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Research Interests

Microbes fascinate me. They can make a living almost anywhere, exhibit complex social lives, and influence the environment on a global scale, all despite their microscopic size. My focus is in the area of environmental microbial ecology, where I am primarily interested in understanding the causes and consequences of microbial diversity, community function, and control on biogeochemical cycling. My long-term goals are to help establish unifying principles that govern microbial interactions, especially in relation to ocean biogeochemistry and climate change.

Amy E. Zimmerman

Current Research

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Resource allocation strategies of prokaryotes (UCI)
Prokaryotes function as the primary recyclers of organic matter in aquatic, terrestrial, and subsurface ecosystems, but despite this critical role and their significant contribution to microbial biomass in many ecosystems, the factors controlling their allocation of carbon, nitrogen, and phosphorus resources to growth or resource acquisition machinery are unclear. The objective of my dissertation work is to characterize the genetic, physiological, and environmental factors that contribute to resource allocation strategies of prokaryotes and their potential impacts on biogeochemistry. Preliminary results support the general conclusion that the resource allocation strategies of prokaryotes can be quite flexible in the face of genetic, physiological, and environmental constraints. Overall this research argues for explicit consideration of the prokaryotic component when linking microbial activity and characteristics to ecosystem processes.

Previous Research

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Bacteriophage therapeutics as an alternative to antibiotics (Kent SeaTech)
Bacterial pathogens cause extensive agriculture losses and directly affect the ability of U.S. producers to compete with foreign products. However, due to the rapid and worldwide emergence of antibiotic-resistant bacterial pathogens in human medicine, agriculture, and aquaculture, regulators are severely limiting antibiotic use in the U.S. We investigated the use of bacteriophages, naturally-occurring anti-bacterial viruses, as an alternative therapeutic to conventional antibiotics. Bacteriophages (phages) are usually species specific and serve as a self-replicating therapy. We characterized candidate phages from environmental samples and evaluated their effectiveness in vivo for disease treatment. Several candidate phages showed promising results in either fish or mouse models.

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Microbial diversity and control of iron (Fe) cycling in the Tijuana Estuary (PLNU)
The Tijuana Estuary is one of the last intact estuaries remaining in California. It is constantly challenged with pollution in the form of untreated sewage, trash, and heavy sediment loading, which has made restoration of natural flora difficult. Reduction of Fe(III) in the estuary may contribute to the bioavailability of Fe to plants, the release of phosphorous and toxic metals from the sediments into the water, and the breakdown of organic compounds. We used molecular techniques to study the diversity of Fe(III)- and sulfate-reducing bacteria in the Tijuana Estuary as well as anaerobic microcosms to study their activities in an attempt to understand the functions they play in this complex ecosystem.