Low O2 level enhances CH4-derived carbon flow into microbial communities in landfill cover soils

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.

Ridge with no-tillage facilitates microbial N2 fixation associated with methane oxidation in rice soil

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.

Iron and nitrogen regulate carbon transformation in a methanotroph-microalgae system

Nutrient supply is important for maintaining a methanotroph and microalgae (MOB-MG) system for biogas valorization. However, there is a lack of understanding regarding how key elements regulate the growth of a MOB-MG coculture. In this study, a MOB-MG coculture with high protein content (0.47 g/g biomass) was established from waste activated sludge using synthetic biogas. An increase in iron availability substantially stimulated the specific growth rate (from 0.18 to 0.62 day-1) and biogas conversion rate (from 26.81 to 106.57 mg-C L-1 day-1) of the coculture. Moreover, the protein content remained high (0.51 g/g biomass), and the total lipid content increased (from 0.09 to 0.14 g/g biomass). Nitrogen limitation apparently constrained the specific growth rate (from 0.64 to 0.28 day-1) and largely reduced the protein content (from 0.51 to 0.31 g/g biomass) of the coculture. Intriguingly, the lipid content remained unchanged after nitrogen was depleted. The eukaryotic community was consistently dominated by MG belonging to Chlorella, while the populations of MOB shifted from Methylococcus/Methylosinus to Methylocystis due to iron and nitrogen amendment. In addition, diverse non-methanotrophic heterotrophs were present in the community. Their presence neither compromised the performance of the coculture system nor affected the protein content of the biomass. However, these heterotrophs may contribute to high carbon conversion efficiency by utilizing the dissolved organic carbon released by MOB and MG. Overall, the findings highlight the vital roles of iron and nitrogen in achieving efficient conversion of biogas, fast growth of cells, and optimal biomass composition in a MOB-MG coculture system.

Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments

Conventional aerobic CH₄-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O₂ gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH₄ with the help of riboflavin when O₂ was unavailable. Within the MOB consortium, MOB transformed CH₄ to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH₄ oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH₄ emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH₄ sink in iron-rich sediments.

Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress

Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH₄ emission from landfills. Here, stable isotope probing microcosms with CH₄ or CH₄ and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH₄ oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO₄^2-) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH₄ in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH₄ and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH₄ and sulfur compounds.

Synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under methanethiol stress

Methanotrophs are able to metabolize volatile organic sulfur compounds (VOSCs), excrete organic carbon during CH₄ oxidation, and influence microbial community structure and function of the ecosystem. In return, microbial community structure and environmental factors can affect the growth metabolism of methanotrophs. In this study, Methylomonas koyamae and Hyphomicrobium methylovorum were used for model organisms, and methanethiol (MT) was chosen for a typical VOSC to investigate the synergy effects under VOSC stress. The results showed that when Hyphomicrobium methylovorum was co-cultured with Methylomonas koyamae in the medium with CH₄ used as the carbon source, the co-culture had better MT tolerance relative to Methylomonas koyamae and oxidized all CH₄ within 120 h, even at the initial MT concentration of 2000 mg m^-3. The optimal co-culture ratios of Methylomonas koyamae to Hyphomicrobium methylovorum were 4:1-12:1. Although MT could be converted spontaneously to dimethyl disulfide (DMDS), H₂S, and CS₂ in air, faster losses of MT, DMDS, H₂S, and CS₂ were observed in each strain mono-culture and the co-culture. Compared with Hyphomicrobium methylovorum, MT was degraded more quickly in the Methylomonas koyamae culture. During the co-culture, the CH₄ oxidation process of Methylomonas koyamae could provide carbon and energy sources for the growth of Hyphomicrobium methylovorum, while Hyphomicrobium methylovorum oxidized MT to help Methylomonas koyamae detoxify. These findings are helpful to understand the synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under MT stress and enrich the role of methanotrophs in the sulfur biogeochemical cycle. KEY POINTS: • The co-culture of Methylomonas and Hyphomicrobium has better tolerance to CH₃SH. • Methylomonas can provide carbon sources for the growth of Hyphomicrobium. • The co-culture of Methylomonas and Hyphomicrobium enhances the removal of CH₄ and CH₃SH.

