Amplicons and isolates:Rhizobiumdiversity in fields under conventional and organic management

Abstract

Background: The influence of farming on plant, animal and microbial biodiversity has been carefully studied and much debated. Here, we compare an isolate-based study of 196 Rhizobium strains to amplicon-based MAUI-seq analysis of rhizobia from 17,000 white clover root nodules. We use these data to investigate the influence of soil properties, geographic distance, and field management on Rhizobium nodule populations. Results: Overall, there was good agreement between the two approaches and the precise allele frequency estimates from the large-scale MAUI-seq amplicon data allowed detailed comparisons of rhizobium populations between individual plots and fields. A few specific chromosomal core-gene alleles were significantly correlated with soil clay content, and core-gene allele profiles became increasingly distinct with geographic distance. Field management was associated with striking differences in Rhizobium diversity, where organic fields showed significantly higher diversity levels than conventionally managed trials. Conclusions: Our results indicate that MAUI-seq is suitable and robust for assessing nodule Rhizobium diversity. We further observe possible profound effects of field management on microbial diversity, which could impact plant health and productivity and warrant further investigation.

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

“…It will be important to validate these observed strain interactions in natural and rhizosphere soil communities in the future. While our results suggest that OE strains could be highly competitive, their frequency is relatively low in white clover nodule populations across Europe, while the gsC strains are often the most abundant (Kumar et al ., 2015; Cavassim et al ., 2020; Moeskjaer et al ., 2020). Relatively higher frequencies of gsE strains have however been observed in pea and faba bean nodules (Boivin et al ., 2020), which suggest that their abundance could also depend on the specific legume host.…”