Research Projects

The study of marine Archaea and Bacteria are much further advanced than those studying more recently evolved unicellular eukaryotes. We are working with other USC collaborators, Drs. Dave Caron and John Heidelberg, to evaluate diversity and genetic complement of marine taxa from uncultured (and unstudied) eukaryotes at a time series station in the San Pedro Time Series Station off the coast of Southern California. By sequencing portions of their genomes, we can begin to evaluate gene compliment and potential function on the oceans. These data will significantly increase genomic information on environmental microbial eukaryotes in the public domain and begin to allow detailed studies of relationships between and among prokaryote and eukaryote taxa. Graduate student Amy Koid is working on this project.

The central theme of the study of hypersaline Lake Tyrrell is to determine the influence of salinity on microbial ecosystems. We want to make Lake Tyrrell in outback Australia the best understood hypersaline ecosystems in the world. To achieve this, we are using a combination of environmental genomics and biomarker geochemistry to quantify the entirety ‘community’ of genes, lipids and pigments in the lake water with the goal of assigning them to different microbes that were identified by their genome (even if these can't be cultured). We are achieving this goal by deep genome sequencing of samples and biolipid and pigment analysis. Our data will provide a very detailed view of how the microbial community in Lake Tyrrell is constructed and how the ecosystem functions. Our data will also augment the scientific foundation for understanding ecosystems response to salinization that accompanies drawdown of groundwater reservoirs and provide data that may be applied to genetic engineering of salt-tolerant crops. Further infromation can be found here.

My lab is studying diversity and gene expression of marine microbial eukaryotic fractions from hydrothermal vent communities (9 North, East Pacific Rise, and Guaymas basin). This sampling effort has just begun, but we expect to find and characterize many previously unknown communities. See our NSF sponsored interactive educational outreach website for the 2008 cruise.

The marine environment around Antarctica have conditions that are very different from conditions in most of the other places that I have worked. On a 2 month cruise in 2008 our lab took part in a collaborative cruise with Dave Caron (USC) and Darcy Longsdale (SUNY Stonybrook) in the Ross Sea to evaluate what special adaptations microbial eukaryotes have evolved to tolerate the cold, and how this affects the flow of energy in marine food chains.

Australian soils are the most fragile in the world because they are low in organic matter, erodible and often subjected to drought. We are using a metagenomic approach (looking at the entire community of genes present in the environment) to inventory microbial communities from agricultural and non-agricultural soils.

Comparative sites are located in SE Victoria, near Manangatang, where the soil is acidic, nutrient-rich and there is high annual rainfall; and in NW Victoria, near Ellinbank, where alkaline, nutrient poor soil is found in a low rainfall region. A subset of samples for land-use comparison was made for the first site, between ‘managed’ (>60 years crop) and ‘remnant’ native vegetation sub-sites.

We are evaluating microbial communities to look for genes that yield insight into ecosystem function and adaptation to varying soil conditions and land use. Our results will be used for crop management decisions in the context of climate change as well as for resource sustainability.