Internship offer – 2021/2022
Title: Biodiversity screening- MarineGEO-Hong Kong: Recording the pulse of the ocean
Name of the researcher(s) responsible for the proposal and affiliation:
Dr. Shelby McIlroy, Dr. Guibert Isis and Dr. David M. Baker

The Baker Lab
Swire Institute of Marine Science
School of Biological Sciences
Kadoorie Biological Sciences Building
The University of Hong Kong
Pokfulam Road, Hong Kong, PRC

Description and scientific objectives of the proposal:
Marine Global Earth Observatory (MarineGEO) is a global network of partners focused on understanding how coastal marine ecosystems function, and how to help conserve biodiversity. We bring together simple sampling technology (ARMS) and next-generation genetic sequencing to fill the large gaps that still exist when estimating marine biodiversity.
Autonomous Reef Monitoring Structures (ARMS) is a multi-layered settlement plate that mimic complex marine substrates. It is designed as a passive and non-invasive collector of marine understudied fauna, from algae, corals, crabs, snails and worms, all without causing damage to the environment. While ARMS has been deployed worldwide to explore the cryptic fauna, bacterial community, which are important component of reefs ecosystems remain poorly studied.

ARMS are deployed for a period of 6 months to 1 year in Hong Kong waters. Once retrieved, ARMS are disassembled and photographed. Large specimens >2mm that reside in the ARMS are collected and sorted into taxonomic groups. Tissues of the specimens will be extracted and sequenced for further identification.
The small motile fraction (106m to 2 mm) is collected by filtration. After collecting all mobile organisms, the remaining sessile organisms on the AMRS are scraped off plates. The DNA of the small motile fraction and sessile fraction is extracted and amplified for metabarcoding analysis.

The candidate will be responsible of DNA extraction and amplification for barcoding analysis and help on the field if necessary. The project proposed for this research internship aims to build an extensive database of marine fauna in Hong Kong by the sample collecting process stated above. With the data from different sites organized, we will analyze the impact of human activities on biodiversity and community composition. Numerous samples will be collected from the ARMS, therefore the candidate will need to keep a good record of sample information, sequences and photos.

Your qualifications
Candidates should have experience and interest in DNA-sequencing and ecology, and the skills to read an interpret scientific literature. Experience of data organizing using R and excel would be appreciated. The successful candidate will have experience in molecular biology laboratory work. A high level of written and spoken English proficiency is required.

Scientific and technical environment:
The successful candidate will perform the sequencing and data organizing processes mentioned above. Dr. Shelby McIlroy and Dr. Guibert Isis will be available to guide the student through this process, but a level of independent working is expected. The intern will participate to all the MarineGEO field work happening during his stay.

Some initial and suggested reading about the topic:
-Chen et al. 2020 A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome
-David et al. 2019 Lessons from photo analyses of Autonomous Reef Monitoring Structures as tools to detect (bio-)geographical, spatial, and environmental effects. Marine Pollution Bulletin
-Ng et al. 2017 Hong Kong’s rich marine biodiversity: the unseen wealth of South China’s megalopolis. Biodiversity and conservation
-Permean et al. 2018 Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority. Scientific Report
-Perman et al 2019. Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS). Molecular Ecology
-Ransom et al. 2017 The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia. Plos one

Contact: and
Review of applications will begin immediately. Your application should include:
1/Detailed curriculum vitae (including your research experience)
2/Academic transcript and rank (M1 & L3)
3/Cover letter

Internship length: 6 months – dates flexibles

Internship location: In person in Hong Kong

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