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PhD scholarship on the temporal and spatial community composition of biofouling on aquaculture structures using eDNA

   Seafood Genomics

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  Assoc Prof Maren Wellenreuther, Mr Peter Bell, Assoc Prof Xavier Pochon  Applications accepted all year round  Funded PhD Project (Students Worldwide)

About the Project

PhD Scholarship on the temporal and spatial community composition of biofouling on aquaculture structures using eDNA


We are seeking a highly motivated PhD student to be part of a group investigating the temporal and spatial changes of biofouling on open ocean aquaculture structures in New Zealand waters.


Biological fouling (biofouling) is the growth of organisms on artificial structures submerged in the sea or other aquatic environments. It develops sequentially from the initial conditioning layer of adsorbed organic and inorganic matter through the formation of a microbial film to a potentially diverse community of bacteria, macroscopic plants and animals. The problem of biofouling is diverse and includes many research aspects, e.g. the role of bacterial biofilms in the early stages of biofouling, patterns of biofouling in the freshwater, estuarine or marine environment, the transmission of invasive species, antifouling technologies and their impact on biofouling and ambient environment. Biofouling of marine structures has serious economic consequences. For example, the increased fuel costs for ships due to hull biofouling are suggested to be as high as US$150 billion annually (Selim et al., 2017). In addition, biofouling of fish and shellfish cages is a serious problem for aquaculture, accounting for, 5-10% of production costs (Bannister et al., 2019). The aim of this project is to understand how biofouling community structure of marine structures varies in space in time in New Zealand waters.

The project

Plant and Food Research (PFR) is making a significant investment in developing the knowledge, capability and innovations needed to undertake the aquaculture of fish at open ocean sites around Aotearoa. Biofouling of marine structures has been identified as a hurdle to farming in the open ocean, and a five year programme called New Open Ocean Ecosystems was designed and launched in 2021 to study the poorly understood topic of biofouling of aquaculture materials at exposed NZ sites. The PhD project will form part of this research programme, specifically, the student will develop a standardised and replicated sampling array for assessing the composition of marine biofilms. To adequately characterise community composition the student will apply optimised DNA extraction methods to extract high quality DNA for metabarcoding to characterize marine bacterial and eukaryotic biofouling communities (Zaiko et al., 2016, Pochon et al., 2015, von Ammon et al., 2018a, Briand et al., 2018, von Ammon et al., 2018b, Zaiko et al., 2020). Sampling will initially be undertaken at an easily accessible inshore location (e.g. Beatrix Bay, Nelson Haven) with the aim of extending these protocols to samples from more exposed open ocean aquaculture sites, to better understand the sources and vectors of propagules and to improve management of biofouling-related risks. Temporal and spatial variation among biofilm settlement will be assessed against the most relevant parameters identified. Additionally filtered planktonic eDNA samples will be collected in close proximity to the settlement arrays to examine linkages between planktonic and settled communities. The opportunity to include eRNA approaches as a proxy for the living portion of the biofouling community will be considered and discussed (Pochon et al., 2017, Wood et al., 2020).

The PhD project will incorporate a range of cutting-edge, next-generation sequencing (NGS)-based techniques to better understand the colonisation process on artificial surfaces and link what is present in the plankton to what occurs in the fouling community under a range of fouling-control conditions. The PhD student will gain experience working in academic and government institutions. They will be a member of a highly active and collaborative group of researchers, and help develop new technological approaches and applied-genomic tools.

The specific PhD project aims are:

(i) catalogue the primary colonizers responsible for causing biofouling and document successional stages and seasonal changes,

(ii) understand the impact of the spatial location and associated environmental factors on biofilm-forming community composition, and

(iii) compare the biofilm-forming and planktonic bacterial community.

The proposed topic leaves sufficient freedom in the selection of specific aspects and the design of a research plan for the doctorate candidate.

How to apply

Applicants should send a CV, contact details of two academic referees and a cover letter that states why you are interested in the position and how your qualifications and experience make you a good fit for the proposed research. Academic qualifications are considered alongside significant relevant non-academic experience. Send these to Maren Wellenreuther ([Email Address Removed]) and Peter Bell ([Email Address Removed]). Applications will be considered until the position is filled. Students will be enrolled at the University of Auckland but be based in Nelson ( We will provide a three-year scholarship that provides a stipend and university (domestic-level) fees.


1.   Main supervisor: Associate Professor Maren Wellenreuther, Auckland University and Plant and Food Research, Nelson, New Zealand.

2.   Co-supervisor: Peter Bell, Plant and Food Research (PFR), Nelson, New Zealand.

3.   Co-supervisor: Associate Professor Xavier Pochon, Cawthron Institute (Nelson) and Auckland University, New Zealand.

Funding Notes

This scholarship is open worldwide, but please pay attention to the New Zealand border entry rules


Cited literature
BANNISTER, J., SIEVERS, M., BUSH, F. & BLOECHER, N. 2019. Biofouling in marine aquaculture: a review of recent research and developments. Biofouling, 35, 631-648.
BRIAND, J.-F., POCHON, X., WOOD, S. A., BRESSY, C., GARNIER, C., RÉHEL, K., URVOIS, F., CULIOLI, G. & ZAIKO, A. 2018. Metabarcoding and metabolomics offer complementarity in deciphering marine eukaryotic biofouling community shifts. Biofouling, 34, 657-672.
POCHON, X., ZAIKO, A., FLETCHER, L. M., LAROCHE, O. & WOOD, S. A. 2017. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PloS one, 12, e0187636.
POCHON, X., ZAIKO, A., HOPKINS, G. A., BANKS, J. C. & WOOD, S. A. 2015. Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices. Biofouling, 31, 241-251.
SELIM, M. S., SHENASHEN, M., EL-SAFTY, S. A., HIGAZY, S., SELIM, M. M., ISAGO, H. & ELMARAKBI, A. 2017. Recent progress in marine foul-release polymeric nanocomposite coatings. Progress in Materials Science, 87, 1-32.
VON AMMON, U., WOOD, S. A., LAROCHE, O., ZAIKO, A., TAIT, L., LAVERY, S., INGLIS, G. & POCHON, X. 2018a. The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: a high-throughput sequencing analysis. Marine Environmental Research, 133, 57-66.
VON AMMON, U., WOOD, S. A., LAROCHE, O., ZAIKO, A., TAIT, L., LAVERY, S., INGLIS, G. J. & POCHON, X. 2018b. Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities. Scientific reports, 8, 1-11.
WOOD, S. A., BIESSY, L., LATCHFORD, J. L., ZAIKO, A., VON AMMON, U., AUDREZET, F., CRISTESCU, M. E. & POCHON, X. 2020. Release and degradation of environmental DNA and RNA in a marine system. Science of the Total Environment, 704, 135314.
ZAIKO, A., SCHIMANSKI, K., POCHON, X., HOPKINS, G. A., GOLDSTIEN, S., FLOERL, O. & WOOD, S. A. 2016. Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management. Biofouling, 32, 671-684.
ZAIKO, A., WOOD, S. A., POCHON, X., BIESSY, L., LAROCHE, O., CROOT, P. & GARCIA-VAZQUEZ, E. 2020. Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses. Environmental Science & Technology, 54, 8443-8454.
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