Novel lambdapapillomavirus in northern sea otters Enhydra lutris kenyoni, associated with oral hyperplastic nodules

A novel papillomavirus (PV) associated with hyperplastic nodules scattered over the muco-cutaneous border of the oral cavity of a dead, wild, subadult northern sea otter Enhydra lutris kenyoni (NSO) in 2004 in Homer, Alaska, USA, was genetically characterized. Primers for the amplification of 2 large overlapping DNA fragments that contained the complete genome of the NSO PV were designed. Sanger methodology generated sequences from which new specific primers were designed for the primer-walking approach. The NSO PV genome consists of 8085 nucleotides and contains an early region composed of E6, E7, E1, and E2 open reading frames (ORFs), an E4 ORF (contained within E2) lacking an in-frame proximal ATG start codon, an unusually long (907 nucleotide) stretch lacking any ORFs, a late region that contains the capsid genes L2 and L1, and a non-coding regulatory region (ncRR). This NSO PV has been tentatively named Enhydra lutris kenyoni PV2 (ElkPV2). Pairwise and multiple sequence alignments of the complete L1 ORF nucleotides and concatenated E1-E2-L1 amino acid sequences showed that the NSO PV is a novel PV, phylogenetically most closely related to southern sea otter PV1. The carboxy end of the E6 oncoprotein does not contain the PDZ-binding motif with a strong correlation with oncogenicity, suggesting a low-risk PV, which is in agreement with histopathological findings. However, the ElkPV2 E7 oncoprotein does contain the retinoblastoma (pRb) binding domain LXCXE (LQCYE in ElkPV2), associated with oncogenicity in some high-risk PVs. Further studies on the prevalence and clinical significance of ElkPV2 infections in NSO are needed.

Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis)

Erysipelothrix spp., including E. rhusiopathiae, are zoonotic bacterial pathogens that can cause morbidity and mortality in mammals, fish, reptiles, birds, and humans. The southern sea otter (SSO; Enhydra lutris nereis) is a federally-listed threatened species for which infectious disease is a major cause of mortality. We estimated the frequency of detection of these opportunistic pathogens in dead SSOs, described pathology associated with Erysipelothrix infections in SSOs, characterized the genetic diversity and antimicrobial susceptibility of SSO isolates, and evaluated the virulence of two novel Erysipelothrix isolates from SSOs using an in vivo fish model. From 1998 to 2021 Erysipelothrix spp. were isolated from six of >500 necropsied SSOs. Erysipelothrix spp. were isolated in pure culture from three cases, while the other three were mixed cultures. Bacterial septicemia was a primary or contributing cause of death in five of the six cases. Other pathology observed included suppurative lymphadenopathy, fibrinosuppurative arteritis with thrombosis and infarction, bilateral uveitis and endophthalmitis, hypopyon, petechia and ecchymoses, mucosal infarction, and suppurative meningoencephalitis and ventriculitis. Short to long slender Gram-positive or Gram-variable bacterial rods were identified within lesions, alone or with other opportunistic bacteria. All six SSO isolates had the spaA genotype-four isolates clustered with spaA E. rhusiopathiae strains from various terrestrial and marine animal hosts. Two isolates did not cluster with any known Erysipelothrix spp.; whole genome sequencing revealed a novel Erysipelothrix species and a novel E. rhusiopathiae subspecies. We propose the names Erysipelothrix enhydrae sp. nov. and Erysipelothrix rhusiopathiae ohloneorum ssp. nov. respectively. The type strains are E. enhydrae UCD-4322-04 and E. rhusiopathiae ohloneorum UCD-4724-06, respectively. Experimental injection of tiger barbs (Puntigrus tetrazona) resulted in infection and mortality from the two novel Erysipelothrix spp. Antimicrobial susceptibility testing of Erysipelothrix isolates from SSOs shows similar susceptibility profiles to isolates from other terrestrial and aquatic animals. This is the first description of the pathology, microbial characteristics, and genetic diversity of Erysipelothrix isolates recovered from diseased SSOs. Methods presented here can facilitate case recognition, aid characterization of Erysipelothrix isolates, and illustrate assessment of virulence using fish models.

