Project Description

The overall aims of this project, ‘Biodegradable plastics as emerging environmental pollutants’ are to establish the biological impacts of biodegradable plastics exposure in a sentinel marine species the shanny (Lipophrys pholis). This project will be carried out under the guidance of Profs Gary Hardiman and Jaimie Dick at Queen’s University Belfast/Queen’s Marine Laboratory and Prof Stuart Piertney at the University of Aberdeen. The plastics industry has pivoted towards the production of ‘compostable’ and ‘degradable’ plastics in response to environmental concerns surrounding conventional plastics. The slow decomposition rate and the accumulation of traditional macro and microplastics are now a global concern particularly as the waste material is inert and persistent in the environment. Plastic debris has been found in sensitive ecosystems such as Antarctica and in a plethora of freshwater, terrestrial and marine organisms. Several actions have been taken in Europe to reduce the use of conventional plastics and many countries have banned their use. The European Commission plans that all plastic will be reusable or recyclable by 2030. Biodegradable bioplastics (BBPs) use has increased exponentially across the globe, with >2.11 million tonnes manufactured in 2018 alone. A concern with BBPs is that they may not degrade completely in natural ecosystems. Most BBPs are comprised of organic polymers (e.g. polylactic acid, polyhydroxyalkanoate) and as they degrade, have the potential to release carbon as well as other chemicals that could affect organisms, food webs, nutrient and energy transfers, ecosystem function, and ultimately ecosystem services. This PhD project will take an interdisciplinary approach that encompasses aquatic biology, marine genomics, metagenomics, toxicology, and fish physiology to allow a holistic understanding of the impacts of BBPs on aquatic organisms using the shanny  as a ‘canary in a coal mine’. This intertidal fish combines many characteristics required in sentinel species. It is abundant and easy to catch, has a wide geographical distribution and a restricted home range. This species is commonly encountered in rockpools in Ireland and the UK. We have piloted, at QML, the use of shanny in ambient and dietary plastics exposure and found the species amenable to such experimental treatments.

To date, much work has been done to understand the effects of conventional plastic pollution in the aquatic environment. It is well established that plastics are a source of endocrine-disrupting chemicals (EDCs) and that they can release or transfer these contaminants to organisms. Based on previous studies from our group, we know that conventional plastics and their additives (e.g. bisphenol A, phthalates) alter hepatic miRNA expression profiles, perturb hepatic metabolism, and energy balance, and decrease reproductive performance. Ingestion of marine microplastic debris impacts intestinal flora disrupting symbiosis between the host and its microbiome. This dysbiosis may interfere with animal health and promote disease onset. At present, there is a lack of information about the potential health effects of biodegradable plastics in marine organisms. Despite their promise, it remains unclear whether they cause environmental damage and this PhD project will address this gap in our knowledge.

Taking into account the low biodegradation rate of bioplastic polymers in the marine environment, and the fact that bioplastics will be ubiquitous in the environment in a few short years the student will focus on the impacts of two bioplastic polymers; 1) A biodegradable biobased polymer: PLA (poly(lactic)acid) derived from corn and a promising candidate to replace conventional plastics and 2) a biodegradable non-biobased plastic: PBAT (polybutylene adipate terephthalate), derived from fossil resources and, after PLA, is the most manufactured biodegradable polymer. This project will undertake a comprehensive research program consisting of three independent, yet complementary objectives to assess the impacts of bioplastics on fish physiology, organismal stress, endocrine disruption, alterations in commensal gut microbial flora, and transcriptional perturbations. The first objective will assess the impacts of BBPs on the hepatic-gonadal axis of the shanny after chronic BBP ingestion. The second objective will examine the gut microbiota and potential dysbiosis following BBPs ingestion. The third objective will assess transcriptomic responses in the hepatic-gonadal axis and integrate findings with data from O1 and O2 (including behavioural observations, e.g. swimming, aggression, feeding rates, hiding, exploring, and correlates with physiology) to allow risk assessment. These data will ultimately provide key insights into the toxic mechanisms of action of biodegradable plastics. The rationale is that once the key mechanisms have been elucidated, a systems-level comprehension of phenotypic, behavioural, metagenomic, and transcriptional perturbations in response to bioplastics exposure will be possible and this will guide the development of risk assessment frameworks using advanced machine learning models.

