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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #382562

Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

Title: Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

item XU, LING - University Of California
item DONG, ZHAOBIN - University Of California
item CHINIQUY, DAWN - University Of California
item PIERROZ, GRADY - University Of California
item DENG, SIWEN - University Of California
item GAO, CHENG - University Of California
item DIAMOND, SPENCER - University Of California
item SIMMONS, TUESDAY - University Of California
item WIPF, HEIDI - University Of California
item Caddell, Daniel
item VAROQUAUX, NIELLE - University Of California
item MADERA, MARY - University Of California
item HUTMACHER, ROBERT - University Of California, Davis
item DEUTSCHBAUER, ADAM - Lawrence Berkeley National Laboratory
item DAHLBERG, JEFFERY - University Of California, Davis
item GUERINOT, MARY LOU - Dartmouth University
item PURDOM, ELIZABETH - University Of California
item BANFIELD, JILLIAN - University Of California
item TAYLOR, JOHN - University Of California
item LEMAUX, PEGGY - University Of California
item Coleman-Derr, Devin

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2021
Publication Date: 5/28/2021
Citation: Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H.M., Caddell, D.F., Varoquaux, N., Madera, M.A., Hutmacher, R., Deutschbauer, A., Dahlberg, J., Guerinot, M., Purdom, E., Banfield, J.F., Taylor, J.W., Lemaux, P.G., Coleman-Derr, D.A. 2021. Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications. 12. Article 3209.

Interpretive Summary: Organisms living in terrestrial ecosystems must be able to adapt to dry conditions that result from shifts in water availability due to diurnal and seasonal fluctuations. Plants, as sessile organisms, have adapted strategies to tolerate, resist, or avoid the stress imposed by drying environments. To respond to moisture gradients in soil, plants alter their physiology, modify root growth and architecture, and close stomata on their aboveground segments. Recently, it has been demonstrated that interactions with microbial partners above and below ground play a role in augmenting a plant’s ability to survive under drought and that drought significantly influences these interactions, altering both structure and function of the root microbiome. As it is hypothesized that droughts in the future are likely to be more frequent, severe, and long-lasting than they have been in recent decades, new and rapidly deployable solutions for improving drought tolerance in crops are needed. An increased understanding of the complex feedback between plants and microbes during and after drought will pave the way for harnessing the rhizosphere microbiome to increase the resilience of crop production to drought

Technical Abstract: Here, we employ genome-resolved metagenomics to recover 55 bacterial genomes from drought-stressed sorghum rhizospheres and use comparative genomics to identify pathways more prevalent within microbial lineages enriched under drought. We identify a group of Actinobacteria with significant enrichment under drought stress in the rhizosphere community and demonstrate that gene copy number of carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. Furthermore, we reveal that an inorganic ion transport and metabolism, is strongly associated with drought enrichment, and that within this category, the most abundant COGs are tied to iron metabolism. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress. Additionally, we show that loss of the maize phytosiderophore iron transporter TOM1/YS3 impacts microbial community composition, leading to significant increases in Actinobacterial abundance. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria and their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome’s response to drought and may inform efforts to improve drought tolerance for increasing food security.