Geology topics

Susan Knowles

Publications and source records attributed to Susan Knowles.

At least 19 recordsLinked to original sources

USGS2025

Nocardia cyriacigeorgica in a Mallard (Anas platyrhynchos) from Arizona, USA

Nocardia spp. are opportunistic pathogens of humans, domestic animals, and wildlife that can cause high levels of morbidity and mortality. Here, we present a unique case of nocardial airsacculitis in a free-ranging mallard ( Anas platyrhynchos ) from Arizona, USA, and compare it to the hosts, geographic distribution, diagnostic methodology, and infection site of known nocardiosis cases in birds. A gross necropsy, histopathology, and bacterial culture were performed. There were no gross findings associated with the nocardiosis. Histopathology showed multiple granulomas expanding the air sac with intralesional filamentous bacteria that were Grocott’s methenamine silver-positive, Fite–Faraco and Ziehl–Neelsen acid-fast, positive with the Periodic acid–Schiff reaction, and variably Gram-positive. The organism was isolated in culture and identified as Nocardia cyriacigeorgica based on the sequencing of a 463 bp portion of the 16S rRNA gene. While reports of nocardiosis in the class Aves are rare and some are possibly misdiagnosed due to limited diagnostics, cases are reported globally, sometimes resulting in epizootics. More information is needed to understand whether immunosuppression plays a role in disease development in birds. Known to be an emerging pathogen in humans, N. cyriacigeorgica can be considered as a differential diagnosis for pulmonary and potentially cutaneous or disseminated infections in birds.

Arizona↗

USGS2025

An enigmatic wild passerine mortality event in the eastern United States

The ability to rapidly respond to wildlife health events is essential. However, such events are often unpredictable, especially with anthropogenic disturbances and climate-related environmental changes driving unforeseen threats. Many events also are short-lived and go undocumented, making it difficult to draw on lessons learned from past investigations. We report on the response to a mortality event observed predominantly in wild passerines in the eastern United States. The event began in May 2021 when wildlife rehabilitators and private citizens reported large numbers of sick and dead juvenile birds, mostly presenting as single cases with neurologic signs and/or ocular and periocular lesions. Early efforts by rehabilitators, veterinarians, state and federal wildlife agencies, and universities helped gather public reports and fuel rapid responses by government agencies. Collective efforts included live bird and carcass collections; submission to diagnostic laboratories and evaluation; information sharing; and coordinated messaging to stakeholders and interested parties. Extensive diagnostic evaluations failed to identify a causative pathogen or other etiology, although congruent results across laboratories have helped drive further investigation into alternative causes, such as nutritional deficiencies. This report highlights the strengths of a multi-agency, interdisciplinary investigation while exposing the need for an operational framework with approaches and resources dedicated to wildlife health.

eastern United States↗

USGS2025

Sampling mass mortality events to enable diagnoses: A protocol using freshwater mussels

Many taxa around the globe are threatened by often unexplained mass mortality events (MMEs), which can decimate populations and compromise key ecosystem functions. One example of a highly threatened taxon facing frequent MMEs is freshwater mussels (Unionida). There has been a recent increase in interest in understanding the causes of freshwater mussel MMEs, but standardised methodologies for how best to respond to them to facilitate diagnoses are unavailable. When an MME is observed, swift and appropriate sample collection is imperative owing to the transient nature of these phenomena. Here we provide structured guidance that will facilitate rapid and appropriate sampling of MMEs, using freshwater mussels as an example. We set out standardised procedures for sample collection, preparation and preservation. The procedures we outline will improve our capacity for diagnostic investigations of MMEs and other mortality events, not only in freshwater mussels but also across many other taxa. This, in turn, can inform appropriate management responses.

Methods in Ecology and Evolution↗

USGS2025

Arsenic accumulation in Sonora Mud Turtles (Kinosternon sonoriense) in an unusual freshwater food web

