Developing the macroalgae (seaweeds) as indicator species for marine mortality events: an -omic approach

Over the past few years, marine life worldwide has suffered many mass mortality events, with a prominent recent UK example being the dead and distressed crabs that washed up around Teesside in Oct 2021. The exact causes of these mortality events are many and varied but there is an urgent need to develop tools that will allow us to distinguish between natural (e.g. harmful algal blooms) and anthropogenic (e.g. pollutant release by sediment displacement) causes.

To do this, environmental toxicology has traditionally relied on chemical analyses of waters, tissues and sediments to look for environmental toxins. These are powerful techniques but a drawback is that the effects of toxins may linger (for example, through bioaccumulation) long after the toxins themselves have dropped below any threshold of detection. Similarly, many mortality events result from the interaction of multiple smaller stressors, any one of which may look innocuous on its own. One way to complement chemical analyses is, therefore, to use increasingly cheap and rapid transcriptomic- and metabolomic- based approaches to look at the acute and chronic responses of indicator species. By looking directly at how indicator species are allocating their metabolic resources, we can deliver more subtle answers about the interrelationships that tie together marine species and human activity.

This studentship will, therefore, develop transcriptomic and metabolomic techniques to look at how coastal macroalgae, or seaweeds, respond during marine mortality events along the North Sea coastline. The brown seaweeds (kelps and wracks) are particularly well suited for this work because they are common species that show a range of growth habits (annuals vs perennials). Prior work (as part of the Supervisor 1’s BBSRC SuBBSea and EU FP7 EnAlgae projects) has already developed a range of -omic protocols in these species.

Progress during the studentship will build towards three main goals:

a. To describe the relationship between transcriptome and metabolome in at least two key brown seaweed indicator genera: the perennial wracks (Fucus spp.) and the annual kelps (Laminaria spp.). Work will focus on the Teesside coastline, which is prone to mortality events, but our CASE partnership with The Fishmongers’ Company will allow us quick and responsive access to other coastal regions around the UK.
b. To create digital models of macroalgal metabolism, which will incorporate their responses to xenobiotics (e.g. pollutants, heavy metals) to allow them to be used as baselines to help diagnose ongoing or past mortality events.
c. To develop and encourage the student as an independent researcher

Marine and coastal ecosystems are increasingly under economic pressure, so this studentship represents a clear opportunity for the UK to lead excellence in this area. More broadly, the proposal addresses two of NERC’s Priority Areas (‘Environmental Solutions‘ and ‘Resilient environment’). Results will be based around the mortality events that recur around Teesside but will inform the study of other mortality events worldwide.


Marine mortality events of various sizes are relatively common in UK waters but are hard to predict and the earliest warnings of their onsets come from coastal end-users. For that reason, we have made this studentship a CASE partnership with The Fishmongers’ Company’s Fisheries Charitable Trust. Our CASE partner will allow us to monitor and track the onset of mortality events and arrange field access to affected areas. Meanwhile, the baseline collection of seaweed samples will be helped by our link with the North East Fishing Collective as end users, because their inshore fishing boats will allow us to harvest kelp samples along the north east coastline that would otherwise be inaccessible by shore sampling.

Our methodology will therefore involve:

1. Field sampling (CASE partner): In a series of field trips, we will collect keystone brown seaweed species (Fucus, Laminaria, Saccharina) during different seasons and from areas around the main UK fishing ports (Peterhead, Scrabster, Brixham, Newlyn, Shoreham, Grimsby). Importantly, we will also sample responsively and rapidly from areas in which mortality events are reported: this will be co-ordinated and arranged with and through our CASE partner, who monitor UK-wide mortalities.
2. Transcriptomic data collection (Supervisor 1): Work will begin using standard RNAseq technology to record the transcriptional signatures of seaweed indicator species, but a particular aim of our project will be to develop Oxford nanopore technology for field transcriptomic work. Lab stresses, including chronic low-level pollution, will complement field samples collected around mortality events.
3. Metabolomic data collection (Supervisor 2): The student will use a range of chemical analytical techniques (GC-MS, fractionation and NMR) to describe acute and chronic (eg cell walls) metabolite levels in seaweed indicator species.
4. Metabolic modelling (Supervisor 1): Bespoke metabolic models for field indicator species will be constructed using e.g. COPASI.

Project Timeline

Year 1

Months 1-12: Induction and training – introduction to seaweed ecology and molecular biology – short placement at Fishmongers’ Hall in London (= CASE partner HQ) to gain an understanding of the structure and organisation of the UK aquaculture sector and to learn how aquaculture research is co-ordinated – field sampling around the UK

Year 2

Months 13-24 (Durham and Newcastle, including several short fieldwork trips): RNAseq and metabolite analysis of field-collected samples – trialling of Oxford nanopore tech for field transcriptomic work – lab stress experiments to complement samples collected from areas with mortality events

Year 3

Months 25-36 (Durham): Creation of metabolic models to describe transcriptomic and metabolomic data – (ongoing with CASE partner) Creation of metabolic metrics to diagnose environmental stressors – Development of the student’s own research ideas.

Year 3.5

Months 37-42 (Durham): Final analysis – Writing up.

& Skills

The student will be fully trained in a range of environmental (sampling, boatwork), biochemical RNAseq, GC-MS, NMR) and computational techniques (R coding), which will be delivered by PDRAs and other team members, including both supervisors as needed; an indicative timeline is given above.

We know that students should benefit from extracurricular training and workshops outside our teams and both supervisors have encouraged past students to attend external training courses (e.g. computational biology, data visualization, Python coding).

This studentship proposal originated as part of a concerted effort across several northeast Universities to help understand large-scale marine mortality events in the North Sea, so the student will be involved from the start in work with a clear real-world application. Both supervisors have strong links to industry and community contacts, from whom the student will also draw.

Finally, we note that our CASE placement will develop the student’s knowledge and skills in three of the Fishmongers’ Company’s four thematic strands, all of which give critical understanding of the UK’s marine resources:
a) Marine fish, fisheries and environmental management
b) The sustainable and innovative development of aquaculture
c) Supporting and developing the fish trade

References & further reading

Supervisor 1 and co-authors (2018). Insights into the Evolution of Multicellularity from the Sea Lettuce Genome. Current Biology 28(18): 2921-2933.e5.
Supervisor 1 and co-authors (2018). The effects of spatial scale and isoscape on consumer isotopic niche width. Functional Ecology 32(4): 904-915.
For background and for the current economic importance of this work to justify CASE partnership, ongoing work in this area by the supervisors is being presented to Government select committees, with a recent example being:

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