The USC Microbial Observatory was established in 2000. The research focus of this observatory is an investigation of the microbial diversity and microbial community composition at a study site in the San Pedro Channel and Basin off the coast of southern California. The Channel area encompasses a diversity of coastal ocean habitats. The near-coast region borders one of the most highly urbanized areas of the country (greater Los Angeles) while open ocean waters impinge on the Channel Island archipelago that extends to within 30 km of the mainland. The San Pedro Basin is a deep-water environment (approximately 890 m) that exhibits very low oxygen concentration. The overarching objective of this project is the derivation of fundamental understanding of how microbial communities in the ocean are organized spatially (with depth) and temporally (at scales of months-to-years), and how environmental and biological factors shape this organization. The basic premise of the research is that "guilds" or "consortia" of microbial species exist that constitute functional subunits within the huge diversity of taxa that comprise planktonic microbial communities. The microbial species forming these guilds are functionally interdependent, and act as ecological units that replace one another in time and space as environmental conditions change. The program consists of monthly sampling at four depths in order to document the abundance, biomass and species composition of all planktonic microorganisms at the mid-channel sampling station. A variety of microscopical and molecular biological approaches are employed to examine archaeal, bacterial and microeukaryote (microalgal, protozoan, micrometazoan) diversity. The observatory is unique in that it entails an assessment of the complete spectrum of microorganisms (from viruses to the largest protists) in the water column. Genetic fingerprinting of the total microbial community is the primary tool for revealing the trophic roles and relationships among microbial taxa (predation, mutualism, commensalism, parasitism/infection), and to generate hypotheses on the interdependences among these species. Experimental studies involve manipulative food web experiments to test hypotheses concerning the relationships and interactions among the various microbial species. The data support extensive statistical analyses to identify relationships between microbial taxa, and with environmental parameters. This research program strives to develop a fundamental understanding of the factors controlling the structure of microbial communities in aquatic ecosystems. Therefore, the results have far-reaching consequences for predicting biogeochemical processes mediated by microbial activities in nature. The project also incorporates a strong educational component aimed at reaching students ranging from elementary school children to graduate students. The information resulting from the research is incorporated into undergraduate and graduate courses taught by the principal investigators, and both types of students participate actively in the research. In addition, the principal investigators and graduate students supported by this project participate directly in an ongoing teacher education program (Centers for Ocean Science Education Excellence; COSEE-West) that reaches middle and high school students, many of whom are Hispanic, African-American or other ethnic minorities and most of whom are economically disadvantaged. This education/outreach goal is accomplished through an existing teacher enhancement and student enrichment program that incorporates the research from this microbial observatory into a learning experience that enhances student awareness of environmental science, microbiology and the natural world. The observatory principal investigators work is featured and publicly available on the internet as a part of the USC Microbial Observatory Website at www.usc.edu/microbialobservatory).
There is an ever-increasing realization of the importance of microbial processes in global biogeochemical cycles in marine ecosystems. Our work has focused on understanding the ecological interactions of the huge diversity of species that comprise the natural microbial assemblage of a coastal oceanic ecosystem. This research project has entailed a study of the diversity all microorganisms (bacteria, archaea and protists) at an oceanographic station in the San Pedro Channel off southern California. The overarching goal of this research project has been the discovery of new microbial life, and the characterization of food web interactions, nutrient uptake and release, and energy flow among microorganisms within the pelagic food web at this site. The San Pedro Basin combines a number of unique environmental features including a deep-water environment (≈890 m) in close proximity to shore, very low oxygen concentration in deep waters (<1 ml L-1 below 150 m), natural inputs from oceanic regions, as well as significant anthropogenic inputs from a major metoropolitan area (greater Los Angeles region). Our objective has been to develop a more complete view of microbial interactions in the region by considering a more complete collection of all the interacting microorganisms than has been attempted in most microbial ecological studies to date. Our guiding hypothesis is that the microbial community is organized into ‘guilds’ of microbes (self-organizing groups of interacting microbial species) that form functional subunits within the huge diversity of taxa that comprise planktonic microbial communities. We speculate that these functional subunits conduct the major biogeochemical processes in the water, and that changes in environmental conditions result in shifts, or substitutions, in the specific guild of species dominating at any given time. This hypothesis has been tested by examining changes in the composition of the microbial community on a monthly basis (sampling started in 2000, as part of a previously-funded project) carried out approximately mid-channel between Long Beach, CA and the USC Wrigley Marine Science Center on Santa Catalina island, in conjunction with the San Pedro Ocean Time Series (SPOT) program. The composition of the microbial community has been carried out using state-of-the-art DNA sequencing approaches and analyses, and standard oceanographic approaches, to characterize the species of microbes present at various depths and on dates of sampling. Trophic linkages between microbial groups during monthly, seasonal and annual changes in community composition have been examined by comparisons of microbial community structure using network analysis, which aids in establishing relationships among microbial species (e.g. predator-prey relationships, parasitic relationships, etc.) and with environmental variables (temperature, nutrients, etc.). This study has also included experimental studies to examine the response of microbial community composition to environmental perturbations. The primary intellectual merit of our research program is that we have uncovered significant relationships among the various microbial species, as consequence of the unique goal of our project to characterize the complete spectrum of microorganisms (from viruses to the largest protists) in the water column at our study site. Few research programs have attempted to simultaneously follow and relate these disparate but highly interdependent assemblages. Through analysis of our extensive monthly time-series (10 years of data), which incorporates both biological and environmental parameters, we have provided new insights into the short-term responses of microbial communities to environmental change, as well as established a dataset from which we can begin to examine the impact of long-term changes (e.g. decadal climate shifts such as El Nino, global warming, oceanic acidification). Genetic fingerprinting of the total microbial community has revealed many of the trophic relationships involving these microbes (predation, mutualism, commensalism, parasitism/infection), and the susceptibility of these relationships to environmental change. Broader impacts of the project have covered a spectrum of activities that broadly disseminate scientific information. These have included: presentations at national and international scientific meetings, and publication in the scientific literature (the USC Microbial Observatory has tallied more than 50 scientific publications in the primary literature and book chapters); participation within a NSF-funded education program (Centers for Ocean Science Education Excellence; COSEE-West) that uses ocean themes to improve math and science education in K-12 schools in disadvantaged parts of Southern California; participation in the University of Southern California NSF/REU program in Geobiology; undergraduate research opportunities for high school and undergraduate students in the PI’s labs; career workshops with local high schools; personal appearances at middle schools; teaching at the undergraduate and graduate level at USC including courses in the Department of Biological Sciences core curriculum, upper division elective in microbial ecology and molecular ecology, and graduate classes in scientific writing and reviewing.
