Search Results (57)

Wetlands are the most important natural sources of methane. Studies on the distribution and diversity of methanotrophs, especially in tropical wetlands, are limited. The studies on wetland methanotrophs help bridge the gap in the literature for understanding the community structure of methanotrophs in tropical wetlands. Our present study documents the methanotroph diversity from various wetland habitats across Western India. Samples from various sites, such as freshwater ponds, lake sediments, mangroves, etc., located in Western India, were collected and enriched for methanotroph isolation. An established protocol for the isolation of methanotrophs from Indian rice fields, involving serial dilution and long-term incubations, was slightly modified and used. Obtaining entirely pure cultures of methanotrophs is a labor-intensive and technically challenging process. Hence, for primary level characterization, ‘methanotroph monocultures’, which have a single methanotroph culture with minimal contamination, were established. Twenty monocultures and eight pure cultures of methanotrophs were obtained in this study. The pmoA gene has been used for the phylogenetic characterization of methanotrophs for the last 25 years. Monocultures were from seven genera: the Methylomonas, Methylocystis, Methylosinus, Methylocaldum, Methylocucumis, Methylomagnum, and Methylolobus genera. Eight pure cultures were obtained, which were strains of Methylomonas koyamae, Methylosinus sporium, and Methylolobus aquaticus. A maximum number of cultures belonged to the Type I genus Methylomonas and to the Type II genus Methylocystis. Thus, the cultivation-based community studies of methanotrophs from wetland habitats in India expanded the current knowledge about the methanotroph diversity in such regions. Additionally, the cultivation approach helped us obtain new methanotrophs from this previously unexplored habitat, which can be used for further biotechnological and environmental applications. The isolated monocultures can either be used as MMCs (mixed methanotroph consortia) for environmental applications or further purified and used as pure cultures. Full article

Oxidation of methane by soil microorganisms is an important mechanism controlling the content of this potent greenhouse gas in the atmosphere. Agricultural soils operate under stressful conditions, and ammonium (N-fertilization) and drying (global warming) may have a significant impact on methane oxidation. In order to investigate how soil methanotrophs respond to drying–rewetting (DW), ammonium addition (100 mg/g) (A), and their combined action (MS), agricultural soil microcosms were incubated over the three months and methane oxidation was measured before and after perturbations, while community composition was monitoring using 16S rRNA gene sequencing. A significant decline in the methane-oxidation activity after perturbations was found, with subsequent restoration, and the combined treatment was more effective than the sum of individual treatments, indicating a synergistic effect. After rewetting, the structure of the bacterial community returned to pre-dry-down levels, but the application of ammonia and combined action lead to irreversible changes in the structure of soil methanotrophic communities. Methanotroph Methylomicrobium were significantly reduced under disturbances, while there was a significant increase in the representation of Methylobacter accompanied by the facultative methylotroph Methylovorus. We concluded that methanotrophic communities in agricultural soil demonstrated flexibility, and even when the abundance of dominant populations drops, ecosystem functions can recover. Full article

Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels, and other valuable compounds, leveraging the power of microbial systems for enhanced yield and sustainability. Genome-scale metabolic (GSM) modeling has become an essential approach in this field, which enables a guide for targeting genetic modifications and the optimization of metabolic pathways for various industrial applications. While single-species GSM models have traditionally been employed to optimize strains like Escherichia coli and Lactococcus lactis, the integration of these models into community-based approaches is gaining momentum. Herein, we present a pipeline for community metabolic modeling with a user-friendly GUI, applying it to analyze interactions between Methylococcus capsulatus, a biotechnologically important methanotroph, and Escherichia coli W3110 under oxygen- and nitrogen-limited conditions. We constructed models with unmodified and homoserine-producing E. coli strains using the pipeline implemented in the original BioUML platform. The E. coli strain primarily utilized acetate from M. capsulatus under oxygen limitation. However, homoserine produced by E. coli significantly reduced acetate secretion and the community growth rate. This homoserine was taken up by M. capsulatus, converted to threonine, and further exchanged as amino acids. In nitrogen-limited modeling conditions, nitrate and ammonium exchanges supported the nitrogen needs, while carbon metabolism shifted to fumarate and malate, enhancing E. coli TCA cycle activity in both cases, with and without modifications. The presence of homoserine altered cross-feeding dynamics, boosting amino acid exchanges and increasing pyruvate availability for M. capsulatus. These findings suggest that homoserine production by E. coli optimizes resource use and has potential for enhancing microbial consortia productivity. Full article

