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Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing.

Brady AL, Sharp CE, Grasby SE, Dunfield PF - Front Microbiol (2015)

Bottom Line: Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g(-1) (wet weight) day(-1) within five selected sites.Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in (13)CO incubations.While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary Calgary, AB, Canada.

ABSTRACT
Carbon monoxide (CO) is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45 to 65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g(-1) (wet weight) day(-1) within five selected sites. Active anaerobic carboxydotrophic bacteria were identified using (13)CO DNA stable isotope probing (SIP) combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in (13)CO incubations. The predominant bacteria that assimilated (13)C derived from CO were closely related (>98% 16S rRNA gene sequence identity) to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter, and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of partial 16S rRNA gene sequences belonging to OTUs identified in heavy fractions from 13CO SIP incubations present at a minimum of 25 fold enrichment. OTUs presented are from those incubations that showed an observable shift in density and are hypothesized to represent microbes that oxidized CO. A skeleton tree was constructed from near complete 16S rRNA gene sequences (>1400 bp) via Neighbor-joining with a Jukes-Cantor correction and 10,000 bootstraps. Shorter sequences produced via 454 pyrosequencing obtained in this study were added by parsimony using ARB (in bold). The scale bar represents 0.1 change per nucleotide position. Bootstrap support values greater than 55% for the major nodes are given. The tree was rooted using 7 Proteobacteria 16S rRNA gene sequences.
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Figure 3: Phylogenetic tree of partial 16S rRNA gene sequences belonging to OTUs identified in heavy fractions from 13CO SIP incubations present at a minimum of 25 fold enrichment. OTUs presented are from those incubations that showed an observable shift in density and are hypothesized to represent microbes that oxidized CO. A skeleton tree was constructed from near complete 16S rRNA gene sequences (>1400 bp) via Neighbor-joining with a Jukes-Cantor correction and 10,000 bootstraps. Shorter sequences produced via 454 pyrosequencing obtained in this study were added by parsimony using ARB (in bold). The scale bar represents 0.1 change per nucleotide position. Bootstrap support values greater than 55% for the major nodes are given. The tree was rooted using 7 Proteobacteria 16S rRNA gene sequences.

Mentions: The taxonomic identifications of OTUs recovered from13CO microcosm heavy fractions that were present at 25 fold enrichment compared to the original environmental sample are shown in Table 2. A 16S rRNA gene phylogenetic tree was constructed using the top OTUs from each 13CO heavy fraction showing an observable shift compared to reference sequences (Figure 3). Taxonomic identifications of OTUs present at >1% of all sequences are presented in Supplementary Table S2. Most of the putative carboxydotrophs identified belonged with >98% sequence identity to genera that include known CO-oxidizers, such as Thermincola, Desulfotomaculum, Carboxydocella, and Thermolithobacter (Sokolova et al., 2002, 2005, 2007; Parshina et al., 2005a,b). For example, the most abundant OTU (OTU_17948) recovered from 13CO heavy fractions from Dewar Creek (DCm2010 and DCmN11) and Lakelse springs showed 99% sequence identity to both Thermincola potens and to Thermincola carboxydiphila, known CO-oxidizing bacteria (Sokolova et al., 2005; Byrne-Bailey et al., 2010) (Table 2). Members of the genus Carboxydocella were also detected in the majority of heavy fractions across all sites. This genus was represented by multiple OTUs, however the top OTU_7600 identified in most samples corresponded to Carboxydocella thermautotrophica (98% similarity). Members of the genus Desulfotomaculum were most predominant in DCs9, a sediment sample collected from Dewar Creek. In DCs9_13CO incubations, 31.9% of sequences were attributed to the genus Desulfotomaculum. 30.0% of sequences were in OTU_3148, which showed 99% sequence identity to D. kuznetsovii and D. luciae.


Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing.

Brady AL, Sharp CE, Grasby SE, Dunfield PF - Front Microbiol (2015)

Phylogenetic tree of partial 16S rRNA gene sequences belonging to OTUs identified in heavy fractions from 13CO SIP incubations present at a minimum of 25 fold enrichment. OTUs presented are from those incubations that showed an observable shift in density and are hypothesized to represent microbes that oxidized CO. A skeleton tree was constructed from near complete 16S rRNA gene sequences (>1400 bp) via Neighbor-joining with a Jukes-Cantor correction and 10,000 bootstraps. Shorter sequences produced via 454 pyrosequencing obtained in this study were added by parsimony using ARB (in bold). The scale bar represents 0.1 change per nucleotide position. Bootstrap support values greater than 55% for the major nodes are given. The tree was rooted using 7 Proteobacteria 16S rRNA gene sequences.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555085&req=5

Figure 3: Phylogenetic tree of partial 16S rRNA gene sequences belonging to OTUs identified in heavy fractions from 13CO SIP incubations present at a minimum of 25 fold enrichment. OTUs presented are from those incubations that showed an observable shift in density and are hypothesized to represent microbes that oxidized CO. A skeleton tree was constructed from near complete 16S rRNA gene sequences (>1400 bp) via Neighbor-joining with a Jukes-Cantor correction and 10,000 bootstraps. Shorter sequences produced via 454 pyrosequencing obtained in this study were added by parsimony using ARB (in bold). The scale bar represents 0.1 change per nucleotide position. Bootstrap support values greater than 55% for the major nodes are given. The tree was rooted using 7 Proteobacteria 16S rRNA gene sequences.
Mentions: The taxonomic identifications of OTUs recovered from13CO microcosm heavy fractions that were present at 25 fold enrichment compared to the original environmental sample are shown in Table 2. A 16S rRNA gene phylogenetic tree was constructed using the top OTUs from each 13CO heavy fraction showing an observable shift compared to reference sequences (Figure 3). Taxonomic identifications of OTUs present at >1% of all sequences are presented in Supplementary Table S2. Most of the putative carboxydotrophs identified belonged with >98% sequence identity to genera that include known CO-oxidizers, such as Thermincola, Desulfotomaculum, Carboxydocella, and Thermolithobacter (Sokolova et al., 2002, 2005, 2007; Parshina et al., 2005a,b). For example, the most abundant OTU (OTU_17948) recovered from 13CO heavy fractions from Dewar Creek (DCm2010 and DCmN11) and Lakelse springs showed 99% sequence identity to both Thermincola potens and to Thermincola carboxydiphila, known CO-oxidizing bacteria (Sokolova et al., 2005; Byrne-Bailey et al., 2010) (Table 2). Members of the genus Carboxydocella were also detected in the majority of heavy fractions across all sites. This genus was represented by multiple OTUs, however the top OTU_7600 identified in most samples corresponded to Carboxydocella thermautotrophica (98% similarity). Members of the genus Desulfotomaculum were most predominant in DCs9, a sediment sample collected from Dewar Creek. In DCs9_13CO incubations, 31.9% of sequences were attributed to the genus Desulfotomaculum. 30.0% of sequences were in OTU_3148, which showed 99% sequence identity to D. kuznetsovii and D. luciae.

Bottom Line: Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g(-1) (wet weight) day(-1) within five selected sites.Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in (13)CO incubations.While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary Calgary, AB, Canada.

ABSTRACT
Carbon monoxide (CO) is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45 to 65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g(-1) (wet weight) day(-1) within five selected sites. Active anaerobic carboxydotrophic bacteria were identified using (13)CO DNA stable isotope probing (SIP) combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in (13)CO incubations. The predominant bacteria that assimilated (13)C derived from CO were closely related (>98% 16S rRNA gene sequence identity) to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter, and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.

No MeSH data available.


Related in: MedlinePlus