Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

Abstract

A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.

Isolation and Characterization of Phosphate Solubilizing Bacteria from Paddy Field Soils in Japan

“…The fertilizer management of paddy rice SAR samples must have affected the occurrence of iPSB. Previous studies demonstrated that the application of chemical fertilizers may reduce the abundance of beneficial taxa for plant health and growth ( Sinong et al , 2021 ). This was reflected in the present results, with the highest portion of total iPSB being obtained at Kagawa sites 1 and 2 and at Nagano, at which organic farming is practiced.…”

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods

“…They contribute to the maintenance of microbial populations across successive plant generations, making them integral to the plant's life cycle. In addition to providing beneficial endosymbionts to the offspring, they also actively contribute to seed Sinong et al 2021). In this study, we employed both culture-independent and culture-dependent approaches to evaluate the endophytic microbial communities within rice seeds produced under conventional and organic farming systems.…”

Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice

“…We present a critical appraisal of bacterial and fungal communities sampled in the bulk soil, rhizosphere soil, the root, leaf, and grain in two different locations of non-symptomatic and symptomatic sample types to provide a comprehensive view of the rice-associated microbiome. Rice-associated bacterial and fungal communities have previously been studied by culture-dependent as well as culture-independent methods (Edwards et al, 2015 ; Bertani et al, 2016 ; Kanasugi et al, 2020 ; Kim and Lee, 2020 ; Sinong et al, 2020 ). We profiled the 16S and ITS2 regions to reveal the composition of bacterial and fungal communities.…”