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Diet in fish is influenced by multiple factors including nutritional requirements, trophic morphology and spatial and temporal variation in resource availability. We examined spatial variation in trophic resources on substrata grazed by scarinine parrotfishes by combining quantitative microhistology with 16S and 18S small subunit rRNA barcoding of feeding substrata in six parrotfish species on outer-shelf reefs of the Great Barrier Reef, Australia. We then compared four of these taxa with conspecific data from mid-shelf reefs differing in incident wave energy, parrotfish assemblage structure and benthic cover of hard corals, crustose coralline algae (CCA) and macroalgae. The dominant biota on outer-shelf feeding substrata in terms of both surface coverage and frequency of occurrence were filamentous cyanobacteria. The density of filamentous cyanobacteria on outer-shelf feeding substrata as measured by microscope did not differ either among the six parrotfish species or within-species cross-shelf. Endolithic and epilithic filamentous cyanobacteria from the order Nostocales were the most frequently observed filamentous cyanobacteria, suggesting that these represent a key feeding target for these parrotfishes. In addition to filamentous Nostocales cyanobacteria, taxa that were consistently present on both mid-shelf and outer-shelf feeding substrata were the euendolithic micro-chlorophytes Ostreobium and Phaeophila, diatoms, fungi, CCA, Peyssonnelia, dinoflagellates of the family Symbiodiniaceae, the sponge taxa Clionaida and Poecilosclerida and the filamentous algae Sphacelaria and Polysiphonia. Our results reveal key nutritional drivers underlying feeding by parrotfish on carbonate reefs and provide further support for the hypothesis that microscopic photoautotrophs are a major dietary target for grazing parrotfishes. [ABSTRACT FROM AUTHOR]

Parrotfish are key agents of bioerosion and sediment production in coral reef ecosystems; however, their dietary targets and therefore potential sources of variation in carbonate cycling lack resolution. Here we address this knowledge shortfall in our current understanding of parrotfish diets by testing the concept that protein-rich micro-photoautotrophs are the target prey for many Scarinine parrotfishes. We focus at fine spatial scales on the feeding substrata of 12 syntopic Indo-Pacific parrotfish species at mid-shelf sites around Lizard Island, Great Barrier Reef, Australia. We followed individual parrotfish on snorkel until biting was observed, and then extracted a reef core around each bite. The surface of each bite core was scraped to ~1 mm for quantitative microscopic analysis (up to 630 × magnification) and for 16S and 18S rRNA metabarcoding. The most dominant photoautotrophic group in terms of surface cover was filamentous cyanobacteria, followed by crustose coralline algae. Epiphytic, epilithic, endophytic and endolithic filamentous cyanobacteria were consistent bite core biota. Although the density of filamentous cyanobacteria on bite cores was largely consistent among the 12 parrotfish species, the quantitative microscopic data and rRNA metabarcoding revealed distinct differences between parrotfish species in the taxonomic composition of core biota. Our data provide further evidence that these syntopic parrotfish species partition feeding resources. [ABSTRACT FROM AUTHOR]

Chaetopteridae forms a monophyletic clade showing an uncertain position within Annelida. The family has 75 ubiquitous species within four genera that cluster in two well-supported clades (Chaetopterus–Mesochaetopterus and Spiochaetopterus–Phyllochaetopterus) and includes several cryptic species complexes. Based on integrative taxonomy and supported by citizen science, here we describe one new and two unnamed species of Caribbean chaetopterids. Partial sequences from the nuclear 18S rRNA and mitochondrial Cytochrome Oxidase I genes of all known chaetopterid genera allowed us to (1) discuss the phylogeny of the family and (2) assign the three species into Mesochaetopterus (two) and Phyllochaetopterus (one). Mesochaetopterus stinapa, sp. nov. clearly diverged from all species of the genus, whereas Mesochaetopterus aff. xerecus forms a separate clade with Mesochaetopterus rogeri (Europe) and Mesochaetopterus xerecus (Brazil). Phyllochaetopterus aff. verrilli forms a separate clade with Phyllochaetopterus arabicus (Red Sea) and the closely related sequences from Hawai’i, Australia and French Polynesia attributed to Phyllochaetopterus verrilli (or cf. verrilli). Despite observing differences in morphology (e.g. palp colour pattern, presence or absence of eyespots, chaetal morphology and arrangement) and biogeographical distributions, only the erection of M. stinapa as a new species is well supported by the genetic distance, barcoding gap and species discrimination analyses. Our results emphasise the existence of cryptic species complexes within Mesochaetopterus and Phyllochaetopterus, whose taxonomy will require further morphological, biogeographical and molecular data to be resolved. [ABSTRACT FROM AUTHOR]

