Machine learning for Real-time Detection of Airborne Fungi

FERGUSON_E25ARIES

Machine learning for Real-time Detection of Airborne Fungi

FERGUSON_E25ARIES

Project Description

Supervisors

Dr Rob Ferguson, School of Life Sciences, University of Essex – contact me

Professor Corinne Whitby, University of Essex School of Life Sciences

Dr Emma Marczylo, UKHSA

Dr  Pippa, Douglas

 

Scientific background

The air we breathe is teaming with microorganisms and other biogenic particulates (collectively referred to as bioaerosols). Many of these have negative effects on human and plant health. For example, Aspergillus emitted from composting can cause asthma, and respiratory infections; crop pathogens such as Phytophthora and Alternaria threaten global food security. Climate change is driving range expansion and seasonality of these taxa, but we lack real-time monitoring data to assess the risk. A major development towards this are optical measurement systems that characterise individual bioaerosols, but their use for fungi remains underdeveloped. We have optimised methods for collecting/characterising bioaerosols from different environments for molecular analysis [1,2]. This project aims to apply novel methods to develop classification algorithms for real-time bioaerosols monitoring to assess exposure and health impacts.

Research methodology

The project will utilise state-of-the-art computational and molecular techniques. Machine leaning will be used to develop novel classification algorithms for key fungal taxa by aerosolizing fungi into a SwisensPoleno air-flow-cytometer in ambient air, compositing sites, and crop systems. For comparison, high-throughput sequencing will be used to characterise airborne fungal communities. Additional data from a SwisensPoleno Jupiter and multi-vial-cyclone sampler will be provided by the UKHSA Chilton’s monitoring station. These data will be used to develop better forecasting tools and assess how bioaerosol exposure will be effected by a changing climate.

Training

The individual will receive training in novel air sampling techniques, molecular microbial, bioinformatic and fieldwork skills. Additionally, they will receive training in data analysis and machine leaning at Swisens. The individual will be encouraged to present at conferences and will gain experience in policy development (UKHSA/Environment Agency). The candidate will also be invited to join the UKHSA’s and Environment Agency’s Chief Scientist’s Group PhD network.

Person specification

This is an exciting opportunity for a highly motivated individual with a background in Computer Science, Bioinformatics, Biological/Environmental Sciences, Molecular Biology, Microbiology who is keen to undertake both lab and fieldwork, engage with regulators and end users. The successful applicant will join a multi-disciplinary team at Essex with time spent at the collaborative partners UKHSA, EA.

Acceptable first degree subjects: Biological/ Environmental Science, Computer science, bioinformatics, Molecular Biology, Microbiology, Ecology or related subject.

References

  • Ferguson RMW, Neath CEE, Nasir ZA, Garcia-Alcega S, Tyrrel S, Coulon F, Dumbrell AJ, Colbeck I, Whitby C (2021) Size fractionation of bioaerosol emissions from green-waste composting. Environment International 147:106327.
  • Ferguson RMW, Garcia-Alcega S, Coulon F, Dumbrell AJ, Whitby C, Colbeck I (2019). Bioaerosol Biomonitoring: Sampling Optimisation for Molecular Microbial Ecology. Molecular Ecology Resources, 19:672-690.
  • Pankhurst L, Whitby C, Pawlett M, Larcombe L, McKew BA, Deacon L, Morgan S, Villa R, Drew G, Tyrrel S, Pollard S, Coulon F (2012). Temporal and spatial changes of the microbial bioaerosol communities in green-waste composting. FEMS Microbiol Ecol, 79:229-239.
  • Whitby C, Ferguson RMW, Colbeck I, Dumbrell AJ, Nasir ZA, Marczylo E, Kinnersley R, Douglas P, Drew G, Bhui K, Lemon M, Jackson S, Tyrrel S, Coulon F (2022). Compendium of analytical methods for sampling, characterization and quantification of bioaerosols. In D. A. Bohan, & A. Dumbrell (Eds.), Functional Microbiomes (pp. 101-229). (Advances in Ecological Research; Vol. 67). Academic Press Inc
  • Lam, Holly CY, et al. "Association between ambient temperature and common allergenic pollen and fungal spores: A 52-year analysis in central England, United Kingdom." Science of the Total Environment 906 (2024): 167607.

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2025. The closing date for applications is 23:59 on 8th January 2025.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£19,237 p.a. for 2024/25) and research funding. A limited number of studentships are available for international applicants, with the difference between 'home' and 'international' fees being waived by the registering university. Please note however that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK, such as visa costs or the health surcharge.
  • ARIES postgradute researcher (PGRs) benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis. International applicants should check whether there are any conditions of visa or imigration permission that preclude part-time study. All advertised project proposals have been developed with consideration of a safe, inclusive, and appropriate research and fieldwork environment with respect to protected characteristics. If you have any concerns please contact us.
  • For further information, please contact the supervisor. To apply for this Studentship follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential, and will be stored on the UEA sharepoint server. Data will not be shared with those involved in making decisions on the award of Studentships, and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be ask to complete the form by the University to which you apply.
  • If funded under the BBSRC-NERC DLA scheme, ARIES studentships will be subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. See https://www.ukri.org/publications/terms-and-conditions-for-training-funding/ for more information

Apply now

Please send your cover letter and CV to:  ariesapp@essex.ac.uk, identifying the project that you’re interested in. Please include the relevant project code.