Microcosm design and evaluation to study stream microbial biofilms

Abstract

Biofilms represent the dominant form of microbial life in stream ecosystems. Research of complex environmental biofilms requires appropriate cultivation techniques to address questions central to biofilm structure‐function‐coupling and ecosystem implications. Whereas the cultivation of medical and industrial biofilms has received considerable attention, cultivation devices for environmental biofilms have not. Here we describe and systematically assess the reproducibility of laboratory‐based microcosms that allow the study of the structure and function of stream biofilms under different flow regimes. Microcosms were assembled from 1.3‐m‐long Plexiglas flumes fed with water that recirculated between a header tank and a sink. Each flume was paved with 104 individual unglazed ceramic coupons that served as growth substratum. We operated 3 microcosms designed to simulate laminar, transitional, and turbulent flow. Each microcosm consisted of two duplicate sets of flumes where two flumes shared the same water. We monitored biofilm coverage, bacterial abundance, and chlorophyll a as bulk biomass parameters over a growth period of 28 days and tested for community composition shifts using denaturing gradient gel electrophoresis (DGGE). Based on these variables, we assessed the reproducibility at different levels of microcosm assembly: (1) within individual flumes (i.e., longitudinal gradients), (2) within a shared water body, and (3) within flow regime treatments. Our results revealed good reproducibility at the various levels of the experimental setup and suggest microcosm flumes as highly valuable tools for biofilm studies with multitreatment and multireference designs.