Environmental microbiology calls for more advanced research methods for resolving microbial functions and regulation in environmental samples. The proposed project introduces an unconventional technology, radioisotope probing (RIP). This approach is based on the invention of radioactivity measurement via pH analysis. When the analysis of radioactivity is now combined with semiconductor sequencing, the technology offers two-dimensional analysis of millions of molecules on a sequencing chip. Hybridization of experimentally labeled RNA and radioactivity measurement would provide a second dimension for the sequencing analysis, facilitating various new applications in environmental microbiology, as well as potential applications for different needs of biochemistry and medical research.The project aims to develop and test three novel RIP applications to analyse functional diversity, transcriptional regulation and mRNA processing in microbial communities, especially focusing on prokaryotic species. The applications are utilized for studying regulation of microbial decomposition, which is the key question, when predicting the effects of climate change. It is hypothesized that more frequent flood, droughts and redox fluctuations can prime the biodegradation of otherwise stable boreal carbon pools.Functional diversity of microbes utilizing model and complex substrates is studied in terrestrial and aquatic environments using time-series samplings and labeling experiments. Prevailing mechanisms in the cellular regulation in microbial communities are investigated using community-level methylation and regulatory RNA patterns. The effect of external stressor (toxicants and changing oxygen regimes) on these patterns is analyzed using sequencing and RIP to reveal the mechanisms regulating the processes beyond mere community composition.