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Microbes need energy to grow, reproduce, repair damage, maintain their metabolisms, and interact with their environment. Phototrophic microbes can harness the power of sunlight while chemotrophs derive energy from chemical compounds. Thermodynamic calculations can tell us whether a chemotrophic metabolic reaction will yield energy in an aqueous environment depending on fluid composition, temperature, and pressure. If the calculation reveals that energy is not available for a reaction, the reaction can be ruled out as a viable metabolic strategy in that system. Similarly, energy supplies can be quantified for energy-yielding reactions to generate hypotheses about how chemotrophic microbes harness energy in a system. Because of its usefulness for interpreting chemotroph metabolic strategies, several recent studies have quantified microbial energy supplies in natural systems and growth experiments using free and open-source software tools developed for the Water-Organic-Rock-Microbe (WORM) Portal online computing environment [1, 2, 3, 4]. The WORM Portal is an NSF-funded geochemical modeling platform for researchers, students, and the public that can be accessed for free through an internet browser. The WORM Portal comes pre-packaged with computational Jupyter notebook tools and educational demos covering a variety of topics in geobiology and geochemistry. In this presentation, we will demonstrate how the WORM Portal can be used to quantify microbial energy supplies, chemical affinities, and power (energy over time) in water samples and growth media under ambient conditions and elevated temperatures and pressures, and how you can apply the WORM Portal to quantify energy supplies in your own systems of interest. [1] Alain et al. (2022). Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents. Environmental Microbiology, 24(5), 2210-2219. [2] Howells et al. (2025). Energetic and genomic potential for hydrogenotrophic, formatotrophic, and acetoclastic methanogenesis in surface-expressed serpentinized fluids of the Samail Ophiolite. Frontiers in Microbiology, 15, 1523912. [3] Parsons et al. "Hydrothermal Seepage of Altered Crustal Formation Water Seaward of the Middle America Trench, Offshore Costa Rica." Geochemistry, Geophysics, Geosystems 25.1 (2024): e2023GC011246. [4] Rhim et al. (2024). Mode of carbon and energy metabolism shifts lipid composition in the thermoacidophile Acidianus. Applied and Environmental Microbiology, 90(2), e01369-23. 

The availability of chemical energy supplies is fundamental to environmental and planetary habitability. However, the presence of a chemical energy supply does not guarantee the presence of microorganisms capable of consuming it. In this study, chemical energy supplies available in Yellowstone National Park (YNP) hot springs were calculated, and the results indicate that ammonia oxidation, calculated using total dissolved ammonia, is one of the major energy supplies. Nevertheless, known ammonia-oxidizers (AO) are only present in a small fraction of the hot springs tested. Where AO are present, they do not dominate the microbial communities (relative abundances <5%), even in cases where total dissolved ammonia oxidation is the richest energy supply. The AO in YNP hot springs are predominantly ammonia-oxidizing archaea (AOA), which tend to favor environments with low total ammonia (sum of NH3 and NH4+) concentrations, despite the requirement of ammonia (NH3) as a substrate. Hot spring pH and temperature determine the ratio of NH3 to NH4+ and, consequently, NH3 availability to resident AOA. In this study, total ammonia measurements were collected from YNP hot spring samples using ion chromatography in coordination with biological sampling. DNA was extracted from simultaneously collected samples for 16S rRNA gene sequencing and analysis, and for the identification of known AOA. The WORM-portal (https://worm-portal.asu.edu/) was used to speciate the total ammonia measurements into ammonia and ammonium activities. By performing speciation calculations, we identified a potential lower limit for substrate (NH3) availability and a potential upper limit for NH4+ concentrations for the YNP hot spring AOA. Thus, the niche for AOA across YNP hot springs is dictated by the form of the total dissolved ammonia present, not by the energy supply available for total dissolved ammonia oxidation. 

Serpentinization, the reaction of water with ultramafic rock, produces reduced, hyperalkaline, and H₂-rich fluids that support a variety of hydrogenotrophic microbial metabolisms. Previous work indicates the occurrence of methanogenesis in fluids from the actively serpentinizing Samail Ophiolite in the Sultanate of Oman. While those fluids contain abundant H₂to fuel hydrogenotrophic methanogenesis (CO₂ + 4H₂➔ CH₄ + 2H₂O), the concentration of CO₂is very low due to the hyperalkalinity (> pH 11) and geochemistry of the fluids. As a result, species such as formate and acetate may be important as alternative methanogenic substrates. In this study we quantified the impact of inorganic carbon, formate and acetate availability for methanogenic metabolisms, across a range of fluid chemistries, in terms of (1) the potential diffusive flux of substrates to the cell, (2) the Affinity (Gibbs energy change) associated with methanogenic metabolism, and (3) the energy “inventory” per kg fluid. In parallel, we assessed the genomic potential for the conduct of those three methanogenic modes across the same set of fluids and consider the results within the quantitative framework of energy availability. We find that formatotrophic methanogenesis affords a higher Affinity (greater energetic yield) than acetoclastic and hydrogenotrophic methanogenesis in pristine serpentinized fluids and, in agreement with previous studies, find genomic evidence for a methanogen of the genusMethanobacteriumto carry out formatotrophic and hydrogenotrophic methanogenesis, with the possibility of even using bicarbonate as a supply of CO₂. Acetoclastic methanogenesis is also shown to be energetically favorable in these fluids, and we report the first detection of a potential acetoclastic methanogen of the familyMethanosarcinaceae, which forms a distinct clade with a genome from the serpentinizing seafloor hydrothermal vent field, Lost City. These results demonstrate the applicability of an energy availability framework for interpreting methanogen ecology in serpentinizing systems. 

ABSTRACT Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs. 

Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure–function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.