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Air samples from hurricanes, clouds, high altitudes (&gt;10km) and low altitudes (~4km)</STUDY_ABSTRACT><CENTER_PROJECT_NAME>air metagenome</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>170715</ID><LABEL>PRJNA170715</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE xmlns="" alias="Transit_20100813" center_name="Georgia Institute of Technology" accession="SRS351343"><IDENTIFIERS><PRIMARY_ID>SRS351343</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01091716</EXTERNAL_ID><SUBMITTER_ID namespace="Georgia Institute of Technology">Transit_20100813</SUBMITTER_ID></IDENTIFIERS><TITLE>Transit flight from CA to FL(Transit_20100813)</TITLE><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Transit flight from CA to FL</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><XREF_LINK><DB>biosample</DB><ID>1091716</ID><LABEL>SAMN01091716</LABEL></XREF_LINK></SAMPLE_LINK></SAMPLE_LINKS></SAMPLE><RUN_SET><RUN xmlns="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Transit_20100813" center_name="Georgia Institute of Technology" accession="SRR521970" total_spots="5315" total_bases="2839479" size="6627813" load_done="true" published="2013-01-31 12:33:31" is_public="true" cluster_name="public" static_data_available="1"><EXPERIMENT_REF accession="SRX160861"/><RUN_ATTRIBUTES><RUN_ATTRIBUTE><TAG>TGACGAC</TAG><VALUE/><UNITS/></RUN_ATTRIBUTE></RUN_ATTRIBUTES><Pool><Member member_name="" accession="SRS351343" sample_name="Transit_20100813" sample_title="Transit flight from CA to FL(Transit_20100813)" spots="5315" bases="2839479"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="16SrRNA_Pyrosequencing+Test_20100810" accession="SRX160133" center_name="Georgia Institute of Technology"><TITLE>The microbiome of the upper troposphere</TITLE><STUDY_REF accession="SRP014337"/><DESIGN><DESIGN_DESCRIPTION/><SAMPLE_DESCRIPTOR accession="SRS350370"/><LIBRARY_DESCRIPTOR><LIBRARY_NAME>GRIP_16S</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>BarCode</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>12</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX Titanium</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="GRIP_Campaign_2010" lab_name="Konstantinidis Lab" center_name="Georgia Institute of Technology" submission_date="2012-07-16T14:52:11Z" accession="SRA056067"/><STUDY alias="PRJNA170715" center_name="BioProject" accession="SRP014337"><DESCRIPTOR><STUDY_TITLE>GRIP campaign air samples 16S amplicon</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Samples from the atmosphere at high altitudes.  Air samples from hurricanes, clouds, high altitudes (&gt;10km) and low altitudes (~4km)</STUDY_ABSTRACT><CENTER_PROJECT_NAME>air metagenome</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>170715</ID><LABEL>PRJNA170715</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE xmlns="" alias="Test_20100810" center_name="Georgia Institute of Technology" accession="SRS350370"><IDENTIFIERS><PRIMARY_ID>SRS350370</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01090408</EXTERNAL_ID><SUBMITTER_ID namespace="Georgia Institute of Technology">Test_20100810</SUBMITTER_ID></IDENTIFIERS><TITLE>Test Flight Off coast CA</TITLE><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Test Flight Off coast CA</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><XREF_LINK><DB>biosample</DB><ID>1090408</ID><LABEL>SAMN01090408</LABEL></XREF_LINK></SAMPLE_LINK></SAMPLE_LINKS></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Test_20100813" center_name="Georgia Institute of Technology" accession="SRR521967" total_spots="8287" total_bases="4392103" size="10244066" load_done="true" published="2013-01-31 12:33:31" is_public="true" cluster_name="public" static_data_available="1"><EXPERIMENT_REF accession="SRX160133"/><RUN_ATTRIBUTES><RUN_ATTRIBUTE><TAG>CAAGAAC</TAG><VALUE/><UNITS/></RUN_ATTRIBUTE></RUN_ATTRIBUTES><Pool><Member member_name="" accession="SRS350370" sample_name="Test_20100810" sample_title="Test Flight Off coast CA" spots="8287" bases="4392103"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="experiment15" center_name="ETHZ" accession="SRX220436"><IDENTIFIERS><PRIMARY_ID>SRX220436</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">experiment15</SUBMITTER_ID><SUBMITTER_ID namespace="ETHZ">run8</SUBMITTER_ID></IDENTIFIERS><TITLE>leaves_RM_epiphyte</TITLE><STUDY_REF accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION>Primer 799F (5'-AACMGGATTAGATACCCKG-3'), which minimizes contamination from plastid DNA (Chelius and Triplett, 2001) and a primer designed for this study, 1193r (5'-ACGTCATCCCCACCTTCC-3'), were used to amplify V5, V6 and V7 of the 16S rRNA gene. The forward primer was fused to the 454 Life Sciences primer B and the reverse primer was fused to the adapter A and a barcode in order to sequence the hypervariable regions V6 and V7.  Each 25 µl PCR reaction contained 10 ng (for the endophytic fraction) or 1 ng (for the epiphytic fraction) of DNA, Mg2+ free PCR buffer (TaKaRa), 3mM MgCl2 (TaKaRa), 200 µM dNTP, 200 nM forward primer, 200 nM reverse primer, 12.5 µg ultrapure BSA (Ambion), and 1 unit Ex Taq HotStart polymerase (TaKaRa). Cycling conditions were 94ºC for 2 min, followed by 25 cycles of 94ºC for 30 sec, 55ºC for 30 sec, 72ºC for 1 min, with a final extension of 72ºC for 10 min. All samples were amplified in quadruplicates, which were combined before purification. Primer 799f and 1193r amplify a mitochondrial product of about 800 bp and a bacterial product of about 500 bp. We isolated the bacterial product by separating the PCR products on a 3% low melt agarose gel (2% agarose for root samples) and excising a band of agarose with size 400 bp to 700 bp. DNA was extracted from the gel using the QIAquick gel extraction kit (Qiagen). After purification, DNA was quantified using the PicoGreen assay (Invitrogen) and the quality was checked using a Bioanalyzer (Agilent). DNA concentration was adjusted to 1 ng/µl. The amplicon libraries were prepared by pooling 10 ng of each PCR.</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS387974"><IDENTIFIERS><PRIMARY_ID>SRS387974</PRIMARY_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME/><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING><PIPELINE><PIPE_SECTION><STEP_INDEX/><PREV_STEP_INDEX/><PROGRAM>mothur</PROGRAM><VERSION>v 1.29.1</VERSION></PIPE_SECTION></PIPELINE></PROCESSING></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Arabido" lab_name="Vorholt" accession="SRA064179" center_name="ETHZ" submission_date="2013-01-09T06:05:46Z"><IDENTIFIERS><PRIMARY_ID>SRA064179</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">Arabido</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="PRJNA73097" center_name="BioProject" accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID><EXTERNAL_ID namespace="BioProject">PRJNA73097</EXTERNAL_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Phyllosphere and Rhizosphere 16S Community Analysis</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>The purpose of this study is to describe the bacterial community associated with Arabidopsis thaliana leaves and roots.

