Understanding the role of benthic fauna and microbes in UK seabed biogeochemical cycles, and how anthropogenic stressors modify these roles and the ecosystem services they generate.


Loss or degradation of natural marine habitats due to human impact (climate change, mining, fishing/ trawling disturbance) is causing widespread reorganisation of natural marine communities, with growing concerns around the sustainability of the critical functions they support. Carbon and nutrient cycling is largely mediated by the marine seabed which is already heavily impacted by multiple stressors, and sediment type, depth, temperature, pelagic input and the functional capability biota all play important roles in driving carbon, nutrient and other biogeochemical cycles. Understanding these contributing components, their interactions and how anthropogenic stressors will alter seafloor processes and environments remains poor. This studentship will aim to disentangle and quantify these effects, with a specific focus on biological activities. For the first time, the studentship will link the biology to the biogeochemistry following a more integrated approach, including interactions and biological groups that have been largely ignored (e.g., microbes, meiofauna). This studentship will adopt a systematic methodology that allows the role of, and impacts on different biological groups to be partitioned and quantified. This will be undertaken through linked ecological and biogeochemical studies conducted at the Lyell Centre’s mesocosm facilities and supported by modelling approaches. This work will increase the confidence in the projection of present baseline functional relationships, and the mechanisms of impact from contrasting pressures acting over different components of the seabed community. Ultimately, this work seeks to improve our predictions of future ecosystem service sustainability in an era of intense anthropogenic impacts. The work will provide datasets and observations that inform the development of biodiversity and seabed function models. The outcomes will aid decision-making by environmental policy makers by identifying whether benefits supported by the specific utilisation of natural capital outweigh those provided by alternative management measures. This studentship has direct relevance to the Blue Economy strategy and links closely to themes on people and the environment relating to resilience and valuation of nature-based solutions.


The PhD studentship will be based at the Lyell Centre under the direct supervision of Prof.  Sweetman and Dr. Shimmield, and directly benefit from advisory input from and exchange visits to meet co-supervisors Drs. Garcia, Parker and Bolam. The studentship will involve undertaking experiments to assess how carbon and nutrients are cycled and buried by benthic fauna (meio and macro) and microbes (bacteria and archaea), and the impacts of anthropogenic stressors such as climate change (e.g. acidification, deoxygenation, warming), and sediment disturbance (e.g. excavation and deposition). The experiments will be undertaken using advanced benthic flux chambers in the Wolfson Climate Change aquarium at the Lyell Centre. Isotope tracer studies will be carried out to document changes in carbon and energy flow through the microbial loop and meio/macrofaunal food-web. The student will also use stable isotope probing (SIP) coupled to metagenomics and metatranscriptomics to further understand the impacts of various stressors on microbial biota and processes. This studentship also aligns with the modelling work achieved under previous projects (NERC/DEFRA SSB and EU project BENTHIS). These early models focused on the macrobenthos (biodiversity, community structure) and its role in the delivery of key ecosystem services (ecosystem processes and functioning involved in carbon and nutrient cycling) but did not include explicitly meiofauna and microbes. Doing so will provide considerable added value and improved predictive capabilities. We will specifically combine theoretical background and existing modelling tools to implement a ‘trait-based’ modelling approach within a Bayesian framework to incorporate the context-dependent (faunal mixture, anthropogenic stressors) variability around the seabed fauna effects on carbon and nutrient cycling. This will make the certainty around the predictions more accurate than existing models, which are currently only considering the macrofaunal component in their projections.

Project Timeline

Year 1

During the first half of the first year, the student will gain proficiency in undertaking benthic flux experiments and begin to grow up the labelled isotope tracers (e.g., 13C-labeled algae) that will be used throughout the experiments. The experimental design, study site(s) and the target stressors will be identified, and final plans made for the main experiments. The experiments will be undertaken in the second half of the year. It is expected the experiments will last for 1-2 months. After undertaking the experiments, work will begin on analysing data (e.g., changes in O2 consumption) and samples (e.g., nutrient analysis).

Year 2

The second year will be exclusively devoted to sample analysis. It is envisaged that the microbial processes work (e.g. SIP, 13C-fatty acid and isoprenoid analysis) will take 4-6 months. Sorting and identifying fauna to family (species if possible) will also be conducted, allowing isotope content analysis to be undertaken towards the end of the second year.

Year 3

The third year will be devoted to the modelling component of the PhD. The student will learn how to use existing trait-based modelling approaches and gain an understanding on Bayesian Hierarchical Models. We will use the outcomes from the experiments with Bayes theorem to relate the effects of stressors tested to a change in fitness of the fauna trait expressions (behaviour or feeding). We will then use fitting methods such as Markov Chain Monte Carlo to estimate each tested variable effect and predict the probability of faunal trait responses along a range of value of natural and anthropogenic stressors. This “fauna-microbesâ€ model will then be coupled with the existing macrofauna model to understand the holistic effect of the seabed fauna on carbon and nutrient cycling.

Year 3.5

The final six months of the PhD will be devoted to finishing data analysis and completion of peer-reviewed papers and the PhD thesis. During the final part of the PhD, the student will also be encouraged to attend international or national marine ecological conferences.

& Skills

Statistics: The student will learn/ develop their statistica/ modelling skills using the R statistical platform especially within the context trait-based approach and Bayesian Hierarchical model
Science communication: Through the specific collaboration with CEFAS, we anticipate opportunities for outreach to decision-making and policy development fora.

References & further reading

Sweetman AK et al. (2016). Jellyfish decomposition at the seafloor rapidly alter biogeochemical cycling and carbon flow through benthic food-webs. Limnology and Oceanography, 61, 1449-1461.
Thomsen M, Garcia C, Bolam, SG, Parker R, et al. (2017). Consequences of biodiversity loss diverge from expectation due to post-extinction compensatory responses. Scientific Reports 7:43695.
Webb C.T. et al. (2010). A structured and dynamic framework to advance traits-based theory and prediction in ecology. Ecology Letters 13: 267-283.

Further Information

For further information, please contact:
1) Professor Andrew K. Sweetman, The Lyell Centre, Email: A.Sweetman@hw.ac.uk
2) Dr. Clement Garcia, Centre for Environment, Fisheries and Aquaculture, Email: clement.garcia@cefas.co.uk

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