Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.)

Hayley E Park; Lucas Nebert; Ryan M King; Posy Busby; James R Myers

doi:10.3389/fpls.2023.1251919

Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.)

Front Plant Sci. 2023 Oct 25:14:1251919. doi: 10.3389/fpls.2023.1251919. eCollection 2023.

Authors

Hayley E Park¹, Lucas Nebert¹, Ryan M King², Posy Busby³, James R Myers¹

Affiliations

¹ Department of Horticulture, Oregon State University, Corvallis, OR, United States.
² National Clonal Germplasm Repository, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States.
³ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.

Abstract

Introduction: We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history.

Methods: Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set.

Results: Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens.

Discussion: The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.

Keywords: breeding history; crop management; microbiome; rhizosphere; snap bean.

Grants and funding

This material is based upon work that is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, through the Western Sustainable Agricultural Research and Extension program under project number GW21-229. USDA is an equal opportunity employer and service provider. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author (s) and do not necessarily reflect the view of the U.S. Department of Agriculture.