Selecting soil microbiomes that optimize drought responsive traits in maize

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Eric R. Moore, Michaeline Nelson Albright, Christina Steadman, Anthony Sabella, Sangeeta Negi and John Dunbar, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, Kelsey R. Carter, John Heneghan, L. Turin Dickman, Dea Musa, Jeffrey Heikoop, Brent D. Newman and Sanna Sevanto, Earth & Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, Abby Nachtsheim, Christine Anderson-Cook, Anastasiia Kim and Nicholas Lubbers, Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, Chris Yeager, Chemical Diagnostics and Engineering Division, Los Alamos National Laboratoy, Los Alamos, NM, Louise H. Comas, Penn State University, University Park, PA

Background/Question/Methods
Soil microorganisms form close associations with plants and can improve plant growth under stressful conditions, including drought. Despite their potential for improving plant performance, microbial inoculations are often limited to a small collection of culturable organisms, and stable establishment of the introduced cells into the native microbiome is not always successful. Approaches that consider both the greater soil microbial community and plant as a whole may be more effective to improve plant performance under drought. We used artificial selection of the soil microbiome to improve the performance of two drought responsive traits, stomata closure point (SCP) and intrinsic water use efficiency (WUEi), in greenhouse grown maize. Using plant SCP or WUEi as performance markers, we identified soil microbiomes that were associated with the best performing plants, and selectively propagated these communities through several generations of plant growth. Changes in SCP, WUEi, soil microbiome composition, biogeochemistry, and other plant morphological and physiological traits were monitored to 1) determine if selection on the microbiome could significantly improve maize performance under water-limited conditions, 2) understand how the microbial community changed during selection, and 3) identify microbiome features associated with improved performance of these traits.
Results/Conclusions
Preliminary results suggest the potential for microbial control of traits related to SCP and WUEi. Inoculations of microbiomes derived from an agricultural field slowed stomatal conductance decline during drought by 20.1 ± 10.5 % and extended the time stomata were open by 2.6 ± 0.9 days, relative to microbiomes from pine forest soils. Inoculum previously subjected to drought also induced stomata closure 3.8 ± 1.8 days earlier under water replete conditions. We identified bacteria whose abundances significantly correlated with SCP or WUEi in each soil tested. Specifically, Dyadobacter, Devosia, Chthoniobacter, Mucilaginibacter, and family Pirellulaceae correlated with WUEi, while Marmoricola, Peredibacter, and family Pedosphaeraceae correlated with SCP, suggesting microbial driven optimization of SCP and WUEi is possible. After only one generation of selection, microbiomes associated with superior WUEi or SCP performance under drought in the previous generation showed no significant improvements in these traits compared to microbiomes associated with the worst performers, suggesting one generation was insufficient to observe shifts in plant performance. Maintaining selective pressure over multiple generations will be necessary to significantly optimize performance. If successful, selectively propagating whole microbiomes may be a solution to robustly optimize plant functions for specific environments and stressors, and to improve crop productivity.