Characterization of anaerobic oxidation of methane and microbial community in landfills with aeration

Landfills are the third largest source of anthropogenic CH₄ emissions. Anaerobic oxidation of methane (AOM) activity and communities of methane-oxidizing bacteria were investigated in three informal landfills in this study, namely, BJ, CH and SZ landfills, among which BJ and CH represent traditional anaerobic landfills, while the SZ landfill was subjected to aeration to accelerate waste stabilization. The AOM rates of the investigated landfilled wastes ranged from 3.66 to 23.91 nmol g^-1 h^-1. Among the three landfills, the AOM rate was highest in the SZ-1-Top sample, which was closest to the aeration pipe. Among the possible electron acceptors for AOM, including NO₃^-, NO₂^-, SO₄^2- and Fe³⁺, the NO₂^--N content was the only variable that was positively correlated with the AOM rate. Compared with α-Proteobacteria methanotrophs, γ-Proteobacteria methanotrophs were more abundant in the landfilled waste, especially Methylobacter, which was detected in nearly all samples. Members of the family Methylomirabilaceae, including Candidatus Methylomirabilis, were also detected in the SZ-1 and SZ-2-Bot samples. The relative abundance of the main methanotrophs in the families Methylomonadaceae, Methylococcaceae, Rokubacteriales and Methylomirabilaceae, the genus Methylocystis and the phylum NC10 were all positive correlations with the contents of NO₂^--N in the landfilled waste samples. Additionally, significantly positive correlations were observed between the AOM rates and the relative abundance of the main methanotrophs except for the family Methylococcaceae. This indicated that aeration could enhance the conversion of nitrogen compounds in the landfilled waste, in which the high contents of NO₂^--N could stimulate the growth of methanotrophs and increase AOM rate. These findings are helpful for understanding the mechanisms of CH₄ oxidation in landfills and for taking effective measures to mitigate CH₄ emissions from landfills.

Heterogeneity of CH4-derived carbon induced by O2:CH4 mediates the bacterial community assembly processes

The mechanism by which O₂:CH₄ controls microbial community assembly in the process of aerobic methane oxidation coupled to denitrification (AMED) remains largely uncharacterized, which hinders the design of engineering microbiomes for the AMED. In this study, the changes in the bacterial community in fed-batch serum bottle reactors under different O₂:CH₄ ratios were systematically characterized. The ratios of CH₄ consumption to the amount of nitrate removal in the treatment with O₂:CH₄ = 1.5:1, O₂:CH₄ = 0.5:1, and O₂:CH₄ = 0.25:1 were 13.1 ± 3.4, 4.7 ± 1.1, and 5.9 ± 3.0 mol-CH₄ mol^-1-NO₃^-, respectively. The α-diversity of the bacterial community increased as O₂:CH₄ decreased. Significantly different selection patterns were found for the high and low O₂:CH₄ ratios. The coherence process dominated the selection at high O₂:CH₄ ratios, while the diversification process played a role when O₂:CH₄ was low. Differences were also observed in the composition of CH₄-derived carbon between treatments with O₂:CH₄ = 1.5:1 and O₂:CH₄ = 0.5:1. Compared with the treatments with O₂:CH₄ = 1.5:1, the concentrations of methanol, formaldehyde, acetate, and ethanol in the treatment with O₂:CH₄ = 0.5:1 were significantly higher, while the concentration of formate was significantly lower. The heterogeneity of CH₄-derived carbon induced by O₂:CH₄ was likely to be responsible for the differences in the selection patterns. Our findings bridge the gaps between the observations of bacterial community perturbations and ecological community assembly theories, highlighting the potential of the bottom-up design approach to improve the nitrate removal rate of the AME-D.

Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N₂ fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N₂ fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. ¹⁵N₂-stable isotope probing showed that N₂-fixing activity was stimulated 160-fold by CH₄ oxidation from 0.27 to 43.3 μmol N g^–1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of ¹⁵N-NH₄⁺ through microbial mineralization. Nitrate amendment almost completely abolished N₂ fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N₂ fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N₂ fixation in CH₄-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N₂ fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.

CS2 increasing CH4-derived carbon emissions and active microbial diversity in lake sediments

Lakes are important methane (CH₄) sources to the atmosphere, especially eutrophic lakes with cyanobacterial blooms accompanied by volatile sulfur compound (VSC) emissions. CH₄ oxidation is a key strategy to mitigate CH₄ emission from lakes. In this study, we characterized the fate of CH₄-derived carbon and active microbial communities in lake sediments with CS₂ used as a typical VSC, based on the investigation of CH₄ and VSC fluxes from Meiliang Bay in Lake Taihu. Stable isotope probing microcosm incubation showed that the efficiency of CH₄-derived carbon incorporated into organic matter was 21.1% in the sediment with CS₂ existence, which was lower than that without CS₂ (27.3%). SO₄^2--S was the main product of CS₂ oxidation under aerobic condition, accounting for 59.3-62.7% of the input CS₂-S. CS₂ and CH₄ coexistence led to a decrease of methanotroph and methylotroph abundances and stimulated the production of extracellular polymeric substances. CS₂ and its metabolites including total sulfur, SO₄^2- and acid volatile sulfur acted as the main drivers influencing the active microbial community structure in the sediments. Compared with α-proteobacteria methanotrophs, γ-proteobacteria methanotrophs Methylomicrobium, Methylomonas, Crenothrix and Methylosarcina were more dominant in the sediments. CH₄-derived carbon mainly flowed into methylotrophs in the first stage. With CH₄ consumption, more CH₄-derived carbon flowed into non-methylotrophs. CS₂ could prompt more CH₄-derived carbon flowing into non-methanotrophs and non-methylotrophs, such as sulfur-metabolizing bacteria. These findings can help elucidate the influence of VSCs on microorganisms and provide insights to carbon fluxes from eutrophic lake systems.