Australian wild deer populations have significantly expanded in size and distribution in recent decades. Due to their role in pathogen transmission, these deer populations pose a biosecurity risk to the livestock industry. However, little is known about the infection status of wild deer in Australia. The intestinal parasite Entamoeba bovis has been previously detected in farm and wild ruminants worldwide, but its epidemiology and distribution in wild ruminants remain largely unexplored. To investigate this knowledge gap, faecal samples of wild deer and domestic cattle from south-eastern Australia were collected and analysed for the presence of Entamoeba spp. using PCR and phylogenetic analysis of the conserved 18S rRNA gene. E. bovis parasites were detected at high prevalence in cattle and wild deer hosts, and two distinct Entamoeba ribosomal lineages (RLs), RL1 and RL8, were identified in wild deer. Phylogenetic analysis further revealed the existance of a novel Entamoeba species in sambar deer and a novel Entamoeba RL in fallow deer. While we anticipated cross-species transmission of E. bovis between wild deer and cattle, the data generated in this study demonstrated transmission is yet to occur in Australia. Overall, this study has identified novel variants of Entamoeba and constitutes the first report of Entamoeba in fallow deer and sambar deer, expanding the host range of this parasite. Epidemiological investigations and continued surveillance of Entamoeba parasites in farm ruminants and wild animals will be required to evaluate pathogen emergence and transmission to livestock. [ABSTRACT FROM AUTHOR]

A new Isospora (Apicomplexa:Eimeriidae) species is described from a single yellow-throated miner bird ( Manorina flavigula ) (subspecies M. f. wayensis ) in Western Australia. Sporulated oocysts (n = 32) of this isolate are spherical to subspherical, 22.8 (20.3–23.8) × 18.3 (17.7–18.7) μm, with a shape index (length/width) of 1.25 (1.2–1.3); and a smooth and bilayered oocyst wall, 1.3 μm thick (outer layer 0.9 μm, inner 0.4 μm). A polar granule is present, but the micropyle and oocyst residuum are absent. The sporocysts are lemon-shaped, 15.5 (14.6–15.8) × 9.5 (9.5–10.2) μm, with a shape index of 1.6. Stieda and substieda bodies are present, the Stieda body being knob-like and the substieda body being subspherical-shaped. A sporocyst residuum is present and composed of numerous granules of different size scattered among the sporozoites, a spheroid or subspheroid refractile body is present in the sporozoite. Morphologically, the oocysts from this isolate are different from those of all known valid Isospora spp. Molecular analysis was conducted at 3 loci; the 18S and 28S ribosomal RNA and the mitochondrial cytochrome oxidase (COI) gene. At the 18S locus, this new isolate exhibited 99.2% similarity to Isospora gryphoni and three other Isospora spp. Further analysis of a subgroup of 300 bp long 18S sequences (8), including Isospora anthochaerae was conducted. This new isolate grouped in a clade with I. anthochaerae and exhibited 99.3% similarity. At the 28S locus, this new isolate grouped with I. anthochaerae with which it shared 99.1% similarity. At the COI locus, this new isolate exhibited 96.8% similarity to Isospora sp. JCI-2015 from a spectacled warbler ( Sylvia conspicillata ) in Spain. Further analysis from a subgroup of shorter COI sequences (n = 13) was performed and this new isolate exhibited 99.1% similarity to I. anthochaerae . Based on morphological and molecular data, this isolate is a new species of Isospora , which is named Isospora manorinae n. sp. after its host, the yellow-throated miner ( Manorina flavigula wayensis ). [ABSTRACT FROM AUTHOR]

The prevalence of Eimeria in sheep in Australia has not been well described, therefore a quantitative PCR (qPCR) was developed, validated and used to study the prevalence and oocyst concentration in lamb faecal samples at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected from approximately 1182 lambs across the 4 states and screened for the presence of Eimeria using this qPCR at the 18S ribosomal RNA (rRNA) locus. A subset of positives was typed by sequence analysis at the 18S locus. The overall prevalence was 18.1% (95% CI 16.8–19.3%) and of the 616 positives, 118 were successfully genotyped. The prevalence of Eimeria was highest in NSW and peaked at 70% during the post-weaning period. The range of oocyst shedding per gram of faeces (g −1 ) at weaning, post-weaning and pre-slaughter overall across all states was 23–2.1 × 10 7 , 23–1.3 × 10 7 and 23–2.1 × 10 5 , respectively. Median Eimeria shedding g −1 was higher during post-weaning (1.1 × 10 3 ) and pre-slaughter (1.1 × 10 3 ) than during weaning (206). The following species were identified: Eimeria crandallis , Eimeria ahsata , Eimeria ovinoidalis , Eimeria weybridgensis and Eimeria cylindrica . Of these, E. crandallis and E. ovinoidalis , the most pathogenic species in sheep were responsible for 58.5% of infections typed. This highlights a need for further research to quantify the production impacts of Eimeria in sheep. [ABSTRACT FROM AUTHOR]

