Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters
Identifieur interne : 000462 ( Ncbi/Merge ); précédent : 000461; suivant : 000463Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters
Auteurs : James T. Hollibaugh [États-Unis] ; Scott M. Gifford [États-Unis] ; Mary Ann Moran [États-Unis] ; Meredith J. Ross [États-Unis] ; Shalabh Sharma [États-Unis] ; Bradley B. Tolar [États-Unis]Source :
- The ISME Journal [ 1751-7362 ] ; 2013.
Abstract
We used a combination of metatranscriptomic analyses and quantitative PCR (qPCR) to study seasonal changes in Thaumarchaeota populations from a salt marsh-dominated estuary. Surface waters (0.5 m depth) were sampled quarterly at Marsh Landing, Sapelo Island, GA, USA over a 3-year period. We found a mid-summer peak in Thaumarchaeota abundance measured by qPCR of either 16S rRNA or
Url:
DOI: 10.1038/ismej.2013.171
PubMed: 24132081
PubMed Central: 3930313
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<author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name>
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<front><div type="abstract" xml:lang="en"><p>We used a combination of metatranscriptomic analyses and quantitative PCR (qPCR) to study seasonal changes in Thaumarchaeota populations from a salt marsh-dominated estuary. Surface waters (0.5 m depth) were sampled quarterly at Marsh Landing, Sapelo Island, GA, USA over a 3-year period. We found a mid-summer peak in Thaumarchaeota abundance measured by qPCR of either 16S rRNA or <italic>amoA</italic>
genes in each of the 3 years. Thaumarchaeota were 100–1000-fold more abundant during the peak than at other times of the year, whereas the abundance of ammonia- and nitrite-oxidizing Bacteria varied <10-fold over the same period. Analysis of the microdiversity of several highly transcribed genes in 20 metatranscriptomes from a 1-year subset of these samples showed that the transcriptionally active population consisted of 2 or 3 dominant phylotypes that differed between successive summers. This shift appeared to have begun during the preceding winter and spring. Transcripts from the same genes dominated the Thaumarchaeota mRNA pool throughout the year, with genes encoding proteins believed to be involved in nitrogen uptake and oxidation, and two hypothetical proteins being the most abundant transcripts in all libraries. Analysis of individual genes over the seasonal cycle suggested that transcription was tied more closely to variation in growth rates than to seasonal changes in environmental conditions. Day–night differences in the relative abundance of transcripts for ribosomal proteins suggested diurnal variation in Thaumarchaeota growth.</p>
</div>
</front>
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<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>
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<article-meta><article-id pub-id-type="pmid">24132081</article-id>
<article-id pub-id-type="pmc">3930313</article-id>
<article-id pub-id-type="pii">ismej2013171</article-id>
<article-id pub-id-type="doi">10.1038/ismej.2013.171</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters</article-title>
<alt-title alt-title-type="running">Seasonality of Thaumarchaeota metatranscriptomes</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Hollibaugh</surname>
<given-names>James T</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>Gifford</surname>
<given-names>Scott M</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="author-notes" rid="note1"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Moran</surname>
<given-names>Mary Ann</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ross</surname>
<given-names>Meredith J</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="author-notes" rid="note2"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sharma</surname>
<given-names>Shalabh</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tolar</surname>
<given-names>Bradley B</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
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<aff id="aff1"><label>1</label>
<institution>Department of Marine Sciences, University of Georgia</institution>
, Athens, GA,<country>USA</country>
</aff>
<aff id="aff2"><label>2</label>
<institution>Department of Microbiology, University of Georgia</institution>
, Athens, GA,<country>USA</country>
</aff>
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<author-notes><corresp id="caf1"><label>*</label>
<institution>Department of Marine Sciences, University of Georgia</institution>
, 226 Marine Sciences Building, Athens, GA 30602-3636, <country>USA</country>
. E-mail: <email>aquadoc@uga.edu</email>
or <email>mmoran@uga.edu</email>
</corresp>
<fn fn-type="present-address" id="note1"><label>3</label>
<p>Present address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.</p>
</fn>
<fn fn-type="present-address" id="note2"><label>4</label>
<p>Present address: Biology Program, Vanderbilt University, Nashville, TN 37203, USA.</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>03</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>10</month>
<year>2013</year>
</pub-date>
<volume>8</volume>
<issue>3</issue>
<fpage>685</fpage>
<lpage>698</lpage>
<history><date date-type="received"><day>01</day>
<month>05</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>22</day>
<month>07</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>01</day>
<month>09</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 International Society for Microbial Ecology</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>International Society for Microbial Ecology</copyright-holder>
</permissions>
<abstract><p>We used a combination of metatranscriptomic analyses and quantitative PCR (qPCR) to study seasonal changes in Thaumarchaeota populations from a salt marsh-dominated estuary. Surface waters (0.5 m depth) were sampled quarterly at Marsh Landing, Sapelo Island, GA, USA over a 3-year period. We found a mid-summer peak in Thaumarchaeota abundance measured by qPCR of either 16S rRNA or <italic>amoA</italic>
genes in each of the 3 years. Thaumarchaeota were 100–1000-fold more abundant during the peak than at other times of the year, whereas the abundance of ammonia- and nitrite-oxidizing Bacteria varied <10-fold over the same period. Analysis of the microdiversity of several highly transcribed genes in 20 metatranscriptomes from a 1-year subset of these samples showed that the transcriptionally active population consisted of 2 or 3 dominant phylotypes that differed between successive summers. This shift appeared to have begun during the preceding winter and spring. Transcripts from the same genes dominated the Thaumarchaeota mRNA pool throughout the year, with genes encoding proteins believed to be involved in nitrogen uptake and oxidation, and two hypothetical proteins being the most abundant transcripts in all libraries. Analysis of individual genes over the seasonal cycle suggested that transcription was tied more closely to variation in growth rates than to seasonal changes in environmental conditions. Day–night differences in the relative abundance of transcripts for ribosomal proteins suggested diurnal variation in Thaumarchaeota growth.</p>
</abstract>
<kwd-group><kwd>ammonia oxidation</kwd>
<kwd>nitrification</kwd>
<kwd>estuary</kwd>
<kwd>Thaumarchaeota</kwd>
<kwd>nitrite</kwd>
<kwd>diurnal</kwd>
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<affiliations><list><country><li>États-Unis</li>
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<name sortKey="Gifford, Scott M" sort="Gifford, Scott M" uniqKey="Gifford S" first="Scott M" last="Gifford">Scott M. Gifford</name>
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<name sortKey="Ross, Meredith J" sort="Ross, Meredith J" uniqKey="Ross M" first="Meredith J" last="Ross">Meredith J. Ross</name>
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