Ceratotherium Simum Simum Research Articles

Progress Toward Genetic Rescue of the Northern White Rhinoceros (Ceratotherium simum cottoni).

The northern white rhinoceros (NWR) is functionally extinct, with only two nonreproductive females remaining. However, because of the foresight of scientists, cryopreserved cells and reproductive tissues may aid in the recovery of this species. An ambitious program of natural and artificial gamete and in vitro embryo generation was first outlined in 2015, and many of the proposed steps have been achieved. Multiple induced pluripotent stem cell lines have been established, primordial germ cell-like cells have been generated, oocytes have been collected from the remaining females, blastocysts have been cryopreserved, and the closely related southern white rhinoceros (SWR) is being established as a surrogate. Recently, the first successful embryo transfer in SWR demonstrated that embryos can be generated by in vitro fertilization and cryopreserved. We explore progress to date in using advanced cellular technologies to save the NWR and highlight the necessary next steps to ensure a viable population for reintroduction. We roll out a holistic rescue approach for a charismatic megavertebrate that includes the most advanced cellular technologies, which can provide a blueprint for other critically endangered mammals. We also provide a detailed discussion of the remaining questions in such an upgraded conservation program.

Trypanosomiasis in Introduced Southern White Rhinoceros (Ceratotherium simum simum) Gifts to Ex Situ Habitat in Aitong, Kenya.

During the opening of diplomatic relations in the 1990s, South Africa gifted 20 southern white rhinoceros (Ceratotherium simum simum) to Kenya. The species is not indigenous to Kenya, and management of the introduction was not clearly addressed in the legislation. Responsibility was left to the private sector and local authorities. Ten of the animals were introduced to land contiguous with the Maasai Mara National Reserve, an area with tsetse-trypanosomiasis challenges, and with rare cases of human sleeping sickness. Mortalities had been previously documented when indigenous naïve black rhinoceros were introduced to areas with tsetse; hence there was no consensus on the management of this introduction. Feasibility was only explored once before with the introduction of two animals in a monitored and managed translocation from Lewa Downs, Laikipia in 1992-1994. Ultimately, Kenyan experts were co-opted to address risk after trypanosomiasis occurred in many animals. Unfortunately, this finding was followed by gradual mortalities of most rhinoceros with only a few being saved by removal to highland private sanctuaries. This event was complicated by many factors. Samples were only sporadically collected, and mainly from sick animals. With no clear responsibility by government agencies, a collaboration between veterinarians and researchers resulted in characterization of the disease challenge, and when invited, assessment of health status. Laboratory diagnostics revealed common and sometimes severe infections with Trypanosoma brucei, a normally infrequent trypanosome. Infection was associated with disturbances in erythropoiesis, especially anemia. Symptoms varied from sudden death associated with intestinal atony, to a semiparalyzed animal that was partially responsive to treatment for trypanosomes. This event should be used as a caution to future movements of this species that are planned or ongoing in Africa, for conservation or other purposes.

The effect of a warmed enema during ovum pick-up on subsequent in vitro oocyte maturation in Southern white rhinoceros (Ceratotherium simum simum).

Rhinoceros are currently one of the most threatened mammal species globally. Slow population growth, increased poaching and habitat destruction have led to increased conservation efforts for each species. Assisted reproductive technologies (ART) have been implemented in an attempt to aid reproductive outputs for the conservation of these endangered species. Developing species-specific ART programmes for wildlife have been challenging. Temperature control during oocyte recovery is essential for ensuring in vitro success. This study is the first to investigate the effect of enema warming prior to trans-rectal ovum pick-up (OPU) on in vitro oocyte maturation in Southern white rhinoceros (Ceratotherium simum simum). OPUs were performed on 20 rhinoceros cows from three different game farms in South Africa; oocytes were transported to one of two in vitro fertilisation laboratories for culture. The enema fluid was either warmed to 32 °C or not warmed prior to the OPU. Location of the farm, the different laboratories, ambient temperature, season, aspiration probe temperature, media type and enema temperature were investigated as predictor variables for oocyte maturation success. After considering all other potential covariates, warming of the enema fluid was the only independent predictor of in vitro oocyte maturation success during this study. Oocytes retrieved from rhinoceros cows that received an enema warmed to 32 °C were 2.3 times more likely to mature in vitro compared to oocytes from cows that received an unwarmed enema; the findings can be implemented in other rhinoceros ART programmes and in conservation efforts of other endangered mammalian species.

Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

Much remains unknown about the reproductive physiology of southern white rhinoceros (SWR) and the effect of ovarian stimulation prior to ovum pickup (OPU) have not been fully elucidated. Granulosa cells (GC) provide valuable insight into follicle growth and oocyte maturation status. The goals of this study were to evaluate transcriptomic changes in GC from three stages of follicle development and to identify biomarkers possibly associated with follicular growth and maturation as a result of ovarian stimulation. GC collected from SWRs following OPU were assigned stages based upon follicle size. Total RNA was isolated, and cDNA libraries were prepared and sequenced on a NovaSeq 6000. All bioinformatics analyses were performed utilizing the Galaxy web platform. Reads were aligned to CerSimCot1.0, and the manual curation was performed with EquCab3.0. Overall, 39,455 transcripts (21,612 genes) were identified across follicle stages, and manual curation yielded a 61% increase in gene identification from the original annotation. Granulosa cells from preovulatory follicles expressed the highest number of unique transcripts. The following seven biomarkers were determined based upon cluster analysis and patterns of expression: COL1A1, JMY, FBXW11, NRG1, TMPO, MACIR and COL4A1. These data can be used to potentially evaluate the effects of different ovarian stimulation protocols on follicle dynamics, improve OPU results, and support conservation efforts in this species.

Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum)†.

Efforts to implement effective assisted reproductive technologies (ARTs) for the conservation of the northern white rhinoceros (NWR; Ceratotherium simum cottoni) to prevent its forthcoming extinction, could be supported by research conducted on the closely related southern white rhinoceros (SWR; Ceratotherium simum simum). Within the follicle, extracellular vesicles (EVs) play a fundamental role in the bidirectional communication facilitating the crucial transport of regulatory molecules such as microRNAs (miRNAs) that control follicular growth and oocyte development. This study aimed to elucidate the dynamics of EV-miRNAs in stage-dependent follicular fluid (FF) during SWR ovarian antral follicle development. Three distinct follicular stages were identified based on diameter: Growing (G; 11-17mm), Dominant (D; 18-29mm), and Pre-ovulatory (P; 30-34mm). Isolated EVs from the aspirated FF of segmented follicle stages were used to identify EV-miRNAs previously known via subsequent annotation to all equine (Equus caballus; eca), bovine (Bos taurus; bta), and human (Homo sapiens; hsa) miRNAs. A total of 417 miRNAs were detected, with 231 being mutually expressed across all three stages, including eca-miR-148a and bta-miR-451 as the top highly expressed miRNAs. Distinct expression dynamics in miRNA abundance were observed across the three follicular stages, including 31 differentially expressed miRNAs that target various pathways related to follicular growth and development, with 13 miRNAs commonly appearing amidst two different comparisons. In conclusion, this pioneering study provides a comprehensive understanding of the stage-specific expression dynamics of FF EV-miRNAs in the SWR. These findings provide insights that may lead to novel approaches in enhancing ARTs to catalyze rhinoceros conservation efforts.

Vesicular stomatitis virus in two species of rhinoceros at a California zoological park.

To describe an outbreak of vesicular stomatitis virus (VSV) in southern white rhinoceros (SWR; Ceratotherium simum simum) and greater one-horned rhinoceros (GOHR; Rhinoceros unicornis) at a safari park in San Diego, CA, from May to September 2023. 21 SWR and 5 GOHR in professionally managed care. Rhinoceros of both species presented with a range of clinical signs and severities. Lesion locations were categorized as cutaneous (coronary bands, heels and soles, limbs, ventrum, neck folds, and ears) and mucocutaneous (lips, nostrils, mucous membranes of the oral cavity, and vulva). Clinical signs included lethargy, lameness, difficulty with prehension, hyporexia to anorexia, and hypersalivation. Severely affected rhinoceros had clinical pathology findings consistent with systemic inflammation. Vesicular stomatitis New Jersey virus was confirmed via PCR from swabs of lesions in 10/26 (38%) rhinoceros. Of these 10 confirmed cases, 9 (90%) were SWR and 1 (10%) was a GOHR. A further 6/26 (24%) were considered probable cases, and 10/26 (38%) were considered suspect cases based on clinical signs, but the inability to appropriately sample due to the housing environment precluded confirmation. Histopathology samples from 3 rhinoceros were consistent with VSV, and viral RNA was localized in histologic lesions via RNA in situ hybridization for 1 case. All rhinoceros survived infection despite severe systemic illness in 2 animals. This case series describes the clinical appearance and progression of VSV in 2 rhinoceros species. To the authors' knowledge, this is the first report of VSV in a rhinoceros.

