Abstract
Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.
Highlights
Plants coexist with complex microbial communities both in above-ground organs and below-ground, the rhizosphere including both the inside of the root tissue and the soil immediately adjacent to and under the influence of the root system
When taking into account pairwise phylogenetic distance between Operational Taxonomic Units (OTUs) in the community structure analysis (NMDS with Weighted UniFrac), plant species had much stronger effect than soil and there was a reduced interaction between the two (ANOSIM: R plant = 0.39, F = 8.5, p = 0.001; R soil = 0.07, F = 1.8, p = 0.001; R plant : soil = 0.417, F = 1.5, p = 0.033, respectively, Figure 3). These analyses reveal that specific bacteria tend to be associated with different host species
Distinct bacterial communities are typically associated with roots of different agricultural crop species in the field (Wieland et al, 2001; Marschner et al, 2004; Haichar et al, 2008)
Summary
Plants coexist with complex microbial communities both in above-ground organs (the phyllosphere) and below-ground (the rhizosphere), the rhizosphere including both the inside of the root tissue and the soil immediately adjacent to and under the influence of the root system. A wide range of physiological benefits for plants may result from the association with bacteria; benefits that include nutrient acquisition, enhanced stress tolerance, host immune regulation, and protection against soil borne pathogens and phytophagous insects (Pineda et al, 2010; Berendsen et al, 2012; Mendes et al, 2013; Turner et al, 2013a; Bakker et al, 2014; Cook et al, 2015). Microbiome effects on host immunity are thought to be crucial. Despite their importance, we are at an early
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