Cubozoans, commonly referred to as box jellyfish, are a class of marine taxa which contain members described as the most venomous organisms on the planet. They are found in warm tropical waters around the globe and have multiple unique attributes which have garnered them significant research interest. These attributes include their visual capabilities, life histories, swimming abilities, and, most notably, their potent venom. Stings from dangerous members can result in severe reactions, hospitalisation, and potentially death. The ability to manage this risk of envenomation is a challenge faced by stakeholders and decision makers globally. Despite this, cubozoan jellyfish are largely understudied and ecological data on the majority of species are limited. To overcome the threats and challenges which these taxa pose, an increased understanding of their ecology is needed. Significant knowledge gaps exist surrounding cubozoan jellyfish life histories and population structures. These gaps stem from the challenges associated with their detection, a result of their elusive nature, transparency, and spatial and temporal variability in abundance. Moreover, these gaps persist due to limitations of current detection and sampling techniques in addressing the logistical difficulties of studying these aspects of cubozoan ecology.
The broad objective of this thesis was to explore the use of eDNA as an innovative technique for detecting and studying deadly cubozoan jellyfish. The development of a robust assay (Chapter 2) was a prerequisite for the application of the technique for studying the ecology of medusae and polyps in open and closed marine environments (Chapters 3 & 4). Finally, estimates of spatiotemporal detection limits were determined by modelling the dispersal of eDNA (Chapter 5).
The development and optimisation of an eDNA assay for Chironex fleckeri revealed the technique’s high utility for the detection of the potentially deadly jellyfish (Chapter 2). The assay was designed to target a region of the mitochondrial 16S rRNA gene which contained both interspecific and intraspecific variability. This allowed for the assay to be highly specific, ensuring it could distinguish C. fleckeri from closely related species, while ensuring its ability to detect the species across its biogeographic distribution. Field trials demonstrated this, with C. fleckeri medusae being detected at locations across the species range, where they were known and confirmed to be present. Multiplexing the assay with an endogenous control allowed for enhanced quality control, ensuring reliability in all stages of the technique’s workflow. This, additionally, enabled reliability and confidence in field detections, limiting the potential for false positive or false negative detections. Additionally, the assay was found to be highly sensitive, with an effective limit of detection of 0.45 copies/reaction when utilising six technical replicates. This sensitivity provided assurance of a powerful and reliable detection tool, especially due to the high spatial and temporal variability in C. fleckeri abundance. Mesocosm experimentation revealed a rapid decay rate of C. fleckeri eDNA (99% within 27 hours), with no detectable variation in this rate across minor temperature changes. This provided essential insights into the temporal resolution of the technique, and with knowledge on the movements and behaviours of C. fleckeri, suggested that detections likely reflected the species’ close proximity. These findings demonstrate that eDNA offers a highly effective and precise tool for detecting C. fleckeri, hence addressing a key challenge in determining the species’ presence.
The application of eDNA in Port Musgrave provided critical evidence that C. fleckeri have spatially small stock populations. The relatively enclosed estuarine system served as a habitat for both medusae and polyps (Chapter 3). eDNA samples were collected across various habitats, including sandy beaches and mangroves, during the jellyfish season, and outside of the season when only polyps would be present. Accordingly, eDNA proved to be an effective tool to locate the elusive benthic polyp stage of C. fleckeri, which are the source of the free-swimming medusae stage. Polyps were detected exclusively within the Port, specifically around rocky substrata along sandy beaches, with no detections in mangrove habitat. This suggested that polyps exhibit distinct habitat preferences, similar to those observed in other cnidarian species, particularly scyphozoan jellyfish. Medusae were detected at a high frequency inside, and more sporadically outside, of the estuarine system, suggesting that the species moves between these areas, aligning with known patterns of the jellyfish’s movement. The distinct spatial distributions of medusae and polyps enabled an evaluation of their population boundaries, suggesting that the Port likely contains a population stock of the species. This finding supports growing evidence of spatially restricted population stocks of some cubozoan jellyfish. Finally, while eDNA proved highly effective for C. fleckeri detection, its use as a proxy for abundance was limited, likely due to the high variability in eDNA shed by the low abundance and spatially dispersed species.
