Relative importance of H2 and H2S as energy sources for primary production in geothermal springs

Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous

Introduction

Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings.

Methods

Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli.

Results and Discussion

Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO₄ ^2- and NH₄ ⁺ concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.

Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents

BACKGROUND

Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems.

RESULTS

Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera.

CONCLUSIONS

The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.

Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales

The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs

Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.

Seasonal hydrologic and geologic forcing drive hot spring geochemistry and microbial biodiversity

Hot springs integrate hydrologic and geologic processes that vary over short- and long-term time scales. However, the influence of temporal hydrologic and geologic change on hot spring biodiversity is unknown. Here, we coordinated near-weekly, cross-seasonal (~140 days) geochemical and microbial community analyses of three widely studied hot springs with local precipitation data in Yellowstone National Park. One spring ('HFS') exhibited statistically significant, coupled microbial and geochemical variation across seasons that was associated with recent precipitation patterns. Two other spring communities, 'CP' and 'DS', exhibited minimal to no variation across seasons. Variability in the seasonal response of springs is attributed to differences in the timing and extent of aquifer recharge with oxidized near-surface water from precipitation. This influx of oxidized water is associated with changes in community composition, and in particular, the abundances of aerobic sulfide-/sulfur-oxidizers that can acidify waters. During sampling, a new spring formed after a period of heavy precipitation and its successional dynamics were also influenced by surface water recharge. Collectively, these results indicate that changes in short-term hydrology associated with precipitation can impact hot spring geochemistry and microbial biodiversity. These results point to potential susceptibility of certain hot springs and their biodiversity to sustained, longer-term hydrologic changes.

The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems

Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.

Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.

Probing the geological source and biological fate of hydrogen in Yellowstone hot springs

Hydrogen (H₂ ) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H₂ concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H₂ that partition into the vapour phase during decompressional boiling of ascending hydrothermal fluids. Variable vapour input leads to differences in H₂ concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapour-phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapour-phase gas and with the most H₂ in YNP were examined to determine the fate of H₂ . SJ3 had the most H₂ , the most 16S rRNA gene templates and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H₂ oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H₂ to hot springs and the distribution of organisms that use H₂ to generate energy.

Sulfur-dependent microbial lifestyles: deceptively flexible roles for biochemically versatile enzymes

A wide group of microbes are able to "make a living" on Earth by basing their energetic metabolism on inorganic sulfur compounds. Because of their range of stable redox states, sulfur and inorganic sulfur compounds can be utilized as either oxidants or reductants in a diverse array of energy-conserving reactions. In this review the major enzymes and basic chemistry of sulfur-based respiration and chemolithotrophy are outlined. The reversibility and versatility of these enzymes, however, means that they can often be used in multiple ways, and several cases are discussed in which enzymes which are considered to be hallmarks of a particular respiratory or lithotrophic process have been found to be used in other, often opposing, metabolic processes. These results emphasize the importance of taking into account the geochemistry, biochemistry and microbiology of an organism and/or environment when trying to interpret the function of a particular sulfur-dependent redox enzyme.

Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs

The geochemistry of hot springs and the availability of oxidants capable of supporting microbial metabolisms are influenced by subsurface processes including the separation of hydrothermal fluids into vapor and liquid phases. Here, we characterized the influence of geochemical variation and oxidant availability on the abundance, composition, and activity of hydrogen (H₂ )-dependent chemoautotrophs along the outflow channels of two-paired hot springs in Yellowstone National Park. The hydrothermal fluid at Roadside East (RSE; 82.4°C, pH 3.0) is acidic due to vapor-phase input while the fluid at Roadside West (RSW; 68.1°C, pH 7.0) is circumneutral due to liquid-phase input. Most chemotrophic communities exhibited net rates of H₂ oxidation, consistent with H₂ support of primary productivity, with one chemotrophic community exhibiting a net rate of H₂ production. Abundant H₂ -oxidizing chemoautotrophs were supported by reduction in oxygen, elemental sulfur, sulfate, and nitrate in RSW and oxygen and ferric iron in RSE; O₂ utilizing hydrogenotrophs increased in abundance down both outflow channels. Sequencing of 16S rRNA transcripts or genes from native sediments and dilution series incubations, respectively, suggests that members of the archaeal orders Sulfolobales, Desulfurococcales, and Thermoproteales are likely responsible for H₂ oxidation in RSE, whereas members of the bacterial order Thermoflexales and the archaeal order Thermoproteales are likely responsible for H₂ oxidation in RSW. These observations suggest that subsurface processes strongly influence spring chemistry and oxidant availability, which in turn select for unique assemblages of H₂ oxidizing microorganisms. Therefore, these data point to the role of oxidant availability in shaping the ecology and evolution of hydrogenotrophic organisms.

