Proving bioremediation of perfluoroalkyl substance (PFAS)

Overview

Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS) are a family of human made chemicals used by industry as part of stain- and water-resistant fabrics, cleaning products, paints, fire-fighting foams and in cookware. They are pollutants of increasing concern as they are now commonly found in waterbodies largely due to industrial waste emissions. PFAS are also highly persistent in the environment and accumulate in fish, birds, plants and animals. PFAS are linked to formation of cancer and organ damage. They are associated with negative impacts on the development of children. Currently PFAS is removed from waters using physical processes which do not, for example, clean contaminated sediments and which generate large volumes of waste that need costly disposal. This studentship will aim to remove PFAS from water and sediment using microbes that can breakdown PFAS in situ through a process known as biotransformation which will be more effective, while reducing both cost and wastes generated.
The main AIM is to exploit the use of microorganisms to clear PFAS from PFAS-contaminated waters. The specific OBJECTIVES are to: (1) Collect water and aquatic annelids samples from Scottish freshwater and estuarine environments; (2) Identify microbial communities from the water & sediment samples able to biotransform PFAS; (3) Microcosm study of biotransformation of PFAS.

Methodology

To achieve the abovementioned objectives, the student will (in collaboration with SEPA):
OBJ 1) Collect surface water samples from a selection of Scottish lochs and estuaries, which have been reported as having high concentrations of pharmaceuticals, nutrients and/or total organic carbon (TOC). S/he will also collect a number of annelids from sediment next to loch/estuary and prepare extracts for analysis. Student will work with SEPA’s Chemistry department and Institute of Aquaculture for PFAS analysis using liquid chromatography – mass spectrometry (LC-MS). (OBJ 2) Use our in-house 3-branch manifold vacuum filter with appropriate membrane filters to filter samples collected (described in OBJ 1). Water-/sediment-borne microbes on filters or excreta from depurated aquatic annelids will be grown on solid media containing commercial PFAS to exploit the potential for microbial transformation. Isolated single colonies of bacteria or yeast will be grown in increasing levels of PFAS in liquid cultures to further screen for PFAS-resistant species. Biochemical tests will be applied to characterise PFAS-resistant microbes and whole genome DNA will be sequenced for species identification. (OBJ 3) Evaluate the biotransforming capabilities of the bacteria or yeast isolated and characterised in OBJ 2, a microcosm study in removing PFAS from groundwater spiked with commercial PFAS.

Project Timeline

Year 1

Conduct a literature review and design an appropriate research strategy for work within the laboratory (microbiology/cell biology);
Sample collection from lochs and estuaries in Scotland;
Isolate and analyse microbial samples;
Undergo training in genomics & RNA-seq data analysis;
Attend and present at one local conference.

Year 2

Repeat Year 1’s work for reproducibility and to observe sample variation: Sample collection from lochs and estuaries in Scotland; Isolate and analyse microbial samples & sequence analysis of interesting microbial samples;
Culturing and/or maintaining a variety of PFAS-resistant microorganisms;
Microcosm study of PFAS-resistant microorganisms;
Attend and present at one local/overseas conference.

Year 3

Expand on Year 2’s work by culturing and/or maintaining a wider variety of PFAS-resistant microorganisms;
Microcosm study of PFAS-resistant microorganisms;
Attend and present at one local/overseas conference.

Year 3.5

Thesis finalisation and paper writing (although it is anticipated that these activities will be ongoing throughout the PhD).

Training
& Skills

The analytical techniques required for this study are already established at the University of Stirling and at SEPA include: SDS-PAGE, western blotting, microbiological / biochemical assays, using microscopy & plate readers. S/he will receive training in ‘Linux for Genomics’‚’RNA-seq Data Analysis’ from Edinburgh Genomics (https://genomics.ed.ac.uk/ ). S/he will be trained in experimental design and data analysis related to the project work. Furthermore, s/he will attend courses on Effective Research, Scientific Writing, Statistics for Environmental Evaluation (and use of R) and Presentation Skills.
The student will also benefit from wider interaction within research groups at Stirling. S/he will be expected to present the results of their research annually at the highly popular BES Student Symposium as well as at SEPA events and workshops. The student will also be expected to present their work at local and international conferences.

References & further reading

1) European Environment Agency (2019) Emerging chemical risks in Europe. [online] Available at: https://www.eea.europa.eu/themes/human/chemicals/emerging-chemical-risks-in-europe [Accessed 29 Oct 2020] 2) United States Environmental Protection Agency (2020) Per- And Polyfluoroalkyl Substances (PFASs) Remediation Technologies. [online] Available at: https://clu-in.org/contaminantfocus/default.focus/sec/Per-_and_Polyfluoroalkyl_Substances_(PFASs)/cat/Remediation_Technologies/ [Accessed 29 Oct 2020].
3) Karnjanapiboonwong A, Deb SK, Subbiah S, Wang D, Anderson TA (2018) Perfluoroalkylsulfonic and carboxylic acids in earthworms (Eisenia fetida): Accumulation and effects results from spiked soils at PFAS concentrations bracketing environmental relevance. Chemosphere 199:168-173
4) Gillespie IM & Philp JC (2013) Bioremediation, an environmental remediation technology for the bioeconomy. Trends Biotechnol 31:329-332.
5) Kotthoff M & Bucking M (2019) Four Chemical Trends Will Shape the Next Decade’s Directions in Perfluoroalkyl and Polyfluoroalkyl Substances Research. Front Chem 6:103.

Further Information

Dr Jenson Lim, jenson.lim@stir.ac.uk , +44 (0)1786 467821
Prof. David Copplestone, david.copplestone@stir.ac.uk , +44 (0) 1786 467852

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