Deciphering the rhizosphere microbiota composition of nature farming soybean (Glycine max L.) with different nodulation phenotypes

Abstract

Background: Nature farming, a sustainable agricultural method which avoids agrochemicals and untreated organic amendments, promotes both agricultural productivity and ecological conservation. This system may foster unique plant-microbiota interactions for growth and fitness; however, the microbiota of nature-farmed plants remains largely unexplored. Second, root nodule symbiosis (RNS) is crucial for nitrogen fixation in legumes; however, its broader impact on rhizosphere microbiota assembly is not well understood. This study examined the dynamics between impaired nodule symbiosis, soil management, and the rhizosphere microbiota composition and growth of soybean (Glycine max L.).

Results: We evaluated the growth and characterized the rhizosphere bacterial and fungal communities of soybean by comparing wildtype soybeans (Enrei) with the non-nodulating mutants (En1282) across four soils under conventional and nature farming, including fumigated and unfumigated conditions. We found that the non-nodulating soybean mutants (En1282) exhibited reduced growth compared with wild-type (Enrei) plants, especially in untreated soils. Soil fumigation decreased microbial diversity and reshaped rhizosphere community composition with a significant reduction in plant growth and nodulation in all soils. Restriction in RNS increased bacterial diversity in untreated soils, possibly as a compensatory mechanism for nitrogen acquisition, whereas fungal diversity remained relatively stable. Nature farming promoted beneficial microbes like Rhizobium, Trichoderma, and Chloridium, whereas conventional soil plants favored Bacillus and Aspergillus. Notably, differential enrichment analysis identified distinct associations for each nodulation phenotype, with Enrei predominantly enriched for Pseudomonas, and En1282 associated primarily with oligotrophic microbes.

Conclusion: Our study sheds light on the complex interplay between legume symbiosis and rhizosphere microbiota assembly and highlights the significance of eco-friendly farming methods like nature farming in cultivating a healthy rhizosphere for plant growth. The results paves way for future strategies to manipulate rhizosphere microbiota, ultimately promoting robust and sustainable farming systems that reduce reliance on chemical inputs.

Keywords: Nature farming; Nodulation phenotype; Rhizobium symbiosis; Rhizosphere microbiota; Soil fumigation; Soybean.

Fig. 1

Effects of root-nodule symbiosis and soil fumigation on plant performance. (a) Image of soybean plants displaying the phenotypic differences between nodulating wildtype (Enrei) and symbiosis defect mutants (En1282) grown in four different soils under natural and fumigant-perturbed conditions. Boxplots showing measured plant growth traits including (b) SPAD value for leaf chlorophyll content (c) plant height (d) shoot fresh weight (e) average number of nodules per plant (the number of nodules were decreased by 64.8% in fumigated soils). Statistical significance is indicated by letters, based on linear mixed effect analysis and Tukey’s HSD test (p < 0.05, n = 16 for aboveground traits, n = 32 for number of nodules)

Fig. 2

Microbial community structure and diversity in the soybean rhizosphere. (a, c) Venn diagrams showing the number of unique and shared ASVs between Enrei and En1282 under non-treated (NT) and fumigant-treated conditions (T) conditions for bacteria and fungi, respectively. (b, d) Boxplots displaying alpha diversity measures (Shannon diversity index and observed species richness) for bacteria and fungi. (e, f) Nonmetric multidimensional distance scaling based on Bray-Curtis distance visualizing the effects of soil condition (fumigation treatment), farming system, and plant genotype on bacterial and fungal communities for bacteria and fungi, respectively

Fig. 3

Taxonomic composition of the most abundant microbial taxa in the soybean rhizosphere. Bar charts show the percent relative abundances of (a) bacterial phyla (b) bacterial genera (c) fungal phyla (d) fungal genera. Only the top 10 most abundant taxa are shown, with all other taxa pooled into “Others”. “NT = non-treated soils, T = fumigant-treated soils, C = conventional soil, N = nature farming soils

Fig. 4

Differential abundance of soybean rhizosphere-associated taxa. Dot plots illustrating taxa differences between the rhizosphere microbiota of nodulating soybean (Enrei) from RNS-impaired mutant (En1282) under untreated and fumigant-treated conditions. (a, b) Taxa differentiating rhizosphere communities between Enrei and En1282 for bacteria and fungi, respectively, in non-treated soils. (c, d) Taxa differentiating rhizosphere communities between Enrei and En1282 for bacteria and fungi, respectively, in fumigant-treated soils. LEfSe analysis was used to identify significantly enriched taxa with an LDA log fold threshold > 3 based on Kruskal-Wallis (p < 0.01), pairwise Wilcoxon (p < 0.01) and LDA analysis

Fig. 5

Putative functional prediction of microbial communities in the soybean rhizosphere. (a) The FAPROTAX annotated functions of bacterial communities in non-treated soils and fumigant-treated soils (b) The predicted guild assignments of soybean-associated fungal communities in non-treated and fumigant-treated soils