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

  • 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
  • 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

 

Publications

  • 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., more
  • 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, more
  • Delacauw, S.; Deneudt, K.; GEANS consortium; Hablützel, P.I. (2020). Non-indigenous species pilot in GEANS, in: Mees, J. et al. Book of abstracts – VLIZ Marine Science Day. Oostende, Belgium, 18 March 2020. VLIZ Special Publication, 84: pp. 53, more
  • Pavloudi, C.; Chrismas, N.; Troncoso, J.S.; Norkko, J.; Viard, F.; Mortelmans, J.; Mavric, B.; Gerovasileiou, V.; Arvanitidis, C.; Kotoulas, G.; Obst, M. (2019). Artificial Reef Monitoring Structures (ARMS) providing insights on the marine biodiversity and community structure. Genomic Observatories/ASSEMBLE/Interreg Balkan-Mediterranean/IMBBS/HCMR: [s.l.]. 1 poster pp., more
  • Kotoulas, G.; Deneudt, K.; GOs ASSEMBLE PLUS Consortium (2018). Current initiatives supporting dynamic evolvement and long term sustainability of Genomic Observatories in a European and international context, in: Mees, J. et al. (Ed.) Book of abstracts – 53rd European Marine Biology Symposium. Oostende, Belgium, 17-21 September 2018. VLIZ Special Publication, 82: pp. 82, more
  • Willemse, S. (2018). Genetic barcoding of marine zooplankton communities in the North Sea using the Minion Sequencer. MSc Thesis. Universiteit Gent - Faculteit Bio-ingenieurswetenschappen: Gent. 64 pp, more
  • Grosemans, T.; Asselman, J.; Boets, P.; Mees, J.; De Schamphelaere, K.; Janssen, C. (2017). Detection and degradation of environmental DNA (eDNA) in the marine environment: a lab and field approach using plaice, in: Mees, J. et al. (Ed.) Book of abstracts – VLIZ Marine Scientist Day. Brugge, Belgium, 3 March 2017. VLIZ Special Publication, 79: pp. 39, more
  • Grosemans, T.; Asselman, J.; Boets, P.; De Schamphelaere, K.; Janssen, C. (2016). Measuring biodiversity with a bottle of water: development and field validation of an eDNA approach with plaice, in: Mees, J. et al. (Ed.) Book of abstracts – VLIZ Marine Scientist Day. Brugge, Belgium, 12 February 2016. VLIZ Special Publication, 75: pp. 56, more
  • 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, more