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

Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii

Microbial syntrophy is a thermodynamically-based cooperation between microbial partners that share the small amounts of free energy for anaerobic growth. To gain insights into the mechanism by which syntrophic microorganisms coordinate their metabolism, we constructed cocultures of propionate-oxidizing Pelotomaculum thermopropionicum and hydrogenotrophic Methanocella conradii and compared them to monocultures. Transcriptome analysis was performed on these cultures using strand-specific mRNA sequencing (RNA-Seq). The results showed that in coculture both P. thermopropionicum and M. conradii significantly upregulated the expression of genes involved in catabolism but downregulated those for anabolic biosynthesis. Specifically, genes coding for the methylmalonyl-CoA pathway in P. thermopropionicum and key genes for methanogenesis in M. conradii were substantially upregulated in coculture compared to monoculture. The putative flavin-based electron bifurcation/confurcation systems in both organisms were also upregulated in coculture. Formate dehydrogenase encoding genes in both organisms were markedly upregulated, indicating that formate was produced and utilized by P. thermopropionicum and M. conradii, respectively. The inhibition of syntrophic activity by formate and 2-bromoethanesulphonate (2-BES) but not H2/CO2 also suggested that formate production was used by P. thermopropionicum for the recycling of intracellular redox mediators. Finally, flagellum-induced signal transduction and amino acids exchange was upregulated for syntrophic interactions. Together, our study suggests that syntrophic organisms employ multiple strategies including global metabolic shift, utilization of electron bifurcation/confurcation and employing formate as an alternate electron carrier to optimize their metabolisms for syntrophic growth

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

NanoFe3O4 as Solid Electron Shuttles to Accelerate Acetotrophic Methanogenesis by Methanosarcina barkeri

Magnetite nanoparticles (nanoFe3O4) have been reported to facilitate direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens thereby improving syntrophic methanogenesis. However, whether or how nanoFe3O4 affects acetotrophic methanogenesis remain unknown. Herein, we demonstrate the unique role of nanoFe3O4 in accelerating methane production from direct acetotrophic methanogenesis in Methanosarcina-enriched cultures, which was further confirmed by pure cultures of Methanosarcina barkeri. Compared with other nanomaterials of higher electrical conductivity such as carbon nanotubes and graphite, nanoFe3O4 with mixed valence Fe(II) and Fe(III) had the most significant stimulatory effect on methane production, suggesting its redox activity rather than electrical conductivity led to enhanced methanogenesis by M. barkeri. Cell morphology and spectroscopy analysis revealed that nanoFe3O4 penetrated into the cell membrane and cytoplasm of M. barkeri. These results provide the unprecedented possibility that nanoFe3O4 in the cell membrane of methanogens serve as electron shuttles to facilitate intracellular electron transfer and thus enhance methane production. This work has important implications not only for understanding the mechanisms of mineral-methanogen interaction but also for optimizing engineered methanogenic processes

Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil

BACKGROUND: Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.). METHODOLOGY/PRINCIPAL FINDINGS: By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254(T) was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAE(T) was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4-2.8 µm long and by 0.2-0.3 µm in width. They grew at 37-60 °C (optimally at 55 °C) and salinity of 0-5 g NaCl l(-1) (optimally at 0-1 g NaCl l(-1)). The pH range for growth was 6.4-7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5-7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254(T) utilized H(2)/CO(2) but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254(T) and SANAE(T) were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254(T) as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254(T) ( = CGMCC 1.5162(T) = JCM 17849(T) = DSM 24694(T)). CONCLUSIONS/SIGNIFICANCE: Strain HZ254(T) could potentially serve as an excellent laboratory model for studying Methanocellales due to its fast growth and consistent cultivability

Structure and function of methanogenic microbial communities in soils from flooded rice and upland soybean fields from Sanjiang plain, NE China.

About 50 years ago, most of the natural wetlands in northeast China, the Sanjiang plain, were converted to either flooded rice fields or to upland soybean fields. After the conversion, natural wetland soils were either managed as artificial wetland or as drained upland resulting in soil microbial community changes. The purpose of our study was to understand how methanogenic microbial communities and their functions had changed in the two different soils upon conversion, and whether these communities now exhibit different resistance/resilience to drying and rewetting. Therefore, we determined function, abundance and composition of the methanogenic archaeal and bacterial communities in two soils reclaimed from a Carex wetland 25 years ago. We incubated the soils under anoxic conditions and measured the rates and pathways of CH4 production by analyzing concentration and ?13C of CH4 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also analyzed the abundance of bacterial and archaeal 16S rRNA genes, and of mcrA (coding for a subunit of the methyl coenzyme M reductase) using qPCR. The composition of the archaeal and bacterial 16S rRNA genes was determined by using MiSeq illumina sequencing. Our results showed clear differences in structure and function of methanogenic archaeal communities in rice field soil versus upland soil. Furthermore, in both soils composition of bacteria and archaea changed after artificial drying and became less diverse. The archaeal and bacterial signature species in the two soils were also different. However, functional changes were similar, with rates of CH4 production and contribution of aceticlastic methanogenesis decreasing upon drying and rewetting in both soils

