A molecular and isotopic assessment of farmed tilapia (Oreochromis niloticus) to improve aquaculture in Papua New Guinea

Aquaculture is the fastest growing food-producing sector worldwide, with much of the recent and ongoing growth attributed to freshwater fish farming. Freshwater fish farming is considered a solution to many global food security and health issues because it has the capacity to provide urban, remote, and rural populations with a regular source of fresh food. Genetically Improved Farmed Tilapia (GIFT) strain Nile tilapia (Oreochromis niloticus) has shown promise in its ability to improve developing nation food security. However, for its full potential to be realised, there is a need to improve yields and increase efficiency, particularly through lower cost farming practices. My thesis aimed to enhance our understanding of GIFT farming and assess the potential for low-cost, locally-available resources to improve fish farm productivity and profitability in Papua New Guinea (PNG). Using a combination of molecular methods, including 16S rRNA gene amplicon sequencing, environmental metabarcoding (eDNA) and stable isotope analysis (SIA) this thesis evaluated how different diets, farming strategies and aquaculture systems influence GIFT performance. Overall, I found that whilst the relationship between the composition of the GIFT gut microbiota and its condition varied based on the type of aquaculture system used (i.e., earthen pond or cage-culture), differences in the microbiota composition always correspond with distinct isotopic signatures (i.e., δ13C and δ15N values) and diets (e.g., pellet or vegetable based, eDNA analysis). Specifically, I found that in earthen pond culture, commercial feed pellets significantly improve fish condition, with profit and productivity further enhanced via the addition of inorganic fertiliser (NPK). In an assessment of cage-culture, I revealed that floating cages affect the composition of naturally occurring foods obtained, digested, and assimilated by GIFT; however, no impacts on fish condition were identified. Overall, my thesis demonstrated that low-cost resources (e.g., NPK) can improve the success of small-scale GIFT farming in PNG. This research provides a foundation to evaluate small scale fish farming in developing nations, with the potential for the multidisciplinary approaches used in this study to improve the food and income security of remote, and rural populations in other developing nations

Correction: Diet type influences the gut microbiome and nutrient assimilation of Genetically Improved Farmed Tilapia (Oreochromis niloticus).

[This corrects the article DOI: 10.1371/journal.pone.0237775.]