My background is in microbial ecology and bioinformatics.
HERBVRE - a multi-year experimental field study analyzing the effects of nutrient amendment and herbivory on corals and their associated microbes. Both overfishing and eutrophication are thought to be harmful to coral reefs. However, the effects of each factor can be difficult to disentangle in descriptive studies, because many stressors to coral reefs are correlated (areas of high human habitation may be subject to both eutrophication, overfishing, pollution, damage from anchors, etc). By experimentally exposing reef plots to nutrient addition (slow diffusing fertilizer) or excluding herbivores, this project aims to directly test how these factors affect microbial communities on the coral surface. By studying DNA samples taken every 6 weeks across years, we are also seeking to understand how these stressors interact with periods of extreme ocean temperature. Understanding these interactions may be important in a changing climate. This project is a collaboration with Deron Burkepile.
Co-evolution of corals and their microbes (the GCMP)- this recently funded NSF Dimensions of Biodiversity project aims to conduct a global microbial survey of the major evolutionary groups of reef-building corals. We aim to study the microbial diversity of coral skeleton, tissue and mucus at 15 sites spanning the globe. This will provide a framework that will allow discoveries in particular corals (e.g. microbe A is important) to be related to coral diversity worldwide. The project will also culture key microorganisms associated with corals, and use high-throughput metabolic characterization to test some of their biochemical capabilities. One overarching goal is to trace when associations with particular microbial groups were acquired in coral's evolutionary history, and to see whether this helps to explain disease resistance or susceptibility of particular coral species. This project is a collaboration with Mónica Medina.
Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUSt)
This software package uses evolutionary modeling of sequenced bacterial and archaeal genomes to predict their contributions to metagenomes. By comparing mostly uncultured microbes from environmental libraries to their sequenced relatives, it is possible to estimate the contents of microbial communities using 16S rRNA libraries as input. It is also able to use this tool to correct 16S rRNA libraries for variation in 16S gene copy number.
You can read more on my blog, Napkin Diagram