Molecular and morphological confirmation of Profilicollis altmani as the cause of acanthocephalan peritonitis in California sea otters (Enhydra lutris nereis)

Acanthocephalan peritonitis (AP; trans-intestinal migration of acanthocephalan parasites into the peritoneal cavity resulting in severe peritonitis), is a common cause of mortality in southern sea otters (Enhydra lutris nereis). Although Profilicollis spp. acanthocephalans have been implicated in these infections, the species causing AP has been an important unresolved question for decades. We used morphological and molecular techniques to characterize acanthocephalans from the gastrointestinal (GI) tract and peritoneal omentum of eighty necropsied southern sea otters. Only P. altmani was found to have perforated through the intestinal wall and migrated into the peritoneal cavity of examined sea otters, resulting in AP. Morphological and molecular criteria confirmed that Profilicollis kenti was synonymous with P. altmani. A second Profilicollis sp., likely P. botulus, was present only in the intestinal lumen, did not penetrate through the intestinal wall, and was not associated with AP.

Macronutrient composition of sea otter diet with respect to recolonization, life history, and season in southern Southeast Alaska

The sea otter (Enhydra lutris) population of Southeast Alaska has been growing at a higher rate than other regions along the Pacific coast. While good for the recovery of this endangered species, rapid population growth of this apex predator can create a human-wildlife conflict, negatively impacting commercial and subsistence fishing. Previous foraging studies throughout the sea otter range have shown they will reduce invertebrate prey biomass when recolonizing an area. The goal of this study was to examine and quantify the energy content of sea otter diets through direct foraging observations and prey collection. Our study area, Prince of Wales Island in southern Southeast Alaska, exhibits a gradient of sea otter recolonization, thus providing a natural experiment to test diet change in regions with different recolonization histories. Sea otter prey items were collected in three seasons (spring, summer, and winter) to measure caloric value and lipid and protein content. We observed 3523 sea otter dives during the spring and summer. A majority of the sea otter diet consisted of clams. Sea otters in newly recolonized areas had lower diet diversity, higher energetic intake rates (EIR, kcal/min), and prey had higher energy content (kcal/g). Females with pups had the highest diet diversity and the lowest EIR. Sea otter EIR were higher in the fall and winter vs. spring and summer. Sea cucumber energy and lipid content appeared to correspond with times when sea otters consumed the highest proportion of sea cucumbers. These caloric variations are an important component of understanding ecosystem-level effects sea otters have in the nearshore environment.

Mercury content in the fur of sea otters (Enhydra lutris) from the Commander Islands

The sea otter (Enhydra lutris) is a keystone species in the ecosystem which is currently in depression in Russia. The objectives of this study were to: (1) establish if the sea otters from the Commander Islands have hazardous levels of mercury (Hg) in their fur; (2) assess Hg pollution in sea otters during a period of high abundance and population depression; (3) identify the age and sex differences in sea otters by Hg content. The sea otters were classified from no to low risk for Hg health effects. Differences in Hg content during periods of low and high population size were not statistically significant. Hg concentrations in adult sea otters were significantly higher than in the young, and higher in males than in females. This study presents the first data on Hg content in sea otters' fur and the first estimate of Hg contamination for the Commander Islands population.

