Microbial and molecular sensors
Lead: IRIS (Catherine Boccadoro)
This task will focus on the development of sensors for the molecular detection of phytoplankton, harmful algae blooms, and pollutants through their effect on microorganisms. This will include the development of novel molecular sensors for the detection and identification of organisms, microbial markers of pollutant exposure or toxin concentrations, which can be adapted to existing platforms to incorporate crucial biological parameters into already existing measures. Another aspect of this task will be the adaptation of a suitable sampling device to the Ferrybox to enable the collection and preservation of sensitive material for further laboratory analysis. This task will be a collaborative effort to develop and integrate complementary molecular sensors into existing platforms.
SubTask: 3.4.1 Microbial molecular markers for pollution detection (led by IRIS): Pollutant exposures in the marine environment trigger specific changes within the microbial communities, resulting in some species and genes becoming much more prominent following contaminant exposure or environmental changes. Subtle microbial population shifts can be very informative about acute spills as well as chronic low levels of exposure, which can be extremely challenging to detect and quantify using more traditional chemical analysis. These can be detected and quantified through qPCR analysis of seawater DNA samples, which will be obtained using existing coastal monitoring platforms. This task will develop the method, focussing on the identification of suitable marker organisms and genes for the detection of pollutants, with a particular focus on chronic and acute low-level hydrocarbon pollution. The collection and preservation of samples will be adapted to the Ferrybox through Sub-Task 3.4.3.
SubTask: 3.4.2 Biosensors for the detection of toxic algae (led by HZG): This talk will aim at developing complementary technologies for monitoring toxic algae based on the detection of the organisms through an autonomous sensor, and the detection of the toxin using a probe. Within the EU project EnviGuard (Project no. 614057) a fully automated sensor module for autonomous monitoring of toxic algae will be developed by the Alfred Wegner Institute (AWI), Germany, in cooperation with HZG. This system includes a remote-controlled automated filtration system coupled to a semi-automated nucleic acid biosensor. The detection principle of a nucleic acid biosensor is based on the specific binding of a molecular probe immobilised to the sensor surface to the target particle. A transducer component transforms this detection event into a measurable signal such as an electrical current for highly sensitive and quantitative nucleic acid based detection of toxic algae. In this activity, this sensor will be adapted and optimised for long term unattended operation on Ferrybox systems. In parallel, a complementary technology for the detection of the toxins will be further developed. An in situ optical biosensor based on surface plasmon resonance for domoic acid detection and quantification has been developed at Ifremer. Tests performed in laboratory and during oceanographic campaigns showed that the system allows a semi-quantitative detection of the toxin in the range 0,1-2ng/mL. Improvements will be made through this task to gain in sensitivity accompanied with a drastic reduction in costs by working in the NIR range with special glass material and low-cost spectrometer. This strategy will allow a rapid adaptation of the in situ prototype and testing in the marine environment in the context of “JERICO-NEXT“. The system will be complementary to the one developed by the HZG. Analysis of the same samples with the two instruments will be carried out to prove the interest to detect the algae species as well as the toxin in coastal waters.
SubTask: 3.4.3 – Automated sampling of rDNA adapted to the Ferrybox (led by SMHI): The detection of biological species through whole sampling of organisms or DNA often require particular methods and care to preserve the quality of the sample for later laboratory analysis. This part of the work will focus on adapting an existing commercially available sampler to the Ferrybox in order to collect sensitive material, which will be used to ultimately generate new biodiversity data on phytoplankton, bacteria and microzooplankton based on sequencing of rDNA. Minor modifications will be necessary to ensure the proper preservation of samples with the use of the necessary toxic preservatives (glutaraldehyde or formaldehyde), while maintaining a safe and healthy working environment. Verification of sample quality will be carried out by sequencing of 16S and 18S rDNA as well as microscopic analysis, qualifying the method as operational for the collection of samples for plankton and bacteria.
Deliverable 3.7: Progress report after development of microbial and molecular sensors (M24). This document will give the status on the developments towards microbial and algae sensors and it will give a status on the Ferrybox adaptation on sample collection for molecular analysis.
Deliverable 3.8: Results after development of microbial and molecular sensors (M42). This document will include results from the deployment of the phycotoxin biosensor and a Compilation of results from the activities carried out to develop microbial and molecular sensors for the detection of pollution and toxic algae, and the development of a suitable sampling device adapted to the Ferrybox.