Widespread soil bacterium that oxidizes atmospheric methane

Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic

Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.

Physiological basis for atmospheric methane oxidation and methanotrophic growth on air

Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.

Global hotspots and trends in microbial-mediated grassland carbon cycling: a bibliometric analysis

Grasslands are among the most widespread environments on Earth, yet we still have poor knowledge of their microbial-mediated carbon cycling in the context of human activity and climate change. We conducted a systematic bibliometric analysis of 1,660 literature focusing on microbial-mediated grassland carbon cycling in the Scopus database from 1990 to 2022. We observed a steep increase in the number of multidisciplinary and interdisciplinary studies since the 2000s, with focus areas on the top 10 subject categories, especially in Agricultural and Biological Sciences. Additionally, the USA, Australia, Germany, the United Kingdom, China, and Austria exhibited high levels of productivity. We revealed that the eight papers have been pivotal in shaping future research in this field, and the main research topics concentrate on microbial respiration, interaction relationships, microbial biomass carbon, methane oxidation, and high-throughput sequencing. We further highlight that the new research hotspots in microbial-mediated grassland carbon cycling are mainly focused on the keywords "carbon use efficiency," "enzyme activity," "microbial community," and "high throughput sequencing." Our bibliometric analysis in the past three decades has provided insights into a multidisciplinary and evolving field of microbial-mediated grassland carbon cycling, not merely summarizing the literature but also critically identifying research hotspots and trends, the intellectual base, and interconnections within the existing body of collective knowledge and signposting the path for future research directions.

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.

Targeting methanotrophs and isolation of a novel psychrophilic Methylobacter species from a terrestrial Arctic alkaline methane seep in Lagoon Pingo, Central Spitsbergen (78° N)

The microbial diversity associated with terrestrial groundwater seepage through permafrost soils is tightly coupled to the geochemistry of these fluids. Terrestrial alkaline methane seeps from Lagoon Pingo, Central Spitsbergen (78°N) in Norway, with methane-saturated and oxygen-limited groundwater discharge providing a potential habitat for methanotrophy. Here, we report on the microbial community's comparative analyses and distribution patterns at two sites close to Lagoon Pingo's methane emission source. To target methane-oxidizing bacteria from this system, we analysed the microbial community pattern of replicate samples from two sections near the main methane seepage source. DNA extraction, metabarcoding and subsequent sequencing of 16S rRNA genes revealed microbial communities where the major prokaryotic phyla were Pseudomonadota (42-47%), Gemmatimonadota (4-14%) and Actinobacteriota (7-11%). Among the Pseudomonadota, members of the genus Methylobacter were present at relative abundances between 1.6 and 4.7%. Enrichment targeting the methane oxidising bacteria was set up using methane seep sediments as inoculum and methane as the sole carbon and energy source, and this resulted in the isolation of a novel psychrophilic methane oxidizer, LS7-T4AT. The optimum growth temperature for the isolate was 13 °C and the pH optimum was 8.0. The morphology of cells was short rods, and TEM analysis revealed intracytoplasmic membranes arranged in stacks, a distinctive feature for Type I methanotrophs in the family Methylomonadaceae of the class Gammaproteobacteria. The strain belongs to the genus Methylobacter based on high 16S rRNA gene similarity to the psychrophilic species of Methylobacter psychrophilus Z-0021T (98.95%), the psychrophilic strain Methylobacter sp. strain S3L5C (99.00%), and the Arctic mesophilic species of Methylobacter tundripaludum SV96T (99.06%). The genome size of LS7-T4AT was 4,338,157 bp with a G + C content of 47.93%. The average nucleotide identities (ANIb) of strain LS7-T4AT to 10 isolated strains of genus Methylobacter were between 75.54 and 85.51%, lower than the species threshold of 95%. The strain LS7-T4AT represents a novel Arctic species, distinct from other members of the genus Methylobacter, for which the name Methylobacter svalbardensis sp. nov. is proposed. The type of strain is LS7-T4AT (DSMZ:114308, JCM:39463).

Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil

Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.

A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps

Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.

Plant-mediated CH4 exchange in wetlands: A review of mechanisms and measurement methods with implications for modelling

Plant-mediated CH4 transport (PMT) is the dominant pathway through which soil-produced CH4 can escape into the atmosphere and thus plays an important role in controlling ecosystem CH4 emission. PMT is affected by abiotic and biotic factors simultaneously, and the effects of biotic factors, such as the dominant plant species and their traits, can override the effects of abiotic factors. Increasing evidence shows that plant-mediated CH4 fluxes include not only PMT, but also within-plant CH4 production and oxidation due to the detection of methanogens and methanotrophs attached to the shoots. Despite the inter-species and seasonal differences, and the probable contribution of within-plant microbes to total plant-mediated CH4 exchange (PME), current process-based ecosystem models only estimate PMT based on the bulk biomass or leaf area index of aerenchymatous plants. We highlight five knowledge gaps to which more research efforts should be devoted. First, large between-species variation, even within the same family, complicates general estimation of PMT, and calls for further work on the key dominant species in different types of wetlands. Second, the interface (rhizosphere-root, root-shoot, or leaf-atmosphere) and plant traits controlling PMT remain poorly documented, but would be required for generalizations from species to relevant functional groups. Third, the main environmental controls of PMT across species remain uncertain. Fourth, the role of within-plant CH4 production and oxidation is poorly quantified. Fifth, the simplistic description of PMT in current process models results in uncertainty and potentially high errors in predictions of the ecosystem CH4 flux. Our review suggest that flux measurements should be conducted over multiple growing seasons and be paired with trait assessment and microbial analysis, and that trait-based models should be developed. Only then we are capable to accurately estimate plant-mediated CH4 emissions, and eventually ecosystem total CH4 emissions at both regional and global scales.

Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.

Effects of nitrogen supply on hydrogen-oxidizing bacterial enrichment to produce microbial protein: Comparing nitrogen fixation and ammonium assimilation

To investigate the effects of nitrogen source supply on microbial protein (MP) production by hydrogen-oxidizing bacteria (HOB) under continuous feed gas provision, a sequencing batch culture comparison (N2 fixation versus ammonium assimilation) was performed. The results confirmed that even under basic cultivation conditions, N2-fixing HOB (NF-HOB) communities showed higher levels of CO2 and N2 fixation (190.45 mg/L Δ CODt and 11.75 mg/L Δ TNbiomass) than previously known, with the highest biomass yield being 0.153 g CDW/g COD-H2. Rich ammonium stimulated MP synthesis and the biomass accumulation of communities (increased by 7.4 ～ 14.3 times), presumably through the enhancement of H2 and CO2 absorption. The micro mechanism may involve encouraging the enrichment of species like Xanthobacter and Acinetobacter then raising the abundance of nitrogenase and glutamate synthase to facilitate the nitrogen assimilation. This would provide NF-HOB with ideas for optimizing their MP synthesis activity.

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.

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.

Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.

One Step Closer to Enigmatic USCα Methanotrophs: Isolation of a Methylocapsa-like Bacterium from a Subarctic Soil

The scavenging of atmospheric trace gases has been recognized as one of the lifestyle-defining capabilities of microorganisms in terrestrial polar ecosystems. Several metagenome-assembled genomes of as-yet-uncultivated methanotrophic bacteria, which consume atmospheric CH4 in these ecosystems, have been retrieved in cultivation-independent studies. In this study, we isolated and characterized a representative of these methanotrophs, strain D3K7, from a subarctic soil of northern Russia. Strain D3K7 grows on methane and methanol in a wide range of temperatures, between 5 and 30 °C. Weak growth was also observed on acetate. The presence of acetate in the culture medium stimulated growth at low CH4 concentrations (~100 p.p.m.v.). The finished genome sequence of strain D3K7 is 4.15 Mb in size and contains about 3700 protein-encoding genes. According to the result of phylogenomic analysis, this bacterium forms a common clade with metagenome-assembled genomes obtained from the active layer of a permafrost thaw gradient in Stordalen Mire, Abisco, Sweden, and the mineral cryosol at Axel Heiberg Island in the Canadian High Arctic. This clade occupies a phylogenetic position in between characterized Methylocapsa methanotrophs and representatives of the as-yet-uncultivated upland soil cluster alpha (USCα). As shown by the global distribution analysis, D3K7-like methanotrophs are not restricted to polar habitats but inhabit peatlands and soils of various climatic zones.

