Products from Photolysis Reactions of Tetracycline Mediated by Clay and Humic Substance Induce Contrasting Expressions of Target Resistance Genes.

Phototransformation is a key process affecting the fate of many antibiotics in the environment, but little is known about whether their photoproducts exert selective pressure on bacteria by inducing antibiotic resistance genes (ARGs). Here, we examined the expression of tetracycline resistance gene tet(M) of a fluorescent Escherichia coli whole-cell bioreporter influenced by the phototransformation of tetracycline. The presence of suspended smectite clay (montmorillonite or hectorite, 1.75 g/L) or dissolved humic substance (Pahokee Peat humic acid or Pahokee peat fulvic acid, 10 mg C/L) in aqueous solutions markedly facilitated the transformation of tetracycline (initially at 400 µg/L) with half-life shortened by 1.4-2.6 times. Despite the similar phototransformation ratios (80-90%) of the total loaded tetracycline after 60 min irradiation, the decreased ratios of cell fluorescence intensity (which was proportional to the expression amount of ARG tet(M)) were much higher with the two clays (94 and 93%) than with the two humic substances (44 and 69%) when compared to the respective dark controls. As illustrated by mass spectroscopic and chemical analyses, tetracycline was proposed to be mainly transformed to amide (ineffective in inducing ARGs) with the presence of clays by reaction with self-photosensitized singlet oxygen (1O2), while the humic substances might catalyze the production of another two demethylated and/or deaminated compounds (still effective in inducing ARGs) in addition to the amide compound via reaction with triplet excited state dissolved organic matter (3DOM*). As clay minerals and humic substances are important soil constituents and ubiquitously present in surface environments, the observed clay and humic-dependent photooxidation pathways of tetracycline and the differing selective pressures of the associated products highlight the need for monitoring the transformation compounds of antibiotics and provide critical insight into the development of antibiotic treatment protocols.

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.

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.

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.

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.

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.

Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments.

Syntrophic interaction occurs during anaerobic fermentation of organic substances forming methane as the final product. H2 and formate are known to serve as the electron carriers in this process. Recently, it has been shown that direct interspecies electron transfer (DIET) occurs for syntrophic CH4 production from ethanol and acetate. Here, we constructed paddy soil enrichments to determine the involvement of DIET in syntrophic butyrate oxidation and CH4 production. The results showed that CH4 production was significantly accelerated in the presence of nanoFe3 O4 in all continuous transfers. This acceleration increased with the increase of nanoFe3 O4 concentration but was dismissed when Fe3 O4 was coated with silica that insulated the mineral from electrical conduction. NanoFe3 O4 particles were found closely attached to the cell surfaces of different morphology, thus bridging cell connections. Molecular approaches, including DNA-based stable isotope probing, revealed that the bacterial Syntrophomonadaceae and Geobacteraceae, and the archaeal Methanosarcinaceae, Methanocellales and Methanobacteriales, were involved in the syntrophic butyrate oxidation and CH4 production. Among them, the growth of Geobacteraceae strictly relied on the presence of nanoFe3 O4 and its electrical conductivity in particular. Other organisms, except Methanobacteriales, were present in enrichments regardless of nanoFe3 O4 amendment. Collectively, our study demonstrated that the nanoFe3 O4 -facilitated DIET occurred in syntrophic CH4 production from butyrate, and Geobacter species played the key role in this process in the paddy soil enrichments.

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate.

Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.

Response of a rice paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses.

Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms' adaptation to low H2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F420-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii. We propose that Methanocella methanogens cope with low H2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formatedependent methanogenesis.

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.

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil.

The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differences in the distribution of bacterial and archaeal ammonia oxidizers, and of Nitrobacter-like and Nitrospira-like nitrite oxidizers were found in the different compartments of planted paddy soil indicating niche differentiation. In bulk soil, ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) were at low abundance and displayed no activity, but in surface soil their activity and abundance was high. Nitrite oxidation in surface soil was dominated by Nitrospira spp. By contrast, ammonia-oxidizing Thaumarchaeota and Nitrobacter spp. seemed to dominate nitrification in rhizospheric soil and on rice roots. In contrast to soil compartment, the level of N fertilization and the time point of sampling had only little effect on the abundance, composition and activity of the nitrifying communities. The results of our study show that in rice fields population dynamics and activity of nitrifiers is mainly differentiated by the soil compartments rather than by nitrogen amendment or season.

Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil.

The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.

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.

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.

Complete genome sequence of a thermophilic methanogen, Methanocella conradii HZ254, isolated from Chinese rice field soil.

Members of the order Methanocellales play a key role in methane emissions in paddy fields. Because of their slow growth and fastidious culture conditions, pure cultures are difficult to isolate and have been unavailable until recently. Here we report the complete genome sequence of a novel isolate in this group, Methanocella conradii strain HZ254.

Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil.

Intermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogen mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that both mcrA gene copies and mcrA transcripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance of mcrA genes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription of mcrA genes was reduced to a greater extent than the abundance of mcrA genes, resulting in very low mcrA transcript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance of mcrA transcripts than of mcrA genes in rice field soil.

Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions.

Propionate is one of the major intermediary products in the anaerobic decomposition of organic matter in wetlands and paddy fields. Under methanogenic conditions, propionate is decomposed through syntrophic interaction between proton-reducing and propionate-oxidizing bacteria and H(2)-consuming methanogens. Temperature is an important environmental regulator; yet its effect on syntrophic propionate oxidation has been poorly understood. In the present study, we investigated the syntrophic oxidation of propionate in a rice field soil at 15°C and 30°C. [U-(13)C]propionate (99 atom%) was applied to anoxic soil slurries, and the bacteria and archaea assimilating (13)C were traced by DNA-based stable isotope probing. Syntrophobacter spp., Pelotomaculum spp., and Smithella spp. were found significantly incorporating (13)C into their nucleic acids after [(13)C]propionate incubation at 30°C. The activity of Smithella spp. increased in the later stage, and concurrently that of Syntrophomonas spp. increased. Aceticlastic Methanosaetaceae and hydrogenotrophic Methanomicrobiales and Methanocellales acted as methanogenic partners at 30°C. Syntrophic oxidation of propionate also occurred actively at 15°C. Syntrophobacter spp. were significantly labeled with (13)C, whereas Pelotomaculum spp. were less active at this temperature. In addition, Methanomicrobiales, Methanocellales, and Methanosarcinaceae dominated the methanogenic community, while Methanosaetaceae decreased. Collectively, temperature markedly influenced the activity and community structure of syntrophic guilds degrading propionate in the rice field soil. Interestingly, Geobacter spp. and some other anaerobic organisms like Rhodocyclaceae, Acidobacteria, Actinobacteria, and Thermomicrobia probably also assimilated propionate-derived (13)C. The mechanisms for the involvement of these organisms remain unclear.

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.

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.

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.