Methane-oxidizing Bacteria Research Articles

Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems

Lakes and ponds are considered as a major natural source of CH4 emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane-oxidizing bacteria (MOB), which utilize CH4 using oxygen as an electron acceptor, are one of the dominant microorganisms in the CH4-rich water columns. Metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions. However, experimental proof of these functions, i.e., organic acid production via fermentation, by lake MOB is lacking. In addition, psychrophilic (i.e., cold-loving) MOB and their CH4-oxidizing process have rarely been investigated. In this study, we isolated, provided a taxonomic description, and analyzed the genome of Methylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs, Methylobacter sp. S3L5C represented a ubiquitous cluster of Methylobacter spp. in boreal aquatic ecosystems. At optimal temperatures (3–12 °C) and pH (6.8–8.3), the specific growth rates (µ) and CH4 utilization rate were in the range of 0.018–0.022 h−1 and 0.66–1.52 mmol l−1 d−1, respectively. In batch cultivation, the isolate could produce organic acids, and the concentrations were elevated after replenishing CH4 and air into the headspace. Up to 4.1 mM acetate, 0.02 mM malate, and 0.07 mM propionate were observed at the end of the test under optimal operational conditions. The results herein highlight the key role of Methylobacter spp. in regulating CH4 emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.

Structure and activity of particulate methane monooxygenase arrays in methanotrophs

Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.

Impact of recovered phosphorus supply on methanotrophic cultivation and microbial protein production

Microbial protein is a promising dietary supplement alternative to traditional sources, being methane oxidising bacteria (MOB) an attractive option to produce it. Though current production processes rely on fossil resources, there is an increasing trend of using recovered residual nutrient streams, with most research focusing on nitrogen and methane, paying little attention to phosphorus. Struvite and precipitated calcium phosphate (PCP) were evaluated as potential residual P sources for microbial protein production after dissolved them with strong acids. MOB growth was studied in batch experiments. Yields ranged from 0.21 to 0.29 g CDW g CH4−1. Crude protein contents above 50% of dried weight were achieved, and neither the P nor the N source affected the amino acid profile significantly. The highest protein content (75%) was observed when using struvite as nutrient source, but also yielded cadmium and lead accumulation above limits set in legislation.

Enhancing the Efficiency of a Plant Microbial Fuel Cell through the Use of Methane-Oxidizing Bacteria

Enhancing the Efficiency of a Plant Microbial Fuel Cell through the Use of Methane-Oxidizing Bacteria

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

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−, SO42− 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.

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts.

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

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.

Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil

Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.

Trait-Based Model Reproduces Patterns of Population Structure and Diversity of Methane Oxidizing Bacteria in a Stratified Lake

In stratified lakes, methane oxidizing bacteria are critical methane converters that significantly reduce emissions of this greenhouse gas to the atmosphere. Efforts to better understand their ecology uncovered a surprising diversity, vertical structure, and seasonal succession. It is an open question how this diversity has to be considered in models of microbial methane oxidation. Likewise, it is unclear to what extent simple microbial traits related to the kinetics of the oxidation process and temperature optimum, suggested by previous studies, suffice to understand the observed ecology of methane oxidizing bacteria. Here we incorporate niche partitioning in a mechanistic model of seasonal lake mixing and microbial methane oxidation in a stratified lake. Can we model MOB diversity and niche partitioning based on differences in methane oxidation kinetics and temperature adaptation? We found that our model approach can closely reproduce diversity and niche preference patterns of methanotrophs that were observed in seasonally stratified lakes. We show that the combination of trait values resulting in coexisting methanotroph communities is limited to very confined regions within the parameter space of potential trait combinations. However, our model also indicates that the sequence of community assembly, and variations in the stratification and mixing behavior of the lake result in different stable combinations. A scenario analysis introducing variable mixing conditions showed that annual weather conditions and the pre-existing species also affect the developing stable methanotrophic species composition of the lake. Both, effect of pre-existing species and the environmental impact suggest that the MOB community in lakes may differ from year to year, and a stable community may never truly occur. The model further shows that there are always better-adapted species in the trait parameter space that would destabilize and replace an existing stable community. Thus, natural selection may drive trait values into the specific configurations observed in nature based on physiological limits and tradeoffs between traits.

Methane Emission Reduction and Biological Characteristics of Landfill Cover Soil Amended With Hydrophobic Biochar.

Biochar-amended landfill cover soil (BLCS) can promote CH4 and O2 diffusion, but it increases rainwater entry in the rainy season, which is not conducive to CH4 emission reduction. Hydrophobic biochar–amended landfill cover soil (HLCS) was prepared to investigate the changes in CH4 emission reduction and biological characteristics, and BLCS was prepared as control. Results showed that rainwater retention time in HLCS was reduced by half. HLCS had a higher CH4 reduction potential, achieving 100% CH4 removal at 25% CH4 content of landfill gas, and its main contributors to CH4 reduction were found to be at depths of 10–30 cm (upper layer) and 50–60 cm (lower layer). The relative abundances of methane-oxidizing bacteria (MOB) in the upper and lower layers of HLCS were 55.93% and 46.93%, respectively, higher than those of BLCS (50.80% and 31.40%, respectively). Hydrophobic biochar amended to the landfill cover soil can realize waterproofing, ventilation, MOB growth promotion, and efficient CH4 reduction.