A bio-augmented system with Methylosarcina sp. LC-4 immobilized on bio-carriers: Towards an integrated approach to mitigate and valorize methane emissions from landfills to biodiesel

Bio-augmented systems based on methanotrophs are indispensable in curbing anthropogenic methane emissions from engineered landfills or dumpsites to curtail rising levels of greenhouse gases. Using a defined methanotroph culture immobilized on an inert material-based bio-carrier makes it possible to harness these methane emissions for creating value-added products, thus contributing to the circular bio-economy. The methane oxidation capacity of the model methanotroph Methylosarcina sp. LC-4, a prospective organism for biodiesel production using methane present in landfill gas, immobilized on several inert bio-carriers, was evaluated to identify a bio-carrier that provided optimum conditions for the process. Among the several bio-carriers evaluated, perlite and vermiculite were selected due to their high specific surface area and superior water-holding capacity, which result in the retention of nutrients and biomass and higher methane elimination capacity. While perlite showed high biomass holding capacity and methane transport, vermiculite supported a high growth of methanotrophs. LC-4 immobilized on perlite and vermiculite as the bio-carrier showed maximum methane elimination capacity (MEC) of 291.3 g m-2 day-1 and 155.5 g m-2 day-1, respectively. The low bed height of only 0.13 m and a short start-up period of 2-4 days are promising for use as alternate daily cover in a landfill. The recovered biomass had 12% (w/w) fatty acid methyl ester (FAME), with a high fraction of (∼85%) of C14-C18 saturated and monounsaturated fatty acids, suitable for biodiesel production. The combination of perlite and vermiculite increased MEC and FAME content levels. The current study demonstrated a new bio-augmented system designed with a pure methanotroph for methane elimination with a short start-up time and the valorization of the assimilated methane.

The intrinsic methane mitigation potential and associated microbes add product value to compost

Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h-1 g dw compost-1 and 25.19 ± 6.75 pmol h-1 g dw compost-1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.

Methylococcus mesophilus sp. nov., the first non-thermotolerant methanotroph of the genus Methylococcus, from a rice field

Strain 16-5T, a mesophilic methanotroph of the genus Methylococcus, was isolated from rice field soil sampled in Chungcheong Province, Republic of Korea. Strain 16-5T had both particulate and soluble methane monooxygenases and could only grow on methane and methanol as electron donors. Strain 16-5 T cells are Gram-negative, white to light tan in color, non-motile, non-flagellated, diplococcoid to cocci, and have the typical type I intracytoplasmic membrane system. Strain 16-5T grew at 18-38 °C (optimum, 27 °C) and at pH 5.0-8.0 (optimum, pH 6.5-7.0). C16 : 1 ω7c (38.8%), C16 : 1  ω5c (18.8%), C16 : 1  ω6c (16.8%) and C16 : 0 (16.9%) were the major fatty acids, and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid were the major polar lipids. The main respiratory quinone was methylene-ubiquinone-8. Strain 16-5T displayed the highest 16S rRNA gene sequence similarities to other taxonomically recognized members of the genus Methylococcus, i.e. Methylococcus capsulatus TexasT (98.62%) and Methylococcus geothermalis IM1T (98.49 %), which were its closest relatives. It did, however, differ from all other taxonomically described Methylococcus species due to some phenotypic differences, most notably its inability to grow at temperatures above 38 °C, where other Methylococcus species thrive. Its 4.34 Mbp-sized genome has a DNA G+C content of 62.47 mol%, and multiple genome-based properties such as average nucleotide identity and digital DNA-DNA hybridization value distanced it from its closest relatives. Based on the data presented above, this strain represents the first non-thermotolerant species of the genus Methylococcus. The name Methylococcus mesophilus sp. nov. is proposed, and 16-5T (=JCM 35359T=KCTC 82050T) is the type strain.

Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new?

Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.

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.

A methanotrophic bacterium to enable methane removal for climate mitigation

The rapid increase of the potent greenhouse gas methane in the atmosphere creates great urgency to develop and deploy technologies for methane mitigation. One approach to removing methane is to use bacteria for which methane is their carbon and energy source (methanotrophs). Such bacteria naturally convert methane to CO2 and biomass, a value-added product and a cobenefit of methane removal. Typically, methanotrophs grow best at around 5,000 to 10,000 ppm methane, but methane in the atmosphere is 1.9 ppm. Air above emission sites such as landfills, anaerobic digestor effluents, rice paddy effluents, and oil and gas wells contains elevated methane in the 500 ppm range. If such sites are targeted for methane removal, technology harnessing aerobic methanotroph metabolism has the potential to become economically and environmentally viable. The first step in developing such methane removal technology is to identify methanotrophs with enhanced ability to grow and consume methane at 500 ppm and lower. We report here that some existing methanotrophic strains grow well at 500 ppm methane, and one of them, Methylotuvimicrobium buryatense 5GB1C, consumes such low methane at enhanced rates compared to previously published values. Analyses of bioreactor-based performance and RNAseq-based transcriptomics suggest that this ability to utilize low methane is based at least in part on extremely low non-growth-associated maintenance energy and on high methane specific affinity. This bacterium is a candidate to develop technology for methane removal at emission sites. If appropriately scaled, such technology has the potential to slow global warming by 2050.

Perspective elucidating the physiology of a microbial cell: Neidhardt's Holy Grail

A living microbial cell represents a system of high complexity, integration, and extreme order. All processes within that cell interconvert free energy through a multitude of interconnected metabolic reactions that help to maintain the cell in a state of low entropy, which is a characteristic of all living systems. The study of macromolecular interactions outside this cellular environment yields valuable information about the molecular function of macromolecules but represents a system in comparative disorder. Consequently, care must always be taken in interpreting the information gleaned from such studies and must be compared with how the same macromolecules function in vivo, otherwise, discrepancies can arise. The importance of combining reductionist approaches with the study of whole-cell microbial physiology is discussed regarding the long-term aim of understanding how a cell functions in its entirety. This can only be achieved by the continued development of high-resolution structural and multi-omic technologies. It is only by studying the whole cell that we can ever hope to understand how living systems function.

Effects of capping on microbial populations and contaminant immobilization in an old unlined landfill

This research aimed at evaluating the effects of capping on the mitigation of impacts generated by a closed unlined landfill in São Carlos, SP, Brazil. Physicochemical and microbiological analyses (16S rRNA sequencing) of buried solid waste samples were performed, in capped and uncapped areas. Even though leachate pockets could still be encountered in capped areas, the capping construction reduced oxygen availability and created more reducing conditions, propitiating the development of sulfate-reducing bacteria and possibly contributing to the precipitation of the metals Pb, Cd, Ni, Co, As, and Zn as metal sulfides, causing their immobilization. The microbial populations adapted to the anaerobic conditions created under capped zones belonged to the phyla Firmicutes, Chloroflexi, and Euryarchaeota and the genera Methanosaeta, Hydrogenispora, Smithella, and Gelria. Differently, the phyla Acidobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria were more abundant in samples from the uncapped zones, in which the abundance of different genera varied homogeneously. Methanogenic activity was not impaired by the intervention measure, as assessed by the specific methanogenic activity (SMA). Capping of old unlined landfills brings benefits to the immobilization of metals and does not impair microbial degradation, being effective for the mitigation of impacts on soils and water resources.

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.