Montezuma Well is an unusual fishless, spring-fed, desert wetland in central Arizona. Water in the wetland is naturally enriched with > 100 µg/l dissolved geogenic arsenic (As) and supports a simple aquatic food web dominated by a small number of endemic invertebrate species that achieve high abundances. Previous studies of As among various environmental compartments and organisms in Montezuma Well did not include omnivorous Sonora Mud turtles ( Kinosternon sonoriense ) despite their potential importance in the As cycle by virtue of their substantial biomass and role as top predators. We measured As concentrations in water, sediment, and organisms (macrophytes, amphipods, insects, leeches, and turtles) representing a range of trophic levels in order to document the importance of turtles at the apex of the Montezuma Well food web and in the As cycle. Concentrations of As in turtles varied according to tissue type. The greatest values (up to 26.77 mg/kg dry weight) were in the scutes of 1 of our oldest turtles (31.5 yrs). These elevated concentrations may be due to the affinity of As to react with sulfur in the keratin of scutes, and therefore might reflect duration of exposure in long-lived turtles. Although As concentrations generally tend to decrease when moving up to higher trophic levels in a food web, our results were different. Relatively elevated concentrations reported in sediments by us and a previous study declined in plant samples as expected. Amphipod concentrations increased but then decreased again in 3 of their invertebrate predators. Arsenic concentrations in endemic leeches were extremely elevated with a mean value of 72.2 mg/kg. The mean concentration of As in turtles was 7.08 mg/kg across tissue types and was greater than the plants or invertebrates they eat, with the notable exception of leeches, which have been proposed to be part of their diet.

Arizona↗

USGS2024

Freshwater mussel viromes increase rapidly in diversity and abundance when hosts are released from captivity into the wild

Freshwater mussels create habitat, filter water, and enhance food webs, but they are also among the world’s most imperiled taxa. Conservation efforts largely rely on captive propagation in which mussels are grown in protected aquaculture environments (hatcheries) for later release. Recent evidence has highlighted the importance of pathogens in population losses of freshwater mussels. In response to ongoing mass mortality events of freshwater mussels in the Upper Tennessee River Basin in Virginia and Tennessee, USA, we conducted a multi-year study to document viruses across multiple restoration sites and compare them to viruses in mussels from the hatchery. Viral communities changed greatly after mussels were released. Of the 681 viruses of the 27 families we documented, only 20 viruses were found exclusively in hatchery mussels, compared to 451 viruses found only in mussels stocked to the wild. After release, mussels rapidly acquired new viruses, and the number of viruses increased steadily over time. These findings have implications for how mussel introduction programs might be managed for greater success, for example, by incorporating acclimatization periods prior to full release.

Tennessee, Virgnia↗

USGS2024

Hirsutonosema embarrassi n. gen. n. sp. (Phylum Microsporidia) in the Ovary of Mucket (Actinonaias ligamentina), Plain Pocketbook (Lampsilis cardium), and Fatmucket (Lampsilis siliquoidea) (Unionidae) from the Embarrass River, Wisconsin, USA

During an epidemiological survey following a mortality event of freshwater mussels in 2018 in the Embarrass River, Wisconsin, USA, we identified a novel microsporidian parasite in the ovaries of mucket ( Actinonaias ligamentina ), plain pocketbook ( Lampsilis cardium ), and fatmucket ( Lampsilis siliquoidea ) (Unionidae). Histopathology showed round-to-oval microsporidian spores in the cytoplasm of oocytes in 60% (3/5) of female mucket, 100% (4/4) of female plain pocketbook, and 50% (1/2) of female fatmucket. Using transmission electron microscopy, we found that mature spores were round-to-oval and measured 4.13 ± 0.64 µm (3.14–5.31) long by 2.88 ± 0.37 µm (2.36–3.68) wide. The spores had a thin electron-dense exospore with a spiky “hairy” coat, a thick electron lucent endospore, diplokaryotic nuclei, a polar vacuole, and 27–28 polar filaments arranged in 1–3 rows. Sequencing of the small subunit rRNA produced a 1356 bp sequence most similar to that of Pseudonosema cristatellae (92%), and phylogenetic analysis grouped it within the freshwater Neopereziida. Genetic, morphological, and ultrastructural characteristics did not closely match those of other Pseudonosema spp., and a new genus and species, Hirsutonosema embarrassi n. gen. n. sp., were designated. Additional studies could evaluate host susceptibility, distribution, seasonality, transmission, and lethal or sub-lethal effects of this parasite on freshwater mussels.

Wisconsin↗

USGS2024

Retrospective review of the pathology of American pikas

American pikas ( Ochotona princeps ) are small lagomorphs that live in mountainous talus areas of western North America. Studies on the histopathology of American pikas are limited. We summarize here the clinical histories, and gross and histologic findings of 12 American pikas, including 9 captive (wild-caught) and 3 wild animals. Death was often attributed to stress (transport, handling, anesthesia) with few-to-no premonitory clinical signs. Infection was the cause of death in 2 cases: 1 had bacterial pyogranulomatous dermatitis, cellulitis, and lymphadenitis with sepsis; the other case had oomycete-induced necrotizing colitis. Incidental parasitic infections included sarcocystosis, nematodosis (oxyurids), and ectoparasitism. Most animals with adequate nutritional status had periportal hepatic lipidosis; this finding was absent in all animals with adipose atrophy, and it is possible that periportal hepatic lipidosis is non-pathologic in American pikas. Three cases had myocardial necrosis that was considered the cause of death; the cause of necrosis was not determined, but it may have been caused by stress or vitamin E–selenium deficiency. Esophageal hyperkeratosis was noted in animals with a history of anorexia and negative energy balance; accumulation of esophageal keratin can result from lack of mucosal abrasion by ingesta. Several histologic findings that are likely normal in American pikas include splenic extramedullary hematopoiesis, thymic tissue in adults, and Clostridium sp. in the enteric lumen.