Conductive Fe3O4 nanoparticles accelerate syntrophic methane production from butyrate oxidation in two different lake sediments

Syntrophic methanogenesis is an essential link in the global carbon cycle and a key bioprocess for the disposal of organic waste and production of biogas. Recent studies suggest direct interspecies electron transfer (DIET) is involved in electron exchange in methanogenesis occurring in paddy soils, anaerobic digesters and specific co-cultures with Geobacter. In this study, we evaluate the possible involvement of DIET in the syntrophic oxidation of butyrate in the enrichments from two lake sediments (an urban lake and a natural lake). The results showed that the production of CH4 was significantly accelerated in the presence of conductive nanoscale Fe3O4 or carbon nanotubes (CNTs) in the sediment enrichments. Observations made with fluorescence in situ hybridization (FISH) and scanning electron microscope (SEM) indicated that microbial aggregates were formed in the enrichments. It appeared that the average cell-to-cell distance in aggregates in nanomaterial-amended enrichments was larger than that in aggregates in the non-amended control. These results suggested that DIET-mediated syntrophic methanogenesis could occur in the lake sediments in the presence of conductive materials. Microbial community analysis of the enrichments revealed that the genera of Syntrophomonas, Sulfurospirillum, Methanosarcina and Methanoregula were responsible for syntrophic oxidation of butyrate in lake sediment samples. The mechanism for the conductive-material-facilitated DIET in butyrate syntrophy deserves further investigation

Table_1_Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii.PDF

<p>Microbial syntrophy is a thermodynamically-based cooperation between microbial partners that share the small amounts of free energy for anaerobic growth. To gain insights into the mechanism by which syntrophic microorganisms coordinate their metabolism, we constructed cocultures of propionate-oxidizing Pelotomaculum thermopropionicum and hydrogenotrophic Methanocella conradii and compared them to monocultures. Transcriptome analysis was performed on these cultures using strand-specific mRNA sequencing (RNA-Seq). The results showed that in coculture both P. thermopropionicum and M. conradii significantly upregulated the expression of genes involved in catabolism but downregulated those for anabolic biosynthesis. Specifically, genes coding for the methylmalonyl-CoA pathway in P. thermopropionicum and key genes for methanogenesis in M. conradii were substantially upregulated in coculture compared to monoculture. The putative flavin-based electron bifurcation/confurcation systems in both organisms were also upregulated in coculture. Formate dehydrogenase encoding genes in both organisms were markedly upregulated, indicating that formate was produced and utilized by P. thermopropionicum and M. conradii, respectively. The inhibition of syntrophic activity by formate and 2-bromoethanesulphonate (2-BES) but not H₂/CO₂ also suggested that formate production was used by P. thermopropionicum for the recycling of intracellular redox mediators. Finally, flagellum-induced signal transduction and amino acids exchange was upregulated for syntrophic interactions. Together, our study suggests that syntrophic organisms employ multiple strategies including global metabolic shift, utilization of electron bifurcation/confurcation and employing formate as an alternate electron carrier to optimize their metabolisms for syntrophic growth.</p

Inhibitory effects of ammonia on syntrophic propionate oxidation in anaerobic digester sludge

Syntrophic propionate oxidation (SPO) coupled with methanogenesis is often inhibited under high ammonium concentrations in anaerobic digesters. However, the inhibitory mechanism remains poorly understood. We conducted two independent laboratory experiments with a swine manure digester sludge. In experiment I, RNA-based stable isotope probing (SIP) was applied to determine the active players of both bacteria and methanogens involved in SPO under different ammonium concentrations (0, 3 and 7 g NE4+-N L-1). In experiment II, the dynamics of the bacterial community under ammonia stress was monitored using the 16S rRNA pyrosequencing and quantitative PCR under similar conditions as in experiment I but without the addition of external propionate. An additional higher ammonium treatment (10 g L-1) was applied in experiment II to maximize the ammonia stress. We identified that the Smithella bacteria and the Methanosaetaceae and Methanospirillaceae archaea were the most active players involved in SPO and methanogenesis. We revealed that Smithella, Methanosaetaceae and Methanospirillaceae were moderately and severely inhibited at 3 and 7-10 g NH4+-N L-1, respectively. However, the fermentative bacteria appeared to be more tolerant to ammonia stress. The microbial responses were corroborated with the accumulation of VFAs and the repression of methanogenesis under high ammonium conditions. (C) 2018 Elsevier Ltd. All rights reserved