Microbial structuring of marine ecosystems

Abstract

In this Review, Azam and Malfatti make a case for the need to elucidate in situ microbiology as a unifying basis for understanding and modelling the influence of microorganisms on marine ecosystems. Bacteria dominate the ocean in abundance, diversity and metabolic activity. The uptake of organic matter by bacteria is a major carbon-flow pathway, and its variability can change the overall flux of carbon in the ocean and, therefore, globally. Organic matter in seawater is present as transparent gels that are composed of colloids, mucus sheets and bundles. It is important to consider how microorganisms interact with organic matter that is present in this form. Growth rates of bacteria in the ocean are important, but estimates based on the bulk phase could be inaccurate. It is feasible that hot spots of nutrients allow bursts of fast growth in a boom-and-bust cycle. Marine snow is an important component of the organic carbon in the ocean on which bacteria can reach high cell densities. Understanding the biochemical bases of the interactions of bacteria with marine snow will enable us to begin to link carbon storage and carbon biochemistry with gene expression in the bacteria that are present on these aggregates. Microbial oceanography is a field that is caught between scales — microbial processes must be understood at the scale of the individual microorganism, but yet we want to understand the cumulative influence of microbial processes on how the ocean works as a biogeochemical system. We argue that understanding how bacteria interact with the ocean system at the nanometre to millimetre scales provides insights into biogeochemical processes of global significance.