Task A) Evaluate microbes and microbial consortia for improving soybean stress tolerance. Individual microbes can enhance the stress tolerance of a range of crops. We have recovered microbes and microbial communities from the endosphere of roots of soybeans grown under water-deficits. We proposed that microbes and microbial communities selected by stressed soybeans have a strong probability of promoting plant health when used as inoculants. Here, we propose to use our collection of microbes, both singly and in combination, and our collection of recovered microbiomes to evaluate the potential for microbes to enhance the resilience of soybeans to abiotic stresses. We will compare inoculated and uninoculated plants for their growth under a range of water deficits, salinity, and low phosphate conditions, using growth parameters that we have validated as indicators of abiotic stress. These results will test the benefits of inoculants as stress protectants for soybeans. These results will also test whether soybeans select for microbial communities that are beneficial under stressful environmental conditions, with this new knowledge providing microbiome targets for soybean breeding aimed at stress tolerance.
Task B) Explore the influence of ROS on interactions within the root microbiome. ROS may influence microbial interactions within microbiomes in various ways, and knowledge of these interactions would be useful to strategies to amplify target beneficial microbes. We hypothesize that stress-induced systemic ROS in soybean enrich for specific microbes by killing those that are not ROS tolerant. Alternatively, ROS in soybean may enrich for specific microbes by activating the production of antibiotics or predation functions that kill non-target microbes. We propose to use our collection of microbial isolates from roots of water-limited soybeans in lab assays to evaluate ROS tolerance and the impact of ROS on antibiotic production and predatory activities. We will use this information to help optimize the inoculants identified in Task A, such as by evaluating the impact of enrichment via ROS exposure to increase their survival in stressed plants. Understanding the processes by which ROS alter root microbiomes is critical to using these processes to direct or reshape soybean microbiomes, as we propose to do with Bradyrhizobium inoculants, below.
Task C) Use ROS-based strategies to improve the efficacy of Bradyrhizobium japonicum inoculants under stressful environmental conditions. Biological nitrogen fixation due to the Bradyrhizobium-soybean symbiosis is highly sensitive to water deficits and high salinity. We hypothesize that stress-associated ROS signaling in soybean contributes to the sensitivity of the symbiosis to these stresses, and that this sensitivity can be attenuated by various ROS-based strategies. We propose to test this, first, by enhancing the tolerance of B. japonicum to ROS by passaging cultures through increasing ROS levels in culture. We predict that pre-adaptation of the symbiont to ROS will enable earlier nodulation and nitrogen fixation, and the resulting fixed nitrogen will help promote continued plant growth under at least low levels of stress. Second, we will screen for microbial isolates that enhance the oxidative stress tolerance of B. japonicum in culture, and will co-evolve B. japonicum in mixed cultures under ROS stress, with cross protection likely resulting from the secretion of antioxidants and enzymes. We predict that inoculants with B. japonicum in mixtures with antioxidant-producing bacteria or in cultures co-evolved to be ROS tolerant will enable earlier nodulation and nitrogen fixation. These results have the potential to boost nitrogen fixation under water deficits, as well as in the presence of other ROS-generating stresses including salinity, low phosphate and acidity.