Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

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

BPEG binning and consensus genome statistics.

*<p>Read assignment. ¹With the exception of homology binning information, all other statistics shown use phylum-level tetranucleotide binning data.</p

Sulfur cycle in BP.

<p>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 (<i>dsr</i>), phosphoadenosine phosphosulfate reductase (<i>apr</i>), and sulfate adenyltransferase (<i>sat</i>). Sulfide oxidation genes counted include sulfite oxidoreductase (<i>sor</i>), adenylylsulfate:phosphate adenylyltransferase (APAT), sulfide oxidase (<i>soxABCDXYZ</i>), thiosulfate quinone oxidoreductase (<i>tqr</i>), sulfide quinone reductase (<i>sqr</i>), and sulfide dehydrogenase flavocytochrome (<i>fcsd</i>), but did not include the <i>dsr</i>, <i>apr</i>, and <i>sat</i> genes which are used in both sulfide oxidation and sulfate reduction.</p

Total counts of genes associated with carbon-fixation via five cycles/pathways.

<p>Shown are genes associated with the reductive tricarboxylic-acid cycle (rTCA), including citryl co-A synthase/lyase, and pyruvate ferridoxin oxidoreductase (<i>oorABCD</i>). 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.</p

Map of BP, showing the five sample locations used in this study.

<p>Modified from Havig et al. (2011) and originally drafted by G.R. Osburn.</p

Selected geochemical trends moving downstream at BP.

<p>Top and middle; chloride and oxygen isotope (of water) measurements, respectively, showing calculated evaporation trendlines imposed on the data; the slopes of the lines are set by the extent of evaporation required to account for the temperature decrease. Bottom; dissolved oxygen concentrations, representing redox processes in BP. All plots show chemosynthetic (far right), transition “fringe” (grey bar), and photosynthetic zones (far left).</p

Nitrogen cycle in BP.

<p>Top plot; concentrations of nitrate (solid circles) and nitrite (open circles) as a function of downstream flow. Plot shows chemosynthetic (far right), transition “fringe” (grey bar), and phostosynthetic zones (far left). Bottom histogram shows total counts of genes associated with denitrification (black bars), N₂-fixation (grey bars), and nitrification (diagonal filled bars) normalized to the smallest total dataset. Denitrification genes included nitrate reductase (<i>nar</i>), nitrite reductase (<i>nir</i>), nitric oxide reductase (<i>nor</i>), and nitrous oxide reductase (<i>nos</i>). N₂-fixation was counted by nitrogenase (<i>nif</i>), and nitrification genes included hydroxylamine oxidase <i>hao</i> and ammonia monooxygenase (<i>amo</i>, which was not found in any sample).</p

BPEG sequence statistics.

<p>BPEG sequence statistics.</p