Health of Antarctic birds: a review of their parasites, pathogens and diseases

Diverse papillomaviruses identified from Antarctic fur seals, leopard seals and Weddell seals from the Antarctic

Papillomaviruses (family Papillomaviridae) are non-enveloped, circular, double-stranded DNA viruses known to infect squamous and mucosal epithelial cells. In the family Papillomaviridae there are 53 genera and 133 viral species whose members infect a variety of mammalian, avian, reptilian, and fish species. Within the Antarctic context, papillomaviruses (PVs) have been identified in Adélie penguins (Pygoscelis adeliae, 2 PVs), Weddell seals (Leptonychotes weddellii, 7 PVs), and emerald notothen (Trematomus bernacchii, 1 PV) in McMurdo Sound and Ross Island in eastern Antarctica. Here we identified 13 diverse PVs from buccal swabs of Antarctic fur seals (Arctocephalus gazella, 2 PVs) and leopard seal (Hydrurga leptonyx, 3 PVs) in western Antarctica (Antarctic Peninsula), and vaginal and nasal swabs of Weddell seals (8 PVs) in McMurdo Sound. These PV genomes group into four genera representing 11 new papillomavirus types, of which five are from two Antarctic fur seals and a leopard seal and six from Weddell seals.

Nearly (?) sterile avian egg in a passerine bird

During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity, and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonized after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate the contribution of these mechanisms to gut microbiota formation in avian embryos. We investigated microbiome of the egg content (day 0; E0-egg), embryonic gut at day 13 (E13) and female faeces in a free-living passerine, the great tit (Parus major), using a methodologically advanced procedure combining 16S rRNA gene sequencing and microbe-specific qPCR assays. Our metabarcoding revealed that the avian egg is (nearly) sterile, but acquires a slightly richer microbiome during the embryonic development. Of the three potentially pathogenic bacteria targeted by qPCR, only Dietzia was found in E0-egg (yet also in negative controls), E13 gut and female samples, which might indicate possible vertical transfer. Unlike in poultry, we have shown that major bacterial colonization of the gut in passerines does not occur before hatching. We emphasize that protocols that carefully check for environmental contamination are critical in studies with low-bacterial biomass samples.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project

Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.

Prevalence of Haemosporidian Parasites in an Arctic Breeding Seabird Species-The Red-Throated Diver (Gavia stellata)

Haemosporida, vector-transmitted blood parasites, can have various effects and may also exert selection pressures on their hosts. In this study we analyse the presence of Haemosporida in a previously unstudied migratory seabird species, the red-throated diver Gavia stellata. Red-throated divers were sampled during winter and spring in the eastern German Bight (North Sea). We used molecular methods and data from a related tracking study to reveal (i) if red-throated divers are infected with Haemosporida of the genera Leucocytozoon, Plasmodium and Haemoproteus, and (ii) how infection and prevalence are linked with the breeding regions of infected individuals. Divers in this study were assigned to western Palearctic breeding grounds, namely Greenland, Svalbard, Norway and Arctic Russia. We found a prevalence of Leucocytozoon of 11.0% in all birds sampled (n = 45), of 33.0% in birds breeding in Norway (n = 3) and of 8.3% in birds breeding in Arctic Russia (n = 25). For two birds that were infected no breeding regions could be assigned. We identified two previously unknown lineages, one each of Plasmodium and Leucocytozoon. Haemosporida have not been detected in birds from Greenland (n = 2) and Svalbard (n = 2). In summary, this study presents the first record of Haemosporida in red-throated divers and reports a new lineage of each, Plasmodium and Leucocytozoon GAVSTE01 and GAVSTE02, respectively.

