|Gary E. Schultz, Jr.||
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My lab is currently exploring the diversity of the bacterial community in various ecosystems. We have gathered data in seagrass beds in Puerto Rico as well as here in the Ohio and Guyandotte Rivers.
Why We Care About Bacterial Diversity
Biogeochemical cycles are fueled by microbial activity. Therefore, the function of any ecosystem is dependent upon which microbes are present and how many of each type are present. Bacterial diversity in marine systems has been demonstrated to be very large (Venter et al. 2004, Massana and Pedrós-Alió 2008, Giovannoni and Stingl 2005, DeLong et al., 2006, Rusch et al., 2007, Dinsdale et al. 2008, Ghai et al., 2010, DeLong et al., 2010). This diversity represents a huge reservoir of genetic information. The controls on the genetic power contained in this diversity, and thus the controls on the world’s biogeochemical cycles, are not known. Determining the diversity and the genetic potential of an ecosystem is important for understanding and manipulating ecosystems, particularly, large managed systems such as the Ohio River.
In the past, the impact of marine bacterioplankton on various biogeochemical cycles (Schultz et al. 2003, Falkowski et al. 2000, Azam et al. 1983, Ducklow and Carlson 1992, Karl and Lucas, 1996, Arrigo 2005) was determined by studying the activity of the bacteria without knowing which bacteria were present. The bacterial community structure was a virtual black box. Without knowing the community structure and the forces that control said structure, predicting future changes in ecosystem function is nearly impossible. The inability to culture a significant number of the microbial species present in natural ecosystems (Aman et al. 1995), however, made this situation unavoidable. In the 1980s and 90s, researchers came up with methods to extract DNA directly from the environment, thus circumventing the need to culture all environmentally relevant microbes (Pace et al. 1986, Giovanonni et al. 1990, Lee and Fuhrman 1990, 1991). These studies were very work intensive and required a great deal of resources to identify a fraction of the total community. With the recent advent of next generation sequencing (Schuster 2008), researchers finally have the tools necessary to examine the bacterial structure within an ecosystem, determine how that structure changes over time and under what conditions, and understand the relationships and interactions between bacteria and the ecosystem.
Aman, R. I., Ludwig, W., and Schleifer, K-H. 1995. Phylogenetic Identification and In Situ Detection of IndividualMicrobial Cells without Cultivation. Micro. Rev. 59: 143–169. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC239358/pdf/590143.pdf
Arrigo, K. R. 2005. Marine microorganisms and global nutrient cyles. Nature 437, 349-355.
Azam, F., Fenchel, T., Field, J. G., Gray, J. S., Meyer-Reil, L. A., and Thingstad, T. F. 1983. The ecological role of water-column microbes in the sea. Marine Ecol. Prog. Ser. 10, 257-263. http://www.freshwaterlife.org/servlet/BinaryDownloaderServlet?filename=1158073821097_The_Ecological_Role_of_Water_Quality_Microbes_in_the_Sea.pdf
DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallum, S. J., Frigaard, N. U., Asuncion, M., Sullivan, M. B., Edwards, R., Brito, B. R., Chisolm, S. W., and Karl, D. M. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496-503.
DeLong, E. F. and Beja, O. 2010. The light driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol 8: e1000359.
Dinsdale, E. A., et al. 2008. Functional metagenomic profiling of nine biomes. Nature. 452, 629-632. http://barkerlab.net/biodiv/2008_Dinsdale_etal_Nature.pdf
Ducklow, H. W. and Carlson, C. A. 1992. Oceanic bacterial production. Vol. 12, New York, Plenum Press, 113-181.
, , , , , et al. 2000. The global carbon cycle: a test of our knowledge of Earth as a system. Science, 290, 291–296. http://www.sciencemag.org/content/290/5490/291.full
Ghai, R., Martin-Cuadrado, A. B., Molto, A. G., Heredia, I. G., Cabrera, R., Martin, J. et al. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME Jour. 4, 1154-1166. http://www.sciencemag.org/content/311/5760/496.abstract?etoc
Giovanonni, S. J., Britschgi, T. B., Moyer, T. L., and Field, K. G. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63.
Giovannoni, S. J., and Stingl, U. 2005. Molecular diversity and ecology of microbial plankton. Nature 437, 343-348. http://www.nature.com/nature/journal/v437/n7057/full/nature04158.html
Karl, D. M. and Lukas, R. 1996. The Hawaii Ocean Time-series (HOT) program: Background, rationale and field implementation. Deep Sea Res. Part II Top Stud. Oceanogr 43, 129-156.
Lee, S. and Fuhrman, J. A. 1990. DNA hybridization to compare species compositions of natural bacterioplankton assemblages. Appl. Env. Microb. 56, 739-746. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC183415/pdf/aem00068-0165.pdf
Lee, S. and Fuhrman, J. A. 1991. Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization. Limnol. Oceanogr. 36, 12777-12787. http://222.aslo.org/lo/toc/vol_36/issue_7/1277.pdf
Massana, R. and Pedrós-Alió, C. 2008. Unveiling new microbial eukaryotes in the surface ocean. Curr. Opin. Microbiol. 11, 213-218. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4SRNYJB-1&_user=6616765&_coverDate=06%2F30%2F2008&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000024899&_version=1&_urlVersion=0&_userid=6616765&md5=c029cb05437805212ee2598c52256558&searchtype=a
Pace, N. R., Stahl, D. A., Lane, D. L. and Olsen, G. J. 1986. The analysis of natural microbial populations by rRNA sequences. Adv. Microb. Ecol. 9, 1-55.
Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., et al. 2007. The Sorceror II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5, 398-431.
Schultz, G. E., White, E. D., and Ducklow, H. W. 2003. Bacterioplankton dynamics in the York River estuary: primary influence of temperature and freshwater inputs. Aquat. Microb. Ecol. 30:135-148.
Schuster, S. C., 2008. Next-generation sequencing transforms today's biology. Nature Methods 5, 16-18. http://www.nature.com/nmeth/journal/v5/n1/full/nmeth1156.html
Venter, J. C., Remington, K., Heidelberg, J. F., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74. http://www.sciencemag.org/content/304/5667/66.full
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