Wu Xiong

BACKGROUND: The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing. RESULTS: We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others. CONCLUSIONS: This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.

A growing body of evidence suggests that microbial α-diversity (local species richness) may have positive effects on ecosystem function. However, less attention has been paid to β-diversity (the variation among local microbial assemblages). Here we studied the impact of microbial α-diversity on stochastic/deterministic microbial community assembly processes, which are related to β-diversity, and the consequences for community function. Bacterial communities differing in α-diversity were generated and their structures and potential community functional traits were inferred from DNA sequencing. Phylogenetic null modeling analysis suggests that stochastic assembly processes are dominant in high-diversity communities. However, in low-diversity communities, deterministic assembly processes are dominant, associating with the reduction of specialized functions that are correlated with specific bacterial taxa. Overall, we suggest that the low-diversity-induced deterministic community assembly processes may constrain community functions, highlighting the potential roles of specialized functions in community assembly and in generating and sustaining the function of soil ecosystems.

BACKGROUND: Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. RESULTS: To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. CONCLUSION: Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function. Video Abstract.