Influenza A(H11N2) Virus Detection in Fecal Samples from Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarcticus) Penguins, Penguin Island, Antarctica

Influenza A viruses infect a range of host species, including a large variety of mammals and more than a hundred species of birds. A total of 95 avian fecal samples were collected from penguin colonies in the South Shetland Islands, close to the Antarctic Peninsula, and tested by reverse transcription-PCR (RT-PCR) to detect avian influenza viruses (AIVs). Five out of seven samples collected from Penguin Island were positive for AIVs. Analysis of the genomes recovered from four samples revealed the detection of influenza A(H11N2) virus in fecal samples from Adélie penguins (Pygoscelis adeliae) and from a colony of chinstrap penguins (Pygoscelis antarcticus). Bayesian phylogeographic analysis revealed the clustering of all currently available H11N2 samples from Antarctica's avifauna in a single cluster that emerged at least in the early 2010s, suggesting its continued circulation on the continent. Our results reinforce the need for continuous surveillance of avian influenza on the Antarctic continent. IMPORTANCE Although wild birds play a role in the transmission and ecology of avian influenza viruses (AIVs) across the globe, there are significant gaps in our understanding of the worldwide distribution of these viruses in polar environments. In this study, using molecular analysis and full-genome sequencing, we describe the detection of distinct influenza A(H11N2) viruses in fecal samples of penguins in the Southern Shetland Islands, Antarctica. We emphasize the need for virus monitoring as AIVs may have implications for the health of endemic fauna and the potential risk of the introduction of highly pathogenic AIVs to the continent.

Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.

The ocular pyogranulomatous lesion in a Gentoo penguin (Pygoscelis papua) from the Antarctic Peninsula: evaluation of microbiological and histopathological analysis outcomes

In this study, it was aimed to present the results of microbiological, cytological, histopathological, and immunohistochemical analyses of ocular samples from an Antarctic (Ardley Island, King George Island) Gentoo penguin chick (Pygoscelis papua) with a pyogranulomatous lesion in the right eye. Samples were taken from both the healthy left eye and the lesion in the right eye. Conventional culture methods and phenotypic and molecular tests were used for bacterial isolation and identification, respectively. None of the isolates could be identified phenotypically. As a result, four of the five isolates obtained from the right eye were considered to belong to putative novel bacterial species and taxa as their similarity to GenBank data was below 98.75%. The isolates were considered to be Pasteurellaceae bacterium, Corynebacterium ciconiae, Cardiobacteriaceae bacterium, Actinomyces sp., and Dermabacteraceae bacterium. The only isolate from the left eye was identified as Psychrobacter pygoscelis. The cytological analysis demonstrated cell infiltrates composed mostly of degenerate heterophils, reactive macrophages, plasma cells, lymphocytes, and eosinophils. Based on histopathological findings, the lesion was defined as a typical pyogranulomatous lesion. Immunohistochemistry demonstrated that the granuloma was positive for TNF-α, IL-4, MMP-9, IL-1β, and IL-6. This is the first documented report of the unilateral pyogranulomatous ocular lesion in a Gentoo penguin chick, living in its natural habitat in Antarctica. This report also describes the isolation of four bacteria from the infected eye, which are considered to belong to novel Genus, species, or taxa. The primary bacterial pathogen that caused the ocular lesion was not able to be detected and remains unclear.

Risk assessment of SARS-CoV-2 in Antarctic wildlife

The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This pathogen has spread rapidly across the world, causing high numbers of deaths and significant social and economic impacts. SARS-CoV-2 is a novel coronavirus with a suggested zoonotic origin with the potential for cross-species transmission among animals. Antarctica can be considered the only continent free of SARS-CoV-2. Therefore, concerns have been expressed regarding the potential human introduction of this virus to the continent through the activities of research or tourism to minimise the effects on human health, and the potential for virus transmission to Antarctic wildlife. We assess the reverse-zoonotic transmission risk to Antarctic wildlife by considering the available information on host susceptibility, dynamics of the infection in humans, and contact interactions between humans and Antarctic wildlife. The environmental conditions in Antarctica seem to be favourable for the virus stability. Indoor spaces such as those at research stations, research vessels or tourist cruise ships could allow for more transmission among humans and depending on their movements between different locations the virus could be spread across the continent. Among Antarctic wildlife previous in silico analyses suggested that cetaceans are at greater risk of infection whereas seals and birds appear to be at a low infection risk. However, caution needed until further research is carried out and consequently, the precautionary principle should be applied. Field researchers handling animals are identified as the human group posing the highest risk of transmission to animals while tourists and other personnel pose a significant risk only when in close proximity (< 5 m) to Antarctic fauna. We highlight measures to reduce the risk as well as identify of knowledge gaps related to this issue.

