Plant and Microbes

Do closely-related microbial taxa living inside plants respond similarly to environmental perturbations?

The microbiome of a plant host, the combination of microbial species inhabiting an individual, represents a diverse and labile community of interacting organisms. They play key functional roles for their hosts, yet our understanding their responses to environmental changes is limited. Evidence is accumulating that endophyte microbial responses to environmental changes are patterned by phylogenetic relationships among co-occurring taxa. As the functional roles played by species in a community are often more complementary when the community is composed of species from different evolutionary clades, phylogenetic analyses can reveal differences not captured by standard measures of species richness. I examined the effects of nutrient addition and herbivory in multiple replicated experimental set-up across four midwestern US sites on the phylogenetic diversity of foliar endophyte fungal communities of host grass species, Andropogon gerardii.

Our experimental set-up

Planting corn in one of our plots

Using metagenomics approach by next-generation sequencing of ITS1 region, we characterized phylogenetic response of fungal communities to the same environmental factors at different spatial scale (from host to site-level scale). Phylogenetic diversity does not increase nor decrease with spatial scale i.e. no scale-dependency although there is a significant phylogenetic turnover in communities among sites. Furthermore, nutrient addition and herbivory have differential impacts on phylogenetic diversity within and among fungal communities regardless of spatial scale. Together, these results highlight the idiosyncrasy of the impacts of environmental factors in fungal phylogenetic community assembly, possibly due to dispersal limitations and different environmental tolerance of microbial communities in an environment, and the importance of scale at which these factors are evaluated. This work provides insights into how sensitive plant-associated microbial communities are to global changes, and how it might potentially feedback into the plant’s health such as resistance to diseases and ability to successfully colonize a new habitat.


Oil spill, oil degradation and the microbes of saltmarsh plant

Species diversity is a fundamental property of ecological communities, relating to resource use, niche partitioning and coexistence, and is related to emergent properties of communities such as productivity and stability. I apply these concepts to address an ongoing environmental problem in Lousiana: Deepwater Horizon oil spill in 2010. I am examining shifts in endophyte fungal communities in leaves, roots and soil inhabiting key grass species in saltmarshes relative to oil spill. This work allows for identifying potential key functions conferred by the endophyte communities e.g. oil degradation to the host environment as well to host/plant physiology e.g. host tolerance by assessing the magnitude and trajectory of fungal community shifts in the presence of oil. Furthermore, comparison of endophyte communities in different compartments of a plant illuminates different mechanisms by which plant-microbe interactions are most affected by extensive environmental perturbations.

Saltmarsh islands near Port Fourchon, Lousiana

Preparing to get muddy and collect Spartina