Variation in soybean root-associated microbiome between lateral roots with and without nodules.

Background: Leguminous crops could fix atmospheric nitrogen through their symbiotic and non-symbiotic associations with different microbes to survive and maintain nutrient in soils that are deficient in nitrogen. Only limited number of lateral roots of the legume prefers to formulate nodules. So far, it is unclear whether microbial communities in lateral roots with/without nodules are different, and whether the selection of microbiome among different types of lateral roots of a plant is a random process or is strictly controlled by the host plant. Methods: We investigated the diversity and community structure of prokaryotic and eukaryotic microorganisms inhabiting in lateral roots with and without nodules of soybean via high-throughput 16S rDNA and 18S rDNA amplicon sequencing. In addition, quantitative microbial element cycling method was applied to estimate the functional genes that are related to carbon, nitrogen, phosphorus, sulfur cycling and methane metabolism. Results: Microbiome in rhizosphere of lateral roots with nodules had significantly lower α-diversity and higher co-occurrence network complexity, compared to those of lateral roots without nodules. The neutral model analysis demonstrated that microbial community of lateral roots with nodules in rhizosphere soil were less affected by neutral process than that of lateral roots without nodules. In addition, we identified a keystone ecological cluster (Module #1) of the rhizosphere cross-kingdom network that positively correlated with multiple functional gene copies, suggesting that the microbial taxa in Module #1 could play important roles in nutrient cycling of rhizosphere microenvironment. Conclusions: Overall, our study revealed the differences in microbial communities in the lateral roots with/without the nodule of root systems and identified a keystone ecological cluster positively linking with multiple functional cycling. [ABSTRACT FROM AUTHOR]