External and gastrointestinal parasites of the Franklin's Gull, Leucophaeus pipixcan (Charadriiformes: Laridae), in Talcahuano, central Chile

Parasitological studies of the Franklin's gull, Leucophaeus pipixcan, are scarce, and knowledge about its endoparasites is quite limited. In order to describe its parasitic community, a total of 60 Franklin's gulls were captured in the coastal area in central Chile, using modified Bal-chatri traps. Ectoparasites were collected from all 60 live individuals through inspection of their plumage, while 30 were examined for endoparasites by standard parasitological necropsy. The prevalence of ectoparasites was 78.3%, including the feather mite Zachvatkinia larica (43.3%) and four species of lice: Actornithophilus piceus lari (15.0%), Austromenopon transversum (6.7%), Quadraceps punctatus (10.0%) and Saemundssonia lari (46.7%). Some 25 of 30 (83.3%) of birds necropsied were parasitized with the following helminths: Aporchis sp. (6.7%), Tetrabothrius cylindraceus (56.7%), Cyclophyllidea gen. sp. (3.3%), Profilicollis altmani (56.7%), Eucoleus contortus (10.0%), Cosmocephalus obvelatus (13.3%), Paracuaria adunca (10.0%), Stegophorus sp. (3.3%) and Tetrameres skrjabini (3.3%). To our knowledge, with the exception of P. altmani, these helminths are reported for first time in the Franklin's gull.

A Review of Pathogen Transmission at the Backyard Chicken-Wild Bird Interface

Habitat conversion and the expansion of domesticated, invasive species into native habitats are increasingly recognized as drivers of pathogen emergence at the agricultural-wildlife interface. Poultry agriculture is one of the largest subsets of this interface, and pathogen spillover events between backyard chickens and wild birds are becoming more commonly reported. Native wild bird species are under numerous anthropogenic pressures, but the risks of pathogen spillover from domestic chickens have been historically underappreciated as a threat to wild birds. Now that the backyard chicken industry is one of the fastest growing industries in the world, it is imperative that the principles of biosecurity, specifically bioexclusion and biocontainment, are legislated and implemented. We reviewed the literature on spillover events of pathogens historically associated with poultry into wild birds. We also reviewed the reasons for biosecurity failures in backyard flocks that lead to those spillover events and provide recommendations for current and future backyard flock owners.

Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula

There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.

Identification of Circovirus Genome in a Chinstrap Penguin (Pygoscelis antarcticus) and Adélie Penguin (Pygoscelis adeliae) on the Antarctic Peninsula

Circoviruses infect a variety of animal species and have small (~1.8–2.2 kb) circular single-stranded DNA genomes. Recently a penguin circovirus (PenCV) was identified associated with an Adélie Penguin (Pygoscelis adeliae) with feather disorder and in the cloacal swabs of three asymptomatic Adélie Penguins at Cape Crozier, Antarctica. A total of 75 cloacal swab samples obtained from adults and chicks of three species of penguin (genus: Pygoscelis) from seven Antarctic breeding colonies (South Shetland Islands and Western Antarctic Peninsula) in the 2015−2016 breeding season were screened for PenCV. We identified new variants of PenCV in one Adélie Penguin and one Chinstrap Penguin (Pygoscelis antarcticus) from Port Charcot, Booth Island, Western Antarctic Peninsula, a site home to all three species of Pygoscelid penguins. These two PenCV genomes (length of 1986 nucleotides) share > 99% genome-wide nucleotide identity with each other and share ~87% genome-wide nucleotide identity with the PenCV sequences described from Adélie Penguins at Cape Crozier ~4400 km away in East Antarctica. We did not find any evidence of recombination among PenCV sequences. This is the first report of PenCV in Chinstrap Penguins and the first detection outside of Ross Island, East Antarctica. Given the limited knowledge on Antarctic animal viral diversity, future samples from Antarctic wildlife should be screened for these and other viruses to determine the prevalence and potential impact of viral infections.

Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.

Do humans spread zoonotic enteric bacteria in Antarctica?

Reports of enteric bacteria in Antarctic wildlife have suggested its spread from people to seabirds and seals, but evidence is scarce and fragmentary. We investigated the occurrence of zoonotic enteric bacteria in seabirds across the Antarctic and subantarctic region; for comparison purposes, in addition to seabirds, poultry in a subantarctic island was also sampled. Three findings suggest reverse zoonosis from humans to seabirds: the detection of a zoonotic Salmonella serovar (ser. Enteritidis) and Campylobacter species (e.g. C. jejuni), typical of human infections; the resistance of C. lari isolates to ciprofloxacin and enrofloxacin, antibiotics commonly used in human and veterinary medicine; and most importantly, the presence of C. jejuni genotypes mostly found in humans and domestic animals but rarely or never found in wild birds so far. We also show further spread of zoonotic agents among Antarctic wildlife is facilitated by substantial connectivity among populations of opportunistic seabirds, notably skuas (Stercorarius). Our results highlight the need for even stricter biosecurity measures to limit human impacts in Antarctica.

Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel

In less than one century, the once-abundant Peruvian diving petrel has become the first endangered seabird of the Humboldt Current System (HCS). This small endemic petrel of the South American Pacific coast is now an important indicator of ongoing habitat loss and of the success of local conservation policies in the HCS - an ecoregion designated as a priority for the conservation of global biodiversity. Yet so far, poorly understood life history traits such as philopatry or dispersal ability may strongly influence the species' response to ecosystem changes, but also our capacity to assess and interpret this response. To address this question, we explore the range-wide population structure of the Peruvian diving petrel, and show that this small seabird exhibits extreme philopatric behavior at the island level. Mitochondrial DNA sequences and genome-wide SNP data reveal significant isolation and low migration at very short distances, and provide strong evidence for questioning the alleged recovery in the Peruvian and Chilean populations of this species. Importantly, the full demographic independence between colonies makes local population rescue through migration unlikely. As a consequence, the Peruvian diving petrel appears to be particularly vulnerable to ongoing anthropogenic pressure. By excluding immigration as a major factor of demographic recovery, our results highlight the unambiguously positive impact of local conservation measures on breeding populations; yet at the same time they also cast doubt on alleged range-wide positive population trends. Overall, the protection of independent breeding colonies, and not only of the species as a whole, remains a major element in the conservation strategy for endemic seabirds. Finally, we underline the importance of considering the philopatric behavior and demographic independence of breeding populations, even at very fine spatial scales, in spatial planning for marine coastal areas.

Molecular characterization and lesions associated with Diomedenema diomedeae (Aproctoidea: Desmidocercidae) from grey-headed albatrosses (Thalassarche chrysostoma) on Subantarctic Marion Island

