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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower Improvement Research » Research » Publications at this Location » Publication #421845
Research Project: Sunflower Yield, Crop Quality, and Interactions with Biotic and Abiotic Stressors

Location: Sunflower Improvement Research

Title: Heritable genetic differences affect sunflower rhizosphere archaeal, bacterial, and fungal communities across all taxonomic levels

Author
item BUENO DE MESQUITA, CLIFTON - University Of Colorado
item KEEPERS, KYLE - University Of Colorado
item KANE, NOLAN - University Of Colorado
item Hulke, Brent

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2025
Publication Date: 3/11/2026
Citation: Bueno De Mesquita, C., Keepers, K.G., Kane, N.C., Hulke, B.S. 2026. Heritable genetic differences affect sunflower rhizosphere archaeal, bacterial, and fungal communities across all taxonomic levels. Phytobiomes Journal. 10:127-137. https://doi.org/10.1094/PBIOMES-05-25-0034-R.
DOI: https://doi.org/10.1094/PBIOMES-05-25-0034-R

Interpretive Summary: Bacteria and fungi are associated with soils and the soil-root contact points in plants, but their biology is only now being carefully studied. In particular, the plant's genetic effect on the bacteria and fungi that come into contact with it is a new area of study. We looked specifically at this issue, and studied the tendency of sunflower lines to change the composition of bacteria and fungi that occur near it. Not only did we discover that sunflower lines can affect microbial composition, but that this ability is inherited throughout generations of sunflowers. This information will be helpful to sunflower breeders who may look to bacteria and fungi associated with roots to improve plant health.

Technical Abstract: All major agricultural crops have multiple genetically-distinct cultivars, and plant genetics can exert a strong effect on soil rhizosphere microbial communities. Here we use 16S and ITS marker gene sequencing data from the rhizosphere soil of 95 sunflower (Helianthus annuus) inbred lines to test the heritability of archaeal, bacterial, and fungal soil rhizosphere communities, as well as alpha- and beta-diversity metrics and differences in the relative abundance of microbial zero-radius operational taxonomic units (ZOTUs). The majority of taxa passing prevalence and relative abundance cutoffs (25%, 0.01%) were heritable across all taxonomic levels for both prokaryotes (archaea and bacteria) and fungi, with higher heritabilities at finer taxonomic resolution. Metrics of alpha-diversity and beta-diversity were also heritable, particularly for prokaryotes. Prokaryotic and fungal communities were both heritable, and at similar levels, but with significantly higher fungal heritability at the ZOTU, genus, and family levels. Prokaryotic and fungal richness were only weakly positively correlated, and beta-diversity was not correlated, which suggests that sunflower inbred lines affect prokaryotes and fungi in different ways. Our work provides valuable information for crop breeding and provides a general methodological framework for assessing the strength and types of genotype-microbial associations.