Characterisation of 'Candidatus Methylobacter titanis' sp. nov., a putative novel species of Methylobacter clade 2 and their distribution in sediments of freshwater lakes in maritime Antarctica

Global warming has a strong impact on the polar regions, in particular, the Antarctic Peninsula and nearby islands. Methane (CH₄) is a major factor in climate change and mitigation of CH₄ emissions can be accomplished through microbial oxidation by methanotrophic bacteria. Understanding this biological process is crucial given the shortage of research carried out in this geographical area. The aim of this study was to characterise psychrophilic enrichment cultures of aerobic methanotrophs obtained from lake sediments of the Fildes Peninsula (King George Island, South Shetland Islands) and revealing the distribution of the genus Methylobacter in different lake sediments of the peninsula. Four stable methanotrophic enrichment cultures were obtained and analysed by metagenome-assembled genomes (MAGs). The phylogeny of methanotroph MAGs recovered from these enrichment cultures based on the 16S rRNA gene showed that K-2018 MAG008 and D1-2020 MAG004^Ts clustered within the Methylobacter clade 2, with high similarity to Methylobacter tundripaludum SV96^T (97.88 and 98.56% respectively). However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with M. tundripaludum were < 95% (84.8 and 85.0%, respectively) and < 70% (30.2 and 30.3%, respectively), suggesting that they represent a putative novel species for which the name 'Ca. Methylobacter titanis' is proposed. This is the first species of clade 2 of the genus Methylobacter obtained from Antarctica. The bacterial diversity assessed by 16S rRNA gene sequencing of 21 samples of different lakes (water column and sediments) revealed 54 ASVs associated with methanotrophs and the genus Methylobacter as the most abundant. These results suggest that aerobic methanotrophs belonging to the Methylobacter clade 2 would be the main responsible for CH₄ oxidation in these sediments.

Plastic-Rock Complexes as Hotspots for Microplastic Generation

Discarded plastics and microplastics (MPs) in the environment are considered emerging contaminants and indicators of the Anthropocene epoch. This study reports the discovery of a new type of plastic material in the environment─plastic-rock complexes─formed when plastic debris irreversibly sorbs onto the parent rock after historical flooding events. These complexes consist of low-density polyethylene (LDPE) or polypropylene (PP) films stuck onto quartz-dominated mineral matrices. These plastic-rock complexes serve as hotspots for MP generation, as evidenced by laboratory wet-dry cycling tests. Over 1.03 × 10⁸ and 1.28 × 10⁸ items·m^-2 MPs were generated in a zero-order mode from the LDPE- and PP-rock complexes, respectively, following 10 wet-dry cycles. The speed of MP generation was 4-5 orders of magnitude higher than that in landfills, 2-3 orders of magnitude higher than that in seawater, and >1 order of magnitude higher than that in marine sediment as compared with previously reported data. Results from this investigation provide strong direct evidence of anthropogenic waste entering geological cycles and inducing potential ecological risks that may be exacerbated by climate change conditions such as flooding events. Future research should evaluate this phenomenon regarding ecosystem fluxes, fate, and transport and impacts of plastic pollution.

Thermal acclimation of methanotrophs from the genus Methylobacter

Methanotrophs oxidize most of the methane (CH₄) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH₄ oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH₄ oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH₄ is consumed to support growth at different CH₄ concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH₄ uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96^T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH₄ oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96^T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH₄ consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH₄ uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH₄ emissions.

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.

Microbial one‑carbon and nitrogen metabolisms are beneficial to the reservoir recovery after cyanobacterial bloom

Cyanobacterial blooms have profound effects on the structure and function of plankton communities in inland waters, but few studies have focused on the effects of microbial-based processes in one‑carbon and nitrogen cycling on water quality improvement following the bloom. Here, we compared the structure and function of the bacterial community, focusing on microbial one‑carbon and nitrogen metabolisms during and after a cyanobacterial Microcystis bloom in a deep subtropical reservoir. Our data showed that microbial one‑carbon and nitrogen cycles were closely related to different periods of the bloom, and the changes of functional genes in microbial carbon and nitrogen cycling showed the same consistent trend as that of Methylomonas sp. With the receding of the bloom, the abundance of Methylomonas as well as the functional genes of microbial one‑carbon and nitrogen cycling reached the peak and then recovered. Our results indicate that microbial one‑carbon and nitrogen metabolisms were beneficial to the recovery of water quality from the cyanobacterial bloom. This study lays a foundation for a deep understanding of the cyanobacterial decomposition mediated by microbes in one‑carbon and nitrogen cycles in inland freshwaters.