The Prince Edward Islands are Subantarctic islands in the southwest Indian Ocean that are of global importance as seabird nesting sites, and are breeding grounds for five species of albatrosses (Procellariiformes: Diomedeidae). In March-April 2016 numerous chicks of one of these species, the grey-headed albatross (Thalassarche chrysostoma), were found dead at colonies on Marion Island (46°57'S 37°42'E), the larger of the two Prince Edward Islands. Affected chicks were weak, prostrated, apathetic, had drooping wings, and many eventually died while sitting on the nest. Five carcasses were necropsied, and samples were obtained for pathological and parasitological analysis. Four chicks appeared to have died from starvation, and one died due to air-sac helminthiasis, with extensive hemorrhage in the air sacs and multifocal pyogranulomatous air-sacculitis. The air sac parasites were identified as Diomedenema diomedeae (Aproctoidea: Desmidocercidae). Phylogenetic analysis of the nuclear 18S rRNA gene and mitochondrial COI gene confirmed that D. diomedeae belongs to the suborder Spirurina and showed that it is most closely related to the Diplotriaenidae (superfamily Diplotriaenoidea), a family of parasites that infect the air sacs and subcutaneous tissues of a variety of bird species. To our knowledge this is the first record of the occurrence of a nematode in the respiratory tract of an albatross and the first study to provide DNA sequences for a species of the superfamily Aproctoidea.

Avian cholera outbreaks threaten seabird species on Amsterdam Island

Infectious diseases may be particularly critical for the conservation of endangered species. A striking example is the recurrent outbreaks that have been occurring in seabirds on Amsterdam Island for the past 30 years, threatening populations of three Endangered seabird species and of the endemic, Critically Endangered Amsterdam albatross Diomedea amsterdamensis. The bacteria Pasteurella multocida (avian cholera causative agent), and to a lesser extent Erysipelothrix rhusiopathiae (erysipelas causative agent), were both suspected to be responsible for these epidemics. Despite this critical situation, demographic trends were not available for these threatened populations, and the occurrence and characterization of potential causative agents of epizootics remain poorly known. The aims of the current study were to (i) provide an update of population trends for four threatened seabird species monitored on Amsterdam Island, (ii) assess the occurrence of P. multocida, and E. rhusiopathiae in live birds from five species, (iii) search for other infectious agents in these samples and, (iv) isolate and genotype the causative agent(s) of epizooties from dead birds. Our study shows that the demographic situation has worsened substantially in three seabird species during the past decade, with extremely low reproductive success and declining populations for Indian yellow-nosed albatrosses Thalassarche carteri, sooty albatrosses Phoebetria fusca, and northern rockhopper penguins Eudyptes moseleyi. Pasteurella multocida or E. rhusiopathiae were detected by PCR in live birds of all five investigated species, while results were negative for eight additional infectious agents. A single strain of P. multocida was repeatedly cultured from dead birds, while no E. rhusiopathiae could be isolated. These results highlight the significance of P. multocida in this particular eco-epidemiological system as the main agent responsible for epizootics. The study stresses the urgent need to implement mitigation measures to alter the course of avian cholera outbreaks threatening the persistence of seabird populations on Amsterdam Island.

Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing

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Summary of identified viruses associated with Antarctic animals.

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Genomes of Antarctic animals viruses have only been determine in the last five years.

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Limited knowledge of animal virology relative to environmental virology in Antarctica.

The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (adenoviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches. This review summaries the knowledge of animal Antarctic virology and discusses potential future directions with the advent of HTS in virus discovery and ecology.

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

Introduction: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host-microbial interactions. Fecal DNA analysis can provide information about the host's microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins. Material and methods: Six DNA extraction kits were first tested according to the manufacturers' instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces. Results: Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders. Conclusion: This study presents an optimized approach to DNA extraction from challenging avian fecal samples.

Isolation of Campylobacter spp. from Three Species of Antarctic Penguins in Different Geographic Locations

The presence of Campylobacter species was studied in three Antarctic penguin species, Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua). A total of 390 penguins were captured in 12 different rookeries along the Antarctic Peninsula with differences in the amount of human visitation: six colonies were highly visited [Stranger Point, King George Island (P. papua and P. adeliae); Hannah Point, Livingston Island (P. papua and P. antarctica); Deception Island (P. antarctica); and Paradise Bay, Antarctic Peninsula (P. papua)], and six colonies were rarely visited [Devil's Point, Byers Peninsula, Livingston Island (P. papua); Cierva Cove, Antarctic Peninsula (P. papua); Rongé Island (P. papua and P. antarctica); Yalour Island (P. adeliae); and Avian Island (P. adeliae)]. A total of 23 strains were isolated from penguins from nine different rookeries. Campylobacter lari subsp. lari was isolated from eight samples (seven from P. papua and one from P. adeliae); C. lari subsp. concheus from 13 (ten from P. adeliae and three from P. antarctica) and C. volucris from two samples (both from P. papua). We did not find any significant differences in the prevalence of Campylobacter spp. between the populations in highly and rarely visited areas. This is the first report of C. lari subsp. concheus and C. volucris isolation from penguins in the Antarctic region.

