Novel methanotrophic and methanogenic bacterial communities from diverse ecosystems and their impact on environment

Variations in microbial community compositions and processes imposed under contrast geochemical contexts in Sicilian mud volcanoes, Italy

Terrestrial mud volcanoes represent surface features of channels for subsurface methane transport and, therefore, constitute an important source of methane emission from natural environments. How microbial processes regulate methane emissions in terrestrial mud volcanoes has yet to be fully addressed. This study demonstrated the geochemical characteristics and microbial communities of four mud volcano and seep sites in two geological settings of Sicily, Italy. At sites within the accretionary wedge that exhibited higher methane and sulfate concentrations, the communities were dominated by members capable of catalyzing methane and sulfate metabolisms and organic degradation. In particular, both anaerobic and aerobic methanotrophs were abundant and their abundance distribution coincided with the geochemical transition. In contrast, the sites near Mount Etna were characterized by high fluid salinity, CO2, and low methane and sulfate concentrations, with communities consisting of halophilic organic degraders and sulfur metabolizers, along with a minor presence of aerobic methanotrophs. Substantial variations in community composition and geochemistry across spatial and vertical redox gradients suggest that physicochemical contexts imposed by the geology, fluid path, and source characteristics play a vital role in shaping community composition and cycling of methane, sulfur and organic carbon in Sicily mud volcanoes.

Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir

Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103-1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.

Additive facilitated co-composting of lignocellulosic biomass waste, approach towards minimizing greenhouse gas emissions: An up to date review

Although the composting of lignocellulosic biomass is an emerging waste-to-wealth approach towards organic waste management and circular economy, it still has some environmental loopholes that must be addressed to make it more sustainable and reliable. The significant difficulties encountered when composting lignocellulosic waste biomass are consequently discussed in this study, as well as the advances in science that have been achieved throughout time to handle these problems in a sustainable manner. It discusses an important global concern, the emission of greenhouse gases during the composting process which limits its applicability on a broader scale. Furthermore, it discusses in detail, how different organic minerals and biological additives modify the physiochemical and biological characteristics of compost, aiming at developing eco-friendly compost with minimum odor, greenhouse gases emission and an optimum C/N ratio. It brings novel insights by demonstrating the effect of additives on the microbial enzymes and their pathways involved in the degradation of lignocellulosic biomass. This review also highlights the limitations of the application of additives in composting and suggests possible ways to overcome these limitations in the future for the sustainable and eco-friendly management of agricultural waste. The present review concludes that the use of additives in the co-composting of lignocellulosic biomass can be a viable remedy for the ongoing issues with the management of lignocellulosic waste.

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Potential methane emission reduction strategies from rice cultivation systems in Bangladesh: A critical synthesis with global meta-data

Methane (CH₄) is one of the dominant greenhouse gases (GHG) that is largely emitted from rice fields and thus, significantly contributes to global warming. Significant efforts have been made to find out suitable strategies to mitigate CH₄ emission from rice culture. However, the effectiveness of these management practices is often diverse with negative, no, or positive impacts making it difficult to adopt under a particular condition. The diversity of rice cultivation in terms of agro-climatic conditions and cultivation practices makes it difficult for providing specific recommendations. Here, we collected data from a total of 198 studies reporting 1052 observations. The management practices are categorized into five different management practices i.e., water, organic and inorganic fertilizer management, crop establishment method, and agronomic practices while major categories were subdivided into different classes. To test statistically significant differences in the effectiveness between major management practices, an analysis of variance (ANOVA) was applied. The Gaussian and bootstrapping model were applied to find out the best estimate of the effectiveness of each practice. In addition, mechanisms controlling the CH₄ emission reductions were synthesized. Next, the adoption potentials of these practices were assessed based on the existing rice cultivation systems in Bangladesh. Our results showed that water and organic matter management were the most effective methods irrespective of the growing conditions. When these technologies are customized to Bangladesh, water management and crop establishment methods seem most feasible. Among the rice-growing seasons in Bangladesh, there is a larger scope to adopt these management practices in the Boro season (December to May), while these scopes are minimal in the other two seasons due to their rain-fed nature of cultivation. Altogether, our study provides fundamental insights on CH₄ reductions strategies from rice fields in Bangladesh.

The rice histone methylation regulates hub species of the root microbiota

Plants have a close relationship with their root microbiota, which comprises a complex microbial network. Histone methylation is an important epigenetic modification influencing multiple plant traits; however, little is known about the role of plant histone methylation in the assembly and network structure of the root microbiota. In this study, we established that the rice (Oryza sativa) histone methylation regulates the structure and composition of the root microbiota, especially the hub species in the microbial network. DJ-jmj703 (defective in histone H3K4 demethylation) and ZH11-sdg714 (defective in H3K9 methylation) showed significant different root microbiota compared with the corresponding wild types at the phylum and family levels, with a consistent increase in the abundance of Betaproteobacteria and a decrease in the Firmicutes. In the root microbial network, 35 of 44 hub species in the top 10 modules in the tested field were regulated by at least one histone methylation-related gene. These observations establish that the rice histone methylation plays a pivotal role in regulating the assembly of the root microbiota, providing insights into the links between plant epigenetic regulation and root microbiota.