Tidal variation and litter decomposition co-affect carbon emissions in estuarine wetlands

Estuarine wetlands play important roles in the regional and global carbon cycle as well as greenhouse gas emissions; however, the driving factors and potential carbon emissions mechanisms are unclear. Here, the carbon emission fluxes were investigated in situ from different vegetated areas in the Chongming wetlands. The results showed that the highest methane (CH4) and carbon dioxide (CO2) emissions of 178.1 and 21,482.5 mg∙m−2∙min−1 were in Scirpus mariqueter and Phragmites australis dominated areas, respectively. A series of microcosms was strategically designed to simulate the influence of tidal variation on carbon emissions and the litter decomposition on daily- and monthly-timescales in estuarine wetlands. All added litter promoted CH4 and CO2 emissions from the wetland soils. The CH4 and CO2 emission fluxes of the S. mariqueter treatment were higher (367.7 vs. 108.4; 1607.9 vs. 1324.3 mg∙m−2∙min−1) than those of the P. australis treatment without tidal variation on a monthly timescale, due to the higher total organic carbon (TOC) content of S. mariqueter. The decomposition of litter also released a large amount of nutrients, which enhanced the abundance of methane-producing archaea (MPA) and methane-oxidizing bacteria (MOB). However, the tidal water level was negatively correlated with CH4 and CO2 emission fluxes. The CH4 and CO2 emission fluxes in the S. mariqueter treatment at the lowest tide were 556.02 and 604.99 mg∙m−2∙min−1, respectively. However, the CH4 and CO2 emission fluxes did not change significantly on the daily timescale in the S. mariqueter treatment without tidal variations. Therefore, the prolonged timescales revealed increases in litter decomposition but a decrease in the contribution of tidal variations to carbon emissions in estuarine wetlands. These findings provide a theoretical basis for evaluating the carbon cycle in estuarine wetlands.

Enhanced Methane Oxidation Potential of Landfill Cover Soil Modified with Aged Refuse

Aged refuse with a landfill age of 1.5 years was collected from a municipal solid waste landfill with high kitchen waste content and mixed with soil as biocover material for landfill. A series of laboratory batch tests was performed to determine the methane oxidation potential and optimal mixing ratio of landfill cover soil modified with aged refuse, and the effects of water content, temperature, CO2/CH4, and O2/CH4 ratios on its methane oxidation capacity were analyzed. The microbial community analysis of aged refuse showed that the proportions of type I and type II methane-oxidizing bacteria were 56.27% and 43.73%, respectively. Aged refuse could significantly enhance the methane oxidation potential of cover soil, and the optimal mixing ratio was approximately 1:1. The optimal temperature and water content were about 25 °C and 30%, respectively. Under the conditions of an initial methane concentration of 15% and an O2/CH4 ratio of 0.8–1.2, the measured methane oxidation rate was negatively correlated with the O2/CH4 ratio. The maximum methane oxidation capacity measured in the test reached 308.5 (μg CH4/g)/h, indicating that the low-age refuse in the landfill with high kitchen waste content is a biocover material with great application potential.

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

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

Phagocytosis of exogenous bacteria by gill epithelial cells in the deep-sea symbiotic mussel Bathymodiolus japonicus.

Animals that live in nutrient-poor environments, such as the deep sea, often establish intracellular symbiosis with beneficial bacteria that provide the host with nutrients that are usually inaccessible to them. The deep-sea mussel Bathymodiolus japonicus relies on nutrients from the methane-oxidizing bacteria harboured in epithelial gill cells called bacteriocytes. These symbionts are specific to the host and transmitted horizontally, being acquired from the environment by each generation. Morphological studies in mussels have reported that the host gill cells acquire the symbionts via phagocytosis, a process that facilitates the engulfment and digestion of exogenous microorganisms. However, gill cell phagocytosis has not been well studied, and whether mussels discriminate between the symbionts and other bacteria in the phagocytic process remains unknown. Herein, we aimed to investigate the phagocytic ability of gill cells involved in the acquisition of symbionts by exposing the mussel to several types of bacteria. The gill cells engulfed exogenous bacteria from the environment indiscriminately. These bacteria were preferentially eliminated through intracellular digestion using enzymes; however, most symbionts were retained in the bacteriocytes without digestion. Our findings suggest that regulation of the phagocytic process after engulfment is a key mechanism for the selection of symbionts for establishing intracellular symbiosis.

Is the role of aerobic methanotrophs underestimated in methane oxidation under hypoxic conditions?