Occurrence of blood parasites in seabirds admitted for rehabilitation in the Western Cape, South Africa, 2001-2013

Blood parasites are generally uncommon in seabirds, and knowledge on their epidemiology is further limited by the fact that they often inhabit remote locations that are logistically difficult or expensive to study. We present a long term data set of blood smear examinations of 1909 seabirds belonging to 27 species that were admitted to a rehabilitation centre in Cape Town (Western Cape, South Africa) between 2001 and 2013. Blood parasites were detected in 59% of species (16/27) and 29% of individuals examined (551/1909). The following blood parasites were recorded: Babesia ugwidiensis, Babesia peircei, Babesia sp., Plasmodium sp., Leucocytozoon ugwidi, Hepatozoon albatrossi, Haemoproteus skuae and Spirochaetales. Several of the records are novel host-parasite associations, demonstrating the potential of rehabilitation centres for parasite and disease surveillance, particularly for species infrequently sampled from which no host-specific parasites have been described.

Health evaluation of African penguins (Spheniscus demersus) in southern Africa

The African penguin (Spheniscus demersus) is an endangered seabird that breeds along the coast of Namibia and South Africa, and disease surveillance was identified as a priority for its conservation. Aiming for the establishment of baseline data on the presence of potential pathogens in this species, a comprehensive health assessment (blood smear examination, haematology, biochemistry and serology) was conducted on samples obtained from 578 African penguins at 11 breeding colonies and a rehabilitation centre. There were 68 penguins that were seropositive for at least one of seven pathogens tested: avian encephalomyelitis virus, avian infectious bronchitis virus, avian reovirus, infectious bursal disease virus, Newcastle disease virus, Mycoplasma gallisepticum and Mycoplasma synoviae. All samples were seronegative for avian influenza virus subtypes H5 and H7 and infectious laryngotracheitis virus. The apparent prevalence of Babesia sp. and Borrelia sp. in blood smears was consistent with previous studies. Babesia-infected individuals had a regenerative response of the erythrocytic lineage, an active inflammatory response and hepatic function impairment. These findings indicate that African penguins may be exposed to conservation-significant pathogens in the wild and encourage further studies aiming for the direct detection and/or isolation of these microorganisms.

A PELAGIC OUTBREAK OF AVIAN CHOLERA IN NORTH AMERICAN GULLS: SCAVENGING AS A PRIMARY MECHANISM FOR TRANSMISSION?

Avian cholera, caused by the bacterium Pasteurella multocida , is an endemic disease globally, often causing annual epizootics in North American wild bird populations with thousands of mortalities. From December 2006 to March 2007, an avian cholera outbreak caused mortality in marine birds off the coast of Atlantic Canada, largely centered 300-400 km off the coast of the island of Newfoundland. Scavenging gulls ( Larus spp.) were the primary species detected; however, mortality was also identified in Black-legged Kittiwakes ( Rissa tridactyla ) and one Common Raven ( Corvus corax ), a nonmarine species. The most common gross necropsy findings in the birds with confirmed avian cholera were acute fibrinous and necrotizing lesions affecting the spleen, air sacs, and pericardium, and nonspecific hepatomegaly and splenomegaly. The etiologic agent, P. multocida serotype 1, was recovered from 77 of 136 carcasses examined, and confirmed or probable avian cholera was diagnosed in 85 cases. Mortality observed in scavenging gull species was disproportionately high relative to their abundance, particularly when compared to nonscavenging species. The presence of feather shafts in the ventricular lumen of the majority of larid carcasses diagnosed with avian cholera suggests scavenging of birds that died from avian cholera as a major mode of transmission. This documentation of an outbreak of avian cholera in a North American pelagic environment affecting primarily scavenging gulls indicates that offshore marine environments may be a component of avian cholera dynamics.

