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BIOTEK2021-Bioteknologi for verdiskaping

KSP: On-site monitoring of aquaculture impact on the environment by open-source nanopore eDNA analysis

Alternative title: Overvåkning av laksenæringa sin påvirkning av miljøet ved bruk ny håndholdt DNA sekvenseringsteknologi

Awarded: NOK 20.7 mill.

In this project, we have developed a database with over 1500 samples from the entire Norwegian coast and Iceland, where we have linked information about macrofauna with microbiological composition. The result of this comparison was striking, as we primarily identified only two groups of microorganisms. However, these groups were strongly associated with the ecological status of the macrofauna. This information has now been published as a preprint: https://www.biorxiv.org/content/10.1101/2024.09.19.613430v1. Based on the information from the large database, we have developed a specialized database for nanopore sequencing data. This database is designed to predict the status of macrofauna based on nanopore sequencing. The analyses provided highly accurate predictions. In parallel, we have developed a protocol for DNA purification that can be performed in under 15 minutes in the field. The combination of these methods now provides us with a complete setup for nanopore-sequencing-based classification of environmental status. In the development of the model for nanopore-based classification of environmental status, it was found that fewer than 10 bacterial groups were sufficient to provide an accurate classification of the status. This opens up the possibility of using quantitative PCR instead of sequencing, which would be much simpler to implement than sequencing. In the final phase of the project, we will design and test primers. We will also work towards further implementation of nanopore-sequencing-based classification.

Based Regional Research Found funded project DigiMiBa we have shown that we can accurately determine the impact of aquaculture on the environment by functional barcoding of bacteria (predicting electron donors and acceptors in metabolism). These approaches will be combined with novel on-site nanopore sequencing strategies developed in the Norwegian Research Council funded project UnveilMe. The monitoring of aquaculture environmental impact currently represents a major bottleneck in developing the aquaculture industry, particularily the lack of rocky bottom analytic . The aim of this application is to implement an open-source database and prototype on-site test systems so that the aquaculture industry can adapt the functional barcode concept in accurate and efficient monitoring of the environmental impact. Functional e-DNA information will 1) be transmitted to environmental index information in the form of an open-source database , 2) e-DNA indexes be compared to the indexes derived from macroorganism counting, 3) simplified sampling and testing systems that are adaptable to the industry, and 4) suggestions for implementation in Norwegian standards. To achieve the main aim we will expand the analyses to include 1750 samples along the whole Norwegian coast, with sampling covering the whole year cycle. The industry partners in the project will do the sampling in conection with traditional analyses. The Three industry partners complement each other by covering the Whole coastline. The project will also include prototype methodology (microarray based, second and third generation sequencing) for service providers can utilize for functional classification based on eDNA. Based on the project results a report will be written for the new revision of the Norwegian standard for environmental monitoring of aquaculture (NS9410) which is expected in 2023. The intention will be the implementing of functional barcoding in the standard.

Funding scheme:

BIOTEK2021-Bioteknologi for verdiskaping