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Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem.

Swingley WD, Meyer-Dombard DR, Shock EL, Alsop EB, Falenski HD, Havig JR, Raymond J - PLoS ONE (2012)

Bottom Line: We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering.We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function.The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability.

View Article: PubMed Central - PubMed

Affiliation: School of Natural Sciences, University of California Merced, Merced, California, United States of America.

ABSTRACT
We have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the "Bison Pool" (BP) Environmental Genome and a complementary contextual geochemical dataset of ~75 geochemical parameters. 2,321 16S rRNA clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of BP, an alkaline hot spring in Sentinel Meadow (Lower Geyser Basin) of Yellowstone National Park. This channel acts as a >22 m gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of biologically important chemical species, such as those containing nitrogen and sulfur. Microbial life at BP transitions from a 92 °C chemotrophic streamer biofilm community in the BP source pool to a 56 °C phototrophic mat community. We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering. We have also assigned environmental genome sequences to individual microbial community members by complementing traditional homology-based assignment with nucleotide word-usage algorithms, allowing more than 70% of all reads to be assigned to source organisms. This assignment yields high genome coverage in dominant community members, facilitating reconstruction of nearly complete metabolic profiles and in-depth analysis of the relation between geochemical and metabolic changes along the outflow. We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function. We have also identified an organism constituting a novel phylum in a metabolic "transition" community, located physically between the chemotroph- and phototroph-dominated sites. The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability.

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Total counts of genes associated with carbon-fixation via five cycles/pathways.Shown are genes associated with the reductive tricarboxylic-acid cycle (rTCA), including citryl co-A synthase/lyase, and pyruvate ferridoxin oxidoreductase (oorABCD). The Calvin cycle (CBB) is represented by the gene for ribulose-1,5-bisphosphate carboxylase, and the reductive acetyl Co-A pathway (rACP) is estimated by CO dehydrogenase. Malonate semialdehyde reductase and 4-hydroxybutyryl-CoA dehydratase are used as proxies for the 3-hydroxypropionate cycle (3-HP), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-4HP), respectively. All columns are normalized to the smallest total dataset.
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pone-0038108-g008: Total counts of genes associated with carbon-fixation via five cycles/pathways.Shown are genes associated with the reductive tricarboxylic-acid cycle (rTCA), including citryl co-A synthase/lyase, and pyruvate ferridoxin oxidoreductase (oorABCD). The Calvin cycle (CBB) is represented by the gene for ribulose-1,5-bisphosphate carboxylase, and the reductive acetyl Co-A pathway (rACP) is estimated by CO dehydrogenase. Malonate semialdehyde reductase and 4-hydroxybutyryl-CoA dehydratase are used as proxies for the 3-hydroxypropionate cycle (3-HP), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-4HP), respectively. All columns are normalized to the smallest total dataset.

Mentions: Concentrations of dissolved organic and inorganic carbon (DOC, and DIC) vary little downstream at BP, ∼5 ppm C and ∼80 ppm C, respectively. In Figure 8, total counts of genes within the consensus genomes associated with five of the six recognized CO2-fixation schemes are given, outlining a progression of CO2-fixation processes as a function of downstream community shifting (Table S5). At site 1, the hottest, strictly chemotrophic location, the majority of carbon cycling genes found in the BPEG are related to the reverse tricarboxylic acid (rTCA) cycle. Here, evidence for carbon fixation rests with citryl-CoA synthase and citryl-CoA lyase genes found in the Aquificae consensus genome, and the Thermoproteales consensus genome, which also code for oorABCD. Values of Δ13C for sites 1–5 were previously reported [2], and those data suggested that the rTCA cycle contributed the most to the Δ13C signature of site 1 biofilms. Further downstream, at sites 2 and 3, the CO2-fixation genes found in the BPEG were dominated by both rTCA and reductive acetyl co-A pathway (rACP) genes. While the rACP gene, CO dehydrogenase, is not unique to this pathway, the bins containing a CO dehydrogenase match are from phyla known to perform this reaction [53]. The Δ13C data from the biofilms at these locations, in the range of ∼ −5 to −12‰, support these assignments [28]. In the photosynthetic zone, sites 4 and 5, it might be expected that the majority of CO2-fixation genes would belong to the Calvin cycle (reductive pentose phosphate cycle), due to the prevalence of photosynthetic organisms. However, total gene counts in the BPEG indicate that more rTCA genes than Calvin cycle genes are found in these samples, and the rACP processes appear to have a larger impact on the Δ13C of the photosynthetic biofilms [2]. In addition, a single set of ribulose-1,5-bisphosphate carboxylase (the key enzyme in the Calvin cycle) genes were identified at site 3 (BPEG3_14745 and BPEG3_14746). This sequence shares 89% amino acid identity with a predicted protein from Meiothermus silvanus DSM 9946 (YP_003686579) [57], though Thermales are not known to be autotrophic. Malonate semialdehyde reductase, associated with the 3-hydroxypropionate cycle (3HP) was also found in the Chloroflexi consensus genome from sites 4 and 5, which was expected as this cycle is specific to the Chloroflexi [58].


Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem.

