Abstract
The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major U.S. growing regions (Michigan, Nebraska, Colorado, and Washington), plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data from beans grown in Colombia. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, the breadth of ecologically important dimensions included in this work (space, time, host genotype, and management) provides an example of how to systematically identify the most stably-associated microbiome members, and can be applied to other hosts or systems.
Highlights
Agriculture requires more efficient use of available resources, and the naturally occurring, soil-dwelling microbiota offers potential to contribute to the responsible
With the cooperation of the U.S Bean Coordinated Agricultural Project (Bean CAP), we executed a first-ofits-kind study of two divergent bean genotypes grown under field conditions in five major North American bean growing regions, including Michigan, Nebraska, Colorado, and Washington. These two genotypes belong to the Mesoamerican (Eclipse genotype) and Andean (California Early Light Red Kidney, CELRK genotype) gene pools that represent the major divergences from the wild bean ancestor [9]
From our effort that was inclusive of both broad biogeography, plant development, and inter-annual plantings, we discovered a stable bean rhizosphere microbiome of 48 members that persistently associated with this nutritionally, agronomically, and economically important crop
Summary
Agriculture requires more efficient use of available resources, and the naturally occurring, soil-dwelling microbiota offers potential to contribute to the responsible. With the cooperation of the U.S Bean Coordinated Agricultural Project (Bean CAP), we executed a first-ofits-kind study of two divergent bean genotypes grown under field conditions in five major North American bean growing regions, including Michigan, Nebraska, Colorado, and Washington These two genotypes belong to the Mesoamerican (Eclipse genotype) and Andean (California Early Light Red Kidney, CELRK genotype) gene pools that represent the major divergences from the wild bean ancestor [9]. From our effort that was inclusive of both broad biogeography (including the U.S and Colombia, and with different U.S management strategies), plant development, and inter-annual plantings, we discovered a stable bean rhizosphere microbiome of 48 members that persistently associated with this nutritionally, agronomically, and economically important crop This stable “core” was discovered in spite of apparent microbiome differences that were attributable to local soil conditions and management. We did not detect an influence of plant genotype, suggesting that this core membership supersedes it
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