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Plant Microbiome Interactions


Plants grow in association with complex communities of organisms (microbiome). Plant-associated microbiomes have an important role in the sustained health and productivity of plants and plant ecosystems. We use innovative approaches to study the functional and structural basis of microbiomes as they relate to agricultural systems and the interactions between agricultural and natural systems. Ongoing projects address the roles of plant, insect, and/or soil-associated microbes in crop-plant performance and fitness. We are interested in examining coevolution of plant hosts with plant-associated microbiomes and the role of the microbiomes in the interactions between insect pests or pathogens and their hosts. The aim of our research is the development of new bioinformatic tools and host/microbiome models that will enable plant breeders and plant ecologists to predict beneficial interactions to achieve improved crop yields and plant resilience to changing environments.

Climate Change

Microbes in soil decompose litter, recycle nutrients, and produce and regulate greenhouse gases that are important at the ecosystem level; but how will climate change impact all these functions? We are using manipulative lab-based studies and long-term climate change experiments in natural and agricultural systems to understand the responses of microbial communities to global change and their feedbacks. In addition, we are also investigating the impact of climate change and extreme weathers on interaction between above and below ground communities and its consequences for ecosystem functioning (Collaborators: Western Sydney University, Australia; University of Minnesota, USA).


Microbiome Engineering

Microbiome engineering is an emerging field that aims to move beyond characterization of microbes, to manipulate, recombine, and control the collective properties, behaviors, and functions of interdependent microbial communities. In an ongoing project we are developing the next generation of tools and capabilities to probe the molecular mechanisms underlying community interactions. We will use this information to manage, analyze, interpret, and model the enormous amounts of data generated by microbiome studies and begin assembling synthetic communities.


Incorporating Microbiome in Ecosystem Models

Earth systems models play an integral role in predicting climate and climate forcing processes in the environment. However, traditional models don’t incorporate microbiome information. We are employing a systems biology approach, which couples modeling and simulation with experiment and theory to provide evidence for microbial regulation of biogeochemical cycles and feedback in response to climate change. The next challenge will be to develop physiological parameterizations that directly interface between molecular, genomic, and physiological datasets scaling the ecological models from the gene to ecosystem level.

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