Current Research
The Breitbart lab studies viruses and bacteria in a wide range of environments. Here are descriptions of just a few of our many current projects. View recent publications on each of these topics.
DNA Barcoding of Fish Eggs
The Spawning Habitat & Early-life Linkages to Fisheries (SHELF) project funded by the Florida RESTORE Act Centers of Excellence Program identifies the taxa of planktonic fish eggs collected across the West Florida Shelf using DNA barcoding. DNA barcoding of fish eggs enables accurate identification of early life stages of ecologically and economically important fish species, locating important fish spawning areas. This long-term project will produce time-series data to detect changes in the amount or location of spawning by individual fish species as well as changes in fish egg community composition over time, which may be linked to climate change, fishing, or changes in habitat quality.
Viruses Associated with Harmful Algal Blooms
As part of the USF Center for Red Tide Tracking and Forecasting, the Breitbart lab is looking at viruses associated with red tides caused by the dinoflagellate Karenia brevis through mining available sequence data, performing viral metagenomics and PCR on field samples collected during blooms, and attempting to culture these viruses in the laboratory. This research recently yielded the first description of viruses associated with K. brevis harmful algal blooms in water samples from southwest Florida. Identifying viruses associated with red tide improves understanding of environmental factors involved in bloom dynamics and is a critical first step towards exploring how viruses could control red tide.
VIDA Seagrass – Viral Infection Dynamics Among Seagrasses
Seagrasses are marine flowering plants (or angiosperms) that create expansive underwater meadows that form the basis of highly productive and valuable ecosystems in coastal oceans. Unlike terrestrial systems where angiosperms dominate plant diversity, seagrasses are the only flowering plants in marine environments. Based on the profound impacts of viral infections on terrestrial plants, viruses are expected to influence seagrass ecology. However, no prior work has investigated viral infection dynamics in seagrasses or the impact of viruses on seagrass health. This NSF-funded project provides fundamental knowledge about seagrass-virus interactions through field and laboratory studies of Thalassia testudinum (i.e., turtlegrass, a climax species and key ecosystem engineer), and turtlegrass virus X (TGVX), the only seagrass virus currently reported from experimental research. By establishing the first seagrass-virus study system, a novel virus-host pathosystem for which virtually nothing is known, this project contributes to a more comprehensive understanding of seagrass ecology and serves as a model for investigating the growing number of seagrass viruses discovered through sequencing efforts.
Emerging Contaminants in Tampa Bay
The Tampa Bay Surveillance Project funded by NOAA’s National Centers for Coastal Ocean Science (NCCOS) includes a comprehensive spatial sampling program collecting water, sediment, fishes and invertebrates of Tampa Bay to characterize the distribution of contaminants of emerging and known concern. As part of this project, the Breitbart lab is helping to investigate the distribution of microbiological indicators and chemical contaminants throughout Tampa Bay, and exploring wastewater as a source of these contaminants. Current research focuses on testing the efficiency of electrocoagulation for removal of chemical contaminants from treated wastewater effluent and developing new methods for detecting viral indicators of human fecal pollution.
https://www.marine.usf.edu/tbs/how-do-you-age-a-fish/
Diadematidae Scuticociliatosis – Studying the Ciliate Responsible for Mass Mortality in Sea Urchins
Sea urchins are critically important herbivores on coral reefs, where they graze algae, providing space for corals to recruit and grow. In 2022, the long-spined sea urchin Diadema antillarum experienced mass mortality throughout the Caribbean. Since then, the condition has spread to additional urchin species in the eastern Mediterranean, Red Sea, Arabian Gulf and Eastern Indian Ocean. Working with Dr. Ian Hewson at Cornell University, Dr. Christina Kellogg at the USGS, and a large team of international collaborators, the Breitbart lab determined that the mass mortality in the Caribbean and elsewhere was caused by a ciliate most closely related to Philaster apodigitiformis. Current efforts are focused on detailed characterization of this ciliate, with the goal of understanding the factors involved in urchin disease.
https://www.usf.edu/marine-science/news/2023/scientists-identify-2022-sea-urchin-killer.aspx
The Effects of SUP05 Cells and Virocells on Nitrogen Cycling in Marine Oxygen Minimum Zones
Bacteria and the viruses that infect them (phages) play a major role in marine ecosystems. Virus-host interactions can alter community structure, preserve genetic diversity, and impact nutrient cycling. Up to a third of the bacteria that dominate marine oxygen minimum zones (OMZs) are infected with phages, yet the consequences of the host-virus interactions are unknown. Environmental DNA sequence data suggest that a dominant lineage of OMZ bacteria (SUP05) is comprised of species and subspecies that carry out different steps in marine nitrogen cycling and that these cells are often infected by viruses. The nitrogen cycling capacity of diverse SUP05 cells can drive the accumulation of nitrogen cycle intermediates in the oceans or lead directly to significant nitrogen loss. The outcome may be driven in part by phages, by causing cell death, metabolic rewiring of infected cells (virocells), or through the expression of phage-encoded auxiliary metabolic genes (AMGs). This NSF-funded project tests the overarching hypothesis that SUP05 populations are comprised of diverse nitrogen respiring cell types and that their interactions with phages can determine the fate of fixed nitrogen. This interdisciplinary study evaluates SUP05 cells and phages in stable OMZ fjord systems using field approaches to study microbial and viral diversity in nature, cultivation studies to test genomic predictions under controlled laboratory conditions, and isotope analyses to identify the rates and mechanisms underlying microbial nitrogen cycling and loss.