Microbial methane oxidation is the major biological methane (CH4) sink in the carbon cycle. Methanotrophs can use various electron acceptors in addition to oxygen; understanding the role and contribution of methanotrophs is thus an important topic. However, anaerobic oxidation of methane (AOM) mediated by methanotrophs is poorly explored and understood. This article summarizes the role aerobic methanotrophic bacteria play in AOM. Though AOM was originally considered to be mediated by anaerobic methanotrophic archaea, intra-aerobic methane-oxidizing bacteria (Candidatus Methylomirabilis oxyfera) appear to be involved in nitrite-dependent AOM. In addition, aerobic methanotrophs of the Methylomonadaceae and Methylocystaceae, are more versatile than previously assumed and can also be involved in nitrate/nitrite- or mineral oxide-dependent AOM under oxygen-limitation. Furthermore, the simultaneous reduction of nitrous oxide and oxidation of CH4 may be another new metabolic trait of aerobic methanotrophs. We discuss the potential metabolic pathways of CH4 oxidation under hypoxic conditions. It is of great ecological importance not only for the quantification of CH4 oxidation and emissions, but also for the definition of a new function of aerobic methanotrophs in anaerobic/hypoxic environments.

Methane-Derived Carbon as a Driver for Cyanobacterial Growth.

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

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.

Redox Zone and Trophic State as Drivers of Methane-Oxidizing Bacterial Abundance and Community Structure in Lake Sediments

Eutrophication is expected to increase methane production in freshwater sediments worldwide over the coming decades. Methane-oxidizing bacteria (MOB) consume a significant fraction of this sedimentary methane, but the factors that control their distributions and activities are not understood. By combining genetic approaches (pmoA, 16S rRNA gene, metagenomics) with geochemical and sedimentological analyses, we investigate the role of trophic state, electron acceptors, oxygen (O2) and methane fluxes, and potential methylotrophic partner organisms in driving the distributions, abundances, and community compositions of MOB across five lakes in central Switzerland. Although methane fluxes were highest in the eutrophic lakes, methanotrophic abundances peaked in oxic and anoxic sediments of an oligotrophic lake. In all lakes, Type I gammaproteobacterial Methylococcaceae dominated oxic and suboxic bottom water and surface sediments, showing strong correlations with abundances of putatively methylotrophic Methylophilaceae, whereas Type II alphaproteobacterial Methylocystaceae increased in deeper, anoxic sediment layers. Methanotrophic bacteria belonging to the NC10 phylum were predominantly detected within denitrifying sediment of the oligotrophic lake, matching their presumed nitrite-dependent lifestyle. While dominant MOB taxa at the genus-level follow vertical distributions of different aerobic and anaerobic respiration reactions, trophic state at the time of sediment deposition was the best predictor of MOB community structure at the operational taxonomic unit (OTU) level. Elevated methane fluxes combined with low MOB abundances in surface sediments of eutrophic lakes, moreover, support the notion that in eutrophic lakes a major portion of sedimentary methane bypasses the biological methane filter and escapes to overlying water.

Use of methanotrophically activated biochar in novel biogeochemical cover system for carbon sequestration: Microbial characterization

Biochar-amended soils have been explored to enhance microbial methane (CH4) oxidation in landfill cover systems. Recently, research priorities have expanded to include the mitigation of other components of landfill gas such as carbon dioxide (CO2) and hydrogen sulfide (H2S) along with CH4. In this study, column tests were performed to simulate the newly proposed biogeochemical cover systems, which incorporate biochar-amended soil for CH4 oxidation and basic oxygen furnace (BOF) slag for CO2 and H2S mitigation, to evaluate the effect of cover configuration on microbial CH4 oxidation and community composition. Biogeochemical covers included a biochar-amended soil (10% w/w), and methanotroph-enriched activated biochar amended soil (5% or 10% w/w) as a biocover layer or CH4 oxidation layer. The primary outcome measures of interest were CH4 oxidation rates and the structure and abundance of methane-oxidation bacteria in the covers. All column reactors were active in CH4 oxidation, but columns containing activated biochar-amended soils had higher CH4 oxidation rates (133 to 143 μg CH4 g−1 day−1) than those containing non-activated biochar-amended soil (50 μg CH4 g−1 day−1) and no-biochar soil or control soil (43 μg CH4 g−1 day−1). All treatments showed significant increases in the relative abundance of methanotrophs from an average relative abundance of 5.6% before incubation to a maximum of 45% following incubation. In activated biochar, the abundance of Type II methanotrophs, primarily Methylocystis and Methylosinus, was greater than that of Type I methanotrophs (Methylobacter) due to which activated biochar-amended soils also showed higher abundance of Type II methanotrophs. Overall, biogeochemical cover profiles showed promising potential for CH4 oxidation without any adverse effect on microbial community composition and methane oxidation. Biochar activation led to an alteration of the dominant methanotrophic communities and increased CH4 oxidation.