Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Identifieur interne : 000003 ( Pmc/Corpus ); précédent : 000002; suivant : 000004Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Auteurs : Marie B. Lund ; Jason M. Smith ; Christopher A. FrancisSource :
- The ISME Journal [ 1751-7362 ] ; 2012.
Abstract
Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (
Url:
DOI: 10.1038/ismej.2012.40
PubMed: 22592819
PubMed Central: 3446794
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PMC:3446794Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Diversity, abundance and expression of nitrite reductase (<italic>nirK</italic>
)-like genes in marine thaumarchaea</title>
<author><name sortKey="Lund, Marie B" sort="Lund, Marie B" uniqKey="Lund M" first="Marie B" last="Lund">Marie B. Lund</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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</affiliation>
</author>
<author><name sortKey="Smith, Jason M" sort="Smith, Jason M" uniqKey="Smith J" first="Jason M" last="Smith">Jason M. Smith</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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<author><name sortKey="Francis, Christopher A" sort="Francis, Christopher A" uniqKey="Francis C" first="Christopher A" last="Francis">Christopher A. Francis</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Diversity, abundance and expression of nitrite reductase (<italic>nirK</italic>
)-like genes in marine thaumarchaea</title>
<author><name sortKey="Lund, Marie B" sort="Lund, Marie B" uniqKey="Lund M" first="Marie B" last="Lund">Marie B. Lund</name>
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<author><name sortKey="Smith, Jason M" sort="Smith, Jason M" uniqKey="Smith J" first="Jason M" last="Smith">Jason M. Smith</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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<author><name sortKey="Francis, Christopher A" sort="Francis, Christopher A" uniqKey="Francis C" first="Christopher A" last="Francis">Christopher A. Francis</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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<series><title level="j">The ISME Journal</title>
<idno type="ISSN">1751-7362</idno>
<idno type="eISSN">1751-7370</idno>
<imprint><date when="2012">2012</date>
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<front><div type="abstract" xml:lang="en"><p>Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (<italic>nirK</italic>
), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal <italic>nirK</italic>
genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the <italic>nirK</italic>
variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the <italic>nirK</italic>
from <italic>Candidatus</italic>
Nitrosopumilus maritimus and <italic>Candidatus</italic>
Nitrosoarchaeum limnia. The two <italic>nirK</italic>
variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal <italic>amoA</italic>
, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used <italic>amoA</italic>
primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal <italic>nirK</italic>
was expressed 10–100-fold more than <italic>amoA</italic>
in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">ISME J</journal-id>
<journal-id journal-id-type="iso-abbrev">ISME J</journal-id>
<journal-title-group><journal-title>The ISME Journal</journal-title>
</journal-title-group>
<issn pub-type="ppub">1751-7362</issn>
<issn pub-type="epub">1751-7370</issn>
<publisher><publisher-name>Nature Publishing Group</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22592819</article-id>
<article-id pub-id-type="pmc">3446794</article-id>
<article-id pub-id-type="pii">ismej201240</article-id>
<article-id pub-id-type="doi">10.1038/ismej.2012.40</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Diversity, abundance and expression of nitrite reductase (<italic>nirK</italic>
)-like genes in marine thaumarchaea</article-title>
<alt-title alt-title-type="running"><italic>nirK</italic>
-like genes in marine thaumarchaea</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Lund</surname>
<given-names>Marie B</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="caf1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Smith</surname>
<given-names>Jason M</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Francis</surname>
<given-names>Christopher A</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<aff id="aff1"><label>1</label>
<institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
</aff>
</contrib-group>
<author-notes><corresp id="caf1"><label>*</label>
<institution>Department of Environmental Earth System Science, Stanford University</institution>
, 473 Via Ortega, Y2E2 Building, Room 140, Stanford, CA 94305-4216, <country>USA</country>
. E-mail: <email>mlund@stanford.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>10</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>05</month>
<year>2012</year>
</pub-date>
<volume>6</volume>
<issue>10</issue>
<fpage>1966</fpage>
<lpage>1977</lpage>
<history><date date-type="received"><day>22</day>
<month>12</month>
<year>2011</year>
</date>
<date date-type="rev-recd"><day>19</day>
<month>03</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>23</day>
<month>03</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2012 International Society for Microbial Ecology</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>International Society for Microbial Ecology</copyright-holder>
</permissions>
<abstract><p>Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (<italic>nirK</italic>
), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal <italic>nirK</italic>
genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the <italic>nirK</italic>
variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the <italic>nirK</italic>
from <italic>Candidatus</italic>
Nitrosopumilus maritimus and <italic>Candidatus</italic>
Nitrosoarchaeum limnia. The two <italic>nirK</italic>
variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal <italic>amoA</italic>
, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used <italic>amoA</italic>
primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal <italic>nirK</italic>
was expressed 10–100-fold more than <italic>amoA</italic>
in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.</p>
</abstract>
<kwd-group><kwd>ammonia-oxidizing archaea</kwd>
<kwd>copper-containing nitrite reductase</kwd>
<kwd>Monterey Bay time series</kwd>
<kwd><italic>nirK</italic>
</kwd>
<kwd>thaumarchaea</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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