Anatomy of the sense of touch in sea otters: Cutaneous mechanoreceptors and structural features of glabrous skin

Sea otters (Enhydra lutris) demonstrate rapid, accurate tactile abilities using their paws and facial vibrissae. Anatomical investigations of neural organization in the vibrissal bed and somatosensory cortex coincide with measured sensitivity, but no studies describe sensory receptors in the paws or other regions of glabrous (i.e., hairless) skin. In this study, we use histology to assess the presence, density, and distribution of mechanoreceptors in the glabrous skin of sea otters: paws, rhinarium, lips, and flipper digits, and we use scanning electron microscopy to describe skin-surface texture and its potential effect on the transduction of mechanical stimuli. Our results confirm the presence of Merkel cells and Pacinian corpuscles, but not Meissner corpuscles, in all sea otter glabrous skin. The paws showed the highest density of Merkel cells and Pacinian corpuscles. Within the paw, relative densities of mechanoreceptor types were highest in the distal metacarpal pad and digits, which suggests that the distal paw is a tactile fovea for sea otters. In addition to the highest receptor density, the paw displayed the thickest epidermis. Rete ridges (epidermal projections into the dermis) and dermal papillae (dermal projections into the epidermis) were developed across all glabrous skin. These quantitative and qualitative descriptions of neural organization and physical features, combined with previous behavioral results, contribute to our understanding of how structure relates to function in the tactile modality. Our findings coincide with behavioral observations of sea otters, which use touch to maintain thermoregulatory integrity of their fur, explore objects, and capture visually cryptic prey.

Pathology and epidemiology of nasopulmonary acariasis (Halarachne sp.) in southern sea otters (Enhydra lutris nereis)

Halarachne sp. nasal mites infest harbor seals (Phoca vitulina) and southern sea otters (Enhydra lutris nereis) in California, but little is known about the pathophysiology of these infestations, or risk factors for exposure. To investigate these questions, a retrospective case-control study was performed using necropsy data from 70 mite-infested sea otters, and 144 non-infested controls. Case records for sea otters examined by pathologists from February 1999 through May 2015 were examined to assess risk factors for infestation, and lesions associated with nasopulmonary acariasis. Animals with a history of captive care within 10 days of death or carcass recovery were 3.2 times more likely to be infested with nasopulmonary mites than those with no history of recent rehabilitation. Sea otters stranding within 1 km of Elkhorn Slough in Monterey Bay were 4.9 times more likely to be infested with nasal mites than other areas; this site is characterized by high sea otter contact with sympatric harbor seals (a common host for Halarachne sp.), and a comparatively large population of rehabilitated and released sea otters. Aged adult otters were 9.4 times more likely to be infested than younger animals, and sea otters with nasopulmonary acariasis were 14.2 times more likely to have upper respiratory inflammation than un-infested animals. Additional findings in otters with nasopulmonary acariasis included lower respiratory tract bacterial infections, presence of medium-sized and/or fresh nose wounds at necropsy (indicators of recent face-to-face interaction between otters during copulation or fighting), and turbinate bone erosion. Our findings, although preliminary, suggest that captive rehabilitation and close contact with harbor seals could facilitate nasopulmonary mite transmission to sea otters. We also identified a high-risk zone for nasopulmonary acariasis in sea otters. We also provide preliminary data to suggest that nasopulmonary mite infestations can cause significant respiratory pathology in sea otters.

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Our data illustrates that nasopulmonary mites can be pathogenic for sea otters.

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High mite loads were associated with captive care, fresh nose wounds, and females.

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Mite-infested otters were 14 times more likely to have nasopharyngeal inflammation.

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Aged adult otters were 9 times more likely to be infested than other age groups.

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Otters hospitalized within 10 days of death were 3 times more likely to be infested.

