Microbial Oceanography

The research mission of this relatively new subdiscipline is anchored at the intersections of oceanography, marine microbiology, and ecology. While the specific disciplinary boundaries are not well defined, the core foci are biogeochemistry, especially element cycles, the microbial loop, and controls on microbial population distributions and dynamics in time and space. This current bibliography is restricted to pelagic ecosystems, those seaward of the continental shelves and above the seafloor. Future microbial oceanography themed bibliographies could focus on benthic habitats (from littoral habitats to the abyss), microbial life in extreme environments (e.g., oxygen minimum zones, hydrothermal and seep habitats, life in polar seas), or other relevant topics, but the pelagic ocean is the largest biome on Earth, so our stated focus is well justified. A central challenge of microbial oceanography is to conduct comprehensive field campaigns to track the physical and chemical variables that define specific marine biomes and to understand how these habitat characteristics influence in situ microbial processes. The key physical processes, ranging in scale from molecular diffusion to global ocean circulation to ocean-atmosphere-climate interactions, cannot be reproduced in a laboratory setting. The target populations in microbial oceanography include bacteria, archaea, protists, microalgae, and small (<150 μm) metazoans, as well as their viruses. Symbiosis, including parasitism and mutualism, syntrophy, and other direct and indirect cell-to-cell interactions are important phenomena in the sea, but they are also difficult to reproduce in a shore-based laboratory setting. Consequently, access to the sea and the ability to conduct at-sea experiments is vital for research success in the discipline of microbial oceanography. Finally, a major challenge in microbial oceanography is the training of the next generation of practitioners and leaders. Because the research foci are transdisciplinary, the formal training should also be at the intersections of oceanography, marine microbiology, and ecology, but few academic degree programs are designed for this purpose. Like many emergent scientific disciplines, microbial oceanography is rapidly evolving, so we have endeavored to select several “classic” publications to provide an intellectual foundation of knowledge rather than rely solely on “last week’s” discovery papers. The hope is that this annotated bibliography will serve as a useful starting point to identify key concepts in the discipline and will help to educate and to inspire those interested in pursuing a career in this important and timely discipline.