EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS). MAPS First Awards are intended to help early career faculty become competitive for funding from the research directorates at the National Science Foundation. The awards do this by encouraging early career faculty to submit proposals to the NSF or other federal funding agency as soon as possible after their first faculty appointment, and by accelerating the pace of their research as well as the quality of their subsequent proposals. First Awards are awarded to a single-investigators to support their research program at their institution. Any tenure track faculty member who: 1) is currently nontenured at the assistant professor rank at the University of Kansas, Kansas State University, Wichita State University, Emporia State University, Fort Hays State University, Pittsburg State University or Washburn University; 2) is within the first three years of his/her faculty appointment; 3) has not previously received a First Award or similar funding from another EPSCoR or EPSCoR-like (Centers of Biomedical Research Excellence, COBRE) program in Kansas; and 4) is not currently nor has previously been a lead Principal Investigator of a research grant funded by a federal agency. Individual investigators may submit a total project budget of up to $100,000 in direct costs to the MAPS First Award program. Only projects with research in areas that are related to the current Kansas NSF EPSCoR focus of microbiomes as broadly construed to be in aquatic, plant and/or soil systems were considered. The following individuals and their research projects were awarded MAPS First Awards in the Spring of 2019:
Wichita State University
The research goal of this project is to design and validate a scaled-down version of the Trapping and Assisted Pairing (TAP) chip, a microuidics
tool for conducting plant cell-microbe interaction studies at the single-cell level meant to advance microbiome research. This goal stems from the big picture idea of smart and sustainable agricultural practices to meet
the future global crop production demands in the era of ecosystem degradation and climate change. The TAP will be capable of screening up to 10,000 cell-microbe pairs for symbiotic/parasitic relationships, help plant biologists devise approaches to maximize the symbiotic functions/minimize the parasitic functions, and engineer stress-tolerant plants. The TAP leverages droplet microuidics to efficiently trap 10,000 pairs of droplets |one set of droplets containing individual plant cells and another set of droplets containing individual microbes |and merge the droplet pairs, initiating 10,000 cell-microbe interactions. For maximizing the cell-microbe pairs, it is critical to understand the droplet trapping and merging physics. The project objective is to describe droplet trapping and merging physics in
the traps, and demonstrate the droplet trapping and merging capabilities of TAP. This project will significantly advance knowledge on two fronts. Biology: Advance the understanding of microbiomes. The TAP chip is a cell handling tool designed to advance microbiome research by enabling plant cell-microbe interaction studies at the single-cell level. By integrating a computer controlled x-y stage, automated data acquisition system, real-time image processing, and traditional imaging infrastructure, the TAP will be a live-cell reporter system that can track the progression in cell-microbe interactions for extended periods of time, and thus allow it to answer a wealth of microbiome questions: What genes in cells/microbes turn ON/OFF during interactions? Are there any yet-to-be-discovered cell microbe relationships? Engineering: A fundamental understanding of the influence of trap geometry and fluid properties on droplet trapping and merging. The TAP leverages droplet microuidics to pair individual plant cells and microbes in a droplet. It is very critical to understand droplet trapping and merging physics for maximizing the plant cell-microbe pairs. Through first principles-based parametric studies, design charts and guidelines necessary for the design of traps will be created.
Kansas State University
Soil water and heat dynamics exert a strong control on soil respiration by modulating the rate of microbial activity, substrate availability, and the diffusion rate of carbon dioxide at the soil aggregate level. Thus, a first order up-scaling of soil respiration from the aggregate level to the
watershed level inevitably requires knowledge of the spatial structure of-, and cross-scale interactions between, soil moisture, soil temperature, and soil respiration. The goal of this study is to accurately quantify watershed scale soil respiration applying a simple up-scaling strategy based on the merger of chamber-based soil CO2 efflux observations with modeling predictions. We hypothesize that combining detailed information about the soil spatial variability of the catchment area with accurate soil respiration observations and a parsimonious model will result in more accurate estimates of soil respiration than the use of chamber observations or model predictions alone. A distinct feature of the proposed method is the integration of time-invariant landscape patterns with the soil moisture information from a cosmic-ray neutron detector capable of large-scale non-invasive soil moisture observations. This project will bridge the gap point-level (i.e. small survey chambers) measurements that leave large unmonitored areas between observations ecosystem-level soil respiration products such as those generated by eddy covariance flux towers. The proposed method will provide a framework for integrating ubiquitous soil respiration measurements and existing models of soil respiration to reconcile soil and tower fluxes and to better measure the exchanges of carbon dioxide of terrestrial ecosystems. Up-scaling methods that account for watershed soil spatial heterogeneity are essential to account for potential soil respiration “hot spots” and “hot moments”, better evaluate factors controlling the spatial variability of soil respiration, and assess the representativeness of eddy covariance tower measurements. This is particularly relevant in a global scenario characterized by the widespread deployment of micrometeorological tower sites that use eddy covariance methods (e.g. FLUXNET), the growing market of automated chamber systems, and new hectometer-level, non-invasive soil moisture sensing technologies.