Sex and occupation time influence niche space of a recovering keystone predator

Predators exert strong effects on ecological communities, particularly when they re-occupy areas after decades of extirpation. Within species, such effects can vary over time and by sex and cascade across trophic levels. We used a space-for-time substitution to make foraging observations of sea otters (Enhydra lutris) across a gradient of reoccupation time (1-30 years), and nonmetric multidimensional scaling (nMDS) analysis to ask whether (a) sea otter niche space varies as a function of occupation time and (b) whether niche space varies by sex. We found that niche space varied among areas of different occupation times. Dietary niches at short occupation times were dominated by urchins (Mesocentrotus and Strongylocentrotus spp; >60% of diets) in open habitats at 10-40 m depths. At longer occupation times, niches were dominated by small clams (Veneroida; >30% diet), mussels (Mytilus spp; >20% diet), and crab (Decapoda; >10% diet) in shallow (<10 m) kelp habitats. Diet diversity was lowest (H' = 1.46) but energy rich (~37 kcal/min) at the earliest occupied area and highest, but energy poor (H' = 2.63, ~9 kcal/min) at the longest occupied area. A similar transition occurred through time at a recently occupied area. We found that niche space also differed between sexes, with bachelor males consuming large clams (>60%), and urchins (~25%) from deep waters (>40 m), and females and territorial males consuming smaller, varied prey from shallow waters (<10 m). Bachelor male diets were less diverse (H' = 2.21) but more energy rich (~27 kcal/min) than territorial males (H' = 2.54, ~13 kcal/min) and females (H' = 2.74, ~11 kcal/min). Given recovering predators require adequate food and space, and the ecological interactions they elicit, we emphasize the importance of investigating niche space over the duration of recovery and considering sex-based differences in these interactions.

Molecular characterization and prevalence of Halarachne halichoeri in threatened southern sea otters (Enhydra lutris nereis)

Parasitism, particularly in concert with other sublethal stressors, may play an important, yet underappreciated role in morbidity and mortality of threatened species. During necropsy of southern sea otters (Enhydra lutra nereis) from California submitted to the Marine Wildlife Veterinary Care and Research Center's Sea Otter Necropsy Program between 1999 and 2017, pathologists occasionally observed nasopulmonary mites infesting the respiratory tracts. Infestation was sometimes accompanied by lesions reflective of mite-associated host tissue damage and respiratory illness. Our objectives were to estimate prevalence of nasopulmonary mites, determine the taxonomic identity of the observed mites, and create a DNA reference for these organisms in southern sea otters as an aid in population management. Using unique morphological characteristics discerned via light and scanning electron microscopy (SEM), we identified the mites as Halarachne halichoeri, a species typically associated with harbor seals (Phoca vitiluna). The 18S, 16S, 28S and ITS1-2 genetic regions were sequenced and submitted to GenBank. We observed H. halichoeri mites in 25.6% (95% CI 19.9-33.4%). of southern sea otters from a subset of necropsies performed between 2012 and 2017. This is the first documentation of H. halichoeri in southern sea otters and is suggestive of parasite exchange between sea otters and harbor seals.

From the predictable to the unexpected: kelp forest and benthic invertebrate community dynamics following decades of sea otter expansion

The recovery of predators has the potential to restore ecosystems and fundamentally alter the services they provide. One iconic example of this is keystone predation by sea otters in the Northeast Pacific. Here, we combine spatial time series of sea otter abundance, canopy kelp area, and benthic invertebrate abundance from Washington State, USA, to examine the shifting consequences of sea otter reintroduction for kelp and kelp forest communities. We leverage the spatial variation in sea otter recovery to understand connections between sea otters and the kelp forest community. Sea otter increases created a pronounced decline in sea otter prey-particularly kelp-grazing sea urchins-and led to an expansion of canopy kelps from the late 1980s until roughly 2000. However, while sea otter and kelp population growth rates were positively correlated prior to 2002, this association disappeared over the last two decades. This disconnect occurred despite surveys showing that sea otter prey have continued to decline. Kelp area trends are decoupled from both sea otter and benthic invertebrate abundance at current densities. Variability in kelp abundance has declined in the most recent 15 years, as it has the synchrony in kelp abundance among sites. Together, these findings suggest that initial nearshore community responses to sea otter population expansion follow predictably from trophic cascade theory, but now, other factors may be as or more important in influencing community dynamics. Thus, the utility of sea otter predation in ecosystem restoration must be considered within the context of complex and shifting environmental conditions.

