Soil aggregation impacts bacterial community assembly and suppression of Ralstonia disease in tomato

Soil aggregation is a key element of soil structure, providing a range of micro-niches for soil-borne microorganisms and creating fine-scale heterogeneity in physical and chemical properties. Soil microorganisms drive a range of critical terrestrial ecosystem functions. The importance of understanding the impact of soil aggregates on microbiome assembly and function is increasingly becoming appreciated. In this study, we used a long-term tomato monoculture field as a model system to investigate the impact of soil aggregates on bacterial community assembly and inhibition of the pathogen Ralstonia solanacearum. Samples were collected after harvest from experimental fields with either no fertilizer (CK), chemical fertilizer (CF), organic fertilizer (BF) or a bio-organic fertilizer (BF) and separated into categories of soil aggregates (e.g. <0.25 mm, 0.25-1 mm, 1-2 mm, >2 mm) by a wet-sieving method. Bacterial community composition was found to differ significantly across aggregate fractions, and bacterial communities from larger aggregate fractions exhibited a higher degree of phylogenetic clustering. Furthermore, we found that soil aggregate size classes differed in the relative importance of deterministic versus stochastic processes Fields with different fertilization differ in soil aggregates distribution and disease suppression. Fields with organic inputs (OF, BF) had a higher abundance of large macro-aggregates and fewer micro-aggregates than inorganic input treatments (CK, CF). Meanwhile, disease incidences were lowest in BF, then increasing in OF, CF and CK, orderly. Interestingly, only relative density of R. solanacearum in micro-aggregates was positively correlated with disease. Furthermore, in experiments involving inoculation of R. solanacearum into aggregate size fractions recovered from field samples, only micro-aggregates (<0.25 mm) from the low disease incidence soil (BF) showed significantly higher resistance against pathogen invasion as compared to the high disease incidence soil (CF). In summary, under agricultural practice, soil aggregates can mediate the ecological assembly processes of bacterial communities, thereby influences the suppression of bacterial wilt disease. Soil structure and aggregation should therefore be considered in strategies to improve soil-borne resistance to plant pathogens.