In Chapter 4, the eDNA data collected in the open coastal environment of Magnetic Island built on the findings from Port Musgrave, providing further insights into the spatial distribution and source locations of C. fleckeri. The study area, encompassing Horseshoe and Maud Bays, featured oceanographic and geomorphic conditions expected to facilitate greater dispersal of the jellyfish, when compared to the semi- enclosed estuarine system of Chapter 3. Environmental DNA samples were collected across nearshore, mid-shore and offshore locations both during the jellyfish season and non-seasonal months. Medusae were detected exclusively in nearshore areas, consistent with their known distribution, confirming the ability of eDNA to accurately capture the spatial presence of the species. Outside of the jellyfish season, polyps were detected near freshwater inflows, with the highest frequency of detections occurring in Horseshoe Bay. This supported the hypothesis, based upon empirical medusae size- distribution data, that Horseshoe Bay serves as a source location for C. fleckeri on the island. Polyps were detected in habitats with rocky substrata, consistent with previous findings. A comparison of the distributions of both life history stages, where medusae were exclusively detected nearshore and polyps consistently detected in Horseshoe Bay, suggested that the northern side of Magnetic Island likely represents a population stock of the jellyfish. Sampling in both semi-enclosed and open environments added further evidence to a developing paradigm of spatially restricted C. fleckeri stocks.
Finally, in Chapter 5, focus shifted to understanding the spatiotemporal dispersion and detectability of C. fleckeri eDNA through the utilisation of biophysical models, to better understand the relationship between eDNA detections and the physical presence of the jellyfish. The spatiotemporal detectability of eDNA was found to be spatially restricted, across 100s of meters to kilometres, despite potential for particles to travel distances of up to 10s of kilometres. This was, as expected, primarily influenced by both particle dilution and decay. Local hydrodynamics, including tidal flows and wind- driven surface currents, played a key role in shaping dispersal patterns, leading to heterogeneous movements and retention of eDNA across small spatial scales. Estimated spatiotemporal detection limits aligned with the results of empirical detections (Chapter 4).
In summary, this thesis has demonstrated the effectiveness of eDNA as a powerful ecological sampling tool for detecting and studying cubozoan jellyfish across their key life history stages. The development of a highly specific and sensitive eDNA assay enabled accurate detection of both medusae and polyp life history stages, and provided critical insights into their spatial distribution, habitat preferences, and population structures. Specifically, the efficient detection of polyps is a crucial advancement, offering a new approach to detect and study this life history stage. This knowledge on polyps is vital for effective management strategies as they are the source of stinging medusae. The findings of this thesis additionally add to growing evidence of some cubozoan species, including C. fleckeri, maintaining spatially small population stocks, to the scale of bays and estuaries, with these findings being ecologically robust across differing environmental settings. The ubiquitous nature of DNA makes this genetic detection tool applicable for all ~50 cubozoan species, highlighting its potential to further ecological understanding on other problematic cubozoans, such as the notorious ‘Irukandji’ jellyfish, Carukia barnesi. Additionally, eDNA shows considerable promise as a potential management tool, offering an efficient method for early detection and potential mitigation of the risks posed by these taxa. While eDNA proved highly effective in detecting presence, limitations as a proxy for abundance, its inability to determine size/age distributions, and behavioural patterns were acknowledged, emphasising the need for a multifaceted approach for the comprehensive study of cubozoan ecology. As molecular genetic techniques advance, future research efforts may refine cubozoan detections by offering finer temporal and spatial resolution, potentially enabling targeted collection and in-situ study of these jellyfish. Collectively, the findings of this thesis contribute significantly to the field of cubozoan jellyfish ecology and showcase the high applicability of eDNA as an ecological sampling tool to detect and study these taxa.