The Properties of Soilless Culture Substrates Determine the Evolutionary Direction of Rhizosphere Microbial Communities in Potato Breeding, Having Potential Impact on Breeding

Abstract

Abstract Background Coconut bran and vermiculite are commonly used substrates in the process of potato germplasm breeding under soilless cultivation conditions, each possessing distinct physicochemical properties and indigenous microbial reservoirs. In comparison to natural soil, there is a lack of evaluation and limited understanding of the root-associated microbial communities in soilless cultivation environments. As soilless cultivation is increasingly applied in agriculture, the evolution of these microorganisms can significantly impact the breeding environment and the microecological environment within the regions involved in breeding. Results The physicochemical characteristics of the substrates significantly influence the composition and evolution of indigenous bacterial communities under similar treatments. Substrate permeability has almost no effect on the microbial community, while WSN (water-stable aggregates), TN (total nitrogen), AK (available potassium), and TOC (total organic carbon) are identified as the most critical influencing factors. They show a positive correlation with bacterial communities but a negative correlation with fungal communities. Coconut bran exhibits higher values for these four indicators. During the two stages of mixed fermentation after basal fertilization and 50 days of potato cultivation, coconut bran consistently maintains higher bacterial diversity and abundance while possessing lower fungal diversity and abundance. Coconut bran substrates exhibit a more complex microbial network and higher bacterial-fungal negative correlations. Each group is enriched with specific functional biomarkers, where coconut bran substrates are associated with polysaccharide degradation and denitrification-related microorganisms, along with an abundance of plant growth-promoting rhizobacteria (PGPRs). In contrast, vermiculite substrates are enriched with Dyella, a microorganism involved in rock weathering, but also contain a higher abundance of plant pathogens, particularly potato pathogenic bacteria and fungi (Pectobacterium and Botryotinia). Conclusion Coconut bran and vermiculite, as distinct soilless cultivation substrates, play a crucial role in shaping the microbial community composition during various stages of potato breeding. Higher levels of WSN, TN, AK, and TOC in coconut bran substrates provide a healthier microecological environment. These findings offer potential insights into the selection of soilless cultivation substrates for healthy and sustainable potato breeding and the adjustment of beneficial microbial community composition.