The prevalence of Cryptosporidium in sheep in the eastern states of Australia has not been well described, therefore a study of the prevalence, oocyst concentration, species and subtypes of Cryptosporidium were assessed from lamb faecal samples at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected from approximately 1182 lambs across the four states and screened for the presence of Cryptosporidium using a quantitative PCR (qPCR) at the actin locus. Positives were typed at the 18S locus and at a second locus using C. parvum and C. hominis specific qPCR primers. The overall prevalence was 16.9% (95% CI: 15.6–18.1%) and of the 576 positives, 500 were successfully genotyped. In general, the prevalence of Cryptosporidium was higher in WA than the eastern states. Cryptosporidium prevalence peaked at 43.9% and 37.1% at Pingelly (WA2) and Arthur River (WA1), respectively during weaning and at Pingelly (WA2) during pre-slaughter (36.4%). The range of oocyst shedding at weaning overall across all states was 63–7.9×106 and the median was 3.2×104 oocystsg−1. The following species were identified; C. xiaoi (69%—345/500), C. ubiquitum (17.6%—88/500), C. parvum (9.8%—49/500), C. scrofarum (0.8%—4/500), mixed C. parvum and C. xiaoi (2.4%—12/500), C. andersoni (0.2%—1/500) and sheep genotype 1 (0.2%—1/500). Subtyping of C. parvum and C. ubiquitum isolates identified IIa and IId subtype families within C. parvum (with IId as the dominant subtype) and XIIa within C. ubiquitum. This is the first published description of C. parvum subtypes detected in lambs in Australia. [ABSTRACT FROM AUTHOR]

Abstract: A total of 421 fecal samples from a variety of captive and wild marsupial hosts in Western Australia, Victoria and South Australia were screened for the presence of Giardia species/genotypes using PCR and sequence analysis of a fragment of the 18S rRNA gene. Giardia spp. were identified in 13.4% (28/209) of samples from captive marsupials and 13.7% (29/212) of samples from wild marsupials. Sequence analysis at the 18S locus identified the zoonotic Giardia duodenalis Genotypes A and B in both captive and wild marsupials. Eight isolates were typed as genotype B3 and B4 at the gdh locus, although 7/8 were typed as genotype A at the 18S rRNA locus. The possible reasons for this discordance are discussed. This is the first report of genotype B and only the second report of genotype A in marsupials. As some of the genotype B isolates were identical to human-derived Giardia gdh sequences, these results suggest that marsupials in catchments may pose a public health risk and therefore warrant further investigation. [Copyright &y& Elsevier]

Wild rabbits ( Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas ( Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR-based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome-specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits. [ABSTRACT FROM AUTHOR]

An Isospora species, Isospora amphiboluri, originally described by Canon in 1967 and later by McAllister et al. (1995), was isolated from a central netted dragon (Ctenophorus nuchalis) housed at a wildlife rehabilitation centre in Perth, Western Australia. Sporulated oocysts of Isospora amphiboluri (n = 30) are spherical, 24.2 (26.5–23.0) μm in length and 23.9 (22.4–25.9) μm in width, with a shape index of 1.01. The bilayered oocyst wall is smooth and light-yellow in color. Polar granule, oocyst residuum and micropyle are absent. The sporocysts are lemon-shaped, 15.7 (15.2–18.0) × 10.2 (8.9–11.2) μm, with a shape index (length/width) of 1.53. Stieda and substieda bodies are present, the Stieda body being small and hemidome-shaped and the substieda half-moon-shaped. Each sporocyst contains four vermiform sporozoites arranged head to tail. The sporozoites are 11.7 (9.9–16.2) × 3.0 (2.4–3.5) μm, with a shape index (length/width) of 3.87. A sporocyst residuum is present. Sporozoites contain a central nucleus with a finely distributed granular residuum. Comparison of oocyst measurements and their features with other valid Isospora species from hosts in the Agamid family confirmed that this Isospora species is Isospora amphiboluri. Molecular characterization of I. amphiboluri at the 18S rRNA and MTCOI loci showed the highest similarity with I. amphiboluri from the central bearded dragon, 99.8% and 99.7% respectively. This is the first report of I. amphiboluri from a central netted dragon in Australia. [Display omitted] • Description of I. amphiboluri in a new host - central netted dragon. • Morphology study: With the same features of I. amphiboluri reported before. • Genetic study: 99.8% and 99.7% similar to I. amphiboluri at 18S and mtCOI locus, respectively. • First time identified I. amphiboluri in Australia. [ABSTRACT FROM AUTHOR]

