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Bacterial pathogens exhibit physiologically distinct forms that enable their survival in an infected host, the environment and following exposure to antimicrobial agents. B. pseudomallei causes the disease melioidosis, which has a high mortality rate and is difficult to treat with antibiotics. The bacterium is endemic to several countries and detected in high abundance in the environment.

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

Abstract Background Helminth infection and infestation in fishes are detrimental and have a major effect on fish health and fish production. Among various factors, parasitic infections are known to modulate antioxidant defences in fish. Similar to other aerobic animals, fish are also susceptible to the effect of reactive oxygen species and thus have well established intrinsic and efficient antioxidant defences. ‘Oxidative stress markers are an important indicator of the physiological state of the parasite and its host’. Indian catfish, Wallago attu is a freshwater fish that serves as the definitive host of the adult piscine trematode Isoparorchis hypselobagri. Our two years prevalence data signifies the intensity of the problem revealing a minimum of 5.5% and a maximum of 54% I. hypselobagri infection in Indian catfish W. attu (unpublished data). The present study aimed to achieve baseline data attributed to changes in some oxidative markers due to parasitic infection. Results During the present study, the level of enzyme activities of Catalase (CAT), Glutathione reductase (GR), Glutathione-S-transferase (GST), Glutathione peroxidase (GPx), Superoxide dismutase (SOD) and lipid peroxidation was investigated to explore the pathogenic impact on the fish host. The level of these oxidative stress markers was monitored in the swim bladder, liver, intestine and muscle of the host. We also recorded the enzyme activities in the parasite I. hypselobagri. Analysis of data revealed an elevation in GST, SOD, GR, GPx and CAT activity in the infected host tissue as compared to the non-infected fish. Further, we observed presence of GST, SOD, GR and GPx enzymes in the parasite I. hypselobagri while CAT did not show any enzyme activity. Conclusions Increased level of enzyme activity in liver, muscle and intestine of infected host has been recorded which indicates increased oxidative stress in the host due to parasitic invasion. The presence of antioxidant enzymes in the parasites suggests an active antioxidant defence system to avoid immune responses to long term survival and establishment in their host.

Aggregated movement and population structure are known in entomopathogenic nematodes, which are obligate insect parasites. Aggregation behavior in the absence of external stimuli suggests communication among individuals, often in the form of trail-following, which has not been shown by nematodes of any kind. Interactions among individuals are an essential basis of following behaviors and can have significant fitness consequences. We explored intraspecific and interspecific interactions among three Steinernema species (S. glaseri, S. carpocapsae, and S. feltiae) in terms of trail following, and fitness outcomes of following heterospecific individuals. We found that the following behavior is context dependent. Following behavior among conspecifics was significantly increased when the lead nematode had prior contact with host cuticle. However, we did not find a clear association between the following response to heterospecific IJs and their reproductive success in a co-infected host.

The foodborne pathogen Salmonella is responsible for a wide variety of pathologies depending on the infected host, the infecting serovars, and its set of virulence factors. However, the implication of each of these virulence factors and their role in the specific host-pathogen interplay are not fully understood.

Lyme borreliosis is a multisystemic disease caused by the pleomorphic bacteria of the Borrelia burgdorferi sensu lato complex. The exact mechanisms for the infection to progress into a prolonged sequelae of the disease are currently unknown, although immune evasion and persistence of the bacteria in the host are thought to be major contributors. The current study investigated B. burgdorferi infection processes in two human cell lines, both non-immune and non-phagocytic, to further understand the mechanisms of infection of this bacterium. By utilizing light, confocal, helium ion, and transmission electron microscopy, borrelial infection of chondrosarcoma (SW1353) and dermal fibroblast (BJ) cells were examined from an early 30-min time point to a late 9-days post-infection. Host cell invasion, viability of both the host and B. burgdorferi, as well as, co-localization with lysosomes and the presence of different borrelial pleomorphic forms were analyzed. The results demonstrated differences of infection between the cell lines starting from early entry as B. burgdorferi invaded BJ cells in coiled forms with less pronounced host cell extensions, whereas in SW1353 cells, micropodial interactions with spirochetes were always seen. Moreover, infection of BJ cells increased in a dose dependent manner throughout the examined 9 days, while the percentage of infection, although dose dependent, decreased in SW1353 cells after reaching a peak at 48 h. Furthermore, blebs, round body and damaged B. burgdorferi forms, were mostly observed from the infected SW1353 cells, while spirochetes dominated in BJ cells. Both infected host cell lines grew and remained viable after 9 day post-infection. Although damaged forms were noticed in both cell lines, co-localization with lysosomes was low in both cell lines, especially in BJ cells. The invasion of non-phagocytic cells and the lack of cytopathic effects onto the host cells by B. burgdorferi indicated one mechanism of immune evasion for the bacteria. The differences in attachment, pleomorphic form expressions, and the lack of lysosomal involvement between the infected host cells likely explain the ability of a bacterium to adapt to different environments, as well as, a strategy for persistence inside a host.

Interkingdom competition occurs between hymenopteran parasitoids and insect viruses sharing the same insect hosts. It has been assumed that parasitoid larvae die with the death of the infected host or as result of competition for host resources. Here we describe a gene family, parasitoid killing factor (pkf), that encodes proteins toxic to parasitoids of the Microgastrinae group and determines parasitism success. Pkfs are found in several entomopathogenic DNA virus families and in some lepidopteran genomes. We provide evidence of equivalent and specific toxicity against endoparasites for PKFs found in entomopoxvirus, ascovirus, baculovirus, and Lepidoptera through a mechanism that elicits apoptosis in the cells of susceptible parasitoids. This highlights the evolutionary arms race between parasitoids, viruses, and their insect hosts.

Bacteriophages that have integrated their genomes into bacterial chromosomes, termed prophages, are widespread across bacteria. Prophages are key components of bacterial genomes, with their integration often contributing novel, beneficial, characteristics to the infected host. Likewise, their induction—through the production and release of progeny virions into the surrounding environment—can have considerable ramifications on bacterial communities. Yet, not all prophages can excise following integration, due to genetic degradation by their host bacterium. Here, we present hafeZ, a tool able to identify 'active' prophages (i.e. those undergoing induction) within bacterial genomes through genomic read mapping. We demonstrate its use by applying hafeZ to publicly available sequencing data from bacterial genomes known to contain active prophages and show that hafeZ can accurately identify their presence and location in the host chromosomes. Availability and Implementation: hafeZ is implemented in Python 3.7 and freely available under an open-source GPL-3.0 license from https://github.com/Chrisjrt/hafeZ. Bugs and issues may be reported by submitting them via the hafeZ github issues page.