&lt;p&gt;Bacterial communities associated with the phyllosphere and rhizosphere of Arabidopsis thaliana were analyzed by PCR amplification of the 16S rDNA gene and 454 sequencing.  Arabidopsis roots and leaves were harvested at 4 different sites. DNA was extracted from the roots and the leaves and amplified with 16S primers.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>uncultured bacterium</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>73097</ID><LABEL>PRJNA73097</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE center_name="BioSample" alias="SAMN01888401" accession="SRS387974"><IDENTIFIERS><PRIMARY_ID>SRS387974</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01888401</EXTERNAL_ID></IDENTIFIERS><TITLE>MIMARKS Survey related sample from leaf_epiphytes</TITLE><SAMPLE_NAME><TAXON_ID>77133</TAXON_ID><SCIENTIFIC_NAME>uncultured bacterium</SCIENTIFIC_NAME></SAMPLE_NAME><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1888401</ID><LABEL>SAMN01888401</LABEL></ENTREZ_LINK></SAMPLE_LINK><SAMPLE_LINK><ENTREZ_LINK><DB>bioproject</DB><QUERY>PRJNA73097</QUERY></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>lat_lon</TAG><VALUE>41.354836, -86.737353</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>biome</TAG><VALUE>temperate grassland</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>collection_date</TAG><VALUE>15-Apr-2008</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>feature</TAG><VALUE>disturbed field</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>investigation_type</TAG><VALUE>miens-survey</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>project_name</TAG><VALUE>Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>geo_loc_name</TAG><VALUE>USA: Route Marker 166, Indiana</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>material</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>env_package</TAG><VALUE>MIGS/MIMS/MIMARKS.plant-associated</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>specific_host</TAG><VALUE>Arabidopsis thaliana</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="run8" accession="SRR671965" center_name="ETHZ" total_spots="15492" total_bases="4140682" size="7562130" load_done="true" published="2013-02-06 00:00:00" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>SRR671965</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">run8</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF accession="SRX220436"/><Pool><Member member_name="" accession="SRS387974" sample_name="SAMN01888401" sample_title="MIMARKS Survey related sample from leaf_epiphytes" spots="15492" bases="4140682"/></Pool><QualityCount><Quality value="0" count="2149"/><Quality value="6" count="68"/><Quality value="7" count="270"/><Quality value="8" count="518"/><Quality value="9" count="494"/><Quality value="10" count="249"/><Quality value="11" count="5461"/><Quality value="12" count="2688"/><Quality value="13" count="11880"/><Quality value="14" count="3704"/><Quality value="15" count="8734"/><Quality value="16" count="6746"/><Quality value="17" count="4478"/><Quality value="18" count="4604"/><Quality value="19" count="4620"/><Quality value="20" count="6989"/><Quality value="21" count="5859"/><Quality value="22" count="12551"/><Quality value="23" count="7239"/><Quality value="24" count="5965"/><Quality value="25" count="13924"/><Quality value="26" count="9192"/><Quality value="27" count="4526"/><Quality value="28" count="20706"/><Quality value="29" count="9385"/><Quality value="30" count="19956"/><Quality value="31" count="74599"/><Quality value="32" count="167663"/><Quality value="33" count="26200"/><Quality value="34" count="37286"/><Quality value="35" count="48056"/><Quality value="36" count="56959"/><Quality value="37" count="2711910"/><Quality value="38" count="177865"/><Quality value="39" count="11393"/><Quality value="40" count="655796"/></QualityCount><Statistics nreads="2" nspots="15492"><Read index="0" count="15492" average="4" stdev="0"/><Read index="1" count="15492" average="263.28" stdev="10.02"/></Statistics><Bases cs_native="false" count="4140682"><Base value="A" count="942746"/><Base value="C" count="1297293"/><Base value="G" count="923224"/><Base value="T" count="975270"/><Base value="N" count="2149"/></Bases></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="experiment11" center_name="ETHZ" accession="SRX220432"><IDENTIFIERS><PRIMARY_ID>SRX220432</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">experiment11</SUBMITTER_ID><SUBMITTER_ID namespace="ETHZ">run6</SUBMITTER_ID></IDENTIFIERS><TITLE>leaves_NL_epiphyte</TITLE><STUDY_REF accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION>Primer 799F (5'-AACMGGATTAGATACCCKG-3'), which minimizes contamination from plastid DNA (Chelius and Triplett, 2001) and a primer designed for this study, 1193r (5'-ACGTCATCCCCACCTTCC-3'), were used to amplify V5, V6 and V7 of the 16S rRNA gene. The forward primer was fused to the 454 Life Sciences primer B and the reverse primer was fused to the adapter A and a barcode in order to sequence the hypervariable regions V6 and V7.  Each 25 µl PCR reaction contained 10 ng (for the endophytic fraction) or 1 ng (for the epiphytic fraction) of DNA, Mg2+ free PCR buffer (TaKaRa), 3mM MgCl2 (TaKaRa), 200 µM dNTP, 200 nM forward primer, 200 nM reverse primer, 12.5 µg ultrapure BSA (Ambion), and 1 unit Ex Taq HotStart polymerase (TaKaRa). Cycling conditions were 94ºC for 2 min, followed by 25 cycles of 94ºC for 30 sec, 55ºC for 30 sec, 72ºC for 1 min, with a final extension of 72ºC for 10 min. All samples were amplified in quadruplicates, which were combined before purification. Primer 799f and 1193r amplify a mitochondrial product of about 800 bp and a bacterial product of about 500 bp. We isolated the bacterial product by separating the PCR products on a 3% low melt agarose gel (2% agarose for root samples) and excising a band of agarose with size 400 bp to 700 bp. DNA was extracted from the gel using the QIAquick gel extraction kit (Qiagen). After purification, DNA was quantified using the PicoGreen assay (Invitrogen) and the quality was checked using a Bioanalyzer (Agilent). DNA concentration was adjusted to 1 ng/µl. The amplicon libraries were prepared by pooling 10 ng of each PCR.</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS387970"><IDENTIFIERS><PRIMARY_ID>SRS387970</PRIMARY_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME/><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING><PIPELINE><PIPE_SECTION><STEP_INDEX/><PREV_STEP_INDEX/><PROGRAM>mothur</PROGRAM><VERSION>v 1.29.1</VERSION></PIPE_SECTION></PIPELINE></PROCESSING></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Arabido" lab_name="Vorholt" accession="SRA064179" center_name="ETHZ" submission_date="2013-01-09T06:05:46Z"><IDENTIFIERS><PRIMARY_ID>SRA064179</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">Arabido</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="PRJNA73097" center_name="BioProject" accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID><EXTERNAL_ID namespace="BioProject">PRJNA73097</EXTERNAL_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Phyllosphere and Rhizosphere 16S Community Analysis</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>The purpose of this study is to describe the bacterial community associated with Arabidopsis thaliana leaves and roots.

&lt;p&gt;Bacterial communities associated with the phyllosphere and rhizosphere of Arabidopsis thaliana were analyzed by PCR amplification of the 16S rDNA gene and 454 sequencing.  Arabidopsis roots and leaves were harvested at 4 different sites. DNA was extracted from the roots and the leaves and amplified with 16S primers.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>uncultured bacterium</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>73097</ID><LABEL>PRJNA73097</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE center_name="BioSample" alias="SAMN01888397" accession="SRS387970"><IDENTIFIERS><PRIMARY_ID>SRS387970</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01888397</EXTERNAL_ID></IDENTIFIERS><TITLE>MIMARKS Survey related sample from leaf_epiphytes</TITLE><SAMPLE_NAME><TAXON_ID>77133</TAXON_ID><SCIENTIFIC_NAME>uncultured bacterium</SCIENTIFIC_NAME></SAMPLE_NAME><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1888397</ID><LABEL>SAMN01888397</LABEL></ENTREZ_LINK></SAMPLE_LINK><SAMPLE_LINK><ENTREZ_LINK><DB>bioproject</DB><QUERY>PRJNA73097</QUERY></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>lat_lon</TAG><VALUE>41.540244, -86.425794</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>biome</TAG><VALUE>temperate grassland</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>collection_date</TAG><VALUE>30-Apr-2008</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>feature</TAG><VALUE>disturbed field</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>investigation_type</TAG><VALUE>miens-survey</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>project_name</TAG><VALUE>Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>geo_loc_name</TAG><VALUE>USA: North Liberty, Indiana</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>material</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>env_package</TAG><VALUE>MIGS/MIMS/MIMARKS.plant-associated</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>specific_host</TAG><VALUE>Arabidopsis thaliana</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="run6" accession="SRR671963" center_name="ETHZ" total_spots="16391" total_bases="4297552" size="7959889" load_done="true" published="2013-02-06 00:00:00" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>SRR671963</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">run6</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF accession="SRX220432"/><Pool><Member member_name="" accession="SRS387970" sample_name="SAMN01888397" sample_title="MIMARKS Survey related sample from leaf_epiphytes" spots="16391" bases="4297552"/></Pool><QualityCount><Quality value="0" count="3574"/><Quality value="6" count="46"/><Quality value="7" count="391"/><Quality value="8" count="882"/><Quality value="9" count="749"/><Quality value="10" count="212"/><Quality value="11" count="8950"/><Quality value="12" count="4451"/><Quality value="13" count="14200"/><Quality value="14" count="3932"/><Quality value="15" count="9930"/><Quality value="16" count="7178"/><Quality value="17" count="5537"/><Quality value="18" count="5397"/><Quality value="19" count="5541"/><Quality value="20" count="7581"/><Quality value="21" count="7301"/><Quality value="22" count="11494"/><Quality value="23" count="7747"/><Quality value="24" count="6828"/><Quality value="25" count="12312"/><Quality value="26" count="10385"/><Quality value="27" count="4721"/><Quality value="28" count="19394"/><Quality value="29" count="9927"/><Quality value="30" count="18862"/><Quality value="31" count="63661"/><Quality value="32" count="129156"/><Quality value="33" count="28047"/><Quality value="34" count="39887"/><Quality value="35" count="53397"/><Quality value="36" count="58617"/><Quality value="37" count="2842383"/><Quality value="38" count="181319"/><Quality value="39" count="12045"/><Quality value="40" count="701518"/></QualityCount><Statistics nreads="2" nspots="16391"><Read index="0" count="16391" average="4" stdev="0"/><Read index="1" count="16391" average="258.19" stdev="10.62"/></Statistics><Bases cs_native="false" count="4297552"><Base value="A" count="997413"/><Base value="C" count="1322244"/><Base value="G" count="957645"/><Base value="T" count="1016676"/><Base value="N" count="3574"/></Bases></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="experiment6" center_name="ETHZ" accession="SRX220261"><IDENTIFIERS><PRIMARY_ID>SRX220261</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">experiment6</SUBMITTER_ID><SUBMITTER_ID namespace="ETHZ">run4</SUBMITTER_ID></IDENTIFIERS><TITLE>leaves_ME_epiphyte</TITLE><STUDY_REF accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION>Primer 799F (5'-AACMGGATTAGATACCCKG-3'), which minimizes contamination from plastid DNA (Chelius and Triplett, 2001) and a primer designed for this study, 1193r (5'-ACGTCATCCCCACCTTCC-3'), were used to amplify V5, V6 and V7 of the 16S rRNA gene. The forward primer was fused to the 454 Life Sciences primer B and the reverse primer was fused to the adapter A and a barcode in order to sequence the hypervariable regions V6 and V7.  Each 25 µl PCR reaction contained 10 ng (for the endophytic fraction) or 1 ng (for the epiphytic fraction) of DNA, Mg2+ free PCR buffer (TaKaRa), 3mM MgCl2 (TaKaRa), 200 µM dNTP, 200 nM forward primer, 200 nM reverse primer, 12.5 µg ultrapure BSA (Ambion), and 1 unit Ex Taq HotStart polymerase (TaKaRa). Cycling conditions were 94ºC for 2 min, followed by 25 cycles of 94ºC for 30 sec, 55ºC for 30 sec, 72ºC for 1 min, with a final extension of 72ºC for 10 min. All samples were amplified in quadruplicates, which were combined before purification. Primer 799f and 1193r amplify a mitochondrial product of about 800 bp and a bacterial product of about 500 bp. We isolated the bacterial product by separating the PCR products on a 3% low melt agarose gel (2% agarose for root samples) and excising a band of agarose with size 400 bp to 700 bp. DNA was extracted from the gel using the QIAquick gel extraction kit (Qiagen). After purification, DNA was quantified using the PicoGreen assay (Invitrogen) and the quality was checked using a Bioanalyzer (Agilent). DNA concentration was adjusted to 1 ng/µl. The amplicon libraries were prepared by pooling 10 ng of each PCR.</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS387832"><IDENTIFIERS><PRIMARY_ID>SRS387832</PRIMARY_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME/><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING><PIPELINE><PIPE_SECTION><STEP_INDEX/><PREV_STEP_INDEX/><PROGRAM>mothur</PROGRAM><VERSION>mothur v.1.29.1</VERSION></PIPE_SECTION></PIPELINE></PROCESSING></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Arabido" lab_name="Vorholt" accession="SRA064179" center_name="ETHZ" submission_date="2013-01-09T06:05:46Z"><IDENTIFIERS><PRIMARY_ID>SRA064179</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">Arabido</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="PRJNA73097" center_name="BioProject" accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID><EXTERNAL_ID namespace="BioProject">PRJNA73097</EXTERNAL_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Phyllosphere and Rhizosphere 16S Community Analysis</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>The purpose of this study is to describe the bacterial community associated with Arabidopsis thaliana leaves and roots.