MODE OF ATTACHMENT AND PATHOLOGY CAUSED BY PARORCHITES ZEDERI IN THREE SPECIES OF PENGUINS: PYGOSCELIS PAPUA, PYGOSCELIS ADELIAE, AND PYGOSCELIS ANTARCTICA IN ANTARCTICA

We identified and compared gross and microscopic lesions associated with the cestode, Parorchites zederi, in the digestive tracts of three species of penguins (Spheniscidae): the Chinstrap ( Pygoscelis antarctica ), Gentoo ( Pygoscelis papua ), and Adélie penguins ( Pygoscelis adeliae ). The gastrointestinal tracts of 79 recently dead individuals (71 chicks and eight adults) were collected in locations throughout the Antarctic Peninsula during summer field trips in 2006-09. Parorchites zederi was found in the small intestine of 37 animals (47%), and 23 (62%) of these had parasite-associated lesions. The cestodes were either free in the intestinal lumen, clustered within mucosal ulcers, or deeply embedded in the intestinal wall. Histopathologic changes were most severe in adult Gentoo Penguins and included transmural fibrogranulomatous enteritis, hemorrhage, and edema. This report of pathology associated with P. zederi in the digestive tracts of penguins can serve as reference to monitor health in Antarctic birds associated with environmental changes.

Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica)

The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.

Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica

The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations.

First record of Babesia sp. in Antarctic penguins

This is the first reported case of Babesia sp. in Antarctic penguins, specifically a population of Chinstrap penguins (Pygoscelis antarctica) in the Vapour Col penguin rookery in Deception Island, South Shetlands, Antarctica. We collected peripheral blood from 50 adult and 30 chick Chinstrap penguins. Examination of the samples by microscopy showed intraerythrocytic forms morphologically similar to other avian Babesia species in 12 Chinstrap penguin adults and seven chicks. The estimated parasitaemias ranged from 0.25×10(-2)% to 0.75×10(-2)%. Despite the low number of parasites found in blood smears, semi-nested PCR assays yielded a 274 bp fragment in 12 of the 19 positive blood samples found by microscopy. Sequencing revealed that the fragment was 97% similar to Babesia sp. 18S rRNA from Australian Little Penguins (Eudyptula minor) confirming presence of the parasite. Parasite prevalence estimated by microscopy in adults and chicks was higher (24% vs. 23.3%, respectively) than found by semi-nested PCR (16% vs. 13.3% respectively). Although sampled penguins were apparently healthy, the effect of Babesia infection in these penguins is unknown. The identification of Babesia sp. in Antarctic penguins is an important finding. Ixodes uriae, as the only tick species present in the Antarctic Peninsula, is the key to understanding the natural history of this parasite. Future work should address the transmission dynamics and pathogenicity of Babesia sp. in Chinstrap penguin as well as in other penguin species, such as Gentoo penguin (Pygoscelis papua) and Adélie penguin (Pygoscelis adeliae), present within the tick distribution range in the Antarctic Peninsula.

