Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing

Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis

Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na+, and SO42- concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2--N concentration and NO2-/NO3- ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.

Isolation of Methane Enriched Bacterial Communities and Application as Wheat Biofertilizer under Drought Conditions: An Environmental Contribution

The search for methanotrophs as plant-growth-promoting rhizobacteria (PGPR) presents an important contribution to mitigating the impact of global warming by restoring the natural soil potential for consuming methane while benefiting plants during droughts. Our in silico simulations suggest that water, produced as a byproduct of methane oxidation, can satisfy the cell growth requirement. In addition to water, methanotrophs can produce metabolites that stimulate plant growth. Considering this, we proposed that applying methanotrophs as PGPR can alleviate the effect of droughts on crops, while stimulating atmospheric methane consumption. In this work, we isolated a series of methanotrophic communities from the rhizospheres of different crops, including Italian sweet pepper and zucchini, using an atmosphere enriched with pure methane gas, to determine their potential for alleviating drought stress in wheat plants. Subsequently, 23 strains of nonmethanotrophic bacteria present in the methanotrophic communities were isolated and characterized. We then analyzed the contribution of the methane-consuming consortia to the improvement of plant growth under drought conditions, showing that some communities contributed to increases in the wheat plants' lengths and weights, with statistically significant differences according to ANOVA models. Furthermore, we found that the presence of methane gas can further stimulate the plant-microbe interactions, resulting in larger plants and higher drought tolerance.

DNA-SIP reveals an overlooked methanotroph, Crenothrix sp., involved in methane consumption in shallow lake sediments

Methanotrophs are the main consumers of methane produced in lake sediments. In shallow lakes suffering from eutrophication, methanogenesis is accelerated by the excess organic carbon input, and thus methanotrophs play a key role in regulating this methane flux as well as carbon cycling. Here, we applied nucleic acid stable isotope probing (SIP) to investigate the active methanotrophic microbial community in sediments of several shallow lakes affected by eutrophication. Our results showed that an active methanotrophic community dominated by gamma-proteobacterial methanotrophs, as well as abundant beta-proteobacterial methanol-utilizers, was involved in methane-derived carbon assimilation. Crenothrix, a filamentous methanotroph, was found to be a key methane consumer in all studied lakes. The ecological role of Crenothrix in lacustrine ecosystems is so far poorly understood, with only limited information on its existence in the water column of stratified lakes. Our results provide a novel ecological insight into this group by revealing a wide distribution of Crenothrix in lake sediments. The active methane assimilation by Crenothrix also suggested that it might represent a so far overlooked but crucial biological sink of methane in shallow lakes.

Pollution alters methanogenic and methanotrophic communities and increases dissolved methane in small ponds

Small ponds have become a hotspot of greenhouse gas emissions, but our understanding of methane (CH₄) cycling and its biological regulation in small polluted ponds remains limited. To assess how pollution affects CH₄ content, we investigated dissolved CH₄ concentrations, water and sediments properties, methanogenic and methanotrophic communities in two types of small polluted ponds. Compared with low pollution (LP) ponds, high pollution (HP) ponds showed significantly (P < 0.05) higher dissolved CH₄ in water. Sequencing of methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) genes showed that HP led to significant (P < 0.05) shifts of CH₄-cycling microbial communities, with increased Shannon index of sediment methanogenic communities and water methanotrophic communities. There were also strong negative associations (P < 0.05) between dissolved CH₄ concentrations and interdomain methanogen-methanotroph network connectivity in water and sediments, respectively. The partial least squares path modeling indicated that dissolved oxygen, total organic carbon, ammonium nitrogen and nitrate nitrogen of water, and total nitrogen and total carbon of sediment, and CH₄-cycling microbes could regulate the CH₄ content. This study clarified the effects of environmental deterioration on CH₄ cycling in small ponds, highlighting the use of methanogen-methanotroph network connectivity to assess the CH₄ production.

