Environmental Microbiology

Research in Dr. Cummings’ lab is focused on understanding the ways in which microorganisms influence the fate and transport of metals in the environment. A typical soil contains between one million and ten billion prokaryotic cells (Bacteria and Archaea) in a single gram (~1 cm3). Metals, such as iron (Fe) and chromium (Cr), are naturally present in these soil ecosystems as well as due to anthropogenic (human caused) contamination. One of the most important microbe-metal interactions is that of reduction, or the addition of electrons. Oxidized metals can serve as respiratory terminal electron acceptors when oxygen is limited, resulting in reduced metal species whose chemistry is dramatically altered from the oxidized form. Insoluble Fe(III) reduction leads to increased soluble Fe (as Fe2+) and release of adsorbed (physically associated) trace elements such as phosphorus (P) and arsenic (As). Reduction of soluble Cr(VI) leads to the less toxic Cr(III) species, which may even precipitate from solution under the right conditions, immobilizing it. Dr. Cummings’ research attempts to better understand the processes that control these reactions in complex communities and in pure cultures.

Acidiphilium cryptum

A. cryptum is a facultative anaerobe that can use either oxygen or Fe(III) as respiratory terminal electron acceptor. The novelty of this organism, though, is that it functions optimally at pH 3, and so is found in various acidic environments around the world including acid mine drainage and acid hot springs. As part of a larger project geared towards understanding how A. cryptum reduces metals, we are also studying its ability to reduce Cr(VI) to Cr(III) at low pH. An exciting new development in this research is the complete sequence of the A. cryptum genome by the Joint Genome Institutes, which will guide much of our future work. This project is funded by the U.S. Department of Energy.

Tijuana River Estuary

The Tijuana River Estuarine Research Reserve, or TJ Estuary for short, is one of the last intact estuaries remaining in California, and one of the most natural left in the entire U.S. It is constantly challenged with pollution in the form of untreated sewage, trash, and heavy sediment loading. Reduction of Fe(III) in the estuary may contribute to the bioavailability of Fe to plants, the release of phosphorus and toxic metals from the sediments into the water, and the breakdown of organic compounds. We are studying the diversity of Fe(III)- and sulfate-reducing bacteria in the TJ Estuary as well as their activities in an attempt to understand the functions they play in this complex ecosystem. To date, this project has been funded by the Howard Hughes Medical Institute, and we are actively seeking other outside funding.

Students directed by David Cummings

Tasha Kopshy (Sacramento, CA), Nathan Singh (Fresno, CA), and Amy Hebling (Chicago, IL)
Numerous metals and metalloids persist in the environment, having been introduced by both natural and anthropogenic routes. In addition to disturbances to ecosystem function, these contaminants pose significant risks to human health. Microbial metal reduction is a process whereby bacteria in soil and sediment use oxidized metals as respiratory electron acceptors, reducing their oxidation state, often dramatically altering their chemistry. The acidophilic bacterium Acidiphilium cryptum is currently the only known metal-reducing bacterium that operates in acidic (low pH) environments. The goal of this research is to understand the physiology and resulting ecology of microbial metal reduction under acidic conditions. We are currently studying the mechanisms and implications of hexavalent chromium reduction by A. cryputm. In 2005, Nathan Singh and Tasha Kopshy studied constraints on Cr(VI) reduction and detoxification by A. cryptum under acidic conditions. The genome of A. cryptum was recently completed by the US DOE at our request, and Nate and Tasha will spend summer 2006 creating mutant strains deficient in Fe(III) and Cr(VI) reduction in order to study the genetic and biochemical pathways involved.

The Tijuana Estuary is one of the few remaining undisturbed salt marshes in California where fresh river water meets the ocean. This habitat is critical for hundreds of plant and animal species that call it home for at least part of the year. For example, the light-footed clapper rail, a shore bird that is endangered due to habitat loss, thrives in the Tijuana Estuary. Although it is already known as a State Park, a Research Reserve, and a Wildlife Refuge, it was recently designated a Wetland of International Importance by a United Nations subcommittee, drawing our local treasure into the international spotlight. In addition to providing critical habitat to migrating birds and ocean fishes, estuaries are natural filters, cleaning pollutants from water discharging from urban watersheds. The health of the Tijuana Estuary is critical to purification of water from Tijuana and San Diego prior to entering the ocean. In 2005 Amy Hebling studied the diversity and activities of anaerobic microorganisms in the surface muds of the Tijuana Estuary. This summer (2006) Amy will be completing a clone library, a list of species present in the estuary sediments and their relative abundances based on the small subunit ribosomal RNA gene as an identifying marker.

Cummings presented some of Nathan and Tasha’s data at a conference in Jackson, WY in August:

D. E. Cummings, S. Fendorf, R. K. Sani, B. M. Peyton, N. Singh, T. J. Kopshy, and T. S. Magnuson. 2005. “Reduction of Cr(VI) under acidic conditions by the facultatively Fe(III)-reducing bacterium Acidiphilium cryptum.” ISSM-ISEB Joint Symposium, Jackson, WY, oral.

None of my students have yet attended meetings. They are all planning to present at the undergrad conference in spring 06.

Nate’s data will be included in a manuscript to be re-submitted spring 06:
Cummings, D. E., S. Fendorf, R. K. Sani, B. M. Peyton, N. Singh, and T. S. Magnuson. 2005. Reduction of Cr(VI) under acidic conditions by the facultatively Fe(III)-reducing bacterium Acidiphilium cryptum. Environ. Sci. Technol. (in revision)

Amy’s data should be ready to write up by the end of summer 06. Amy’s data will also be used to prepare a 3-year grant proposal to California Sea Grant in March.

Funding:

Singh and Cummings were supported by a grant from the U.S. Department of Energy’s Natural and Acceleration Bioremediation Research (NABIR) Program entitled, “Comparative biochemistry and physiology of iron-respiring bacteria from acidic and neutral-pH environments” (T. S. Magnuson and D. E. Cummings, FY04-FY06).
Hebling was supported by a grant from the Howard Hughes Medical Institute (HHMI) to PLNU.