&lt;p&gt;Bacterial communities associated with the phyllosphere and rhizosphere of Arabidopsis thaliana were analyzed by PCR amplification of the 16S rDNA gene and 454 sequencing.  Arabidopsis roots and leaves were harvested at 4 different sites. DNA was extracted from the roots and the leaves and amplified with 16S primers.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>uncultured bacterium</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>73097</ID><LABEL>PRJNA73097</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE center_name="BioSample" alias="SAMN01888393" accession="SRS387832"><IDENTIFIERS><PRIMARY_ID>SRS387832</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01888393</EXTERNAL_ID></IDENTIFIERS><TITLE>MIMARKS Survey related sample from leaf_epiphytes</TITLE><SAMPLE_NAME><TAXON_ID>77133</TAXON_ID><SCIENTIFIC_NAME>uncultured bacterium</SCIENTIFIC_NAME></SAMPLE_NAME><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1888393</ID><LABEL>SAMN01888393</LABEL></ENTREZ_LINK></SAMPLE_LINK><SAMPLE_LINK><ENTREZ_LINK><DB>bioproject</DB><QUERY>PRJNA73097</QUERY></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>lat_lon</TAG><VALUE>42.0927, -86.356322</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>biome</TAG><VALUE>temperate grassland</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>collection_date</TAG><VALUE>25-Apr-2008</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>feature</TAG><VALUE>disturbed field</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>investigation_type</TAG><VALUE>miens-survey</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>project_name</TAG><VALUE>Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>geo_loc_name</TAG><VALUE>USA: Michigan Extension, Michigan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>material</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>env_package</TAG><VALUE>MIGS/MIMS/MIMARKS.plant-associated</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>specific_host</TAG><VALUE>Arabidopsis thaliana</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="run4" accession="SRR671961" center_name="ETHZ" total_spots="16777" total_bases="4446081" size="8111002" load_done="true" published="2013-02-06 00:00:00" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>SRR671961</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">run4</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF accession="SRX220261"/><Pool><Member member_name="" accession="SRS387832" sample_name="SAMN01888393" sample_title="MIMARKS Survey related sample from leaf_epiphytes" spots="16777" bases="4446081"/></Pool><QualityCount><Quality value="0" count="3616"/><Quality value="6" count="13"/><Quality value="7" count="375"/><Quality value="8" count="726"/><Quality value="9" count="588"/><Quality value="10" count="168"/><Quality value="11" count="8075"/><Quality value="12" count="3604"/><Quality value="13" count="12169"/><Quality value="14" count="3205"/><Quality value="15" count="8202"/><Quality value="16" count="4891"/><Quality value="17" count="4172"/><Quality value="18" count="4770"/><Quality value="19" count="4855"/><Quality value="20" count="5755"/><Quality value="21" count="6355"/><Quality value="22" count="10014"/><Quality value="23" count="7674"/><Quality value="24" count="6586"/><Quality value="25" count="12769"/><Quality value="26" count="9085"/><Quality value="27" count="4172"/><Quality value="28" count="19956"/><Quality value="29" count="9372"/><Quality value="30" count="20441"/><Quality value="31" count="72838"/><Quality value="32" count="170379"/><Quality value="33" count="26951"/><Quality value="34" count="41334"/><Quality value="35" count="48602"/><Quality value="36" count="51186"/><Quality value="37" count="2939332"/><Quality value="38" count="184993"/><Quality value="39" count="11779"/><Quality value="40" count="727079"/></QualityCount><Statistics nreads="2" nspots="16777"><Read index="0" count="16777" average="4" stdev="0"/><Read index="1" count="16777" average="261.01" stdev="8.25"/></Statistics><Bases cs_native="false" count="4446081"><Base value="A" count="1001137"/><Base value="C" count="1397610"/><Base value="G" count="992859"/><Base value="T" count="1050859"/><Base value="N" count="3616"/></Bases></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="experiment2" center_name="ETHZ" accession="SRX219208"><IDENTIFIERS><PRIMARY_ID>SRX219208</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">experiment2</SUBMITTER_ID><SUBMITTER_ID namespace="ETHZ">run2</SUBMITTER_ID></IDENTIFIERS><TITLE>leaves_LMC_epiphyte</TITLE><STUDY_REF accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION>Primer 799F (5'-AACMGGATTAGATACCCKG-3'), which minimizes contamination from plastid DNA (Chelius and Triplett, 2001) and a primer designed for this study, 1193r (5'-ACGTCATCCCCACCTTCC-3'), were used to amplify V5, V6 and V7 of the 16S rRNA gene. The forward primer was fused to the 454 Life Sciences primer B and the reverse primer was fused to the adapter A and a barcode in order to sequence the hypervariable regions V6 and V7.  Each 25 µl PCR reaction contained 10 ng (for the endophytic fraction) or 1 ng (for the epiphytic fraction) of DNA, Mg2+ free PCR buffer (TaKaRa), 3mM MgCl2 (TaKaRa), 200 µM dNTP, 200 nM forward primer, 200 nM reverse primer, 12.5 µg ultrapure BSA (Ambion), and 1 unit Ex Taq HotStart polymerase (TaKaRa). Cycling conditions were 94ºC for 2 min, followed by 25 cycles of 94ºC for 30 sec, 55ºC for 30 sec, 72ºC for 1 min, with a final extension of 72ºC for 10 min. All samples were amplified in quadruplicates, which were combined before purification. Primer 799f and 1193r amplify a mitochondrial product of about 800 bp and a bacterial product of about 500 bp. We isolated the bacterial product by separating the PCR products on a 3% low melt agarose gel (2% agarose for root samples) and excising a band of agarose with size 400 bp to 700 bp. DNA was extracted from the gel using the QIAquick gel extraction kit (Qiagen). After purification, DNA was quantified using the PicoGreen assay (Invitrogen) and the quality was checked using a Bioanalyzer (Agilent). DNA concentration was adjusted to 1 ng/µl. The amplicon libraries were prepared by pooling 10 ng of each PCR.</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS387494"><IDENTIFIERS><PRIMARY_ID>SRS387494</PRIMARY_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME/><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING><PIPELINE><PIPE_SECTION><STEP_INDEX/><PREV_STEP_INDEX/><PROGRAM>mothur</PROGRAM><VERSION>v.1.29.1</VERSION></PIPE_SECTION></PIPELINE></PROCESSING></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Arabido" lab_name="Vorholt" accession="SRA064179" center_name="ETHZ" submission_date="2013-01-09T06:05:46Z"><IDENTIFIERS><PRIMARY_ID>SRA064179</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">Arabido</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="PRJNA73097" center_name="BioProject" accession="SRP018030"><IDENTIFIERS><PRIMARY_ID>SRP018030</PRIMARY_ID><EXTERNAL_ID namespace="BioProject">PRJNA73097</EXTERNAL_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Phyllosphere and Rhizosphere 16S Community Analysis</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>The purpose of this study is to describe the bacterial community associated with Arabidopsis thaliana leaves and roots.

