As theory of science is subject to conflicting ideas, the role of micr
obiology in marine ecosystem analysis is viewed from extremely differe
nt positions. Combined descriptive and experimental approaches have el
ucidated key functions of microorganisms that challenge the traditiona
l, macro-organism-dominated concepts in ecosystem ecology. This point
is illustrated, in particular, by examples of microbe-mediated pathway
s in the benthic-pelagic coupling of energy flow and carbon cycling. I
n this context, the role of bacterial biofilms and benthic macrofauna
as well as their interaction in marine sediment biogeochemistry is emp
hasized.