Marine genomic observations | Lifewatch regional portal

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Marine genomic observations

General

DNA sequencing technology has come a long way since the rise of automated sequencing in the 1990s. Today, it is possible to generate huge amounts of sequence data in a relatively straight-forward and affordable way. High throughput sequencing allows a more complete and deeper investigation of environmental samples than ever possible before, leading to new possibilities in biodiversity research.

In the marine domain, LifeWatch applies innovative DNA-based techniques to create high-resolution data series on the biodiversity in the Belgian Part of the North Sea (BPNS). For its long-term observations, LifeWatch works towards standardization in collaboration with various international consortia in the framework of GEANS, AssemblePlus, Jerico-Next, Ocean Sampling Day consortium, the European ARMS program and EMBRC. State-of-the-art bioinformatics pipelines are developed in close collaboration with the LifeWatch ERIC.

 

Approach and infrastructure

During monthly multidisciplinary sampling campaigns with RV Simon Stevin, various water samples for sequencing are collected in the BPNS.

Collected water samples are filtered onboard and stored for further processing in line with the Ocean Sampling Day protocol for metagenomics and metabarcoding of microbial and eukaryote plankton communities. Samples are either processed in the framework of various projects (see below) or are made available as part of the sample library. In addition, unfiltered samples are stored for species-specific analysis of environmental DNA.

  

Fig 1. RV Simon Stevin. Fig 2. Filtrations for bacterial DNA by Sterivex according to the OSD protocol.

 

In order to observe the marine fauna near the sea floor a number of fixed Artificial Reef Monitoring Structures (ARMS) are set out each year at a number of points in the BPNS. This standardized passive sampling and consecutive DNA-based analysis is done in line with the protocols of the European ARMS/MBON program. Organisms growing on the settlement plates are collected and are pooled into samples for DNA metabarcoding.

   

Fig 3. Recovery of tripod with the Automated Reef Monitoring Structure (ARMS) attached. Fig 4. Detailed image of the Automated Reef Monitoring Structure (ARMS).

 

Depending on the project, samples are processed in the molecular lab making use of the in-house infrastructure (thermal cycler for qPCR, BioAnalyzer for DNA quality control, MinION for nanopore sequencing, etc.) or making use of external sequencing facilities.

Bioinformatics pipelines for standardized processing of the sequence reads are developed in close collaboration with the LifeWatch ERIC and making use of the ICT infrastructure offered by Ghent University and the Flemish Supercomputing Centre (VSC).

 

Projects

  • Genomic Observatories - Ocean Sampling Day
  • Genomic Observatories - ARMS
  • Micro-B3
  • AssemblePlus
  • Jerico-Next
  • GEANS
  • BPNS Long-term series E
  • PhD (R. de Blok) - Spatial and temporal phytoplankton dynamics in the Southern part of the North Sea
  • PhD (N. Dillen) - Artifical Intelligence based integration of genomic, morphological and environmental plankton
  • PhD (M. Perneel) – Understanding plankton environment interactions by investigating pysiological pathways and selective sequencing of expressed genes.
  • Development of nanopore sequencing procedures for detection and identification of marine species

 

Data

  • Phytoplankton biodiversity in the Belgian part of the North Sea: a microscopic and molecular inventory, more
  • LifeWatch observatory data: genomic observations in the Belgian Part of the North Sea, more
  • LifeWatch 2016 monthly genomic observation (16S & 18S) in the Belgian Part of the North Sea, more
  • LifeWatch/Jerico cruise 2017 - genomic observations (18S) in the Belgian and Dutch Part of the North Sea and the English channel, more
  • Ocean Sampling Day 2012 pilot genomic observations (16S) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2017 genomic observations (16S) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2018 genomic observations (16S) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2019 genomic observations (16S) in the Belgian Part of the North Sea, more
  • 2018 ARMS observations invasive and indigenous hard-bottom communities by Flanders Marine Institute, more
  • 2019 ARMS observations invasive and indigenous hard-bottom communities by Flanders Marine Institute, more
  • 2020 ARMS observations invasive and indigenous hard-bottom communities by Flanders Marine Institute, more
  • 2021 ARMS observations invasive and indigenous hard-bottom communities by Flanders Marine Institute, more
  • LifeWatch June 2014 genomic observations (16S V3 & V4) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2014 genomic observations (16S V4) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2020 monthly genomic observations (16S) in the Belgian Part of the North Sea, more
  • Ocean Sampling Day 2021 genomic observations (16S) in the Belgian Part of the North Sea
  • European Marine Omics Biodiversity Observation Network (EMO BON) 2021 bimonthly sampling

 

Selection of publications

  • Semmouri, I.; De Schamphelaere, K.A.C.; Van Nieuwerburgh, F.; Deforce, D.; Janssen, C.R.; Asselman, J. (2020). Spatio-temporal patterns in the gene expression of the calanoid copepod Temora longicornis in the Belgian part of the North Sea. Mar. Environ. Res. 160: 105037. https://dx.doi.org/10.1016 [link to IMIS record]
  • Hablützel, P.I.; Rombouts, I.; Dillen, N.; Lagaisse, R.; Mortelmans, J.; Ollevier, A.; Perneel, M.; Deneudt, K. (2021). Exploring New Technologies for Plankton Observations and Monitoring of Ocean Health, in: Kappel, E.S. et al. Frontiers in ocean observing: Documenting ecosystems, understanding environmental changes, forecasting hazards. Oceanography, Suppl. 34(4): pp. 20-25. https://dx.doi.org/10.5670/oceanog.2021.supplement.02-09 [link to IMIS record]
  • Lagaisse, R. (2020). Phytoplankton biodiversity in the Belgian part of the North Sea: a microscopic and molecular inventory. MSc Thesis. Ghent University, Biology Department: Gent. 117 pp. [link to IMIS record]
  • Semmouri, I.; De Schamphelaere, K.A.C.; Mees, J.; Janssen, C.R.; Asselman, J. (2020). Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community. Mar. Environ. Res. 153: 104836. https://hdl.handle.net/10.1016/j.marenvres.2019.104836 [link to IMIS record]
  • ten Hoopen, A.; Pesant, S.; Kottmann, R.; Kopf, A.; Bicak, M.; Claus, S.; Deneudt, K.; Borremans, C.; Thijssen, P.; Dekeyzer, S.; Schaap, D.M.A.; Bowler, C.; Glóckner, F.O.; Cochrane, G. (2015). Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards. Stand Genomic Sci. 10: 20 [1-10]. hdl.handle.net/10.1186/s40793-015-0001-5 [link to IMIS record]