Marine Environmental Genomics: New Secrets from a Mysterious Ocean

powerful as these studies are, they do not provide information on which microbes are responsible for specific biogeochemical processes. Additional studies were designed to evaluate ocean function with the use of culturing technologies. However, a significant challenge to our ability to study and understand these microorganisms is that the vast majority are not easily cultured on typical growth media, the traditional approach in much of microbiology dating back to the early days of medical microbiology and Koch’s principles. Culturing methods were thought to be the necessary first step towards evaluating microbial diversity and function, but we now know that studying only microbial populations that can be grown in culture provides very little information on natural diversity or environmental function (e.g. Beja et al., 2002a). Consequently, over the past decade, scientists have developed molecular tools to explore environmental diversity without relying on culturing technologies. The most commonly used culture-independent method relies on comparisons of homologous genes between organisms by using techniques such as polymerase chain reaction (PCR) products typically targeting phylogentic genes. Amplification and sequencing of the conserved regions of the 16S ribosomal RNA (rRNA) gene (part of the protein synthesis machinery found in all living cells), can provide the identity of the specific organisms in the sample. Initial application of this methodology resulted in an explosion of information, providing for the first time a mechanism to evaluate microbial diversity for the > 99% of the microbial population that could not be grown in the laboratory (e.g. DeLong et al., 1989; Giovannoni et al.; 1990; Pace, 1996, 1997). Despite the impact of these rRNA based surveys, a phylogenetic identification of a microorganism based solely on an rRNA sequence does not allow inference of physiology, biochemistry, or ecological significance. Therefore, the specific biological properties of abundant uncultured microorganisms remain almost entirely unknown. Another limitation of the 16S rRNA sequencing technique is that it does not distinguish between strains of the same species that may fill significantly different biological niches and habitats. For example, Escherichia coli, which persist in the human gut in a mutualistic relationship, may not be disT oday we are witnessing an explosion in interest in marine microbial communities. Microscopic marine organisms, including communities of phytoplankton, Bacteria, Archaea, protists and viruses, play critical roles in the biosphere by participating in virtually all of the Earth’s biogeochemical cycles and thereby affecting geology, hydrology, and even possibly global climate change. These prolific and diverse microbial communities, while not seen by casual observers, by some estimates account for more than 90 percent of the ocean’s biomass and 98 percent of the primary production in the marine environment (e.g. Whitman et al., 1998). Therefore, for humans to truly begin to understand the impact of our activities on our environment, and to being to develop new tools to combat negative effects, it is important for us to understand both diversity and function of the marine microbial assemblages. Traditional ‘black box’ microbial ecology set the foundation for understanding ocean function and taught us that unseen biology is of critical importance in the ocean. Through these studies we learned that microbes were at the core of virtually all the biogeochemical carbon (e.g. Carlson et al., 2001) and nutrient (e.g. Redfeld, 1958) cycles. For example, the global dissolved organic carbon pool is estimated to be approximately 700 Pg C, a value comparable to the mass of inorganic C in the atmosphere. Interaction of microbes within the dissolved organic pool could strongly impact the balance between oceanic and atmospheric carbon dioxide. However,