Summary

This training course will provide and introduction to sample collection and sorting, including taxonomy and processing for DNA extraction, eDNA and qPCR analyses, as well as a quick guide on the use of the bioinformatics for sequence analysis to in-country (Fiji) managers and technical staff.

Learning outcomes

By the end of the course the participants should be able to:

1. Collect samples through the various methods used in PacMAN
2. Understand the benefits and challenges of eDNA sampling and its use in biodiversity monitoring.
3. Understand the processes involved in taxonomy (e.g. gross sorting, routine simplified processing and identification steps to group organisms and record this information appropriately).
4. Know how to conduct DNA extractions on 3 different marine sample types as well as troubleshooting any problems
5. Know how to conduct PCR amplification and understand teh principles of metabarcoding
6. Run qPCR analyses for target organisms using established probes
7. Run a query search on global databases after sequence information is received
8. Entering data and understand the basics of sequence analysis with bioinformatics

Target audience

Target audience should be managers and technical staff from Fiji key organisations working in the field of marine conservation, monitoring and surveillance, curators of marine collections, fisheries resource personnel, researchers in marine sciences including students in academia and mariculture practitioners.

Course content (Topics and activities to be covered)

Online/remotely (via OTeL) (~ 6 hours workload, asynchronously)

Topic 1: Introduction to marine invasive species - why monitoring is needed?

• Biodiversity loss & CBD
• Existing gaps and areas of concern from PacMAN survey
• The difference between monitoring for early detection (the purpose of PacMAN) and managing existing known incursions (not the focus of PacMAN)

Topic 2: Monitoring plan & protocols, high risk species, eDNA and qPCR

• Introduction to molecular methods for monitoring using eDNA
• DNA amplification using PCR
• DNA Quality control through Gel Electrophoresis and Clean-Up
• DNA sequencing

Topic 3: Fiji as a Case Study

• Introduction to marine biosecurity in Fiji
• Overview of the PacMAN project and methods used within
• Port baseline survey
• Routine monitoring in the operational phase

Onsite (40 hours onsite, 09:00 – 16:30 local time, Monday - Friday)

Topic 4:

4A Field protocols for monitoring, deployment and sample collections

• Field work to be conducted at the USP jetty.
• Workplace health and safety procedures for risk reduction

4B Laboratory Plates Sampling

Transfer of samples from Port to Laboratory

• Morphological identification/Gross sorting of specimens
• Record keeping & Photographic method
• Taxa list generation/Linking across sampling trips
• Linking to USP marine collections protocols

Topic 5: Laboratory Molecular protocols

• DNA extraction
• Metabarcoding PCR (CO1 and 18S)

Topic 6: Laboratory Targeted monitoring protocols

• Quantitative PCR (Species specific targeting)

Topic 7 & 8: Data Management & Quality Controls

• Importance of sharing data and the standards linked to it
• How data is collected, checked & processed locally
• Principles of the PacMAN data workflow
• Preparation of data for upload
• Demonstration of data upload and analysis?
• How data will be shared

Instructors/Trainers

• Craig Sherman (Deakin University- Lead trainer)
• Dr. Chaminda Dissanayake (BAF qPCR specialist)
• Mr. Joape Ginigini, USP (Co-facilitator and training coordinator)
• Dr. Gilianne Brodie, USP (Marine scientific advisor and Assistant facilitator)
• Miri Vuiyasawa, USP (Assistant facilitator and Training liaison for communications and logistics)
• Mr. Ward Appeltans (OBIS project manager)
• Mr. Pieter Provoost (OBIS data manager)
• Dr. Saara Suominen (OBIS scientific officer)
• Dr. Elizabeth Lawrence (OBIS training officer)

Language

• English

Pre-course Activities or Assessment

Mandatory online phase between 31 Oct – 14 November 2022 ~ 6 hours workload (self paced).

Learner assessment  

A certificate will be issued to learners achieving a minimum of 70% in the evaluation (quizzes and assignements).

Pre-requisites:

Language and computer skills required:

Applicants are expected to have:

• a working knowledge of English
• background knowledge in biological and marine sciences
• basic computer skills (operating either with Windows or Mac systems)
• finding resources through search engines
• downloading and installing software
• the ability to be self-directed in learning new technology skills (e.g. following a step-by-step tutorial, online video help, or access to support to learn necessary skills)

Technology requirements

To complete this course, participants should have access to:

• Latest version of either Chrome, Edge, Firefox, or Safari web browsers
• Access to internet
• Webcam and speaker/phone

Other requirements for onsite phase (field and lab component)

• Participants need to bring individual protective equipment (safety shoes or proper closed shoes and lab coat)
• Declare any health issues with chemical exposure including existing illnesses (e.g. liver)
• Full disclosure of any injuries that may affect one’s coordination in a laboratory environment