Diversity and function of soybean rhizosphere microbiome under nature farming

Abstract

Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.

Keywords: fumigation; microbiome; nature farming; rhizosphere; soybean; symbiosis.

Figure 1

The effect of soils, fumigation, and soybean genotypes on average number of nodules (A,B) and the rate of AMF colonization in soybean roots based on the presence of arbuscles, vesicles, and hyphae (C,D). Different letters indicate significant differences between samples based on the SNK test (p < 0.05). C, conventional farming soil, N, nature farming soil, n = 4.

Figure 2

Rhizosphere bacterial and fungal community of soybean as influenced by cultivar, farming system, and chloropicrin treatment. Alpha diversity (Shannon index) of bacteria (A) and fungi (B). Principal coordinate analysis (PCoA) based on Bray Curtis dissimilarity index for bacteria (C) and fungi (D). C, conventional farming soil, N, nature farming soil.

Figure 3

Taxonomic composition of microbial communities inhabiting the rhizosphere of soybean grown in conventional and nature farming soils with and without chloropicrin treatment. The bar graphs represent the relative abundance of bacterial (A) and fungal (B) communities at the genus level. Only taxa with abundance >1% are shown. WT = Enrei cv. C, conventional farming soil, N, nature farming soil.

Figure 4

Linear discriminant analysis effect size (LEfSe) results of top 20 bacteria (A) and fungi (B) that were significantly enriched in either conventional or nature farming soil, and bacteria (C) and fungi (D) with significant abundance in either non-treated or chloropicrin-treated soils. Red boxes show a high abundance and blue boxes show a low abundance of a particular genera.

Figure 5

Putative functional prediction of bacterial communities in the rhizosphere of soybean grown under different farming systems (A), and the treatment of chloropicrin (B) using PICRUSt. The top 25 significantly dominant functional pathways are shown.

Figure 6

Network co-occurrence analysis of rhizosphere bacterial communities of soybean grown in non-treated conventional soil (A), chloropicrin-treated conventional soil (B), non-treated nature farming soil (C), and chloropicrin-treated nature farming soil (D). Correlation network generated using SparCC algorithm, with nodes representing taxa at the genus level and edges representing correlations between bacterial taxa. Co-occurrence networks are based on Pearson correlation with a threshold of r > 0.5.