This transdisciplinary approach will leverage supervisory expertise in Big Data, genomics, toxicology, and marine biology at QUB/QML and UoA and world-class research infrastructure for computing, analytical chemistry, genomics, and marine research at the Institute for Global Food Security (IGFS) QUB and the Queen’s Marine Laboratory (QML). The project’s multidisciplinary approach provides an excellent opportunity for training in various aspects of ecotoxicogenomics and advanced environmental and risk assessment analysis. Moreover, it provides an exceptional opportunity for research training in both Northern Ireland and Scotland whereby the successful candidate will work collaboratively across disciplines and research cultures to generate new insights that transcend traditional boundaries. The project will combine aspects of marine biology, environmental chemistry, genetics, bioinformatics, and systems biology.  Consequently, subject-specific training will be offered in each of these areas. This will comprise a mix of appropriate postgraduate level training (e.g. molecular biology, bioinformatics, genetics, biogeochemistry, computer science, environmental change) and ‘hands-on’ training in the advanced systems-level methods.

Funding and eligibility information available here.

Supervisors

Gary Hardiman

Primary Supervisor:

Profile: Gary Hardiman
Email: g.hardiman@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Stuart Piertney

Secondary Supervisor:

Profile: Stuart Piertney
Email: s.piertney@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Jaimie TA Dick

Additional Supervisor:

Profile: Jaimie TA Dick
Email: j.dick@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

References

Horton, A. A. et al. Science of the Total Environment 738, 140349 (2020)

Pagliaro, M. Chem. Today 37, (2019)

Kakadellis, S. et al. Journal of Cleaner Production 274, 122831 (2020)

Research Methods

  1. A cohort of 100 fish will ensure robust sample sizes with n = 10 males and females per experimental group. Bioplastics will be prepared using an Alpine Shredder to minimize particle size. Specimens will be weighed, and total length measured. Exposure via diet will take place for 28 days (OECD Test 407) during the breeding season. BBPs will be manually incorporated into 100 mg herring chunks. Fish will be fed with PLA or PBAT microplastics (< 5 mm) at doses representative of environmental levels of polyethylene (1.6 mp/L) and 16 mp/L (10x reported environmental concentrations). A control group will receive fish food without microplastics. Behaviour will be video recorded, and measures (e.g. swimming, aggression, feeding rates, hiding, exploring) analysed using JWatcher software. After 28 days, fish will be euthanized. Total size, length, and spermiation index will be assessed and sperm collected. The gonads and liver will be weighed to calculate condition factor (K), gonadosomatic index (GSI) and the hepatosomatic index (HSI). Plasma concentrations of 17β-estradiol, testosterone (to assess endocrine disruption), and cortisol (to assess stress) will be measured. Histological analysis will be performed on hepatic and gonadal tissue.
  2. 16S rRNA surveys will provide a unbiased view of diversity and abundance of the microbiota in shanny exposed to BBPs using Quantitative Insights into Microbial Ecology (QIIME 2).
  3. RNAseq will determine if the gene expression patterns (GEP) in liver, testis, and ovary correlate with adverse phenotype endpoints. Spearman correlation analyses will investigate the relationship between gene expression and the concentrations of steroid hormones, GSI, HSI, K, standard length, weight, and behaviour.
  4. Deep machine learning approaches e.g., Logic Forest will integrate phenotypic and behavioural endpoints, metagenomic and transcriptomic signatures to identify predictors of BBP safety, followed by confirmation of the association between those predictors and the interactions identified using logistic regression.

Expected Training Provision

The project’s multidisciplinary approach provides an excellent opportunity for training in various aspects of fish biology and advanced environmental and risk assessment analysis. Moreover, it provides an exceptional opportunity for research training in both Northern Ireland and Scotland whereby the successful candidate will work collaboratively across disciplines and research cultures to generate new insights that transcend traditional boundaries. The project will combine aspects of marine biology (Dick & Hardiman), environmental chemistry (Dick & Hardiman), genetics, bioinformatics, and systems biology (Hardiman & Piertney). Consequently, subject-specific training will be offered in each of these areas. This will comprise a mix of appropriate postgraduate level training (e.g. molecular biology, bioinformatics, genetics, biogeochemistry, computer science, environmental change) and ‘hands-on’ training in the advanced systems-level methods used.

In addition to the in-depth advanced training detailed above and the broad understanding, the student will obtain of their subject area, the students will be encouraged to comprehend how their research will have societal and environmental impacts. The student will receive training in good research conduct. The project will embrace FAIR principles guaranteeing ‘Findable, Accessible, Interoperable and Reusable’ data, providing rigor and transparency in research and helping to maximize the research impact by peers and collaborators. The student will receive training in compliance with relevant ethical, legal, and professional frameworks.

