Changes in rhizosphere soil bacterial, fungal, and protistan communities during tomato (Solanum lycopersicum) growth after reductive soil disinfestation

Reductive soil disinfestation (RSD) is an effective agricultural practice to improve the soil microbial community. However, most RSD research has focused on single bacteria or fungi, little is known about the combined influence on the entire microbiome, particularly impacts on protists and the relationships of these groups linked to plant biomass in rhizosphere soil.

In this study, four treatments, i.e., untreated control (CK), RSD with 1% corn straw (CS), 1% miscanthus (MS), and 1% arundo donax (Ad) were performed.

RSD treatment decreased bacterial and fungal community diversity, but increased the diversity of protistan community, along with the relative abundances of Cercozoa and Amoebozoa belonging to phagotrophic protists. The bacterial community diversity rapidly increased with plant growth in the RSD treatment, and we observed that the bacterial community diversity and structure were the major predictors of plant biomass. The RSD treatment had significantly lower relative abundances of potential pathogenic fungi (e.g., Fusarium and Cladosporium) compared to the CK treatment, and the CK treatment showed a dramatic decrease in fungal community diversity. Additionally, RSD treatment increased both bacteria-bacteria and bacteria-protist connections, as reflected by co-occurrence network analysis. The Mantel test demonstrated that soil pH and NO₃⁻-N contents were intensively correlated with bacterial and protistan community diversity, respectively. Moreover, the Ad treatment had notably higher soil LOC and NO₃⁻-N contents compared to the CK treatment after 90 days of plant growth.

RSD treatment promoted plant biomass by increasing soil nutrient turnover and inhibiting pathogen persistence through affecting more connections among soil microbial communities within the rhizosphere.