Project: Experimentally linking identification and function of marine bacteria

Marine bacteria are tremendously abundant in seawater and are major driving forces in global biogeochemical cycles. Molecular biological techniques have permitted us to start to identify the different kinds of bacteria present in various parts of the sea, but there is still a major disconnect between knowing the identity of the organisms and who does what in a biogeochemical or ecological sense. Yet such information is important to understand the workings of the system and to model it accurately. This may become particularly critical in understanding global change. This question has been addressed to date with techniques like combined autoradiography & fluorescence in situ hybridization, stable isotope probing, large metagenomic projects, and statistical analysis of field data, each with its strengths and weaknesses.

While no single approach provides the whole answer, each new result provides useful pieces to the puzzle of how the different microbial components contribute to system functions. This project will use an experimental approach, by manipulating field samples various ways and then using molecular techniques to observe the growth reactions of various members of the microbial community (by DNA and RNA analysis). This approach has been used successfully in a limited way, and new information permits us to refine it and minimize ambiguity in organism identification. Dr. Fuhrman proposes to apply this approach broadly to an array of field samples collected at various locations, depths, and seasons. Specific manipulations will involve changes in light, pH, inorganic nutrients, and organic substances. The experimental plans are expected to benefit from new results including large amounts of metagenomic data soon to be released and also whole genome sequences from marine bacteria. Experiments will be done with samples collected primarily at a well-studied station between Los Angeles to the USC Wrigley Marine Laboratory Santa Catalina Island, to which we have frequent free access and for which he has several years of substantial background data on oceanographic parameters and microbiology (as part of the San Pedro Ocean Time Series and USC Microbial Observatory). He also anticipates additional samples on cruises of opportunity and other cruises along California and elsewhere. All experiments will employ controls for effects of containment and other possible artifacts, and he will endeavor to minimize artifacts through large volumes and use of the shortest incubations that yield an effect.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Fuhrman, JA. "Microbial community structure and its functional implications," NATURE, v.459, 2009, p. 193-199. View record at Web of Science

Fuhrman, JA; Schwalbach, MS; Stingl, U. "Opinion - Proteorhodopsins: an array of physiological roles?," NATURE REVIEWS MICROBIOLOGY, v.6, 2008, p. 488-494. View record at Web of Science

Fuhrman, JA; Steele, JA. "Community structure of marine bacterioplankton: patterns, networks, and relationships to function," AQUATIC MICROBIAL ECOLOGY, v.53, 2008, p. 69-81. View record at Web of Science