Detection of oomycetes on seagrasses using state-of-the-art Nanopore sequencing
Date of publication: Aug 23, 2023

In a short research project, Kaïn van Calcar, a BSc student at the University of Amsterdam, investigated the role of oomycetes in the decline of seagrass meadows. Seagrass meadows are essential for providing various ecosystem services, including acting as habitats for marine organisms and effectively storing carbon. Unfortunately, these meadows have been experiencing a rapid worldwide decline. Oomycetes are fungus-like protists, ubiquitous on land and in the ocean. Recently, some oomycete pathogens have been identified as the cause of the decline of seagrass meadows in some areas; they are known to infect seagrasses, reducing seed germination and impairing seedling development. Therefore, identifying pathogenic species and understanding the underlying conditions leading to infection is extremely important to restoring seagrass meadows. 

Kaïn van Calcar presenting his research at the University of Amsterdam

           To explore the presence of oomycetes and their potential contribution to seagrass decline, Kaïn employed Oxford Nanopore sequencing. Specifically, he used this state-of-the-art method to sequence PCR-amplified gene fragments containing both the 18S rRNA and ITS gene regions, allowing for detecting and identifying oomycetes. These genes vary between species and are commonly used to identify eukaryotic species. 

           Oomycetes were not detected in samples of the seagrasses Zostera marina, Zostera noltii and Cymodocea nodosa obtained from the Ria Formosa coastal lagoon in Faro, Portugal. However, positive results were obtained with isolated oomycete strains used as reference.

Seagrass meadow (Photo by Fee Smulders)

           This study highlights the significance of Oxford Nanopore sequencing for achieving accurate and reliable taxonomic classification by analysing large DNA fragments with specific gene regions. Kaïn received oomycete isolates from Christiana do Couto Pereira Maia (CCMAR, Portugal) and Thomas Jung (Mendel University in Bro, Czech Republic), as well as seagrass samples from Aschwin Engelen (CCMAR, Portugal). The collaborative nature of the study demonstrates the importance of cooperation between different partners, a big goal of the RESTORESEAS project.

Written by Gerard Muyzer, University of Amsterdam