As a microbial ecologist, my primary research goal is to understand the ecological processes and mechanisms that govern microbial interactions, including among microbes as well as between microbes and their environment. Because microbes function at the interface between abiotic and biotic components of the environment, microbial activity regulates nearly all biogeochemical processes, from photosynthesis to decomposition. Advances in sequencing technologies and bioinformatic analyses have allowed an unprecedented view into the diversity and distribution of microorganisms; yet we have a surprisingly superficial understanding of how microbial communities really function in the environment.

Broadly, my research focuses on how microbial interactions and functional diversity regulate cycling of essential elements through ecosystems. I use quantitative lab and field investigations to identify ecological and physiological mechanisms that underlie the dynamics of microbial communities. My work integrates aspects of ecology, microbiology, evolution, bioinformatics, and oceanography to understand ecosystem-level consequences for carbon and nutrient cycling. My research contributes to a framework for linking microbial activity with ecosystem processes. By understanding how ecological, environmental, and evolutionary factors affect microbial resource use and interactions, we can predict with greater confidence how ecosystems will respond under changing environmental conditions.

Recent Projects

Quantifying nutrient-virus-phytoplankton interactions in marine picoeukaryotes(MBARI)

Viruses are the most abundant and diverse biological entities in marine systems. Viral infection of marine phytoplankton can be a significant source of mortality and disrupt the canonical flow of carbon and nutrients through the microbial loop, turning over as much as 150 Gt of carbon per year. To understand the potential ecosystem-level influences of microbial activities we must take the community context into account and the concurrent effects of bottom-up and top-down regulatory processes. While the ecological importance of marine viruses is now recognized, many fundamental first-order questions about how viruses interact with their hosts and influence carbon and nutrient cycles still remain unanswered. As part of a coordinated effort to compare virus-host dynamics across key marine pico-phytoplankton lineages (i.e., photosynthetic cyanobacteria and eukaryotic algae <2 μm in diameter), I have established a virus-host model system for the picoeukaryotic alga Ostreococcus and two infecting viruses. This model system is supported by sequenced host and viral genomes, which indicate that the viruses selected represent the same genetic clade. Results from parallel infections indicate major differences in the infection strategies these two viruses, despite their genetic relatedness. In addition to differences in viral infectivity, host mortality, and viral production, work is under way to quantify potential chemical and transcriptional differences between infections of these two viruses, as well as to identify how infection dynamics shift under nutrient limitation. This work is supported by the Gordon and Betty Moore Foundation, in collaboration with Maureen Coleman, Jacob Waldbauer (University of Chicago), Seth John (University of Southern California), Matt Sullivan (Ohio State University), and Alexandra Worden (Monterey Bay Aquarium Research Institute).

Resource allocation strategies of prokaryotes(UCI)

Prokaryotes function as the primary recyclers of organic matter in aquatic, terrestrial, and subsurface ecosystems. Despite this critical ecological role and their significant contribution to microbial biomass, the factors controlling their allocation of carbon and nutrient resources to cellular machinery are unclear. The partitioning of carbon and nutrient resources to different types of cellular machinery (e.g., proteins or nucleic acids) is directly related to cycling of these elements via structural differences that drive cellular elemental composition. The aim of this project is to analyze the phylogenetic, physiological, and environmental factors that contribute to microbial resource allocation strategies. We addressed this through quantitative laboratory and field investigations that used a combination of bioinformatic, molecular, and biochemical methods.

Our results provide strong evidence for the diversity and flexibility of resource allocation strategies in marine microbes. Significant variation in traits related to resource allocation among closely related organisms supports that these traits evolve rapidly in relation to traditional phylogenetic markers, highlighting the importance of considering both ecological and evolutionary processes when interpreting patterns of microbial resource use. We also found that allocation to macromolecules and cellular elemental composition in both laboratory cultures and natural microbial communities deviated from several assumed patterns, which are frequently used in predicting interactions among major nutrient cycles. By exploring several potential constraints on allocation strategies across biological scales, this work serves to improve the current framework for understanding the impact of microbial resource use on biogeochemical cycling under changing nutrient conditions. This work was supported by the National Science Foundation, in collaboration with Adam Martiny, Steve Allison (University of California Irvine), Juan Bonachela (University of Strathclyde), Simon Levin (Princeton University), and Michael Lomas (Bigelow Laboratory for Ocean Sciences).

Relavant Papers

Resource allocation by the marine cyanobacterium Synechococcus WH8102 in response to different nutrient supply ratios


Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria.


Phosphate supply explains variation in nucleic acid allocation but not C:P stoichiometry in the western North Atlantic


Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes


Previous Projects

Targeted bacteriophage therapeutics as replacements for conventional antibiotics in aquaculture(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- or strain-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. This proprietary work was conducted at Kent SeaTech Corporation, which is now Kent BioEnergy Corporation.

Activity and diversity of iron reducing bacteria in estuarine sediments(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.

Relavant Papers

Influence of microbially reducible Fe(III) on the bacterial community structure of estuarine surface sediments


© 2018 - Amy E. Zimmerman

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