Search

Summary: Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant–mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil–plant continuums (rhizosphere, phyllosphere and endosphere) in the maize–wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop‐associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub‐community is mainly determined by stochastic processes. In contrast, the rare sub‐community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co‐occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions. [ABSTRACT FROM AUTHOR]

Summary: Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro‐ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate‐active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate‐binding modules. These results demonstrate that virus‐encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil. [ABSTRACT FROM AUTHOR]

Summary: Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known.Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)‐wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites.Our results demonstrate that microbiome assembly along the soil‐plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize.Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Soil microbial communities play an important role in driving a variety of ecosystem functions and ecological processes and are the primary driving force in maintaining the biogeochemical cycle. It has been observed that soil microbial diversity decreases with land use intensification and climate change in the global background. It is essential to investigate whether the reduction in soil microbial diversity can affect soil multifunctionality. Thus, in this study, the dilution-to-extinction method was used to construct the gradient of soil microbial diversity, combined with high-throughput sequencing to explore the impact of the reduction in bacterial, fungal, and protist diversity on soil multifunctionality. The results showed that the soil microbial alpha diversity (richness and Shannon index) was significantly lower than that of the original soil. Principal coordinate analysis (PCoA) showed that the microbial community structure of original soil was significantly different from that of diluted soil, and the response of bacterial and fungal communities to diluted soil was higher than that of protists. The regression model showed that there was a significant negative linear relationship between the average response value of soil multi-function and the index of microbial diversity, indicating that the change in soil microbial community was the key factor in regulating soil multifunctionality. The regression model showed that there was a significant negative linear relationship between soil multifunctionality and microbial diversity, indicating that the change in soil microbial community was the key factor to regulate soil multi-kinetic energy. Through the aggregated boosted tree analysis (ABT) and regression model, we found that some specific microbial groups, such as the Solacocozyma and Holtermaniella of fungi and Rudaea of bacteria, could significantly promote the change in soil multifunctionality, which showed that key microbial taxa play an indicative role in biological processes. Furthermore, the structural equation model revealed that bacteria could affect soil multifunctionality through the interaction between microbiomes, which was the key biological factor driving the change in soil multifunctionality. This study provided experimental evidence for the impact of soil microbial diversity on soil multifunctionality, and promoted the notion that maintaining a certain diversity of soil microbial community in a single agricultural ecosystem, especially the diversity of key microbial taxa, is of great significance to the sustainable development of ecosystem function in the future.