Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation
Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, origina...
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| Veröffentlicht in: | The ISME Journal 2016-05, Vol.10 (5), p.1051-1063 |
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| creator | Bayer, Barbara Vojvoda, Jana Offre, Pierre Alves, Ricardo J E Elisabeth, Nathalie H Garcia, Juan AL Volland, Jean-Marie Srivastava, Abhishek Schleper, Christa Herndl, Gerhard J |
| description | Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel
Nitrosopumilus
strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems. |
| doi_str_mv | 10.1038/ismej.2015.200 |
| format | Article |
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Nitrosopumilus
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Nitrosopumilus
strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.</description><subject>14/32</subject><subject>45/23</subject><subject>45/77</subject><subject>631/158/2446/2447</subject><subject>631/158/855</subject><subject>Ammonia</subject><subject>Ammonia - metabolism</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - physiology</subject><subject>Biomedical and Life Sciences</subject><subject>Carbon - metabolism</subject><subject>Ecology</subject><subject>Ecosystem</subject><subject>Energy Metabolism</subject><subject>Evolutionary Biology</subject><subject>Genomics</subject><subject>Life Sciences</subject><subject>Marine ecosystems</subject><subject>Microbial Ecology</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Microenvironments</subject><subject>Niches</subject><subject>North Sea</subject><subject>Original</subject><subject>original-article</subject><subject>Oxidation-Reduction</subject><subject>Oxidoreductases - genetics</subject><subject>Phylogeny</subject><subject>Physiology</subject><subject>Seawater - microbiology</subject><subject>Surface water</subject><subject>Urea</subject><subject>Water column</subject><issn>1751-7362</issn><issn>1751-7370</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptkctrFTEUxoNYbK1uXUrAjZt7m8fkMRtBii8o1IWuQ5qcuZPLTFKTTKX-9eb21kst3ZwcOL_z5Tt8CL2hZE0J12ehzLBdM0JFK-QZOqFK0JXiijw_9JIdo5elbAkRSkr1Ah0zKZjWXJ2g-n28LSFNaROcnbCNHm8gpjk47EabrauQwx9bQ4o4Dbj-TjimG5jwbHOIgOtol9Y2Ftp6qdmGWHCIvslVKDgGNwL2YRggQ6zhTukVOhrsVOD1_XuKfn7-9OP86-ri8su3848XKydYV1dcA1PO9b2HXisqqb7y3jonrdSqk04xweXQCTEILxX1VAgFfc-40AMDpfkp-rDXvV6uZvCuGch2Mtc5NMu3Jtlg_p_EMJpNujGd5r0grAm8vxfI6dcCpZo5FAfTZCOkpRiqNNOcyK5v6LtH6DYtObbzdhTVVHWCNmq9p1xOpWQYDmYoMbtAzV2gZhdoK6QtvH14wgH_l2ADzvZAaaO4gfzg36cl_wLnla-a</recordid><startdate>20160501</startdate><enddate>20160501</enddate><creator>Bayer, Barbara</creator><creator>Vojvoda, Jana</creator><creator>Offre, Pierre</creator><creator>Alves, Ricardo J E</creator><creator>Elisabeth, Nathalie H</creator><creator>Garcia, Juan AL</creator><creator>Volland, Jean-Marie</creator><creator>Srivastava, Abhishek</creator><creator>Schleper, Christa</creator><creator>Herndl, Gerhard J</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><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>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160501</creationdate><title>Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation</title><author>Bayer, Barbara ; Vojvoda, Jana ; Offre, Pierre ; Alves, Ricardo J E ; Elisabeth, Nathalie H ; Garcia, Juan AL ; Volland, Jean-Marie ; Srivastava, Abhishek ; Schleper, Christa ; Herndl, Gerhard J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c524t-38e27cc99de9871618bddacc6a68746c72536f455f5d671d1557e992358f2e783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>14/32</topic><topic>45/23</topic><topic>45/77</topic><topic>631/158/2446/2447</topic><topic>631/158/855</topic><topic>Ammonia</topic><topic>Ammonia - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The ISME Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bayer, Barbara</au><au>Vojvoda, Jana</au><au>Offre, Pierre</au><au>Alves, Ricardo J E</au><au>Elisabeth, Nathalie H</au><au>Garcia, Juan AL</au><au>Volland, Jean-Marie</au><au>Srivastava, Abhishek</au><au>Schleper, Christa</au><au>Herndl, Gerhard J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation</atitle><jtitle>The ISME Journal</jtitle><stitle>ISME J</stitle><addtitle>ISME J</addtitle><date>2016-05-01</date><risdate>2016</risdate><volume>10</volume><issue>5</issue><spage>1051</spage><epage>1063</epage><pages>1051-1063</pages><issn>1751-7362</issn><eissn>1751-7370</eissn><abstract>Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel
Nitrosopumilus
strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26528837</pmid><doi>10.1038/ismej.2015.200</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 14/32 45/23 45/77 631/158/2446/2447 631/158/855 Ammonia Ammonia - metabolism Archaea - classification Archaea - genetics Archaea - physiology Biomedical and Life Sciences Carbon - metabolism Ecology Ecosystem Energy Metabolism Evolutionary Biology Genomics Life Sciences Marine ecosystems Microbial Ecology Microbial Genetics and Genomics Microbiology Microenvironments Niches North Sea Original original-article Oxidation-Reduction Oxidoreductases - genetics Phylogeny Physiology Seawater - microbiology Surface water Urea Water column |
| title | Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation |
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