Evolving perspectives in microbial oceanography from genomes to biomes

The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Preface The ocean's biota is numerically dominated by microbial species. Yet the population dynamics, metabolic complexity and synergistic interactions hidden within marine microbial assemblages remain largely uncharted. A full understanding of the living ocean requires moving beyond the 'parts list' of marine microbial taxa and genome sequences. New experimental techniques and analytical approaches have potential to provide the required model systems, experimental data, and ecosystem observations to facilitate construction of predictive models to interrelate microbial dynamics with the biogeochemical matter and energy fluxes that comprise the living ocean ecosystem. At the same time astronauts were walking on the moon, the total number of (micro)organisms living in each milliliter of seawater had been underestimated by over three orders of magnitude ! While we were looking toward the skies, the majority of microbial life on Earth was left largely unknown, and certainly under appreciated. A large paradigm shift in microbial oceanography occurred in the late 1970s and early 1980s, when accurate estimates of total cell numbers and bulk rates of microbial production became available. Over the next 25 years or so, local, regional, and global estimates of microbial numbers, and their bulk production and consumption rates in ocean surface waters were quantified and mapped. These data have provided more accurate estimates of total planktonic microbial biomass and its turnover, enlarging the perceived role and significance of bulk microbial biomass and activity in oceanic food webs. While this information has been extremely useful, only recently has more specific information on the biology of planktonic microbial organisms become available. Questions that are now being more specifically addressed include : Which taxa of marine 2 Bacteria and Archaea are most dominant, representative, or biogoechemically relevant in particular ocean provinces or depth strata ? What are the most common microbial energy and carbon sources, and the most relevant catabolic and anabolic pathways ? How do dynamic population shifts (regular or sporadic) and species interactions shape the ecology and biogeochemistry of the seas ? Unlike eukaryotic plankton, that can often be taxonomically and metabolically categorized based on directly observable phenotypes, planktonic Bacteria and Archaea have remained more enigmatic with respect to their core identifies and physiological properties. Consequently, advances in cultivation-independent metagenomics, as well as new cultivation technologies, have had specific and dramatic influence on our knowledge of …