Beneath the Surface: Fungal Community Associated with Brown Alga Saccharina latissima A Molecular Characterization through DNA Extraction, PCR Amplification, Nanopore sequencing and BLAST Analysis

Abstract

Fungi can be found in every marine habitat, but our knowledge about their diversity, function, and potential is still limited Studies show that marine fungi play an important role in ecosystems by contributing to nutrient cycling and forming symbiotic relationships with marine organisms. Saccharina latissima, also known as sugar kelp, is a brown algae with a circumpolar distribution in the Northern Hemisphere and has generated increased interest for cultivation in Europe and Norway.

The objective of this study was to identify the fungal communities on S. latissima through molecular characterization using DNA extraction, PCR amplification, Nanopore sequencing, and BLAST analysis. I aimed to investigate the fungal communities on S. latissima, the diversity of fungi in wild S. latissima compared to cultivated, and the diversity changes of fungi throughout the seasons. This research would expand the knowledge about marine fungi associated with S. latissima, laying the foundation for future research to ensure the sustainable cultivation of S. latissima. I collected 12 S. latissima samples from a kelp forest outside the student diving club in Tromsø and 8 samples from a kelp cultivation facility at Krakens operated by Akvaplan-niva and Oceanfood. The samples were collected from February 2023 to October 2023.

I encountered difficulties in my methodology. The extraction of fungal DNA for the algal samples was not optimal, and I hypothesize that inhibitors were in the DNA extracts and did inhibit further analysis. These inhibitors could have inhibited DNA amplification or our choice of primers and blocking oligonucleotide were suboptimal and could limit the amplification of fungal DNA. Further, the purification of PCR products before sequencing resulted in a loss of DNA, making some samples unviable for sequencing due to low DNA concentration.

Nevertheless, I was able to document the presence of 10 different fungal taxa within an individual S. latissima sampled from the kelp forest. Future research should focus on optimizing DNA extraction and PCR amplification of fungal DNA from S. latissima and other kelp and brown algal species.