Bacillus-derived cycle lipopeptides modulate microbiome structure and enzymatic activity of soil and increase productivity of Solanum tuberosum

Abstract Cyclic lipopeptides (CLPs) are well-known secondary metabolites produced by Bacillus bacteria. Current research into the role of lipopeptides in soil microbial ecology suggests that their importance goes beyond the suppression of phytopathogens. Aims. In our work, we studied CLPs (bacillomycins and fengycins) as modulators of agroecosystem microbiome structure (taxonomic) and its functional properties (enzymatic activity) that lead to improved soil health and consequently productivity of growing plants. Methods. In a 56-day study, we conducted microcosm and field experiments to assess the biodiversity of soil bacterial and fungal communities using DNA metabarcoding; and the activity of extracellular enzymes using fluorometric microplate enzyme assays with fluorogenic-labelled substrates. The obtained data were subjected to static and mathematical processing in order to predict the enzymatic activity of the soil based on metabarcoding data. Results. The metabolic activity of the soil microbial community has been found to be stimulated by the application of CLPs to soil. Microbial enzymes involved in the cycling of carbon (3 enzymes), nitrogen (2 enzymes) and phosphorus (1 enzyme) were activated in the experimental condition. Exposure to CLPs did not alter the alpha diversity of the bacteria but increased the alpha diversity of the fungi. DNA metabarcoding showed that the action of CLPs altered the relative abundance of approximately 20% of the bacterial and fungal ASVs that comprised the dominants. The effect was the same for both bacteria and fungi: the relative abundance of most of these ASVs increased. The constructed network of relationships between enzyme activity and changes in the microbial community allowed us to identify potential taxa of bacteria and fungi that determine the activity of specific enzymes. Finally, we tested the CLPs-based preparation on potato tubers and found that it improved the physiological and biochemical parameters of plants. Conclusions. Thus, the use of purified Bacillus-derived CLPs allowed better characterization of the biological effects exerted by soil bacilli on the soil microbiome. In addition, CLPs were found to be non-toxic and stimulating to soil microbiota, which may lead to the development of biopreparations to improve crop productivity.