Nematode community dynamics in Australian vertebrates: impacts of contemporary captive management practices

Captive management practices may alter host-parasite ecology, driving the emergence of disease in species of commercial or conservation significance. The development of sustainable, integrated techniques for the control of potentially pathogenic taxa requires an understanding of the factors influencing parasite transmission, establishment and intracommunity competition in captive environments. In this study, the community dynamics of parasitic nematodes (suborders; Trichocephalatina and Strongylida) were examined under two captive management regimes; intensively farmed saltwater crocodiles (Crocodylusporosus) and non-commercial populations of red kangaroos (Macropus rufus). Four aspects of parasite ecology were investigated; genetic diversity within nematode populations, the role of extrinsic environmental factors in mediating nematode-associated helminthosis, the development of high-throughput molecular methods for characterising parasite communities and structuring of nematode assemblages within and between conspecific host populations. 18S ribosomal RNA gene sequences (n=55) were obtained from Paratrichosoma sp (nematoda: Trichosomoididae) eggs present in the epidermis of C. porosus. The level of genetic diversity distributed within the Paratrichosoma sp population was relatively high (241 variable positions in the 1094 bp alignment), suggesting that rates of nucleotide basepair substitution are accelerated in this genus of nematodes. A significant negative linear relationship (P=0.011, R2=0.327) was identified between mean monthly rainfall and the monthly incidence of Paratrichosoma-associated helminthosis. The accuracy with which terminal restriction fragment length polymorphism (TRFLP) analysis, was capable of distinguishing between the constituent taxa of macropodid parasite communities was assessed by comparing sequence data from ~20 species of nematode (suborder Strongylida). Our results demonstrate that, with fluorescent labelling of the forward and reverse terminal restriction fragments (T-RFs) of the ITS+ rDNA region, the restriction endonuclease Hinf1 was capable of generating species specific T-RFLP profiles. A notable exception was within the genus Cloacina, in which closely related species often shared identical T-RFs. This may be a consequence of the group’s comparatively recent evolutionary radiation. The strongylid nematode communities of M. rufus were characterised across seven captive sites, using T-RFLP and Illumina MiSeq next-generation sequencing of the ITS2 locus. The prevalence (P=<0.001) and mean intensity (df=6, F=17.494, P=<0.001) of strongylid nematode infection differed significantly between the sites. Significant levels of parasite community structure were observed (ANOSIM, P = 0.01), with most of the variation being distributed within, rather than between, captive sites. The range of nematode taxa that occured in captive red kangaroos appeared to differ from that of wild conspecifics, with representatives of the genus Cloacina, a dominant nematode parasite of the macropodid forestomach, being detected at only two of the seven study sites. This study also provides the first evidence for the presence of the genus Trichostrongylus in a macropodid marsupial. Our results demonstrate that contemporary species management practices may exert a profound influence on the structure of parasite communities in captive systems. Results from this thesis demonstrate a strong anthropogenic influence on the structure of nematode assemblages in captive host populations. Studies of this nature will contribute to the development of more effective captive management practices by elucidating the factors influencing community structure and infection dynamics in a group of parasites that can exert a profound influence on the health and viability of their host populations.