Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere

Abstract

Aim Most culture‐independent studies of bacterial biogeography have been at genus or higher taxonomic levels, although many important processes mediated by bacteria are at the strain or species level, such as the competitive nodulation of rhizobia on legumes. Here, at the intra‐species level, we characterized the structural variation in rhizobial populations in soybean rhizosphere under field conditions across 32 sampling sites in three eco‐regions. Location North‐east (Heilongjiang), north (Hebei–Shandong) and south (Jiangxi) China. Methods The intra‐species diversity of rhizobia in soybean rhizospheres was investigated by rpoB pyrosequencing. Soybean nodule isolates were characterized using repetitive extragenic palindromic PCR, restriction fragment length polymorphism of 16S‐23S intergenic sequences and rpoB PCR sequencing. Patterns and processes of biogeography of identified rhizobia were studied. Results Significant biogeographical patterns of rhizosphere rhizobia at the species level were found, and the abundant species in the rhizosphere were generally the dominant microsymbionts in soybean nodules. The distribution of rhizobial species in the rhizosphere across eco‐regions correlated with combined effects of spatial, vegetative, edaphic and climatic variables. Gene flow and genetic differentiation analyses revealed that there was no dispersal limitation among geographical populations of the same rhizobial species, and drift or subsequent diversification might be involved in shaping the biogeographical pattern in addition to environmental factors. Main conclusions These results constitute the first report of the existence of rhizobial biogeography in legume rhizospheres at the species level, contrasting with most studies, which focused on nodule isolates. The method developed in this study could be used to uncover, at high resolution, the diversity of local rhizobial populations in soils. This information is crucial for choosing suitable strains or species as inoculants for a specific legume host under local field conditions. Moreover, a similar strategy could be used to study other bacteria with important ecological functions.

Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean

“…A well-known example of this is the substantial differences in nodulation rates of Sinorhizobium and Bradyrhizobium in soybean grown in soils with different pH values; the differences in the pH tolerance of Sinorhizobium and Bradyrhizobium may explain the geographic distribution patterns of these rhizobia [15,19,22,23]. Comparative genomic analysis revealed that genus-specific genes, known to be involved in alkaline-saline adaptations, likely contribute to the observed biogeographic patterns of Bradyrhizobium and Sinorhizobium nodulation in soybean [24]. Here, we found that the soybean rhizosphere microbiota, especially the B. cereus group, affect the growth and nodulation of Sinorhizobium and Bradyrhizobium, which may also affect the nodulation of these two kinds of rhizobia.…”

“…It has been proposed that the adaptability of these rhizobia to soils with different pH values underlies the biogeographic patterns of soybean root nodulation mediated by Bradyrhizobium and Sinorhizobium [22]. Indeed, Sinorhizobium species are dominant in alkaline-saline soils, whereas Bradyrhizobium are dominant in neutral to acidic soils [23][24][25].…”

The nitrate‐reduction gene cluster components exert lineage‐dependent contributions to optimization of Sinorhizobium symbiosis with soybeans

“…Sinorhizobium fredii predominates Glycine max (cultivated soybean) and G. soja (wild soybean) nodules in the alkaline‐saline soils, while Sinorhizobium sp. III and S. sojae show limited abundance in few sampling sites (Wu et al ., ; Tian et al ., ; Guo et al ., ; Zhang et al ., ). In this study, representative strains of three species SF45436 ( S. fredii CCBAU45436), SS05631 ( S .…”

“…Indeed, SF45436 represents the most abundant sublineage of S. fredii, which dominates soybean nodules and rhizospheres in alkaline-saline soils and has a larger accessory genome than Sinorhizobium sp. III (SS05631) and S. sojae (SJ05684) Zhang et al, 2017).…”

“…(Fig. 6), although it might be either subsequently lost in the genome of S. sojae or not received by this species with limited geographical distributions Zhang et al, 2017).…”