Past Research
MERA
An innovative, beach water quality investigation that considers human behavior, water pollution, and risk of illness. Learn more on the MERA website
Only 10% of the world’s household wastewater is properly treated and disinfected prior to flowing into rivers and ultimately, coastal beaches. Since this wastewater contains millions of pathogens, swimming and playing at beaches polluted by wastewater can greatly impact your health. In total, millions of cases of illness occur each year due to playing at contaminated beaches and this costs the global community 12 billion USD annually. Despite scientific advancements, government beach management approaches rely on outdated compliance practices that do not accurately identify public health risks. This innovative investigation will advance local management practices, serve as an example from a tropical region, as well as contribute to our global achievement of the 2030 Agenda for Sustainable Development. The Investigation MERA research team is composed of anthropologists and natural scientists, from a variety of backgrounds, from Universities, private laboratories, governmental institutions, as well as non-governmental non-profit organizations from the United States of America and Costa Rica. Together, we will execute a holistic beach water quality investigation that will consider human behavior, water pollution, and risk of illness at a Costa Rican beach. Our ultimate goal is to improve beach management and ensure the protection of public health.
Polonies
Gokushovirinae, a subfamily of the Microviridae family, are single-stranded DNA (ssDNA) phages that are ubiquitous in marine environments, but little is known about their diversity and abundance. This knowledge gap is partly due to the methodological limitations associated with studying ssDNA phages. This project focuses on quantifying ssDNA phage abundance and assessing ssDNA phage diversity in the Red Sea through molecular techniques. The polony method is a solid phase PCR that immobilizes the template DNA in an acrylamide gel, then hybridizes the PCR products with a fluorescent probe to determine the abundance of targeted viral groups. Unlike quantitative PCR, the polony approach is compatible with degenerate primer sets, allowing us to quantify the abundance of a diverse group of gokushoviruses instead of targeting a specific subgroup. The gokushovirus major capsid protein was amplified and sequenced from water samples collected from 9 depths (0 m, 20 m, 40 m, 60 m, 80 m, 100 m, 140 m, 200 m, and 400 m) in the Gulf of Aqaba in the Red Sea in September 2015, during a period of water column stratification. Based on the sequences recovered, a probe was designed for the quantification of the gokushoviruses using the polony method. These will provide the first estimates of gokushovirus abundances in the oceans. Insight into the spatiotemporal changes in gokushovirus diversity along with their abundance will elucidate their ecological role in the marine environment.
Ferrojan Horse Hypothesis
Iron (Fe) is an essential micronutrient, required by all living things. However, the bioavailable form of Fe is particularly limited in the marine environment. Fe tends to be speciated into complex forms, including binding to ligands (sticky compounds), rendering it unusable to organisms. Bacteria have developed mechanisms to recruit Fe, for example by using siderophores and cell receptors to bind Fe to their cell surfaces. These receptors have potentially left them vulnerable to the most abundant predator of the oceans, viruses. Viruses that infect bacteria are called bacteriophage (phage). Through data mining it was found that many phage have Fe binding sites on their tail fibers, which was hypothesized as a decoy to allow for phage attachment and infects, similar to a Trojan horse or Ferrojan horse in this case. This project tested the hypothesis in a model organism (E. coli) and now aims to test the hypothesis in the marine environment using Vibrio as a model organism.
Submerged Aquatic Vegetation Viral Diversity
Submerged aquatic vegetation (SAV) are plants that live beneath the water’s surface. These plants are taxonomically diverse, including angiosperms, liverworts and macroalgae. Our study focuses on SAV found in the Florida springs & Tampa Bay. Viral-like particles were isolated from each SAV species using chloroform (to kill bacteria), nuclease treatment (to get rid of free nucleic acids), and extraction methods (to break open the viral capsid) to obtain viral nucleic acids, with a focus on single stranded RNA viruses. SAV ecosystems are declining in Florida and we need to figure out why. This project aims to elucidate the role these viruses could play in the health of these ecosystems.
Bacterial & Viral Communities of the Florida Springs
Florida has one of the highest spring densities in the world, with upwards of 7,000 springs. Twenty-three of these are first magnitude springs, which discharge greater than 65 millions gallons of freshwater each day from the Floridan aquifer. The Floridan aquifer is an essential source of drinking water in and around the state. Despite these ecosystems’ importance, there is little is known about the microbial and viral communities which inhabit them. This project assesses the bacterial and viral communities within five Florida springs to understand the compositions of these populations and their spatio-temporal variations.