Response of methanotrophic activity and community structure to temperature changes in a diffusive CH4/O2 counter gradient in an unsaturated porous medium

The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.

Research on aerobic oxidation of methane bacteria and its influencing factors in Chongqing central city section of the Yangtze River, China

Bacterial communities play an important role in the carbon cycle of freshwater ecosystems. In order to understand the influencing factors of bacterial community in the process of carbon cycle and search for measures to reduce carbon emissions, Chongqing central city section of the Yangtze River and its tributaries were selected to be the study area in this research. High-throughput sequencing was applied to study aerobic oxidation of methane bacteria (MOB) in sampling area. The results showed that there were spatial differences in the community diversity of aerobic MOB in the Yangtze River in central Chongqing. The Shannon index in the sediment (2.389-2.728) was higher than that in the water (1.820-2.458), and the community diversity in the middle reaches of the main river was higher than that in the upstream and the downstream. The aerobic MOB community was mainly dominated by Type II (Methylocystis). Most of operational taxonomic units (OTUs) in the top ten had high homology with MOB from river and lake sediments, and a few OTUs had high homology with MOB from paddy fields, forests and wetland soils. The main environmental factors affecting the community structure of aerobic MOB were NH4+-N, dissolved oxygen (DO), temperature (T, p ≤ 0.001), pH (p ≤ 0.05), methane (CH4) and carbon dioxide (CO2).

Community structure and network interaction of aerobic methane-oxidizing bacteria in Chongqing's central urban area in the Three Gorges Reservoir, China

A reservoir is an important source of methane (CH₄), which is consumed by aerobic methane-oxidizing bacteria (MOB), representing the main CH₄ sink in water. The central urban area of Chongqing in the Three Gorges Reservoir (TGR) area was selected as the study area in 2021. High-throughput sequencing was used to analyze the community structure and abundance of MOBs. The results showed that Methylocystis (Type II) was the dominant MOB in water, whereas Methylococcus (Type I) and Methylocystis co-dominated the sediments. High water temperature in the study area largely accounted for the predominance of Type II MOBs in the two habitats. Moreover, the influence of environmental factors on MOB community and its interspecific relationship were significantly regulated by the operation of the TGR. In the low-water-level period, NO₂^--N and CO₂ concentration significantly correlated with Methylocystis, whereas in the high-water-level period, the higher discharge and velocity weakened the influence of all environmental factors on Methylocystis. In addition, the scouring of sediments by increasing discharge in the high-water-level period caused a significant decrease in dissolved CH₄ concentration. The decrease in substrate increased interspecific competition within the MOB community, especially between different types of MOBs, in the high-water-level period.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH₄) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH₄ oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH₄ gdw^–1 day^–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH₄ oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH₄ emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH₄ oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

Hyperthermophilic composting significantly decreases methane emissions: Insights into the microbial mechanism

Methane (CH₄) emissions from thermophilic composting (TC) are a substantial contributor to climate change. Hyperthermophilic composting (HTC) can influence CH₄-related microbial communities at temperatures up to 80 °C, and thus impact the CH₄ emissions during composting. This work investigated CH₄ emissions in sludge-derived HTC, and explored microbial community succession with quantitative PCR and high-throughput sequencing. Results demonstrated that HTC decreased CH₄ emissions by 52.5% compared with TC. In HTC, the CH₄ production potential and CH₄ oxidation potential were nearly 40% and 64.1% lower than that of TC, respectively. There was a reduction in the quantity of mcrA (3.7 × 10⁸ to 0 g^-1 TS) in HTC, which was more significant than the reduction in pmoA (2.0 × 10⁵ to 2.1 × 10⁴ g^-1 TS), and thus lead to reduce CH₄ emissions. It was found that the abundance of most methanogens and methanotrophs was inhibited in the hyperthermal environment, with a decline in Methanosarcina, Methanosaeta and Methanobrevibacter potentially being responsible for reducing the CH₄ emissions in HTC. This work provides important insight into mitigating CH₄ emissions in composting.

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.

Methane emissions respond to soil temperature in convergent patterns but divergent sensitivities across wetlands along altitude

Among the global coordinated patterns in soil temperature and methane emission from wetlands, a declining trend of optimal soil temperature for methane emissions from low to high latitudes has been witnessed, while the corresponding trend along the altitudinal gradient has not yet been investigated. We therefore selected two natural wetlands located at contrasting climatic zones from foothill and mountainside of Nepal Himalayas, to test: (1) whether the optimal temperature for methane emissions decreases from low to high altitude, and (2) whether there is a difference in temperature sensitivity of methane emissions from those wetlands. We found significant spatial and temporal variation of methane emissions between the two wetlands and seasons. Soil temperature was the dominant driver for seasonal variation in methane emissions from both wetlands, though its effect was perplexed by the level of standing water, aquatic plants, and dissolved organic carbon, particularly in the deep water area. When integrative comparison was conducted by adding the existing data from wetlands of diverse altitudes, and the latitude-for-altitude effect was taken into account, we found the baseline soil temperatures decrease whilst the altitude rises with respect to a rapid increase in methane emission from all wetlands, however, remarkably higher sensitivity of methane emissions to soil temperature (apparent Q₁₀ ) was found in mid-altitude wetland. We provide the first evidence of an apparent decline in optimal temperature for methane emissions with increasing elevation. These findings suggest a convergent pattern of methane emissions with respect to seasonal temperature shifts from wetlands along altitudinal gradient, while a divergent pattern in temperature sensitivities exhibits a single peak in mid-altitude.

