Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake

Recent findings in methanotrophs: genetics, molecular ecology, and biopotential

The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.

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.

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.

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs

Methane-oxidizing bacteria (MOB) have long been recognized as an important bioindicator for oil and gas exploration. However, due to their physiological and ecological diversity, the distribution of MOB in different habitats varies widely, making it challenging to authentically reflect the abundance of active MOB in the soil above oil and gas reservoirs using conventional methods. Here, we selected the Puguang gas field of the Sichuan Basin in Southwest China as a model system to study the ecological characteristics of methanotrophs using culture-independent molecular techniques. Initially, by comparing the abundance of the pmoA genes determined by quantitative PCR (qPCR), no significant difference was found between gas well and non-gas well soils, indicating that the abundance of total MOB may not necessarily reflect the distribution of the underlying gas reservoirs. 13C-DNA stable isotope probing (DNA-SIP) in combination with high-throughput sequencing (HTS) furthermore revealed that type II methanotrophic Methylocystis was the absolutely predominant active MOB in the non-gas-field soils, whereas the niche vacated by Methylocystis was gradually filled with type I RPC-2 (rice paddy cluster-2) and Methylosarcina in the surface soils of gas reservoirs after geoscale acclimation to trace- and continuous-methane supply. The sum of the relative abundance of RPC-2 and Methylosarcina was then used as specific biotic index (BI) in the Puguang gas field. A microbial anomaly distribution map based on the BI values showed that the anomalous zones were highly consistent with geological and geophysical data, and known drilling results. Therefore, the active but not total methanotrophs successfully reflected the microseepage intensity of the underlying active hydrocarbon system, and can be used as an essential quantitative index to determine the existence and distribution of reservoirs. Our results suggest that molecular microbial techniques are powerful tools for oil and gas prospecting.

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.

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.

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

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.

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.

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.

Variations in Concentration and Carbon Isotope Composition of Methanotroph Biomarkers in Sedge Peatlands Along the Altitude Gradient in the Changbai Mountain, China

Northern peatlands are one of the largest natural sources of atmospheric methane globally. As the only biological sink of methane, different groups of methanotrophs use different carbon sources. However, the variations in microbial biomass and metabolism of different methanotrophic groups in peatlands along the altitude gradient are uncertain. We measured the concentrations and metabolic characteristics of type I (16:1ω7c and 16:1ω5c) and type II (18:1ω7c) methanotroph biomarkers using biomarkers and stable isotopes in eight Carex peatlands along an altitude gradient from 300 to 1,500 m in the Changbai Mountain, China. We found that the trends with altitude in concentrations of the type I and type II methanotroph biomarkers were different. The dominating microbial group changed from type I to type II methanotroph with increasing altitude. The concentrations of type I and type II methanotroph biomarkers were significantly affected by the total phosphorus, total nitrogen, and dissolved organic carbon, respectively. The δ¹³C values of type II methanotroph biomarkers changed significantly along the altitude gradient, and they were more depleted than type II methanotroph biomarkers, which indicates the difference in carbon source preference between type I and type II methanotrophs. This study highlights the difference in the concentration and carbon source utilization of type I and type II methanotrophic groups along the altitude gradient, and enhances our understanding of the metabolic process of methane mediated by methanotrophs and its impact on carbon-sink function in northern peatlands.

Reduced methane emissions in former permafrost soils driven by vegetation and microbial changes following drainage

In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon-rich wetlands, although 71% of this carbon pool is stored in faster-thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short-term thawing experiments, investigations of the long-term changes following final thaw and co-occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25 years of natural drainage, that resulted in a 10-fold decrease in CH₄ emissions (3.2 ± 2.2 vs. 0.3 ± 0.4 mg C-CH₄  m^-2  day^-1 ), while CO₂ emissions were comparable. These data extend the time perspective from earlier studies based on short-term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH₄ oxidation due to the longer residence time of CH₄ in the oxidation zone, while the observed loss of aerenchyma plants reduced CH₄ diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long-term effects of climate change on CH₄ emissions and underscores the need for data from different soil types and thaw histories.

