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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.

Show MeSH
Sulfur cycle in BP.Top plot; concentrations of sulfate (solid circles) and “total sulfide” (open circles), which includes H2S and HS–, as a function of downstream flow. Calculated evaporation trends are shown (solid lines). Plot shows chemosynthetic (far right), transition “fringe” (grey bar), and phostosynthetic zones (far left). Bottom histogram shows total counts of genes associated with sulfate reduction (black bars) and sulfide oxidation (grey bars), normalized to the smallest total dataset. Sulfate reduction genes counted include desulfite reductase (dsr), phosphoadenosine phosphosulfate reductase (apr), and sulfate adenyltransferase (sat). Sulfide oxidation genes counted include sulfite oxidoreductase (sor), adenylylsulfate:phosphate adenylyltransferase (APAT), sulfide oxidase (soxABCDXYZ), thiosulfate quinone oxidoreductase (tqr), sulfide quinone reductase (sqr), and sulfide dehydrogenase flavocytochrome (fcsd), but did not include the dsr, apr, and sat genes which are used in both sulfide oxidation and sulfate reduction.
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pone-0038108-g006: Sulfur cycle in BP.Top plot; concentrations of sulfate (solid circles) and “total sulfide” (open circles), which includes H2S and HS–, as a function of downstream flow. Calculated evaporation trends are shown (solid lines). Plot shows chemosynthetic (far right), transition “fringe” (grey bar), and phostosynthetic zones (far left). Bottom histogram shows total counts of genes associated with sulfate reduction (black bars) and sulfide oxidation (grey bars), normalized to the smallest total dataset. Sulfate reduction genes counted include desulfite reductase (dsr), phosphoadenosine phosphosulfate reductase (apr), and sulfate adenyltransferase (sat). Sulfide oxidation genes counted include sulfite oxidoreductase (sor), adenylylsulfate:phosphate adenylyltransferase (APAT), sulfide oxidase (soxABCDXYZ), thiosulfate quinone oxidoreductase (tqr), sulfide quinone reductase (sqr), and sulfide dehydrogenase flavocytochrome (fcsd), but did not include the dsr, apr, and sat genes which are used in both sulfide oxidation and sulfate reduction.

Mentions: Overall concentrations of SO4−2 and total sulfide decrease with downstream sampling, and are examples of ions that do not appear to respond to strictly abiological influences in the runoff channel. Variation in sulfate and total sulfide concentrations between the source pool and site 5 are far below what is predicted by evaporation models, indicating that biological intervention is likely (Figure 6). Total sulfide decreases at a rate that is too high for abiological oxidation as found in previous studies [50], [51], and concentrations of sulfate do not in total account for the loss of sulfide. The largest loss of total sulfide in the BP outflow occurs between sites 1 and 2 (Figure 6). In general, there is energy available via H2S oxidation throughout BP, but only minimal energy available for SO4−2 reduction with inorganic reductants (Table S3). For example, oxidation of H2S or S with O2, NO3−, or NO2− is estimated to yield between 7.3–24.3 kcal/(mol e­ transferred) across all sites sampled. Conversely, the reduction of SO4−2 is rarely energy yielding in BP, yielding at most 3.4 kcal/mol e− transferred, written as strictly a chemoautotrophic process. There is also ∼6 kcal/mol e− transferred if SO4−2 is coupled to formate oxidation in ∼pH 8 environments in Yellowstone [49], and sulfate reduction coupled to other organic compounds (such as acetate) are likely energetically favorable. Using the results from BPEG phylum-level binning, as described above, we are able to assign genes associated specifically with sulfur cycling and metabolism to specific dominant taxa (Table S5). Total counts of identified genes associated with S oxidation and reduction in the BPEG consensus genomes are shown in Figure 6. The total sum of S oxidation genes at site 1, which includes the genes sor, APAT, sox, tqo, and sqr, is more than twice that found at site 2. At sites 1 and 2, the Aquificae consensus genomes appear to have the genetic capacity for H2S oxidation, as soxABXYZ were identified, in addition to other S-oxidation genes. These Aquificae appear to lack the soxCD genes, which indicates they likely possess a version of the “branched” S-oxidation system and may have the capacity to deposit sulfur globules internally (periplasmic deposition), or externally to their cellular membranes [52]. At site 3, the role of S-oxidation passes to the Deinococcus-Thermus consensus genomes, which possesses a variety of S-oxidation genes, including sor, soxABCDF, fcsd, and dsr, apr, and sat. The latter three genes are also used in SO4−2 reduction, and while the Deinococcus-Thermus at site 3 does not have a full complement of S-oxidation genes, it is likely that these organisms are capable of S-oxidation in some capacity. Members of both Thermus and Aquificae are known to oxidize S in pure cultures [53]. The only apparent genetic capacity for chemotrophic SO4−2 reduction is shown by the Thermoproteales consensus genomes identified at sites 1 and 2. These organisms have all three critical genes for SO4−2 reduction (dsr, apt, and sat), and no genes associated strictly with S-oxidation. In pure cultures, strains of Pyrobaculum and other Thermoproteales are known to reduce SO4−2 coupled to the oxidation of organic carbon. While discussion has thus far been focused primarily on the strictly chemotrophic portions of the BP outflow channel, the Cyanobacterial, Chloroflexi, and Proteobacterial species at sites 4 and 5 also have copies of dsr, apt, and sat, indicating the capacity for SO4−2 reduction within the photosynthetic mat communities.