Journal of Veterinary Diagnostic Investigation↗

USGS2024

Bacteriological analysis of unionid hemolymph collected from freshwater mussel populations in the Pacific northwestern United States

Native freshwater mussel (Unionidae) mortality events have been occurring with increased frequency in recent decades, with few investigations into potential etiological agents. In the western United States, no surveys have been published regarding the bacteria associated with unionid mussels. Herein, we examine locations of known mussel mortality events in the Chehalis River (Washington), in the Crooked River (Oregon), and Owyhee River (Oregon). Mussel populations considered healthy were sampled in the Skookumchuck River (Washington) for comparison. A variety of bacteria were isolated from these populations, and most notably, Acinetobacter spp. were identified from 82% of moribund individuals of Gonidea angulata in the Owyhee River. Future work evaluating whether Acinetobacter spp. are pathogenic to freshwater mussels could be valuable in unraveling the factors associated with these enigmatic mortality events.

Oregon, Washington↗

USGS2024

Little brown bats (Myotis lucifugus) are resistant to SARS-CoV-2 infection

It has been proposed that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that spread through human populations as a pandemic originated in Asian bats. There is concern that infected humans could transmit the virus to native North American bats; therefore, the susceptibility of several North American bat species to the pandemic virus has been experimentally assessed. Big brown bats ( Eptesicus fuscus ) were shown to be resistant to infection by SARS-CoV-2, whereas Mexican free-tailed bats ( Tadarida brasiliensis ) became infected and orally excreted moderate amounts of virus for up to 18 d postinoculation. Little brown bats ( Myotis lucifugus ) frequently contact humans, and their populations are threatened over much of their range due to white-nose syndrome, a fungal disease that is continuing to spread across North America. We experimentally challenged little brown bats with SARS-CoV-2 to determine their susceptibility and host potential and whether the virus presents an additional risk to this species. We found that this species was resistant to infection by SARS-CoV-2. These findings provide reassurance to wildlife rehabilitators, biologists, conservation scientists, and the public at large who are concerned with possible transmission of this virus to threatened bat populations.

Journal of Wildlife Diseases↗

USGS2023

Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola , little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons ( Furcifer pardalis ) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis , although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan- Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assay’s performance will require additional follow up due to the small number of clinical samples ( n = 14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

Frontiers in Microbiology↗

USGS2023

Mussel mass mortality in the Clinch River, USA: Metabolomics detects affected pathways and biomarkers of stress

Biologists monitoring freshwater mussel (order Unionida) populations rely on behavioral, often subjective, signs to identify moribund (“sick”) or stressed mussels, such as gaping valves and slow response to probing, and they lack clinical indicators to support a diagnosis. As part of a multi-year study to investigate causes of reoccurring mortality of pheasantshell ( Ortmanniana pectorosa; synonym Actinonaias pectorosa ) in the Clinch River, Virginia and Tennessee, USA, we analyzed the hemolymph metabolome of a subset of mussels from the 2018 sampling period. Mussels at the mortality sites were diagnosed in the field as affected (case) or unaffected (control) based on behavioral and physical signs. Hemolymph was collected in the field by non-lethal methods from the anterior adductor muscle for analysis. We used ultra-high-performance liquid chromatography with quadrupole time-of-flight mass spectroscopy to detect targeted and untargeted metabolites in hemolymph and compared metabolomic profiles by field assessment of clinical status. Targeted biomarker analysis found 13 metabolites associated with field assessments of clinical status. Of these, increased gamma-linolenic acid and N -methyl- L -alanine were most indicative of case mussels, while adenine and inosine were the best indicators of control mussels. Five pathways in the targeted analysis differed by clinical status; two of these, purine metabolism and glycerophospholipid metabolism, were also indicated in the untargeted analysis. In the untargeted nalysis, 22 metabolic pathways were associated with clinical status. Many of the impacted pathways in the case group were catabolic processes, such as degradation of amino acids and fatty acids. Hierarchical clustering analysis matched clinical status in 72% (18 of 25) of mussels, with control mussels more frequently (5 of 16) not matching clinical status. Our study demonstrated that metabolomic analysis of hemolymph is suitable for assessing mussel condition and complements field-based indicators of health.

