Trace gas oxidizers are widespread and active members of soil microbial communities

Atmospheric Trace Gas Oxidizers Contribute to Soil Carbon Fixation Driven by Key Soil Conditions in Terrestrial Ecosystems

Microbial oxidizers of trace gases such as hydrogen (H2) and carbon monoxide (CO) are widely distributed in soil microbial communities and play a vital role in modulating biogeochemical cycles. However, the contribution of trace gas oxidizers to soil carbon fixation and the driving environmental factors remain unclear, especially on large scales. Here, we utilized biogeochemical and genome-resolved metagenomic profiling, assisted by machine learning analysis, to estimate the contributions of trace gas oxidizers to soil carbon fixation and to predict the key environmental factors driving this process in soils from five distinct ecosystems. The results showed that phylogenetically and physiologically diverse H2 and CO oxidizers and chemosynthetic carbon-fixing microbes are present in the soil in different terrestrial ecosystems. The large-scale variations in soil carbon fixation were highly positively correlated with both the abundance and the activity of H2 and CO oxidizers (p < 0.05-0.001). Furthermore, soil pH and moisture-induced shifts in the abundance of H2 and CO oxidizers partially explained the variation in soil carbon fixation (55%). The contributions of trace gas oxidizers to soil carbon fixation in the different terrestrial ecosystems were estimated to range from 1.1% to 35.0%. The estimated rate of trace gas carbon fixation varied from 0.04 to 1.56 mg kg-1 d-1. These findings reveal that atmospheric trace gas oxidizers may contribute to soil carbon fixation driven by key soil environmental factors, highlighting the non-negligible contribution of these microbes to terrestrial carbon cycling.

Comparative Genomics Reveal Distinct Environment Preference and Functional Adaptation Among Lineages of Gemmatimonadota

Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats.

Microbiome associated to an H2-emitting zone in the São Francisco basin Brazil

BACKGROUND

Dihydrogen (H₂) natural gas is a clean and renewable energy source of significant interest in the transition to sustainable energy. Unlike conventional petroleum-based fuels, H₂ releases only water vapor upon combustion, making it a promising alternative for reducing carbon footprints in the future. However, the microbial impact on H₂ dynamics in H2-emitting zones remains unclear, as does the origin of H2 - whether it is produced at greater depths or within shallow soil layers. In the São Francisco Basin, soil hydrogen concentrations of approximately 200 ppm were identified in barren ground depressions. In this study, we investigated the microbiome associated with this area using the 16S rRNA gene sequencing, with a focus on metabolic processes related to H₂ consumption and production. Soil samples were collected from two monitored (< 1 m) depths - 10 cm and 1 m - in the emission zone, which is predominantly covered with pasture vegetation, and from an adjacent area with medium and small trees.

RESULTS

Our findings suggest that the H2-emitting zone significantly influences the composition and function of the microbiome, with Bacillus emerging as the dominant genus. In contrast to typical Cerrado soil, we observed a higher prevalence of Actinobacteriota (∼ 40%) and Firmicutes (∼ 20%). Additionally, we identified an abundance of sporulating bacteria and taxonomic groups previously described as H2-oxidizing bacteria.

CONCLUSIONS

The H2-emitting zone in the São Francisco Basin presents a unique opportunity to deepen our understanding of the impact of H₂ on microbial communities. This study is the first to characterize a natural H2-associated bacterial community in Cerrado soil using a culture-independent approach.

3775-year-old wood burial supports "wood vaulting" as a durable carbon removal method

Six-times more carbon dioxide (CO2) is removed each year by terrestrial photosynthesis than fossil fuel emissions. However, the carbon is mostly returned to the atmosphere by decomposition. We found a 3775-year-old ancient wood log buried 2 meters belowground that was preserved far beyond its expected lifetime. The wood had near-perfect preservation, with carbon loss less than 5% compared to a modern sample. The lack of decay is likely due to the low permeability of the compact clay soil at the burial site. Our observation suggests a hybrid nature-engineering approach for carbon removal by burying woody biomass in similar anoxic environments. We estimate a global sequestration potential of up to 10 gigatonnes CO2 per year with existing technology at a low cost of $30 to $100 per tonne after optimization.

