Research Projects
The ChUMPS use chromatographic and other physical fractionation techniques to isolate microbial populations directly from complex communities. Our goal is to move beyond metagenomics and to couple genomics with proteomics and other phenotypic analyses of uncultivated microorganisms. One of the methods we use to determine the progress of our fractionation is pulsed field gel electrophoresis (PFGE) of viral genomes. A methods chapter on the use of PFGE for analysis of viral communities is available here (PDF). Seed funding has been provided by the NSF.
The PERPHECTO team has tackled a number of projects dealing with the ecology of bacterial pathogens (Vibrio vulnificus, Staphylococcus aureus). We are interested in the environmental and biological controls on pathogen abundance and virulence and, in particular, how bacteriophages contribute to the population dynamics and virulence of these bacteria.
Project VECTOR
Vulnificus Ecology in Costal Tropical Ocean Regions - We are investigating the ecology of Vibrio vulnificus in coastal waters of Oahu. Our primary interests are in determining the physical chemical and biological mechanisms that control the abundance of clinical versus environmental strains of this serious human pathogen. Funding has been provided by the NSF and the NIEHS.
Project SAPPHIRES
Staphylococcus aureus Pathogen Phage-Host Interactions in the Recreational Environment of Seawater - We are investigating the abundance and diversity of the human opportunistic pathogen, Staphylococcus aureus, in coastal waters. We are particularly interested in the contribution of bacteriophages to the genetic diversity of S. aureus and the possible role of the coastal ocean as a melting pot for the creation of new strains of increased virulence. We have reports on the presence of virulence and antibiotic resistance genes (PDF) and on the presence of multiple prophages in S. aureus isolates from seawater at a recreational beach (PDF). Funding has been provided by the NSF and the NIEHS.
The Katrina Project
We were involved in a multi-institutional project that investigated the microbiological water quality in Lake Pontchartrain, New Orleans, following Hurricane Katrina. Our group focused on characterizing the spatial and seasonal variability of Vibrio bacteria. We isolated and characterized hundreds of the pathogens Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. for the presence of virulence-associated genes. Initial results appeared in a synthesis paper in the Proceedings of the National Academy of Sciences of the USA (PDF) and a paper with a more detailed analysis of the entire seasonal cycle of vibrios is in preparation. Funding was provided by the NSF and NIEHS.
The devotees of DERVISH investigate the abundance, diversity and ecology of RNA-containing viruses in seawater. We have identified new picorna-like viruses in local coastal waters by analysis of the viral RNA-dependent RNA polymerase gene sequences (PDF of a recent paper) and we are analyzing the total RNA virus community using environmental shotgun sequencing. We are attempting of new virus-host systems from local waters. Seed funding was provided by the NSF.
The LOCO-MOCO contingent is investigating the microbiology of thin layers of plankton that frequently form at density discontinuities in the ocean. As narrow zones of highly elevated plankton concentrations, thin layers have significant implications for our understanding of all manner of marine ecological processes. One consideration is how these layers may affect strategies for detecting harmful algal blooms (a paper on this topic is here: PDF). Work on this project has been funded by NOAA National Undersea Research Program. Sampling in 2005 and 2006 was conducted in collaboration with researchers in the ONR-funded LOCO program.
This team is hot on learning more about the abundance, diversity, and ecology of the large, very large, and huge DNA-containing viruses in the ocean and other aquatic environments.
The Hawaii Ocean Observing System is the Hawaiian Islands component of the Pacific Islands Ocean Observing System (PacIOOS). HiOOS is a coastal observing system that is intended to provide ocean data of use to the public, government agencies, businesses with links to the ocean, and marine researchers. Our lab is involved in the Automated Water Quality Sensing component of HiOOS. More information on the NOAA-funded HiOOS initiative can be found here.