The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'

The ammonia monooxygenase (AMO) is a key enzyme in ammonia-oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (K_i ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia-oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one-carbon (C1) compounds in ammonia-oxidizing archaea.

Characterization and DNA Stable-Isotope Probing of Methanotrophic Bioaerosols

The growth and activity of bacteria have been extensively studied in nearly every environment on Earth, but there have been limited studies focusing on the air. Suspended bacteria (outside of water droplets) may stay in the atmosphere for time frames that could allow for growth on volatile compounds, including the potent greenhouse gas methane. We investigated the ability of aerosolized methanotrophic bacteria to grow on methane in the airborne state in rotating gas-phase bioreactors. The physical half-life of the aerial bacterium-sized particles was 3 days. To assess the potential for airborne growth, gas-phase bioreactors containing the aerosolized cultures were amended with 1,500 ppmv 13CH4 or 12CH4. Three of seven experiments demonstrated 13C incorporation into DNA, indicating growth in air. Bacteria associated with the genera Methylocystis and Methylocaldum were detected in 13C-DNA fractions, thus indicating that they were synthesizing new DNA, suggesting growth in air. We conclude that methanotrophs outside of water droplets in the air can potentially grow under certain conditions. Based on our data, humidity seems to be a major limitation to bacterial growth in air. Furthermore, low biomass levels can pose problems for detecting 13C-DNA synthesis in our experimental system. IMPORTANCE Currently, the cellular activities of bacteria in the airborne state outside of water droplets have not been heavily studied. Evidence suggests that these airborne bacteria produce ribosomes and metabolize gaseous compounds. Despite having a potentially important impact on atmospheric chemistry, the ability of bacteria in the air to metabolize substrates such as methane is not well understood. Demonstrating that bacteria in the air can metabolize and grow on substrates will expand knowledge about the potential activities and functions of the atmospheric microbiome. This study provides evidence for DNA synthesis and, ultimately, growth of airborne methanotrophs.

Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves

Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH₄  g^-1 DW h^-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH₄ and CO₂ concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.

Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia

Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N₂O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.

Microbial roles in cave biogeochemical cycling

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.

The CoQ biosynthetic di-iron carboxylate hydroxylase COQ7 is inhibited by in vivo metalation with manganese but remains functional by metalation with cobalt

Coenzyme Q (CoQ; ubiquinone) is an obligate component of the mitochondrial electron transport chain. COQ7 is a mitochondrial hydroxylase that is required for CoQ biosynthesis. COQ7 belongs to di-iron carboxylate enzymes, a rare type of enzyme that carries out a wide range of reactions. We found that manganese exposure of mouse cells leads to decreased COQ7 activity, but that pre-treatment with cobalt interferes with the inhibition by manganese. Our findings suggest that cobalt has greater affinity for the active site of COQ7 than both iron and manganese and that replacement of iron by cobalt at the active site preserves catalytic activity.

