Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Identifieur interne : 000511 ( Main/Merge ); précédent : 000510; suivant : 000512Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Auteurs : Marie B. Lund [États-Unis] ; Jason M. Smith [États-Unis] ; Christopher A. Francis [États-Unis]Source :
- 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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<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 wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></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 wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Francis, Christopher A" sort="Francis, Christopher A" uniqKey="Francis C" first="Christopher A" last="Francis">Christopher A. Francis</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22592819</idno><idno type="pmc">3446794</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446794</idno><idno type="RBID">PMC:3446794</idno><idno type="doi">10.1038/ismej.2012.40</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000003</idno><idno type="wicri:Area/Pmc/Curation">000003</idno><idno type="wicri:Area/Pmc/Checkpoint">000422</idno><idno type="wicri:Area/Ncbi/Merge">000314</idno><idno type="wicri:Area/Ncbi/Curation">000314</idno><idno type="wicri:Area/Ncbi/Checkpoint">000314</idno><idno type="wicri:doubleKey">1751-7362:2012:Lund M:diversity:abundance:and</idno><idno type="wicri:Area/Main/Merge">000511</idno></publicationStmt><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><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></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 wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Francis, Christopher A" sort="Francis, Christopher A" uniqKey="Francis C" first="Christopher A" last="Francis">Christopher A. Francis</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>, Stanford, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><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></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></record>Pour manipuler ce document sous Unix (Dilib)
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