Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Identifieur interne : 000314 ( Ncbi/Curation ); précédent : 000313; suivant : 000315Diversity, 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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)-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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, Stanford, CA,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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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 wicri:level="1"><nlm:aff id="aff1"><institution>Department of Environmental Earth System Science, Stanford University</institution>
, Stanford, CA,<country>USA</country>
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<country xml:lang="fr">États-Unis</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>
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, Stanford, CA,<country>USA</country>
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<country xml:lang="fr">États-Unis</country>
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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>
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