Complete genome sequence of a novel sea otterpox virus

Members of the Poxviridae family are large, double-stranded DNA viruses that replicate in the cytoplasm of their host cells. The subfamily Chordopoxvirinae contains viruses that infect a wide range of vertebrates including marine mammals within the Balaenidae, Delphinidae, Mustelidae, Odobenidae, Otariidae, Phocidae, and Phocoenidae families. Recently, a novel poxvirus was found in a northern sea otter pup (Enhydra lutris kenyoni) that stranded in Alaska in 2009. The phylogenetic relationships of marine mammal poxviruses are not well established because of the lack of complete genome sequences. The current study sequenced the entire sea otterpox virus Enhydra lutris kenyoni (SOPV-ELK) genome using an Illumina MiSeq sequencer. The SOPV-ELK genome is the smallest poxvirus genome known at 127,879 bp, is 68.7% A+T content, is predicted to encode 132 proteins, and has 2546 bp inverted terminal repeats at each end. Genetic and phylogenetic analyses based on the concatenated amino acid sequences of 7 chorodopoxvirus core genes revealed the SOPV-ELK is 52.5-74.1% divergent from other known chordopoxviruses and is most similar to pteropoxvirus from Australia (PTPV-Aus). SOPV-ELK represents a new chordopoxvirus species and may belong to a novel genus. SOPV-ELK encodes eight unique genes. While the function of six predicted genes remains unknown, two genes appear to function as novel immune-modulators. SOPV-ELK-003 appears to encode a novel interleukin-18 binding protein (IL-18 BP), based on limited sequence and structural similarity to other poxviral IL-18 BPs. SOPV-ELK-035 appears to encode a novel tumor necrosis factor receptor-like (TNFR) protein that may be associated with the depression of the host's antiviral response. Additionally, SOPV-ELK-036 encodes a tumor necrosis factor-like apoptosis-inducing ligand (TRAIL) protein that has previously only been found in PTPV-Aus. The SOPV-ELK genome is the first mustelid poxvirus and only the second poxvirus from a marine mammal to be fully sequenced. Sequencing of the SOPV-ELK genome is an important step in unraveling the position of marine mammal poxviruses within the larger Poxviridae phylogenetic tree and provides the necessary sequence to develop molecular tools for future diagnostics and epidemiological studies.

Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim

Pathogens entering the marine environment as pollutants exhibit a spatial signature driven by their transport mechanisms. The sea otter (Enhydra lutris), a marine animal which lives much of its life within sight of land, presents a unique opportunity to understand land-sea pathogen transmission. Using a dataset on Toxoplasma gondii prevalence across sea otter range from Alaska to California, we found that the dominant drivers of infection risk vary depending upon the spatial scale of analysis. At the population level, regions with high T. gondii prevalence had higher human population density and a greater proportion of human-dominated land uses, suggesting a strong role for population density of the felid definitive host of this parasite. This relationship persisted when a subset of data were analysed at the individual level: large-scale patterns in sea otter T. gondii infection prevalence were largely explained by individual exposure to areas of high human housing unit density, and other landscape features associated with anthropogenic land use, such as impervious surfaces and cropping land. These results contrast with the small-scale, within-region analysis, in which age, sex and prey choice accounted for most of the variation in infection risk, and terrestrial environmental features provided little variation to help in explaining observed patterns. These results underscore the importance of spatial scale in study design when quantifying both individual-level risk factors and landscape-scale variation in infection risk.

MORTALITY TRENDS IN NORTHERN SEA OTTERS ( ENHYDRA LUTRIS KENYONI) COLLECTED FROM THE COASTS OF WASHINGTON AND OREGON, USA (2002-15)

During 2002-15 we examined the causes of mortality in a population of northern sea otters ( Enhydra lutris kenyoni). Beachcast sea otters were collected primarily from the US coast of Washington. Although there are no permanent sea otter residents in Oregon, several beachcast otters were collected from the Oregon coast. Infectious diseases were the primary cause of death (56%) for otters we examined. Sarcocystosis was the leading infectious cause of death (54%) and was observed throughout the study period. Some infectious diseases, such as morbilliviral encephalitis and leptospirosis, were documented for a limited number of years and then not detected again despite continued testing for these pathogens in necropsied animals. Trauma was the second most common cause of death (14%) during the study period. The continued stable growth of the Washington population of otters suggests they are able to tolerate current mortality rates.

