Submarine groundwater discharge is one of the largest sources of nutrients and contaminants into coastal marine environments. This creates a highly reactive intertidal mixing zone where microbes can interact with these compounds before ultimately entering the global oceans. How microbes function in these areas and affect the fate of nutrients and contaminants remains largely understudied. Currently at Cape Shores, Lewes, DE we are conducting in-depth geochemical and microbial functional gene analyses, mineralogical characterizations, and laboratory cultivation studies in an effort to understand how microbes in this intertidal mixing zone are influencing C, N, Fe, and S cycling.
Iron-oxidizing bacteria: their role in biogeochemical cycling
Iron is one of the most abundant metals on Earth and microbes have the ability to use it as an electron acceptor and electron donor to gain energy. Biologically produced iron oxides, a product of iron oxidation metabolism, are highly reactive and can sequester nutrients such as phosphorous, nitrogen, or organic carbon as well as heavy metals. Therefore, these organisms may play a profound role in contaminant mobility, water treatment, biocorrosion, and biogeochemical cycling in the environment. My research focuses largely on marine iron-oxidizing bacteria in estuaries, coastal regions, and hydrothermal vents, but these interactions are also very important in terrestrial and freshwater environments. By integrating microbial and geochemical analyses through comparative genomics, laboratory experiments with environmental isolates, and field studies we can begin to answer many critical questions about iron-oxidizers in the environment including:
- How do iron-oxidizing bacteria influence the cycling of other elements such
as nitrogen, sulfur, and carbon?
- How do iron-oxidizers respond to sequestration of nutrients and heavy metals at a genetic level due to toxicity, fluctuating concentrations, and co-occurrence?
Using -omics techniques to cultivate novel environmental microbes
The majority of microorganisms found in the environment cannot be grown in the laboratory. This is due in large part to our inability to provide the appropriate growth conditions. Omics-based techniques helps us answer some of these questions (who are they? what are they doing?) so we can design better enrichments in an effort to grow these novel microbes and study them in the lab.
Single cell genomics, one of these methods, allows us to obtain genomic information from the environment at the most fundamental level- a single cell- while avoiding the difficulties of cultivation. We can then answer questions about the physiology, ecology, and evolution of microbes from a variety of environments including hydrothermal vents, hot springs, near-shore, and the deep subsurface.
A Case Study: The Zetaproteobacteria, a class of iron-oxidizers has been found in a wide range of marine environments. They have been implicated in the corrosion of steel ships and pilings causing billions of dollars a year in structural damage. Unfortunately, many fundamental questions remain unanswered about their metabolic capabilities because they are difficult to grow in the lab. By using single cell genomics we are able to learn more about their metabolism, physiology, and design new enrichment strategies. Single cell genomics data has already led to the successful cultivation a novel Zetaproteobacteria isolate which we can now use in laboratory studies.
We are applying this technique to a variety of environments in order to make exciting discoveries about elusive, uncultivated microbes in the environment!