Paddy fields are important anthropogenic emission sources of methane (CH₄). However, it is not clear how rice root development and rhizosphere soil properties affect CH₄ emissions. Therefore, we selected rice varieties with similar growth periods but different root traits in the local area. We measured CH₄ emission fluxes, cumulative CH₄ emissions, root dry weight, root length, and the dissolved organic carbon (DOC), microbial biomass carbon (MBC), redox potential (Eh), ammonium nitrogen (${\mathrm{N}\mathrm{H}}_4^{+}$–N), and nitrate nitrogen (${\mathrm{N}\mathrm{O}}_3^{-}$–N) contents in rhizosphere soil. Methanogens and methanotrophs are crucial factors influencing CH₄ emissions; thus, their abundance and community composition were also assessed. The result showed that CH₄ fluxes of each rice variety reached the peak at tillering stage and jointing-booting stage. The CH₄ emissions in tillering stage were the largest in each growth period. CH₄ emissions had negative correlations with root length, root dry weight, Eh ${\mathrm{N}\mathrm{O}}_3^{-}$–N, methanotroph abundance, and the pmoA/mcrA ratio, and positive correlations with ${\mathrm{N}\mathrm{H}}_4^{+}$–N, MBC, DOC, and methanogen abundance. Path analysis confirmed methanogens and methanotrophs as direct influences on CH₄ emissions. Root development and rhizosphere soil properties affect CH₄ emissions indirectly through these microbes. This study suggests that choosing rice varieties with good root systems and managing the rhizosphere soil can effectively reduce CH₄ emissions. Full article

The effects of fallow season water and straw management on methane (CH₄) emissions during the fallow season and the subsequent rice-growing season are rarely reported, and the underlying microbial mechanisms remain unclear. A field experiment was conducted with four treatments: (1) fields flooded in both the fallow and rice seasons (FF), (2) fields drained in the fallow season and flooded in the rice season (DF), (3) FF with straw retention (FFS), and (4) DF with straw retention (DFS). The CH₄ emissions in fields under different water and straw treatments were monitored using the static closed chamber method. Methanogenic and methanotrophic communities in these fields were examined using terminal restriction fragment length polymorphism (T-RFLP) analysis based on the mcrA gene and pmoA gene encoding methyl coenzyme M reductase and particulate methane monooxygenase, respectively. The results showed that CH₄ emissions were significantly affected by water management, straw retention, season, and their interactions. Over 80% of CH₄ emissions occurred during the rice season. Field drainage during the fallow season reduced CH₄ emissions by 47.0% and 53.8% with and without straw during the rice season, respectively. Water management altered the abundance and composition of methanogens and methanotrophs, whereas the effects of straw retention were less pronounced. The quantitative polymerase chain reaction (qPCR) assay revealed that field drainage in the fallow season decreased the mcrA gene abundance by 30.0% and 23.2% with and without straw in rice season, respectively, and increased the pmoA gene abundance by 108.9% and 213.7% with and without straw in rice season, respectively. CH₄ flux was significantly positively associated with mcrA gene copy number and the ratio of mcrA to pmoA gene copy number, whereas it was significantly negatively correlated with the pmoA gene copy number. Results indicated that fallow drainage greatly decreased CH₄ emission not only during the fallow season but also during the subsequent rice season by altering the community composition of methanogens and methanotrophs. These findings provide scientific insight into the role of water and straw management in controlling CH₄ emissions through microbial community dynamics. Full article

