Thermal responses of dissolved organic matter under global change.

The diversity of intrinsic traits of different organic matter molecules makes it challenging to predict how they, and therefore the global carbon cycle, will respond to climate change. Here we develop an indicator of compositional-level environmental response for dissolved organic matter to quantify the aggregated response of individual molecules that positively and negatively associate with warming. We apply the indicator to assess the thermal response of sediment dissolved organic matter in 480 aquatic microcosms along nutrient gradients on three Eurasian mountainsides. Organic molecules consistently respond to temperature change within and across contrasting climate zones. At a compositional level, dissolved organic matter in warmer sites has a stronger thermal response and shows functional reorganization towards molecules with lower thermodynamic favorability for microbial decomposition. The thermal response is more sensitive to warming at higher nutrients, with increased sensitivity of up to 22% for each additional 1 mg L-1 of nitrogen loading. The utility of the thermal response indicator is further confirmed by laboratory experiments and reveals its positive links to greenhouse gas emissions.

Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil.

BACKGROUND: Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic investigation into the mechanism of straw decomposition in a paddy soil. RESULTS: The chemical analysis of 16-day soil microcosm incubation revealed that straw decomposition could be divided into two stages based on the dynamics of methane, short chain fatty acids, dissolved organic carbon and monosaccharides. Metagenomic analysis revealed that the relative abundance of glucoside hydrolase (GH) encoding genes for cellulose decomposition increased rapidly during the initial stage (3-7 days), while genes involved in hemicellulose decomposition increased in the later stage (7-16 days). The increase of cellulose GH genes in initial stage was derived mainly from Firmicutes while Bacteroidota contributed mostly to the later stage increase of hemicellulose GH genes. Flagella assembly genes were prevalent in Firmicutes but scarce in Bacteroidota. Wood-Ljungdahl pathway (WLP) was present in Firmicutes but not detected in Bacteroidota. Overall, Bacteroidota contained the largest proportion of total GHs and the highest number of carbohydrate active enzymes gene clusters in our paddy soil metagenomes. The strong capacity of the Bacteroidota phylum to degrade straw polymers was specifically attributed to Bacteroidales and Chitinophagales orders, the latter has not been previously recognized. CONCLUSIONS: This study revealed a collaborating sequential contribution of microbial taxa and functional genes in the decomposition of straw residues in a paddy soil. Firmicutes with the property of mobility, WLP and cellulose decomposition could be mostly involved in the initial breakdown of straw polymers, while Bacteroidota became abundant and possibly responsible for the decomposition of hemicellulosic polymers during the later stage.

Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism.

The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.

Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments.

Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms.

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Coupling methanogenesis with iron reduction by acetotrophic Methanosarcina mazei zm-15.

Application of ferric iron is conventionally considered to inhibit methanogenesis in anoxic environments. Here we show that Methanosarcina mazei zm-15, a strain isolated from the natural wetland of Tibetan plateau, is capable of Fe(III) reduction, which significantly promotes its growth and methanogenesis. We grew Ms. mazei zm-15 in a medium containing acetate supplemented with Fe(III) in ferric citrate or ferrihydrite and to some cultures anthraquinone-2,6-disulfonate (AQDS) was applied as an electron shuttle. The reduction of Fe(III) species occurred immediately. Ferric citrate was more readily reduced than ferrihydrite. The X-ray diffraction spectra analysis showed the formation of magnetite from ferrihydrite and amorphous reduced products from ferrihydrite plus AQDS. The analysis of protein contents revealed that Fe(III) reduction contributed 36%-46% of the cell growth. The growth yield, estimated as protein increment per acetate consumed for Fe(III) reduction, increased by 20- to 30-fold compared with methanogenesis, which is in consistence with the difference in free energy available by Fe(III) reduction relative to methanogenesis. We propose that the outer-surface multiheme c-type cytochrome predicted from Ms. mazei zm-15 genome serves as the terminal reductase with the energy-converting hydrogenase and F420 H2 dehydrogenase involved in electron transport chain for Fe(III) reduction. The findings shed a light to better understand the ecophysiology of Methanosarcina in anaerobic environments.

