Extensive TREC expedition provides land and sea samples needed to develop Microbiome Ocean Health Index
The completion of the 15-month long Traversing European Coastlines (TREC) expedition marks the beginning of an exciting research phase that involves the analysis of 23,000 marine samples and 70,000 terrestrial samples. Combining marine sampling with sampling of soil, sediment and shallow water, researchers from the TREC expedition gathered biological and environmental data along the European coastline at more than 120 land-sea transects.
For the EU-funded BlueRemediomics project, which aims to develop novel tools and approaches to explore marine microbiome data, these samples provide an exciting opportunity to study human impact on coastal ecosystems in unprecedented detail. They also provide critical insights into the search for novel products and cosmeceuticals derived from valuable marine bioresources.
Using Microbiome Data to Understand Ocean Health
The marine microbiome plays a critical role in ocean health, cleaning up contaminated conditions and performing critical functions such as oxygen generation and recycling key nutrients. Although central to managing ocean health, the marine microbiome is still vastly underexplored, especially when assessing its role in ocean health. Previous scientific efforts have established a framework for an Ocean Health Index (OHI), which measures how well ocean systems are providing benefits and services to people based on the status of, for example, carbon storage, natural products, coastal protection, food provision, biodiversity and livelihoods. Yet, the index, in its current state, does not incorporate the status of the ocean microbiome.
To fully understand ocean health and our human impact on it we need to integrate ocean microbiome data into such assessment frameworks. Catering to this need, the BlueRemediomics project is establishing a “Microbiome Ocean Health Index”, which specifically aims at determining coastal anthropogenic impacts on marine microbiomes.
TREC Expedition – Providing New Insights
Once the TREC sampling data is publicly available – following the sequencing and analysis phase – it will play a key role in validating the Microbiome Ocean Health Index. Scientists on the BlueRemediomics project are currently working towards establishing this index based on already available datasets. To this end, researchers are identifying microbes and gene modules that co-vary with specific environments and pollutants, to derive biomarkers and a new metric for assessing ocean health. Although currently available datasets offer a good starting point for this work, project Co-Coordinator and CNRS Director of Research Chris Bowler considers this data as “just setting the scene” for what could be done at a much deeper level with the TREC data. According to him, one of the issues with currently available datasets is that they are often disparate and disconnected, making it harder to establish the Microbiome Ocean Health Index. For instance, in some cases “good biological datasets are available that describe the microbial diversity in a certain environment, but there are no chemical datasets available. In other cases, there is quite good chemical data available on the presence of pollutants, but there is no microbial data from the same environment”, says Chris Bowler.
The combination of land-sea sampling activities along the coastline as part of TREC promises to change this with unprecedented insights into microbial activities and chemical data (including the presence of pesticides, antibiotics and other pollutants). This will allow a precise focus on human-induced impacts and provide answers to the interplay between pollution through for instance antibiotics and related changes in the ocean microbiome. As Chris Bowler explains, it will provide answers to questions such as: “If a particular antibiotic is present in high levels, is there a set of microbial activities that correlate very strongly with the presence of that antibiotic?” Such insights can feed back into the Microbiome Ocean Health Index.
“We can consider the TREC samples as a gold standard for connecting the dots between human impacts and microbial activities in the seas and oceans. This is perhaps the most comprehensive sampling programme that has been done to try to connect the chemical water content in coastal areas, with the microbial content of those coastal areas.”
Chris Bowler
MGnify – The Mining Resource for TREC Data
The application of the TREC data in BlueRemediomics does not end with the Microbiome Ocean Health Index. Quite the contrary, the proteins derived from the TREC data will pave new ways for the identification of novel enzymes and natural products, such as pharmaceuticals. The TREC data will be incorporated into the MGnify resource coordinated by BlueRemediomics co-coordinator Rob Finn at the European Molecular Biology Laboratory (EMBL-EBI). MGnify offers a publicly accessible resource enabling researchers to analyse, discover and compare microbiome data. Adding the TREC data will enrich the genomic and protein catalogues, which in turn can be mined to identify bioactives with cosmeceutical, phytostimulant, antimicrobial or pharmaceutical value.
The data will also have applications for the aquaculture research done in the project, which aims to improve our understanding of the fish microbiome in different environments and production systems. The final goal is to develop innovative microbiome-based solutions that will enhance the sustainability of aquaculture practices. Although not reliant on TREC data, most of the aquaculture activities in BlueRemediomics will be contextualised using the TREC data shared through MGnify, which will especially play a role in comparing artificial aquaculture-associated environments with natural ecosystems to gain insights into fish-environment interactions.
Beyond BlueRemediomics, the data products from environmental samples in MGnify, including TREC, will be made publicly available and flow through established routes to the well-known open-access biodiversity platforms OBIS and GBIF. Through these efforts, the data will contribute to other initiatives such as the Digital Twin of the Ocean. Collectively, this brings the data into the context of ecological modelers, policymakers and governments, achieving wider impact beyond the project’s remit.
Future Outlook
The TREC samples promise to provide unprecedented insights connecting the dots between human impacts and microbial activities in the ocean. Yet, what does that mean in practical terms for the future of the Microbiome Ocean Health Index?
Ultimately, the vision is to set up highly standardised and reliable protocols that can be applied by local governments, regions and ecosystem managers, to assess the microbial health of their coastal ecosystems in actual numerical values. The potential commercialisation of this index as a protocol or “kit” could generate economic returns, thereby increasing the monetary value of the Microbiome Ocean Health Index developed in BlueRemediomics. Although it will be several years before the index will be close to commercialisation, BlueRemediomics will lay the groundwork for the necessary protocols and standardisations.