Heritable Genetic Differences Affect Sunflower Rhizosphere Archaeal, Bacterial, and Fungal Communities Across All Taxonomic Levels

Plant genetics can exert a strong effect on soil rhizosphere microbes. Broad-sense heritability estimates quantify the degree to which plant genotype predicts microbiome composition, enabling characterization of plant genotype effects on rhizosphere microbes. We used 16S rRNA and internal transcribed spacer marker gene sequencing data from rhizosphere soil from 95 field-grown sunflower ( Helianthus annuus) inbred lines to test the heritability of archaeal, bacterial, and fungal 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 of 25 and 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 and beta diversity were also heritable, particularly for prokaryotes. Prokaryotic and fungal communities were both heritable, but there was significantly higher fungal heritability at the ZOTU, genus, and family levels. Prokaryotic richness and fungal richness were only weakly positively correlated, and beta diversity was not correlated, suggesting 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. Because of high heritability for individual microbial taxa, as well as for microbial diversity metrics more broadly, sunflowers are clearly an important species to study the ecology, evolution, and genetics of plant–microbe interactions, and this knowledge can be used to improve sustainability of the crop. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .