PERPHECTO - Pathogen Evolution Resulting from Phage-Host Ecology in the Coastal Tropical Ocean

DERVISH - Diversity and Ecology of RNA Viruses in Saline Habitats

ChUMPS - Characterizing Uncultivated Microbes using Physical Separation

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 NSF, NIEHS, and is supported at present by Sea Grant.  Photo and Video Gallery.


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 NSF and 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 pathogenic bacteria in the genus Vibrio. 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). A paper with a detailed analysis of the entire seasonal cycle of vibrios is soon to be submitted and a paper evaluating different media for isolating pathogenic vibrios is in preparation. Funding was provided by NSF. Photo and Video Gallery.

This project has been supported by NSF through a seed grant (0621729) and a subsequent grant (0826650; PIs G.F. Steward, A. I. Culley, G. Poisson). We are investigating the abundance, diversity and ecology of RNA-containing viruses in seawater. A review of RNA viruses in the sea is available here (PDF). We have identified new picorna-like viruses in coastal waters of Hawaii and California by analysis of the viral RNA-dependent RNA polymerase gene sequences (PDF). We are also analyzing the total RNA virus community using environmental shotgun sequencing and isolating eukaryotic phytoplankton to establish new virus-host systems (more information).

One of our objectives has been to improve methods of studying viruses and we have published on laboratory and bioinformatic analyses. These include laboratory methods for purification of viruses (PDF), extraction of viral nucleic acids (PDF), and characterization of RNA viruses (PDF), as well as bioinformatic tools for comparative genomics (Request Reprint) and a program for classification of viral sequence fragments (Request Reprint).

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. These viruses infect phytoplankton and heterotrophic protists. A paper on the diversity of large viruses in the family Phycodnaviridae in local coastal waters is available here (PDF).  Funding provided by Sea Grant and NSF. A brief description of some of our current efforts to isolate new phytoplankton viruses can be found here

HOT LAVA - Hawaii Oceanographic Team for Large Aquatic Virus Analyses

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.  Photos and video of an AUV survey of the Ala Wai canal can be found in the Photo and Video Gallery. Funding provided by NOAA.

HiOOS - Hawaii Ocean Observing System

We 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). The value of fractionation for metagnomic analyses has been articulated here (PDF) and the mathematical basis of this advantage established here (PDF). An evaluation of viral fractionation methods was recently published (Brum and Steward 2011) and an application of these methods to analysis of a viral metagenome (Brum et al. 2013). Seed funding was provided by NSF.

Viral Ecology in Mono Lake

In this project we investigated the ecology of viruses in Mono Lake, a moderately hypersaline lake in the eastern Sierra Nevada Mountains of California.  This was a collaborative project with Sunny Jiang at the University of California, Irvine. Several of the publications resulting from this project are available here for download including a brief description of viruses in the lake written for the Mono Lake Newsletter (PDF), an investigation of the abundance and diversity of viruses in the lake (PDF), and a seasonal study of viruses and viral infections of bacteria (PDF). A morpholgical study of viruses at different depths in Mono Lake is currently in press. Photos of one of the sampling trips can be viewed here. Funding provided by NSF.

Ecology of viruses in the summer plankton bloom of the Western Antarctic Peninsula

Members of the MarVEL team have embarked on an expedition to the Western Antarctic Peninsula to investigate how viruses affect the massive summer blooms of phytoplankton. A short report about our upcoming adventure appeared on Hawaii Public Radio and can be heard here.  A an article about our project by journalist Susan Moran who interviewed Alex Culley while in Antarctica can be found here. Some photos from the first group’s trip and their first sampling can be found in the Gallery here. Funding for this project is provided by NSF.

LOCO-MOCO - Layered Organization in the Coastal Ocean - Microbial Observations of Community Organization

The LOCO-MOCO contingent is investigating the microbiology of thin layers of phytoplankton 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 was funded by NOAA National Undersea Research Program. Sampling in 2005 and 2006 was conducted in collaboration with researchers in the ONR-funded LOCO program. Information on thin layers can be found here, and here.

Past Projects