This report presents results from a project investigating the use of microbes as indicators of mercury (Hg) pollution in sediments. Microbes respond rapidly to environmental change, making them excellent bioindicators. However, to ensure reliable results, it is essential to analyze microbial communities soon after sampling to prevent degradation or loss of activity. To address this, a portable molecular sequencing laboratory, OmiBox, was developed, enabling near in situ analysis of microbial taxonomic composition and gene expression. Additionally, microbial community composition was studied in Hg-contaminated fiber banks in the Gulf of Bothnia. The results revealed that certain taxonomic groups, such as bacteria from the phyla Campylobacterota and Desulfobacterota, were enriched in fiber-rich, Hg-polluted sediments.