Microbial Community Analysis of Rhizosphere of Healthy and Wilted Pepper (Capsicum Annuum L.) in An Organic Farming System

Abstract

\n Rhizosphere microorganisms play an important role in the growth and health of plants. Around the world, diverse soil-borne pathogens attack Capsicum annuum causing significant damage and economic losses; however, very little is known about how rhizosphere microbial communities are altered by infestation with root pathogens. This work aimed to determine whether the diversity and structure of microbial communities in the rhizosphere soil of C. annuum plants is significantly changed by wilt disease. We used 16S rRNA for bacteria and the internal transcribed spacer region for fungi, to characterize the rhizosphere microbiomes of healthy and wilted plants. The most abundant bacterial phyla were Proteobacteria and Gemmatimonadetes, while the most abundant fungal phyla were Ascomycota and Mucoromycota. The bacterial α-diversity did not show significant differences in richness and diversity, but did show a significant difference in evenness and dominance of species. Rare taxa were present in both healthy and wilted conditions with relative abundances\u2009<\u20091%. In the fungi, all evaluated estimators showed a significant reduction in the wilted condition. The β-diversity showed significant differences in the structure of bacterial and fungal communities, which were segregated according to plant health condition. The differential abundance analysis did not show significant results in the bacterial communities; however, in the fungal communities, Rhizopus, Thanatephorus, Curvularia, Fusarium, Cladosporium, and Alternaria were more abundant in the rhizosphere of wilted than healthy plants. Species from these genera have been previously reported as phytopathogens of several plants, including in reports on individual species as disease agents in C. annuum.