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.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Atmospheric Methane Consumption and Methanotroph Communities in West Siberian Boreal Upland Forest Ecosystems

Upland forest ecosystems are recognized as net sinks for atmospheric methane (CH4), one of the most impactful greenhouse gases. Biological methane uptake in these ecosystems occurs due to the activity of aerobic methanotrophic bacteria. Russia hosts one-fifth of the global forest area, with the most extensive forest landscapes located in West Siberia. Here, we report seasonal CH4 flux measurements conducted in 2018 in three types of stands in West Siberian middle taiga–Siberian pine, Aspen, and mixed forests. High rates of methane uptake of up to −0.184 mg CH4 m−2 h−1 were measured by a static chamber method, with an estimated total growing season consumption of 4.5 ± 0.5 kg CH4 ha−1. Forest type had little to no effect on methane fluxes within each season. Soil methane oxidation rate ranged from 0 to 8.1 ng CH4 gDW−1 h−1 and was negatively related to water-filled pore space. The microbial soil communities were dominated by the Alpha- and Gammaproteobacteria, Acidobacteriota and Actinobacteriota. The major group of 16S rRNA gene reads from methanotrophs belonged to uncultivated Beijerinckiaceae bacteria. Molecular identification of methanotrophs based on retrieval of the pmoA gene confirmed that Upland Soil Cluster Alpha was the major bacterial group responsible for CH4 oxidation.

Aerobic methanotrophs in an urban water cycle system: Community structure and network interaction pattern

Aerobic methane-oxidizing bacteria (MOB) play an important role in reducing methane emissions in nature. Most current researches focus on the natural habitats (e.g., lakes, reservoirs, wetlands, paddy fields, etc.). However, methanotrophs and the methane-oxidizing process remain essentially unclear in artificial habitat, such as the urban water cycle systems. Here, high-throughput sequencing and qPCR were used to analyze the community structure and abundance of MOB. Six different systems were selected from Yunyang City, Chongqing, China, including the raw water system (RW), the water supply pipe network system (SP), the wastewater pipe network system (WP), the hospital wastewater treatment system (HP), the municipal wastewater treatment plant system (WT) and the downstream river system (ST) of a wastewater treatment plant. Results clearly showed that the MOB community structure and network interaction patterns of the urban water cycle system were different from those of natural water bodies. Type I MOB was the dominant clade in HP. Methylocysis in Type II was the most abundant genus among the whole urban water cycle system, indicating that this genus had a high adaptability to the environment. Temperature, dissolved oxygen, pH and concentration significantly affected the MOB communities in the urban water cycle system. The network of MOB in WT was the most complicated, and there were competitive relationships among species in WP. The structure of the network in HP was unstable, and therefore, it was vulnerable to environmental disturbances. Methylocystis (Type II) and Methylomonas (Type I) were the most important keystone species in the entire urban water cycle system. Overall, these findings broaden the understanding of the distribution and interaction patterns of MOB communities in an urban water cycle system and provide valuable clues for ecosystem restoration and environmental management.

Heavy metal reduction coupled to methane oxidation：Mechanisms, recent advances and future perspectives

Methane emission has contributed greatly to the global warming and climate change, and the pollution of heavy metals is an important concern due to their toxicity and environmental persistence. Recently, multiple heavy metals have been demonstrated to be electron acceptors for methane oxidation, which offers a potential for simultaneous methane emission mitigation and heavy metal detoxification. This review provides a comprehensive discussion of heavy metals reduction coupled to methane oxidation, and identifies knowledge gaps and opportunities for future research. The functional microorganisms and possible mechanisms are detailed in groups under aerobic, hypoxic and anaerobic conditions. The potential application and major environmental significances for global methane mitigation, the elements cycle and heavy metals detoxification are also discussed. The future research opportunities are also discussed to provide insights for further research and efficient practical application.

Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.

Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil

Biochar addition can reduce methane (CH₄) emissions from paddy soils while the mechanisms involved are not entirely clear. Here, we studied the effect of biochar addition on CH₄ emissions, and the abundance and community composition of methanogens and methanotrophs over two rice cultivation seasons. The experiment had the following five treatments: control (CK), chemical fertilizer application only (BC0), and 0.5% (w/w) (BC1), 1% (BC2), and 2% of biochar applied with chemical fertilizers (BC3). The season-wide CH₄ emissions were decreased (P < 0.05) by 22.2-95.7% in biochar application compared with BC0 in the two rice seasons (2017 and 2018). In 2017, biochar application decreased methanogenic archaea (mcrA) but increased methanotrophic bacteria (pmoA) abundances, and decreased the ratio of mcrA/pmoA, as compared with BC0 (P < 0.05). In 2018, the abundance of mcrA was lower in BC2 and BC3 than in BC0 (P < 0.05) but was not different between BC0 and BC1, and the abundance of pmoA was lower in BC1, BC2 and BC3 than in BC0 (P < 0.05). The CH₄ emissions were positively related to abundances of the mcrA gene (P < 0.01) but not to that of the pmoA gene in two rice seasons. Rice grain yield was increased by 62.2-94.1% in biochar addition treatments compared with BC0 in the first year (P < 0.01) and by 29.9-37.6% in BC2 and BC3 compared with BC0 in the second year (P < 0.05). Biochar application decreased CH₄ emissions by reducing methanogenic archaea abundance in the studied flooded paddy soil.

Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs

Upland soils of tundra function as a constant sink for atmospheric CH₄ but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of -0.4 to -0.6 mg CH₄-C m^-2 day^-1 were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH₄ oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~10⁷pmoA gene copies g^-1 dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96-100 and 95-98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and "Methylocapsa gorgona" MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs.

Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China

Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH₄⁺-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.

Denitrifying anaerobic methane oxidation in marsh sediments of Chongming eastern intertidal flat

Denitrifying anaerobic methane oxidation (DAMO) and associated microbial diversity and abundance in the marsh sediments of Chongming eastern intertidal flat, the Yangtze Estuary, were investigated using carbon-isotope tracing and molecular techniques. Co-existence of nitrate-DAMO archaea and nitrite-DAMO bacteria was evidenced, with higher biodiversity of DAMO archaea than DAMO bacteria. Abundance of DAMO archaeal mcrA gene and DAMO bacterial pmoA gene ranged from 4.2 × 10³ to 3.9 × 10¹⁰ copies g^-1 and from 4.5 × 10⁵ to 6.4 × 10⁶ copies g^-1, respectively. High DAMO potential was detected, ranging from 0.6 to 46.7 nmol ¹³CO₂ g^-1 day^-1 for nitrate-DAMO and from 1.3 to 39.9 nmol ¹³CO₂ g^-1 day^-1 for nitrite-DAMO. In addition to playing an important role as a CH₄ sink, DAMO bacteria also removed a substantial amount of reactive nitrogen (29.4 nmol N g^-1 day^-1) from the intertidal sediments. Overall, these results indicate the importance of DAMO bioprocess as methane and nitrate sinks in intertidal marshes.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.

Widespread soil bacterium that oxidizes atmospheric methane

The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

Salinity stress changed the biogeochemical controls on CH4 and N2O emissions of estuarine and intertidal sediments

Elevated salinity is expected to drive changes in biogeochemical cycling and microbial communities in estuarine and intertidal wetlands. However, limited information regarding the role of salinity in shaping biogeochemical controls and mediating greenhouse gas emissions is currently available. In this study, we used incubation experiment across salinity gradients of the estuarine and intertidal sediments to reveal the underlying interconnections of CH₄ and N₂O emissions, biogeochemical controls and salinity gradients. Our results indicated that sediment biogeochemical properties were significantly affected by the increasing salinity, which were attributed to the accelerated sediment enzyme activities. The increasing salinity promoted CH₄ and N₂O emission rates by stimulating organic carbon decomposition and nitrogen transformation rates. In addition, the copy number of mcrA, nirS and nirK genes increased along with the salinity gradients, which strongly mediated the CH₄ and N₂O emission rates. Stepwise regression analysis suggested that labile organic carbon and denitrification were the most crucial determinants of CH₄ and N₂O emission rates, respectively. Overall, salinity could enhance CH₄ and N₂O emission mainly by altering sediment geochemical variables, microbial activity and functional gene abundance in estuarine and intertidal environments. Furthermore, increasing salinity could enhance the carbon and nitrogen export, which may pose a threat to the ecological function of estuarine and intertidal ecosystems. This study may contribute to the knowledge about the importance of biogeochemical controls induced by salinity in mediating greenhouse gas emissions.

