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Invertebrate-microbe interactions in the breakdown of the lignocellulose complex: implications for biotechnology, biodeterioration and biosphere function

Project Description

Applications are invited for a competition-funded three year PhD studentship to commence in October 2019.

The supervisors are Prof. Simon Cragg, Dr. Joy Watts, Dr Sam Robson and Prof Dan Distel (Ocean Genome Legacy and Northeastern University USA).

The project will focus on:
· Collecting samples at field sites and work with whole organisms.
· Profiling microbial communities in different regions of the organisms.
· Extracting and characterise native protein from promising portions of the digestive tract
· Investigating microbial endosymbionts using metatransciptomics and characterise the products they supply to the host.
· Using our existing knowledge of complex polymer degradation determine if new metabolic pathways are expressed using sophisticated in house bioinformatics resources and those of collaborators- such as Ocean Genome Legacy (USA).
· Promising candidate enzymes may then be further characterised by the team using a range of structural, biophysical and computational approaches.

Project description

This project will build upon the research at the Centre for Enzyme Innovation (in collaboration with the Universities of York and Cambridge) into how the highly recalcitrant lignocellulose complex is broken down by specialist wood feeders (1-5). It will focus on wood digesting bivalves (shipworms) that house symbiotic bacteria in specialised gill cells and in different areas of their gastrointestinal tract. It will investigate the various microbial contributions towards digestion, using a range of species from temperate and tropical waters. Field sampling will be conducted in collaboration with partners in the USA, the Mediterranean, the Caribbean and SE Asia.

Samples will be examined by microscopy, microbial community profiling, metatranscriptomics and promising protein sequences will be explored using our established pipelines for characterising the capabilities of novel proteins (5,6). This characterisation will be supported by the CEI team of postdoctoral researchers with skills in bioinformatics, molecular modelling, structural biology and enzymology. In addition to a full program of training provided by the Graduate School, you will have opportunities to broaden your range of expertise and to acquire extra practical skills with the excellent range of molecular biology and biophysics equipment used by CEI and also National
facilities such as the NERC Mass Spectrometry Facility and the Diamond Synchrotron.
The understanding to be gained from this study will have application in:
• biotechnological use of woody wastes;
• providing fundamental knowledge on a complex symbiosis:
• development of novel non-toxic enzyme-inhibiting methods of wood protection;
• clarifying poorly understood, but globally important carbon flows derived from woody detritus.

General admissions criteria
You should have a good first degree (minimum 2.1 or equivalent) in a project-relevant discipline such as Biology, Microbiology or Biochemistry, and a desire to excel as a disciplined scientist within a cohesive research team. Potential applicants with a Masters-level qualification, or equivalent experience in a relevant field, are strongly encouraged to apply.
We require English language proficiency at a minimum of IELTS band 6.5 with no component score below 6.0.

Specific candidate requirements
We are looking for a talented student with a strong background in biology, microbiology and molecular biology. An understanding of ecological processes and a specific interest in examining novel aspects of symbiosis in wood degrading organisms would also be valuable. We will provide specialist training in the range of skills required for this project.

How to Apply
We’d encourage you to contact Prof. Simon Cragg () or Dr Joy Watts () to discuss your interest before you apply, quoting both the project code and the project title.

When you are ready to apply, you can use our online application form making sure you submit a personal statement, proof of your degrees and grades, details of two referees, proof of your English language proficiency and an up-to-date CV. Our ‘How to Apply’ page offers further guidance on the PhD application process.

When applying to the University, please quote project code: BIOL4590219

Funding Notes

This competition-funded studentship (subject to funding) is available to UK and EU students only and covers tuition fees and an annual maintenance grant of £14,777 (RCUK 2018/19 rate) for three years.

This studentship is subject to the University of Portsmouth’s successful funding investment to grow its newly developed Centre for Enzyme innovation. The Centre focuses on the discovery, engineering and deployment of enzymes with potential application to the circular economy.


1. Cragg, S et al (2015) Lignocellulose degradation mechanisms across the Tree of Life. Current Opinion in Chemical Biology 29: 108-119.
2. Watts J et al 2017 Investigation into the fungal diversity within different regions of the gastrointestinal tract of Panaque nigrolineatus, a wood-eating fish AIMS Microbiology 3: 749-761.
3. Besser, K. et al., (in press) Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans. Nature Communications.Austin HP et al. (2018) Characterization and engineering of a plastic-degrading aromatic polyesterase. PNAS 115(19):E4350-E4357.
4. Sabbadin et al (2018) Uncovering the molecular mechanisms of lignocellulose digestion in shipworms. Biotechnology for Biofuels 11:59, 14pp.
5. Kern M et al. (2013) Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance. PNAS 18;110(25):10189-94
6. Mallinson SJB et al. (2018) A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion, Nature Communications 9, 2487.

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

FTE Category A staff submitted: 25.73

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

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