Kansas State University
Cheaters threaten the evolutionary persistence of cooperative traits. When cheaters and cooperative individuals co-occur, cheaters have an advantage because they benefit from the costly action of their competitors while themselves avoiding cooperative costs. The investigators will examine the prevalence and degree of co-occurrence of a cooperative pathogen and the avirulent cheaters that exploit it. The generalist pathogen Agrobacterium tumefaciens infects plant hosts at great cost to itself. Infected plants produce a public good resource that the pathogen and any present cheaters can catabolize. Our work has experimentally demonstrated that the cooperative pathogen is vulnerable to invasion by avirulent, cheating genotypes of agrobacteria that out compete the pathogen in disease environments. However, the degree to which there is opportunity for this to occur in nature is poorly understood. Accordingly, we propose to assess how common cheating genotypes are and the degree to which cooperative and cheater agrobacteria co-occur in natural environments. We will sample agrobacteria from Konza Prairie from the rhizosphere of Helianthus annuus plants. Characterization of the pathogenesis functions, opine catabolism functions, and phylogenetic relationships of this sample of natural agrobacteria strains as well as those from an experimental mesocosm will allow us to determine the degree and distribution of agrobacterial genetic diversity and evaluate the prevalence and diversity of cheater strains. The investigators will also measure the rate and spatial scale of cooperator and cheater dispersal in experimental mesocosms to access how dispersal influences cooperative benefits and the spread of cooperative pathogens and cheaters. The proposed research will provide insight into the ecological dynamics mediating the evolution of cooperation. This proposal bridges concepts and approaches from ecology, evolutionary biology, and genomics to examine how competition and dispersal influence the dynamics of microbial populations. The findings are also relevant to understanding how microbial dynamics influence the spread of a facultative pathogen in both environmental reservoir and infected host environments. These issues are of key importance to understanding the epidemiology of pathogens that can live independent of their hosts. The plant pathogen A. tumefaciens has been a productive study system for determining the mechanisms of microbial interactions but the ecological consequences of these mechanisms are poorly characterized. The investigators have previously leveraged this mechanistic information to identify factors shaping key ecological and evolutionary processes like the fitness costs and benefits of cooperative pathogenesis.
Ecology and Evolutionary Biology
University of Kansas
A simplified community to enable manipulative study of maize microbiome function
Plants live in close association with hundreds to thousands of bacterial and fungal species, both on and inside their roots. This diverse and complex microbial community—the plant microbiome—can profoundly affect the health of the host plant. For this reason, plant microbiomes have great promise as a sustainable tool for protecting both crops and wild plants against environmental challenges. However, the enormous complexity of natural microbiomes has been an obstacle to understanding the principles and mechanisms that determine their composition and function. One powerful approach to overcoming this challenge is experimentation with “synthetic communities” (SynComs), which typically consist of dozens to a few hundred known microbial strains, contained within an otherwise sterile environment. SynComs enable precise manipulation of microbiome composition and analysis of the effects on community function. The goal of this project is to create a SynCom specifically for maize and use it to explore the role of microbe-microbe interactions in root microbiome function under drought conditions. Maize is critically important both as a crop plant and a model system in genetics research. However, the existing maize SynCom contains only seven bacterial species, which limits its value and versatility. The proposed experiments will investigate maize root microbiome assembly from farm and prairie soils across a natural precipitation gradient in Kansas (Objective 1), generate a curated collection of microbes isolated from maize roots growing in these soils (Objective 2), and use the resulting SynCom to test how key organisms influence the rest of the microbiome and function of the whole community, in a water-limited environment (Objective 3). The proposed work would be the most thorough study to date of the maize root microbiome response to drought conditions, as well as the first to investigate the role of legacy effects (land-use and historical precipitation levels) on soil microbiome function. It would also increase the number of microbial strains available for maize SynCom experiments by approximately 30-fold, thus massively improving the microbial functional diversity that can be studied. The effects of SynCom strains on maize phenotype and microbiome structure under water-stressed conditions will be directly tested under reproducible germ-free growth conditions. The expanded SynCom may form the basis of a wide variety of follow-up projects, investigating plant-microbiome interactions at levels ranging from genes to ecosystems.
Funding for the Spring 2019 MAPS First Awards is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.