Exploring the mechanisms of decreased methane during pig manure and wheat straw aerobic composting covered with a semi-permeable membrane

It is very important to reduce methane production and emission during aerobic composting. In this study, the effects of covering with a semi-permeable membrane during pig manure and wheat straw composting were investigated. Two laboratory-scale composting reactors were used: the membrane covered treatment (treatment A) and the control treatment (treatment B). Composting in treatment A effectively improved the oxygen utilization rate and decreased methane emissions by 22.42% relative to the control treatment. Quantification of functional genes and Pearson rank correlations showed that the mcrA and mcrA/pmoA gene abundances were significantly positively correlated with temperature and negatively correlated with the interstitial oxygen concentration, and that the pmoA gene abundance was positively correlated with the carbon: nitrogen ratio and moisture content. Therefore, increasing the aeration rate and optimizing the carbon: nitrogen ratio and moisture content will decrease methane emissions. Together, the results demonstrate that coverage membrane could be a novel strategy for reducing methane emissions during composting.

An assessment of the potential use of compost filled plastic void forming units to serve as vents on historic landfills and related sites

Much of the solid municipal waste generated by society is sent to landfill, where biodegrading processes result in the release of methane, a major contributor to climate change. This work examined the possibility of installing a type of biofilter within paved areas of the landfill site, making use of modified pervious paving, both to allow the escape of ground gas and to avoid contamination of groundwater, using specially designed test models with provision for gas sampling in various chambers. It proposes the incorporation of an active layer within a void forming box with a view to making dual use of the pervious pavement to provide both a drainage feature and a ground gas vent, whilst providing an active layer for the oxidation of methane by microbial action. The methane removal was observed to have been effected by microbial oxidation and as such offers great promise as a method of methane removal to allow for development of landfills.

Methanotrophy across a natural permafrost thaw environment

The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ¹³C-CH₄ isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils

Recent dynamics and uncertainties in global methane budgets necessitate a dissemination of current knowledge on the controls of sources and sinks of atmospheric methane. Forest soils are considered to be efficient methane sinks; however, as they are microbially mediated they are sensitive to anthropogenic influences and tend to switch from being sinks to being methane sources. With regard to global changes in land use, the present study aimed at (i) investigating the influence of grazing on flux rates of methane in forest soils, (ii) deducing possible (a)biotic factors regulating these fluxes, and (iii) gaining an insight into the complex interactions between methane-cycling microorganisms and ecosystem functioning. Here we show that extensive grazing significantly mitigated the soil's sink strength for atmospheric methane through alterations of both microbial activity and community composition. In situ flux measurements revealed that all native, non-grazed areas were net methane consumers, while the adjacent, grazed areas were net methane producers. Whereas neither parent material nor soil properties including moisture and organic matter showed any correlation to the ascertained fluxes, significantly higher archaeal abundances at the grazed study sites indicated that small inputs of methanogens associated with cattle grazing may be sufficient to sustainably increase methane emissions.

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high-affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal

We conducted a study to examine the effect of seasonal variations and the disruptive effects of the 2015 Nepal earthquake on microbial communities associated with drinking water sources. We first characterized the microbial communities of water samples in two Nepali regions (Kathmandu and Jhapa) to understand the stability of microbial communities in water samples collected in 2014. We analyzed additional water samples from the same sources collected from May to August 2015, allowing the comparison of samples from dry-to-dry season and from dry-to-monsoon seasons. Emphasis was placed on microbes responsible for maintaining the geobiochemical characteristics of water (e.g., ammonia-oxidizing and nitrite-oxidizing bacteria and archaea and sulfate-reducing bacteria) and opportunistic pathogens often found in water (Acinetobacter). When examining samples from Jhapa, we identified that most geobiochemical microbe populations remained similar. When examining samples from Kathmandu, the abundance of microbial genera responsible for maintaining the geobiochemical characteristics of water increased immediately after the earthquake and decreased 8 months later (December 2015). In addition, microbial source tracking was used to monitor human fecal contamination and revealed deteriorated water quality in some specific sampling sites in Kathmandu post-earthquake. This study highlights a disruption of the environmental microbiome after an earthquake and the restoration of these microbial communities as a function of time and sanitation practices.

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.

Aerated biofilters with multiple-level air injection configurations to enhance biological treatment of methane emissions

Aiming to improve conventional methane biofilter performance, a multiple-level aeration biofilter design is proposed. Laboratory flow-through column experiments were conducted to evaluate three actively-aerated methane biofilter configurations. Columns were aerated at one, two, and three levels of the bed depth, with air introduced at flow rates calculated from methane oxidation reaction stoichiometry. Inlet methane loading rates were increased in five stages between 6 and 18mL/min. The effects of methane feeding rate, levels of aeration, and residence time on methane oxidation rates were determined. Samples collected after completion of flow-through experiments were used to determine methane oxidation kinetic parameters, V_max, K_m, and methanotrophic community distribution across biofilter columns. Results obtained from mixed variances analysis and response surfaces, as well as methanotrophic activity data, suggested that, biofilter column with two aeration levels has the most even performance over time, maintaining 85.1% average oxidation efficiency over 95days of experiments.