Tennessee, Virginia↗

USGS2023

Pathology and infectious agents of unionid mussels: A primer for pathologists in disease surveillance and investigation of mortality events

Freshwater mussels are one of the most imperiled groups of organisms in the world, and more than 30 species have gone extinct in the last century. While habitat alteration and destruction have contributed to the declines, the role of disease in mortality events is unclear. In an effort to involve veterinary pathologists in disease surveillance and the investigation of freshwater mussel mortality events, we provide information on the conservation status of unionids, sample collection and processing techniques, and unique and confounding anatomical and physiological differences. We review the published accounts of pathology and infectious agents described in freshwater mussels including neoplasms, viruses, bacteria, fungi, fungal-like agents, ciliated protists, Aspidogastrea, Digenea, Nematoda, Acari, Diptera, and Odonata. Of the identified infectious agents, a single viral disease, Hyriopsis cumingii plague disease, that occurs only in cultured mussels is known to cause high mortality. Parasites including ciliates, trematodes, nematodes, mites, and insects may decrease host fitness, but are not known to cause mortality. Many of the published reports identify infectious agents at the light or ultrastructural microscopy level with no lesion or molecular characterization. Although metagenomic analyses provide sequence information for infectious agents, studies often fail to link the agents to tissue changes at the light or ultrastructural level or confirm their role in disease. Pathologists can bridge this gap between identification of infectious agents and confirmation of disease, participate in disease surveillance to ensure successful propagation programs necessary to restore decimated populations, and investigate mussel mortality events to document pathology and identify causality.

Veterinary Pathology↗

USGS2023

A bacteriological comparison of the hemolymph from healthy and moribund unionid mussel populations in the upper Midwestern U.S.A. prompts the development of diagnostic assays to detect Yokenella regensburgei

Recent bacteriological investigations of freshwater mussel mortality events in the southeastern United States have identified a variety of bacteria and differences in bacterial communities between sick and healthy mussels. In particular, Yokenella regensburgei and Aeromonas spp. have been shown to be associated with moribund mussels, although it remains unclear whether these bacteria are causes or consequences of disease. To further understand the role of bacteria in mussel epizootics, we investigated mortality events that occurred in the upper Midwest in the Embarrass River (Wisconsin) and the Huron River (Michigan). For comparison, we also studied mussels from an unaffected population in the St. Croix River (Wisconsin). Diverse bacterial genera were identified from these sites, including Y. regensburgei from moribund mussels in the Embarrass River (Wisconsin). This bacterium has also been consistently isolated during ongoing mortality events in the Clinch River (Virginia). Subsequently, we developed and validated molecular assays for the detection of Yokenella to use in future investigations of mussel mortality events and to identify environmental reservoirs of this bacterium.

Michigan, Minnesota, Wisconsin↗

USGS2023

Experimental infection of Mexican free-tailed bats (Tadarida brasiliensis) with SARS-CoV-2

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus is thought to have originated in wild bats from Asia, and as the resulting pandemic continues into its third year, concerns have been raised that the virus will expand its host range and infect North American wildlife species, including bats. Mexican free-tailed bats ( Tadarida brasiliensis ) live in large colonies in the southern United States, often in urban areas and, as such, could be exposed to the virus from infected humans. We experimentally challenged wild T. brasiliensis with SARS-CoV-2 to determine the susceptibility, reservoir potential, and population impacts of infection in this species. Of 10 bats oronasally inoculated with SARS-CoV-2, 5 became infected and orally excreted moderate amounts of virus for up to 18 days postinoculation. These five subjects all seroconverted and cleared the virus before the end of the study with no obvious clinical signs of disease. We additionally found no evidence of viral transmission to uninoculated subjects. These results indicate that while T. brasiliensis are susceptible to SARS-CoV-2 infection, infection of wild populations of T. brasiliensis would not likely cause mortality. However, the transmission of SARS-CoV-2 from T. brasiliensis to or from humans, or to other animal species, is a possibility requiring further investigation to better define.

mSphere↗

USGS2023

Further bacteriological analysis of annual Pheasantshell (Actinonaias pectorosa) mussel mortality events in the Clinch River (Virginia/Tennessee), USA, reveals a consistent association with Yokenella Regensburgei

