Paddy soils make up the largest anthropogenic wetlands on earth, and are characterized by a prominent potential for organic carbon (C) sequestration. By quantifying the plant- and microbial-derived C in soils across four climate zones, we identified that organic C accrual is achieved via contrasting pathways in paddy and upland soils. Paddies are 39%-127% more efficient in soil organic C (SOC) sequestration than their adjacent upland counterparts, with greater differences in warmer than cooler climates. Upland soils are more replenished by microbial-derived C, whereas paddy soils are enriched with a greater proportion of plant-derived C, because of the retarded microbial decomposition under anaerobic conditions induced by the flooding of paddies. Under both land-use types, the maximal contribution of plant residues to SOC is at intermediate mean annual temperature (15-20 °C), neutral soil (pH~7.3) and low clay/sand ratio. By contrast, high temperature (~24 °C), low soil pH (~5) and large clay/sand ratio are favorable for strengthening the contribution of microbial necromass. The greater contribution of microbial necromass to SOC in water-logged paddies in warmer climates is likely due to the fast anabolism from bacteria, whereas fungi are unlikely to be involved as they are aerobic. In the scenario of land-use conversion from paddy to upland, a total of 504 Tg C may be lost as CO from paddy soils (0-15 cm) solely in eastern China, with 90% released from the less protected plant-derived C. Hence, preserving paddy systems and other anthropogenic wetlands and increasing their C storage through sustainable management are critical for maintaining global soil C stock and mitigating climate change.This article is protected by copyright. All rights reserved.

Sustainable soil carbon sequestration practices need to be rapidly scaled up and implemented to contribute to climate change mitigation. We highlight that the major potential for carbon sequestration is in cropland soils, especially those with large yield gaps and/or large historic soil organic carbon losses. The implementation of soil carbon sequestration measures requires a diverse set of options, each adapted to local soil conditions and management opportunities, and accounting for site-specific trade-offs. We propose the establishment of a soil information system containing localised information on soil group, degradation status, crop yield gap, and the associated carbon-sequestration potentials, as well as the provision of incentives and policies to translate management options into region- and soil-specific practices.

利用微生物回收和固定CO₂气体的生物固碳方法,成为解决“温室效应”这一重大环境问题的焦点,本研究目的是分离筛选固碳微生物菌株。利用无碳源无机培养基从活性污泥、沼液和设施土壤中分离筛选出以CO₂为碳源的菌株24株,选取其中生长较快的8株菌进行cbbL基因、形态观察、生理生化反应测定和16S rDNA测序分析,将测序结果在BlAST数据库中比对,进行固碳菌株的分子鉴定,并对其菌体含量和RubisCO酶活性进行比较。选取RubisCO酶活性最高的菌株C2-8R,进行土壤施用试验,通过土壤RubisCO酶活性的测定,确定分离筛选的固碳菌的固碳能力。研究表明,可通过无碳源培养基进行固碳微生物菌株的筛选,筛选的固碳菌分别隶属于假单胞菌属和嗜甲基菌属,并可通过RubisCO 酶活性来反映微生物的固碳能力。

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b–3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

Innovative fermentation processes are necessary for the cost-effective production of bulk chemicals from renewable resources. Current microbial processes are either anaerobic processes, with high yield and productivity, or less-efficient aerobic processes. Oxygen utilization plays an important role in energy generation and redox metabolism that is necessary for product formation. The aerobic productivity, however, is relatively low because of rate-limiting volumetric oxygen transfer; whereas the product yield in the presence of oxygen is generally low because part of the substrate is completely oxidized to CO₂. Hence, new microbial conversion processes for the production of bulk chemicals should be anaerobic. In this opinion article, we describe different scenarios for the development of highly efficient microbial conversion processes for the anaerobic production of bulk chemicals.Copyright © 2010 Elsevier Ltd. All rights reserved.

It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data.The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

A novel methanotroph, designated strain E10T, was isolated from a rice paddy field in Uruguay. Strain E10T grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30–35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2T (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10T formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14LT, respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C16 : 0 (62.05 %). Thus, strain E10T ( = JCM 16910T  = DSM 23452T) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed.

Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.

\n Methylosinus trichosporium\n OB3b (for “oddball” strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from\n M. trichosporium\n OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the\n M. trichosporium\n OB3b genome is the first reported from a member of the\n Methylocystaceae\n family in the order\n Rhizobiales\n.\n

Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names “Candidatus Methanoperedens manganicus” and “Candidatus Methanoperedens manganireducens” for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.© 2024. The Author(s).

Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane. Long-term performance data, in conjunction with the 13C- and 57Fe-labelling batch experiments, demonstrated that AOM was coupled to Fe(III) reduction to Fe(II) in this bioreactor. Metagenomic analysis showed that this archaeon belongs to a novel genus within family Candidatus Methanoperedenaceae, and possesses genes encoding the “reverse methanogenesis” pathway, as well as multi-heme c-type cytochromes which are hypothesised to facilitate dissimilatory Fe(III) reduction. Metatranscriptomic analysis revealed upregulation of these genes, supporting that this archaeon can independently mediate AOM using Fe(III) as the terminal electron acceptor. We propose the name Candidatus “Methanoperedens ferrireducens” for this microorganism. The potential role of “M. ferrireducens” in linking the carbon and iron cycles in environments rich in methane and iron should be investigated in future research.

\n Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH\n 4\n ) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH\n 4\n oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and\n 13\n CH\n 4\n -DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH\n 4\n oxidation in supporting denitrification. Our results reveal positive relationships between CH\n 4\n oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH\n 4\n and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover,\n 13\n CH\n 4\n -DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating\n 13\n C, which are mostly belonged to\n Rubrivivax\n,\n Magnetospirillum\n, and\n Bradyrhizobium\n. Combined analyses of\n 13\n C-metagenome-assembled genomes and\n 13\n C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH\n 4\n oxidation, for the coupling of CH\n 4\n oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH\n 4\n oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.\n

Microbial composition and functions in the rhizosphere-an important microbial hotspot-are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin-antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11-182%), while genes involved in nitrification were strongly depleted.© 2022. The Author(s).