Swingley WD, Meyer-Dombard DR, Shock EL, Alsop EB, Falenski HD, Havig JR, Raymond J - PLoS ONE (2012)

Total counts of genes associated with carbon-fixation via five cycles/pathways.Shown are genes associated with the reductive tricarboxylic-acid cycle (rTCA), including citryl co-A synthase/lyase, and pyruvate ferridoxin oxidoreductase (oorABCD). The Calvin cycle (CBB) is represented by the gene for ribulose-1,5-bisphosphate carboxylase, and the reductive acetyl Co-A pathway (rACP) is estimated by CO dehydrogenase. Malonate semialdehyde reductase and 4-hydroxybutyryl-CoA dehydratase are used as proxies for the 3-hydroxypropionate cycle (3-HP), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-4HP), respectively. All columns are normalized to the smallest total dataset.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3367023&req=5

pone-0038108-g008: Total counts of genes associated with carbon-fixation via five cycles/pathways.Shown are genes associated with the reductive tricarboxylic-acid cycle (rTCA), including citryl co-A synthase/lyase, and pyruvate ferridoxin oxidoreductase (oorABCD). The Calvin cycle (CBB) is represented by the gene for ribulose-1,5-bisphosphate carboxylase, and the reductive acetyl Co-A pathway (rACP) is estimated by CO dehydrogenase. Malonate semialdehyde reductase and 4-hydroxybutyryl-CoA dehydratase are used as proxies for the 3-hydroxypropionate cycle (3-HP), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-4HP), respectively. All columns are normalized to the smallest total dataset.
Mentions: Concentrations of dissolved organic and inorganic carbon (DOC, and DIC) vary little downstream at BP, ∼5 ppm C and ∼80 ppm C, respectively. In Figure 8, total counts of genes within the consensus genomes associated with five of the six recognized CO2-fixation schemes are given, outlining a progression of CO2-fixation processes as a function of downstream community shifting (Table S5). At site 1, the hottest, strictly chemotrophic location, the majority of carbon cycling genes found in the BPEG are related to the reverse tricarboxylic acid (rTCA) cycle. Here, evidence for carbon fixation rests with citryl-CoA synthase and citryl-CoA lyase genes found in the Aquificae consensus genome, and the Thermoproteales consensus genome, which also code for oorABCD. Values of Δ13C for sites 1–5 were previously reported [2], and those data suggested that the rTCA cycle contributed the most to the Δ13C signature of site 1 biofilms. Further downstream, at sites 2 and 3, the CO2-fixation genes found in the BPEG were dominated by both rTCA and reductive acetyl co-A pathway (rACP) genes. While the rACP gene, CO dehydrogenase, is not unique to this pathway, the bins containing a CO dehydrogenase match are from phyla known to perform this reaction [53]. The Δ13C data from the biofilms at these locations, in the range of ∼ −5 to −12‰, support these assignments [28]. In the photosynthetic zone, sites 4 and 5, it might be expected that the majority of CO2-fixation genes would belong to the Calvin cycle (reductive pentose phosphate cycle), due to the prevalence of photosynthetic organisms. However, total gene counts in the BPEG indicate that more rTCA genes than Calvin cycle genes are found in these samples, and the rACP processes appear to have a larger impact on the Δ13C of the photosynthetic biofilms [2]. In addition, a single set of ribulose-1,5-bisphosphate carboxylase (the key enzyme in the Calvin cycle) genes were identified at site 3 (BPEG3_14745 and BPEG3_14746). This sequence shares 89% amino acid identity with a predicted protein from Meiothermus silvanus DSM 9946 (YP_003686579) [57], though Thermales are not known to be autotrophic. Malonate semialdehyde reductase, associated with the 3-hydroxypropionate cycle (3HP) was also found in the Chloroflexi consensus genome from sites 4 and 5, which was expected as this cycle is specific to the Chloroflexi [58].

Bottom Line: We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering.We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function.The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability.

View Article: PubMed Central - PubMed

Affiliation: School of Natural Sciences, University of California Merced, Merced, California, United States of America.

ABSTRACT
We have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the "Bison Pool" (BP) Environmental Genome and a complementary contextual geochemical dataset of ~75 geochemical parameters. 2,321 16S rRNA clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of BP, an alkaline hot spring in Sentinel Meadow (Lower Geyser Basin) of Yellowstone National Park. This channel acts as a >22 m gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of biologically important chemical species, such as those containing nitrogen and sulfur. Microbial life at BP transitions from a 92 °C chemotrophic streamer biofilm community in the BP source pool to a 56 °C phototrophic mat community. We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering. We have also assigned environmental genome sequences to individual microbial community members by complementing traditional homology-based assignment with nucleotide word-usage algorithms, allowing more than 70% of all reads to be assigned to source organisms. This assignment yields high genome coverage in dominant community members, facilitating reconstruction of nearly complete metabolic profiles and in-depth analysis of the relation between geochemical and metabolic changes along the outflow. We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function. We have also identified an organism constituting a novel phylum in a metabolic "transition" community, located physically between the chemotroph- and phototroph-dominated sites. The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability.

Show MeSH