SEP 12, 2019 9:00 AM PDT

Investigating the common bean microbiome

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Postdoctoral Scholar, Michigan State University
    Biography
      Nejc Stopnisek is a post-doctoral research associate in the Department of Microbiology and Molecular Genetics at Michigan State University. His research revolves around the use of Next-Generation Sequencing, metabolomics, bioinformatics, and physiological methods to characterize soil and plant associated microbial communities, uncover their functional importance, and decipher molecular and metabolic mechanisms underpinning their responses to anthropogenic perturbations and climate change processes. Recently his work is focused on unravelling the beneficial microbes of the common bean and their integration in plant breeding strategies. Before joining Michigan State University, Dr. Stopnisek worked as a post-doctoral research associate at the University of Washington, applying synthetic microbial ecology approaches to better understand syntrophic interactions in anaerobic systems. He holds a Ph.D. degree from the University of Zurich, Switzerland and Undergraduate diploma from the University of Ljubljana, Slovenia.

    Abstract

    Plants 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 two evolutionarily-distinct genotypes, grown in field conditions across five major growing regions in the United States. We discovered a conserved core microbiome of 271 bacterial, archaeal and fungal taxa that were consistently associated with the common bean, despite different soil types, management, climates and genotypes. Neutral models of abundance-occupancy relationships and co-occurrence networks suggest that these core taxa are in intimate relationships with the plant, rather than important members of the local soil microbiome. We expanded our study to leverage rhizosphere samples inclusive of eight additional common bean genotypes that were grown in Colombian soils. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets for functional investigation in support of sustainable common bean agriculture. More generally, our approach provides insights into microbial taxa that can be prioritized towards translational studies of plant-microbiome. management.

    Learning objectives:

    1. Rhizosphere is one of the most diverse ecosystems harboring a great number of plant beneficial microbes and functions.
    2. Plants consistently recruit a number of ecological important microbial taxa which represent the core microbiome.
    Members of the core microbiome have potential to be implemented in plant breeding strategies.


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