Geobiological feedbacks and the evolution of thermoacidophiles

Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O₂. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O₂, and that these events likely occurred in the recent evolutionary past. Comparative genomic analyses indicated that archaeal thermoacidophiles from independent lineages are enriched in similar protein-coding genes, consistent with convergent evolution aided by horizontal gene transfer. Because the generation of acidic environments and their successful habitation characteristically require O₂, these results suggest that thermoacidophilic Archaea and the acidity of their habitats co-evolved after the evolution of oxygenic photosynthesis. Moreover, it is likely that dissolved O₂ concentrations in thermal waters likely did not reach levels capable of sustaining aerobic thermoacidophiles and their acidifying activity until ~0.8 Ga, when present day atmospheric levels were reached, a time period that is supported by our estimation of divergence times for archaeal thermoacidophilic clades.

Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs

Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism.

Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH₄, CO₂, H₂, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO₄^2-, O₂ and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day⁻¹, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O₂ into the Fe(III)-oxide mat. The formation of microterracettes also implicated O₂ as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73–0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41–95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

Microsensor measurements of hydrogen gas dynamics in cyanobacterial microbial mats

We used a novel amperometric microsensor for measuring hydrogen gas production and consumption at high spatio-temporal resolution in cyanobacterial biofilms and mats dominated by non-heterocystous filamentous cyanobacteria (Microcoleus chtonoplastes and Oscillatoria sp.). The new microsensor is based on the use of an organic electrolyte and a stable internal reference system and can be equipped with a chemical sulfide trap in the measuring tip; it exhibits very stable and sulfide-insensitive measuring signals and a high sensitivity (1.5–5 pA per μmol L^-1 H₂). Hydrogen gas measurements were done in combination with microsensor measurements of scalar irradiance, O₂, pH, and H₂S and showed a pronounced H₂ accumulation (of up to 8–10% H₂ saturation) within the upper mm of cyanobacterial mats after onset of darkness and O₂ depletion. The peak concentration of H₂ increased with the irradiance level prior to darkening. After an initial build-up over the first 1–2 h in darkness, H₂ was depleted over several hours due to efflux to the overlaying water, and due to biogeochemical processes in the uppermost oxic layers and the anoxic layers of the mats. Depletion could be prevented by addition of molybdate pointing to sulfate reduction as a major sink for H₂. Immediately after onset of illumination, a short burst of presumably photo-produced H₂ due to direct biophotolysis was observed in the illuminated but anoxic mat layers. As soon as O₂ from photosynthesis started to accumulate, the H₂ was consumed rapidly and production ceased. Our data give detailed insights into the microscale distribution and dynamics of H₂ in cyanobacterial biofilms and mats, and further support that cyanobacterial H₂ production can play a significant role in fueling anaerobic processes like e.g., sulfate reduction or anoxygenic photosynthesis in microbial mats.

Carbon source preference in chemosynthetic hot spring communities

Rates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73 °C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (K(m)) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in high-temperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available.

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.

Two new Beggiatoa species inhabiting marine mangrove sediments in the Caribbean

Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperate waters, as well as hydrothermal vents, where they form dense mats on the floor. However, they have never been described in tropical marine mangroves. Here, we describe two new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangrove roots. We combined phylogenetic and lipid analysis with electron microscopy in order to describe these organisms. Furthermore, oxygen and sulphide measurements in and ex situ were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as Candidatus Maribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves.

Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.

Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines

The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.

Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin

Microrespirometry showed that several organic and inorganic electron donors stimulated oxygen consumption in two ∼80°C springs. Sediment and planktonic communities were structurally and functionally distinct, and quantitative PCR revealed catabolically distinct subpopulations of Thermocrinis. This study suggests that a variety of chemolithotrophic metabolisms operate simultaneously in these springs.

Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park

We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (≥ 99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park

Geothermal and hydrothermal waters often contain high concentrations of dissolved sulfide, which reacts with oxygen (abiotically or biotically) to yield elemental sulfur and other sulfur species that may support microbial metabolism. The primary goal of this study was to elucidate predominant biogeochemical processes important in sulfur biogeochemistry by identifying predominant sulfur species and describing microbial community structure within high-temperature, hypoxic, sulfur sediments ranging in pH from 4.2 to 6.1. Detailed analysis of aqueous species and solid phases present in hypoxic sulfur sediments revealed unique habitats containing high concentrations of dissolved sulfide, thiosulfate, and arsenite, as well as rhombohedral and spherical elemental sulfur and/or sulfide phases such as orpiment, stibnite, and pyrite, as well as alunite and quartz. Results from 16S rRNA gene sequencing show that these sediments are dominated by Crenarchaeota of the orders Desulfurococcales and Thermoproteales. Numerous cultivated representatives of these lineages, as well as the Thermoproteales strain (WP30) isolated in this study, require complex sources of carbon and respire elemental sulfur. We describe a new archaeal isolate (strain WP30) belonging to the order Thermoproteales (phylum Crenarchaeota, 98% identity to Pyrobaculum/Thermoproteus spp. 16S rRNA genes), which was obtained from sulfur sediments using in situ geochemical composition to design cultivation medium. This isolate produces sulfide during growth, which further promotes the formation of sulfide phases including orpiment, stibnite, or pyrite, depending on solution conditions. Geochemical, molecular, and physiological data were integrated to suggest primary factors controlling microbial community structure and function in high-temperature sulfur sediments.

Metagenomic and biochemical characterizations of sulfur oxidation metabolism in uncultured large sausage-shaped bacterium in hot spring microbial mats

So-called “sulfur-turf” microbial mats in sulfide containing hot springs (55–70°C, pH 7.3–8.3) in Japan were dominated by a large sausage-shaped bacterium (LSSB) that is closely related to the genus Sulfurihydrogenibium. Several previous reports proposed that the LSSB would be involved in sulfide oxidation in hot spring. However, the LSSB has not been isolated yet, thus there has been no clear evidence showing whether it possesses any genes and enzymes responsible for sulfide oxidation. To verify this, we investigated sulfide oxidation potential in the LSSB using a metagenomic approach and subsequent biochemical analysis. Genome fragments of the LSSB (a total of 3.7 Mb sequence including overlapping fragments) were obtained from the metagenomic fosmid library constructed from genomic DNA of the sulfur-turf mats. The sequence annotation clearly revealed that the LSSB possesses sulfur oxidation-related genes coding sulfide dehydrogenase (SD), sulfide-quinone reductase and sulfite dehydrogenase. The gene encoding SD, the key enzyme for sulfide oxidation, was successfully cloned and heterologously expressed in Escherichia coli. The purified recombinant enzyme clearly showed SD activity with optimum temperature and pH of 60°C and 8.0, respectively, which were consistent with the environmental conditions in the hot spring where the sulfur-turf thrives. Furthermore, the affinity of SD to sulfide was relatively high, which also reflected the environment where the sulfide could be continuously supplied. This is the first report showing that the LSSB harbors sulfide oxidizing metabolism adapted to the hot spring environment and can be involved in sulfide oxidation in the sulfur-turf microbial mats.

Modeling the habitat range of phototrophs in yellowstone national park: toward the development of a comprehensive fitness landscape

The extent to which geochemical variation shapes the distribution of phototrophic metabolisms was modeled based on 439 observations in geothermal springs in Yellowstone National Park (YNP), Wyoming. Generalized additive models (GAMs) were developed to predict the distribution of phototrophic metabolism as a function of spring temperature, pH, and total sulfide. GAMs comprised of temperature explained 38.8% of the variation in the distribution of phototrophic metabolism, whereas GAMs comprised of sulfide and pH explained 19.6 and 11.2% of the variation, respectively. These results suggest that of the measured variables, temperature is the primary constraint on the distribution of phototrophs in YNP. GAMs comprised of multiple variables explained a larger percentage of the variation in the distribution of phototrophic metabolism, indicating additive interactions among variables. A GAM that combined temperature and sulfide explained the greatest variation in the dataset (53.4%) while minimizing the introduction of degrees of freedom. In an effort to verify the extent to which phototroph distribution reflects constraints on activity, we examined the influence of sulfide and temperature on dissolved inorganic carbon (DIC) uptake rates under both light and dark conditions. Light-driven DIC uptake decreased systematically with increasing concentrations of sulfide in acidic, algal-dominated systems, but was unaffected in alkaline, cyanobacterial-dominated systems. In both alkaline and acidic systems, light-driven DIC uptake was suppressed in cultures incubated at temperatures 10°C greater than their in situ temperature. Collectively, these quantitative results indicate that apart from light availability, the habitat range of phototrophs in YNP springs is defined largely by constraints imposed firstly by temperature and secondly by sulfide on the activity of these populations that inhabit the edges of the habitat range. These findings are consistent with the predictions from GAMs and provide a quantitative framework from which to translate distributional patterns into fitness landscapes for use in interpreting the environmental constraints that have shaped the evolution of this process through Earth history.

