Bacterial diversity and function shift of strawberry root in different cultivation substrates

Abstract

With the increasing use of soilless cultivation, artificial substrates are becoming more common, which inevitably leads to changes in the crop root environment. However, the impact of artificial substrate application on crop root microflora remains incompletely investigated. This study collected strawberry root samples from two artificial substrates and one greenhouse soil and used. 16S rRNA amplicon sequencing method to analyze the changes in the bacterial communities surrounding strawberry roots in different cultivation substrates. The corresponding root microbiota was predicted by PICRUSt. The results demonstrated that the α and β diversity of bacterial microbiota in samples from artificial substrates and greenhouse soil were significantly different. Almost all bacteria detected in root samples from greenhouse soils were also found in root samples from artificial substrates. The abundance of the genera Cellvibrio and Streptomyces in root samples from greenhouse soil were significantly higher than those of artificial substrate 1 and substrate 2. Bacteria found in substrate 1 including Acidocella, Vibrio and other 8 genera were significantly enriched compared to greenhouse soil; Bacteria identified in substrate 2 including Asticcacaulis, Bordetella, and other 13 genera were significantly higher than those in greenhouse soil. According to PICRUSt prediction, there were 34 pathways in substrate 1 and 47 pathways in substrate 2, including pathways related to cellular processes, environmental information processing, genetic information processing, human diseases, metabolism, and organismal systems in root microbiota from different substrates might significantly shifted. Among these pathways, those related to plant growth promotion, such as flavonoids and flavanols synthesis, were significantly up-regulated and pathways regarding antimicrobial compound synthesis including clavulanic acid, stilbenoid, and macrolides were significantly down-regulated in root microbiota from artificial substrates. This work provides basic information on root bacterial diversity of strawberries grown in different substrates and help to explore beneficial root microorganisms for sustainable strawberry production.