Pheasantshell ( Actinonaias pectorosa ) mussels in the Clinch River (Tennessee/Virginia, USA) have declined dramatically in recent years. The bacterium Yokenella regensburgei was first isolated with high prevalence from Pheasantshells during the peak of a 2017 mortality event, but it was not identified after mortality subsided a few months later. Since 2017, Pheasantshell mortality in the Clinch River has occurred each autumn. We extended the investigation of culturable bacterial communities in the Clinch River during mussel mortality events in 2018, 2019, and 2020 and examined the spatial and temporal distribution of bacterial genera among Pheasantshells, as well as among other unionid mussels. We identified Y. regensburgei each year, almost exclusively during active mortality events. The significance of Y. regensburgei remains unclear, but the continued association of this bacterium with mussel mortality events warrants further study.

Tennessee, Virginia↗

USGS2022

Freshwater mussels show elevated viral richness and intensity during a mortality event

Freshwater mussels (Unionida) are among the world’s most imperiled taxa, but the relationship between freshwater mussel mortality events and infectious disease is largely unstudied. We surveyed viromes of a widespread and abundant species (mucket, Actinonaias ligamentina ; syn: Ortmanniana ligamentina ) experiencing a mortality event of unknown etiology in the Huron River, Michigan, in 2019–2020 and compared them to viromes from mucket in a healthy population in the St. Croix River, Wisconsin and a population from the Clinch River, Virginia and Tennessee, where a mortality event was affecting the congeneric pheasantshell ( Actinonaias pectorosa ; syn: Ortmanniana pectorosa ) population. We identified 38 viruses, most of which were associated with mussels collected during the Huron River mortality event. Viral richness and cumulative viral read depths were significantly higher in moribund mussels from the Huron River than in healthy controls from each of the three populations. Our results demonstrate significant increases in the number and intensity of viral infections for freshwater mussels experiencing mortality events, whereas individuals from healthy populations have a substantially reduced virome comprising a limited number of species at low viral read depths.

Michigan, Tennessee, Virginia, Wisconsin↗

USGS2022

Divergent gene expression profiles in Alaskan sea otters: An indicator of chronic domoic acid exposure?

An opportunistic investigation into ecosystem instability in Kachemak Bay (KBay), Alaska, has led us to investigate exposure to toxic algae in sea otters. We used gene expression to explore the physiological health of sea otters sampled in KBay in May 2019. We found altered levels of gene transcripts in comparison with reference sea otters from clinically normal, oil-exposed, and nutritionally challenged populations sampled over the past decade. KBay sea otters were markedly divergent from the other groups for five genes, which indicated the involvement of neurological, cardiac, immune, and detoxification systems. Further, analyses of urine and fecal samples detected domoic acid in the KBay sea otters. In combination, these results may point to chronic, low-level exposure to an algal toxin, such as domoic acid. With a warming climate, the frequency and severity of harmful algal blooms in marine environments is anticipated to increase, and novel molecular technologies to detect sublethal or chronic exposure to algal toxins will help provide an early warning of threats to the stability of populations and ecosystems.

Alaska↗

USGS2022

A novel gonadotropic microsporidian parasite (Microsporidium clinchi n. sp.) infecting a declining population of pheasantshell mussels (Actinonaias pectorosa) (Unioinidae) from the Clinch River, USA

Freshwater mussels of the order Unionida are among the most endangered animal groups globally, but the causes of their population decline are often enigmatic, with little known about the role of disease. In 2018, we collected wild adult pheasantshell ( Actinonaias pectorosa ) and mucket ( Actinonaias ligamentina ) during an epidemiologic survey investigating an ongoing mussel mass mortality event in the Clinch River, Virginia and Tennessee, USA. Histopathology and transmission electron microscopy showed a novel microsporidian parasite primarily infecting the ovary of pheasantshell. Sequencing of the small subunit rRNA gene produced a 1333 bp sequence with the greatest similarity to Pseudonosema cristatellae (AF484694.1; 86.36%; e-value = 0), a microsporidium infecting the freshwater bryozoan ( Cristatella mucedo ). Microsporidia were observed in 65% (17/26) of the examined female pheasantshell ( A. pectorosa ) and in no (0/2) female muckets ( A. ligamentina ) and occurred at mortality and non-mortality sites. Our findings indicate that a novel parasite, Microsporidium clinchi n. sp., is present in pheasantshell in the Clinch River, and while likely not a cause of mass mortality, could reduce fecundity and recruitment in this declining population and threaten the success of reintroductions. Surveillance of M. clinchi n. sp. and evaluation of broodstock and their progeny for microsporidia would therefore be prudent.

Tennessee, Virginia↗