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The rhizosphere and phyllosphere of plants are home to a diverse range of microorganisms that play pivotal roles in ecosystem services. Consequently, plant growth‐promoting bacteria (PGPB) are extensively utilized as inoculants to enhance plant growth and boost productivity. Despite this, the interactions between the rhizosphere and phyllosphere, which are influenced by PGPB inoculation, have not been thoroughly studied to date. In this study, we inoculated Bacillus velezensis SQR9, a PGPB, into the bulk soil, rhizosphere or phyllosphere, and subsequently examined the bacterial communities in the rhizosphere and phyllosphere using amplicon sequencing. Our results revealed that PGPB inoculation increased its abundance in the corresponding compartment, and all treatments demonstrated plant growth promotion effects. Further analysis of the sequencing data indicated that the presence of PGPB exerted a more significant impact on bacterial communities in both the rhizosphere and phyllosphere than in the inoculation compartment. Notably, the PGPB stimulated similar rhizosphere‐beneficial microbes regardless of the inoculation site. We, therefore, conclude that PGPB can promote plant growth both directly and indirectly through the interaction between the rhizosphere and phyllosphere, leading to the enrichment of beneficial microorganisms. [ABSTRACT FROM AUTHOR]

Background and Aims: Understanding microbial compositions and functions in arable soils is crucial for effective agroecosystem management. While many studies have explored this topic, large-scale investigations are lacking, resulting in the absence of consistent and reliable patterns of communities and functions of soil microorganisms. Methods: To address this gap, we performed an integrated analysis of published sequencing data from the soils of three main arable fields: upland, paddy, and paddy-upland rotation. Results: Bacterial diversity (richness, Shannon) was highest in upland soils. Actinobacteria and Planctomycetes were enriched in upland soils, while Proteobacteria, Chloroflexi, and Nitrospirae preferred paddy and paddy-upland rotation soils. Bacteria in upland soils have a greater functional potential to decompose aromatic compounds, as well as for chitinolysis and ureolysis. Methanotrophy, methylotrophy, sulfur-related respiration, and most nitrogen metabolic processes were enriched in paddy fields. Bacteria in upland soils are characterized by increased dormancy potential and a faster response to resource input than those in paddy and paddy-upland rotation soils. Stochastic processes poorly contribute to the bacterial assembly in paddy soils, indicating strong environmental filtering due to anaerobic conditions. The spatial turnover in bacterial community composition was much faster than the functional potential, indicating high functional redundancy, especially in paddy soils. Edaphic factors were the major contributors to bacterial composition, whereas the cropland type influenced the predicted functions. Conclusions: Land use defines microbial composition, functional attributes, and ecological characteristics (e.g., dormancy potential, assembly processes, and functional redundancy). These findings deepen our knowledge of microbial biogeographic patterns in soils of agricultural ecosystems and provide new insights into sustainable cropland management. [ABSTRACT FROM AUTHOR]

The assembly of bacterial communities in the rhizosphere is well‐documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator–prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems. [ABSTRACT FROM AUTHOR]

[Display omitted] • Inoculation of thermophilic bacterial consortia promoted the compost efficiency. • P V , n/P III , n values revealed the humification degree in different treatments. • Core microbes drove the variations in compost temperature, TOC, TN, and HAC. • Microbial community functions were closely related to compost quality. The objective of this study was to investigate the potential effects of thermophilic bacterial consortia on compost efficiency and quality. The application of bacterial consortia resulted in an earlier onset of the thermophilic period (THP), an increased upper temperature limit, and an extended duration of the THP by 3–5 days compared to the control group (CK). Microbial inoculation significantly improved the efficiency of organic matter degradation, as well as the content of water-soluble nitrogen (WSN) and humic acid-carbon (HAC). In the case of consortium Ⅱ inoculation (T2), the activities of cellobiohydrolase, β-glucosidase, and protease were increased by 81.81 %, 70.13 %, and 74.09 % at the THP respectively compared to CK. During the maturation stage, T2 also exhibited the highest P V , n/P III , n value (1.33) and HAC content (39.53 mg·g−1), indicating that inoculation of consortium Ⅱ effectively promoted substrate maturity and product quality. Moreover, this inoculation effectively optimized the bacterial communities, particularly the growth of Planococcus, Chelatococcus, and Chelativorans during the composting, which were involved in carbon and nitrogen conversion or HAC synthesis. Carbohydrate and amino acid metabolism, and membrane transport were predominant in the consortia-inoculated samples, with an increased gene abundance, suggesting that inoculation contributed to promoting the biodegradation of lignocellulose and the exchange of favorable factors. In conclusion, this study demonstrates that inoculating thermophilic bacterial consortia has a positive impact on enhancing the resource utilization efficiency of agricultural waste and improving the quality of compost products. [ABSTRACT FROM AUTHOR]

Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1–2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats. [ABSTRACT FROM AUTHOR]

