Dean of Postgraduate Research
Vice-Chancellor’s Office
Extension: 7285
Email:
lucy.johnston@canterbury.ac.nz
Summer Research Scholarship Scheme
2014-2015
Project Application Form
Please complete and submit the application form as a WORD document and send to
summerscholarships@canterbury.ac.nz
The Project
Title of Project (max 30 words):
Bioinformatics analysis of groundwater communities – linking structure and function.
Project Leader(s):
Dr Louise Weaver (ESR)
Host Department/Organization:
Institute of Environmental Science and Research (ESR) (in collaboration with BIC)
Other persons involved in this topic/activity:
(List other significant members involved along with their affiliation to the research project.)
Name
Affiliation to project
Dr Wendy Williamson (Microbial ecology)
Senior Scientist (ESR)
Dr Brent Gilpin (Molecular biology)
Dr Paul Gardner
Science Leader (ESR)
BIC/Biology
Brief outline of project
Describe the proposed research project – maximum of 400 words (box will expand as you type).
Note that this information will be published on the web in order to attract student applicants and therefore be
mindful of any Intellectual Property issues
More than half of New Zealander’s consume drinking-water accessed from groundwater sources
which means that considerable effort must be given to protecting this life-giving resource. Current
methods used to assess water quality in groundwater systems rely on measuring physico-chemical
changes; i.e., nitrate accumulation or microbial faecal indicator organisms such as E. coli.. These
methods are retrospective to contamination, providing an alert for public health only after
substantial contamination has occurred, which is a high risk strategy for health protection.
Therefore, development of alternative methods for groundwater monitoring is warranted to reflect
1
our high dependence on this resource.
Until recently, gaining a clear picture of microbial community composition and function in the
aquifers has been hindered by a lack of methods able to detect the entire population; traditional
microbial culture techniques permitted only a small fraction (<1%) of the complex community
present in groundwater to be detected and thereby identified and their function speculated.
Compounding microbial culture-dependence limitations, the subsurface environment is studied less
than above-ground freshwater ecosystems, mainly due to sampling issues, and has resulted in this
environment being significantly underrepresented in the literature. Next generation sequencing
(NGS) offers an alternative approach for biota detection that provides a culture-independent method
which overcomes traditional shortcomings.
The research team has already completed preliminary NGS experiments investigating how
microbial communities form in groundwater systems. The NGS data sets have been generated and
have had some analysis work done on them. The specific goal of this summer studentship will be to
extend the bioinformatics analysis to examine how the population structure of the groundwater
communities differs to other freshwater environments and what are the key drivers for this. Analysis
will involve bioinformatics analysis alongside some statistical analyses to determine key drivers.
If the project involves work away from the University campus (e.g., at fieldwork sites) please detail all locations.
The majority of the work will occur at ESR which is located adjacent to the University of Canterbury at 27
Creyke Rd, Ilam, Christchurch
If the student be required to work outside of normal university hours (8am-5pm) please provide details
N/A
Benefits student will gain from involvement in the project
Describe the research experience and skills that the student will acquire through involvement in this research project –
maximum of 100 words.
The student will gain an insight into the complex nature of groundwater ecosystems and the vital role they
play in protecting our drinking water sources. Valuable experience in analysing a number of next generation
sequencing data sets a number of software programmes will also be gained during the project. They will also
experience working within a larger scientific team and to develop relationships with scientists at both the
University and at a Crown Research Institute (CRI).
Specific student requirements
Please provide details of all requirements you have for the student to work on this project – for example, if specific
courses/experience are necessary.
This project is suitable for a senior (Year 3 or 4) student who has an interest in microbiology/groundwater
ecology and has completed molecular biology and bioinformatics classes. A high level of computer literacy is
required. Experience with statistical analysis is desirable.
2