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The extent of mixing of juveniles is a fundamental aspect of southern bluefin tuna (SBT) ecology that continues to be debated. Juvenile SBT are found either side of the Indian Ocean, south of Africa and off southern Australia. By the 1980s it was generally accepted that some juveniles migrated directly from waters off Western Australia as far west as the south eastern Atlantic Ocean. Although little was known about the movements of these individuals, they were assumed to remain mostly separate from juveniles off southern Australia. However, the introduction of electronic archival tags in the 1990s has strongly influenced theories of juvenile migration of SBT. Some researchers have claimed the archival tag recoveries suggest the great majority of two- to four-year-old juveniles summer in the Great Australian Bight, while others argue that conventional and archival tag recoveries are better described by juveniles either side of the Indian Ocean remaining separate. I provide a synthesis of historical catch and archival tag recovery data to assess the relative support for the two alternative theories about juvenile spatial dynamics. I develop a generalised linear mixed modelling approach that allows more comprehensive assessment of evidence of incomplete mixing in tag recovery data. My analysis supports the hypothesis of juvenile subgroups remaining mostly separate either side of the Indian Ocean. Specifically, I describe evidence of a juvenile population consisting of contingents with distinct migratory behaviour. Recoveries of tags released from longline vessels provide evidence of fidelity to overwintering grounds. I argue the tag recovery data are consistent with contingents governed by the “entrainment” mechanism. An updated model of juvenile spatial dynamics reconciles archival tag recoveries with catch and conventional tag recovery data. The spatial dynamics I propose have important implications for the interpretation of existing datasets and for future research priorities. Contingents governed by entrainment would influence how the population responds to fishing. I argue the entrainment mechanism contributed to the collapse of a commercial fishery for SBT off New South Wales during the 1980s. Additional findings from analyses of tag shedding and growth are included as appendices.

Salmonella can survive and persist in the environment, acting as a reservoir for infection of animals and ultimately humans through the food chain. Biofilm formation contributes to Salmonella survival and compromises cleaning and disinfection. The overall objective of the research detailed in this thesis was to further understand biofilm formation by Salmonella in pig and poultry production environments. Biofilm formation by 132 Salmonella enterica subspecies enterica environmental isolates was studied by phenotypic characterisation, genomic analysis, and representative in vitro biofilm models. Biofilm-forming ability was assessed using the crystal violet microplate assay at environmentally relevant temperatures, with analysis of the influence of serovar, culture conditions and source environment. Bacterial motility, growth kinetics, antimicrobial resistance (AMR) profiles and colony morphology were also studied. A subset of isolates were analysed using whole-genome sequencing and then screened for genes associated with biofilm formation, AMR, and tolerance to quaternary ammonium compounds (QACs), with comparative genomic analysis of phenotype-genotype associations. A subset of S. 13,23:i:- isolates were evaluated for their tolerance to commercial disinfectants using modified coupon-based and metabolic microplate-based assays. Finally, biofilm formation was assessed in a developed in vitro model of a poultry drinking water system (DWS). Most Salmonella isolates (130/132), representing a range of serovars, formed in vitro biofilms to varying degrees. Differences were observed, particularly between serovars, in planktonic and biofilm phenotypes and the prevalence of biofilm-associated genes and AMR determinants. However, any definitive conclusions regarding the factors influencing in vitro biofilm formation could not be reached. The findings suggest that the persistence of S. 13,23:i:- in the hatchery environment and its observed tolerance to Benzalkonium-chloride and QAC-/glutaraldehyde-based disinfectants may be facilitated by biofilm formation and/or the presence of QAC tolerance genes. In the poultry DWS model, biofilms were formed and quantified successfully, despite inoculation with low levels of bacteria. The studies presented in this thesis provide new information about biofilm formation by Salmonella originating from pig and poultry production environments, and the poultry DWS provides a novel in vitro method for the study of biofilm formation under realistic conditions. These findings may be used to inform improved Salmonella control during primary production of food-producing animals.