[Display omitted] • The mesocosm experiment was used to track bacterial community dynamics. • Organic amendments increase the bacterial diversity during drought stress. • Organic amendments increase the compositional resilience during rewetting. • Pathogen inhibition ability in NOF was enhanced after rewetting. • NOF possesses a strategy-balancing community during whole drought event. The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought. This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers. In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes. Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting. Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning. [ABSTRACT FROM AUTHOR]

Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability. [ABSTRACT FROM AUTHOR]

Summary: Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive.Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long‐term field experiment where continuous application of bio‐organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain.Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance.We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance. [ABSTRACT FROM AUTHOR]

Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules. [ABSTRACT FROM AUTHOR]

• Organic matter degradation and humification point to the maturation of compost. • Bacillales , Eurotiales and Glomerellales dominate bacterial and fungal communities. • Function of bacterial metabolism and fungal saprotroph jointly dominate composting. • Microbial community changed greatly at the second thermophilic period. • Synergistic effect of bacteria and fungi may depend on their metabolite exchange. While both bacteria and fungi are important for the degradation and humification of organic matter during composting, it is unclear to what extent their roles are associated with abiotic compost properties. This study evaluated changes in abiotic compost properties and the succession of bacterial and fungal communities during pig manure composting for 90 days. The compost rapidly reached thermophilic phase (>58 ℃), which lasted for 15 days. Both bacterial and fungal community compositions changed drastically during composting and while bacterial diversity increased, the fungal diversity decreased during the thermophilic phase of composting. Two taxa dominated both bacterial (Bacillales and Clostridiales) and fungal (Eurotiales and Glomerellales) communities and these showed alternating abundance fluctuations following different phases of composting. The abundance fluctuations of most dominant bacterial and fungal taxa could be further associated with decreases in the concentrations of fulvic acid, cellulose, hemicellulose and overall biodegradation potential in the compost. Moreover, bacterial predicted metabolic gene abundances dominated the first three phases of composting, while predicted fungal saprotrophic functional genes increased consistently, reaching highest abundances towards the end of composting. Finally, redundancy analysis (RDA) showed that changes in abiotic compost properties correlated with the bacterial community diversity and carbohydrate metabolism and fungal wood saprotrophic function. Together these results suggests that bacterial and fungal community succession was associated with temporal changes in abiotic compost properties, potentially explaining alternating taxa abundance patterns during pig manure composting. [ABSTRACT FROM AUTHOR]

Summary: A host‐plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host‐associated microbiota are poorly understood.Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties.Plant microhabitat, rather than subspecies type, was the major driver shaping plant‐associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root‐associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host‐plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms.Overall, bacterial microbiota is assembled by host‐plant interactions in a deterministic‐based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance. [ABSTRACT FROM AUTHOR]

Although interactions between plants and microbes at the plant–soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow‐ and fast‐growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient‐depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate‐treated soils, with similar responses observed for slow‐growing and fast‐growing plant exudate treatments. The fast‐growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow‐growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth. Here, we found that the fast‐growing stage root exudates induced higher nutrients mineralization resulted in better plant growth as compared to treatments with slow‐growing stage exudates and the controls. Plants appear to recruit specific beneficial microbiomes throughout their different growth phases, thereby tailoring microbial activities to meet increased nutrient demands during fast‐growing stages. [ABSTRACT FROM AUTHOR]

Soil microbial communities mix and interact, a widespread phenomenon known as community coalescence. However, in the context of different coalescence degrees, the effects and potential applicability of soil mixing on plant disease resistance have not been studied. Here, we mixed soils from two habitats (healthy and diseased soils) at different mixing ratios for watermelon planting. Rhizosphere soils were collected for amplicon sequencing to study the effects of different degrees of bacterial community coalescence on plant growth and disease resistance, as well as on the characteristics, network complexity and stability of rhizosphere microbial communities. Combined with network and cohesion analyses, we found that mixing in more healthy soil reduced the plant disease index and increased biomass by improving the stability and complexity of the network; positive cohesion, reflecting degree of cooperation, was also negatively correlated with the plant disease index. The rhizosphere from healthy soils enriched the core taxa, Nitrospirillum and Singulisphaera. These core taxa were significantly associated with disease suppression and important for regulating the positive cohesion and modularity of the networks. Overall, these findings revealed that the soil bacterial community coalescence enhanced the stability and complexity of the rhizobacterial network, simultaneously core taxa enhanced microbial potential cooperation and network complexity, ultimately enhancing plant health and biomass. Our results provide insights into the understanding of microbial community coalescence as a potentially effective mechanism for improving plant microbial community function and suggest promising new tools for improving plant fitness via mixing soil microbiota. • Community coalescence by soil mixing had positive effects on plant growth and disease-suppression. • More healthy soils resulted in higher positive cohesion and network stability and complexity. • Cooperative behaviours among taxa improved plant resistance to disease. • Core bacterial species strengthen microbial cooperation and network complexity. [ABSTRACT FROM AUTHOR]

Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere. [ABSTRACT FROM AUTHOR]

This study focused on the legacy effects of 8-year application of N (in gradient of 0, 140, 280, 470, and 660 kg N ha−1 year−1) on the bacterial community diversity, interactions, and assembly processes in the wheat rhizosphere. The rhizosphere bacterial α-diversity increased with the rate of historical N input, while it did not change at N addition rates of over 280 kg N ha−1 year−1. Historical N input clearly shifted the rhizosphere bacterial community composition, and soils with more N input were more dissimilar to those without N input. The net relatedness index (NRI) and nearest taxon index (NTI) analysis revealed that the rhizosphere bacterial communities in most samples were phylogenetically clustered, and the treatments with high N (> 470 kg N ha−1 year−1) showed higher levels of clustering than those with low N (< 140 kg N ha−1 year−1), indicating more environmental selection stress in soil with higher historical N input. Increased co-occurrence network size and connectivity were accompanied by increased aboveground biomass of wheat. Overall, with the increase in historical N input, the resulting legacy effects forced the bacterial community in the rhizosphere to undergo higher environmental selection pressure, and indirectly affected the complexity of wheat rhizosphere assemblages during subsequent crop growth. [ABSTRACT FROM AUTHOR]

Background: Rhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology. Results: There is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance. Conclusions: The dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability. [ABSTRACT FROM AUTHOR]

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant–bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe–pathogen and microbe–plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems. [ABSTRACT FROM AUTHOR]

Aims: Plant growth-promoting rhizobacteria (PGPR) substantially improve plant growth and health, but their effects on the succession of rhizosphere microbiota throughout the growth period triggered by pre-inoculation have not yet been considered. Methods: Pepper seedlings cultured from a bio-nursery substrate containing Bacillus velezensis NJAU-Z9 and ordinary nursery substrate were used in this study to evaluate the effects of pre-colonization of a PGPR strain at the seedling stage on yield enhancement. To elucidate the underlying mechanisms involved in the rhizosphere microbiota succession during the whole growth period and their association with yield enhancement, high-throughput sequencing combined with qPCR was conducted. Results: The results showed that, compared to the control without inoculation, pre-inoculation led to a steady yield enhancement in two-season field trials, as well as higher rhizosphere bacterial richness (Chao1) and diversity (Shannon-Wiener). The plant growth stage as the first driving factor, followed by pre-colonization drove the variations of the rhizosphere microbial community composition according to multivariate regression tree analysis and principal coordinate analysis. Variance partitioning analysis (VPA) and Mantel test results showed that the previous plant growth period induced variations in the fungal and bacterial communities at the next stage. Compared to the seedling and flowering stages, the mature-stage microbial community showed a higher degree of explanation of yield enhancement. Additionally, pre-inoculation led to distinctive rhizosphere microbiota succession compared to the control, due to alteration of the initial community. The heat map analysis showed that the rhizosphere microbiota was related to crop yield. In addition to Bacillus velezensis NJAU-Z9, which showed stable abundance in the pepper rhizosphere, stable higher relative abundance of the bacterial genera Sphingomonas, Sphingopyxis, Bradyrhizobium, Chitinophaga, Dyadobacter, Streptomyces, Lysobacter, Pseudomonas and Rhizomicrobium, and the fungal genera Cladorrhinum, Cladosporium and Aspergillus throughout the growth period induced by pre-colonization was associated with yield enhancement. Conclusions: Overall, we conclude that pre-colonization with PGPR changed the initial rhizosphere microbiota and that the plant was triggered to further select distinctive microbes to form unique rhizosphere microbial consortia at the later growth stages, which resulted in plant growth promotion. [ABSTRACT FROM AUTHOR]

Although the precipitation and dissolution of iron (Fe)-containing-minerals are driven by microbially-mediated iron-redox cycling, we still have a limited understanding of complex response of such microbial communities to fertilisation. Here, using chemical and synchrotron-based spectral analyses, we show that the distribution of poorly crystalline Fe minerals and crystalline Fe minerals is different in organically- and inorganically-fertilised soils, and that compared to no fertilisation (Control), Fe redox cycling bacteria were present at higher abundance and diversity in organically-fertilised soils but lower in inorganically-fertilised soil. During Fe(III) reduction, Geobacter were important active Fe(III) reducers, with a higher relative abundance in both organically- and inorganically-fertilised soils than in Control, and their higher abundance was responsible for greater dissolution of ferrihydrite in inorganically-fertilised soil than in organically-fertilised soil. However, during the Fe(II) oxidation, Pseudomonas and Anaerolinea were more abundant, and produced higher levels of poorly crystalline Fe oxides under organic fertilisation. Thus, for the first time, we demonstrate that inorganic and organic fertilisation regimes have contrasting effects on the Fe redox bacterial communities, which then influence Fe cycling in soils. [ABSTRACT FROM AUTHOR]