The role of halophyte-induced saline fertile islands in soil microbial biogeochemical cycling across arid ecosystems

Halophyte shrubs, prevalent in arid regions globally, create saline fertile islands under their canopy. This study investigates the soil microbial communities and their energy utilization strategies associated with tamarisk shrubs in arid ecosystems. Shotgun sequencing revealed that high salinity in tamarisk islands reduces functional gene alpha-diversity and relative abundance compared to bare soils. However, organic matter accumulation within islands fosters key halophilic archaea taxa such as Halalkalicoccus, Halogeometricum, and Natronorubrum, linked to processes like organic carbon oxidation, nitrous oxide reduction, and sulfur oxidation, potentially strengthening the coupling of nutrient cycles. In contrast, bare soils harbor salt-tolerant microbes with genes for autotrophic energy acquisition, including carbon fixation, H2 or CH4 consumption, and anammox. Additionally, isotope analysis shows higher microbial carbon use efficiency, N mineralization, and denitrification activity in tamarisk islands. Our findings demonstrate that halophyte shrubs serve as hotspots for halophilic microbes, enhancing microbial nutrient transformation in saline soils.

Kinetics and pathways of sub-lithic microbial community (hypolithon) development

Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.

Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

Quality analysis and function prediction of soil microbial communities of Polygonatum cyrtonema in two indigenous-origins

Polygonatum cyrtonema Hua (PCH), as an important economic crop, is used as raw industrial materials and traditional Chinese medicine. There are significant variations in the quality of PCH from different geographical origins. It can be due to the change of the endophytic fungi and soil microbial communities of PCH. Therefore, the aim of this study is to investigate the composition and functional prediction of the main microbial communities in the rhizomes and soil of PCH and explore their impact on medicinal quality. High-throughput sequencing techniques targeting ITS and 16S rDNA were employed to compare the structure and biodiversity differences of endophytic fungi in the rhizomes and soil microbial communities of PCH from 12 different locations in Sichuan and Guangxi province. Heatmap analysis was used for comprehensive statistics and visualization of the richness of rhizome and soil microbial communities from all locations. Venn analysis was conducted to determine the total number of shared fungi between rhizomes and soil, and GraphPad Prism analysis was employed to predict and compare the microbial communities related to phenotypes at the genus level in Sichuan and Guangxi. Tax4Fun and Fungild were used for metabolic function prediction of microbial communities in the rhizomes and soil of PCH. The results revealed the identification of 19,387 bacterial amplicon sequence variants (ASVs) in the rhizomes and 37,990 bacterial ASVs in the soil, with 6,889 shared bacterial ASVs. In addition, 2,948 fungal ASVs were identified in the rhizomes and 8,868 in the soil, with 1,893 shared fungal ASVs. Microbial sequencing results indicated that the fungal communities between soil and rhizomes were mainly composed of Ascomycota and Basidiomycota, while bacterial communities included Proteobacteria, Acidobacteria, Bacteroidota, Gammatimonadota, and Firmicutes. Dominant bacterial groups such as Nitrospira, Acidibacter, and fungal groups including Mortierella, Ceratobasidium, and Fusarium were identified as potential contributors to the observed traits. In the top 15 microbial genera, both Sichuan and Guangxi contain 15 bacterial genera, but there are differences in their abundance. Guangxi has three unique fungal genera, including the genera Scleroderma, Russula, and Gliocladiopsis. On the other hand, Sichuan has the unique fungal genus Chamaeota. The correlation analysis between the microbiota and the chemical content from 12 different collecting spots was performed by GraphPad Prism. Burkholderia-Caballeronia-Paraburkholderia, Acidibacter, and Amycolatopsis show an inverse proportionality to total polysaccharides and saponins, while Enterobacter shows a direct proportionality to total polysaccharides and inverse proportionality to saponins. The metabolism pathways show a significant positive correlation with PCH polysaccharides and saponins. This study provide new insights into the mechanisms underlying the quality differences between the two major indigenous areas.

