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Autonomous Monitoring of Marine Organisms with Novel Technologies

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  • Full or part time
    Dr J Robidart
    Dr M Rius
    Dr Robert Young
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Healthy marine ecosystems are essential to humankind, as they provide services such as primary nutrition for human populations (fisheries) and production of half of the oxygen in the atmosphere (phytoplankton). A comprehensive understanding of marine ecosystems is crucial because increasing anthropogenic impacts are accelerating changes in these environments.

Changes in marine ecosystems can be difficult to observe because biodiversity assessments are labour intensive, requiring rigorous field studies which often cannot be sustained over seasonal and annual cycles. With the advent of new molecular biology techniques, analysis of the DNA of environmental samples (e.g. water and sediment samples) has recently allowed biodiversity assessments of entire ecosystems at unprecedented resolution. Biological Essential Ocean Variables require continuous observation and have been defined and prioritized based on relevance, feasibility and cost effectiveness by the Global Ocean Observing System expert panels1. At this stage, no mature sensor exists for global implementation to address biological and ecosystems’ variables. This project seeks to apply novel samplers, sensors and molecular biology tools to assess the use of autonomous environmental DNA (eDNA) sampling technologies to characterize important marine organisms including phytoplankton, jellyfish and metazoan species. In this project, specific and sensitive eDNA tools will be applied on autonomously collected samples from field deployments to understand temporal changes in biotic communities.

The capture and analysis of DNA encapsulated in organisms’ sloughed cells, fecal pellets, and related matter is revolutionising the way scientists study aquatic ecosystems. The rapidly expanding research field of eDNA allows spatial and temporal monitoring of aquatic organisms to occur at an unprecedented rate. This advancement is due to the universal nature of the genetic code among life on Earth, and the sensitivity of eDNA methodologies compared to other community ecological analyses, which for example require diverse taxonomic expertise to classify organisms.

This project will deploy novel technology from the Ocean Technology and Engineering Group at the National Oceanography Centre Southampton (NOCS) for high-yield recovery of nucleic acids over long-term deployments. Stage 1 of the project will involve familiarisation and calibration of eDNA tools in a laboratory environment using cultures and aquaria. Stage 2 will incorporate the optimised molecular autonomous planktonic sampler (MAPS) technology relative to conventional sampling methods. Stage 3 will examine temporal and spatial variation of eDNA to better understand drivers of change in marine communities including phenology shifts, species introductions and early bloom detection. This study will characterize the impact of these new tools across the tree of life, by answering specific research questions:

1) Are morphologically identical phytoplankton responsible for major blooms also genetically identical, or do different genotypes dominate over the course of the bloom?

2) Can we detect temporal patterns and population dynamics of marine invasive species by using high-resolution autonomous sampling and sensitive eDNA detection methodologies?

3) Would autonomous eDNA sampling and detection of jellyfish enable early bloom warning for tourism, the desalination industry and power plants?

The NEXUSS CDT provides state-of-the-art, highly experiential training in the application and development of cutting-edge Smart and Autonomous Observing Systems for the environmental sciences, alongside comprehensive personal and professional development. There will be extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial / government / policy partners. The student will be registered at The University of Southampton, and hosted in the Ocean Technology and Engineering Group at the National Oceanography Centre. Specific training will include:

Knowledge of mechanical and fluidic platforms will result from instrumentation development and application in the student’s role as part of an experienced and highly skilled engineering team. The PhD student will be trained in gathering and bioinformatics analysis of metagenomic and metatranscriptomic sequence data, using the Environmental Genomics Facility and Molecular Biological Laboratory at NOCS/UoS. The teamwork skills involved to achieve advanced engineering goals will be attractive to future employers. Personnel trained in this breadth of techniques are uncommon and therefore sought after by a variety of scientific fields (biotechnology, ecology, evolutionary biology, engineering and oceanography).

The successful candidate will write scientific papers that will be submitted in highly ranked international journals and present research at international conferences / workshops. This person will directly interface with stakeholders including coastal managers and policymakers.

Funding Notes

To be eligible for a full NEXUSS award (stipend and fees) a student must have:

No restrictions on how long they can stay in the UK
Been 'ordinarily resident' in the UK for 3 years prior to the start of the grant.
Not been residing in the UK wholly or mainly for the purpose of full-time education. (This does not apply to UK/EU nationals)

Potential PhD students are requested to apply using the University of Southampton postgraduate application form. For information on the application process and documents required please refer to the following webpage:
http://noc.ac.uk/education/gsnocs/how-apply

References

http://www.goosocean.org/index.php?option=com_content&view=article&id=79&Itemid=27

Darling JA, Galil BS, Carvalho GR, Rius M, Viard F, Piraino S (2017) Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems. Marine Policy 85: 54-64.

McQuillan J, Robidart J (2017). Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities. Current Opinion in Biotechnology 45: 43-50.

How good is research at University of Southampton in Earth Systems and Environmental Sciences?

FTE Category A staff submitted: 68.62

Research output data provided by the Research Excellence Framework (REF)

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