Skipjack tuna (Katsuwonus pelamis) as an indicator of ecosystem and environmental changes using real-time genomic technology

Abstract

The Pacific Ocean, the world’s largest oceanic division, sustains numerous important fishery, economic, and ecological functions (Hills et al., 2011). Marine ecosystems in the Pacific Ocean are under severe threats from human activities and anthropogenic climate change (Hoegh-Guldberg & Bruno, 2010; Pauly et al., 2002). Monitoring marine biodiversity more efficiently and at the community level is critical but challenging due to ecosystem complexity and the large number of inaccessible taxa in marine ecosystems. DNA barcoding and metabarcoding, species identification approaches empowered by high throughput sequencing (HTS) technologies, provide opportunities to monitor marine biodiversity using DNA fragments collected from a wide range of sources, such as ocean water, sediment, feces or gut content of marine species (Hebert et al., 2003). The guts of marine opportunistic predators can provide valuable information, such as food web structure and species interactions through the diet analysis (Olson et al., 2014), and responses to external pressures through the gut microbiome analysis (Apprill, 2017). DNA metabarcoding is especially useful for analysing diet and gut microbiomes efficiently and accurately in marine predators. However, few studies have explored the feasibility of DNA metabarcoding for diet and gut microbiome analyses in wild marine fish, or how their diet and gut microbiome are related to climate and human activities.
The general aim of this research is to evaluate the diet and gut microbiome of skipjack tuna (Katsuwonus pelamis) using DNA metabarcoding to enable monitoring of marine ecosystems in the western and central Pacific Ocean (WCPO). However, several knowledge gaps limit the reliability of this approach, including the reliability of DNA barcode reference databases and gut sample degradation in wild-caught marine fish. Therefore, we first evaluated reference databases for DNA barcode records (Chapter 2) and assessed gut microbiome community changes after the catch of skipjack tuna (Chapter 3), which established baselines for reference database evaluation and curation, and sampling timing for wild-caught skipjack tuna. The fourth chapter examined the diet and gut microbiome of skipjack tuna using DNA metabarcoding and explored the influences of El Nino-Southern Oscillation (ENSO) events. We then explored a cutting-edge HTS technology, Oxford Nanopore Technology (ONT), and its feasibility for monitoring diet and gut microbiome of skipjack tuna in a more convenient and real-time manner (Chapter 5). The final chapter (Chapter 6) provides a comprehensive discussion of the key findings, possible applications of the findings, and general recommendations for stakeholders and researchers involved in skipjack tuna fishery studies based on this research.
This study highlighted the importance of DNA barcode reference database evaluation and curation (Chapter 2) and sampling timing for wild-caught marine fish (Chapter 3). A significant correlation between the gut microbiome of skipjack tuna and ENSO events was identified (Chapter 4). Additionally, ONT MinION was found to be a feasible real-time and field-friendly technology for monitoring the gut microbiome of skipjack tuna (Chapter 5). We suggest increased efforts in monitoring diet and gut microbiome in wild marine fish predators, extending the findings from this study to a larger geographical area, long-term monitoring, and to multiple species.

Date of Award	2026
Original language	English
Supervisor	Dianne GLEESON (Supervisor), Stephen SARRE (Supervisor) & Alejandro TRUJILLO GONZALEZ (Supervisor)