Rare Species-Driven Diversity-Ecosystem Multifunctionality Relationships are Promoted by Stochastic Community Assembly.

The relative functional importance of rare and abundant species in driving relationships between biodiversity and ecosystem functions (BEF) remains unknown. Here, we investigated the functional roles of rare and abundant species diversity (multitrophic soil organism groups) on multifunctionality derived from 16 ecosystem functions in 228 agricultural fields relating to soil and crop health. The results revealed that the diversity of rare species, rather than of abundant species, was positively related to multifunctionality. Abundant taxa tended to maintain a larger number of functions than rare taxa, while rare subcommunity contributed more phylotypes supporting to the single ecosystem functions. Community assembly processes were closely related to the ecosystem functional performance of soil biodiversity, only observed in rare subcommunity. Higher relative contributions of stochastic assembly processes promoted the positive effects of diversity of rare taxa on multifunctionality, while reducing their diversity and multifunctionality overall. Our results highlight the importance of rare species for ecosystem multifunctionality and elucidate the linkage between ecological assembly processes and BEF relationships. IMPORTANCE The relative functional importance of rare and abundant species in driving relationships between biodiversity and ecosystem functions remains unknown. Here, we highlighted the importance of rare species for ecosystem multifunctionality. In addition, community assembly processes were closely related to the ecosystem functional performance of soil biodiversity in rare subcommunity. Stochastic assembly processes promoted the positive effects of diversity of rare taxa on multifunctionality, while reducing their diversity and multifunctionality overall. This study expands current understanding of the mechanisms underpinning the relationships between biodiversity and ecosystem functions and suggests that stochastic community assembly enhances BEF relationships.

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems.

Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity-ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.

Growth Coordination Between Butyrate-Oxidizing Syntrophs and Hydrogenotrophic Methanogens.

Syntrophy is a thermodynamically required mutualistic cooperation between fatty acid-oxidizing bacteria and methanogens that plays the important role in organic decomposition and methanogenesis in anoxic environments. In this study, three experiments were conducted to evaluate the cell-to-cell interaction in a thermophilic coculture consisting of Syntrophothermus lipocalidus and Methanocella conradii and a mesophilic coculture consisting of Syntrophomonas wolfei and Methanococcus maripaludis. First, syntrophs and methanogens were inoculated at different initial cell ratios to evaluate the growth synchronization. The quantitative PCR analysis revealed that the organism with a lower relative abundance at the beginning always grew faster, and the cell ratio converged over time to relative constant values in both the thermophilic and mesophilic cocultures. Next, intermittent ultrasound and constant shaking treatments were used to evaluate the influence of physical disturbance on microbial aggregation in the mesophilic coculture. The fluorescence in situ hybridization and scanning electron microscopy revealed that the tendency of syntrophic aggregation was not affected by the physical disturbances, although the activity was slightly depressed. Syntrophomonas dominated in the initial microbial aggregates, which, however, did not grow until Methanococcus was attached and increased to a significant extent, indicating the local growth synchronization during the formation and maturation of syntrophic aggregates. Last, microfluidic experiments revealed that whether or not Syntrophomonas or Methanococcus was loaded first, the second organism preferred moving to the place where the first organism was located, suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus. Collectively, our study demonstrated the growth synchronization and cell-to-cell attraction between the butyrate-oxidizing bacteria and methanogens for optimizing the syntrophic cooperation.

Response of Methanogen Communities to the Elevation of Cathode Potentials in Bioelectrochemical Reactors Amended with Magnetite.

Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO2 to CH4. Setting low cathode potentials is essential for this process. In this study, we tested if magnetite, an iron oxide mineral widespread in the environment, can facilitate the adaptation of methanogen communities to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from paddy field soil. We elevated cathode potentials stepwise from the initial -0.6 V versus the standard hydrogen electrode (SHE) to -0.5 V and then to -0.4 V over the 130 days of acclimation. Only weak current consumption and CH4 production were observed in the bioreactors without magnetite. However, significant current consumption and CH4 production were recorded in the magnetite bioreactors. The robustness of electroactivity of the magnetite bioreactors was not affected by the elevation of cathode potentials from -0.6 V to -0.4 V. However, the current consumption and CH4 production were halted in the bioreactors without magnetite when the cathode potentials were elevated to -0.4 V. Methanogens related to Methanospirillum were enriched on the cathode surfaces of magnetite bioreactors at -0.4 V, while Methanosarcina relatively dominated in the bioreactors without magnetite. Methanobacterium also increased in the magnetite bioreactors but stayed off electrodes at -0.4 V. Apparently, the magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite, Methanospirillum spp. can adapt to the high cathode potentials, performing efficient electromethanogenesis. IMPORTANCE Converting CO2 to CH4 through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. In this study, we tested if magnetite, a conductive iron mineral, can facilitate the adaptation of methanogens to the elevation of cathode potentials. In two-chamber reactors constructed by using inoculants obtained from paddy field soil, biocathodes developed robustly in the presence of magnetite, whereas only weak activities in CH4 production and current consumption were observed in the bioreactors without magnetite. The elevation of cathode potentials did not affect the robustness of electroactivity of the magnetite bioreactors over the 130 days of acclimation. Methanospirillum strains were identified as the key methanogens associated with the cathode surfaces during the operation at high potentials. The findings reported in this study shed new light on the adaptation of methanogen communities to the elevated cathode potentials in the presence of magnetite.

Thermodynamics shapes the biogeography of propionate-oxidizing syntrophs in paddy field soils.

Soil biogeochemical processes are not only gauged by the dominant taxa in the microbiome but also depend on the critical functions of its 'rare biosphere' members. Here, we evaluated the biogeographical pattern of 'rare biosphere' propionate-oxidizing syntrophs in 113 paddy soil samples collected across China. The relative abundance, activity and growth potential of propionate-oxidizing syntrophs were analysed to provide a panoramic view of syntroph biogeographical distribution at the continental scale. The relative abundances of four syntroph genera, Syntrophobacter, Pelotomaculum, Smithella and Syntrophomonas were significantly greater at the warm low latitudes than at the cool high latitudes. Correspondingly, propionate degradation was faster in the low latitude soils compared with the high latitude soils. The low rate of propionate degradation in the high latitude soils resulted in a greater increase of the total syntroph relative abundance, probably due to their initial low relative abundances and the longer incubation time for propionate consumption. The mean annual temperature (MAT) is the most important factor shaping the biogeographical pattern of propionate-oxidizing syntrophs, with the next factor being the soil's total sulfur content (TS). We suggest that the effect of MAT is related to the thermodynamic conditions, in which the endergonic constraint of propionate oxidation is leveraged with the increase of MAT. The TS effect is likely due to the ability of some propionate syntrophs to facultatively perform sulfate respiration.

Putative Extracellular Electron Transfer in Methanogenic Archaea.

It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H2 or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

BACKGROUND: Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. RESULTS: The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. CONCLUSIONS: These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.

Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields.

Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro-ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large-scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change.

Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems.

The factors determining stochastic and deterministic processes that drive microbial community structure, specifically the balance of abundant and rare bacterial taxa, remain underexplored. Here we examined biogeographic patterns of abundant and rare bacterial taxa and explored environmental factors influencing their community assembly processes in agricultural fields across eastern China. More phylogenetic turnover correlating with spatial distance was observed in abundant than rare sub-communities. Homogeneous selection was the main assembly process for both the abundant and rare sub-communities; however, the abundant sub-community was more tightly clustered phylogenetically and was more sensitive to dispersal limitations than the rare sub-community. Rare sub-community of rice fields and abundant sub-community of maize fields were more governed by stochastic assembly processes, which showed higher operational taxonomic unit richness. We propose a conceptual paradigm wherein soil pH and mean annual temperature mediate the assembly of the abundant and rare sub-communities respectively. A higher soil pH leads to deterministic assembly of the abundant sub-community. For the rare sub-community, the dominance of stochasticity in low-temperature regions indicates weaker niche-based exclusion and the arrival of more evolutionary lineages. These findings suggest that the community assembly processes for abundant and rare bacterial taxa are dependent on distinct environmental variables in agro-ecosystems.

