Marine bacteria and archaea: Diversity, adaptations, and culturability

Abstract

With an estimated total number of 6.6 × 1029 cells, Bacteria and Archaea in marine waters and sediments constitute a major fraction of global microbial biomass. Most marine bacterial communities are highly diverse and individual samples can comprise over 20,000 species. Different marine habitats such as coastal surface waters, subsurface open ocean waters and sediments are colonized by distinct bacterial communities. Consequently, global marine bacterial diversity must be very high but has remained largely uncharted to date. One major obstacle that needs to be overcome is the persisting difficulty to culture most of the dominant marine bacterial and archaeal phylotypes. Typically, these difficulties relate to an insufficient appreciation of the specific physiological requirements and adaptations of marine Bacteria and Archaea. In many marine environments, concentrations of readily utilizable dissolved organic carbon (DOC) compounds or inorganic nutrients are present at submicromolar concentrations whereas suspended marine particles constitute spatially discrete hot spots of growth substrates. Known bacterial adaptations to oligotrophic growth conditions include high affinity uptake systems, low growth rates and cell sizes, streamlined genomes, little regulatory flexibility, physiological specialization and low loss rates due to grazing and viral lysis. On the opposite, lineages adapted to exploitation of nutrient hot spots are motile, chemotactically active, have large cells, adhere to particles, employ specialized uptake systems for high molecular weight substrates, excrete exoenzymes, and feature a broad substrate spectrum. Besides these canonical types of adaptations, interesting novel traits have been discovered over the past years, like the widely distributed proton-pumping bacteriorhodopsins, a multitude of carbohydrate-active enzymes, TonB-like receptors, thiosulfate oxidation, methylotrophic pathways, carbon monoxide oxidation, metabolism of compatible solutes, and heavy-metal resistance. In order to retrieve and study representatives of not-yet-cultured bacterial lineages in the laboratory, future culture attempts need to be modified according to this improved knowledge of the specific adaptations of marine Bacteria and Archaea.