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Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub‐communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub‐communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub‐communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils. [ABSTRACT FROM AUTHOR]

Beneficial host-associated bacteria can assist plant protection against pathogens. In particular, specific microbes are able to induce plant systemic resistance. However, it remains largely elusive which specific microbial taxa and functions trigger plant immune responses associated with disease suppression. Here, we experimentally studied this by setting up two independent microcosm experiments that differed in the time at which plants were exposed to the pathogen and the soil legacy (i.e., soils with historically suppressive or conducive). Overall, we found soil legacy effects to have a major influence on disease suppression irrespective of the time prior to pathogen exposure. Rhizosphere bacterial communities of tomato plants were significantly different between the two soils, with potential beneficial strains occurring at higher relative abundances in the suppressive soil. Root transcriptome analysis revealed the soil legacy to induce differences in gene expression, most importantly, genes involved in the pathway of phenylpropanoid biosynthesis. Last, we found genes in the phenylpropanoid biosynthesis pathway to correlate with specific microbial taxa, including Gp6, Actinomarinicola, Niastella, Phaeodactylibacter, Longimicrobium, Bythopirellula, Brevundimonas, Ferruginivarius, Kushneria, Methylomarinovum, Pseudolabrys, Sphingobium, Sphingomonas, and Alterococcus. Taken together, our study points to the potential regulation of plant systemic resistance by specific microbial taxa, and the importance of soil legacy on disease incidence and eliciting plant-defense mechanisms. [ABSTRACT FROM AUTHOR]

A pineapple-banana rotation was studied as a model system to investigate the potential emergence of a fungal-mediated disease-suppression in a soil highly infested with the pathogen Fusarium oxysporum causing the banana wilt disease. By using both field and pot experiments, the pineapple-banana rotation system resulted in a significant decrease of the pathogen number and next-stubble banana disease incidence (P < 0.05). This pathogen-suppression phenomenon was linked with detectable shifts in the soil resident fungal taxa tracked in the pineapple season. Most importantly, taxa affiliated with Talaromyces pinophilus and Clonostachys rossmaniae were found to be significantly enriched in the bulk soils due to the pineapple cultivation (P < 0.05). The taxon T. pinophilus was also significantly enriched in the rhizosphere of banana after the rotation (P < 0.05). Later, we used fungal isolation and pot inoculation to validate that both T. pinophilus and C. rossmaniae taxa are able to significantly decrease the pathogen number in the banana rhizosphere soil (P < 0.05), thus confirming their biocontrol effects suppressing the disease. Taken together, this study provides evidence on how crop rotation affects the resident soil microbiome and the development of disease suppressiveness. Besides, this study highlights the importance of understanding the dynamic changes in soil biology mediated by crop rotation and validates the mechanisms underpinning suppression toward promoting practical and directed manipulation of protective microbiomes in agroecosystems. [ABSTRACT FROM AUTHOR]

Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina , Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration. [ABSTRACT FROM AUTHOR]

Background and Scope: Microorganisms exhibit an astonishing diversity and wide genetic variability even within species, in particular with respect to their metabolic pathways and host-interactive capabilities. The mosaic genomes that encode these capacities are accountable for the abilities of environmental microbes to survive and thrive in highly complex systems such as soil and the rhizosphere. Whereas credits are to be given to traditional microbiology studies, e.g. with rhizobia and their interaction with the plant, an explosive enhancement of our understanding of the plant-microorganism interactive system has been recently achieved by the broad application of the molecular toolbox, in particular high-throughput sequencing (HTS) technologies. The latter have allowed to access thousands to millions of microbial phylotypes and functions at relatively low cost and effort. While such techniques have improved the accessibility of the taxonomic and functional diversity of rhizosphere and soil microbial communities, detailed insights into organismal ecology and physiology (reflecting the behaviour of populations of cells) within the community in the natural environment are still required. Conclusions: In this review, we first examine the current ‘state-of-the-art’ of rhizosphere ecology studies and what HTS strategies have added to our understanding of the system. We posit that our capacity to develop and test refined ecological hypotheses is hindered if we solely depend on deep-sequencing methods. Plant-soil-microorganism systems represent one of the most intriguing ‘playgrounds’ for assessments of ecological theories, since they offer a myriad of ways to investigate ecological interactions (i.e. intra- and inter-specifically), physiological and behavioural traits. In addition, the evolutionary processes that lead to innovation in the microbiota are likely prominent in the rhizosphere. Thus, there is a perceived need to shift our attention from the HTS studies, that extensively map the local microbiota in an overall fashion, to studies focusing on as-yet-unaddressed fundamental questions about the plant-soil microbiota system. Such a paradigm shift will certainly assist us in the unravelling of the building blocks of rhizosphere (and soil) microbial communities, as well as form a basis for targeted manipulation of these in their natural settings. [ABSTRACT FROM AUTHOR]

Conservation farming and crop diversity increase soil health, organic matter content, and soil microbial activity. However, the design and implementation of sustainable practices often lack a detailed understanding of their impacts on microbial communities in soil. Here, we studied the effects of an Arabica coffee (Coffea arabica) – Brachiaria (Urochloa spp.) intercropping system on soil microbial properties by partitioning at the centimeter-scale the topsoil layers. In particular, we collected and analyzed four soil layers in a vertical stratification gradient of 0–2.5 cm (layer 1), 2.5–5.0 cm (layer 2), 5–10 cm (layer 3), and 10–15 cm (layer 4). Soil samples were subjected to chemical analysis, bacterial community profiling, and quantification of microbial enzymatic activity for β-glucosidase and acid-phosphatase, in addition to the quantification of N-fixation and P-solubilization gene abundances. We found that intercropping increased acid-phosphatase activity at layer 1, β-glucosidase activity at layers 2 and 3, and the amount of soil organic matter and total magnesium at layers 2 and 3. Intercropping increased the relative abundance of the N-fixation gene at layer 3 and bacterial diversity at layers 1 and 3. Overall, intercropping significantly changed the soil bacterial community structure and resulted in a more interconnected co-occurrence network (i.e., greater node connectivity, network density, and lower edges average path length). Taken together, this study provides evidence for the positive impact of intercropping in the soil at a centimeter-scale vertical stratification. It corroborates the notion that plant diversity stimulates microbial activity and species interactions in soil. • Intercropping had positive impacts on soil organic matter and microbial activity. • Soil coverage shifted soil bacterial community structure, richness, and diversity. • nifH gene abundance increased at a specific soil depth in the intercropping system. • Intercropping resulted in a more complex co-occurrence network of bacterial taxa. [ABSTRACT FROM AUTHOR]