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TREC

Traversing European Coastlines

An expedition to study coastal ecosystems and their response to the environment, from molecules to communities

Projects

One major aim of the TREC expedition is to reach a new and comprehensive understanding of coastal ecosystems and their responses to changing environments at the molecular and mechanistic levels. Through the mechanistic understanding of ecosystems and how they are changing, we can help provide new knowledge and discoveries, as well as diagnostic tools, preventative measures, and potential solutions to reverse detrimental changes in the future.

Specific research goals:

  • Identification of key factors (natural and man-made) driving coastal community composition
  • Understanding molecular mechanisms of phenotypic plasticity and adaptation at species and community levels
  • Tracking gene flux between soil and ocean species via horizontal gene transfer or species assimilation, both regionally and globally
  • Elucidating mechanisms of co-adaptation across species and communities
  • A better definition of coastal ecosystems biodiversity, causes of biodiversity loss, and its impact
  • Unravelling new molecular mechanisms from coastal species and symbionts

TREC projects are highly collaborative, involving research groups at EMBL and all collaborating institutes. See below the expanding TREC projects portfolio with plug-in projects submitted by the growing network of collaborators.

Submit a TREC plug-in project

Join in!

If you would like to participate in the TREC project with your samples, data, or analysis, please write to us: TREC@embl.org  

Check out some of the planned TREC projects!

Microbial community interactions between land and water

This project aims to assess how microbial biodiversity is impacted by sea, freshwater and estuaries, pollution, and other environmental factors. In the Bork lab at EMBL, for example, one of the focuses is on the gene flux between land and water. More specifically, soil is a major reservoir of antimicrobial resistance (AMR) and this project will study local AMR profiles and mechanisms of AMR spreading from soils to waters and humans.

Selected species and environmental change

The Arendt Group at EMBL has established the marine annelid Platynereis dumerilii as a new model system for evo-devo and environmental adaptation. Taking advantage of a newly established cellular atlas of three-segmented young worms, the TREC project will correlate the genetic standing variation and  single-cell gene expression with morphological variation, to identify hotspots of cellular adaptation to environmental change.

Planktonic microorganisms and symbiosis

The Decelle Group at the CNRS in collaboration with the Schwab Team at EMBL, and other collaborating groups, are focusing on understanding the morpho-genetic plasticity of free-living and symbiotic microplankton to changing environments. Harnessing the power of the mobile laboratory, the project will combine single-cell omics studies with state-of-the-art  subcellular imaging.

Soundscapes, environmental changes & noise pollution

As part of the EU BIOcean5D project, L. Di Iorio and co-workers at UPVD will assess the biogeography of bioacoustic diversity and investigate environmental state-pressure relationships using soundscapes. Noise pollution will be quantified to study its impact on model systems. The collaboration with the CNRS & EMBL involved in other TREC projects will allow to appraise functional aspects of soundscapes.

Coastal biodiversity changes assessed by sedimentary paleogenomics

In the frame of the EU BIOcean5D project, Dr Siano (Ifremer) will lead a multidisciplinary research team to assess the effect of human pollution across European coastal ecosystems over the Anthropocene period. Using sediment core bio-geochemical archives, human pollution traces will be associated with inter-site community changes, invasive species dynamics, and emergent risk for human and coastal resources.

Revealing planktonic ultrastructural diversity with Expansion Microscopy (ExM)

An international EMBL-EPFL-UNIGE team (Dey, Schwab, Saka, Dudin, Hamel, Guichard) are coupling expansion microscopy (Cryo-ExM and U-ExM) to FISH for species ID and sub-cellular imaging. We aim to create an atlas of native eukaryotic cellular biodiversity with unprecedented 3D spatial resolution, with a long-term view to assess the repercussions of climate change on free-living microplankton populations.

Biogeochemical cycles driven by biodiversity at the land-sea interface

The biogeochemical cycles are strongly related to the living organisms of the ecosystems, from the photosynthesis to the decomposition and persistence functions. With our team from CNRS and Ecole Normale Supérieure Ulm, we will take advantage of the TREC expedition to study carbon, nitrogen and phosphorus cycles in soils, sediments and water, and relate their dynamics and long term persistence to the living organisms.

Mechanisms of environmental adaptation in planarian flatworms

Why can some species live in a wide range of habitats, while others cannot? The Vu group (in collaboration with many folks at EMBL and beyond) aims to answer this question by first, carrying out a systematic field sampling of planarian flatworms along the coastline of Europe; and second, applying cutting-edge single cell multiomics and targeted perturbations to wild planarians brought back to the lab.

FunLeaf – citizen science

Citizen science project, led by Prof. Tedersoo Group at the University of Tartu, aims to describe the biodiversity of organisms associated with plant leaves across the globe. Using DNA-based methods for identification, the aim is to determine the environmental features that lead to the increase or loss of leaf-associated microbial diversity and add one piece to the puzzle of global biodiversity.

