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Dihydrogen (H 2 ) is an important intermediate in anaerobic microbial processes, and concentrations are tightly controlled by thermodynamic limits of consumption and production. However, recent studies reported unusual H 2 accumulation in permeable marine sediments under anoxic conditions, suggesting decoupling of fermentation and sulfate reduction, the dominant respiratory process in anoxic permeable marine sediments. Yet, the extent, prevalence and potential triggers for such H 2 accumulation and decoupling remain unknown. We surveyed H 2 concentrations in situ at different settings of permeable sand and found that H 2 accumulation was only observed during a coral spawning event on the Great Barrier Reef. A flume experiment with organic matter addition to the water column showed a rapid accumulation of hydrogen within the sediment. Laboratory experiments were used to explore the effect of oxygen exposure, physical disturbance and organic matter inputs on H 2 accumulation. Oxygen exposure had little effect on H 2 accumulation in permeable sediments suggesting both fermenters and sulfate reducers survive and rapidly resume activity after exposure to oxygen. Mild physical disturbance mimicking sediment resuspension had little effect on H 2 accumulation; however, vigorous shaking led to a transient accumulation of H 2 and release of dissolved organic carbon suggesting mechanical disturbance and cell destruction led to organic matter release and transient decoupling of fermenters and sulfate reducers. In summary, the highly dynamic nature of permeable sediments and its microbial community allows for rapid but transient decoupling of fermentation and respiration after a C pulse, leading to high H 2 levels in the sediment., Competing Interests: None declared., (© 2023 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography.)

Molecular hydrogen (H 2 ) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H 2 to support growth. Genes for H 2 -uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H 2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H 2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H 2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H 2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry., (© 2023. The Author(s).)

Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate ( Hymenobacter roseosalivarius ) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists., Competing Interests: The authors declare no competing interest.

Organoheterotrophs are the dominant bacteria in most soils worldwide. While many of these bacteria can subsist on atmospheric hydrogen (H 2 ), levels of this gas are generally insufficient to sustain hydrogenotrophic growth. In contrast, bacteria residing within soil-derived termite mounds are exposed to high fluxes of H 2 due to fermentative production within termite guts. Here, we show through community, metagenomic, and biogeochemical profiling that termite emissions select for a community dominated by diverse hydrogenotrophic Actinobacteriota and Dormibacterota. Based on metagenomic short reads and derived genomes, uptake hydrogenase and chemosynthetic RuBisCO genes were significantly enriched in mounds compared to surrounding soils. In situ and ex situ measurements confirmed that high- and low-affinity H 2 -oxidizing bacteria were highly active in the mounds, such that they efficiently consumed all termite-derived H 2 emissions and served as net sinks of atmospheric H 2 Concordant findings were observed across the mounds of three different Australian termite species, with termite activity strongly predicting H 2 oxidation rates ( R 2 = 0.82). Cell-specific power calculations confirmed the potential for hydrogenotrophic growth in the mounds with most termite activity. In contrast, while methane is produced at similar rates to H 2 by termites, mounds contained few methanotrophs and were net sources of methane. Altogether, these findings provide further evidence of a highly responsive terrestrial sink for H 2 but not methane and suggest H 2 availability shapes composition and activity of microbial communities. They also reveal a unique arthropod-bacteria interaction dependent on H 2 transfer between host-associated and free-living microbial communities., Competing Interests: The authors declare no competing interest.