Community diversity affects the survival of newly introduced species via resource competition. Competitive interactions can be modulated by resource availability and we hypothesized that this may alter biodiversity-invasion relationships. To study this, we assessed the growth of a bacterial invader, Ralstonia solanacearum, when introduced into communities comprised of one to five closely related resident species under different resource concentrations. The invader growth was then examined as a function of resident community richness, species composition and resource availability. We found that the relative density of the invader was reduced by increasing resident community richness and resource availability. Mechanistically, this could be explained by changes in the competitive interactions between the resident species and the invader along the resource availability gradient. At low resource availability, resident species with a high catabolic similarity with the invader efficiently reduced the invader relative density, while at high resource availability, fast-growing resident species became more important for the invader suppression. These results indicate that the relative importance of different resident community species can change dynamically along to resource availability gradient. Diverse communities could be thus more robust to invasions by providing a set of significant species that can take suppressive roles across different environments. [ABSTRACT FROM AUTHOR]

Animal production contributes substantially to the dissemination of antibiotic resistance genes (ARGs) in the environment. Thermophilic composting is cost-effective for reducing hazards in animal wastes. However, ARGs can still persist in composts and the mechanism remains largely unclear. In the present study, metagenomics and real-time quantitative PCR were employed to assess the dynamics of ARGs, especially those of high risk to human health, their host species and pathogenicity of the bacterial community during thermophilic composting of chicken manure. The results showed that thermophilic composting was effective at reducing the majority of the spreading risk of antibiotic resistance by 1) eliminating more than half of allARGs that accounted for 80% of the total abundance, 2) reducing the number and abundance of high-risk ARGs significantly, and 3) removing the ARG hosts and the pathogenicity of the bacterial community substantially. The attenuation of ARGs was primarily driven by the bacterial community succession. However, the abundance of some ARGs, especially those associated with plasmids, rebounded during the cooling phase, likely caused by horizontal gene transfer. Our research reveals that minimising the horizontal transfer of plasmid-associated ARGs during the cooling phase of thermophilic composting is crucial for a more effective reduction of the hazards associated with the spread of antibiotic resistance. [Display omitted] • Thermophilic composting reduced the bulk antibiotic resistance in animal manure. • Bacterial community succession drove the attenuation of ARGs. • Plasmid-associated ARGs rebounded via horizontal gene transfer during cooling phase. • Ratios of high-risk ARGs and plasmid-associated ARGs increased during composting. • Minimising ARG revival during cooling phase is key to improving ARG removal. [ABSTRACT FROM AUTHOR]

The influence of fertilization on crop nutrient use efficiency (NUE) and productivity remain unclear. Here, to assess how fertilization management influences the soil microbial communities and their functional profiles and consequently affects NUE and crop productivity, we established a field experiment with mineral and combined organic-mineral fertilization as well as mineral fertilizer reduction practices. The composition of the microbial community was measured by high-throughput amplicon sequencing, and its functional profile was predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software. Our results demonstrated that fertilization management significantly shifted the rhizosphere bacterial community and regulated the compensation intensity of nutrient cycling-related functions, which means the rhizosphere bacterial community assembles to harbour greater nutrient cycling-related functions in lower available nutrient conditions to meet the nutrient requirements of the host plant. Moderate compensation intensity of nutrient cycling functions contributed to the highest NUE and crop productivity being achieved in the combined organic-mineral fertilization treatment. However, insufficient fertilizer input induced intense functional compensation, while standard mineral fertilizer input resulted in weakened functional compensation of nutrient cycling functions, both of which decreased NUE and crop productivity. Overall, this study provides new insights into the key roles of the rhizosphere microbiome in improving NUE, and suggests that the functional compensation characteristics of the rhizosphere microbial community may be a sensitive indicator of nutrient supply and demand relationships as well as a predictor of NUE. • Fertilization alters the compensation intensity of rhizospheric nutrient cycling functions. • Moderate compensation of nutrient cycling functions triggers high nutrient use efficiency (NUE). • Both intensified and marginalized functional compensation decrease the NUE. [ABSTRACT FROM AUTHOR]

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha straw incorporation and 300 kg ha straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria ( Proteobacteria, Betaproteobacteria, and Actinobacteria) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems. [ABSTRACT FROM AUTHOR]

