Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities

Authors: BUENO DE MESQUITA, CLIFTON - University Of Colorado; WALSH, CORINNE - University Of Colorado; ATTIA, ZIV - University Of Colorado; Koehler, Brady; Tarble, Zachary; VAN TASSEL, DAVID - The Land Institute; KANE, NOLAN - University Of Colorado; Hulke, Brent

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Plant associations with beneficial bacteria and fungi, particularly at the root-soil contact space, are important for plant health. One particular sunflower health problem is Sclerotinia (white mold) infection of the roots, which has been shown to be inhibited by the presence of certain bacteria in the rhizosphere. An unanswered question is how root-associated bacteria and fungi, including those that inhibit white mold disease, are affected by the genetics of the sunflower plant, the environment they are grown in, and the interaction of the two. After growing a representative sample of 10 sunflower lines in replicated trials across the Great Plains and sampling their root-associated bacteria and fungi, we found that environment plays the largest role, but for many beneficial bacteria, sunflower genetics and interaction of genetics with environment also mattered. This information is helpful in developing methods to combat white mold infection of sunflower roots by breeding for better genotypes as well as changing the environment to be more conducive to these bacteria.

Technical Abstract: Plant associations with soil microorganisms are crucial for their overall health and functioning. While much work has been done to understand the drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unsolved, as results across studies and focal plants have been mixed and comprehensive studies across many sites and genotypes are limited. Furthermore, how plant genotypes affect soil microbiomes in ways that are crucial for key crop outcomes such as resistance to fungal pathogens is a critical unanswered question. Here we present 16S and ITS marker gene sequencing data from rhizosphere soils of 10 genotypes of the common sunflower (Helianthus annuus) from 15 sites across a broad geographic range in the Great Plains of the United States. We found that while site generally far outweighed genotype overall in terms of effects on both prokaryote and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a stronger influence on prokaryotic and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Genotypes varied in their susceptibility to the fungal pathogen Sclerotinia sclerotiorum but this was not related to their genetic distance or microbiome composition. Taxa that were previously found to be associated with Sclerotinia resistance were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and future manipulations of microbiomes for the improvement of agriculture across different geographic regions.