1. Development of a field-based nanopore sequencing service. Partners: KU Leuven – UGent (GhenToxLab)

Access to genetic data in the field (either during a cruise or on an isolated field station) is limited by access to capital- and data-intensive sequencing platforms. The benchtop ONT MinION system of long read sequencing has made field access to sequence data feasible, albeit not without some challenges such as computational power. We have developed a protocol to deal with ONT MinION sequencing outside an urban lab environment. We successfully applied our protocol through a comparison of Illumina-based short fragment reads and ONT MinION-based reads on a metabarcoding project of zooplankton sampled in the North Sea and the stomach content of polar fish. The protocol has been validated under lab and field conditions and is available to the community.          

  1. Genetic broodstock characterisation for pedigree management in whiteleg shrimp Penaeus vannamei Partners: (KU Leuven – UGent (ARC)

Commercial farmers of fish and shellfish purchase fingerlings from a small number of established breeders without any knowledge of the genetic status. Omics provides opportunities to quantify the genetic diversity and relatedness of the shipments. We used hiIgh-density SNP profiling of larval whiteleg shrimp batches bought for grow-out in Europe. This information is crucial for stock management, as European shrimp farmers aim at independence of external suppliers. We developed a bioinformatic pipeline for analyzing large genomic datasets. A 40,000 SNP chip was used to genotype and characterize 700+ samples of juvenile shrimp collected throughout Europe. The first results point to the first insights into breeding approaches for crustaceans.

  1. Single-cell genomics for marine organisms  Partners: KU Leuven – UGent (PAE, Phycology)

Single-cell genomics may detect genomic and epigenomic variation at the cellular level and link the observation directly to the phenotype. When using traditional omics approaches, which rely on pooled samples, individual variation is lost. Here we developed bioinformatic pipelines allowing single-cell resolution for typical non-model algal organisms (marine macroalgae and diatoms). The output will facilitate future research questions to address cell-to-cell heterogeneity, plasticity or stress at gene-expression level of a single cell, either of a marine microbe or a multicellular organism. A bench protocol and bioinformatic pipeline was tailored for the analysis of single-cell transcriptomic data for a marine unicellular alga. PAE successfully pioneered single cell transcriptomics for the diatom model Cylindrotheca closterium allowing us to study the differentiation of sexual cell types and validated them using a site of cell reporter lines (Bilcke et al. in prep). This approach is now being tested for centric model diatoms.

  1. A broadly applicable workflow to visualize nanoparticles and micro-organisms in small aquatic organisms Partners: UHasselt, UGent (Marbiol, Ghentoxlab)

A bench protocol to visualize nanoparticles simultaneously with micro-organisms in small aquatic organisms. The challenge is to overcome the autofluorescence that is inherently present in these small aquatic organisms. The bench protocol will overcome this to allow researchers to improve their understanding of nanoparticle effects on aquatic organisms.

  1. Optimisation of in-situ sampling from ARMS in dynamic coastal environments Partners: RBINS, VLIZ, UGent (Marbiol)

ARMS are standard artificial structures used to study and monitor biodiversity and are particularly useful for studying species that may be difficult to detect using traditional survey. Using ARMS in dynamic coastal environments is not trivial as physical disruption, sedimentation and biofouling can challenge their usage and researchers need to adapt monitoring techniques. Retrieving an ARMS from a mooring unit with an acoustic release increases possible loss of organisms. Divers can prevent that but diving opportunities in dynamic North Sea conditions are limited due to tides and weather conditions. A standard technique retrieving an ARMS module from coastal north sea environments with divers has been developed and has been compared with retrieval without divers

In addition to these 5 Belgian JDAs, two EMBRC-BE partners were selected to run European JDA projects (2 projects of 100.000€ each, supported by EMBRC HQ).

  1.  MacroC-MicroB fosters a collaboration among EMBRC partners UGent - Phycology (Belgium), CCMAR (Portugal), SBR (France) and Tjarno Marine Laboratories (Sweden) to establish culture collections of economically important marine macroalgae and their associated microbiomes. Furthermore, the joint research activity will establish best practices to biobank microbiomes of cultured organisms. Cultures will be made available to the scientific community through the centralised EMBRC algal culture collection.
  1. A research infrastructure for chronic noise pollution studies in coastal waters and sediments, a collaboration among EMBRC partners UGent - Marbiol (Belgium) and the Institute of Marine Research, IMR (Norway).