The biofilm composition is determined by metagenomic sequencing. This approach, allied to bioinformatics, is also used to analyse community transcription, metaproteomics (whole community protein identification) and for analysis of small molecules by metabolomics (including stable isotope mass spectrometry) to reveal the expression and modification of all gene products, and identify key points of control of community output. The overall communal biology is assessed using a systems biology approach that identifies the network of interactions within the community, the responses to environmental and engineering conditions and hence key points of regulation and control of community output. The 3D spatial distribution and activity of the various members within biofilm communities are determined using in situ fluorescent tagging techniques, and high-resolution imaging and microscale sensors. This combined whole community experimental approach provides unprecedented understanding of community composition and properties of environmental and engineered biofilms. The data on community activity are used to develop ecological models that explain the behaviour and emergent properties of biofilm communities. These are calibrated with laboratory model biofilm systems (Biofilm Biology) and at the process scale (Environmental Engineering) to translate the fundamental understanding of biofilm behaviour to process management strategies. Crucially, translation from fundamental knowledge to engineering solutions requires the robust quantitative analysis of this cluster.