Impacts of the Deepwater Horizon Oil Spill on fungal microbiomes in salt marshes

Large-scale environmental disturbances such as oil pollution can alter the diversity and composition of microbiomes, yet remarkably little is known about how disturbance alters plant-fungal associations. Using Next-Generation sequencing of the 18S rDNA internal transcribed spacer (ITS1) region, we examined outcomes of oil exposure on aboveground leaf and belowground endophytic root and rhizosphere fungal communities of Spartina alterniflora, a highly valued ecosystem engineer in southeastern Louisiana marshes affected by the 2010 Deepwater Horizon accident. This study offers novel perspectives on how environmental contaminants and perturbations can influence plant microbiomes, highlighting the importance of assessing long-term ecological outcomes of oil pollution to better understand how shifts in microbial communities influence plant performance and ecosystem function.

Spatial scaling of the effects of nutrient addition and herbivory on leaf endophytic microbial community in grasslands

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.

Ice age cycle impacts on genetic diversity of diverse plant taxa

After the last Ice Age, temperate European trees migrated northward, experiencing genetic bottlenecks and founder effects, which left high haplotype endemism in southern populations and clines in genetic diversity northward. These patterns are thought to be ubiquitous across temperate forests, and are therefore used to anticipate the potential genetic consequences of future warming. I examined whether these patterns do indeed hold across various taxa between two continents, Eastern North America (ENA) and Europe. Unlike their European counterparts, ENA trees do not share common southern centers of haplotype endemism and they generally maintain high genetic diversity even at their northern range limits. Differences between the genetic impacts of Quaternary climate cycles across continents suggest refined lessons for managing genetic diversity in today’s warming world.

Ancient DNA approach to reconstruct Holocene vegetation shifts and track genetic changes through time

Rapid changes in climate are causing species to shift their ranges. Plants are known to have individualistic response to climatic changes over the past 10,000 years, where climate warmed as much as it is warming today, leading to shifting plant community compositions in a given space and time. Long-term records of forest or vegetation shifts throughout Holocene are inferred from pollen and macrofossil analyses, however, these analyses have inherent limitations e.g. long pollen dispersal and uncertainty in detecting small populations. Ancient DNA from lake sediments can complement these paleoecological analyses. With training from our collaborator Dr. Poinar at McMaster University, I successfully extracted beech chloroplast DNA (cpDNA) from mud and macrofossils preserved in lake sediments for five thousand years (ancient DNA). I cored lakes in Michigan and extracted DNA from lake sediments to characterize how forests have changed over the last 10,000 years. Using a metagenomics approach, I targeted ancient chloroplast DNA from different plant species and sequenced them in Illumina. Characterizing the magnitude of past vegetation changes in response to past climate changes provides an empirical long-term record of how biodiversity was shaped through time and lends insights into the population process of range shifts.

Humans and trees

Large-scale forest clearance for agriculture had occurred following the European settlement starting in the 1600s, followed by forest regeneration as these lands were abandoned in the mid-1800s. In New England, these caused massive population declines, then regeneration, in disturbance-sensitive species such as American beech and Eastern hemlock. Such demographic shifts impact genetic diversity of populations. The magnitude of these impacts can be more pronounced in smaller populations at marginal habitat.