Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Ponds of a Marine Saltern in Santa Pola, Spain
Identifieur interne : 000237 ( Pmc/Corpus ); précédent : 000236; suivant : 000238Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Ponds of a Marine Saltern in Santa Pola, Spain
Auteurs : Ana B. Fernandez ; Rohit Ghai ; Ana Belen Martin-Cuadrado ; Cristina Sanchez-Porro ; Francisco Rodriguez-Valera ; Antonio VentosaSource :
- Genome Announcements [ 2169-8287 ] ; 2013.
Abstract
Marine salterns are composed of several shallow ponds with a salinity gradient, from seawater to salt saturation, with gradually changing microbial populations. Here, we report the metagenome sequencing of the prokaryotic microbiota of two ponds with 13% and 33% salinity from a saltern in Santa Pola, Spain.
Url:
DOI: 10.1128/genomeA.00933-13
PubMed: 24233589
PubMed Central: 3828313
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Ponds of a Marine Saltern in Santa Pola, Spain</title><author><name sortKey="Fernandez, Ana B" sort="Fernandez, Ana B" uniqKey="Fernandez A" first="Ana B." last="Fernandez">Ana B. Fernandez</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ghai, Rohit" sort="Ghai, Rohit" uniqKey="Ghai R" first="Rohit" last="Ghai">Rohit Ghai</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Martin Cuadrado, Ana Belen" sort="Martin Cuadrado, Ana Belen" uniqKey="Martin Cuadrado A" first="Ana Belen" last="Martin-Cuadrado">Ana Belen Martin-Cuadrado</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Sanchez Porro, Cristina" sort="Sanchez Porro, Cristina" uniqKey="Sanchez Porro C" first="Cristina" last="Sanchez-Porro">Cristina Sanchez-Porro</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Rodriguez Valera, Francisco" sort="Rodriguez Valera, Francisco" uniqKey="Rodriguez Valera F" first="Francisco" last="Rodriguez-Valera">Francisco Rodriguez-Valera</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Ventosa, Antonio" sort="Ventosa, Antonio" uniqKey="Ventosa A" first="Antonio" last="Ventosa">Antonio Ventosa</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24233589</idno><idno type="pmc">3828313</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828313</idno><idno type="RBID">PMC:3828313</idno><idno type="doi">10.1128/genomeA.00933-13</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000237</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Ponds of a Marine Saltern in Santa Pola, Spain</title><author><name sortKey="Fernandez, Ana B" sort="Fernandez, Ana B" uniqKey="Fernandez A" first="Ana B." last="Fernandez">Ana B. Fernandez</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ghai, Rohit" sort="Ghai, Rohit" uniqKey="Ghai R" first="Rohit" last="Ghai">Rohit Ghai</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Martin Cuadrado, Ana Belen" sort="Martin Cuadrado, Ana Belen" uniqKey="Martin Cuadrado A" first="Ana Belen" last="Martin-Cuadrado">Ana Belen Martin-Cuadrado</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Sanchez Porro, Cristina" sort="Sanchez Porro, Cristina" uniqKey="Sanchez Porro C" first="Cristina" last="Sanchez-Porro">Cristina Sanchez-Porro</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Rodriguez Valera, Francisco" sort="Rodriguez Valera, Francisco" uniqKey="Rodriguez Valera F" first="Francisco" last="Rodriguez-Valera">Francisco Rodriguez-Valera</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Ventosa, Antonio" sort="Ventosa, Antonio" uniqKey="Ventosa A" first="Antonio" last="Ventosa">Antonio Ventosa</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Genome Announcements</title><idno type="eISSN">2169-8287</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Marine salterns are composed of several shallow ponds with a salinity gradient, from seawater to salt saturation, with gradually changing microbial populations. Here, we report the metagenome sequencing of the prokaryotic microbiota of two ponds with 13% and 33% salinity from a saltern in Santa Pola, Spain.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ventosa, A" uniqKey="Ventosa A">A Ventosa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ventosa, A" uniqKey="Ventosa A">A Ventosa</name></author><author><name sortKey="Nieto, Jj" uniqKey="Nieto J">JJ Nieto</name></author><author><name sortKey="Oren, A" uniqKey="Oren A">A Oren</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oren, A" uniqKey="Oren A">A Oren</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rodriguez Valera, F" uniqKey="Rodriguez Valera F">F Rodriguez-Valera</name></author><author><name sortKey="Ventosa, A" uniqKey="Ventosa A">A Ventosa</name></author><author><name sortKey="Juez, G" uniqKey="Juez G">G 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id><journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">ga</journal-id><journal-id journal-id-type="publisher-id">GA</journal-id><journal-title-group><journal-title>Genome Announcements</journal-title></journal-title-group><issn pub-type="epub">2169-8287</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24233589</article-id><article-id pub-id-type="pmc">3828313</article-id><article-id pub-id-type="publisher-id">genomeA00933-13</article-id><article-id pub-id-type="doi">10.1128/genomeA.00933-13</article-id><article-categories><subj-group subj-group-type="heading"><subject>Prokaryotes</subject></subj-group></article-categories><title-group><article-title>Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Ponds of a Marine Saltern in Santa Pola, Spain</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Fernandez</surname><given-names>Ana B.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ghai</surname><given-names>Rohit</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Martin-Cuadrado</surname><given-names>Ana Belen</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sanchez-Porro</surname><given-names>Cristina</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rodriguez-Valera</surname><given-names>Francisco</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Ventosa</surname><given-names>Antonio</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1">Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain<label>a</label></aff><aff id="aff2">Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain<label>b</label></aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Antonio Ventosa, <email>ventosa@us.es</email>.</corresp></author-notes><pub-date pub-type="epub"><day>14</day><month>11</month><year>2013</year></pub-date><pub-date pub-type="collection"><season>Nov-Dec</season><year>2013</year></pub-date><volume>1</volume><issue>6</issue><elocation-id>e00933-13</elocation-id><history><date date-type="received"><day>4</day><month>10</month><year>2013</year></date><date date-type="accepted"><day>10</day><month>10</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © 2013 Fernandez et al.</copyright-statement><copyright-year>2013</copyright-year><copyright-holder>Fernandez et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported license</ext-link>.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="jga00613753001.pdf"></self-uri><abstract><p>Marine salterns are composed of several shallow ponds with a salinity gradient, from seawater to salt saturation, with gradually changing microbial populations. Here, we report the metagenome sequencing of the prokaryotic microbiota of two ponds with 13% and 33% salinity from a saltern in Santa Pola, Spain.</p></abstract><counts><page-count count="2"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>November/December 2013</meta-value></custom-meta><custom-meta><meta-name>access-type</meta-name><meta-value>free</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec><title>GENOME ANNOUNCEMENT</title><p>Hypersaline environments are widely distributed habitats characterized by their high salt concentrations, e.g., solar salterns, saline soils, salted foods, and other salted products (<xref ref-type="bibr" rid="B1">1</xref>). Among these, salterns are probably the most widely studied habitats and are excellent models for studying the microbial populations inhabiting the ponds along a natural salinity gradient up to NaCl saturation (<xref ref-type="bibr" rid="B2">2</xref>, <xref ref-type="bibr" rid="B3">3</xref>). One of the more extensively studied salterns is located in Santa Pola, near Alicante in southeastern Spain. These salterns have been the subjects of a variety of studies, with approaches ranging from the classical culture-dependent to the more recent culture-independent methods, over nearly 30 years (<xref ref-type="bibr" rid="B4">4</xref>–<xref ref-type="bibr" rid="B10">10</xref>). A recent metagenomic study described the microbiota of two of these saltern ponds, one of intermediate salinity (19% salt) and an NaCl-saturated crystallizer pond (37% salt), using direct pyrosequencing (<xref ref-type="bibr" rid="B11">11</xref>).