Abstract
Anthropogenic activities continue to impact the marine environment, causing shifts in both the physical and chemical properties of the oceans. Of particular concern are regions such as the Great Barrier Reef and the broader Indo-Pacific as they contain some of the highest levels of biodiversity on the planet. The predicted changes in temperature and ocean acidification are expected to negatively impact habitat-forming species such as corals and sea sponges, potentially leading to reduced biodiversity and diminished ecosystem functionality. Traditional methods of monitoring biodiversity have demonstrated biases, inaccuracies, and in some cases, destructive effects, therefore, novel methods that overcome these limitations are required. Recent advances in genomics have developed techniques capable of monitoring biodiversity, specifically, the use of environmental DNA (eDNA). The overall aim of this thesis was to provide evidence of alternative eDNA methods that can be employed for biodiversity monitoring, both contemporary and historical.
To achieve this, artificial and historical sponge specimens were examined. Firstly, the use of artificial sponges to absorb eDNA and detect fish taxa was investigated on the Great Barrier Reef, Australia (15/05/2022 - 23/05/2022). Artificial sponges were deployed over four submersion times (5 min, 30 min, 3 h, and 24 h) on Davies Reef. Results demonstrated that submersion time significantly affected both the number of reads absorbed and the amount of fish taxa detected. A notable reduction in reads was observed over longer durations (>3 h), however, a larger proportion of fish taxa were detected, with the most observed in the 3 h deployment, suggesting that longer submersion times provide more comprehensive biodiversity estimates. Additionally, artificial sponges were deployed on Cairns and Moore Reefs (for 24 h) to investigate whether differences in the composition of fish taxa among the three reefs could be detected. Results indicate that artificial sponges could detect differences in fish composition, although these were not statistically significant, potentially due to the connectivity among reefs across the Great Barrier Reef.
In a second, related study, an analysis of 197 historical sea sponge specimens collected across the Indo-Pacific between 1977-2008 and archived in the Queensland Museum was conducted. The aim was to provide evidence that historical museum specimens, specifically, sponge specimens stored in ethanol, could offer historical genetic information useful for observing past fish biodiversity.
Of these, 75 fish eDNA signals were successfully recovered from 42 sponge specimens. Fish taxonomic composition differed among locations, with an increasing number of fish species detected as latitude decreased. Notably, this spatial pattern is consistent with current knowledge, however, several common fish families unexpectedly weren't detected in any locations. These included: Apogonidae (cardinalfishes), Blenniidae (combtooth blennies), Carangidae (jacks and trevallies), Lethrinidae (emperors), Lutjanidae (snappers), Monacanthidae (filefishes), Mullidae (goatfishes), Scorpaenidae (scorpionfish), and Serranidae (groupers and sea basses). Additionally, a weak relationship was observed between the age of the sample and the reads and fish taxa detected, with older samples showing fewer reads and less fish taxa detected.
Further research should explore how different sponge species and artificial materials impact eDNA acquisition, considering the microbial composition, submersion time and eDNA decay rates. Additional studies should also examine DNA extraction protocols for various preservation methods to understand the impact of preservation time on DNA retrieval. Overall, this thesis demonstrated the potential for the practical applications of artificial and historical sponge specimens in eDNA collection and fish taxa detection, highlighting their value in informing conservation strategies for vulnerable tropical coral reefs.