This paper synthesizes current ideas on the role of the microbial loop
in carbon fluxes in the ocean and proposes some directions for future
research. Organic matter flux into bacteria is highly variable, which
can significantly influence the pathways of carbon flow in the ocean.
A goal for future research is to elucidate the mechanistic bases of b
acteria-organic matter coupling. This research should take into consid
eration the micrometer-scale distribution of bacteria and the composit
ion, structure, and dynamics of the organic matter field in the bacter
ium's microhabitat. The ideas on the interactions of bacteria with the
particulate organic phase need to be revised in view of recent findin
gs of highly abundant, previously unknown particles ranging in size fr
om nanometers to hundreds of micrometers. The ''hot-spots'' in the dis
tribution of organic matter and remineralized nutrients can influence
the rates as well as the direction of biogeochemical fluxes. Slow-to-d
egrade dissolved organic matter (DOM) may be produced because of loose
bacteria-organic matter coupling resulting in DON storage. Its use at
a later time and place has profound implications for carbon fluxes an
d food web dynamics. A fundamental research need for the future is to
understand the ecological interactions among the members of the microb
ial loop in an appropriate microhabitat context. While this goal was p
reviously intractable, new molecular and optical techniques should mak
e it possible to understand the biogeochemical activities of the micro
bial loop in terms of the ecology and evolution of pelagic microbial c
ommunities.