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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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Related in: MedlinePlus

Taxonomic diversity and richness in “Bison Pool”.Left panel shows diversity and richness as measured by 16S rRNA clone libraries, middle panel shows 16S rRNA genes identified in the BPEG, and right panel shows phylum-level assignments for BPEG reads. 16S rRNA sequences from the clone library and the BPEG (metagenome) were assigned using RDP’s classifier. Unassigned sequences represent those scoring below their respective S_ab cutoff (80% for clones and 50% for metagenome sequences). The percentage of total Archaea (Crenarchaeota plus Euryarchaeota) in each clone library are shown normalized to the metagenome total. Metagenome reads were assigned using coordinated homology and tetranucleotide binning. All assignments to phyla containing less than 1% of any community are included within the unassigned.
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pone-0038108-g004: Taxonomic diversity and richness in “Bison Pool”.Left panel shows diversity and richness as measured by 16S rRNA clone libraries, middle panel shows 16S rRNA genes identified in the BPEG, and right panel shows phylum-level assignments for BPEG reads. 16S rRNA sequences from the clone library and the BPEG (metagenome) were assigned using RDP’s classifier. Unassigned sequences represent those scoring below their respective S_ab cutoff (80% for clones and 50% for metagenome sequences). The percentage of total Archaea (Crenarchaeota plus Euryarchaeota) in each clone library are shown normalized to the metagenome total. Metagenome reads were assigned using coordinated homology and tetranucleotide binning. All assignments to phyla containing less than 1% of any community are included within the unassigned.

Mentions: Initial estimates of community composition and diversity were performed on a clone library of 2,359 16S rRNA sequences covering the five BP sites (Figure 4, left panel, and Figure S2). 16S rRNA data suggest that phylum-level microbial diversity (Shannon Index and Simpson Index) and evenness (Shannon Index and Pielou Index) generally increase along the outflow channel, interrupted by a large decrease in these measures at site 4 (where Cyanobacteria dominate the clone library) (Table S2).


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)

Taxonomic diversity and richness in “Bison Pool”.Left panel shows diversity and richness as measured by 16S rRNA clone libraries, middle panel shows 16S rRNA genes identified in the BPEG, and right panel shows phylum-level assignments for BPEG reads. 16S rRNA sequences from the clone library and the BPEG (metagenome) were assigned using RDP’s classifier. Unassigned sequences represent those scoring below their respective S_ab cutoff (80% for clones and 50% for metagenome sequences). The percentage of total Archaea (Crenarchaeota plus Euryarchaeota) in each clone library are shown normalized to the metagenome total. Metagenome reads were assigned using coordinated homology and tetranucleotide binning. All assignments to phyla containing less than 1% of any community are included within the unassigned.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038108-g004: Taxonomic diversity and richness in “Bison Pool”.Left panel shows diversity and richness as measured by 16S rRNA clone libraries, middle panel shows 16S rRNA genes identified in the BPEG, and right panel shows phylum-level assignments for BPEG reads. 16S rRNA sequences from the clone library and the BPEG (metagenome) were assigned using RDP’s classifier. Unassigned sequences represent those scoring below their respective S_ab cutoff (80% for clones and 50% for metagenome sequences). The percentage of total Archaea (Crenarchaeota plus Euryarchaeota) in each clone library are shown normalized to the metagenome total. Metagenome reads were assigned using coordinated homology and tetranucleotide binning. All assignments to phyla containing less than 1% of any community are included within the unassigned.
Mentions: Initial estimates of community composition and diversity were performed on a clone library of 2,359 16S rRNA sequences covering the five BP sites (Figure 4, left panel, and Figure S2). 16S rRNA data suggest that phylum-level microbial diversity (Shannon Index and Simpson Index) and evenness (Shannon Index and Pielou Index) generally increase along the outflow channel, interrupted by a large decrease in these measures at site 4 (where Cyanobacteria dominate the clone library) (Table S2).

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
Related in: MedlinePlus