Monterey Bay Microbial Study

Monterey Bay is a well-studied coastal environment characterized by strong seasonal upwelling, with active local fisheries and adjacent to one of the most productive agriculture areas in the country, and within the Monterey Bay National Marine Sanctuary. The microbial communities in the Bay have been studied for over a decade and have produced important insights into coastal marine microbial community composition (e.g. Beja et al., 2002a, 2002b, Suzuki et al., 2000, 2001, 2004), community dynamics (e.g. Suzuki et al., 2004), potential to mediate biogeochemistry (e.g. Ward, 2005, O'Mullan and Ward, 2005, Mincer et al., 2007), and novel biochemistry (e.g. Beja et al., 2000, de la Torre et al., 2003). The Monterey Bay Aquarium Research Institute.s Biological Oceanography Group has conducted monthly monitoring cruises transecting the Bay (Figure 1) over the last 19 years, and microbial fraction samples were synoptically collected over seven of those years (1997-2004). As part of ongoing research using these time-series samples (Rich et al. in prep.), three surface water samples from mid-bay station M1 (36.747d N, 122.022d W) were pyrosequenced. These samples were selected based on environmental parameters and on DNA yield, and span October 2000 to May 2001 (Figure 2). They represent non-bloom conditions (10/15/00) and two post-bloom response points (4/25/01 and 5/15/01).

The surface water picoplankton DNA samples that were pyrosequenced are being analyzed for taxon and functional gene content, as well as for use in validating and intercalibrating .genome proxy. microarray experiments (Rich et al., 2008; Rich et al. in prep.), conducted with the same samples.

Figure 1: (Click for larger image)
Monterey Bay and the M1 and M2 sampling stations. Monterey Bay is along the central coast of California (inset), on the west coast of the United States.

Figure 2: (Click for larger image)
Environmental and time-series context of pyrosequenced samples. Red arrows denote the three 0m samples that were pyrosequenced, in the context of temperature, and silicate, nitrate and nitrite concentrations. Black diamonds indicate all samples hybridized to the genome-proxy microarray.

References:
Beja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P. et al. (2000) Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
Beja, O., Koonin, E.V., Aravind, L., Taylor, L.T., Seitz, H., Stein, J.L. et al. (2002) Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 68: 335-345.
Beja, O., Suzuki, M.T., Heidelberg, J.F., Nelson, W.C., Preston, C.M., Hamada, T. et al. (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.
de la Torre, J.R., Christianson, L.M., Beja, O., Suzuki, M.T., Karl, D.M., Heidelberg, J., and DeLong, E.F. (2003) Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proceedings of the National Academy of Sciences U S A 100: 12830-12835.
Mincer, T.J., Church, M.J., Taylor, L.T., Preston, C., Karl, D.M., and DeLong, E.F. (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Env. Micro. 9: 1162-1175.
O'Mullan, G.D., and Ward, B.B. (2005) Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California. Appl. Environ. Microbiol. 71: 697-705.
Rich, V.I., Konstantinidis, K., and DeLong, E.F. (2008) Design and testing of 'genome-proxy' microarrays to profile