Alkaline coal mine drainage represents one of the most critical issues in the coal industry, driven by complex hydro-biogeochemical processes. However, the interplay of hydrogeochemical and biogeochemical interactions in alkaline coal mine drainage is still poorly understood. To this end, water samples were systematically collected from alkaline coal mine drainage sites from five coal mining areas in Chongqing coal mining district, located in southwestern China. Hydrogeochemical analyses showed that the main water type of the coal mine drainage sample was HCO₃-SO₄~K-Na, which primarily originated from local meteoric water. The microbial community compositions in the studied alkaline coal drainage were critically associated with sulfate, bicarbonate, DOC, nitrate, and pH, and linked to three putative keystone genera via network analysis (Thiothrix, Methylophilaceae_MM1, and an unclassified genus from Comamonadaceae family). Functional predictions from FAPROTAX suggested a high abundance of metabolic pathways involving the oxidation of sulfide and sulfur compounds, potentially underscoring their importance in controlling sulfate enrichment in alkaline coal mine drainage. Interestingly, members of the Methylomonadaceae family (methanotrophs) and the Methylotenera genus (methylotrophs) had positive Spearman correlations with both ammonium and sulfate, potentially inferring that the enhanced activities of methanotrophs might help capture methane in the alkaline coal mine drainage. This study further enhances our comprehension of the intricate interplay between hydrogeochemical and biogeochemical interactions in alkaline coal mine drainage, contributing to the carbon budget. Full article

As the main contributor to greenhouse gas (GHG) in paddy soil, information on methane (CH₄) emission characteristics under different tillage and cultivation practices are limited. A five-year field trial was conducted from 2019 in a single-cropping rice system in Taihu Lake region, east of China. The experiment had a completely randomized block design, and the treatments included rotary tillage plus rice dry direct seeding (RD), rotary tillage plus rice mechanical transplanting (RT), and plowing tillage plus rice mechanical transplanting (PT). We determined the rice yield, GHG emission, soil traits, and methanogens and methanotrophs in 2022 and 2023. The results revealed that PT and RT significantly increased rice yield compared to RD, whereas PT simultaneously increased CH₄ emissions. The year-averaged cumulative CH₄ emissions in PT were increased by 38.5% and 61.4% higher than RT and RD, respectively. Meanwhile, yield-scaled global warming potentials (GWPs) in RT and RD were lower than those in PT. Tillage and cultivation practices shifted mcrA and pmoA abundances, and PT significantly decreased pmoA abundance. The community structure and diversity of the methanogens and methanotrophs were not significantly affected. Structural equation model analyses illustrated that CH₄ emissions were regulated by mcrA and pmoA directly, which in turn, regulated by soil carbon and nitrogen. Overall, rotary tillage plus mechanism transplanting was a feasible agronomic technology in a single-cropping rice system in Taihu Lake region, exhibiting higher and more stable rice productivity, accompanied with lower CH₄ emissions and yield-scaled GWP. Full article

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH₄ cm⁻³ day⁻¹ in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65–99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO₂ fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes. Full article

An ever-increasing amount of research is being performed on the stability and recovery of soil methane-oxidizing bacteria since this is one of the fundamental processes controlling the amount of methane in the atmosphere. Mineral fertilizers may alter the methane oxidation processes in agricultural soils when they are introduced. Although ammonium (NH₄⁺) is believed to have a significant impact on aerobic methane oxidation activity in soils, there is still little data on how it reacts with lanthanum (La). The recent identification of a novel class of lanthanum-containing enzymes in methanotrophic bacteria may be the foundation for controlling the function of the soil “methane filter” and related microbiota. In the current study, microcosms with agricultural sod-podzolic soils were created and incubated in air or 20% CH₄ in the gas phase with the addition of NH₄⁺ (100 µg/g) and La (5 µg/g) to the soil. Using GC analysis and high-performance 16S rRNA sequencing, the methane oxidation potential and composition of soil bacterial communities were studied over the month of incubation. A negative impact of NH₄⁺ on the oxidation of methane was observed, whereas La had a somewhat beneficial effect. Ammonium had an impact on the composition of methanotrophs, and a significant shift was observed upon La addition. Proteobacteria made up a larger share of the soil microbial community, and Gammaproteobacteria dominated the methanotrophic populations. Methylobacter, a methanotroph, and Methylotenera, an obligatory methylotroph, were the two absolute dominants in the La-amended variants. These findings could help evaluate how lanthanum regulates methanotrophic communities in agricultural soils and lead to the creation of new strategies for controlling the “methane filter” in soil. Full article

