Revised preprint out: Common bean core microbiome levels up to include plant developmental series

We're pleased to announce a revision to a preprint posted today on the bioRXiv.

We're pleased to announce a revision to a preprint posted today on the bioRXiv.  After using primary data from US common bean growers across the major production regions in the US, expanding the data set to include meta-analysis of beans grown in South America to discover a cross-continentally persistent core microbiome across the major divergent bean lineages, we now have leveled up to also detect these same core bacterial taxa persistently over plant development in the field! 



Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere

by Nejc Stopnisek and Ashley Shade


lants recruit soil microbes that provide nutrients, promote growth and protect against pathogens. However, the full potential of microbial communities for supporting plant health and agriculture is unrealized, in part because rhizosphere members key for plant health are difficult to prioritize. Microbes that ubiquitously associate with a plant species across large spatial scales and varied soil conditions provide a practical starting point for discovering beneficial members. Here, we quantified the structures of bacterial/archaeal and fungal communities in the common bean rhizosphere (Phaseolus vulgaris), and assessed its core membership across space and time. To assess a spatial core, two divergent bean genotypes were grown in field conditions across five major growing regions in the United States, and then also compared to eight genotypes grown in Colombian soil. To assess a temporal core, we conducted a time course of rhizosphere and rhizoplane microbiome members over bean development in the field. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans and over plant development, suggesting cosmopolitan enrichment and time-independence. Neutral models of abundance-occupancy relationships and co-occurrence networks show that many of these core taxa are deterministically selected and likely in intimate relationships with the plant. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets in support of translational plant-microbiome management. More generally, this work reveals that core members of the plant microbiome can have both broad ranges and temporal persistence with their host, suggesting intimate, albeit possibly opportunistic, interactions.



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