Tree stems are an important and unconstrained source of methane, yet it is uncertain whether internal microbial controls (i.e. methanotrophy) within tree bark may reduce methane emissions. Here we demonstrate that unique microbial communities dominated by methane-oxidising bacteria (MOB) dwell within bark of Melaleuca quinquenervia, a common, invasive and globally distributed lowland species. In laboratory incubations, methane-inoculated M. quinquenervia bark mediated methane consumption (up to 96.3 µmol m -2 bark d -1 ) and reveal distinct isotopic δ 13 C-CH 4 enrichment characteristic of MOB. Molecular analysis indicates unique microbial communities reside within the bark, with MOB primarily from the genus Methylomonas comprising up to 25 % of the total microbial community. Methanotroph abundance was linearly correlated to methane uptake rates (R 2  = 0.76, p = 0.006). Finally, field-based methane oxidation inhibition experiments demonstrate that bark-dwelling MOB reduce methane emissions by 36 ± 5 %. These multiple complementary lines of evidence indicate that bark-dwelling MOB represent a potentially significant methane sink, and an important frontier for further research.

Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.

Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH 4 ) emissions, but the aerobic CH 4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH 4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil samples. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis-Menten kinetics of CH 4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH 4 source such as landfill cover soils. The rate constant of CH 4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH 4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH 4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH 4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH 4 concentrations and suggest a higher functional diversity within this group than previously recognised.

Termites are responsible for ∼1 to 3% of global methane (CH 4 ) emissions. However, estimates of global termite CH 4 emissions span two orders of magnitude, suggesting that fundamental knowledge of CH 4 turnover processes in termite colonies is missing. In particular, there is little reliable information on the extent and location of microbial CH 4 oxidation in termite mounds. Here, we use a one-box model to unify three independent field methods-a gas-tracer test, an inhibitor approach, and a stable-isotope technique-and quantify CH 4 production, oxidation, and transport in three North Australian termite species with different feeding habits and mound architectures. We present systematic in situ evidence of widespread CH 4 oxidation in termite mounds, with 20 to 80% of termite-produced CH 4 being mitigated before emission to the atmosphere. Furthermore, closing the CH 4 mass balance in mounds allows us to estimate in situ termite biomass from CH 4 turnover, with mean biomass ranging between 22 and 86 g of termites per kilogram of mound for the three species. Field tests with excavated mounds show that the predominant location of CH 4 oxidation is either in the mound material or the soil beneath and is related to species-specific mound porosities. Regardless of termite species, however, our data and model suggest that the fraction of oxidized CH 4 ( f ox ) remains well buffered due to links among consumption, oxidation, and transport processes via mound CH 4 concentration. The mean f ox of 0.50 ± 0.11 (95% CI) from in situ measurements therefore presents a valid oxidation factor for future global estimates of termite CH 4 emissions., Competing Interests: The authors declare no conflict of interest.

Glacier forefield soils can provide a substantial sink for atmospheric CH 4 , facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH 4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH 4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH 4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH 4 uptake rates ranging from -3.7 to -0.03 mg CH 4 m -2 day -1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH 4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH 4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH 4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH 4 inventories. IMPORTANCE Oxidation of methane (CH 4 ) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH 4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH 4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH 4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH 4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH 4 inventories., (Copyright © 2017 American Society for Microbiology.)

Soil-gas turnover is important in the global cycling of greenhouse gases. The analysis of soil-gas profiles provides quantitative information on below-ground turnover and fluxes. We developed a poly-use multi-level sampling system (PMLS) for soil-gas sampling, water-content and temperature measurement with high depth resolution and minimal soil disturbance. It is based on perforated access tubes (ATs) permanently installed in the soil. A multi-level sampler allows extraction of soil-gas samples from 20 locations within 1 m depth, while a capacitance probe is used to measure volumetric water contents. During idle times, the ATs are sealed and can be equipped with temperature sensors. Proof-of-concept experiments in a field lysimeter showed good agreement of soil-gas samples and water-content measurements compared with conventional techniques, while a successfully performed gas-tracer test demonstrated the feasibility of the PMLS to determine soil-gas diffusion coefficients in situ. A field application of the PMLS to quantify oxidation of atmospheric CH4 in a field lysimeter and in the forefield of a receding glacier yielded activity coefficients and soil-atmosphere fluxes well in agreement with previous studies. With numerous options for customization, the presented tool extends the methodological choices to investigate soil-gas transport in the vadose zone.