Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton
Identifieur interne : 000508 ( Istex/Corpus ); précédent : 000507; suivant : 000509Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton
Auteurs : Xiaozhen Mou ; Maria Vila-Costa ; Shulei Sun ; Weidong Zhao ; Shalabh Sharma ; Mary Ann MoranSource :
- Environmental Microbiology Reports [ 1758-2229 ] ; 2011-12.
Abstract
The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.
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DOI: 10.1111/j.1758-2229.2011.00289.x
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<front><div type="abstract" xml:lang="en">The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</div>
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<titleGroup><title type="main">Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title>
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<title type="short">Polyamine‐transforming genes in marine bacterial communities</title>
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<supportingInformation><p><b>Fig. S1.</b>
Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes.</p>
<p><b>Fig. S2.</b>
Phylogenetic placement of <i>spuC</i>
(A) and <i>kauB</i>
(B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen <i>et al</i>
., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura <i>et al</i>
., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes.</p>
<p><b>Table S1.</b>
Initial environmental and biological conditions in the microcosms.</p>
<p><b>Table S2.</b>
Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL.</p>
<p><b>Table S3.</b>
Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (<i>argD</i>
) has a sequence similar to <i>spuC</i>
but a different function unrelated to polyamine degradation<i>.</i>
To distinguish between these two genes, the blast hits that met the cut‐off criteria for <i>spuC</i>
but had a higher bit score against <i>argD</i>
were removed from the final list of <i>spuC</i>
homologues.</p>
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<abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title>
<p>The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (<i>Gammaproteobacteria</i>
, <i>Betaproteobacteria</i>
, <i>Actinobacteria</i>
and <i>Bacteroidetes</i>
) also contributed to polyamine‐related gene transcription.</p>
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<noteGroup><note xml:id="fn1"><p>Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</p>
</note>
<note xml:id="fn2"><p> University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</p>
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<mods version="3.6"><titleInfo lang="en"><title>Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title>
</titleInfo>
<titleInfo type="abbreviated" lang="en"><title>Polyamine‐transforming genes in marine bacterial communities</title>
</titleInfo>
<titleInfo type="alternative" contentType="CDATA" lang="en"><title>Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title>
</titleInfo>
<name type="personal"><namePart type="given">Xiaozhen</namePart>
<namePart type="family">Mou</namePart>
<affiliation>Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.</affiliation>
<description>Correspondence: E‐mail ; Tel. (+1) 330 672 3625; Fax (+1) 330 672 3713</description>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Maria</namePart>
<namePart type="family">Vila‐Costa</namePart>
<affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation>
<description>Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</description>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Shulei</namePart>
<namePart type="family">Sun</namePart>
<affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation>
<description>University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</description>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Weidong</namePart>
<namePart type="family">Zhao</namePart>
<affiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Shalabh</namePart>
<namePart type="family">Sharma</namePart>
<affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Mary Ann</namePart>
<namePart type="family">Moran</namePart>
<affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation>
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<dateIssued encoding="w3cdtf">2011-12</dateIssued>
<edition>Received 28 February, 2011; accepted 2 August, 2011.</edition>
<copyrightDate encoding="w3cdtf">2011</copyrightDate>
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<abstract lang="en">The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</abstract>
<relatedItem type="host"><titleInfo><title>Environmental Microbiology Reports</title>
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<note type="content"> Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues.Supporting Info Item: Supporting info item - </note>
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