The high cost of reproduction in sea otters necessitates unique physiological adaptations

Superimposed on inherently high basal metabolic demands, the additional energetic requirements of reproduction can push female sea otters beyond physiological limits. Indeed, the resulting energy imbalance contributes to disproportionately high rates of mortality at the end of lactation in this species. To examine and quantify metabolic changes associated with reproduction, we measured the resting metabolic rate (RMR) of a female sea otter across gestation, lactation and non-reproductive periods. Concurrently, measurements were made on a non-breeding control female. Our results suggest that RMR declines during gestation. Conversely, RMR increases during lactation, reaches a peak at 3-4 months postpartum, and remains elevated until weaning. Combining these direct measurements with published data, we found the cost of pup rearing to be significantly higher than previously estimated. High baseline energy demands and limited energy reserves, combined with significant lactation and pup rearing costs, appear to necessitate metabolic and thermal lability during key reproductive stages.

Oral papillomatosis caused by Enhydra lutris papillomavirus 1 (ElPV-1) in southern sea otters (Enhydra lutris nereis) in California, USA

The southern sea otter (Enhydra lutris nereis) is a threatened marine sentinel. During postmortem investigations of stranded sea otters from 2004 to 2013 in California, US, papillomas were detected in the oral cavity of at least seven otters via necropsy and histopathology. Next-generation sequencing of viral particles purified from a single papilloma revealed a novel papillomavirus, Enhydra lutris papillomavirus 1 (ElPV-1). The genome of ElPV-1 was obtained, representing the first fully sequenced viral genome from southern sea otters. Phylogenetic analysis of the entire L1 gene, as well as a concatenated protein identities plot of all papillomaviral genes revealed that ElPV-1 is a λ-papillomavirus, related to a raccoon papillomavirus (Procyon lotor papillomavirus type 1) and a canine oral papillomavirus. Immunohistochemical staining, using a cross-reactive bovine papillomavirus antibody, suggested that ElPV-1 is present in intranuclear inclusions and intracytoplasmic keratin granules. Virus-infected cells were scattered throughout the stratum granulosum and stratum spinosum of the gingival and buccal papillomas. Using ElPV-1-specific PCR, we confirmed viral DNA in oral papillomas from all seven stranded sea otters, with identical L1 sequences. This virus is associated with the development of oral papillomatosis in southern sea otters.

Assessing Risks to Sea Otters and the Exxon Valdez Oil Spill: New Scenarios, Attributable Risk, and Recovery

The Exxon Valdez oil spill occurred more than two decades ago, and the Prince William Sound ecosystem has essentially recovered. Nevertheless, discussion continues on whether or not localized effects persist on sea otters (Enhydra lutris) at northern Knight Island (NKI) and, if so, what are the associated attributable risks. A recent study estimated new rates of sea otter encounters with subsurface oil residues (SSOR) from the oil spill. We previously demonstrated that a potential pathway existed for exposures to polycyclic aromatic hydrocarbons (PAHs) and conducted a quantitative ecological risk assessment using an individual-based model that simulated this and other plausible exposure pathways. Here we quantitatively update the potential for this exposure pathway to constitute an ongoing risk to sea otters using the new estimates of SSOR encounters. Our conservative model predicted that the assimilated doses of PAHs to the 1-in-1000th most-exposed sea otters would remain 1-2 orders of magnitude below the chronic effects thresholds. We re-examine the baseline estimates, post-spill surveys, recovery status, and attributable risks for this subpopulation. We conclude that the new estimated frequencies of encountering SSOR do not constitute a plausible risk for sea otters at NKI and these sea otters have fully recovered from the oil spill.