&lt;p&gt;Bacterial communities associated with the phyllosphere and rhizosphere of Arabidopsis thaliana were analyzed by PCR amplification of the 16S rDNA gene and 454 sequencing.  Arabidopsis roots and leaves were harvested at 4 different sites. DNA was extracted from the roots and the leaves and amplified with 16S primers.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>uncultured bacterium</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>73097</ID><LABEL>PRJNA73097</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE center_name="BioSample" alias="SAMN01888389" accession="SRS387494"><IDENTIFIERS><PRIMARY_ID>SRS387494</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01888389</EXTERNAL_ID></IDENTIFIERS><TITLE>MIMARKS Survey related sample from leaf_epiphytes</TITLE><SAMPLE_NAME><TAXON_ID>77133</TAXON_ID><SCIENTIFIC_NAME>uncultured bacterium</SCIENTIFIC_NAME></SAMPLE_NAME><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1888389</ID><LABEL>SAMN01888389</LABEL></ENTREZ_LINK></SAMPLE_LINK><SAMPLE_LINK><ENTREZ_LINK><DB>bioproject</DB><QUERY>PRJNA73097</QUERY></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>lat_lon</TAG><VALUE>42.090114, -86.393408</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>biome</TAG><VALUE>temperate grassland</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>collection_date</TAG><VALUE>16-Apr-2008</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>feature</TAG><VALUE>disturbed field</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>investigation_type</TAG><VALUE>miens-survey</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>project_name</TAG><VALUE>Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>geo_loc_name</TAG><VALUE>USA: Lake Michigan College, Michigan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>material</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>env_package</TAG><VALUE>MIGS/MIMS/MIMARKS.plant-associated</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>specific_host</TAG><VALUE>Arabidopsis thaliana</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="run2" accession="SRR671959" center_name="ETHZ" total_spots="17175" total_bases="4612155" size="8542345" load_done="true" published="2013-02-06 00:00:00" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>SRR671959</PRIMARY_ID><SUBMITTER_ID namespace="ETHZ">run2</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF accession="SRX219208"/><Pool><Member member_name="" accession="SRS387494" sample_name="SAMN01888389" sample_title="MIMARKS Survey related sample from leaf_epiphytes" spots="17175" bases="4612155"/></Pool><QualityCount><Quality value="0" count="3982"/><Quality value="6" count="43"/><Quality value="7" count="459"/><Quality value="8" count="1071"/><Quality value="9" count="968"/><Quality value="10" count="573"/><Quality value="11" count="10610"/><Quality value="12" count="4868"/><Quality value="13" count="19445"/><Quality value="14" count="7026"/><Quality value="15" count="19875"/><Quality value="16" count="12139"/><Quality value="17" count="11506"/><Quality value="18" count="8126"/><Quality value="19" count="8283"/><Quality value="20" count="11312"/><Quality value="21" count="10473"/><Quality value="22" count="20777"/><Quality value="23" count="9943"/><Quality value="24" count="8584"/><Quality value="25" count="21139"/><Quality value="26" count="15721"/><Quality value="27" count="7606"/><Quality value="28" count="31148"/><Quality value="29" count="12554"/><Quality value="30" count="29013"/><Quality value="31" count="97604"/><Quality value="32" count="176984"/><Quality value="33" count="33017"/><Quality value="34" count="49801"/><Quality value="35" count="75499"/><Quality value="36" count="87691"/><Quality value="37" count="2898750"/><Quality value="38" count="195070"/><Quality value="39" count="16849"/><Quality value="40" count="693646"/></QualityCount><Statistics nreads="2" nspots="17175"><Read index="0" count="17175" average="4" stdev="0"/><Read index="1" count="17175" average="264.54" stdev="13.05"/></Statistics><Bases cs_native="false" count="4612155"><Base value="A" count="1120523"/><Base value="C" count="1399430"/><Base value="G" count="973328"/><Base value="T" count="1114892"/><Base value="N" count="3982"/></Bases></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT xmlns="" alias="Run 13 Socompa Stromatolite 3" center_name="INDEAR" accession="SRX090643"><TITLE>Socompa Stromatolite 16S pyrotags</TITLE><STUDY_REF accession="SRP007748"/><DESIGN><DESIGN_DESCRIPTION>Whole DNA was extracted from 0.5 g of  freeze-dried stromatolite was washed in 10 ml of 10% NaCl and incubated at 40°C for  15 min and then centrifuged at 8200 x g for 15 min (three times).  The SN (approx. 15 ml) is maintained for the precipitation of the EPS (a), while the  pellet is retained for the extraction of genomic DNA (b). Precipitation of EPS was  done according to Hong Liu, et al, with some adaptation2: The supernatant is mixed  with 100% ethanol and taken to a concentration of 70% ethanol and incubated O.N  at 4°C. Centrifuged 15 min at 4000 x g at 20°C. The supernatant is discarded and the  resulting pellet was solubilized in sterile H2O and dialyzed against H2Od in a 10.000 Da  MWCO membrane for 3 hours (3 times) at 4°C. Half was lyophilized for dry weight  determination, while the other half was used for chemical analysis and HPLC. Genomic  DNA extraction was done according to Falcon et al1, whit modifications : The cell pellet  of sediment was resuspended in lysis buffer (Tris-HCl, pH 8, 100 mM NaCl 1.5 M,  EDTA, pH 8, 100 mM; Na3PO4, pH 8, 100 M; CTAB 1%). The cells were frozen and  thawed first in N2 (l) and then in a water bath at 65°C (three times). The mixture was  incubated with lysozyme (1 mg / ml) for 30 min at 37°C, then added Proteinase K (0.1  mg / ml), 3% final SDS and incubated ON at 60°C. Supernatant were collected after  10 min of centrifugation at 5000 x g. Organic extractions are made first with 1 Vol.  of phenol:chloroform:isoamyl acohol (25:24:1) and then with 1 Vol. of chloroform:  isoamyl alcohol (24:1). DNA (aqueous phase) is separated and precipitated with cold  Isopropanol (0.7 Vol.) and Sodium Acetate 3M (0,1 Vol), incubated 2 hours at -20°C  and then, the DNA precipitate is washed (three times) with cold 70% ethanol, collecting  the DNA between each wash with centrifugation for 15 min 15000 x g at 4°C. Finally,  the DNA is dried in sterile air and resuspended in DNAse-free H2O.  The V4 hyper variable region of the 16s rRNA gene was amplified using the following  universal primers containing the Roche 454 sequencing A and B adaptors (underlined)  and a 10 nucleotide “multiple identifier” (MID) to sort samples (bold): 520F (5’-  CGTATCGCCTCCCTCGCGCCATCAGAGCACTGTAGAYTGGGYDTAAAGNG-3’,  CTATGCGCCTTGCCAGCCCGCTCAGTACCRGGGTHTCTAATCC,  CTATGCGCCTTGCCAGCCCGCTCAGTACCAGAGTATCTAATTC,  and CTATGCGCCTTGCCAGCCCGCTCAGCTACDSRGGTMTCTAATC,  CTATGCGCCTTGCCAGCCCGCTCAGTACNVGGGTATCTAATCC) obtained from  RDP’s Pyrosequencing Pipeline: http://pyro.cme.msu.edu/pyro/help. Five independent  PCRs were performed. The PCR mix (final volume 25 ul) contained 2.5 ulFastStart  High Fidelity 10X Reaction Buffer (Roche Applied Science, Mannheim, Germany),  20 ng of template DNA, 0.4 uM each primer, 1.25 U FastStart High Fidelity Enzyme  Blend (Roche Applied Science), and 0.2 mM DNTPs. The PCR conditions were 95 °C  for 5 minutes for initial denaturalization, followed by 95 °C for 45 seconds, 57 °C for  45 seconds, 72 °C for 60 seconds in 30 cycles, and a final elongation step at 72°C for  4 minutes. Two negative control reactions containing all components were performed  without the template. The five reactions were pooled and purified using AMPure  beads XP. Quantification of the purified PCR product was performed by using Quant-  iTPicoGreendsDNA Kit (Invitrogen Molecular Probes Inc, Oregon, USA).  Purified PCR product were immobilized onto DNA capture beads, amplified  through emulsion-based clonal amplification (emPCR), and sequenced together  in a PicoTiterPlate device on a Genome Sequencer FLX (Roche Applied Science)  using Titanium Chemistry according to the manufacturer’s instructions at INDEAR  (Argentina) Genome sequencing facility.</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS256213"/><LIBRARY_DESCRIPTOR><LIBRARY_NAME>Socompa Stromatolite</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX Titanium</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Socompa" lab_name="Genomics and Bioinformatics" center_name="INDEAR" submission_date="2011-08-08T21:56:47Z" accession="SRA044035"/><STUDY xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Socompa Stromatolite" center_name="INDEAR" accession="SRP007748"><DESCRIPTOR><STUDY_TITLE>STROMATOLITES AT SOCOMPA LAKE:  MICROBIALCOMMUNITIES DEVELOPING UNDER ALKALINE,  HIPERARSENIC AND HIPERSALYNE VOLCANIC ASSOCIATED  ECOSYSTEM OVER 4000 M IN THE ARGENTINEAN PUNA</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>The High-Altitude Andean Lakes (HAAL) in the Argentinian Puna-High Andes region  represent an almost unexplored ecosystem of shallow lakes at altitudes from 3,000  to 6,000 m. Although exposed to extreme conditions: i.e. volcanic settings, high UV  irradiation, hypersalinity, drastic temperature changes, desiccation, and high pH, an  outstanding microbial biodiversity has developed, most of them ordered in multi-  layered flat mats and stubby pillars called microbialites. Calcareous cyanobacterial  microbialites defined as stromatolites and thrombolites were common in ancient  shallow marine environments. Today, they are restricted to a few lacustrine and  perimarine settings. Compared to them, those from HAAL are the only ones that exist  under such hostile environmental conditions. Moreover, they experience environmental  conditions resembling those that prevailed at the early Earth, making their study even  more promising as a modern template of Early Life development. The present dataset of bacterial diversity assessed by pyrosequencingV4 region of 16S rRNA gene correspond to the  first observation of extreme microbialites harboring a diverse eu-endolythic microbiota  at Laguna Socompa (4000 m asl, pH 9; salinity: 83 ppm; 35 mg L-1 As) at the bottom of  Socompa Volcano Northwest Argentina.