Both nitrogen (N) and phosphorus (P) may limit plant production in steppes and affect plant community structure. However, few studies have explored in detail the differences and similarities in the responses of belowground microbial communities to long-term N and P inputs. Using a high-throughput Illumina Miseq sequencing platform, we characterized the bacterial communities in a semi-arid steppe subjected to long-term N or P additions. Our results showed that both the Chao richness and Shannon's diversity were negatively correlated to N input rate, while only Chao richness was significantly and negatively correlated to P input rate. Also, both N and P additions altered the bacterial community structure. The bacterial community between plots of the same N or P input rate was much more dissimilar with the higher input level, indicating more severe niche differentiation in pots with higher N or P input. N Inputs significantly increased the relative abundance of the predicted copiotrophic groups ( Proteobacteria and Firmicutes ) but reduced the predicted oligotrophic groups ( Acidobacteria , Nitrospirae , Chloroflexi ), with the order Rhizobiales being most affected. P additions significantly affected only two phyla (Armatimonadetes and Chlorobi ), which were positively correlated with P source. Results from the structural equation modelling (SEM) showed that N additions affected the bacterial community primarily by changing the pH, while P additions did so mainly by improving P availability. Our results suggest that the below-ground bacterial communities are more sensitive to N inputs, but P inputs can also play an important role in bacterial niche differentiation. These findings improve our understanding of bacterial responses to N and P inputs, and their impacts on bacterial-mediated processes, especially in the context of increasing anthropogenic nutrient inputs. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have recently made it possible to interrogate the phylogenetic diversity of soils at considerable depth. This ability has led to the development of many computational tools to infer interaction networks from environmental samples. Although such tools have widely been used, they have more often served as a visual means to compare microbial communities across environmental gradients than as a means to appreciate microbial interactions associated with certain ecological processes. Previous studies have often regarded a subnetwork (module) as a functional unit but its functionality in ecological context has never been evidenced. To make better use of these tools in appreciating microbial interactions, we propose the combinational use of different inference tools. This ensemble approach permits the use of more independent predictors and the removal of tool-specific predictions in order to increase prediction accuracy. The purpose of the present study is to identify ecologically meaningful bacterial associations using multi-tool approach. Soil samples were collected in time series from experimental paddy rice plots. Bacterial communities were characterized by high-throughput tag sequencing of 16S rRNA gene fragments. We used three tools, Co-occurrence Network inference (CoNet), Molecular Ecological Network Analysis (MENA) and extended Local Similarity Analysis (eLSA), to infer networks from abundance profiles, partitioned the networks into modules, screened for the modules with ≥50% of genus-/species-level nodes, captured the modules that were derived from different tools and shared ≥ 50% of order-level nodes (tool-agreed modules) and tested their robustness against the changes in the tool parameters. By these procedures, two three-tool-agreed modules were found. One represented a guild that is phenotypically associated with aerobic respiration and fermentation and the other represented a guild phenotypically associated with metal/sulphur cycles, all of which are essential processes of water-submerged paddy soils that are mediated by bacteria. These data suggested that the linked members in a module were functionally associated taxa that work together to achieve a distinct function or an ecological process, and thus were ecologically meaningful to the environment. We selected three linked species from a three-tool-agreed module and validated their interactions using co-culture methods. Results showed that the interaction type between Janthinobacterium lividum and Leuconostoc lactis in the two-species mixture was validated to be ambivalent, positive for one partner and negative for the other. However, this type of interaction was not retained when a third party Lactococcus piscium was introduced, signifying the complexity of multi-species interactions. Validation results suggested that the selected species were interacting partners in laboratory but the validated interaction types were different from those inferred. By multi-tool approach, we also found that highly linked nodes, which are often referred to as “keystone species” and are frequently interpreted as the species playing important roles in soils, are tool dependent. Among top ten highly linked nodes, only four are conserved across three tools. These results suggest more research is required on the ecological significance of degree-based identification of keystone species. Overall, the present study highlights the potential utility of combined use of inference tools to identify ecologically meaningful bacterial associations in soils and other environmental samples. It is interesting to see what type of ecologically meaningful bacterial associations can be found in other soils. [ABSTRACT FROM AUTHOR]

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria. [ABSTRACT FROM AUTHOR]

Plant-derived root exudates modulate plant-microbe interactions and may play an important role in pathogen suppression. Root exudates may, for instance, directly inhibit pathogens or alter microbiome composition. Here, we tested if plants modulate their root exudation in the presence of a pathogen and if these shifts alter the rhizosphere microbiome composition. We added exudates from healthy and Ralstonia solanacearum-infected tomato plants to an unplanted soil and followed changes in bacterial community composition. The presence of pathogen changed the exudation of phenolic compounds and increased the release of caffeic acid. The amendment of soils with exudates from the infected plants led to a development of distinct and less diverse soil microbiome communities. Crucially, we could reproduce similar shift in microbiome composition by adding pure caffeic acid into the soil. Caffeic acid further suppressed R. solanacearum growth in vitro. We conclude that pathogen-induced changes in root exudation profile may serve to control pathogen both by direct inhibition and by indirectly shifting the composition of rhizosphere microbiome. [ABSTRACT FROM AUTHOR]

Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile- C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant- C-degrading genes but a lower intensity of labile- C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil. [ABSTRACT FROM AUTHOR]

