Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).

Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane

Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.

Shift in hemocyte immune parameters of marine bivalve Mytilus galloprovincialis (Lamarck, 1819) after exposure to methane

Methane are widely used in industry as an emerge source may be released significantly higher aquatic ecosystems due to gas seepages. In this study, short-term (90 min) methane effects on bivalve hemocytes were investigated using flow cytometry. Hemocyte parameters including hemolymph cellular composition, phagocytosis activity, mitochondrial membrane potential and reactive oxygen species (ROS) content were evaluated in the mussel Mytilus galloprovincialis (Lamarck, 1819) exposed to hypoxia (control group), pure methane and industrial methane (industrial hydrocarbon mixture). Comparison of biomarkers showed that the mussel was more sensitive to methane than to low oxygen concentration, supporting the effects of methane on the mussel's immune system. After exposure to pure and industrial methane, the number of granulocytes decreased dramatically and the levels of reactive oxygen species, mitochondrial membrane potential and phagocytosis capacity increased significantly. It was shown that the methane type-dependent effect was pronounced, with industrial methane leading to more pronounced changes.

Methane emission from water level fluctuation zone of the Three Gorges Reservoir: Seasonal variation and microbial mechanism

Periodic and significant water level fluctuations within the Three Gorges Reservoir (TGR) create a complex water level fluctuation zone (WLFZ) that can significantly influence greenhouse gas emissions. However, the scarcity of comprehensive studies investigating long-term monitoring and analysis of CH4 flux patterns and underlying mechanisms concerning water level variations, environmental characteristics, and microbial communities has limited our understanding. This study conducted a four-year monitoring campaign to examine in situ CH4 emissions from three representative sampling sites. Results indicated that the CH4 flux remained relatively stable at lower water levels, specifically at the control site (S1). However, water level fluctuations significantly influenced CH4 emissions at the sampling sites situated within the WLFZ. Notably, the highest CH4 flux of 0.252 ± 0.089 mg/(m2·h) was observed during the drying period (June to August), while the lowest CH4 flux of 0.048 ± 0.026 mg/(m2·h) was recorded during the flooding period. Moreover, CH4 emissions through the water-air interface surpassed those through the soil-air interface. The CH4 flux positively correlated with organic carbon, temperature, and soil moisture. The relative abundance of methane metabolism microorganisms peaked during the drying period and decreased during the impounding and flooding periods. The primary methanogenesis pathway was hydrogenotrophic, whereas methanotrophic processes were mainly aerobic, with Ca. Methylomirabilis governing the anaerobic methanotrophic process. Overall, the current findings serve as crucial theoretical references for understanding CH4 emissions and carbon metabolism processes within WLFZ environments.

Appropriately Reduced Nitrogen and Increased Phosphorus in Ratooning Rice Increased the Yield and Reduced the Greenhouse Gas Emissions in Southeast China

Reducing greenhouse gas emissions while improving productivity is the core of sustainable agriculture development. In recent years, rice ratooning has developed rapidly in China and other Asian countries, becoming an effective measure to increase rice production and reduce greenhouse gas emissions in these regions. However, the lower yield of ratooning rice caused by the application of a single nitrogen fertilizer in the ratooning season has become one of the main reasons limiting the further development of rice ratooning. The combined application of nitrogen and phosphorus plays a crucial role in increasing crop yield and reducing greenhouse gas emissions. The effects of combined nitrogen and phosphorus application on ratooning rice remain unclear. Therefore, this paper aimed to investigate the effect of combined nitrogen and phosphorus application on ratooning rice. Two hybrid rice varieties, 'Luyou 1831' and 'Yongyou 1540', were used as experimental materials. A control treatment of nitrogen-only fertilization (187.50 kg·ha-1 N) was set, and six treatments were established by reducing nitrogen fertilizer by 10% (N1) and 20% (N2), and applying three levels of phosphorus fertilizer: N1P1 (168.75 kg·ha-1 N; 13.50 kg·ha-1 P), N1P2 (168.75 kg·ha-1 N; 27.00 kg·ha-1 P), N1P3 (168.75 kg·ha-1 N; 40.50 kg·ha-1 P), N2P1 (150.00 kg·ha-1 N; 13.50 kg·ha-1 P), N2P2 (150.00 kg·ha-1 N; 27.00 kg·ha-1 P), and N2P3 (150.00 kg·ha-1 N; 40.50 kg·ha-1 P). The effects of reduced nitrogen and increased phosphorus treatments in ratooning rice on the yield, the greenhouse gas emissions, and the community structure of rhizosphere soil microbes were examined. The results showed that the yield of ratooning rice in different treatments followed the sequence N1P2 > N1P1 > N1P3 > N2P3 > N2P2 > N2P1 > N. Specifically, under the N1P2 treatment, the average two-year yields of 'Luyou 1831' and 'Yongyou 1540' reached 8520.55 kg·ha-1 and 9184.90 kg·ha-1, respectively, representing increases of 74.30% and 25.79% compared to the N treatment. Different nitrogen and phosphorus application combinations also reduced methane emissions during the ratooning season. Appropriately combined nitrogen and phosphorus application reduced the relative contribution of stochastic processes in microbial community assembly, broadened the niche breadth of microbial communities, enhanced the abundance of functional genes related to methane-oxidizing bacteria and soil ammonia-oxidizing bacteria in the rhizosphere, and decreased the abundance of functional genes related to methanogenic and denitrifying bacteria, thereby reducing greenhouse gas emissions in the ratooning season. The carbon footprint of ratooning rice for 'Luyou 1831' and 'Yongyou 1540' decreased by 25.82% and 38.99%, respectively, under the N1P2 treatment compared to the N treatment. This study offered a new fertilization pattern for the green sustainable development of rice ratooning.

Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.

Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.

Variation in methane uptake by grassland soils in the context of climate change - A review of effects and mechanisms

Grassland soils are climate-dependent ecosystems that have a significant greenhouse gas mitigating function through their ability to store large amounts of carbon (C). However, what is often not recognized is that they can also exhibit a high methane (CH₄) uptake capacity that could be influenced by future increases in atmospheric carbon dioxide (CO₂) concentration and variations in temperature and water availability. While there is a wealth of information on C sequestration in grasslands there is less consensus on how climate change impacts on CH₄ uptake or the underlying mechanisms involved. To address this, we assessed existing knowledge on the impact of climate change components on CH₄ uptake by grassland soils. Increases in precipitation associated with soils with a high background soil moisture content generally resulted in a reduction in CH₄ uptake or even net emissions, while the effect was opposite in soils with a relatively low background moisture content. Initially wet grasslands subject to the combined effects of warming and water deficits may absorb more CH₄, mainly due to increased gas diffusivity. However, in the longer-term heat and drought stress may reduce the activity of methanotrophs when the mean soil moisture content is below the optimum for their survival. Enhanced plant productivity and growth under elevated CO₂, increased soil moisture and changed nutrient concentrations, can differentially affect methanotrophic activity, which is often reduced by increasing N deposition. Our estimations showed that CH₄ uptake in grassland soils can change from -57.7 % to +6.1 % by increased precipitation, from -37.3 % to +85.3 % by elevated temperatures, from +0.87 % to +92.4 % by decreased precipitation, and from -66.7 % to +27.3 % by elevated CO₂. In conclusion, the analysis suggests that grasslands under the influence of warming and drought may absorb even more CH₄, mainly because of reduced soil water contents and increased gas diffusivity.

Overview on agricultural potentials of biogas slurry (BGS): applications, challenges, and solutions

The residual slurry obtained from the anaerobic digestion (AD) of biogas feed substrates such as livestock dung is known as BGS. BGS is a rich source of nutrients and bioactive compounds having an important role in establishing diverse microbial communities, accelerating nutrient use efficiency, and promoting overall soil and plant health management. However, challenges such as lower C/N transformation rates, ammonia volatilization, high pH, and bulkiness limit their extensive applications. Here we review the strategies of BGS valorization through microbial and organomineral amendments. Such cohesive approaches can serve dual purposes viz. green organic inputs for sustainable agriculture practices and value addition of biomass waste. The literature survey has been conducted to identify the knowledge gaps and critically analyze the latest technological interventions to upgrade the BGS for potential applications in agriculture fields. The major points are as follows: (1) Bio/nanotechnology-inspired approaches could serve as a constructive platform for integrating BGS with other organic materials to exploit microbial diversity dynamics through multi-substrate interactions. (2) Advancements in next-generation sequencing (NGS) pave an ideal pathway to study the complex microflora and translate the potential information into bioprospecting of BGS to ameliorate existing bio-fertilizer formulations. (3) Nanoparticles (NPs) have the potential to establish a link between syntrophic bacteria and methanogens through direct interspecies electron transfer and thereby contribute towards improved efficiency of AD. (4) Developments in techniques of nutrient recovery from the BGS facilities' negative GHGs emissions and energy-efficient models for nitrogen removal. (5) Possibilities of formulating low-cost substrates for mass-multiplication of beneficial microbes, bioprospecting of such microbes to produce bioactive compounds of anti-phytopathogenic activities, and developing BGS-inspired biofertilizer formulations integrating NPs, microbial inoculants, and deoiled seed cakes have been examined.

Effects of Soil Moisture and Temperature on Microbial Regulation of Methane Fluxes in a Poplar Plantation

Improved mechanistic understanding of soil methane (CH4) exchange responses to shifts in soil moisture and temperature in forest ecosystems is pivotal to reducing uncertainty in estimates of the soil-atmospheric CH4 budget under climate change. We investigated the mechanism behind the effects of soil moisture and temperature shifts on soil CH4 fluxes under laboratory conditions. Soils from the Huai River Basin in China, an area that experiences frequent hydrological shifts, were sampled from two consecutive depths (0–20 and 20–50 cm) and incubated for 2 weeks under different combinations of soil moisture and temperature. Soils from both depths showed an increase in soil moisture and temperature-dependent cumulative CH4 fluxes. CH4 production rates incubated in different moisture and temperature in surface soil ranged from 1.27 to 2.18 ng g−1 d−1, and that of subsurface soil ranged from 1.18 to 2.34 ng g−1 d−1. The Q10 range for soil CH4 efflux rates was 1.04–1.37. For surface soils, the relative abundance and diversity of methanotrophs decreased with moisture increase when incubated at 5 °C, while it increased with moisture increase when incubated at 15 and 30 °C. For subsurface soils, the relative abundance and diversity of methanotrophs in all samples decreased with moisture increase. However, there was no significant difference in the diversity of methanogens between the two soil depths, while the relative abundance of methanogens in both depths soils increased with temperature increase when incubated at 150% water-filled pore space (WFPS). Microbial community composition exhibited large variations in post incubation samples except for one treatment based on the surface soils incubated at 15 °C, which showed a decrease in the total and unique species number of methanotrophs with moisture increase. In contrast, the unique species number of methanogens in surface soils increased with moisture increase. The analysis of distance-based redundancy analysis (db-RDA) showed that soil pH, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), microbial biomass carbon (MBC), NO3−-N, and NH4+-N mainly performed a significant effect on methanotrophs community composition when incubated at 60% WFPS, while they performed a significant effect on methanogens community composition when incubated at 150% WFPS. Overall, our findings emphasized the vital function of soil hydrology in triggering CH4 efflux from subtropical plantation forest soils under future climate change.