Project Description - Monterey Bay Coastal Ocean Microbial Observatory

Project Description

Single celled marine picoplankton (plankton in the size range between 0.2-2.0 m) represent the most abundant, biogeochemically important organisms in the oceans. At concentrations ranging between 104 - 106 cells/ml, an estimated 20-50% of marine primary productivity is channeled through bacterioplankton assemblages (Azam et al., 1983; Cho and Azam, 1990; Ducklow and Carlson, 1992). In the ocean's interior, microbes consume an estimated 75 % of the sinking particulate organic carbon flux in the upper 500 m (Karl et al., 1988; Cho and Azam, 1990). Small prokaryotes can dominate the biomass in the oligotrophic open seas (Cho and Azam, 1990; Fuhrman et al., 1989). Beyond bulk abundance and estimates, the qualitative attributes and activities of individual components of these microbial communities are crucial to ecosystem function. It is well established that many central biogeochemical processes including nitrogen fixation, anaerobic respiration, chemolithoautotrophy, and nitrification, are mediated solely by prokaryotic species (Madigan et al., 1999). The cycling of the elements in the sea is critically dependent on such microbial activities, yet in the marine environment the specific microbes mediating these processes, and their genetic and biochemical properties, are poorly characterized or unknown.

Traditional cultivation methods introduce several qualitative and quantitative biases in ecological studies. It is now well documented that cultivation approaches typically recover only a small, skewed fraction of the total cells present in a typical seawater sample. In support of this contention, molecular ecological surveys of PCR amplified rRNA genes have revealed unsuspected phylogenetic diversity contained within natural microbial populations. These cultivation-independent surveys have greatly expanded the known phylogenetic variety of microbial species on Earth (Pace, 1997). Accepted distributions of major prokaryotic groups, including archaea (DeLong, 1998a, b), have been dramatically altered by these environmental studies. It is now apparent that some newly discovered, uncultivated bacteria and archaea represent major components of natural marine microbial populations (DeLong, 1992; DeLong 1998b; DeLong et al., 1999; Field et al., 1997; Giovanonni et al., 1990; Gordon and Giovanonni, 1996; Fuhrman and Davis, 1997; Rappe et al., 1997). Despite the impact of these rRNA-based gene surveys, phylogenetic identification based solely on rRNA sequence does not allow inference of physiology, biochemistry, and ecological significance. The specific biological properties of these abundant uncultivated microorganisms therefore remain almost entirely unknown.

Both cultivation approaches and rRNA gene surveys are insufficient for characterizing the specific biological properties or biogeochemical activities of oceanic microbes. Each approach also has its own inherent biases and artifacts. This lack of appropriate methodologies currently imposes serious barriers to comprehensive monitoring efforts of any Microbial Observatory. Better methods need to be refined to overcome these serious problems. In the proposed work, we plan to apply newly developed genomic approaches to characterize globally significant, uncultivated planktonic marine bacteria and archaea. This will result in the first genetic characterization of these cosmopolitan globally distributed microbial groups. It will also provide new approaches, protocols and data generally useful for other Microbial Observatory efforts. Finally, this work will lay the necessary foundation for constructing DNA microarrays for high throughput monitoring of the presence, variability, and gene expression of globally important marine microbial groups. This development will be crucial for future studies of the function and response of these communities to natural environmental variability, anthropogenic impacts, and potential global climate change. We will apply the genomic information derived from this proposed study, in follow up studies involving the use of DNA microarrays and Microbial Observatory efforts in Monterey Bay and surrounding coastal waters.

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Rapp�, M.S., P.F. Kemp, and S.J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42:811-826.

This work was supported by the National Science Foundation
and the David and Lucille Packard Foundation