Abstract
The rhizosphere microbiome (rhizobiome) plays a critical role in plant health and development. However, the processes by which the constituent microbes interact to form and maintain a community are not well understood. To investigate these molecular processes, we examined pairwise interactions between 11 different microbial isolates under select nutrient-rich and nutrient-limited conditions. We observed that when grown with media supplemented with 56 mM glucose, two microbial isolates were able to inhibit the growth of six other microbes. The interaction between microbes persisted even after the antagonistic microbe was removed, upon exposure to spent media. To probe the genetic basis for these antagonistic interactions, we used a barcoded transposon library in a proxy bacterium, Pseudomonas putida, to identify genes which showed enhanced sensitivity to the antagonistic factor(s) secreted by Acinetobacter sp. 02. Iron metabolism-related gene clusters in P. putida were implicated by this systems-level analysis. The supplementation of iron prevented the antagonistic interaction in the original microbial pair, supporting the hypothesis that iron limitation drives antagonistic microbial interactions between rhizobionts. We conclude that rhizobiome community composition is influenced by competition for limiting nutrients, with implications for growth and development of the plant.
Highlights
Microbial communities are being increasingly appreciated for their impact on larger biological systems, such as in relation to human health (Chu et al, 2016) or crop productivity (Mendes et al, 2018)
We examined a larger set of pairwise microbial interactions by competing a set of six (Acinetobacter sp. 01, Acinetobacter sp. 02, B. flexus, Brevundimonas sp., Flavobacterium sp., and Paenibacillus sp.; n ≥ 3 replicates) against the same set, plus the following five microbes: A. rhizogenes, Arthrobacter sp., Chryseobacterium sp., Leifsonia sp., and Ralstonia sp. (n ≥ 2)
In this report we dissect the pairwise interactions which may occur between several representative bacterial members of the Arabidopsis root microbiome
Summary
Microbial communities are being increasingly appreciated for their impact on larger biological systems, such as in relation to human health (e.g., the gut microbiome) (Chu et al, 2016) or crop productivity (e.g., the rhizobiome) (Mendes et al, 2018). A better understanding of microbial communities and their relation to the plant root is of specific interest to understand plant development, biogeochemical carbon cycling, and applications in agriculture. Photosynthetic bioproducts are exuded through the roots, modifying the rhizosphere through the accumulation of sugars and secondary plant metabolites. The composition of root exudate is complex (Chaparro et al, 2013; Kawasaki et al, 2016); simple sugars (such as D-glucose) have often been detected as major components of the root exudate in terrestrial plants such as the model dicot Arabidopsis thaliana (Okubo et al, 2016). Changes in exudate profile correlate with compositional and functional changes in the rhizobiome (Chaparro et al, 2013)
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