Soil microbial communities represent a largely untapped source for yield improvement in crops. In comparison to plants grown without microbes in the soil, yields can be twice as great when plants are grown with their full complement of soil microbes. Microbes may improve plant growth by making soil nitrogen more available to plants. From the point of view of plant growth and eventual yield, nitrogen is important as it is a critical component of one enzyme, Rubisco, which takes carbon dioxide from the air and converts it to sugars for growth through the process of photosynthesis. To identify how microbes improve plant growth, the current research examines 1. how microbes modify soil chemistry, 2. what plant genes are selectively turned on in response to the presence of microbes, 3. how plant processes like photosynthesis respond to microbes, and 4. what the identity and functions are of the soil microbes. Connecting results from these four sets of data will reveal what it is that promotes plant growth, from the soil to the whole-plant level. This research also includes ways to predict plant growth and yield in response to soil microbes when different amounts of nitrogen are added to the soil, which should enable reduced use of fertilizers. The plant being studied is Brassica rapa, which is grown around the world as root (turnip), leaf (cabbage, pak choi), and oilseed (canola) crops; because of the diverse uses of this crop, results from this species are expected to apply to a wide range of other crops. Soil microbes are an important part of the ecosystem, and connect plants to the physical environment. While much is known about the plants in natural and agricultural settings, less is known about the distributions, types, and functions of beneficial soil microbes, and how they help crops cope with poor growing conditions such as drought or lack of nitrogen. The current research fills these knowledge gaps, and will provide recommendations on how to manage soils for beneficial microbes. Broader impacts to this work include development of guided tours within the Williams Conservatory, Geology Museum, and Berry Center for Biodiversity at the University of Wyoming as well as teaching modules related to the study of evolution and crop domestication.
Soil microorganisms serve a range of ecosystem services that promote plant growth under stressful abiotic conditions, including nitrogen limitation. Yet, soil microbial communities represent a largely untapped source for yield improvement in crop species. Analyzing plant transcriptomic and physiological responses to taxonomically and functionally diverse soil microbiomes will provide insights as to the mechanisms by which microbes enhance plant growth. Further, Bayesian systems modeling of plant transcriptomic, hydraulic, and gas-exchange responses to the soil microbial environment can provide a predictive understanding of plant growth promotion by microbes under variable nitrogen amendments. When grown with an intact vs. reduced soil microbiome, crops of Brassica rapa upregulate gas-exchange and increase biomass accumulation up to two-fold, suggesting one physiological link between plant transcriptomic responses to soil microbes and eventual plant biomass accumulation. Because B. rapa is domesticated as root, leaf, and oilseed crops, mechanisms of growth promotion characterized in this species could translate to a range of other crops. Further, the microbiome associated with the rhizosphere of B. rapa is highly differentiated from that of bulk soils more distant from the roots, suggesting the species is an effective model for studying the assembly dynamics, identity, and function of beneficial plant-associated soil microbes. Using next-generation amplicon and metagenome sequencing of rhizosphere DNA in combination with plant genomic, transcriptomic, and physiological experiments, the research will characterize mechanisms of plant growth promotion by soil microbes and test predictive systems models. The research addresses the PGRP 2014 focal areas: to develop a genome-level link between genes and physiological functions in crop plants and to develop a genome to systems-level understanding of plant-environmental interactions, especially with respect to abiotic stress. Broader impacts to this work include development of guided tours and teaching modules related to crop domestication and improvement as well as development of management practices for beneficial microbes. Information on this project can be accessed at www.RhizoBiomics.org.
