Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics
Abstract A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two...
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| Veröffentlicht in: | FEMS microbiology ecology 2014-06, Vol.88 (3), p.623-635 |
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| creator | Fernández, Ana B. Ghai, Rohit Martin-Cuadrado, Ana-Belen Sánchez-Porro, Cristina Rodriguez-Valera, Francisco Ventosa, Antonio |
| description | Abstract
A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium ‘Spiribacter salinus’ were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the ‘salt-in’ strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.
Metagenomic-based phylogenomics and metabolic microbial diversity of an intermediate salinity saltern pond (13% salts) is described. New groups of Euryarchaeota and Bacteria are found. |
| doi_str_mv | 10.1111/1574-6941.12329 |
| format | Article |
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A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium ‘Spiribacter salinus’ were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the ‘salt-in’ strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.
Metagenomic-based phylogenomics and metabolic microbial diversity of an intermediate salinity saltern pond (13% salts) is described. New groups of Euryarchaeota and Bacteria are found.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1111/1574-6941.12329</identifier><identifier>PMID: 24661078</identifier><identifier>CODEN: FMECEZ</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Actinobacteria ; Archaea - classification ; Archaea - genetics ; Archaea - isolation & purification ; Archaea - metabolism ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteria - metabolism ; Carbon cycle ; compatible solutes ; Ecology ; Ecosystem ; Energy sources ; Euryarchaeota ; Euryarchaeota - classification ; Euryarchaeota - genetics ; extreme environments ; Gammaproteobacteria - classification ; Gammaproteobacteria - genetics ; Habitats ; haloarchaea ; Halobacteriaceae ; halophilic bacteria ; Lagoons ; Metagenome ; Metagenomics ; Microbiology ; Microorganisms ; Phylogeny ; Ponds ; Ponds - microbiology ; Principal components analysis ; Salinity ; saltern ; Solutes ; Verrucomicrobia ; Water Microbiology</subject><ispartof>FEMS microbiology ecology, 2014-06, Vol.88 (3), p.623-635</ispartof><rights>2014 Federation of European Microbiological Societies 2014</rights><rights>2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved</rights><rights>2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.</rights><rights>Copyright © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4399-cca8c19d7636b30fbb901fd44131a412a55720d52922b1e0a8a4b2061dec7d73</citedby><cites>FETCH-LOGICAL-c4399-cca8c19d7636b30fbb901fd44131a412a55720d52922b1e0a8a4b2061dec7d73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1574-6941.12329$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1574-6941.12329$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24661078$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fernández, Ana B.</creatorcontrib><creatorcontrib>Ghai, Rohit</creatorcontrib><creatorcontrib>Martin-Cuadrado, Ana-Belen</creatorcontrib><creatorcontrib>Sánchez-Porro, Cristina</creatorcontrib><creatorcontrib>Rodriguez-Valera, Francisco</creatorcontrib><creatorcontrib>Ventosa, Antonio</creatorcontrib><title>Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>Abstract
A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium ‘Spiribacter salinus’ were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the ‘salt-in’ strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.
Metagenomic-based phylogenomics and metabolic microbial diversity of an intermediate salinity saltern pond (13% salts) is described. New groups of Euryarchaeota and Bacteria are found.</description><subject>Actinobacteria</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - isolation & purification</subject><subject>Archaea - metabolism</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteria - metabolism</subject><subject>Carbon cycle</subject><subject>compatible solutes</subject><subject>Ecology</subject><subject>Ecosystem</subject><subject>Energy sources</subject><subject>Euryarchaeota</subject><subject>Euryarchaeota - classification</subject><subject>Euryarchaeota - genetics</subject><subject>extreme environments</subject><subject>Gammaproteobacteria - classification</subject><subject>Gammaproteobacteria - genetics</subject><subject>Habitats</subject><subject>haloarchaea</subject><subject>Halobacteriaceae</subject><subject>halophilic bacteria</subject><subject>Lagoons</subject><subject>Metagenome</subject><subject>Metagenomics</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Phylogeny</subject><subject>Ponds</subject><subject>Ponds - microbiology</subject><subject>Principal components analysis</subject><subject>Salinity</subject><subject>saltern</subject><subject>Solutes</subject><subject>Verrucomicrobia</subject><subject>Water Microbiology</subject><issn>0168-6496</issn><issn>1574-6941</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkdFr1TAUxoMo7jp99k0KvojQ7Zw0TZtHGZsKk-1h7yFpUpfZNtcknfa_N713GzIGeggkJ-d3PpLzEfIW4QhzHGPdsJILhkdIKyqekc3DzXOyAeRtyZngB-RVjDcAWFcMXpIDyjhHaNoNub0M_ocKi0-uK5L67Sc_5pOaTDHapLQfcmbcrQ3RpaXwfS4Vbko2jNY4lWwR1eCmtXa9bDO1Zra4VtollQoVo83LFHrZ6X23O_34mrzo1RDtm7v9kFydnV6dfCnPLz5_Pfl0XnasEqLsOtV2KEzDK64r6LUWgL1hDCtUDKmq64aCqamgVKMF1SqmKXA0tmtMUx2SD3vZbfA_ZxuTHF3s7DCoyfo5SqwZaxhFwP9BgeYQkNH3j9AbP4cp_yNTFQjWguCZOt5TXfAxBtvLbXBjHrVEkKt5crVKrlbJnXm5492d7qzzdB_4e7cyUO-BX26wy7_05Nnpt3vhj_s-P2-f7Cr_esUf-rmwug</recordid><startdate>201406</startdate><enddate>201406</enddate><creator>Fernández, Ana B.</creator><creator>Ghai, Rohit</creator><creator>Martin-Cuadrado, Ana-Belen</creator><creator>Sánchez-Porro, Cristina</creator><creator>Rodriguez-Valera, Francisco</creator><creator>Ventosa, Antonio</creator><general>Blackwell Publishing Ltd</general><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7ST</scope><scope>7TN</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>SOI</scope><scope>7X8</scope></search><sort><creationdate>201406</creationdate><title>Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics</title><author>Fernández, Ana B. ; 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A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium ‘Spiribacter salinus’ were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the ‘salt-in’ strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.
Metagenomic-based phylogenomics and metabolic microbial diversity of an intermediate salinity saltern pond (13% salts) is described. New groups of Euryarchaeota and Bacteria are found.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>24661078</pmid><doi>10.1111/1574-6941.12329</doi><tpages>13</tpages></addata></record> |
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| subjects | Actinobacteria Archaea - classification Archaea - genetics Archaea - isolation & purification Archaea - metabolism Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteria - metabolism Carbon cycle compatible solutes Ecology Ecosystem Energy sources Euryarchaeota Euryarchaeota - classification Euryarchaeota - genetics extreme environments Gammaproteobacteria - classification Gammaproteobacteria - genetics Habitats haloarchaea Halobacteriaceae halophilic bacteria Lagoons Metagenome Metagenomics Microbiology Microorganisms Phylogeny Ponds Ponds - microbiology Principal components analysis Salinity saltern Solutes Verrucomicrobia Water Microbiology |
| title | Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics |
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