The use of organic compost combined with inorganic fertilizer can enable balanced fertilization under intensive farming conditions, but little is known about how these fertilization practices affect the composition of microbial in arable soils. In this study, a field trial of a rice-wheat cropping system was established to examine the effects of 8 years of fertilization with inorganic fertilizers (IFs) and the organic manure-inorganic fertilizers (OMIFs) on composition of microbial communities. The fungal 18S and bacterial 16S rRNA gene fragments were amplified from each soil sample and sequenced. Significantly lower fungal richness and higher bacterial richness were observed for the OMIF treatment compared to the other treatments. No obvious changes in fungal diversity were observed among the treatments, with a decrease bacterial diversity detected in the IF treatment. Variations in relative abundance were observed in the fungal phyla Glomeromycota, Blastocladiomycota, and Schizoplasmodiida and in the bacterial phyla Acidobacteria, Gemmatimonadetes, and Cyanobacteria, most of which were significantly correlated with soil organic matter (OM) and/or nitrate N (NO-N) contents. Additionally, the fungal abundance-based coverage estimator (ACE) showed a significant negative correlation with the soil NO-N/OM content, while the correlation was positive for the bacterial ACE estimate. This study suggests that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO-N/OM content of soil on the composition of fungal and bacterial communities. [ABSTRACT FROM AUTHOR]

Red soil is a kind of Ferralic Cambisol. Good hydrothermal resources but usually acidic and low base saturation make it very easy to be acidified under unreasonable fertilizer managements in agricultural area. In 1990, a series of fertilizer applications were established on a homogeneous field to investigate the soil fertility changes under different fertilizations in Hunan province, among them, long-term chemical nitrogen fertilization (NPK) induced severe soil acidification, whereas long-term chemical plus swine manure fertilization (NPKM) exhibited an overwhelming advantage in terms of nutrient concentration and bacterial diversity. In 2010, to investigate the effect of short-term quicklime and swine manure applications on the acid red soil, a remediation experiment was established on the NPK treatment. Quicklime (CaO) and swine manure (the same as the swine manure in NPKM) applications on NPK soil had different effects on remediating the soil acidification: short-term quicklime application (NPK + Ca) increased soil pH and bacterial diversity more rapidly, whereas short-term swine manure application (NPK + M) improved soil nutrient concentration more effectively. Alteration of environmental conditions caused significant changes of bacterial community: oligotrophic groups were in greater relative abundances with quicklime treatment, whereas copiotrophic groups were in greater relative abundances with swine manure treatment. This study provides insights into the two major remediation approaches for an acidic red soil; these insights are important for soil remediating and improving fertility. Taken together, we recommended short-term quicklime application to increase the soil pH quickly and long-term swine manure fertilization to improve soil fertility. [ABSTRACT FROM AUTHOR]

The development of more stable and sustainable agroecosystems for improving food production has caused wide public concern in recent years. In the present study, we conducted a field experiment to investigate the effect of pig manure organic–inorganic compound fertilizer with reduced chemical fertilizer on the crop yields, soil physicochemical properties, biological activities and bacterial community structure in a rice–wheat cropping system over two crop seasons (rice and wheat). The results showed that at all sampling times, this fertilizer regime enhanced the soil nutrient availability, microbial biomass, enzymatic activities, and soil nitrogen processes and, to some extent, promoted crop yields. Across all soil samples, bacterial communities were dominated by Proteobacteria , Acidobacteria , and Chloroflexi at the phylum level. Hierarchical cluster analysis based on the weighted UniFrac distance revealed that the bacterial community structures were strongly separated by the sampling time, and the treatments in the wheat harvest soils. A Venn diagram of shared OTUs showed a core microbiome across different treatments and sampling times, in which the relative abundance of each abundant phylum (class) was stable in the different treatments and at different sampling times. Specifically, the relative abundance of Alphaproteobacteria , Gammaproteobacteria , Nitrospirae , Bacteroidetes , and Actinobacteria was largely and particularly enriched under the organic–inorganic compound fertilizer regime, indicating that soil functions, such as nitrification and the turnover of organic matter, might be strengthened under this treatment. Collectively, these results indicate that the application of organic–inorganic compound fertilizer may reduce chemical fertilizer use and improve the long-term productivity and sustainability of agroecosystems. [ABSTRACT FROM AUTHOR]

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. [ABSTRACT FROM AUTHOR]

