Development of microbial and molecular sensors

Type Contract report
Date 2019-08-08
Language English
Ref. JERICO-NEXT-WP3-D3.8 Aug 2019 V7
Other localization
Author(s) Boccadoro Catherine1, Karlson Bengt2, Colas FlorentORCID3
Version 7

The aim of Task 3.4 was to develop and test innovative methods for the molecular detection of phytoplankton, harmful algal blooms and pollutants through their effect on microbial communities. This included the development of novel molecular sensors for the detection, quantification and identification of organisms, microbial markers of pollutant exposure or toxin concentrations in marine coastal waters.

Bacterial species and genes which can be used as markers of high nutrient load or hydrocarbon contamination in the marine environment were identified through bacterial community analysis in contaminated environments and literature reviews. Assays using quantitative Polymerase Chain Reaction (qPCR) for the quantification of these organisms were developed and tested through environmental sampling campaigns and laboratory exposure studies. The most promising markers and assays were selected for further study in conjunction with other biological and chemical sensors, and tested through campaigns performed through WP4.

Complementary technologies were developed through this task to monitor toxic algae, combining an approach based on the detection of the organisms through an autonomous sensor, and the detection of toxins using a probe. The fully automated sensor module for autonomous monitoring of toxic algae includes a remote-controlled automated filtration system coupled to a semi-automated nucleic acid biosensor. In parallel, for the direct detection of algae toxins, the capabilities of an in situ optical biosensor were extended, to reduce the device size and its increase its efficiency and test it in laboratory conditions.

For investigating plankton diversity and harmful algal blooms rDNA metabarcoding methods were developed and evaluated by analyzing samples collected using a Ferrybox system in the Baltic Sea area. Results based on 16S and 18S rDNA metabarcoding revealed a much higher phytoplankton diversity compared to microscopy. However, metabarcoding only gives qualitative results on relative abundance of genes (OTU, Operational Taxonomical Units) in samples and does not give information about biomass. Microscopy gives cell numbers and biomass based on cell volumes, making the two methods complementary. Metabarcoding was evaluated through comparison with in situ imaging flow cytometry and microscopy in a study of harmful algal blooms on the Swedish Skagerrak coast.

This report includes the work and results from the development and testing of the novel biosensors and molecular markers performed during JERICO-NEXT project.

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