Effects of heat perturbation to rhinoceros’ cellular metabolism

Climate change is associated with increasing global mean temperatures and extreme heat events. These drastic changes in temperature can have significant deleterious physiological effects, particularly on large strict homeothermic mammals such as the threatened Southern White Rhino (SWR - Ceratotherium simum simum). Developing alternative strategies to understand how climatic events impact species that are logistically challenging to study are crucial. Dermal fibroblasts have proven to be effective in vitro models for studying species resilience to climate since they can reflect an organism's thermosensitivity. These cells can provide an integrative and mechanistic explanation on how cellular function can inform organismal responses to environmental changes. We investigated the effects of heat on mitochondrial function and cellular biology by exposing SWR primary dermal fibroblasts (n = 10 biological replicates) to 24 hours of heat (41°C) or 37°C as a control in culture. Then, we evaluated mitochondrial function using mitochondrial stress test, glycolytic rate test and immunofluorescence (IF) to track nucleus size and mitochondrial distribution in the cytoplasm. Metabolic function was assessed using Agilent Seahorse analyzer and IF images were analyzed on CellProfilerTM software. Our results indicate that compared to the control (37°C), heat exposure decreases mitochondrial respiration (basal: t = 3.7, df = 9, p < 0.01; maximum: t = 3.0, df = 9, p < 0.02), ATP production (t = 5.8, df = 9, p < 0.001), and coupling effciency (t = 7.6, df = 9, p < 0.001). No changes were observed in spare respiratory capacity (t = 0.7, df = 9, p = 0.5), proton leak (t = 0.7, df = 9, p = 0.5) and glycolysis (basal: t = 0.3, df = 4, p = 0.4; compensatory: t = 0.6, df = 4, p = 0.6). Furthermore, heat exposure increases nucleus size and mitochondrial distribution area (Nucleus area: t = 6.8, d.f. = 9, P < 0.001, Mitochondrial coverage area: t = 5.3, d.f. = 9, p < 0.001) and decreases fluorescence intensity of the mitochondrial dye and solidity area covered by mitochondria (Fluorescence: t = 2.3, d.f. = 9, p = 0.04, Mitochondrial area solidity: t = 5.6, d.f. = 9, p < 0.001). These findings show that acute heatwaves trigger a series of complex and interconnected responses in SWR fibroblasts resulting in mitochondrial disfunction, possibly mitophagy and/or mitochondria disintegration, and larger dispersion through the cytoplasm. The thermosensitive phenotype exhibited by SWR fibroblasts provides insights into the likely consequences of global warming on the performance of this species, as cellular and mitochondrial functioning plays a fundamental role in an organism's ability to adjust and thrive under environmental change. Funded by NSF and San Diego Zoo Wildlife Alliance. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Application of positive reinforcement training to assist in voluntary dental evaluation for Southern white rhinoceros (Cerathotherium simum)

Application of positive reinforcement training to assist in voluntary dental evaluation for Southern white rhinoceros (Cerathotherium simum)

Genetic load and viability of a future restored northern white rhino population.