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Socompa Stromatolite Bacterial Diversity</CENTER_PROJECT_NAME><STUDY_DESCRIPTION>DNA from Stromatolite was extracted. 16S rDNA was amplified using RDP designed primers and where sequenced using 454 titanium chemistry, obtaining 113,255 high quality-filtered sequences.</STUDY_DESCRIPTION></DESCRIPTOR></STUDY><SAMPLE alias="Socompa 08-24-2010" center_name="INDEAR" accession="SRS256213"><IDENTIFIERS><PRIMARY_ID>SRS256213</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN00704299</EXTERNAL_ID><SUBMITTER_ID namespace="INDEAR">Socompa 08-24-2010</SUBMITTER_ID></IDENTIFIERS><TITLE>Socompa stromatolite homogenate 24-Aug-2010</TITLE><SAMPLE_NAME><TAXON_ID>496921</TAXON_ID></SAMPLE_NAME><DESCRIPTION/><SAMPLE_LINKS><SAMPLE_LINK><XREF_LINK><DB>biosample</DB><ID>704299</ID><LABEL>SAMN00704299</LABEL></XREF_LINK></SAMPLE_LINK></SAMPLE_LINKS></SAMPLE><RUN_SET><RUN xmlns="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Socompa Stromatolite" center_name="INDEAR" accession="SRR329490" total_spots="113255" total_bases="28400267" size="14844396" load_done="true" published="2012-07-31 00:00:00" is_public="true" cluster_name="public" static_data_available="1"><EXPERIMENT_REF accession="SRX090643"/><Pool><Member member_name="" accession="SRS256213" sample_name="Socompa 08-24-2010" sample_title="Socompa stromatolite homogenate 24-Aug-2010" spots="113255" bases="28400267"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT alias="BACT16S_TSP_28_05" center_name="DISAT" broker_name="EMG" accession="ERX149297"><IDENTIFIERS><PRIMARY_ID>ERX149297</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_28_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><STUDY_REF refname="Airborne bacteria in Milan" accession="ERP001381" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION/><SAMPLE_DESCRIPTOR refname="TSP_28_05" accession="ERS132565" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERS132565</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_28_05</SUBMITTER_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME>BACT16S_TSP_28_05_lib</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED NOMINAL_LENGTH="282"/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><ILLUMINA><INSTRUMENT_MODEL>Illumina Genome Analyzer IIx</INSTRUMENT_MODEL></ILLUMINA></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION accession="ERA122915" broker_name="EMG" alias="Andrea Franzetti" center_name="DISAT" lab_name="Environmental Microbiology"><IDENTIFIERS><PRIMARY_ID>ERA122915</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Andrea Franzetti</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="Airborne bacteria in Milan" center_name="DISAT" broker_name="EMG" accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_28_05" center_name="DISAT" broker_name="EMG" accession="ERS132565"><IDENTIFIERS><PRIMARY_ID>ERS132565</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_28_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_28_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797502</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (longitude)</TAG><VALUE>9.2125</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (country:region,area)</TAG><VALUE>Italy</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Collection date</TAG><VALUE>2010-05-28</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (biome)</TAG><VALUE>terrestrial biome ENVO:00000446</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (featurel)</TAG><VALUE>aerial habitat ENVO:00000568</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (material)</TAG><VALUE>aerosol ENVO:00010505</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Depth</TAG><VALUE/><UNITS>m</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Elevation</TAG><VALUE>122 </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Amount or size of sample collected</TAG><VALUE>360000 litres of air</VALUE><UNITS>g</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>multiplex identifiers</TAG><VALUE>AGATGC</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>pcr primers</TAG><VALUE>783F:CAGGATTAGATACCC , 1064R:CGACRRCCATGCANCACCT</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN alias="BACT16S_TSP_28_05_1_run" center_name="DISAT" broker_name="EMG" accession="ERR117253" total_spots="2720" total_bases="413440" size="322315" load_done="true" published="2012-10-30 23:11:10" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>ERR117253</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_28_05_1_run</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF refname="BACT16S_TSP_28_05" accession="ERX149297" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERX149297</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_28_05</SUBMITTER_ID></IDENTIFIERS></EXPERIMENT_REF><Pool><Member member_name="" accession="ERS132565" sample_name="TSP_28_05" sample_title="" spots="2720" bases="413440"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT alias="BACT16S_TSP_27_05" center_name="DISAT" broker_name="EMG" accession="ERX149296"><IDENTIFIERS><PRIMARY_ID>ERX149296</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_27_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><STUDY_REF refname="Airborne bacteria in Milan" accession="ERP001381" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION/><SAMPLE_DESCRIPTOR refname="TSP_27_05" accession="ERS132564" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERS132564</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_27_05</SUBMITTER_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME>BACT16S_TSP_27_05_lib</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED NOMINAL_LENGTH="282"/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><ILLUMINA><INSTRUMENT_MODEL>Illumina Genome Analyzer IIx</INSTRUMENT_MODEL></ILLUMINA></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION accession="ERA122915" broker_name="EMG" alias="Andrea Franzetti" center_name="DISAT" lab_name="Environmental Microbiology"><IDENTIFIERS><PRIMARY_ID>ERA122915</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Andrea Franzetti</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="Airborne bacteria in Milan" center_name="DISAT" broker_name="EMG" accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_27_05" center_name="DISAT" broker_name="EMG" accession="ERS132564"><IDENTIFIERS><PRIMARY_ID>ERS132564</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_27_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_27_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
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                particulate matter. A seasonal variability in the composition of microbial
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                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_26_05" center_name="DISAT" broker_name="EMG" accession="ERS132563"><IDENTIFIERS><PRIMARY_ID>ERS132563</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_26_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_26_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
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                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_28_02" center_name="DISAT" broker_name="EMG" accession="ERS132557"><IDENTIFIERS><PRIMARY_ID>ERS132557</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_28_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_28_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_25_02" center_name="DISAT" broker_name="EMG" accession="ERS132554"><IDENTIFIERS><PRIMARY_ID>ERS132554</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_25_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_25_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
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                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_27_11" center_name="DISAT" broker_name="EMG" accession="ERS132584"><IDENTIFIERS><PRIMARY_ID>ERS132584</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_27_11</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_27_11</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_25_11" center_name="DISAT" broker_name="EMG" accession="ERS132582"><IDENTIFIERS><PRIMARY_ID>ERS132582</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_25_11</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_25_11</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
