Bolstad, KatHermans, SyrieLee, KevinMaranzana, Marina2026-04-302026-04-302025http://hdl.handle.net/10292/21005Microbial symbiosis with marine hosts facilitates the adaptation and survival of the host, expanding the range of habitable niches available to them in the deep ocean. Research on the microbiomes of deep-sea organisms is increasing due to their recognised importance for providing insight into the physiology, ecology, and behaviour of host organisms; however, much remains to be studied. The microbiota of deep-sea oegopsid squids is an emerging field, with the majority of oegopsid squids' microbiota still unknown. Deep-sea squids are of considerable economic, scientific, and ecological importance, yet there is a lack of data on their life histories and ecologies. This is due to the challenges of studying them in situ and the inaccessibility of deep-sea samples, which limits research availability. Therefore, this PhD thesis aimed to increase our limited understanding of Southern Ocean deep-sea oegopsid squids by investigating their bacterial communities for the first time using 16S rRNA gene amplicon sequencing. Nine different squid species from five distinct families belonging to the order Oegopsida were sequenced. To start, a single species was used to assess the intraspecific variability between sexes by analysing the digestive tract microbiota of five females and five males of Aotearoa’s endemic Southern arrow squid, Nototodarus sloanii. The core microbial taxa observed were Mycoplasma and Brachybacterium, and no significant differences were observed between the sexes. When no significant differences were observed among any individuals within a species, the bacterial community composition variability among species within the same genus and between genera within the same family was investigated. No significant difference in microbial richness was observed among species or between genera; however, a significant difference in microbial beta diversity was observed between squid genera. Mycoplasma and Brachybacterium (which has not been previously reported in cephalopods) are the two most common and abundant microbial taxa found in all researched deep-sea squids. Mycoplasma was seen to be mainly associated with the digestive tract and beak of all squid species, and the BD1-7 clade was the most abundant bacterium in the gills of all the ommastrephid squids. The opportunistic collection of a single species, Todarodes filippovae, at two distinct locations (the Chatham Rise and the sub-Antarctic) enabled a preliminary description of differences in body site microbiota between the two locations within a single species. Both the Chatham Rise and sub-Antarctic digestive tract samples mainly consisted of Brachybacterium. However, the sub-Antarctic beak samples were primarily composed of Mycoplasma, while the Chatham Rise beak samples were mainly made up of Aurantivirga. Once the intra- and inter-genus variability was established, the four ommastrephid deep-sea squids were compared with four different deep-sea oegopsid squids known for storing ammonia in their muscle tissues for buoyancy. This was done to assess variability in the microbiota among deep-sea squids with different body chemistries. A significant difference was observed between the ammoniacal and non-ammoniacal squids. Across all squids except Onykia robsoni, the beaks harboured similar bacterial communities but with different relative abundances. For all squid species, the same was true for the brain, inner eye fluid, and ommastrephid gills. In contrast, for all squid species except Taningia danae, the siphon and reproductive organs showed the greatest variation in both microbial abundance and diversity among squid taxa, although some general trends could be observed within the ammoniacal (which contained more Mycoplasma) and non-ammoniacal squid groupings (which had more BD1-7 clade). Lastly, due to the opportunistic collection of a rare deep-sea oegopsid squid in the Ross Sea, the colossal squid (Mesonychoteuthis hamiltoni), and the availability of a public dataset on NCBI on the microbiota of seawater from the Ross Sea a preliminary assessment of the transfer of microorganisms between the surrounding environment and host organism was conducted, as well as a first description of the microbiota of six body sites of the colossal squid. The bacterial genus Pseudomonas was the only observed taxon in both datasets; however, another bacterial taxon, Pseudoalteromonas, which was observed in all the Ross Sea seawater depth samples, was also observed in several deep-sea squids investigated in this thesis. Mycoplasma, which was seen to be the most abundant bacterium in the colossal squid, was not present in any of the seawater samples from the Ross Sea dataset. Investigating the microbiota of deep-sea squids is essential in furthering our understanding of their life history and ecology. This will also provide insights into how changes in oceanic conditions resulting from anthropogenic pressures could affect their health, as their microbial symbionts are thought to be linked to pathogen prevention and nutrient assimilation. This body of work represents the first microbiota study of cephalopods of the Southern Ocean and the first microbiota study worldwide of deep-sea squids belonging to the families: Octopoteuthidae, Onychoteuthidae, and Cranchiidae.enThesisOpenAccess