Project title: Plastic oceans, can microbes clean our mess?
Host institution: University of Warwick
Key words: Marine ecology, microbial community, plastics degradation, metagenomics, metaproteomics
Supervisory team (including institution & email address):
Joseph A. Christie-Oleza, University of Warwick,
Matthew I. Gibson, University of Warwick,
Overview:
Are marine microbes capable of degrading synthetic polymers such as plastics? Who and how do they carry out this process?
Plastics have become the major contaminant in the world’s oceans (Law et al 2010). The existence of a “plastic island” twice the size of Texas drifting around the North Pacific gyre has become a public concern. In fact, there is data that shows the existence of giant plastic islands in each one of the five ocean gyres as hundreds of thousands of tonnes of plastic waste have been dumped into the oceans since the start of the plastic era.
Recent studies have focussed on the microbial surface colonisation of these floating plastics indicating a high diverse community that differs enormously from the indigenous free-living marine community (Zettler et al 2013; Oberbeckmann et al 2014). These studies have also raised concerns on the fact that polymers, mainly in the form of microplastics, accumulate persistent organic pollutants and harbour harmful microbial species that can easily enter the food chain. Biodegradation of plastics in aquatic systems has been suggested by pits visualised by scanning electron microscopy (Figure 1). Plastic degradation has been reported for land waste plastics and is mainly carried out by fungi and bacteria (reviewed in Ghosh et al 2013). Unfortunately, very little is known on this process in marine systems.
Methodology:
This PhD Project aims to answer key ecological questions on the biodegradation of plastics in marine systems. The successful student will analyse the microorganisms that carry out such vital bioremediation process, investigate the enzymes involved and the biodegradability of different polymers.
Different well-defined polymers generated in the Department of Chemistry will be subject to in situ colonisation by natural marine microbes. Colonised plastics will be processed in the lab to determine: microbial community evolution, metagenomic analysis (using high-throughput sequencing), metaproteomic analysis of the exoproteome (looking for relevant secreted enzymes; using high-throughput proteomics), biodegradation of the polymers (light scattering and chromatography systems to determine the kinetics of degradation), visualisation of the polymer surface after colonisation (scanning electron microscopy) and, ultimately, isolation and characterisation of microbial degraders.
The student will have the opportunity to develophis own experiments comparing the biodegradability of different polymers in natural aquatic environments and the conditions that may accelerate the process. The identification of microbial degraders and the repertoire of exoenzymes used to hydrolyse polymers will have important biotechnological applications.
Training and skills:
This multidisciplinary PhD project will offer a unique opportunity for the student to learn state-of-the-art techniques in environmental –OMICS (such as high-throughput proteomics and genomics), microbial ecology and biochemistry, and analytical chemistry of plastic polymers. The laboratories of supervisors Dr Christie-Oleza (School of Life Sciences) and Dr Gibson (Department of Chemistry) are excellently equipped to carry out this cutting-edge project.
Applicants: We are looking for enthusiastic applicants with BSc or MSci in Biology, Biochemistry or related fields. Applicants with 1st class degrees and laboratory experience will be valued.
Possible timeline:
Year 1: Synthesis of different polymers and in situ colonisation of marine microbes. Analysis of community evolution, metagenomics and exoproteomics analysis. Search for hydrolytic exoenzymes. Evaluation of polymer degradation under different incubation conditions.
Year 2: Collectionof old marine plastic debris with well established microbial communities. Characterisation and evaluation of polymer degradation. Co-incubation of marine debris with newly synthesised polymers to visualise colonisation and evaluate faster biodegradation rates when compared to experiments carried out in year 1.
Year 3: Isolation of potential microbial degraders. Characterise their exoenzymatic repertoire for degrading polymers.
Further reading:
Christie-Oleza et al (2012) Mol Cel Proteomics, 11: M111.013110.
Ghosh et al (2013)Environ Sci Pollut Res Int, 20:4339-4355
Law et al (2010) Science, 329:1185-1188
Oberbeckmann et al (2014) FEMS Microbiol Ecol, doi: 10.1111/1574-6941.12409
Zettler et al (2013) Env Sci Tech, 47: 7137-7146
Further details:
Potential applicants are invited to contact:
Joseph Christie-Oleza ()