Background – The microscopic world of the freshwater biofilm is a complex association of organisms from prokaryotes to metazoans. Understanding the relationships between these organisms, and between them and their environment, is complicated by the processes by which biofilms are studied. Whilst it is possible to observe and minutely describe the individual organisms which comprise biofilms, inter-relationships within the ‘community’ are often destroyed during sample collection and investigation under the microscope. Ecologists often focus on particular groups of organisms (e.g. diatoms) and interrogate data using multivariate statistics. This offers valuable insights that enable us to understand how associations of particular taxonomic groups respond to key environmental gradients yet offers an essentially abstract view of the microscopic world.

Approach – In this essay we contrast the great detail achieved when we see and describe individual cells with the gross approximations necessary when the response of communities is considered. A focus on the diatom assemblage (one part of the intricate biofilm community) and the use of multivariate statistics to interpret responses along ecological gradients offers opportunities to understand environmental change in space and time but at the expense, perhaps, of local detail which may account for some of the unexplained variation in models. We cannot envisage a change in approach in the near future but, instead, encourage a greater awareness of the complexity of stream biofilms to better inform interpretation.