We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas

We thank the organizers of the SAME 10 meeting for the nice environment and the very fruitful meeting. P. del Giorgio pushed us to write down our thoughts, and shared many with us. D. Kirchman commented on some of the issues raised, and C. Pedrós-Alió commented on one of the first drafts. J.M.G. and J.P. summarized and reported on our discussion. Our work was supported by the following grants: NSF grant 0217282 (H.D.), Spanish MEC grant MODIVUS (J.M.G.), the Swedish Science Council (J.P.), the IEO time-series RADIALES programme (X.A.G.M.), the Earth and Life Science Division of the Dutch Science Foundation, ARCHIMEDES project, #835.20.023 (G.J.H.). Work of some of the authors was carried out within the frame of the ‘Networks of Excellence’ MarBef and EurOceans (6th FP of the EU)

AME Special 1, Symposium on Aquatic Microbial Ecology (SAME 10), Progress and Perspectives in Aquatic Microbial Ecology: Highlights of the SAME 10, 2-7 September 2077, Faro , Portugal.-- 18 pages, 2 figures

Peer reviewed