Progress report after development of microbial and molecular sensors. WP3, D3.7, Version 2.0.

Abstract

The aim of Task 3.4 is to develop and test innovative methods for the molecular detection of phytoplankton, harmful algal blooms and pollutants through their effect on microbial communities. This will include 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 environment 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 will be further tested through campaigns to be performed through WP4. Complementary technologies are being 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 based on the specific binding of a molecular. This sensor will be adapted and optimised for long term unattended operation on Ferrybox systems through this task. In parallel, for the direct detection of algae toxins, the capabilities of an in situ optical biosensor were extended. This was done to reduce the device size, increase its efficiency, and potentially extend its performance to detect more than domoic acid, which was the toxin that the sensor was initially designed for. In this first phase of the project, the sensor was successfully redesigned and is planned to be tested in laboratory conditions prior to deployment at sea. For investigating plankton diversity and harmful algal blooms rDNA meta barcoding 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 show that metabarcoding reveals a much higher diversity in phytoplankton compared to microscopy. However, metabarcoding only gives 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. The two different approaches complement each other. Metabarcoding is being further evaluated through comparison with in situ imaging flow cytometry and microscopy in a study of harmful algal blooms on the Swedish Skagerrak coast. This progress report includes the work performed during the first two years of the project. During this first phase of the project, much of the focus has been on the development and improvements of the different types of sensors and biosensors before the sensor testing through laboratory and field campains, which will involve sensor tests in a common setting and integration of the results and responses from the different devices and tools.