Utilisation of low methane concentrations by methanotrophs

The growing urgency regarding climate change points to methane as a key greenhouse gas for slowing global warming to allow other mitigation measures to take effect. One approach to both decreasing methane emissions and removing methane from air is aerobic methanotrophic bacteria, those bacteria that grow on methane as sole carbon and energy source and require O2. A subset of these methanotrophs is able to grow on methane levels of 1000 parts per million (ppm) and below, and these present an opportunity for developing both environmental- and bioreactor-based methane treatment systems. However, relatively little is known about the traits of such methanotrophs that allow them to grow on low methane concentrations. This review assesses current information regarding how methanotrophs grow on low methane concentrations in the context of developing treatment strategies that could be applied for both decreasing methane emissions and removing methane from air.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Black soldier fly larvae mitigate greenhouse gas emissions from domestic biodegradable waste by recycling carbon and nitrogen and reconstructing microbial communities

Black soldier fly larvae have been proven to reduce greenhouse gas emissions in the treatment of organic waste. However, the microbial mechanisms involved have not been fully understood. The current study mainly examined the dynamic changes of carbon and nitrogen, greenhouse gas emissions, the succession of microbial community structure, and changes in functional gene abundance in organic waste under larvae treatment and non-aeration composting. Thirty percent carbon and 55% nitrogen in the organic waste supplied were stored in larvae biomass. Compared to the non-aeration composting, the larvae bioreactor reduced the proportion of carbon and nitrogen converted into greenhouse gases (CO2, CH4, and N2O decreased by 62%, 87%, and 95%, respectively). 16S rRNA sequencing analysis indicated that the larvae bioreactor increased the relative abundance of Methanophaga, Marinobacter, and Campylobacter during the bioprocess, enhancing the consumption of CH4 and N2O. The metagenomic data showed that the intervention of larvae reduced the ratio of (nirK + nirS + nor)/nosZ in the residues, thereby reducing the emission of N2O. Larvae also increased the functional gene abundance of nirA, nirB, nirD, and nrfA in the residues, making nitrite more inclined to be reduced to ammonia instead of N2O. The larvae bioreactor mitigated greenhouse gas emissions by redistributing carbon and nitrogen and remodeling microbiomes during waste bioconversion, giving related enterprises a relative advantage in carbon trading.

Survival and rapid resuscitation permit limited productivity in desert microbial communities

Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Chemical structure of hydrocarbons significantly affects removal performance and microbial responses in gas biotrickling filters

The control of emissions of short-chain hydrocarbons with different structures is critical for the petrochemical industry. Herein, three two-carbon-containing (C2) hydrocarbons, ethane, ethylene, and acetylene, were chosen as pollutants to study the effects of chemical structure of hydrocarbons on removal performance and microbial responses in biotrickling filters. Results showed that the removal efficiency (RE) of C2 hydrocarbons followed the sequence of acetylene > ethane > ethylene. When the inlet loading rate was 30 g/(m3·h) and the empty bed residence time was 60 s, the RE of ethane, ethylene, and acetylene was 57 ± 4.0 %, 49 ± 1.0 %, and 84 ± 2.7 %, respectively. The high water solubility resulted in the high removal of C2 hydrocarbons, while a low surface tension enhanced the removal of C2 hydrocarbons. Additionally, the microbial community, enzyme activity, and extracellular properties of microorganisms also contributed to the difference in C2 hydrocarbon removal. These results could be referred for the effective control of light hydrocarbon emissions.

Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica

Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.

Carbon Monoxide Poisoning: From Microbes to Therapeutics

Carbon monoxide (CO) poisoning leads to 50,000-100,000 emergency room visits and 1,500-2,000 deaths each year in the United States alone. Even with treatment, survivors often suffer from long-term cardiac and neurocognitive deficits, highlighting a clear unmet medical need for novel therapeutic strategies that reduce morbidity and mortality associated with CO poisoning. This review examines the prevalence and impact of CO poisoning and pathophysiology in humans and highlights recent advances in therapeutic strategies that accelerate CO clearance and mitigate toxicity. We focus on recent developments of high-affinity molecules that take advantage of the uniquely strong interaction between CO and heme to selectively bind and sequester CO in preclinical models. These scavengers, which employ heme-binding scaffolds ranging from organic small molecules to hemoproteins derived from humans and potentially even microorganisms, show promise as field-deployable antidotes that may rapidly accelerate CO clearance and improve outcomes for survivors of acute CO poisoning.

