We use a combination of biophysical experiments and computer modelling to understand and manipulate the collective behaviour of microorganisms in environmental, industrial, and clinical settings. These range from bacterial biofilms/flocs in wastewater treatment plants to the formation of microbial railway tracks by pathogenic sea-grass colonising protists. Such systems are very complex , therefore we adopt an interdisciplinary approach combining Physics, Biochemistry, Ecology, Environmental Engineering and Molecular Biology in order to unravel the underpinning science.