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)

Sulfur cycle in BP.Top plot; concentrations of sulfate (solid circles) and “total sulfide” (open circles), which includes H2S and HS–, as a function of downstream flow. Calculated evaporation trends are shown (solid lines). Plot shows chemosynthetic (far right), transition “fringe” (grey bar), and phostosynthetic zones (far left). Bottom histogram shows total counts of genes associated with sulfate reduction (black bars) and sulfide oxidation (grey bars), normalized to the smallest total dataset. Sulfate reduction genes counted include desulfite reductase (dsr), phosphoadenosine phosphosulfate reductase (apr), and sulfate adenyltransferase (sat). Sulfide oxidation genes counted include sulfite oxidoreductase (sor), adenylylsulfate:phosphate adenylyltransferase (APAT), sulfide oxidase (soxABCDXYZ), thiosulfate quinone oxidoreductase (tqr), sulfide quinone reductase (sqr), and sulfide dehydrogenase flavocytochrome (fcsd), but did not include the dsr, apr, and sat genes which are used in both sulfide oxidation and sulfate reduction.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038108-g006: Sulfur cycle in BP.Top plot; concentrations of sulfate (solid circles) and “total sulfide” (open circles), which includes H2S and HS–, as a function of downstream flow. Calculated evaporation trends are shown (solid lines). Plot shows chemosynthetic (far right), transition “fringe” (grey bar), and phostosynthetic zones (far left). Bottom histogram shows total counts of genes associated with sulfate reduction (black bars) and sulfide oxidation (grey bars), normalized to the smallest total dataset. Sulfate reduction genes counted include desulfite reductase (dsr), phosphoadenosine phosphosulfate reductase (apr), and sulfate adenyltransferase (sat). Sulfide oxidation genes counted include sulfite oxidoreductase (sor), adenylylsulfate:phosphate adenylyltransferase (APAT), sulfide oxidase (soxABCDXYZ), thiosulfate quinone oxidoreductase (tqr), sulfide quinone reductase (sqr), and sulfide dehydrogenase flavocytochrome (fcsd), but did not include the dsr, apr, and sat genes which are used in both sulfide oxidation and sulfate reduction.
Mentions: Overall concentrations of SO4−2 and total sulfide decrease with downstream sampling, and are examples of ions that do not appear to respond to strictly abiological influences in the runoff channel. Variation in sulfate and total sulfide concentrations between the source pool and site 5 are far below what is predicted by evaporation models, indicating that biological intervention is likely (Figure 6). Total sulfide decreases at a rate that is too high for abiological oxidation as found in previous studies [50], [51], and concentrations of sulfate do not in total account for the loss of sulfide. The largest loss of total sulfide in the BP outflow occurs between sites 1 and 2 (Figure 6). In general, there is energy available via H2S oxidation throughout BP, but only minimal energy available for SO4−2 reduction with inorganic reductants (Table S3). For example, oxidation of H2S or S with O2, NO3−, or NO2− is estimated to yield between 7.3–24.3 kcal/(mol e­ transferred) across all sites sampled. Conversely, the reduction of SO4−2 is rarely energy yielding in BP, yielding at most 3.4 kcal/mol e− transferred, written as strictly a chemoautotrophic process. There is also ∼6 kcal/mol e− transferred if SO4−2 is coupled to formate oxidation in ∼pH 8 environments in Yellowstone [49], and sulfate reduction coupled to other organic compounds (such as acetate) are likely energetically favorable. Using the results from BPEG phylum-level binning, as described above, we are able to assign genes associated specifically with sulfur cycling and metabolism to specific dominant taxa (Table S5). Total counts of identified genes associated with S oxidation and reduction in the BPEG consensus genomes are shown in Figure 6. The total sum of S oxidation genes at site 1, which includes the genes sor, APAT, sox, tqo, and sqr, is more than twice that found at site 2. At sites 1 and 2, the Aquificae consensus genomes appear to have the genetic capacity for H2S oxidation, as soxABXYZ were identified, in addition to other S-oxidation genes. These Aquificae appear to lack the soxCD genes, which indicates they likely possess a version of the “branched” S-oxidation system and may have the capacity to deposit sulfur globules internally (periplasmic deposition), or externally to their cellular membranes [52]. At site 3, the role of S-oxidation passes to the Deinococcus-Thermus consensus genomes, which possesses a variety of S-oxidation genes, including sor, soxABCDF, fcsd, and dsr, apr, and sat. The latter three genes are also used in SO4−2 reduction, and while the Deinococcus-Thermus at site 3 does not have a full complement of S-oxidation genes, it is likely that these organisms are capable of S-oxidation in some capacity. Members of both Thermus and Aquificae are known to oxidize S in pure cultures [53]. The only apparent genetic capacity for chemotrophic SO4−2 reduction is shown by the Thermoproteales consensus genomes identified at sites 1 and 2. These organisms have all three critical genes for SO4−2 reduction (dsr, apt, and sat), and no genes associated strictly with S-oxidation. In pure cultures, strains of Pyrobaculum and other Thermoproteales are known to reduce SO4−2 coupled to the oxidation of organic carbon. While discussion has thus far been focused primarily on the strictly chemotrophic portions of the BP outflow channel, the Cyanobacterial, Chloroflexi, and Proteobacterial species at sites 4 and 5 also have copies of dsr, apt, and sat, indicating the capacity for SO4−2 reduction within the photosynthetic mat communities.

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