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Although plant microbiome assembly involves a series of both plant–microbe and microbe–microbe interactions, the latter is less often directly tested. Here, we investigate a role for Streptomyces strains to influence assembly of other bacteria into root microbiomes through the use of two synthetic communities (SynComs): a 21-member community including four Streptomyces strains and a 17-member community lacking those Streptomyces strains. Following inoculation with these SynComs on wild-type Arabidopsis thaliana Col-0, differential abundance modeling on root endosphere 16S ribosomal RNA gene amplicon sequencing data revealed altered abundance of four diverse SynCom members: Arthrobacter sp. 131, Agrobacterium sp. 33, Burkholderia sp. CL11, and Ralstonia sp. CL21. Modeling results were tested by seedling coinoculation experiments with the four Streptomyces strains and differentially abundant members, which confirmed the predicted decreased abundance for Arthrobacter sp. 131, Agrobacterium sp. 33, and Ralstonia sp. CL21 when Streptomyces strains were present. We further characterized how the phytohormone salicylic acid (SA) mediates Streptomyces strains’ influence over Agrobacterium sp. 33 and Burkholderia sp. CL11 seedling colonization. Although decreased colonization of Ralstonia sp. CL21 and Arthrobacter sp. 131 when Streptomyces spp. are present were not influenced by SA, direct antibiosis of Arthrobacter sp. 131 by Streptomyces was observed. These results highlight a role for Streptomyces-mediated microbial interactions during plant root microbiome assembly as well as distinct mechanisms that mediate them. Understanding the role of microbial interactions during microbiome assembly will inform the production of beneficial microbial treatments for use in agricultural fields.
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Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
Abstract Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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- Award ID(s):
- 1917270
- PAR ID:
- 10379969
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- The ISME Journal
- Volume:
- 16
- Issue:
- 8
- ISSN:
- 1751-7362
- Format(s):
- Medium: X Size: p. 1957-1969
- Size(s):
- p. 1957-1969
- Sponsoring Org:
- National Science Foundation
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