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                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_26_08" center_name="DISAT" broker_name="EMG" accession="ERS132574"><IDENTIFIERS><PRIMARY_ID>ERS132574</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_26_08</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_26_08</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_25_08" center_name="DISAT" broker_name="EMG" accession="ERS132573"><IDENTIFIERS><PRIMARY_ID>ERS132573</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_25_08</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_25_08</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_27_02" center_name="DISAT" broker_name="EMG" accession="ERS132556"><IDENTIFIERS><PRIMARY_ID>ERS132556</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_27_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_27_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_04_03" center_name="DISAT" broker_name="EMG" accession="ERS132561"><IDENTIFIERS><PRIMARY_ID>ERS132561</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_04_03</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_04_03</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_01_03" center_name="DISAT" broker_name="EMG" accession="ERS132558"><IDENTIFIERS><PRIMARY_ID>ERS132558</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_01_03</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_01_03</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_03_12" center_name="DISAT" broker_name="EMG" accession="ERS132590"><IDENTIFIERS><PRIMARY_ID>ERS132590</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_03_12</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_03_12</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797527</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_02_12" center_name="DISAT" broker_name="EMG" accession="ERS132589"><IDENTIFIERS><PRIMARY_ID>ERS132589</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_12</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_02_12</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797526</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_01_12" center_name="DISAT" broker_name="EMG" accession="ERS132588"><IDENTIFIERS><PRIMARY_ID>ERS132588</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_01_12</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_01_12</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_26_02" center_name="DISAT" broker_name="EMG" accession="ERS132555"><IDENTIFIERS><PRIMARY_ID>ERS132555</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_26_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_26_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797532</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_24_02" center_name="DISAT" broker_name="EMG" accession="ERS132553"><IDENTIFIERS><PRIMARY_ID>ERS132553</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_24_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_24_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797530</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_23_02" center_name="DISAT" broker_name="EMG" accession="ERS132552"><IDENTIFIERS><PRIMARY_ID>ERS132552</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_23_02</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_23_02</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_28_11" center_name="DISAT" broker_name="EMG" accession="ERS132585"><IDENTIFIERS><PRIMARY_ID>ERS132585</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_28_11</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_28_11</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797522</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_26_11" center_name="DISAT" broker_name="EMG" accession="ERS132583"><IDENTIFIERS><PRIMARY_ID>ERS132583</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_26_11</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_26_11</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797520</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location 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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_01_09" center_name="DISAT" broker_name="EMG" accession="ERS132580"><IDENTIFIERS><PRIMARY_ID>ERS132580</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_01_09</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_01_09</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
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                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_31_05" center_name="DISAT" broker_name="EMG" accession="ERS132568"><IDENTIFIERS><PRIMARY_ID>ERS132568</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_31_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_31_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_30_05" center_name="DISAT" broker_name="EMG" accession="ERS132567"><IDENTIFIERS><PRIMARY_ID>ERS132567</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_30_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_30_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_03_06" center_name="DISAT" broker_name="EMG" accession="ERS132571"><IDENTIFIERS><PRIMARY_ID>ERS132571</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_03_06</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_03_06</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_02_06" center_name="DISAT" broker_name="EMG" accession="ERS132570"><IDENTIFIERS><PRIMARY_ID>ERS132570</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_06</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_02_06</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_01_06" center_name="DISAT" broker_name="EMG" accession="ERS132569"><IDENTIFIERS><PRIMARY_ID>ERS132569</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_01_06</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_01_06</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
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            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_29_05" center_name="DISAT" broker_name="EMG" accession="ERS132566"><IDENTIFIERS><PRIMARY_ID>ERS132566</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_29_05</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_29_05</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
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            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797537</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (longitude)</TAG><VALUE>9.2125</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (country:region,area)</TAG><VALUE>Italy</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Collection date</TAG><VALUE>03/03/201004/03/2010</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (biome)</TAG><VALUE>terrestrial biome ENVO:00000446</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (featurel)</TAG><VALUE>aerial habitat ENVO:00000568</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (material)</TAG><VALUE>aerosol ENVO:00010505</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Depth</TAG><VALUE/><UNITS>m</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Elevation</TAG><VALUE>122 </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Amount or size of sample collected</TAG><VALUE>360000 litres of air</VALUE><UNITS>g</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>multiplex identifiers</TAG><VALUE>AGAGAG</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>pcr primers</TAG><VALUE>783F:CAGGATTAGATACCC , 1064R:CGACRRCCATGCANCACCT</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN alias="BACT16S_TSP_03_03_1_run" center_name="DISAT" broker_name="EMG" accession="ERR117248" total_spots="2024" total_bases="307648" size="248064" load_done="true" published="2012-10-30 23:11:10" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>ERR117248</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_03_03_1_run</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF refname="BACT16S_TSP_03_03" accession="ERX149291" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERX149291</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_03_03</SUBMITTER_ID></IDENTIFIERS></EXPERIMENT_REF><Pool><Member member_name="" accession="ERS132560" sample_name="TSP_03_03" sample_title="" spots="2024" bases="307648"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT alias="BACT16S_TSP_02_03" center_name="DISAT" broker_name="EMG" accession="ERX149290"><IDENTIFIERS><PRIMARY_ID>ERX149290</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_03</SUBMITTER_ID></IDENTIFIERS><TITLE/><STUDY_REF refname="Airborne bacteria in Milan" accession="ERP001381" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION/><SAMPLE_DESCRIPTOR refname="TSP_02_03" accession="ERS132559" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERS132559</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_03</SUBMITTER_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME>BACT16S_TSP_02_03_lib</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED NOMINAL_LENGTH="282"/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><ILLUMINA><INSTRUMENT_MODEL>Illumina Genome Analyzer IIx</INSTRUMENT_MODEL></ILLUMINA></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION accession="ERA122915" broker_name="EMG" alias="Andrea Franzetti" center_name="DISAT" lab_name="Environmental Microbiology"><IDENTIFIERS><PRIMARY_ID>ERA122915</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Andrea Franzetti</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="Airborne bacteria in Milan" center_name="DISAT" broker_name="EMG" accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_02_03" center_name="DISAT" broker_name="EMG" accession="ERS132559"><IDENTIFIERS><PRIMARY_ID>ERS132559</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_03</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_02_03</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797536</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (longitude)</TAG><VALUE>9.2125</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (country:region,area)</TAG><VALUE>Italy</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Collection date</TAG><VALUE>2010-03-02</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (biome)</TAG><VALUE>terrestrial biome ENVO:00000446</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (featurel)</TAG><VALUE>aerial habitat ENVO:00000568</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (material)</TAG><VALUE>aerosol ENVO:00010505</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Depth</TAG><VALUE/><UNITS>m</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Elevation</TAG><VALUE>122 </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Amount or size of sample collected</TAG><VALUE>360000 litres of air</VALUE><UNITS>g</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>multiplex identifiers</TAG><VALUE>AGAGAG</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>pcr primers</TAG><VALUE>783F:CAGGATTAGATACCC , 1064R:CGACRRCCATGCANCACCT</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN alias="BACT16S_TSP_02_03_1_run" center_name="DISAT" broker_name="EMG" accession="ERR117247" total_spots="16597" total_bases="2522744" size="1765682" load_done="true" published="2012-10-30 23:11:10" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>ERR117247</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_03_1_run</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF