Physico-chemical factors (‘microenvironments’) are the seminal forces that determine the abundance and activity of microbial communities. By measuring essential parts of microenvironments we can start to unravel the dynamic relationship of microbes with their natural habitat, knowledge that is key to our understanding of ecosystem functioning, resilience and microbial resource utilization. Work in these projects combines microenvironmental sensing technologies (e.g. microsensors or optodes) with general descriptors of microbial abundance (e.g. microscopy, 16S amplicons) and/or activity (transcriptomics, metabolomics, and quantitative imaging technologies). This interdisciplinary approach is highly versatile and has been used on a range of ecosystems, ranging from coral reefs to subterranean caves. The resulting data provides important insights into the mechanisms mediating the nexus between microbes and microenvironments under current and future environmental regimes.