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China.

Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.

Redox cycling of Fe(II) and Fe(III) in magnetite accelerates aceticlastic methanogenesis by Methanosarcina mazei.

It has been recently shown that magnetite nanoparticles (nanoFe3 O4 ) can facilitate methanogenic syntrophy but the effect of magnetite on methanogenesis alone remains elusive. Here we show that aceticlastic methanogenesis by Methanosarcina mazei is accelerated by magnetite and is correlated with the redox cycling of structural Fe(II) and Fe(III) in the mineral. An enrichment and its closest pure culture relative, Ms. mazei zm-15, both obtained from a natural wetland of the Tibetan plateau were tested in this experiment. The Fe(II) to Fe(III) ratios in magnetite, as measured by multiple approaches, show an initial increase in both the methanogenic cultures and the blank preparations containing no microbes. The Fe(II)/Fe(III) ratio then displays a distinct decline followed by an increase towards the end of incubation only in the enrichment and pure culture cultivations. This redox cycling of magnetite is in accordance with the stimulation of aceticlastic methanogenesis. Microscopic observation reveals the precipitation of nanoFe3 O4 on methanogen cell surface. The genomic analysis predicts that in addition to electron transfer components essential for aceticlastic methanogenesis, Ms. mazei zm-15 contains an outer-surface multiheme c-type cytochrome (MHC) and a few function-unknown surface proteins that harbour monoheme motif. We hypothesize that the redox cycling of nanoFe3 O4 delivers a positive influence via the MHC to the membrane electron transfer chain and hence promote the aceticlastic methanogenesis.

Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing.

Metatranscriptomics is a powerful tool for capturing gene expression patterns in microbial communities and investigating their responses to environmental conditions. Stable isotope probing (SIP) is a method to target specific functional groups of microorganisms in environmental samples. The combination of RNA-SIP with metatranscriptomic analysis enhances the detection and identification of mRNA from target microorganisms. In this chapter we provide a protocol for RNA-SIP, mRNA enrichment, and mRNA preparation for high-throughput sequencing using an example of targeting methanotrophs in rice field soil.

Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances.

Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.

Sulfate-reducing bacteria and methanogens are involved in arsenic methylation and demethylation in paddy soils.

Microbial arsenic (As) methylation and demethylation are important components of the As biogeochemical cycle. Arsenic methylation is enhanced under flooded conditions in paddy soils, producing mainly phytotoxic dimethylarsenate (DMAs) that can cause rice straighthead disease, a physiological disorder occurring widely in some rice growing regions. The key microbial groups responsible for As methylation and demethylation in paddy soils are unknown. Three paddy soils were incubated under flooded conditions. DMAs initially accumulated in the soil porewater, followed by a rapid disappearance coinciding with the production of methane. The soil from a rice straighthead disease paddy field produced a much larger amount of DMAs than the other two soils. Using metabolic inhibition, quantification of functional gene transcripts, microbial enrichment cultures and 13C-labeled DMAs, we show that sulfate-reducing bacteria (SRB) and methanogenic archaea are involved in As methylation and demethylation, respectively, controlling the dynamics of DMAs in paddy soils. We present a model of As biogeochemical cycle in paddy soils, linking the dynamics of changing soil redox potential with arsenite mobilization, arsenite methylation and subsequent demethylation driven by different microbial groups. The model provides a basis for controlling DMAs accumulation and incidence of straighthead disease in rice.