Impact

In the past few years, marine plastic pollution has become one of the most commented environmental issues in the media, NGOs, and academic circles. Reduction of plastic pollution has turned into a global societal priority. Several agencies have stressed the importance of reducing plastics use. For example, in the list of Sustainable Development Goals of the United Nations ‘Life below water: avoid plastic bags to keep the oceans clean’ is currently the 14th goal; the European Commission has banned single-use plastic under the EU Strategy for Plastics in a Circular Economy and Environmental America has selected plastic pollution as one of its legislative agenda priorities. The current focus on plastics is slowly shifting to encompass a new class of biodegradable plastics to ameliorate plastic contamination, however, no information is available regarding the potential impacts on the environment. In the aquatic environment, not all biodegradable plastics exhibit the same rates of decay and consequently, biodegradation of bioplastics can take an extended time. A comprehensive understanding of the potentially toxic effects of BBPs under natural conditions is urgently required to understand the implications of switching from legacy plastics to BBPs. This research is important as it will address this knowledge deficit. The impact of this PhD will be the delivery of comprehensive data set using a sentinel species which will facilitate the development of risk assessment frameworks using advanced machine learning models.

Proposed Supervision

Professor Hardiman will serve as the primary supervisor at QUB. Professor Jaimie Dick will serve as an additional supervisor at QUB. Prof Stuart Piertney will serve as the secondary supervisor at UOA. The PhD student will be integrated into the Hardiman laboratory which will serve as his/her academic home. They will avail of the computational infrastructure and expertise in plastics research, ecotoxicogenomics, bioinformatics and systems biology. They will participate in weekly Hardiman laboratory meetings. Jaimie Dick, Director of QML, Portaferry, will provide supervision by incorporating the student into the research environment at QML and ensuring the student is trained in all aspects of fish biology. Hardiman & Dick have a keen interest, and existing research strengths (grants, PhDs) in the study of microplastics in terrestrial and aquatic environments, so this dual supervision will greatly benefit the PhD student. Prof Dick will assist with the integration of the student into QML academic activities including journal clubs, seminars, and symposia. Profs Hardiman & Dick will ensure that the student is integrated into the Northern Ireland microplastics working group which encompasses researchers from QUB, AFBI, DAERA, and DEFRA. Prof Piertney will provide supervision alongside Prof Hardiman on the transcriptomic and microbiome data analyses.

Proposed Timetable

The 42-month project is based on a research strategy with 3 key objectives. In the first 3 months, the candidate will carry out their literature review and become proficient in handling shanny. They will receive training in field sampling and acclimation of the fish to the QML environment.

O1 will involve biodegradable bioplastics (BBP) exposure and assessment of fish for endocrine, behavioral, and physiological alterations. The exposure experiments will commence at the beginning of the shanny breeding season (March-April Y1). Exposure to BBPs will be adapted to 28 days, to balance chronic exposure (in accordance with OECD guidelines). Y1 deliverables will include sampling, exposure via diet to BBPs; collection of tissues for lab analysis; health status and behavioral assessments of shanny; plasma concentrations of steroid hormones; analysis of liver conformation and composition & assessment of reproductive performance.

O2 is a comprehensive Gut microbiota study which will start at the beginning of Y2. DNA will be extracted from fecal samples and fish intestines. 16S rRNA library construction will be carried out to allow metagenomics comparative analysis of control and BBPs diets. The milestone from O2 will be a comprehensive analysis of microbial gut community dysfunctionality in response to BBPs.

O3 will assess transcriptomic responses in hepatic and gonadal tissue in response to BBPs exposures. This will commence in late Y2. RNA will be extracted for RNAseq. Data analysis will be a major focus in Y3 examining hepatic and gonadal deregulated biological pathways O3 will perform an integrative analysis of the transcriptomic, metagenomics, and phenotypic data and provide a risk assessment for the impacts of BBPs. Milestones will be a correlative analysis of metagenomic and transcriptomic data with adverse health, behavioral & phenotypic endpoints. The remainder of Y3 and partial Y4 will involve thesis writing, dissemination, & an internship at AFBI/DAERA.

QUADRAT Themes

  • biodiversity
  • environmental-management

Partners

Non-CASE partners: AFBI, DAERA, & DEFRA

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