Herpesvirus-like respiratory infection in African penguins Spheniscus demersus admitted to a rehabilitation centre

Rehabilitation is an important strategy for the conservation of the Endangered African penguin Spheniscus demersus, and disease has been raised as a concern in the management of the species, both in the wild and in rehabilitation centres. We report 8 cases of herpesvirus-like respiratory infection in African penguin chicks undergoing rehabilitation between 2010 and 2013 at a facility in Cape Town, South Africa. Infection was confirmed through the identification of viral inclusions in the tracheal epithelium and demonstration of particles consistent with herpesvirus by electron microscopy, whereas virus isolation in eggs, serology and PCR testing failed to detect the virus. Only penguin chicks were affected; they were in poor body condition, and in 2 cases infection occurred prior to admission to the rehabilitation centre. The role played by the herpesvirus-like infection in the overall respiratory disease syndrome is uncertain, due to identification of lesions in only a small proportion of the chicks as well as to the occurrence of other concurrent pathological processes. Further studies are advised to characterise the specific virus involved through the development of sensitive diagnostic methods and to clarify the epidemiology and significance of these infections in wild African penguins.

Morphological, molecular and phylogenetic analyses of the spirurid nematode Stegophorus macronectes (Johnston & Mawson, 1942)

Stegophorus macronectes (Johnston & Mawson, 1942) is a gastrointestinal parasite found in Antarctic seabirds. The original description of the species, which was based only on females, is poor and fragmented with some unclear diagnostic characters. This study provides new morphometric and molecular data on this previously poorly described parasite. Nuclear rDNA sequences (18S, 5.8S, 28S and internal transcribed spacer (ITS) regions) were isolated from S. macronectes specimens collected from the chinstrap penguin Pygoscelis antarctica Forster on Deception Island, Antarctica. Using 18S rDNA sequences, phylogenetic analyses (maximum likelihood, maximum parsimony and Bayesian inference) of the order Spirurida were performed to determine the phylogenetic location of this species. Primer pairs of the ITS regions were designed for genus-level identification of specimens, regardless of their cycle, as an alternative to coprological methods. The utility of this molecular method for identification of morphologically altered specimens is also discussed.

Identification of an avian polyomavirus associated with Adélie penguins (Pygoscelis adeliae)

Little is known about viruses associated with Antarctic animals, although they are probably widespread. We recovered a novel polyomavirus from Adélie penguin (Pygoscelis adeliae) faecal matter sampled in a subcolony at Cape Royds, Ross Island, Antarctica. The 4988 nt Adélie penguin polyomavirus (AdPyV) has a typical polyomavirus genome organization with three ORFs that encoded capsid proteins on the one strand and two non-structural protein-coding ORFs on the complementary strand. The genome of AdPyV shared ~60 % pairwise identity with all avipolyomaviruses. Maximum-likelihood phylogenetic analysis of the large T-antigen (T-Ag) amino acid sequences showed that the T-Ag of AdPyV clustered with those of avipolyomaviruses, sharing between 48 and 52 % identities. Only three viruses associated with Adélie penguins have been identified at a genomic level, avian influenza virus subtype H11N2 from the Antarctic Peninsula and, respectively, Pygoscelis adeliae papillomavirus and AdPyV from capes Crozier and Royds on Ross Island.

Gastrointestinal parasite fauna of Emperor Penguins (Aptenodytes forsteri) at the Atka Bay, Antarctica

In general, the knowledge on parasites infecting Antarctic birds is scarce. The present study intends to extend the knowledge on gastrointestinal parasites of Emperor Penguins (Aptenodytes forsteri) at the Atka Bay, Antarctica. Fecal samples of 50 individual Emperor Penguins were collected at the Atka Bay and analyzed using the sodium-acetate-formaldehyde (SAF) method for the identification of intestinal helminth eggs and/or protozoan parasite stages. In addition, coproantigen ELISAs were performed to detect Cryptosporidium and Giardia infections. Overall, 13 out of 50 penguins proved parasitized (26%). The following stages of gastrointestinal parasites were identified: One Capillaria sp. egg, Tetrabothrius spp. eggs, Diphyllobothrium spp. eggs, and proglottids of the cestode Parorchites zederi. The recorded Capillaria infection represents a new host record for Emperor Penguins. All coproantigen ELISAs for the detection of Cryptosporidium spp. and Giardia spp. were negative. This paper provides current data on parasites of the Emperor Penguin, a protected endemic species of the Antarctica.