Our research uses ‘omics’ data to link the role of microorganisms to the (geo)chemistry of the environment and biotechnological applications. These omics techniques are applied to several different (mostly extreme) environments including acidophilic microorganisms (optimum pH for growth <5) in natural and anthropogenic milieu, Baltic Sea sediments influenced by climate change, and microorganisms inhabiting the deep biosphere and the information is combined with geochemistry data to understand their interactions. We use several techniques including sequencing the whole genome of microorganisms (genomics) or the mixed microbial population in an environment (metagenomics), sequencing RNA transcripts from pure cultures and communities to identify which genes are switched on, and bioinformatics to elucidate the metabolic potential encoded in the DNA.