refname="BACT16S_TSP_02_03" accession="ERX149290" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERX149290</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_03</SUBMITTER_ID></IDENTIFIERS></EXPERIMENT_REF><Pool><Member member_name="" accession="ERS132559" sample_name="TSP_02_03" sample_title="" spots="16597" bases="2522744"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT alias="BACT16S_TSP_02_09" center_name="DISAT" broker_name="EMG" accession="ERX149270"><IDENTIFIERS><PRIMARY_ID>ERX149270</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_09</SUBMITTER_ID></IDENTIFIERS><TITLE/><STUDY_REF refname="Airborne bacteria in Milan" accession="ERP001381" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION/><SAMPLE_DESCRIPTOR refname="TSP_02_09" accession="ERS132581" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERS132581</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_09</SUBMITTER_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME>BACT16S_TSP_02_09_lib</LIBRARY_NAME><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED NOMINAL_LENGTH="282"/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><ILLUMINA><INSTRUMENT_MODEL>Illumina Genome Analyzer IIx</INSTRUMENT_MODEL></ILLUMINA></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION accession="ERA122915" broker_name="EMG" alias="Andrea Franzetti" center_name="DISAT" lab_name="Environmental Microbiology"><IDENTIFIERS><PRIMARY_ID>ERA122915</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Andrea Franzetti</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="Airborne bacteria in Milan" center_name="DISAT" broker_name="EMG" accession="ERP001381"><IDENTIFIERS><PRIMARY_ID>ERP001381</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">Airborne bacteria in Milan</SUBMITTER_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Temporal variability of airborne bacterial communities and relations with the environmental factors in milan urban area</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Bacteria represent a relevant fraction of atmospheric suspended
                particles. It is known that airborne bacteria can significantly affect human health
                and ecosystems. However, the abundance and diversity of airborne microorganisms and
                the factors influencing their diversity remain poorly investigated. In the present
                work we used quantitative polymerase chain reaction (PCR) and Illumina technology to
                provide a thorough description of airborne microbial communities of the Milan urban
                area (Northern Italy). We collected 40 air samples, ten per season. Total bacterial
                abundance was about 104 ribosomal operons m-3 of sampled air. Communities were
                dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and a few
                proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales,
                Pseudomonadales). A significant abundance of Chloroplasts was detected, especially
                in warmer seasons, due to the presence of plant debris and pollens in the
                particulate matter. A seasonal variability in the composition of microbial
                communities was found, mainly due to a higher abundance of Actinobacteridae and
                lower abundance of Chloroplasts in samples collected on cold days. At the same time,
                intra-season variation in community composition was comparable to inter-season
                variation. Soil and plants were the sources which most affected airborne bacterial
                communities. This study demonstrated the potential of the Illumina technology and
                quantitative real-time PCR to investigate the microbiological component of the
                atmosphere, an environment largely neglected by previous studies.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>Airborne bacteria in Milan</CENTER_PROJECT_NAME></DESCRIPTOR><STUDY_LINKS><STUDY_LINK><URL_LINK><LABEL>ENA-CITATION</LABEL><URL>http://dx.doi.org/10.1007/s00253-012-4450-0</URL></URL_LINK></STUDY_LINK></STUDY_LINKS></STUDY><SAMPLE alias="TSP_02_09" center_name="DISAT" broker_name="EMG" accession="ERS132581"><IDENTIFIERS><PRIMARY_ID>ERS132581</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">TSP_02_09</SUBMITTER_ID></IDENTIFIERS><TITLE/><SAMPLE_NAME><TAXON_ID>655179</TAXON_ID><COMMON_NAME>air metagenome</COMMON_NAME><ANONYMIZED_NAME>TSP_02_09</ANONYMIZED_NAME><SCIENTIFIC_NAME>air metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><DESCRIPTION>Total suspended particulate matter (TSP) sampled on quartz fibre filters with a
            high-volume sampler (ECHO HiVol, TCR TECORA, Milan, Italy) with a flux speed of 250 L
            per minute for 24 hours. The sampler was placed at approximately 20 m from the nearest
            roads and 50 m from the nearest traffic lights. TSP sampling was performed at
            approximately 1.5 m from the ground.</DESCRIPTION><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1797518</ID></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>Investigation type</TAG><VALUE>MIxS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Project name</TAG><VALUE>Airborne bacteria in Milan</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-CHECKLIST</TAG><VALUE>GSC:MIxS v2.1</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>ENA-KEYWORD</TAG><VALUE>GSC, MIxS, MIMARKS</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Target gene</TAG><VALUE>16S rRNA</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Sequencing method</TAG><VALUE>Pyrosequencing</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Enviornmental package</TAG><VALUE>air</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (latitude)</TAG><VALUE>45.52222</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (longitude)</TAG><VALUE>9.2125</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Geographic location (country:region,area)</TAG><VALUE>Italy</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Collection date</TAG><VALUE>2010-09-02</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (biome)</TAG><VALUE>terrestrial biome ENVO:00000446</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (featurel)</TAG><VALUE>aerial habitat ENVO:00000568</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Environment (material)</TAG><VALUE>aerosol ENVO:00010505</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Depth</TAG><VALUE/><UNITS>m</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Elevation</TAG><VALUE>122 </VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>Amount or size of sample collected</TAG><VALUE>360000 litres of air</VALUE><UNITS>g</UNITS></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>multiplex identifiers</TAG><VALUE>CAGCAG</VALUE></SAMPLE_ATTRIBUTE><SAMPLE_ATTRIBUTE><TAG>pcr primers</TAG><VALUE>783F:CAGGATTAGATACCC , 1064R:CGACRRCCATGCANCACCT</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN alias="BACT16S_TSP_02_09_1_run" center_name="DISAT" broker_name="EMG" accession="ERR117269" total_spots="16349" total_bases="2485048" size="1773105" load_done="true" published="2012-10-30 23:12:11" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>ERR117269</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_09_1_run</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF refname="BACT16S_TSP_02_09" accession="ERX149270" refcenter="DISAT"><IDENTIFIERS><PRIMARY_ID>ERX149270</PRIMARY_ID><SUBMITTER_ID namespace="DISAT">BACT16S_TSP_02_09</SUBMITTER_ID></IDENTIFIERS></EXPERIMENT_REF><Pool><Member member_name="" accession="ERS132581" sample_name="TSP_02_09" sample_title="" spots="16349" bases="2485048"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE><EXPERIMENT_PACKAGE><EXPERIMENT accession="SRX196098" center_name="University Laval" alias="exp2010"><IDENTIFIERS><PRIMARY_ID>SRX196098</PRIMARY_ID><SUBMITTER_ID namespace="University Laval">Exp 2010</SUBMITTER_ID><SUBMITTER_ID namespace="University Laval">exp2010</SUBMITTER_ID></IDENTIFIERS><TITLE>Dispersal barrier of bacteria between the freshwater and marine biomes</TITLE><STUDY_REF accession="SRP016496"><IDENTIFIERS><PRIMARY_ID>SRP016496</PRIMARY_ID></IDENTIFIERS></STUDY_REF><DESIGN><DESIGN_DESCRIPTION>3 lakes were sampled due to their difference in their proximity to sea coast. Air bacteria were resuspended in sterile lake water using vacuum cleaner with a water tank (AquaStream DS 5600, 1400W, Kärcher, Winnenden, Germany). Air and water samples from lakes were filtered onto 0.2-µm 47 mm Supor-200 filters (Pall Corp.) and stored at -80°C until processing. The same procedure was done with approximately 1g of the top 2cm of lake sediment. DNA was extracted using the Easy-DNA kit (Invitrogen, Carlsbad, CA, USA). Bacterial 16S rRNA genes were PCR amplified using forward primer 341 (5'-CCTACGGGNGGCWGCAG-3') and individually bar-coded reverse primers 805 (5'-GACTACHVGGGTATCTAATCC-3'). The total PCR products were divided into 2 pooled samples where in each, equal amounts of 86 amplicons with different sample-specific barcode sequences were mixed in order to get equal number of reads per sample. Pooled samples were sequenced using Roche/454 GS FLX Titanium technology. The resulting reads carried the sample-specific molecular barcodes and barcodes resemble samples as given:   pooled sample #1: Sample ID: 100ML1a, tag_sequence: TATCGCA; Sample ID: 100ML1b, tag_sequence: TACTAGC; Sample ID:100ML1c, tag_sequence:TACTCTC; Sample ID: 100MabL1a, tag_sequence: TACTCGA; Sample ID: 100MabL1b, tag_sequence: TACTGAC; Sample ID:100MabL1c, tag_sequence: TACTGCA; Sample ID: 100MsedL1a, tag_sequence:TACGTCA; Sample ID: 100MsedL1b, tag_sequence: TACGAGT; Sample ID: 100MsedL1c, tag_sequence: TACGCTA; Sample ID: 75ML1a, tag_sequence: TAGTCAC; Sample ID: 75ML1b, tag_sequence: TAGACTC; Sample ID:75ML1c, tag_sequence: TAGACGA; Sample ID: 75MabL1a, tag_sequence: TAGAGAC; Sample ID:75MabL1b, tag_sequence: TAGAGCA; Sample ID: 75MabL1c, tag_sequence: TAGCTCA; Sample ID: 75MsedL1a, tag_sequence: TAGCACT; Sample ID: 75MsedL1b, tag_sequence: TAGCAGA; Sample ID: 75MsedL1c, tag_sequence: TAGCGTA; Sample