Validation and optimization of key biochar properties through iron modification for improving the methane oxidation capacity of landfill cover soil

Knowledge of various BC properties in stimulating the methane (CH₄) oxidation capacity of landfill cover soil (LCS) is still limited, restricting the optimization of BC performance. To validate key BC properties and seek a feasible way for enhancing BC performance, this study prepared BCs with distinctly varying characteristics through iron (Fe) modification. Then, batch incubation experiments under different CH₄ and oxygen concentrations were conducted. Pore volume, cation exchange capacity (CEC), and surface area of BC collectively accounted for 78.5% of the variances in the microbial community structures, with pore volume being the most important factor. These correlated well with the differences in the CH₄ oxidation capacities among the different BC-amended LCS. At a low ratio of 15% (v/v) in LCS, BCs' pH not affected their performance but homogeneity could be a limiting factor. Fe modification proved a promising approach to more efficiently improve the three key BC properties (especially pore volume) and thus optimize BC performance than increasing pyrolysis temperature did. Fe-modified BCs encouraged a bacterial consortium (methanotroph, methylotrophs, and nitrogen-fixing bacteria) in the soil with significantly improved CH₄ oxidation capacities by up to 26%-74% compared to that of pristine BC.

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O2 levels

Aerobic methane (CH₄) oxidation coupled to denitrification (AME-D) can not only mitigate CH₄ emission into the atmosphere, but also potentially alleviate nitrogen pollution in surface waters and engineered ecosystems, and it has attracted substantial research interest. O₂ concentration plays a key role in AME-D, yet little is understood about how it impacts microbial interactions. Here, we applied isotopically labeled K¹⁵NO₃ and ¹³CH₄ and metagenomic analyses to investigate the metabolic and microbial link of AME-D at different O₂ levels. Among the four experimental O₂ levels of 21%,10%, 5% and 2.5% and a CH₄ concentration of 8% (i.e., the O₂/CH₄ ratios of 2.62, 1.26, 0.63 and 0.31), the highest NO₃^--N removal occurred in the AME-D system incubated at the O₂ concentration of 10%. Methanol and acetate may serve as the trophic linkage between aerobic methanotrophs and denitrifers in the AME-D systems. Methylotrophs including Methylophilus, Methylovorus, Methyloversatilis and Methylotenera were abundant under the O₂-sufficient condition with the O₂ concentration of 21%, while denitrifiers such as Azoarcus, Thauera and Thiobacillus dominated in the O₂-limited environment with the O₂ concentration of 10%. The competition of denitrifiers and methylotrophs in the AME-D system for CH₄-derived carbon, such as methanol and acetate, might be influenced by chemotactic responses. More methane-derived carbon flowed into methylotrophs under the O₂-sufficient condition, while more methane-derived carbon was used for denitrification in the O₂-limited environment. These findings can aid in evaluating the distribution and contribution of AME-D and in developing strategies for mitigating CH₄ emission and nitrogen pollution in natural and engineered ecosystems.

Active Methanotrophs in Suboxic Alpine Swamp Soils of the Qinghai-Tibetan Plateau

Methanotrophs are the only biofilters for reducing the flux of global methane (CH4) emissions in water-logged wetlands. However, adaptation of aerobic methanotrophs to low concentrations of oxygen and nitrogen in typical swamps, such as that of the Qinghai-Tibetan Plateau, is poorly understood. In this study, we show that Methylobacter-like methanotrophs dominate methane oxidation and nitrogen fixation under suboxic conditions in alpine swamp soils. Following incubation with 13C-CH4 and 15N-N2 for 90 days under suboxic conditions with repeated flushing using an inert gas (i.e., argon), microbial carbon and nitrogen turnover was measured in swamp soils at different depths: 0-20 cm (top), 40-60 cm (intermediate), and 60-80 cm (deep). Results show detectable methane oxidation and nitrogen fixation in all three soil depths. In particular, labeled carbon was found in CO2 enrichment (13C-CO2), and soil organic carbon (13C-SOC), whereas labeled nitrogen (15N) was detected in soil organic nitrogen (SON). The highest values of labeled isotopes were found at intermediate soil depths. High-throughput amplicon sequencing and Sanger sequencing indicated the dominance of Methylobacter-like methanotrophs in swamp soils, which comprised 21.3-24.0% of the total bacterial sequences, as measured by 13C-DNA at day 90. These results demonstrate that aerobic methanotroph Methylobacter is the key player in suboxic methane oxidation and likely catalyzes nitrogen fixation in swamp wetland soils in the Qinghai-Tibetan Plateau.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.