As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and invitro gametogenesis of biobanked cells. However, restoration of populations can be hindered by low genetic diversity and deleterious genetic load. The persistence of the northern white rhino (Ceratotherium simum cottoni) now depends on the cryopreserved cells of 12 individuals. These banked genomes have higher genetic diversity than southern white rhinos (C. s. simum), a sister subspecies that successfully recovered from a severe bottleneck, but the potential impact of genetic load is unknown. We estimated how demographic history has shaped genome-wide genetic load in nine northern and 13 southern white rhinos. The bottleneck left southern white rhinos with more fixed and homozygous deleterious alleles and longer runs of homozygosity, whereas northern white rhinos retained more deleterious alleles masked in heterozygosity. To gauge the impact of genetic load on the fitness of a northern white rhino population restored from biobanked cells, we simulated recovery using fitness of southern white rhinos as a benchmark for a viable population. Unlike traditional restoration, cell-derived founders can be reintroduced in subsequent generations to boost lost genetic diversity and relieve inbreeding. In simulations with repeated reintroduction of founders into a restored population, the fitness cost of genetic load remained lower than that borne by southern white rhinos. Without reintroductions, rapid growth of the restored population (>20-30% per generation) would be needed to maintain comparable fitness. Our results suggest that inbreeding depression from genetic load is not necessarily a barrier to recovery of the northern white rhino and demonstrate how restoration from biobanked cells relieves some constraints of conventional restoration from a limited founder pool. Established conservation methods that protect healthy populations will remain paramount, but emerging technologies hold promise to bolster these tools to combat the extinction crisis.

Dehorning Does Not Alter the Stress Response in Southern White Rhinoceroses (Ceratotherium simum simum) during Transport: A Preliminary Investigation.

Translocation and dehorning are common and important practices for rhinoceros management and conservation. It is not known if dehorning causes a stress response or negatively affects rhinoceroses during transport. Twenty-three subadult wild Southern white rhinoceros (Ceratotherium simum simum) bulls were immobilized and translocated >280 km for population management reasons. Ten animals were dehorned at capture, and 13 animals were transported without dehorning. For transport, five dehorned and six nondehorned rhinoceroses were sedated with azaperone (62.38±9.54 μg/kg) and five dehorned and seven nondehorned rhinoceroses with midazolam (64.61±9.28 μg/kg). Blood samples were collected at capture, start of transport, and after 6 h of transport. Measurements included 10 physiologic variables: hematocrit, total serum protein, creatine kinase (CK), aspartate aminotransferase, gamma-glutamyl transferase (GGT), creatinine, urea, cholesterol, β-hydroxybutyrate, and glucose; and four stress response variables: cortisol, epinephrine, neutrophil-to-lymphocyte ratio, and leukocyte coping capacity. Using a linear mixed model, CK and GGT were higher in dehorned compared with nondehorned rhinoceroses. There were no significant differences in the other variables between the two groups. The likely cause of these differences is that dehorned animals spent more time in the crate before the start of transport than nondehorned rhinoceroses (3:11±0:54 h vs. 1:12±0:56 h, P<0.001). These results indicate that dehorning does not negatively alter the white rhinoceros' physiologic and stress responses during translocation, supporting its use for antipoaching measures.

Sperm collection in rhinoceros via urethral catheterization

Assisted reproductive technologies are playing an ever-increasing role in the management of ex situ rhinoceros populations. Traditionally, sperm collection in rhinos is conducted via electroejaculation (EEJ) or gamete rescue. Sperm collection via urethral catheterization (UC) is gaining popularity in wildlife reproductive sciences as it requires less specialized equipment, is faster, and less stimulatory than EEJ. This study investigated the use of UC to collect sperm from Southern white (Ceratotherium simum simum; n = 3) and Eastern black (Diceros bicornis michaeli; n = 6) rhinoceros as an alternative or complementary to collection via EEJ. UC samples (n = 14) exhibited high sperm concentration (1.6 ± 0.49 ×109 sperm/mL) and low volume (0.98 ± 0.26 mL). Samples obtained via EEJ (n = 11) were of moderate sperm concentration (0.14 ± 0.05 ×109 sperm/mL) and high volume (30.6 ± 7.2 mL). UC samples were processed for cryopreservation in OptiXcell extender. Motility of UC sperm decreased post-thaw (56 ± 2.4%) over pre-freeze (77.1 ± 3.2%; P < 0.05), with longevity data consistent to prior results published for sperm collected via EEJ. These results suggest sperm quality and cryo-survival are not impacted by the collection method. Since EEJ was conducted after UC, sperm parameters could not be compared between the two methods. Results indicate that UC is a viable alternative to EEJ for sperm collection in rhinoceros.

