Drought Drives Spatial Variation in the Millet Root Microbiome

Abstract

Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.

Loss of Arabidopsis matrix metalloproteinase‐5 affects root development and root bacterial communities during drought stress

“…Library preparation and amplicon sequence data processing was performed according to Simmons et al (2018Simmons et al ( , 2020. To account for differences in sequencing read depth across samples, the data per sample were normalized by dividing its reads per ASV by the sum of usable reads, resulting in a table of relative abundance frequencies.…”

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective

“…Drought stress not only perturbs the plant phenotype, but also the microbial community structure, leading to a decrease in the community diversity [13] , [48] , [49] , [50] . Interestingly, we witnessed opposite response patterns: the community diversity significantly decreased in the soil under drought treatment, but it did not differ or rather increased in the endosphere community.…”

Drought shifts sorghum root metabolite and microbiome profiles and enriches the stress response factor pipecolic acid

“…16S amplicon sequencing reads were demultiplexed in QIIME2 (86) and then passed to DADA2 (87) to generate Amplicon Sequence Variants (ASVs), with taxonomies assigned using the August 2013 version of GreenGenes 16S rRNA gene database as described previously (16). All subsequent 16S statistical analyses were performed in R-v3.6.1 (88).…”

“…For example, enrichment of monoderm bacteria, such as Actinobacteria, during drought has been observed across diverse plant clades (6, 7, 13, 14). Notably, recent studies have demonstrated that plants mediate the shifts in bacterial communities during drought (15), and Actinobacterial enrichment during drought is dependent on signals produced by living roots (16). While monoderm bacteria are dominant during drought, their enrichment is transitory, with diderm bacteria reestablishing after rewatering (13).…”