Project proposal form
Project title: From
seagrass debris to natural bioreactors
Project code:
Host institution: University of Warwick
Theme: theme 1, environmental sustainability; and theme 4, microbial ecology and biogeochemistry
Key words: Marine ecology, microbial community, biopolymer degradation, meta-genomics/proteomics
Supervisory team (including institution & email address):
Joseph A. Christie-Oleza, University of Warwick, J.Christie-Oleza@warwick.ac.uk
Elizabeth Wellington, University of Warwick, E.M.H.Wellington@warwick.ac.uk
Project Highlights: Tonnes of seagrass debris are
annually generated and washed to the shore where
they accumulate and decompose in large stacks.
Who can degrade it and how? What can be learned
from these natural bioreactors? Can they have a
biotechnological use?
Overview:
Humankind has historically copied nature and will
continue to exploit its biotechnological capabilities for
many years to come. This PhD project aims to learn
the biological processes that take place during
seagrass degradation on marine coasts, from the
ecological understanding of microbial communities to
the molecular characterisation of hydrolytic enzymes
and generation of biogas.
Debris generated from the vascular angiosperm
Posidonia oceanica will be used as a case study. This
seagrass is found in the Mediterranean Sea and in
South Australia when coastal ecosystems reach
ecological climax. These coastal “sea-forests” produce
large amounts of debris that is washed to shore where
it accumulates. Despite its inherent protective action
avoiding sand beaches to be washed away during
winter storms, local authorities remove it from
touristic beaches as it is considered an unpleasant
solid waste with consequent economic cost. In
unmanaged beaches, this debris can accumulate year
after year generating large stratified piles or be
covered by sand causing anaerobic digestion.
The natural bioreactors that are developed in these
ecosystems are environments with an enormous
enzymatic potential for hydrolysing biopolymers (e.g.
lignin and cellulose) and ideal locations for the
isolation of extremophile
microbes with
biotechnological uses (e.g. high salinity).
Figure 1: Meadow of Posidonia oceanica and large debris
deposits on coastal environments.
Methodology:
This PhD Project aims to answer key ecological
questions on the biodegradation of seagrass debris in
marine systems. The successful student will analyse
the microorganisms that carry out such vital process
in these natural bioreactors, investigating the
enzymes involved and the processes that take place.
Side products such as depolymerised compounds or
generation of biogas will be monitored. The microbial
community of natural samples will be compared to
those developed in mini-bioreactors setup in the lab
under different conditions. The student will analyse
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) and, ultimately, isolation
and characterisation of microbial degraders and
fermenters. Finally, the student will setup a controlled
synthetic community that will mimic the natural
reactor and that could be re-wired for
biotechnological purposes.
Training and skills:
CENTA students are required to complete 45 days
training throughout their PhD including a 10 day
placement. In the first year, students will be trained as
a single cohort on environmental science, research
methods and core skills. Throughout the PhD, training
will progress from core skills sets to master classes
specific to the student's projects and themes.
This multidisciplinary PhD project will offer a unique
opportunity for the student to learn state-of-the-art
techniques in environmental –OMICS (such as highthroughput proteomics and genomics), microbial
ecology and biochemistry, and analytical chemistry of
biopolymer degradation. The laboratories of
supervisors Dr Christie-Oleza and Prof Wellington
(School of Life Sciences) 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.
Partners and collaboration (including CASE): This
project has a high potential in becoming CASE,
building collaborations with the biopolymer and
biotechnology industry.
Possible timeline:
Year 1: Field sampling with our collaborators in the
Balearic Islands (Spain) and microbial community
analysis of both natural and lab-based seagrass
biodegradation reactors. Isolation of key players with
interesting biodegradative capabilities.
Year 2: Analysis of community evolution under lab
conditions, metagenomics and exoproteomics
analysis. Search for hydrolytic exoenzymes both in
natural communities and microbial isolates.
Evaluation of biopolymer degradation under different
incubation conditions.
Year 3: Setup of synthetic communities that will carry
out the key processes in the biodegradation of
seagrass and generate genetically modified organisms
to re-direct the use of nutrients.
Further reading:
 Christie-Oleza et al (2015) Proteomics, doi:
10.1002/pmic.201400562.
 Christie-Oleza et al (2012) Mol Cel Proteomics, 11:
M111.013110.
 Johnson-Rollings et al (2014) ISME J, 8: 2148-2150.
 Panno et al (2013) N Biotechnol, 30: 685–694.
 Cuomo et al (1987) Biochem System Ecol, 15: 635637.
 Pilavtepe et al (2013) Indust Crops Prod, 51: 348–
354.
Further details:
Enthusiastic applicants with 1st class BSc or MSci
degrees in Biology, Biochemistry or related fields and
laboratory experience are welcome to apply. Contact:
j.christie-oleza@warwick.ac.uk