Understanding how distinct processes operate in mediating community assembly is a long-standing theme in (microbial) ecology. Particularly in soil microbial communities, we still lack a fundamental appreciation of how assembly processes structure communities at the fine-scale level of soil aggregates. In this study, samples from a long-term agricultural field subjected to different fertilization regimes were used to quantify the relative influences of stochastic and deterministic processes on soil bacterial community assembly. First, we found bacterial communities to be more phylogenetically clustered in larger soil aggregates comparatively to small aggregates (Spearman's r = −0.366, P < 0.05). Second, we found the overall relative influence of selection to gradually decrease with an increase of aggregate size (Mantel r = 0.161, P < 0.01). By partitioning aggregate sizes and fertilization regimes, we found that sites subjected to fertilization (including chemical, organic, and bio-organic fertilizers) displayed a stronger relaxation of selection and an increased influence of stochasticity with an increase in aggregate size; a pattern not significantly observed at the control (unfertilized) treatment. Collectively, our results highlight the importance of evaluating community assembly at the fine-scale levels of soil aggregates and illustrate how regional level disturbances (i.e., agricultural management) exert an influence on the dynamic interplay of stochastic and deterministic processes. • Bacterial communities are more phylogenetically clustered in larger soil aggregates. • Soil aggregates mediate the balance between stochastic and deterministic processes. • Deterministic process of homogeneous selection is dominated in all soil aggregates. [ABSTRACT FROM AUTHOR]

A large amount of organic compost, produced with agricultural and breeding industry wastes by composting, is widely used in agriculture in China. The microbial decomposition of organic compost is a major flux in the nutrition cycle in sustainable agricultural soils. To explore the mechanism of organic compost mineralization in soil, in situ decomposition experiments of organic compost buried in soils were arranged in three different latitude regions located in Jilin, Jiangsu, and Yunnan in China. The results showed that organic compost had different decomposition rates at the three different sites, with the highest decomposition rate in Yunnan, followed by Jiangsu and Jilin. The decomposition rates of unsterilized organic compost were significantly greater than those of sterilized organic compost, indicating that the microorganisms in organic compost also made important contributions to the decomposition process. The soil microbial diversity and community structure among the three sites were significantly different. The fungal community, especially fungal richness, rather than the bacterial community in the soil, plays a major role in the decomposition of organic compost. The annual average temperature is an important environmental factor affecting fungal richness. This study will provide a reference for formulating agricultural fertilization models in different regions. • Organic composts had the highest decomposition rate in Yunnan, followed in Jiangsu and Jilin. • The microorganism in organic compost also made important contributions to the decomposition process. • The soil microbial diversity and community structure among the three sites are significantly different. • The fungal community in the soil plays a major role in the decomposition of organic composts, especially fungal richness. [ABSTRACT FROM AUTHOR]

PhoD -harboring microorganisms are crucial for the regulation of soil phosphorus (P) cycling through the secretion of alkaline phosphomonoesterases and are also known to be sensitive to fertilizer inputs. However, the impacts of long-term mineral and organic fertilizer inputs on active phoD -harboring functional communities in soils remain largely unknown. In the present study, 18O-DNA-stable isotope probing coupled with high-throughput sequencing was utilized in order to characterize active phoD -harboring functional bacterial communities in soils subjected to long-term no-fertilizer (Control), mineral-only fertilizer (NPK), organic-only fertilizer (M), and the combination of mineral and organic fertilizer (NPKM) amendments. Total and active phoD gene abundance decreased in soils amended with long-term mineral fertilizer, but increased in soils under organic fertilizer amendment, compared with the non-fertilized soils. A total of 51 active phoD -harboring bacterial OTUs, mainly belonging to Actinobacteria, were identified in this study. Organically amended soils harbored a higher diversity of active bacterial community. In the active phoD -harboring functional community, Rhodococcus comprised approximately 99% of the total relative abundance in the unfertilized soil, whereas Nocardiopsis and Bacillus accounted for approximately 62% and 24%, respectively, in mineral-only fertilized soils. Active phoD -harboring communities were dominated by members of the genera Streptomyces (26–60%), Nocardia (5–9%) and Gordonia (23–41%) in all organically fertilized soils, including M and NPKM. Overall, these long-term fertilization regimes altered the abundance, richness and composition of the active phoD -harboring functional microbial community. This study provides novel insights into the responses of the active functional bacterial community that is responsible for soil P mineralization to differing long-term fertilization regimes. • The active phoD -harboring bacteria was identified by 18O-DNA-SIP technique. • Organic amendment increased the abundance and diversity of active phoD bacteria. • Different fertilization regimes shaped distinctive active phoD bacterial community. • The active phoD bacterial OTUs in fertilized soils was dominated by Actinobacteria. • In unfertilized soil, ~99% active phoD -harboring OTUs belonged to the Rhodococcus. [ABSTRACT FROM AUTHOR]

