Microbial communities as environmental indicators
The overall aim of this project is to evaluate the use of microbial communities as bioindicators of environmental pollution in contaminated marine sediments and under predicted climate change conditions.
Sampling cruise on board the KBV181 vessel
For this project, we went on board the research vessel KBV181. This vessel includes an on-board laboratory for routine environmental monitoring activities, two lab containers, and an electrical Gemini sediment corer system, among other research equipment. Given that some research cruises can take up to several days on board, KBV181 also includes different living quarters such as kitchen, rest area, bedrooms, and even a small but cosy gym. All these living spaces make prolonged research activities much more pleasant.
Deployment of OmiBox on board
This expedition also aimed to test the performance of OmiBox for its potential use in future environmental monitoring activities in the Baltic Sea. Thanks to its high portability, we could easily carry OmiBox inside one of the lab containers on board and deploy all the equipment even in this reduced space. Processing environmental samples and making genomic libraries while staring at the sea landscape... what a nice experience!
Sample collection
This project aims to compare marine sediments with different loads of Hg (highly toxic heavy metal) from various areas throughout the Baltic Sea. On board KBV181, we carried out sample collection from South to North at different monitoring stations and areas known to be contaminated by Hg due to industrial activities, including paper fiber banks. At these contaminated areas, we collected in transects to establish gradients: from highly contaminated to non-contaminated sediments. We use an electrically operated Gemini sediment corer to collect sediment cores, from which the top 10 cm were homogenised, placed in jars, and frozen at -20°C for later analyses of Hg and MeHg content.
Microbial samples and sequencing
From the homogenised top 10 cm layer, around 300 mg of sediment were collected for microbial DNA/RNA analyses. The samples were collected in Eppendorf tubes and immediately processed, from DNA/RNA extraction to Nanopore sequencing.
However, only DNA samples from one of the sampling transect could be successfully analysed due to very rough weather conditions. We could barely walk on board due to the extreme and constant swing of the vessel! Fortunately, extra samples were previously frozen in liquid nitrogen for further analyses in our in-house laboratories. An additional sampling cruise will be planned soon for a new attempt to perform DNA/RNA analyses on all samples.