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

Glacier forefield soils can provide a substantial sink for atmospheric CH₄, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH₄ oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH₄ flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH₄ increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH₄ uptake rates ranging from -3.7 to -0.03 mg CH₄ m^-2 day^-1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH₄ emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH₄ flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH₄ sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH₄ inventories.IMPORTANCE Oxidation of methane (CH₄) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH₄ oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH₄ oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH₄ in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH₄ oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH₄ inventories.

Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers

Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.

Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy

Aerated soils form the second largest sink for atmospheric CH₄. A near-complete genome of uncultured upland soil cluster Gammaproteobacteria that oxidize CH₄ at <2.5 ppmv was obtained from incubated Antarctic mineral cryosols. This first genome of high-affinity methanotrophs can help resolve the mysteries about their phylogenetic affiliation and metabolic potential.

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms

Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.

Diversity of Methane-Oxidizing Bacteria in Soils from "Hot Lands of Medolla" (Italy) Featured by Anomalous High-Temperatures and Biogenic CO2 Emission

"Terre Calde di Medolla" (TCM) (literally, "Hot Lands of Medolla") refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting. The 16S rRNA gene analysis assessed the predominance of Actinobacteria, Acidobacteria, Proteobacteria, and Bacillus in TCM samples collected at a depth of 0.6 m along with the presence of methanotrophs (Methylocaldum and Methylobacter) and methylotrophs (Methylobacillus). The phylogenetic analysis of pmoA sequences showed the presence of MOB affiliated with Methylomonas, Methylocystis, Methylococcus, and Methylocaldum in addition to as yet uncultivated and uncharacterized methanotrophs. Jaccard's analysis of T-RFLP profiles at different ground depths revealed a similar MOB composition in soil samples at depths of 0.6 m and 0.7 m, while this similarity was weaker between these samples and those taken at a depth of 2.5 m, in which the genus Methylocaldum was absent. These results correlate the anomalously high temperatures of the farming area of "Terre Calde di Medolla" with the presence of microbial methane-oxidizing bacteria.

Composition of microbial PLFAs and correlations with topsoil characteristics in the rare active travertine spring-fed fen

We studied soil PLFAs composition and specific soil properties among transect of small-scale fen in Stankovany, Slovakia. The aim of this study was to determine potential differences in the microbial community structure of the fen transect and reveal correlations among PLFAs and specific soil characteristics. PCA analyses of 43 PLFAs showed a separation of the samples along the axis largely influenced by i14:0, 16:1ω5, br17:0, 10Me16:0, cy17:0, cy17:1, br18:0 and 10Me17:0. We measured a high correlation of sample scores and distance from fen edge (Kendall’s test τ = 0.857, P < 0.01). Kendall’s test showed a negative correlation of PLFAs content (mol%) and distance from the fen border for Gram (+) bacteria, Actinomycetes, mid-chain branched saturated PLFAs and total PLFAs. The redundancy analysis of the PLFA data set for the eight samples using PLFAs as species and 21 environmental variables identified soil properties significantly associated with the PLFA variables, as tested by Monte Carlo permutation showing most significant environmental variables including dichlormethan extractables, water extractables, Klason lignin, acid-soluble lignin, holocellulose, total extractables, organic matter content, total PLFA amount, bacterial PLFA and total nitrogen negatively correlated to axis 1 and dry weight and carbonate carbon positively correlated to axis 1. The amounts of Klason lignin, acid-soluble lignin, holocellulose total extractables, total PLFA, bacterial PLFA and total nitrogen were significantly correlated positively to the distance from fen border while moisture and total carbonate carbon were correlated negatively.

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.

Atmospheric methane may be consumed by microorganisms in soil, but the mechanisms behind high-affinity methane oxidization remain poorly understood. Here, Jia et al. show that known methanotrophic bacteria are responsible for atmospheric methane uptake in periodically drained wetland ecosystems.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.

Landscape position influences microbial composition and function via redistribution of soil water across a watershed

Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R = 0.72, P < 0.001) and negatively with soil oxygen (R = -0.53, P = 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.

Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems

Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.

Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability

Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.