Chemolithoautotroph distributions across the subsurface of a convergent margin

Exploring microbial diversity in relation to hydrological signatures and anthropic pressures in the Beauce Aquifer, France

Groundwater is one of the largest reservoirs of liquid fresh water on earth. Aquifers are complex environments where water quality can be affected by geological origins, geochemistry and biological activity. These environments are under pressure due to climate change and pollution. Strongly involved in the biogeochemistry of groundwater ecosystems, microorganisms can also contribute to reducing pollution and potentially be used as indicators of water quality. However, the diversity and role of microorganisms in groundwater remains largely unknown. The present work aimed to characterize bacterial diversity in 60 wells over 8000 km2 in the Beauce Aquifer, France, determine the baseline diversity expected in relation to the hydro geochemical signatures and identify variations that could be due to anthropogenic pressures. We analysed amplicon sequence variants (ASVs) of the 16S rRNA gene as well as the abundance of functional genes associated to arsenic and nitrate (aioA, arsB, narG), organic carbon contents and the geochemical composition. Bacterial diversity and bacterial co-occurrences were found to change according to the hydrogeochemical signatures identified in the aquifer. A lower diversity was measured in confined aquifers, where low oxygen and reducing conditions occurred with high levels of dissolved iron and manganese. This could indicate a higher vulnerability in the face of pressure. Finally, a baseline bacterial diversity composition was found to be linked to each hydrogeochemical signature and several wells that differed from the expected variations of this diversity were identified.

The effects of perfluoroalkyl substance pollution on microbial community and key metabolic pathways in the Pearl River Estuary

The extensive use of perfluoroalkyl substances (PFASs) has raised significant concerns regarding their adverse environmental implications. However, the understanding of their behaviors and biological effects in natural estuarine ecosystems remain limited. This study employed a multidisciplinary approach integrating chemical analysis, biological sequencing, and statistical modeling to comprehensively investigate the distribution of PFASs, as well as their intrinsic relationship with microbial community in the Pearl River Estuary (PRE), a rapidly urbanized area. Our findings demonstrate that the total PFAS concentrations ranged from 52-127 ng L-1 in water, and 2-70 μg kg-1 dry weight in sediment, with notably distinct compositions across habitats. Aquatic microbial communities exhibited higher sensitivity to environmental variables, including PFAS concentrations, attributed to increased stochasticity and reduced spatial turnover. Conversely, sediments harbored microbial communities with higher phylogenetic diversity, rendering them less susceptible to PFAS-induced stress. Furthermore, PFAS concentrations significantly affected microbial carbon, nitrogen, and phosphorus cycling, predominantly through indirect alterations in characteristic genus composition. Importantly, noteworthy variations in impacts were observed between perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), which might contingent upon C-F bond dissociation energies. The findings shed light on PFAS ecological roles and interaction patterns with microbial communities in human-impacted estuarine environments.

Enhanced microbial degradation of hexabromocyclododecane in riparian sediments through regulating flooding regimes

Hexabromocyclododecane (HBCD), a persistent halogenated organic pollutant, has been commonly detected in river sediments, especially in riparian zones, but strategies for promoting its microbial degradation remain insufficiently explored. This study hypothesized that regulating the flooding regime of sediments could accelerate microbial degradation of HBCD in riparian zones and evaluated the underlying mechanisms. Results showed that, compared with high-frequency flooding-drying or no alternations, the low-frequency flooding-drying alternation (6 weeks of flooding and 6 weeks of drying, 6F:6D) significantly promoted microbial degradation of HBCD. This may be due to changes in sediment redox potential under the 6F:6D regime, facilitating the sequential reductive debromination and aerobic degradation process of HBCD. The abundances of organohalide-respiring bacteria (Dehalococcoides spp. and Dehalogenimonas spp.) were always high in the 6F:6D regime, irrespective of flooding or drying periods. Furthermore, the complex bacterial co-occurrence patterns, specific ecological clusters, and potential keystone species including the genera Methylibium, Nitrospira, and Dehalococcoides, may play important degradative roles of HBCD in the 6F:6D regime. Overall, microbial degradation of HBCD can be promoted under low-frequency flooding-drying alternation regulated by hydraulic structures, providing an effective and eco-friendly strategy for ecological restoration.

Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.

Microbial communities and functions are structured by vertical geochemical zones in a northern peatland

Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.

Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N)

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.

Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota

Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.

Targeting deeply-sourced seeps along the Central Volcanic Zone

At convergent margins, plates collide producing a subduction process. When an oceanic plate collides with a continental plate, the denser (i.e., oceanic) plate subducts beneath the less dense (continental) plate. This process results in the transportation of carbon and other volatiles into Earth's deep interior and is counterbalanced by volcanic outgassing. Sampling deeply-sourced seeps and fumaroles throughout a convergent margin allows us to assess the processes that control the inventory of volatiles and their interaction with the deep subsurface microbial communities. The Andean Convergent Margin is volcanically active in four distinct zones: the Northern Volcanic Zone, the Central Volcanic Zone, the Southern Volcanic Zone and the Austral Volcanic Zone, which are each characterised by significantly different subduction parameters like crustal thickness, age of subduction and subduction angle. These differences can change subduction dynamics along the convergent margin, possibly influencing the recycling efficiency of carbon and volatiles and its interaction with the subsurface microbial communities. We carried out a scientific expedition, sampling along a ~800 km convergent margin segment of the Andean Convergent Margin in the Central Volcanic Zone of northern Chile, between 17 °S and 24 °S, sampling fluids, gases and sediments, in an effort to understand interactions between microbiology, deeply-sourced fluids, the crust, and tectonic parameters. We collected samples from 38 different sites, representing a wide diversity of seep types in different geologic contexts. Here we report the field protocols and the descriptions of the sites and samples collected.

Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics

BACKGROUND

Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.

RESULTS

The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.

CONCLUSIONS

Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.

Standard operating procedure for the analysis of major ions in hydrothermal fluids by ion chromatography

This standard operating procedure (SOP) describes an ion chromatography (IC) procedure for the major cations and anions in hydrothermal fluids. Hydrothermal fluids are aqueous solutions with a wide range of temperature, salinity, pH and ion species that can be used by microbial metabolism as electron donors and electron acceptors. Due to the high variability of the environmental physical-chemical parameters in these samples, we have developed this protocol taking into account the special features of the matrices analyzed. An Eco IC Metrohm system equipped with a conductivity detector was used. Calibration curves are linear in the 0.1 to 10 mg/L concentration range for cations Ca 2+, Na +, K +, Mg 2+, NH 4 + and anions Cl -, Br -, NO 3 -, NO 2 -, SO 4 2- , PO 4 3-.

Standard Operating Procedure for the determination of trace elements in hydrothermal fluids by Inductively Coupled Plasma Mass Spectrometry (ICP-MS)

This standard operating procedure (SOP) validates an inductively coupled plasma mass spectrometry (ICP-MS) procedure for the determination of trace elements in hydrothermal fluids. Hydrothermal fluids are aqueous solutions with a wide range of temperature, salinity, pH and trace elements that can be used by a set of microbial proteins containing redox-sensitive transition metals as their catalytic core. Due to the high variability of these samples, we have developed this protocol taking into account the special features of the matrices analyzed. An ICP-MS 7900 Agilent system was used. Calibration curves are linear in the 0.01 to 100 μg/L concentration range.

Marine Science Can Contribute to the Search for Extra-Terrestrial Life

Life on our planet likely evolved in the ocean, and thus exo-oceans are key habitats to search for extraterrestrial life. We conducted a data-driven bibliographic survey on the astrobiology literature to identify emerging research trends with marine science for future synergies in the exploration for extraterrestrial life in exo-oceans. Based on search queries, we identified 2592 published items since 1963. The current literature falls into three major groups of terms focusing on (1) the search for life on Mars, (2) astrobiology within our Solar System with reference to icy moons and their exo-oceans, and (3) astronomical and biological parameters for planetary habitability. We also identified that the most prominent research keywords form three key-groups focusing on (1) using terrestrial environments as proxies for Martian environments, centred on extremophiles and biosignatures, (2) habitable zones outside of "Goldilocks" orbital ranges, centred on ice planets, and (3) the atmosphere, magnetic field, and geology in relation to planets' habitable conditions, centred on water-based oceans.

Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways

Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.

Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy

The Ansanto Valley's Mefite, one of the Earth's largest non-volcanic CO2 gas emissions, is distinguished by its cold natural carbon dioxide springs. These emissions originate from the intricate tectonics and geodynamics of the southern Apennines in Italy. Known for over two millennia for its lethal concentration of CO2 and other harmful gases, the Mefite has a reputation for being toxic and dangerous. Despite its historical significance and unique geological features, there is a lack of information on the microbial diversity associated with the Mefite's gas emissions. This study presents an integrated exploration of the microbial diversity in the mud soil, using high-throughput sequencing of 16S rRNA (Prokaryotes) and ITS2 (Fungi), alongside a geochemical site characterisation. Our findings reveal that the Mefite's unique environment imposes a significant bottleneck on microbial diversity, favouring a select few microbial groups such as Actinobacteria and Firmicutes for Prokaryotes, and Basidiomycota for Fungi.

Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert

High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs shows that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.

Tectonic and geological setting influence hot spring microbiology

Hydrothermal systems form at divergent and convergent boundaries of lithospheric plates and within plates due to weakened crust and mantle plumes, playing host to diverse microbial ecosystems. Little is known of how differences in tectonic setting influence the geochemical and microbial compositions of these hydrothermal ecosystems. Here, coordinated geochemical and microbial community analyses were conducted on 87 high-temperature (>65°C) water and sediment samples from hot springs in Yellowstone National Park, Wyoming, USA (n = 41; mantle plume setting), Iceland (n = 41, divergent boundary), and Japan (n = 5; convergent boundary). Region-specific variation in geochemistry and sediment-associated 16S rRNA gene amplicon sequence variant (ASV) composition was observed, with 16S rRNA gene assemblages being nearly completely distinguished by region and pH being the most explanatory parameter within regions. Several low abundance ASVs exhibited cosmopolitan distributions across regions, while most high-abundance ASVs were only identified in specific regions. The presence of some cosmopolitan ASVs across regions argues against dispersal limitation primarily shaping the distribution of taxa among regions. Rather, the results point to local tectonic and geologic characteristics shaping the geochemistry of continental hydrothermal systems that then select for distinct microbial assemblages. These results provide new insights into the co-evolution of hydrothermal systems and their microbial communities.

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.

Identifying and Understanding Microbial Methanogenesis in CO2 Storage

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO₂ can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO₂, yet there has been little consideration of the subsurface microbial impact on CO₂ storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO₂ that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO₂ storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H₂ generation. We expect that the bioavailability of H₂ (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO₂ storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO₂ storage sites and its potential impact.

Tectonic settings influence the geochemical and microbial diversity of Peru hot springs

Tectonic processes control hot spring temperature and geochemistry, yet how this in turn shapes microbial community composition is poorly understood. Here, we present geochemical and 16 S rRNA gene sequencing data from 14 hot springs from contrasting styles of subduction along a convergent margin in the Peruvian Andes. We find that tectonic influence on hot spring temperature and geochemistry shapes microbial community composition. Hot springs in the flat-slab and back-arc regions of the subduction system had similar pH but differed in geochemistry and microbiology, with significant relationships between microbial community composition, geochemistry, and geologic setting. Flat-slab hot springs were chemically heterogeneous, had modest surface temperatures (up to 45 °C), and were dominated by members of the metabolically diverse phylum Proteobacteria. Whereas, back-arc hot springs were geochemically more homogenous, exhibited high concentrations of dissolved metals and gases, had higher surface temperatures (up to 81 °C), and host thermophilic archaeal and bacterial lineages.

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.

An overview of experimental simulations of microbial activity in early Earth

Microbial activity has shaped the evolution of the ocean and atmosphere throughout the Earth history. Thus, experimental simulations of microbial metabolism under the environment conditions of the early Earth can provide vital information regarding biogeochemical cycles and the interaction and coevolution between life and environment, with important implications for extraterrestrial exploration. In this review, we discuss the current scope and knowledge of experimental simulations of microbial activity in environments representative of those of early Earth, with perspectives on future studies. Inclusive experimental simulations involving multiple species, and cultivation experiments with more constraints on environmental conditions similar to early Earth would significantly advance our understanding of the biogeochemical cycles of the geological past.