</p><p>This study is aimed toward investigating the prokaryotic microbiota of the surface water of two additional hypersaline ponds, with 13% and 33% salinity, in the same location (Bras del Port saltern, Santa Pola, Spain; GPS coordinates: for the 13% pond [SS13], 38°12′05″N, 0°35′44″W; and for the 33% pond [SS33], 38°11′59″N, 0°35′11″W). Fifty-liter water samples were collected on 20 September 2010 and sequentially filtered through 5.0-µm and 0.22-µm pore polycarbonate filters (Millipore, USA). Metagenomic DNA was extracted and purified as previously described (<xref ref-type="bibr" rid="B11">11</xref>, <xref ref-type="bibr" rid="B12">12</xref>). The purified total prokaryotic DNA was sequenced by pyrosequencing (Roche 454 GS-FLX system, Titanium chemistry) by GATC, Konstanz, Germany. The average read lengths obtained were 305 bp and 367 bp for the SS13 and SS33 metagenomes, respectively. A total of 1,443,593 reads and 842,872 reads were obtained for SS13 and SS33, respectively.</p><p>The sequences were compared against the Ribosomal Database Project (RDP) (<xref ref-type="bibr" rid="B13">13</xref>) to analyze and identify 16S rRNA genes. Metagenomic reads were also annotated using the MG-RAST server (<xref ref-type="bibr" rid="B14">14</xref>), CAMERA (<xref ref-type="bibr" rid="B15">15</xref>), and IMG (<xref ref-type="bibr" rid="B16">16</xref>).</p><p>The most abundant phylum detected in both samples was <italic>Euryarchaeota</italic>, while the phyla <italic>Bacteroidetes</italic> and <italic>Euryarchaeota</italic> were the only two prokaryotic groups shared by the metagenomic datasets. At 13% salinity, the diversity found at the phylum and genus level was higher than in the 33% salinity saltern, but the number of sequences unclassified at the genus level was higher in the 13% salinity saltern.</p><p>The data from these metagenomic datasets reveal the genetic diversity in these ponds and the changes in microbial community composition along the salinity gradient in this environment compared to the metagenomic data available from different ponds from this saltern.</p><sec id="h1"><title>Nucleotide sequence accession number.</title><p>The DNA sequences from this metagenomic project have been deposited in the NCBI Sequence Read Archive under the accession no. <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra/?term=SRP028290">SRP028290</ext-link>.</p></sec></sec></body><back><fn-group><fn fn-type="other"><p><bold>Citation</bold> Fernandez AB, Ghai R, Martin-Cuadrado AB, Sanchez-Porro C, Rodriguez-Valera F, Ventosa A. 2013. Metagenome sequencing of prokaryotic microbiota from two hypersaline ponds of a marine saltern in Santa Pola, Spain. Genome Announc. 1(6):e00933-13. doi:10.1128/genomeA.00933-13.</p></fn></fn-group><ack><title>ACKNOWLEDGMENTS</title><p>This work was supported by grants from <funding-source id="GS1">the Spanish Ministry of Science and Innovation</funding-source> (<award-id rid="GS1">CGL2010-19303</award-id>), <funding-source id="GS2">MAGYK</funding-source> (<award-id rid="GS2">BIO2008-02444</award-id>), MICROGEN (Programa CONSOLIDER-INGENIO 2010 <award-id id="G1">CDS2009-00006</award-id>), and <award-id id="G2">CGL2009-12651-C02-01</award-id>; the Generalitat Valenciana (<funding-source id="GS5">DIMEGEN</funding-source><award-id rid="GS5">PROMETEO/2010/089</award-id> and <award-id rid="GS5">ACOMP/2009/155</award-id>); the <funding-source id="GS6">MaCuMBA Project</funding-source><award-id rid="GS6">311975</award-id> of the European Commission FP7; and the Junta de Andalucía (<award-id id="G3">P10-CVI-6226</award-id>). FEDER funds also supported this project. 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