This study designed surface flow constructed wetlands (SFCWs) with Myriophyllum aquaticum (M. aquaticum) to evaluate how different influent C/N ratios (0:1 (C₀N), 5:1 (C₅N), 10:1 (C₁₀N), and 15:1 (C₁₅N)) affect pollutant removal, greenhouse gas (GHG) emissions, and microbial communities. The results showed that effluent ammonia nitrogen (${\mathrm{N}\mathrm{H}}_4^{+}$-N), nitrate nitrogen (${\mathrm{N}\mathrm{O}}_3^{-}$-N), and total nitrogen (TN) concentrations decreased, but effluent chemical oxygen demand (COD) concentration increased with increasing influent C/N ratios. The highest removal rates of TN (73.17%) and COD (74.56%) were observed with C₅N. Regarding GHG emissions, a few changes in CO₂ fluxes were caused by the influent C/N ratio, whereas CH₄ fluxes obviously increased with the increasing influent C/N ratio. The highest N₂O emission occurred with C₀N (211.03 ± 44.38 mg-N·m⁻²·h⁻¹), decreasing significantly with higher C/N ratios. High-throughput sequencing revealed that different influent C/N ratios directly influenced the microbial distribution and composition related to CH₄ and N₂O metabolism in SFCWs. The highest abundance (46.24%) of denitrifying bacteria (DNB) was observed with C₅N, which helped to achieve efficient nitrogen removal with a simultaneous reduction in N₂O emissions. Methanogen abundance rose with higher C/N ratios, whereas methanotrophs peaked under C₅N and C₁₀N conditions. Additionally, the random forest model identified influent C/N ratio and Rhodopseudomonas as primary factors influencing CH₄ and N₂O emissions, respectively. This highlights the importance of the influent C/N ratio in regulating both pollutant removal and GHG emissions in constructed wetlands. Full article

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N₂) fixation and as a promising strategy to mitigate methane (CH₄) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH₄ cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH₄ emissions by 20 times. Yet, the effect on CH₄ cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria–methanotrophs and their respective traits. Full article

Soil greenhouse gas (GHG) fluxes relate to soil carbon and nitrogen budgets and have a significant impact on climate change. Nevertheless, the temporal variation and magnitude of the fluxes of all three major GHGs (CO₂, CH₄ and N₂O) and their influencing factors have not been elucidated clearly in primary forests on the eastern Qinghai-Tibetan Plateau. Herein, field chamber GHG fluxes from May to November, soil microbial community and enzyme activity were analyzed in a fir-dominated (Abies fargesii var. faxoniana) primary forest. The emission rates of CO₂ and N₂O ranged between 64.69–243.22 mg CO₂ m⁻² h⁻¹ and 1.69–5.46 ug N₂O m⁻² h⁻¹, exhibiting a temporally unimodal pattern with a peak in July. The soil acted as a CH₄ sink, and the uptake rate varied between 52.96 and 84.67 μg CH₄ m⁻² h⁻¹ with the higher uptake rates in June and November. The temporal variation in the CO₂ flux was significantly correlated with the geometric mean of enzyme activities, suggesting that the soil CO₂ flux was determined by microbial activity rather than soil microbial biomass. The soil N₂O flux was positively related to nitrate concentration with marginal significance, probably because N₂O was a byproduct of nitrification and denitrification processes. The soil CH₄ uptake was closely associated with methanotrophic biomass (18:1ω7c). The results highlight divergent temporal dynamics of GHG fluxes owing to different driving mechanisms and an important CH₄ sink in the primary forest soil, helping to evaluate the carbon and nitrogen budgets of primary forests on the eastern Qinghai-Tibetan Plateau. Full article

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH_4 mL⁻¹ day⁻¹. Full article

Termites’ digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites’ guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host’s existence, growth, and development. Full article

We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH₄ metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities. Full article