Divergent responses of wetland methane emissions to elevated atmospheric CO2 dependent on water table

Elevated atmospheric CO₂ may have consequences for methane (CH₄) emissions from wetlands, yet the magnitude and direction remain unpredictable, because the associated mechanisms have not been fully investigated. Here, we established an in situ macrocosm experiment to compare the effects of elevated CO₂ (700 ppm) on the CH₄ emissions from two wetlands: an intermittently inundated Calamagrostis angustifolia marsh and a permanently inundated Carex lasiocarpa marsh. The elevated CO₂ increased CH₄ emissions by 27.6-57.6% in the C. angustifolia marsh, compared to a reduction of 18.7-23.5% in the C. lasiocarpa marsh. The CO₂-induced increase in CH₄ emissions from the C. angustifolia marsh was paralleled with (1) increased dissolved organic carbon (DOC) released from plant photosynthesis and (2) reduced (rate of) CH₄ oxidation due to a putative shift in methanotrophic community composition. In contrast, the CO₂-induced decrease in CH₄ emissions from the C. lasiocarpa marsh was associated with the increases in soil redox potential and pmoA gene abundance. We synthesized data from worldwide wetland ecosystems, and found that the responses of CH₄ emissions to elevated CO₂ was determined by the wetland water table levels and associated plant oxygen secretion capacity. In conditions with elevated CO₂, plants with a high oxygen secretion capacity suppress CH₄ emissions while plants with low oxygen secretion capacity stimulate CH₄ emissions; both effects are mediated via a feedback loop involving shifts in activities of methanogens and methanotrophs.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Heavy metal pollution increases CH4 and decreases CO2 emissions due to soil microbial changes in a mangrove wetland: Microcosm experiment and field examination

Mangrove plays an important role in modulating global warming through substantial blue carbon storage relative to their greenhouse gas emission potential. The presence of heavy metals in mangrove wetlands can influence soil microbial communities with implications for decomposition of soil organic matter and emission of greenhouse gases. In this study, field monitoring and a microcosm experiment were conducted to examine the impacts of heavy metal pollution on soil microbial communities and greenhouse gas fluxes. The results show that heavy metal pollution decreased the richness and diversity of the overall soil microbial functional groups (heterotrophs and lithotrophs); however, it did not inhibit the activities of the methanogenic communities, possibly due to their stronger tolerance to heavy metal toxicity compared to the broader soil microbial communities. Consequently, the presence of heavy metals in the mangrove soils significantly increased the emission of CH₄ while the emission of CO₂ as a proxy of soil microbial respiration was decreased. The soil organic carbon content could also buffer the effect of heavy metal pollution and influence CO₂ emissions due to reduced toxicity to microbes. The findings have implications for understanding the complication of greenhouse gas emissions by heavy metal pollution in mangrove wetlands.

Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India

Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH₄) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH₄ utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, K_s of 1.92 ± 0.092 mg CH₄ L^-1. Besides the ability to utilize CH₄, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.

The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review

New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.

Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh

Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50-70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.

Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3

AIMS

Microbial consortia can be more efficient at biological processes than single isolates. The purposes of this study were to design and evaluate a synthetic microbial consortium containing the methanotroph Methylocystis sp. M6 and the helper Hyphomicrobium sp. NM3, and develop a novel methanotrophic process for this consortium utilizing a dialysis membrane.

METHODS AND RESULTS

Hyphomicrobium increased the methane-oxidation rate (MOR), biomass and stability at a dilution rate of 0·067 day^-1 in fed-batch co-culture. qRT-PCR showed that Methylocystis population increased gradually with time, whereas Hyphomicrobium population remained stable despite cell washing, confirming synergistic population interaction. At 0·1 day^-1 , spiking of Hyphomicrobium effectively increased the methanotrophic activity, after which Hyphomicrobium population decreased with time, indicating that the consortium is optimal at <0·1 day^-1 . When Hyphomicrobium was grown in dialysis membrane within the bioreactor, MOR increased linearly up to 155·1 ± 1·0 mmol l^-1  day^-1 at 0·067, 0·1, 0·2 and 0·4 day^-1 , which is the highest observed value for a methanotrophic reactor.

CONCLUSIONS

Hyphomicrobium sp. NM3 is a promising helper micro-organism for methanotrophs. Hyphomicrobium-methanotroph consortia used concurrently with existing methods can produce an efficient and stable methane oxidation system.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel methanotrophic process is superior to those previously reported in the literature, and can provide efficient and stable methane oxidation.