Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens

Abstract

Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and ITS amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we catalogued a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.

Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species

“…In recent years, several publications have reported that pathogen infections may result in changes to the microbiome in many pathosystems ( 33 , 58 , 59 ). In this study, we observed a higher alpha diversity of bacterial communities than that of fungal communities, and similarly, an elevated bacterial alpha diversity was observed in Arabidopsis root and soybean rhizosphere systems in previous studies ( 60 , 61 ). Notably, we observed that the alpha diversity of both bacterial and fungal communities in healthy Kelsey leaves increased progressively from the first to the fifth stage, with a slight decrease in the sixth stage; this suggests a potential mechanism by which the highly diverse microbial communities in healthy leaves can trigger increasingly intensive interactions with the plant immune systems to avoid pathogens ( 62 ).…”

“…For the phyllosphere fungal community, we found that Diaporthaceae and Didymellaceae were significantly enriched in the sixth stage of G. yamadae -infected leaves. Diaporthe and Didymella are major pathogenic members of the families Diaporthaceae and Didymellaceae , respectively, which have been significantly enriched in diseased plant roots in previous studies ( 61 , 70 ). Therefore, these fungal groups may be opportunistic pathogens that colonize highly vulnerable diseased plants ( 61 ).…”

“…Diaporthe and Didymella are major pathogenic members of the families Diaporthaceae and Didymellaceae , respectively, which have been significantly enriched in diseased plant roots in previous studies ( 61 , 70 ). Therefore, these fungal groups may be opportunistic pathogens that colonize highly vulnerable diseased plants ( 61 ).…”

An updated assessment of the soybean–Phytophthora sojae pathosystem

“…Rhizobiomes dominated by Pseudomonadaceae , Bacillaceae , Solibacteraceae and Cytophagaceae were realized for Fusarium oxysporum ‐resistant varieties of common bean (Mendes et al, 2018), whilst approximately 20 rhizosphere‐dwelling taxa were correlated with the prevalence of Fusarium virguliforme in soybean (Srour et al, 2017). Recently, Díaz‐Cruz and Cassone (2022) profiled fungal and prokaryotic communities in the soybean rhizosphere and phyllosphere upon infection with P . sojae and Septoria glycines .…”

“…sojae and Septoria glycines . For both plant compartments, alpha diversity indices were influenced negligibly by the presence of pathogens, although community structure and composition were affected considerably (Díaz‐Cruz & Cassone, 2022). The defined study is the first to correlate microbial dynamics in the soybean rhizosphere with P .…”