Our research

Whether on a farm or in the wild, plants encounter highly complex and variable environmental conditions, both abiotic and biotic. What role does the plant microbiome play in adaptation to environmental challenges? How do phenotypic plasticity and microbial endophytes affect plants’ evolutionary success or agricultural productivity? How do a plant’s genes influence its microbiome and its response to environmental variation? What is the best way to optimize the plant microbiome to improve crop resilience?

To answer these questions, we combine a quantitative genetics framework with sequencing-based microbiome censuses, metagenomics, and isolation-reinoculation experiments. We work with both natural microbial communities in the field and simplified, synthetic communities in the lab and greenhouse. Currently our main study organisms are maize (Zea mays ssp. mays) and the wild perennial mustard Boechera stricta.

Heritability of the metagenome in crops and wild plant species
A plant’s phenotype influences which microbes from the ambient community colonize and thrive within the plant. Clarifying the relationship between host genotype and metagenome composition is a crucial step towards incorporating endophyte communities into sustainable agriculture and understanding the evolution of plant-microbe interactions.

Microbial mutualists and drought resistance in maize
Drought causes serious loss of agricultural productivity across the globe, and is expected to worsen over the coming decades. We are using a combination of greenhouse experiments, field collections, and molecular data to discover microbial mutualists that improve drought resistance in maize and potentially other grass species. This work is funded by Kansas NSF EPSCoR.

Ecological causes and evolutionary consequences of phenotypic plasticity
Environmental variation influences complex trait evolution both by interacting with genotype to produce a phenotype (“plasticity”) and by determining the selection pressure on that phenotype. We use common-garden field and greenhouse experiments to study the intersection of these processes, which determines how or whether plasticity affects reproductive fitness within habitats or after a habitat change. Our particular focus is on microbial neighbors as a driver of plasticity and selection.

Inferring “beneficial” microbiomes from host evolutionary history
It is clear that microbiome disruption can have negative consequences for host health, but what makes a microbiome “beneficial” is poorly understood. Plants that are well adapted to particular environmental stresses may have evolved to recruit symbionts that alleviate those stresses; alternatively, maladapted plants may recruit helpful symbionts to compensate for a lack of genetic resistance. By comparing metagenomes assembled by adapted versus maladapted plants, we aim to identify candidate organisms and microbial genes that confer stress resistance and to validate their effects using re-inoculation experiments.