ID: 50ML1a, tag_sequence: TCTACTC; Sample ID: 50ML1b, tag_sequence: TCTCTCA; Sample ID: 50ML1c, tag_sequence:TCTCATC; Sample ID:50MabL1a, tag_sequence:TCTCACT; Sample ID: 50MabL1b, tag_sequence: TCTCAGA; Sample ID: 50MabL1c, tag_sequence: TCTGAGT; Sample ID: 50MsedL1a, tag_sequence: TCATAGC; Sample ID:50MsedL1b, tag_sequence:TCATCTC; Sample ID:50MsedL1c, tag_sequence:TCATCGA; Sample ID:25ML1a, tag_sequence: TCATGAC; Sample ID: 25ML1b, tag_sequence:TCATGCA; Sample ID:25ML1c,tag_sequence:TCACTAC; Sample ID:25MabL1a, tag_sequence: TCACTCT; Sample ID:25MabL1b, stag_sequence:TCACTGA; Sample ID:25MabL1c, tag_sequence:TCACACA; Sample ID: 25MsedL1a, tag_sequence:TCACAGT; Sample ID:25MsedL1b, tag_sequence:TCACGTA; Sample ID:25MsedL1c, tag_sequence:TCACGAT; Sample ID: 0ML1a, tag_sequence: TCAGTCA; Sample ID: 0ML1b, tag_sequence: TCAGATC; Sample ID:0ML1c, tag_sequence:TCAGAGA; Sample ID: 0MabL1a, tag_sequence:TCAGCTA; Sample ID:0MabL1b, tag_sequence:TCGTAGA; Sample ID:0MabL1c, tag_sequence:TCGTGTA; sample ID:0MsedL1a, tag_sequence:TCGATCA; Sample ID: 0MsedL1b, tag_sequence:TCGACTA; Sample ID: 0MsedL1c, tag_sequence:TCGCATA; Sample ID: controlL1a, tag_sequence:TGTACGA; Sample ID: controlL1b, tag_sequence:TGTAGCA; Sample ID:controlL1c, tag_sequence:TGTCACA; Sample ID: 100ML2a, tag_sequence: TGTCGTA; Sampel ID: 100ML2b, tag_sequence:TGTGTCA; Sample ID:100ML2c, tag_sequence: TGTGCTA; Sample ID: 100MabL2a, tag_sequence:TGATCAC; Sample ID: 100MabL2b, tag_sequence:TGACTCA; Sample ID:100MabL2c, tag_sequence: TGACACT; sample ID:100MsedL2a, tag_sequence: TGAGTAC; Sample ID: 100MsedL2b, tag_sequence: TGAGTCT; Sample ID: 100MsedL2c, tag_sequence: TGAGTGA; Sample ID: 75ML2a, tag_sequence: TGAGCAT; Sample ID: 75ML2b, tag_sequence: TGCTAGA; Sample ID: 75ML2c, tag_sequence:TGCTGTA; Sample ID: 75MabL2a, tag_sequence: TGCATCA; Sample ID: 75MabL2b, tag_sequence: TGCACTA; Sample ID: 75MabL2c, tag_sequence: TGCGATA; Sample ID: 75MsedL2a, tag_sequence: ATACTGC; Sample ID: 75MsedL2b, tag_sequence: ATACGCT; Sample ID: 75MsedL2c, tag_sequence: ATAGCGT; Sample ID: 50ML2a, tag_sequence: ATCTCAC; Sample ID: 50ML2b, tag_sequence: ATCATGC; Sample ID: 50ML2c, tag_sequence: ATCACTC; Sample ID: 50MabL2a, tag_sequence: ATCACGT; Sample ID: 50MabL2b, tag_sequence: ATCAGAC; Sample ID: 50MabL2c, tag_sequence: ATCAGCT; Sample ID: 50MsedL2a, tag_sequence: ATCGTGT; Sample ID: 50MsedL2b, tag_sequence: ATCGACT; Sample ID: 50MsedL2c, tag_sequence: ATCGCAT; Sample ID: 25ML2a, tag_sequence: ATGTCGT; Sample ID:25ML2b, tag_sequence: ATGTGCT; Sample ID: 25ML2c, tag_sequence: ATGAGTC; Sample ID: T0 Sed L1, tag_sequence: ATGAGCA; Sample ID: T0 Sed L2, tag_sequence: ATGCTGT; Sample ID: T0 Sed L3, tag_sequence: ATGCACT; Sample ID: T0 M, tag_sequence: ATGCGAT; Sample ID: T0 L1, tag_sequence: ACTATGC; Sample ID: T0 L2, tag_sequence: ACTACAC; Sample ID:T0 L3, tag_sequence: ACTACGT; Sample ID: T0 B, tag_sequence: ACTAGTC  pooled sample #2: Sample ID: 25MabL2a, tag_sequence: TATCGCA; Sample ID: 25MabL2b, tag_sequence: TACTAGC; Sample ID: 25MabL2c, tag_sequence: TACTCTC; Sample ID: 25MsedL2a, tag_sequence: TACTCGA; Sample ID: 25MsedL2b, tag_sequence: TACTGAC; Sample ID: 25MsedL2c, tag_sequence: TACTGCA; Sample ID: 0ML2a, tag_sequence: TACGTCA; Sample ID: 0ML2b, tag_sequence: TACGAGT; Sample ID: 0ML2c, tag_sequence: TACGCTA; Sample ID:  0MabL2a, tag_sequence: TAGTCAC; Sample ID: 0MabL2b, tag_sequence: TAGACTC; Sample ID: 0MabL2c, tag_sequence: TAGACGA; Sample ID: 0MsedL2a, tag_sequence: TAGAGAC; Sample ID: 0MsedL2b, tag_sequence: TAGAGCA; Sample ID: 0MsedL2c, tag_sequence: TAGCTCA; Sample ID: controlL2a, tag_sequence: TAGCACT; Sample ID: controlL2b, tag_sequence: TAGCAGA, Sample ID: controlL2c, tag_sequence: TAGCGTA; Sample ID: 100ML3a, tag_sequence: TCTACTC; Sample ID: 100ML3b, tag_sequence: TCTCTCA; Sample ID: 100ML3c, tag_sequence: TCTCATC; Sample ID: 100MabL3a, tag_sequence: TCTCACT; Sample ID: 100MabL3b, tag_sequence: TCTCAGA; Sample ID: 100MabL3c, tag_sequence: TCTGAGT; Sample ID: 100MsedL3a, tag_sequence: TCATAGC; Sample ID: 100MsedL3b, tag_sequence: TCATCTC; Sample ID: 100MsedL3c, tag_sequence: TCATCGA; Sample ID: 75ML3a, tag_sequence: TCATGAC; Sample ID: 75ML3b, tag_sequence: TCATGCA; Sample ID: 75ML3c, tag_sequence: TCACTAC; Sample ID: 75MabL3a, tag_sequence: TCACTCT; Sample ID: 75MabL3b, tag_sequence: TCACTGA; Sample ID: 75MabL3c, tag_sequence: TCACACA; Sample ID:75MsedL3a, tag_sequence: TCACAGT; Sample ID: 75MsedL3b, tag_sequence: TCACGTA; Sample ID: 75MsedL3c, tag_sequence: TCACGAT; Sample ID: 50ML3a, tag_sequence: TCAGTCA; Sample ID: 50ML3b, tag_sequence: TCAGATC; Sample ID: 50ML3c, tag_sequence: TCAGAGA; Sample ID: 50MabL3a, tag_sequence: TCAGCTA; Sample ID: 50MabL3b, tag_sequence: TCGTAGA; Sample ID: 50MabL3c, tag_sequence: TCGTGTA, Sample ID: 50MsedL3a, tag_sequence: TCGATCA; Sample ID: 50MsedL3b, tag_sequence: TCGACTA; Sample ID: 50MsedL3c, tag_sequence: TCGCATA; Sample ID: 25ML3a, tag_sequence: TGTACGA; Sample ID: 25ML3b, tag_sequence: TGTAGCA; Sample ID: 25ML3c, tag_sequence: TGTCACA; Sample ID: 25MabL3a, tag_sequence: TGTCGTA; Sample ID: 25MabL3b, tag_sequence: TGTGTCA; Sample ID: 25MabL3c, tag_sequence: TGTGCTA; Sample ID: 25MsedL3a, tag_sequence: TGATCAC; Sample ID: 25MsedL3b, tag_sequence: TGACTCA; Sample ID: 25MsedL3c, tag_sequence: TGACACT; Sample ID: 0ML3a, tag_sequence: TGAGTAC; Sample ID: 0ML3b, tag_sequence: TGAGTCT; Sample ID: 0ML3c, tag_sequence: TGAGTGA; Sample ID: 0MabL3a, tag_sequence: TGAGCAT; Sample ID: 0MabL3b, tag_sequence: TGCTAGA; Sample ID: 0MabL3c, tag_sequence: TGCTGTA; Sample ID: 0MsedL3a, tag_sequence: TGCATCA; Sample ID: 0MsedL3b, tag_sequence: TGCACTA; Sample ID: 0MsedL3c, tag_sequence: TGCGATA; Sample ID: controlL3a, tag_sequence: ATACTGC; Sample ID: controlL3b, tag_sequence: ATACGCT; Sample ID: controlL3c, tag_sequence: ATAGCGT; Sample ID: M.M, tag_sequence: ATCTCAC; Sample ID: M.M, tag_sequence: ATCATGC; Sample ID: M.M, tag_sequence: ATCACTC; Sample ID: control M, tag_sequence: ATCACGT; Sample ID: control M, tag_sequence: ATCAGAC; Sample ID: control M, tag_sequence: ATCAGCT; Sample ID: B.B, tag_sequence: ATCGTGT; Sample ID: B.B, tag_sequence: ATCGACT; Sample ID: B.B, tag_sequence: ATCGCAT; Sample ID: control B, tag_sequence: ATGTCGT; Sample ID: control B, tag_sequence: ATGTGCT; Sample ID: control B, tag_sequence: ATGAGTC; Sample ID: T0 Sed L1, tag_sequence: ATGAGCA; Sample ID: T0 Sed L2, tag_sequence: ATGCTGT; Sample ID: T0 Sed L3, tag_sequence: ATGCACT; Sample ID: T0 M, tag_sequence: ATGCGAT; Sample ID: T0 L1, tag_sequence: ACTATGC; Sample ID: T0 L2, tag_sequence: ACTACAC; Sample ID: T0 L3, tag_sequence: ACTACGT; Sample ID: T0 B, tag_sequence: ACTAGTC</DESIGN_DESCRIPTION><SAMPLE_DESCRIPTOR accession="SRS371332"><IDENTIFIERS><PRIMARY_ID>SRS371332</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01766609</EXTERNAL_ID></IDENTIFIERS></SAMPLE_DESCRIPTOR><LIBRARY_DESCRIPTOR><LIBRARY_NAME/><LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY><LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>PCR</LIBRARY_SELECTION><LIBRARY_LAYOUT><SINGLE/></LIBRARY_LAYOUT></LIBRARY_DESCRIPTOR><SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR></DESIGN><PLATFORM><LS454><INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL></LS454></PLATFORM><PROCESSING/></EXPERIMENT><SUBMISSION xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="exp2010" lab_name="IBIS" accession="SRA059612" center_name="University Laval" submission_date="2012-10-16T14:11:52Z"><IDENTIFIERS><PRIMARY_ID>SRA059612</PRIMARY_ID><SUBMITTER_ID namespace="University Laval">exp2010</SUBMITTER_ID></IDENTIFIERS></SUBMISSION><STUDY alias="PRJNA177753" center_name="BioProject" accession="SRP016496"><IDENTIFIERS><PRIMARY_ID>SRP016496</PRIMARY_ID><EXTERNAL_ID namespace="BioProject">PRJNA177753</EXTERNAL_ID></IDENTIFIERS><DESCRIPTOR><STUDY_TITLE>Freshwater communities response to marine conditions Targeted Locus (Loci)</STUDY_TITLE><STUDY_TYPE existing_study_type="Metagenomics"/><STUDY_ABSTRACT>Batch cultures of natural bacterial communities (sediment, lake and air) were built along a gradient in marine conditions. 3 regions in Sweden were sampled to collect original communities that differ to their proximity to sea coast. The ultimate objective is to determine whether marine taxa can be retrieved from freshwater communities. In particular, we aimed at investigating which source contributes the most to marine taxa recruitment.</STUDY_ABSTRACT><CENTER_PROJECT_NAME>aquatic metagenome</CENTER_PROJECT_NAME><RELATED_STUDIES><RELATED_STUDY><RELATED_LINK><DB>bioproject</DB><ID>177753</ID><LABEL>PRJNA177753</LABEL></RELATED_LINK><IS_PRIMARY>true</IS_PRIMARY></RELATED_STUDY></RELATED_STUDIES></DESCRIPTOR></STUDY><SAMPLE center_name="BioSample" alias="SAMN01766609" accession="SRS371332"><IDENTIFIERS><PRIMARY_ID>SRS371332</PRIMARY_ID><EXTERNAL_ID namespace="BioSample">SAMN01766609</EXTERNAL_ID></IDENTIFIERS><TITLE>General Sample for uncultured bacterium</TITLE><SAMPLE_NAME><TAXON_ID>1169740</TAXON_ID><SCIENTIFIC_NAME>aquatic metagenome</SCIENTIFIC_NAME></SAMPLE_NAME><SAMPLE_LINKS><SAMPLE_LINK><ENTREZ_LINK><DB>biosample</DB><ID>1766609</ID><LABEL>SAMN01766609</LABEL></ENTREZ_LINK></SAMPLE_LINK><SAMPLE_LINK><ENTREZ_LINK><DB>bioproject</DB><QUERY>PRJNA177753</QUERY></ENTREZ_LINK></SAMPLE_LINK></SAMPLE_LINKS><SAMPLE_ATTRIBUTES><SAMPLE_ATTRIBUTE><TAG>isolate</TAG><VALUE>bacteria</VALUE></SAMPLE_ATTRIBUTE></SAMPLE_ATTRIBUTES></SAMPLE><RUN_SET><RUN xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" alias="Exp 2010" accession="SRR594956" center_name="University Laval" total_spots="760325" total_bases="395631455" size="889979778" load_done="true" published="2012-10-19 11:17:59" is_public="true" cluster_name="public" static_data_available="1"><IDENTIFIERS><PRIMARY_ID>SRR594956</PRIMARY_ID><SUBMITTER_ID namespace="University Laval">Exp 2010</SUBMITTER_ID></IDENTIFIERS><EXPERIMENT_REF accession="SRX196098"/><Pool><Member member_name="" accession="SRS371332" sample_name="SAMN01766609" sample_title="General Sample for uncultured bacterium" spots="760325" bases="395631455"/></Pool></RUN></RUN_SET></EXPERIMENT_PACKAGE>
</EXPERIMENT_PACKAGE_SET>