The Role of Thermokarst Lake Expansion in Altering the Microbial Community and Methane Cycling in Beiluhe Basin on Tibetan Plateau

One of the most significant environmental changes across the Tibetan Plateau (TP) is the rapid lake expansion. The expansion of thermokarst lakes affects the global biogeochemical cycles and local climate regulation by rising levels, expanding area, and increasing water volumes. Meanwhile, microbial activity contributes greatly to the biogeochemical cycle of carbon in the thermokarst lakes, including organic matter decomposition, soil formation, and mineralization. However, the impact of lake expansion on distribution patterns of microbial communities and methane cycling, especially those of water and sediment under ice, remain unknown. This hinders our ability to assess the true impact of lake expansion on ecosystem services and our ability to accurately investigate greenhouse gas emissions and consumption in thermokarst lakes. Here, we explored the patterns of microorganisms and methane cycling by investigating sediment and water samples at an oriented direction of expansion occurred from four points under ice of a mature-developed thermokarst lake on TP. In addition, the methane concentration of each water layer was examined. Microbial diversity and network complexity were different in our shallow points (MS, SH) and deep points (CE, SH). There are differences of microbial community composition among four points, resulting in the decreased relative abundances of dominant phyla, such as Firmicutes in sediment, Proteobacteria in water, Thermoplasmatota in sediment and water, and increased relative abundance of Actinobacteriota with MS and SH points. Microbial community composition involved in methane cycling also shifted, such as increases in USCγ, Methylomonas, and Methylobacter, with higher relative abundance consistent with low dissolved methane concentration in MS and SH points. There was a strong correlation between changes in microbiota characteristics and changes in water and sediment environmental factors. Together, these results show that lake expansion has an important impact on microbial diversity and methane cycling.

Diversity and Composition of Methanotroph Communities in Caves

Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH₄). Recent studies have demonstrated methanotrophs are abundant and contribute to CH₄ dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH₄ concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH₄ concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH₄ concentrations, suggesting these microorganisms contribute to CH₄ flux in subterranean ecosystems.

IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH₄) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH₄ oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH₄ sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH₄ concentrations in cave air.

Sulfur and methane oxidation by a single microorganism

Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands.

Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S₄I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO₂ fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.

Divergence of Biocrust Active Bacterial Communities in the Negev Desert During a Hydration-Desiccation Cycle

Rain events in arid environments are highly unpredictable and intersperse extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during rain events, in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active bacterial communities in the Negev Desert biological soil crust (biocrust). Biocrust samples were collected during, and after a medium rainfall and dry soil was used as a control; we evaluated the changes in active bacterial composition, potential function, potential photosynthetic activity, and extracellular polysaccharide (EPS) production. We hypothesized that rain would activate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. As expected, biocrust rewetting activated Cyanobacteria, which replaced the former dominant Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting led to modifications in ecosystem services. We propose that following a rain event, the response of the active bacterial community lagged behind the biocrust water content due to the production of EPS which delayed desiccation and temporarily sustained the biocrust community activity.

Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes

Soil CH₄ fluxes are driven by CH₄-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH₄-cycling microbiomes to net surface CH₄ fluxes throughout a year in two grassland soils. CH₄ fluxes were highly dynamic: both soils were net CH₄ sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH₄ fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH₄ sinks. CH₄ uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH₄ emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH₄ sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH₄-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH₄ ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH₄ oxidation. CH₄ oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH₄ oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH₄ uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH₄ uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal Ralstonia pickettii associates with CH₄ uptake across soils along with pertinent CH₄ and inorganic N metabolism associated genes. This study highlights the critical relationship between CH₄ and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types

Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction

Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin–Benson–Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N₂ fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.

Microbial oxidation of atmospheric trace gases

The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H₂), carbon monoxide (CO) and methane (CH₄). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H₂ and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH₄, H₂ and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.

The methane-driven interaction network in terrestrial methane hotspots

BACKGROUND

Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa.

RESULTS

We applied stable isotope probing (SIP) using ¹³C-CH₄ coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the ¹³C-CH₄ incubation exhibited a less connected and complex topology than the networks derived from the ^unlabelledC-CH₄ incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity.

CONCLUSION

We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.

Methane-Derived Carbon as a Driver for Cyanobacterial Growth

Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH₄ oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO₂) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ¹³C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO₂ released by MOB. On the other hand, ¹³C-CH₄ labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.

Environmental Factors Affecting the Community of Methane-oxidizing Bacteria

Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000‍ ‍mg N L^–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH₄⁺ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.

Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin

Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N₂O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N₂O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N₂O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N₂O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.