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.

Taxonomic and genomic attributes of oligotrophic soil bacteria

Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum-from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the "slow lane." However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils.

Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis

SUMMARY

Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.

Microbial gas fermentation technology for sustainable food protein production

The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.

Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa

IMPORTANCE

The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.

Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition

High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.

A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion

The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome

Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.

Widespread Distribution of the arsO Gene Confers Bacterial Resistance to Environmental Antimony

Microbial oxidation of environmental antimonite (Sb(III)) to antimonate (Sb(V)) is an antimony (Sb) detoxification mechanism. Ensifer adhaerens ST2, a bacterial isolate from a Sb-contaminated paddy soil, oxidizes Sb(III) to Sb(V) under oxic conditions by an unknown mechanism. Genomic analysis of ST2 reveals a gene of unknown function in an arsenic resistance (ars) operon that we term arsO. The transcription level of arsO was significantly upregulated by the addition of Sb(III). ArsO is predicted to be a flavoprotein monooxygenase but shows low sequence similarity to other flavoprotein monooxygenases. Expression of arsO in the arsenic-hypersensitive Escherichia coli strain AW3110Δars conferred increased resistance to Sb(III) but not arsenite (As(III)) or methylarsenite (MAs(III)). Purified ArsO catalyzes Sb(III) oxidation to Sb(V) with NADPH or NADH as the electron donor but does not oxidize As(III) or MAs(III). The purified enzyme contains flavin adenine dinucleotide (FAD) at a ratio of 0.62 mol of FAD/mol protein, and enzymatic activity was increased by addition of FAD. Bioinformatic analyses show that arsO genes are widely distributed in metagenomes from different environments and are particularly abundant in environments affected by human activities. This study demonstrates that ArsO is an environmental Sb(III) oxidase that plays a significant role in the detoxification of Sb(III).

Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov

Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.

Arctic soil methane sink increases with drier conditions and higher ecosystem respiration

Arctic wetlands are known methane (CH4) emitters but recent studies suggest that the Arctic CH4 sink strength may be underestimated. Here we explore the capacity of well-drained Arctic soils to consume atmospheric CH4 using >40,000 hourly flux observations and spatially distributed flux measurements from 4 sites and 14 surface types. While consumption of atmospheric CH4 occurred at all sites at rates of 0.092 ± 0.011 mgCH4 m-2 h-1 (mean ± s.e.), CH4 uptake displayed distinct diel and seasonal patterns reflecting ecosystem respiration. Combining in situ flux data with laboratory investigations and a machine learning approach, we find biotic drivers to be highly important. Soil moisture outweighed temperature as an abiotic control and higher CH4 uptake was linked to increased availability of labile carbon. Our findings imply that soil drying and enhanced nutrient supply will promote CH4 uptake by Arctic soils, providing a negative feedback to global climate change.

Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands

Atmospheric trace gases, such as H2 and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H2 and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.

Pollution characteristics and microbial community succession of a rural informal landfill in an arid climate

Informal landfills pose potential threats to the environment and human health due to the lack of anti-seepage measures. However, little research has been conducted on the distribution of pollutants in informal landfill sites situated in arid climates, as well as the underlying interaction mechanisms between environmental factors and microbial structure. In this study, we sought to investigate the pollution characteristics and microbial community succession of the landfill in northern China. The results revealed that heavy metals in the landfill showed poor mobility and migration. The lower layers of the garbage samples had higher water-soluble contents of heavy metals compared to the upper layers. The landfill-derived dissolved organic matter (DOM) was found to originate from microbial production, and four fluorescent components were identified, including fulvic acid-like substances, humus-like substances, and protein-like components. Fluorescence intensity and humification degree increased with increasing depth. The microbial diversity and richness decreased with sampling depth. The most abundant phyla in the samples were Proteobacteria, unidentified_Bacteria, Bacteroidota, Firmicutes, Myxococcota, Gemmatimonadota, Actinobacteria, and Deinococcota. As the sampling depth increased, Proteobacteria decreased, while Bacteroidota and Firmicutes showed a remarkable increase, with little variation observed in the other phyla. The partial least-squares path model (PLS-PM) results indicated that pH had the most significant effect on microbial abundance and diversity (direct effect value = -5.560), while DOM and heavy metals had the opposite effect, with direct effects of 1.838 and 3.231, respectively. DOM was identified as the driving factor for the variation in other environmental factors. The redundancy analysis (RDA) showed that the dominant genera were greatly influenced by Cu, humic-like substances, and protein-like substances. Among them, Bacillus, Alcanivorax, Devosia, and Chryseolinea may play important roles in the remediation of landfills. Our study not only gains a deeper understanding of the pollution risk of informal landfills in arid climates, but also provides a scientific basis for the future treatment and restoration of contaminated sites associated with landfills.

