MinION in the marine environment: from identifying tetrodotoxin producers to tracing sharks and rays using eDNA
About Reindert Nijland
Reindert Nijland is an Assistant Professor at the Marine Animal Ecology group at Wageningen University, Netherlands. Since obtaining his PhD in molecular microbiology at University of Groningen, Netherlands, he has studied the interaction of bacteria with a diversity of hosts. At the Dove Marine Laboratory, Newcastle University, UK, he worked on biofilms of marine Bacillus species isolated from seaweed. After returning to the Netherlands, he studied bacterial pathogens and their interactions with the human and bovine immune systems at UMC Utrecht. In 2014, he again switched host organism, and joined Wageningen University to study the interactions of bacterial pathogens with their plant hosts. Reindert has a strong passion for marine biology, especially crabs. He enjoys scuba diving, underwater photography and underwater filming. In 2017, he could no longer resist the attraction of the marine environment, and joined the Marine Animal Ecology group. His current focus is on the interaction between marine hosts and their microbes. He developed approaches to identify microbial toxin gene clusters in shellfish. He also works on the development of methods for rapid on-site identification of eukaryotes such as crabs, fish and marine mammals by analysing environmental DNA (eDNA) using nanopore sequencing with the MinION.
We study marine ecology using molecular biology. In recent years, every summer the neurotoxic Tetrodotoxin (TTX) is found in Dutch mussels and oysters, exceeding levels allowed for human consumption. TTX is produced by bacteria, and accumulates in the animal host. The gene cluster encoding TTX biosynthesis is unknown, and the microbial source of the Dutch TTX outbreak is not identified. We therefore isolated metagenomic DNA from TTX positive shellfish and used nanopore sequencing to identify TTX producing microorganisms and their TTX biosynthetic gene clusters. In another project we survey marine biodiversity. Offshore wind farms in the North Sea are assumed to attract large marine animals, since they provide a diverse habitat with increased biodiversity and shelter. Using a mobile sequencing laboratory, we aim to amplify and sequence environmental DNA (eDNA) directly on-site, to investigate the presence of large marine animals such as sharks and rays. Both applications demonstrate the opportunities of mobile, real-time, long-read sequencing enabled by the MinION.