Cryptosporidium species are a major cause of diarrhoea worldwide. In the present study, a retrospective analysis of 109 microscopically Cryptosporidium-positive faecal specimens from Western Australian patients, collected between 2015 and 2018 was conducted. Sequence analysis of the 18S rRNA and the 60 kDa glycoprotein (gp60) gene loci identified four Cryptosporidium species: C. hominis (86.2%, 94/109), C. parvum (11.0%, 12/109), C. meleagridis (1.8%, 2/109) and C. viatorum (0.9%, 1/109). Subtyping at the gp60 locus identified a total of 11 subtypes including the emergence of the previously rare C. hominis IfA12G1R5 subtype in 2017 as the dominant subtype (46.7%, 21/45). This subtype has also recently emerged as the dominant subtype in the United States but the reasons for its emergence are unknown. This is also the first report of C. viatorum in humans in Australia and a novel subtype (XVaA3g) was identified in the one positive patient., (Copyright © 2019 Elsevier B.V. All rights reserved.)

A new Isospora (Apicomplexa: Eimeriidae) species is described from an Australian raven (Corvus coronoides) in Western Australia. Sporulated oocysts (n = 21) are ovoid, 21.2 (18.4-23.9) μm in length and 18.8 (16.9-20.6) μm in width, with a shape index of 1.13. The bi-layered oocyst wall is smooth and colourless, 1.2 μm thick. A polar granule and oocyst residuum is present, but the micropyle is absent. The sporocysts are ovoid-shaped, 16.3 (13.7-18.9) × 10.7 (8.4-12.9) μm, with a shape index (length/width) of 1.52. Stieda and substieda bodies are present, the Stieda body being small and hemidome-shaped and the substieda being indistinct. Each sporocyst with four vermiform sporozoites arranged head to tail. The sporozoites are crescent-shaped, 9.0 (8.9-9.2) × 2.7 (2.3-3.0) μm, with a shape index (length/width) of 3.33. The sporocyst residuum is present. The isolated oocysts had different morphological characteristics when compared with all known Isospora spp. The coccidian parasite was analysed at the 18S and 28S ribosomal RNA and the mitochondrial cytochrome oxidase (COI) loci. At the 18S locus, I. coronoideae n. sp. exhibited 98.9% similarity to I. neochmiae from a captive-bred red-browed finch (KT224380) and Isospora sp. from domestic pigeons (Columba livia domestica) (AB757860), 98.5% similarity to I. gryphoni (AF080613) from an American goldfinch and 98.3% similarity to I. manorinae (KT224379) from a yellow-throated miner. At the 28S locus, it exhibited 95.4% and 94.8% similarity to I. manorinae (KT224381) and I. anthochaerae (KF766053), respectively. At the COI locus, it exhibited 99.8% and 99.7% similarity to I. butcherae (KY801687) and I. neochmiae (KT224378), respectively. Based on morphological and molecular data, this isolate is a new species of Isospora, which is named Isospora coronoideae n. sp. after its host, the Australian raven (Corvus coronoides) (Passeriformes: Corvidae) (Linnaeus, 1758).

The nematodes Abbreviata antarctica von Linstow, 1899, and Abbreviata hastaspicula Jones, 1979 , are predominant spirurid nematodes in species of Varanus lizards in Australia. However, genetic knowledge of these two species of nematode is lacking. In this study, nematodes removed from Varanus gouldii were examined using integrated morphologic and molecular methods. We extracted DNA from A. hastaspicula and A. antarctica for PCR and sequencing. Specific 18S small subunit ribosomal RNA (rRNA) primers were designed on the basis of existing 18S rRNA sequences of Physalopterinae strains. Species of Abbreviata, which are closely similar morphologically, may be misidentified, especially the larvae of different species of Abbreviata that cannot be differentiated. The findings of this study will improve the accuracy in identification of A. hastaspicula and A. antarctica, both morphologically and molecularly.

Recent molecular and sero-surveillance studies of the tick-borne pathogen Hepatozoon canis have identified new hosts, potential vector species, and have revealed that H. canis is more widespread than previously thought. We report the first diagnosed case of canine hepatozoonosis in Australia from a Maremma Sheepdog in Sarina, Queensland. Hepatozoon canis was detected with blood smear examination and 18S rRNA sequencing. It is unknown when or how the organism was introduced into Australia, which raises questions about border biosecurity policies and the H. canis infection status of its potential vectors and hosts in Australia. Surveillance for this pathogen is required to determine whether H. canis has established in Australia., (Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.)