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

Lake methane (CH₄ ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH₄ oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH₄ oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH₄ oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH₄ oxidation rates in lakes and that information on the MOB community can help predict CH₄ oxidation rates and thus emissions from lakes.

Effect of temperature on methane oxidation and community composition in landfill cover soil

Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH₄) emissions in the United States. The majority of CH₄ generated in landfills is converted to carbon dioxide (CO₂) by CH₄-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH₄ oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH₄ oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH₄ oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH₄ oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH₄ g^-1 day^-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH₄ oxidation in vitro and that changing rates of CH₄ oxidation are in part driven by changes in methylotroph community structure.

Effect of temperature on methane oxidation and community composition in landfill cover soil

Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH₄) emissions in the United States. The majority of CH₄ generated in landfills is converted to carbon dioxide (CO₂) by CH₄-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH₄ oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH₄ oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH₄ oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH₄ oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH₄ g^-1 day^-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH₄ oxidation in vitro and that changing rates of CH₄ oxidation are in part driven by changes in methylotroph community structure.

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.

Riverbed methanotrophy sustained by high carbon conversion efficiency

Our understanding of the role of freshwaters in the global carbon cycle is being revised, but there is still a lack of data, especially for the cycling of methane, in rivers and streams. Unravelling the role of methanotrophy is key to determining the fate of methane in rivers. Here we focus on the carbon conversion efficiency (CCE) of methanotrophy, that is, how much organic carbon is produced per mole of CH₄ oxidised, and how this is influenced by variation in methanotroph communities. First, we show that the CCE of riverbed methanotrophs is consistently high (~50%) across a wide range of methane concentrations (~10–7000 nM) and despite a 10-fold span in the rate of methane oxidation. Then, we show that this high conversion efficiency is largely conserved (50%± confidence interval 44–56%) across pronounced variation in the key functional gene (70 operational taxonomic units (OTUs)), particulate methane monooxygenase (pmoA), and marked shifts in the abundance of Type I and Type II methanotrophs in eight replicate chalk streams. These data may suggest a degree of functional redundancy within the variable methanotroph community inhabiting these streams and that some of the variation in pmoA may reflect a suite of enzymes of different methane affinities which enables such a large range of methane concentrations to be oxidised. The latter, coupled to their high CCE, enables the methanotrophs to sustain net production throughout the year, regardless of the marked temporal and spatial changes that occur in methane.

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

Methane (CH(4)) flux to the atmosphere is mitigated via microbial CH(4) oxidation in sediments and water. As arctic temperatures increase, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is important to predicting future CH(4) emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), and pyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH(4) oxidation activity was measured in microcosm incubations containing sediments at all temperatures, with the highest CH(4) oxidation potential of 37.5 μmol g(-1) day(-1) in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and of the 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in (13)C-labeled DNA obtained by SIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisition from CH(4) in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature. Methylotrophs were also abundant in the microbial community that derived carbon from CH(4), especially in the deeper sediments (depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R = 0.82) with the relative abundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophic communities in arctic lake sediments respond to temperature variations.

Methanotrophic community structure and activity under warming and grazing of alpine meadow on the Tibetan Plateau

Knowledge about methanotrophs and their activities is important to understand the microbial mediation of the greenhouse gas CH(4) under climate change and human activities in terrestrial ecosystems. The effects of simulated warming and sheep grazing on methanotrophic abundance, community composition, and activity were studied in an alpine meadow soil on the Tibetan Plateau. There was high abundance of methanotrophs (1.2-3.4 × 10(8) pmoA gene copies per gram of dry weight soil) assessed by real-time PCR, and warming significantly increased the abundance regardless of grazing. A total of 64 methanotrophic operational taxonomic units (OTUs) were obtained from 1,439 clone sequences, of these OTUs; 63 OTUs (98.4%) belonged to type I methanotrophs, and only one OTU was Methylocystis of type II methanotrophs. The methanotroph community composition and diversity were not apparently affected by the treatments. Warming and grazing significantly enhanced the potential CH(4) oxidation activity. There were significantly negative correlations between methanotrophic abundance and soil moisture and between methanotrophic abundance and NH(4)-N content. The study suggests that type I methanotrophs, as the dominance, may play a key role in CH(4) oxidation, and the alpine meadow has great potential to consume more CH(4) under future warmer and grazing conditions on the Tibetan Plateau.