Abstract
Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.
Highlights
Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny
Surveys of root microbiomes associated with angiosperms such as Arabidopsis thaliana[1, 2], maize[3], oak[4], barley[5], rice[6], lettuce[7], and sugarcane[8] typically reveal Actinobacteria and Proteobacteria as the dominant phyla, suggesting that certain members of these lineages may be consistently enriched in the plant root environment
We identified significant correlation between root community composition and host phylogeny in a survey encompassing plant species from multiple plant phyla growing in close proximity
Summary
Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin[329], and FW68 We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. Surveys comparing root-associated communities in maize, sorghum, and wheat[11] (all monocots), as well as Arabidopsis and the related species Cardamine hirsuta[12] (eudicots), report greater variation in root community composition between more distantly related plants These studies hint at a broader influence of host phylogeny on root microbiome composition than is currently appreciated. A core root microbiome was identified at the study site that comprises both well-known plant-associated taxa and poorly characterized and as yet uncultured taxa
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