Microorganisms are the driving catalysts of biogeochemical cycles sustaining life in the ocean. Thus, the determination of their metabolic processes is fundamental for the understanding of marine ecosystems. Nevertheless, these are practically absent from current monitoring programs because of the considerable analysis complexity. Nowadays, advanced molecular techniques overcome former challenges. One of the promising approaches is the analysis of the transcripts in natural microbial assemblages (metatranscriptomes). Unfortunately, transcripts can degrade in less than 30 sec. Their unbiased detection in nature, especially from hypoxic or deep water habitats, is a challenge because they are subject to considerable modification simply due to sampling procedures. We developed already an adequate sampling technique for use at the CTD rosette. However, for monitoring of temporal and spatial variations autonomous event and/or time triggered in situ fixation instruments are essential on ocean observatories. Based on our system these independent instruments will be developed and tested in hypoxic waters. The procedure will be optimized concerning the sampling volume, fixative, and storage time under varying conditions, but also concerning bioinformatics to get reproducible data. Project outcome will be an AFISmon prototype applicable for the monitoring of biogeochemical processes.