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.