I am interested in how microbial interactions and functional diversity regulate cycling of essential elements through ecosystems. Because microbes function at the interface between the abiotic and biotic components of the environment, microbial activity regulates nearly all biogeochemical processes, from photosynthesis to decomposition. I primarily use molecular tools for quantitative lab and field investigations to identify ecological and physiological mechanisms that govern microbial activities. My work contributes to a framework for linking microbial activity with ecosystem processes by integrating aspects of ecology, microbiology, evolution, bioinformatics, and oceanography. 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.

Current Projects

Quantitative proteomics of nitrogen limitation(U Chicago)

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 microbial activities in the environment. Proteins provide a crucial link between function and diversity catalogues. Since transcript abundances only weakly correlate with protein abundances (Rocca et al., 2015; Waldbauer et al., 2012), direct assessment of these biochemical catalysts through proteomic analysis is required to understand protein-level processes. Proteomic analysis can enable mechanistic connections between specific members of the microbial community and the chemical context of the environment. This project focuses on addressing the molecular basis of nitrogen limitation in the ocean through complementary lab and field experiments.

Previous 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. 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 developed a robust virus-host experimental system for the picoeukaryotic alga Ostreococcus and two infecting viruses, supported by sequenced host and viral genomes. In addition to differences in viral infectivity, host mortality, and viral production, analyses are under way to evaluate chemical and transcriptional differences during infections, as well as the impact of irradiance and phosphate availability on infection dynamics. This work was 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).

Relevant Papers

Closely-related viruses of the marine picoeukaryotic alga, Ostreococcus lucimarinus, exhibit different ecological strategies

In revision

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 was to analyze the phylogenetic, physiological, and environmental factors that contribute to microbial resource allocation strategies by using 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 (Rutgers University), Simon Levin (Princeton University), and Michael Lomas (Bigelow Laboratory for Ocean Sciences).

Relevant 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


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.

Relevant Papers

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


© 2019 - Amy E. Zimmerman

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