The win-win effects of nitrification inhibitors on soil-crop systems: Decreasing carbendazim residues but promoting soil bacterial community diversities and stabilities and crop yields

Applying nitrogen (N)-cycling inhibitors is an effective measure to improve N fertilizer utilization efficiency, but the effects of N-cycling inhibitors on fungicide residues in soil-crop systems are unclear. In this study, nitrification inhibitors dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP) and urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) were applied into agricultural soils with fungicide carbendazim applications. The soil abiotic properties, carrot yields, carbendazim residues, bacterial communities and their comprehensive relationships were also quantified. Compared to the control treatment, the DCD and DMPP significantly decreased soil carbendazim residues by 96.2% and 96.0%, and the DMPP and NBPT significantly reduced carrot carbendazim residues by 74.3% and 60.3%, respectively. The nitrification inhibitor applications also generated significant and positive effects on carrot yields and soil bacterial community diversities. The DCD application significantly stimulated soil Bacteroidota and endophytic Myxococcota and modified soil and endophytic bacterial communities. Meanwhile, the DCD and DMPP applications also positively stimulated the co-occurrence network edges of soil bacterial communities by 32.6% and 35.2%, respectively. The linear correlation coefficients between soil carbendazim residues and pH, ETSA and NH₄⁺-N contents were - 0.84, - 0.57 and - 0.80, respectively. The nitrification inhibitor applications generated win-win effects on the soil-crop systems by decreasing carbendazim residues but promoting soil bacterial community diversities and stabilities and crop yields.

Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands

Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2  h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.

Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression

Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.

Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil

Endogenous hydrogen (H₂) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H₂ leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H₂ from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H₂. Based on metagenomes of ¹³C-enriched DNA fractions, endogenous H₂ selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H₂ of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H₂ is a significant energy source for active PCB-degrading communities and suggests that elevated H₂ can influence the microbial ecology and biogeochemistry of the legume rhizosphere.

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.

Structural basis for bacterial energy extraction from atmospheric hydrogen

Diverse aerobic bacteria use atmospheric H₂ as an energy source for growth and survival¹. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments^2,3. Atmospheric H₂ oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily^4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H₂ amid ambient levels of the catalytic poison O₂ and how the derived electrons are transferred to the respiratory chain¹. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H₂ to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H₂ at the expense of O₂, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H₂ oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H₂ oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H₂ in ambient air.

The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga

The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Molecular hydrogen in seawater supports growth of diverse marine bacteria

Molecular hydrogen (H₂) 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 H₂ to support growth. Genes for H₂-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H₂ oxidation increases with depth and decreases with oxygen concentration, suggesting that H₂ is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H₂ 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, H₂ is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.

Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs

Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

Risk of the hydrogen economy for atmospheric methane

Hydrogen (H₂) is expected to play a crucial role in reducing greenhouse gas emissions. However, hydrogen losses to the atmosphere impact atmospheric chemistry, including positive feedback on methane (CH₄), the second most important greenhouse gas. Here we investigate through a minimalist model the response of atmospheric methane to fossil fuel displacement by hydrogen. We find that CH₄ concentration may increase or decrease depending on the amount of hydrogen lost to the atmosphere and the methane emissions associated with hydrogen production. Green H₂ can mitigate atmospheric methane if hydrogen losses throughout the value chain are below 9 ± 3%. Blue H₂ can reduce methane emissions only if methane losses are below 1%. We address and discuss the main uncertainties in our results and the implications for the decarbonization of the energy sector.

Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage

Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.