Internship offer – 2021/2022
Title: Bioinformatic adventure – MarineGEO-Hong Kong: Taking 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:
Microbial communities are responsible for fundamental ecological process and are critical for the resilience of marines ecosystems. However, studies have mainly focused on microbiome communities associated to key species organisms such as corals or sponges. While bacterial communities are an essential part of the marine biodiversity they remains understudied.
However, the investigation of marine biodiversity have increased over the last decade especially through the Marine Global Earth Observatory (MarineGEO) global network of partners focusing on understanding how coastal marine ecosystems function, and how to help conserve biodiversity. This network bring together simple sampling technology (Autonomous Reef Monitoring Structures) and next-generation genetic sequencing to fill the large gaps that still exist when estimating marine biodiversity.
ARMS, a passive and non-invasive collector of marine fauna, were deployed for 6 months to one year in Hong Kong waters. Once retrieved, ARMS were disassembled and photographed. DNA extraction and PCR was performed for the mobile organisms (three groups: >2mm, >500μm and >106μm) and the sessile organisms.
With this project we are aiming to investigate the applicability of ARMS in elucidating the microbial changes in sessile organisms along a pollution gradient in Hong Kong. We propose to use metabarcoding analysis to investigate the microbiome composition associated with the sessile organisms of the Hong Kong reefs. Candidate will be responsible for the metabarcoding pipeline development, sequence analysis and subsequent community ecology research.
Environmental data such as the total carbon, Chemical Oxygen demand or Copper concentration will be available from the Hong Kong Environmental Protection Department. Also, biodiversity data obtained from the vouchers (>2mm mobile organisms) have been organized for all the ARMS sites. With these existing data and the input of candidate, we hope to test the hypothesize that the pollution gradient observed in Hong Kong might reveals drivers of bacterial community structure and function.
A goal of this research would be the publication in a peer reviewed journal.

Your qualifications
Candidates should have experience and interest in bio-informatics and ecology, and the skills to read an interpret scientific literature. Experience using Qiime2 would be appreciated. The successful candidate will have experience in statistical analysis (R). A high level of written and spoken English proficiency is required.

Scientific and technical environment:
The successful candidate will analyze the 16S data using Qiime2 and R. The intern will be expected to participate in writing a scientific paper. 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 or work remotely

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