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.

Effects of trace element concentrations on culturing thermophiles

The majority of microorganisms in natural environments resist laboratory cultivation. Sometimes referred to as 'unculturable', many phylogenetic groups are known only by fragments of recovered DNA. As a result, the ecological significance of whole branches of the 'tree of life' remains a mystery; this is particularly true when regarding genetic material retrieved from extreme environments. Geochemically relevant media have been used to improve the success of culturing Archaea and Bacteria, but these efforts have focused primarily on optimizing pH, alkalinity, major ions, carbon sources, and electron acceptor-donor pairs. Here, we cultured thermophilic microorganisms from 'Sylvan Spring' (Yellowstone National Park, USA) on media employing different trace element solutions, including one that mimicked the source fluid of the inocula. The growth medium that best simulated trace elements found in 'Sylvan Spring' produced a more diverse and faster growing mixed culture than media containing highly elevated trace element concentrations. The elevated trace element medium produced fewer phylotypes and inhibited growth. Trace element concentrations appear to influence growth conditions in extreme environments. Incorporating geochemical data into cultivation attempts may improve culturing success.

Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea

Many thermophiles catalyse free energy-yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in source water and sediments of two ≈ 80°C springs in the US Great Basin. Ammonia oxidation and denitrification occurred mainly in sediments. Ammonia oxidation rates measured using (15)N-NO(3)(-) pool dilution ranged from 5.5 ± 0.8 to 8.6 ± 0.9 nmol N g(-1) h(-1) and were unaffected or only mildly stimulated by amendment with NH(4) Cl. Denitrification rates measured using acetylene block ranged from 15.8 ± 0.7 to 51 ± 12 nmol N g(-1) h(-1) and were stimulated by amendment with NO(3)(-) and complex organic compounds. The DNRA rate in one spring sediment measured using an (15)N-NO(3)(-) tracer was 315 ± 48 nmol N g(-1) h(-1). Both springs harboured distinct planktonic and sediment microbial communities. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both spring sediments by 16S rRNA gene pyrotag analysis. Quantitative PCR (qPCR) indicated that 'Ca. N. yellowstonii'amoA and 16S rRNA genes were present at 3.5-3.9 × 10(8) and 6.4-9.0 × 10(8) copies g(-1) sediment. Potential denitrifiers included members of the Aquificales and Thermales. Thermus spp. comprised <1% of 16S rRNA gene pyrotags in both sediments and qPCR for T. thermophilus narG revealed sediment populations of 1.3-1.7 × 10(6) copies g(-1) sediment. These data indicate a highly active nitrogen cycle (N-cycle) in these springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production.

Archaea in Yellowstone Lake

The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.

Yellowstone Lake: high-energy geochemistry and rich bacterial diversity

Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H(2)S, CH(4), CO(2) and H(2), although CH(4) and H(2) levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-µm-, 3.0-µm-, 0.8-µm- and 0.1-µm-pore-size filters, with the >0.1 to <0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α- and β-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.

Enhanced CO2 fixation by a non-photosynthetic microbial community under anaerobic conditions: optimization of electron donors

To enhance the CO(2) fixation efficiency of the non-photosynthetic microbial community (NPMC) isolated from sea water under anaerobic conditions without hydrogen, the concentration of inorganic compounds as electron donors and their ratios were optimized by response surface methodology design (RSMD). The results indicated that the CO(2) fixation efficiency of NPMC using NaNO(2), Na(2)S(2)O(3) and Na(2)S as the electron donors was increased about 90%, 75% and 207%, respectively. Additionally, there were interactions between two electron donors and three electron donors. Central composite RSMD experimentation predicted that the optimal concentration and ratios of these inorganic compounds was 1.04% NaNO(2), 1.07% Na(2)S(2)O(3) and 0.98% Na(2)S. Under these conditions, the fixed CO(2) was 139.89 mg/L, which obviously exceeded the amount prior to optimization, as well as when H(2) was used as an electron donor. The established electron donor system can effectively enhance the CO(2) fixation efficiency of NPMC without hydrogen under anaerobic conditions.

Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera

A culture-independent community census was combined with chemical and thermodynamic analyses of three springs located within the Long Valley Caldera, Little Hot Creek (LHC) 1, 3, and 4. All three springs were approximately 80 degrees C, circumneutral, apparently anaerobic and had similar water chemistries. 16S rRNA gene libraries constructed from DNA isolated from spring sediment revealed moderately diverse but highly novel microbial communities. Over half of the phylotypes could not be grouped into known taxonomic classes. Bacterial libraries from LHC1 and LHC3 were predominantly species within the phyla Aquificae and Thermodesulfobacteria, while those from LHC4 were dominated by candidate phyla, including OP1 and OP9. Archaeal libraries from LHC3 contained large numbers of Archaeoglobales and Desulfurococcales, while LHC1 and LHC4 were dominated by Crenarchaeota unaffiliated with known orders. The heterogeneity in microbial populations could not easily be attributed to measurable differences in water chemistry, but may be determined by availability of trace amounts of oxygen to the spring sediments. Thermodynamic modeling predicted the most favorable reactions to be sulfur and nitrate respirations, yielding 40-70 kJ mol(-1) e(-) transferred; however, levels of oxygen at or below our detection limit could result in aerobic respirations yielding up to 100 kJ mol(-1) e(-) transferred. Important electron donors are predicted to be H(2), H(2)S, S(0), Fe(2+) and CH(4), all of which yield similar energies when coupled to a given electron acceptor. The results indicate that springs associated with the Long Valley Caldera contain microbial populations that show some similarities both to springs in Yellowstone and springs in the Great Basin.

CO(2) uptake and fixation by a thermoacidophilic microbial community attached to precipitated sulfur in a geothermal spring

Carbon fixation at temperatures above 73 degrees C, the upper limit for photosynthesis, is carried out by chemosynthetic thermophiles. Yellowstone National Park (YNP), Wyoming possesses many thermal features that, while too hot for photosynthesis, presumably support chemosynthetic-based carbon fixation. To our knowledge, in situ rates of chemosynthetic reactions at these high temperatures in YNP or other high-temperature terrestrial geothermal springs have not yet been reported. A microbial community attached to precipitated elemental sulfur (S(o) floc) at the source of Dragon Spring (73 degrees C, pH 3.1) in Norris Geyser Basin, YNP, exhibited a maximum rate of CO(2) uptake of 21.3 +/- 11.9 microg of C 10(7) cells(-1) h(-1). When extrapolated over the estimated total quantity of S(o) floc at the spring's source, the S(o) floc-associated microbial community accounted for the uptake of 121 mg of C h(-1) at this site. On a per-cell basis, the rate was higher than that calculated for a photosynthetic mat microbial community dominated by Synechococcus spp. in alkaline springs at comparable temperatures. A portion of the carbon taken up as CO(2) by the S(o) floc-associated biomass was recovered in the cellular nucleic acid pool, demonstrating that uptake was coupled to fixation. The most abundant sequences in a 16S rRNA clone library of the S(o) floc-associated community were related to chemolithoautotrophic Hydrogenobaculum strains previously isolated from springs in the Norris Geyser Basin. These microorganisms likely contributed to the uptake and fixation of CO(2) in this geothermal habitat.

Cloning and in situ expression studies of the Hydrogenobaculum arsenite oxidase genes

Novel arsenite [As(III)] oxidase structural genes (aoxAB) were cloned from Hydrogenobaculum bacteria isolated from an acidic geothermal spring. Reverse transcriptase PCR demonstrated expression throughout the outflow channel, and the aoxB cDNA clones exhibited distribution patterns relative to the physicochemical gradients in the spring. Microelectrode analyses provided evidence of quantitative As(III) transformation within the microbial mat.

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

A coordinated study of water chemistry, sediment mineralogy, and sediment microbial community was conducted on four >73 degrees C springs in the northwestern Great Basin. Despite generally similar chemistry and mineralogy, springs with short residence time (approximately 5-20 min) were rich in reduced chemistry, whereas springs with long residence time (>1 day) accumulated oxygen and oxidized nitrogen species. The presence of oxygen suggested that aerobic metabolisms prevail in the water and surface sediment. However, Gibbs free energy calculations using empirical chemistry data suggested that several inorganic electron donors were similarly favorable. Analysis of 298 bacterial 16S rDNAs identified 36 species-level phylotypes, 14 of which failed to affiliate with cultivated phyla. Highly represented phylotypes included Thermus, Thermotoga, a member of candidate phylum OP1, and two deeply branching Chloroflexi. The 276 archaeal 16S rDNAs represented 28 phylotypes, most of which were Crenarchaeota unrelated to the Thermoprotei. The most abundant archaeal phylotype was closely related to "Candidatus Nitrosocaldus yellowstonii", suggesting a role for ammonia oxidation in primary production; however, few other phylotypes could be linked with energy calculations because phylotypes were either related to chemoorganotrophs or were unrelated to known organisms.