• • Absolute quantification of microbial abundance makes the result more accurate. • • PICRUSt was applied to predict probable functions across composting ecosystem. • • Relationship between bacterial compositions and FRI parameters were established. • • Vital bacteria as biomarkers were used to predict composting ecosystem functions. This study aimed to provide insights into prediction of composting ecological functioning through analyzing the critical bacterial populations and functions. The bacterial ecosystem functioning was essential, and cow dung, chicken manure, mushroom dreg and Chinese medicine residues were used as raw materials to quantify and predict the functioning of bacterial communities through synthetic spike-in standards accompanied Illumina sequencing and PICRUSt. Bacterial community of wheat straw and chicken manure compost (SCM) was similar to mushroom dreg and chicken manure compost (MCM), and Sinibacillus dominated in both treatments with the abundance of 20.73% and 41.36%, respectively. The correlation analysis between bacterial community and fluorescence EEM regional integration parameters showed that Lactobacillus (0.889), Enterococcus (0.888) and Erysipelothri (0.903) were positively correlated with P V , n / P III , n. The ontology analysis results showed that metabolism, genetic information processing, environmental information processing and cellular processes were the primary functions for bacterial community in all treatments. [ABSTRACT FROM AUTHOR]

Plant rhizosphere microbes play a key role in plant-soil feedbacks. However, the intrinsic principles governing the assembly of the rhizosphere microbial community remain unclear. To understand these principles, we studied the taxonomical and functional characteristics of the reassembled maize rhizosphere bacterial communities after transplanting between soils. The composition of the rhizosphere bacterial community was measured by high-throughput amplicon-based Illumina MiSeq sequencing of the V4 region of the 16S ribosomal RNA (rRNA) gene. The rhizosphere functional profile was assessed using 16S rRNA data in the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved State) software. We found that the reassembled rhizosphere bacterial community was recruited from both soil and endosphere communities. The assembly and functional traits of the rhizosphere bacterial community were associated with the concentrations of soil available nutrients. The most important rhizospheric functions were to improve host stress tolerance, followed by nutrient cycling functions. The rhizosphere bacterial taxa that improved host stress tolerance were in low abundance and were primarily derived from the surrounding bulk soil. Moreover, the rhizosphere nutrient cycling functions were marginalized in nutrient-excessive soils. Plants may sacrifice stress tolerance functions and enhance compensatory colonization of nutrient cycling-related endophytes in the rhizosphere in nutrient-deficient soils. Our results demonstrate that the levels of soil available nutrients mediate the assembly of rhizosphere bacterial communities to satisfy plant-required functions. This assembly principle is useful for manipulating the bacterial communities of plant roots to improve agricultural sustainability. • The rhizosphere bacterial community is recruited from both soil and endosphere communities. • The rhizosphere bacterial communities are compositionally divergent among soils. • The rhizosphere bacterial communities are functionally less divergent among soils. • Soil available nutrient concentrations drive the assembly of rhizosphere microbiome. [ABSTRACT FROM AUTHOR]

• Applying microbial inoculants and mature compost both accelerated composting process. • Bacterial rather than fungal community turnover predetermined composting efficiency. • Initial bacterial community turnover played a key role in composting process. • Microbial inoculation accelerated the composting by stimulating key resident microbes. • Key OTUs (Thermicanus and Tepidimicrobium) played key role in material transformation. The aim of this work was to study the influence of inoculation with microbial inoculants (MI) or mature compost (MC) by comparing the resultant composting efficiency with that in a noninoculated (CK) treatment. MI and MC application both accelerated the composting process according to fluorescence excitation-emission matrix (EEM) detection and germination index testing. Bacterial and fungal community composition both differed significantly over the composting period. However, the turnover of the initial bacterial community played a significant role in the composting process, and the key operational taxonomic units (OTUs) of MI (OTU_26, Thermicanu s) and MC (OTU_48, Tepidimicrobium) showed significant explanatory power for the formation of humic acid-like and fulvic acid-like substances, respectively, during the stage of composting. Thus, our results indicate that microbial inoculation accelerates the composting process by stimulating key resident microbes in the initial stage. [ABSTRACT FROM AUTHOR]

Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants. [ABSTRACT FROM AUTHOR]

• Feasible C/N ratios enhanced composting efficiency. • Composting treatment and phase influenced bacterial community. • Variations of enzymes were related to bacterial community succession. • Functional enzymes related to key taxa enhanced composting efficiency. A consortium of key bacterial taxa plays critical roles in the composting process. In order to elucidate the identity and mechanisms by which specific bacterial species drive high-efficiency composting, the succession of key bacterial consortia and extracellular enzymes produced during the composting process were monitored in composting piles with varying initial C/N ratios. Results showed that C/N ratios of 25 and 35 enhanced composting efficiency through elevated temperatures, higher germination indices, enhanced cellulose and hemicellulose degradation, and higher cellulase and dehydrogenase activities. The activities of cellulase and β-glucosidase, cellulase and protease, and cellulase and β-glucosidase exhibited significant relationships with bacterial community composition within the mesophilic, thermophilic, and mature phases, respectively. Putative key taxa, linked to a higher composting efficiency, such as Nonomuraea , Desemzia , Cellulosimicrobium , Virgibacillus , Clostridium , and Achromobacter , exhibited significantly positive relationships with extracellular enzyme activities, suggesting a significant contribution to these taxa to the development of composting maturity. [ABSTRACT FROM AUTHOR]