Bioaerosols across the land-ocean interface

Bioaerosols remain one of the least studied microbiomes on Earth. Airborne microbes impact the health of humans, plants and animals, and drive key climatological processes. The TREC project enables the Sunagawa lab at ETH Zurich to team up with the Ocean-atmosphere interactions group, led by Michel Flores at the Weizmann Institute of Science, and explore the diversity, function and dispersal of airborne microbial communities at the land-ocean interface. (BIOcean5D)

‘Seatizen’ science to change the scale of measuring aquatic microbiomes

De Vargas and Lombard (CNRS & SU) will deploy innovative frugal tools in research and sea-worker/user communities along the TREC voyage, toward a cooperative and long-term measure of aquatic biodiversity. ‘Seatizen’ will be trained to use the ‘Planktoscope’ and ‘Lamprey’ systems, and generate consistent quantitative imaging and molecular data across ecologically and economically relevant regions,  integrated into global databases. (BIOcean5D)

Resurrection ecology to test for marine phytoplankton adaptation

The Sjöqvist group at Turku University will document potential evolution in marine phytoplankton across European waters to clarify the adaptation potential in key species to ongoing climate change. The field of resurrection ecology offers a “backward-in-time” approach via hatching of dormant life stages. This enables the direct quantification of phenotypes and comparison of genetic material across temporal scales.

cryOcean: Molecular architecture of algal photosynthesis

The Engel group at the University of Basel uses cryo-electron tomography (cryo-ET) to visualize structures inside native cells with molecular resolution. In the cryOcean project, we aim to chart the molecular organization of photosynthetic organelles (light-harvesting thylakoid membranes and carbon-fixing pyrenoids) in diverse marine algae species sampled directly from the ocean.

Nematodes

Nematodes are microscopic worms that dominate soils and sediments and play diverse functions in nutrient cycling. While we have gained some information on the most important drivers of nematode communities in soils and sediments, information on land-sea transitions is missing. Geisen lab at the Laboratory of Nematology WUR will fill this gap by enumerating and identifying nematode taxonomic and functional diversity using various amplicon sequencing approaches.

Discovering new culturable relatives of animals

The Brunet lab at the Institut Pasteur (Paris) studies choanoflagellates, the closest living relatives of animals. Many choanoflagellates can switch between unicellular and multicellular forms and thus offer a proxy to the origin of animal development. However, only a fraction of existing species are known. We will try to systematically describe and isolate new culturable choanos from plankton to understand the natural environment for the emergence of multicellularity.  

Characterising microbial behaviours at the continental scale

Microbial behavior will be quantified during TREC through the deployment of a novel sea-going microfluidic platform, the In Situ Chemotaxis Assay (ISCA). This international collaboration (Stocker: ETH Zurich, Raina + Seymour: University of Technology Sydney, Vincent: EMBL) will leverage the contextual data gathered during the expedition to identify environmental drivers influencing microbial behaviors.

Morphological and genomic diversity of coastal giant viruses

Giant viruses influence the mortality, population structure and gene flux of various protists. The Fischer lab at the MPI for Medical Research studies the diversity and biogeography of giant viruses by electron microscopy, metagenomics, and cultivation on heterotrophic flagellates.
We aim to compare coastal virus communities from water and soil and to isolate new giant viruses for a better understanding of their ecology.

Microbial variation and individuality in a marine sponge

The Hentschel lab at GEOMAR will define the effects of environmental gradients on microbiome variation and individuality in the sponge H. panicea. We will explore taxonomic and functional gene variation of the dominant microbial symbiont clade and immune gene variation on the host side. Our overarching aim is to move marine sponge symbioses from an exploratory to experimental arena for host-microbe interactions.

Animal-algae symbiosis across coastal marine gradients

Led by the Hambleton lab (Uni Vienna), this project will use transcriptomics and lipidomics to assess the biogeography and function of dinoflagellate algae in marine sediments and in symbiosis with marine invertebrates. We aim to reveal how key symbiotic organisms are affected along evolutionary and environmental gradients, allowing predictions of how these symbioses will respond to accelerating climate change.

Diversity and impact of phytoplankton interactions

The Vincent Group (EMBL) will be dedicated to understanding the diversity, distribution and impact of intimate interactions involving diatoms, major primary producers in the ocean. By using a combination of single cell live imaging, high-throughput phenotyping approaches, and in situ chemotactic assays, we ask how microbial interactions can affect diatom behaviour, development and survival in a changing ocean.

Microbe-DOM interactions along coastal gradients

Environmental factors control Microbe-DOM (dissolved organic matter) interactions that result in the consumption, modification and extreme diversification of dissolved organic compounds and are central to marine carbon cycling and sequestration. The interrelations between environmental gradients along the European coast and the fate of DOM will be the focus of Thorsten Dittmar’s lab at the University of Oldenburg during the TREC expedition.


Previous TREC pilot expeditions

TREC pilots

Learn more about our pilot projects

Iceland 2022

The final TREC pilot expedition took place in August 2022. It was co-organised by the Icelandic biodiversity research network BIODICE, which is providing local knowledge and infrastructure, as well as participation in TREC plug-in projects. Several Icelandic coastal habitats were sampled across temperature and pollution gradients.

Villefranche 2021

EMBRC in Villefranche-sur-Mer hosted the TREC pilot expedition that enabled unprecedented high-definition ultrastructure images from fresh samples, such as this plankton which was frozen under high pressure on the beach. Soil and sediments were also sampled along the Villefranche sea-land transects and the river Var estuary.

Naples 2019

The first pilot project testing the sampling and analysis capacity was done in Stazione Zoologica Anton Dohrn, Naples. Soil collected from Naples volcanic habitats revealed new Archaea taxa with specific metabolic adaptations. Annelid worms (Platynereis) were collected across water acidity gradients and analysed down to the single-cell resolution.

Contact

TREC@embl.org

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