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.

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.


DNA Barcoding of Fish Eggs          

DNA barcoding of fish eggs is a relatively new technique that enables more accurate identification of early life stages of ecologically and economically important fish species. Using DNA barcoding of individual planktonic percomorph eggs, we can determine putative spawning locations of neritic and oceanic fish species in the Gulf of Mexico (GoM). Surveys at 40 stations in the Gulf of Mexico showed a clear delineation of spawning sites, with neritic fish eggs generally found on continental shelves, and oceanic fish eggs found at the surface of deeper waters. However, samples collected between Florida and Cuba revealed exceptions to this trend driven by physical oceanographic processes, with mesoscale eddies transporting eggs of neritic fishes off the Florida continental shelf into the deep Florida Straits. Better understanding of the distribution of fish eggs can help identify regions where additional protection of spawners and recruits may be appropriate.

 


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.


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.


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.

Parasite-associated viruses

Parasitic infections represent a public health and economic burden. Parasite-associated microbes may positively or negatively affect parasite fitness and, as consequence, the outcome of parasitic infection. Moreover, parasite-associated microbes may interact with the infected host’s microbiota and/or directly affect the parasite’s host. However, there is scarce information regarding the microbiome of parasites, including viruses. We are working in collaboration with Dr. Nolwenn Dheilly (@DheillyNM) to identify viruses in parasitic flatworms (Phylum Platyhelminthes), whose viromes have been largely overlooked. By investigating parasite-associated viruses, we seek to understand the role of parasites in virus evolution, assess host-parasite-virus interactions,  determine the role of parasite-associated viruses in parasite fitness and host diseases, and identify patterns and processes of host-parasite-virus coevolution. These are important knowledge gaps in the parasitology field as identified by the Parasite Microbiome Project initiative.

Viruses in alternative freshwater supplies

The reuse of municipal wastewater (water reuse) is an important strategy for expanding freshwater resources. To reuse water, it is critical that we safeguard public health by removing microbial pathogens prior to water reuse through natural (e.g., managed aquifer recharge systems) or engineered (e.g., reverse osmosis; RO) wastewater treatment processes.  In collaboration with Dr. Walter Q. Betancourt, we aim to characterize virus occurrence, diversity, and frequency in RO permeates (reusable product) and concentrates (rejected waste product). Although RO is considered an efficient method for virus removal, we discovered single-stranded DNA viruses in RO permeates. Through this collaborative effort we hope to establish adequate viral indicators of treatment performance of RO, an engineered treatment that has been increasingly being implemented for advanced treatment of wastewater for potable reuse applications. Additionally, we will evaluate the potential use of RO concentrates for agricultural irrigation by performing a comprehensive survey of plant viruses in these concentrates.

genomics1Research