22 Transcriptomic analysis of granulosa cells in growing, dominant, and preovulatory follicles in the southern white rhinoceros (Ceratotherium simum simum)

22 Transcriptomic analysis of granulosa cells in growing, dominant, and preovulatory follicles in the southern white rhinoceros (Ceratotherium simum simum)

25 In vivo gene expression analysis of southern white rhinoceros (Ceratotherium simum simum) granulosa cells collected from growing, dominant, and preovulatory follicles after ovum pickup

25 In vivo gene expression analysis of southern white rhinoceros (Ceratotherium simum simum) granulosa cells collected from growing, dominant, and preovulatory follicles after ovum pickup

Parturition and Neonatal Parameters of Three Species of Rhinoceros under Managed Care in the United States

Rhinoceros species range from near threatened to critically endangered due to habitat loss and poaching. A sustainable ex situ breeding population is critically important to maintain genetic diversity and help ensure the survival of the species; however, not all populations under human care are self-sustaining. While rhinoceros reproductive physiology and pathology have been well studied, there is still a paucity of information describing the normal parameters of parturition and neonatal landmarks. Using video recordings, medical records, and keeper logs, we reviewed and compared data regarding the parturition of three rhinoceros species (black rhinoceros (BR) (Diceros bicornis), n = 4; greater one-horned rhinoceros (GOHR) (Rhinoceros unicornis), n = 21; and southern white rhinoceros (SWR) (Ceratotherium simum simum), n = 22) managed under human care in the United States. Using equine parameters as a model for comparison, we compiled the following data: the signs of impending parturition, durations of the parturition phases, calving presentation, frequency of dystocia or stillbirth, and time from birth to neonatal landmarks. Data from 47 births, including 26 videos, were examined. The durations of parturition phases I, II, and III had median lengths of 153 min (n = 18), 28 min (n = 21), and 205 min (n = 15), respectively. Anterior presentation of the calf was observed in 59% births, whereas posterior presentation occurred in 41% births. Posterior calving presentation was associated with a longer phase II of parturition (p = 0.04), although more data are needed to determine whether the posterior presentation of the calf carries a higher risk for stillbirth. Most (83%) stillbirths occurred in GOHR, indicating that this species might be at a higher risk for stillbirth compared to SWR (17%) (p = 0.07). The median time from birth to the calf standing was longer in the GOHR (64 min) compared to the SWR (30 min) (p = 0.02). Detailed descriptions of the parturition parameters and neonatal landmarks in rhinoceros will aid facilities with rhinoceros breeding programs to recognize abnormalities in the parturient or post-partum periods and guide indications for veterinary intervention.

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome.

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.

The neonatal southern white rhinoceros ovary contains oogonia in germ cell nests

The northern white rhinoceros is functionally extinct with only two females left. Establishing methods to culture ovarian tissues, follicles, and oocytes to generate eggs will support conservation efforts using in vitro embryo production. To the best of our knowledge, this is the first description of the structure and molecular signature of any rhinoceros, more specifically, we describe the neonatal and adult southern white rhinoceros (Ceratotherium simum simum) ovary; the closest relation of the northern white rhinoceros. Interestingly, all ovaries contain follicles despite advanced age. Analysis of the neonate reveals a population of cells molecularly characterised as mitotically active, pluripotent with germ cell properties. These results indicate that unusually, the neonatal ovary still contains oogonia in germ cell nests at birth, providing an opportunity for fertility preservation. Therefore, utilising ovaries from stillborn and adult rhinoceros can provide cells for advanced assisted reproductive technologies and investigating the neonatal ovaries of other endangered species is crucial for conservation.

In vitro fertilization program in white rhinoceros.

To save endangered rhinoceros species, assisted reproductive technologies are warranted. We here report in vitro blastocyst generation of the Near-Threatened Southern white rhinoceros and, for the first time, also of the technically Extinct Northern white rhinoceros. The Anthropocene is marked by a dramatic biodiversity decline, particularly affecting the family Rhinocerotidae. Three of five extant species are listed as Critically Endangered (Sumatran, Javan, black rhinoceros), one as Vulnerable (Indian rhinoceros), and only one white rhino (WR) subspecies, the Southern white rhinoceros (SWR), after more than a century of successful protection is currently classified as Near Threatened by the IUCN, while numbers again are declining. Conversely, in 2008, the SWR's northern counterpart and second WR subspecies, the Northern white rhinoceros (NWR), was declared extinct in the wild. Safeguarding these vanishing keystone species urgently requires new reproductive strategies. We here assess one such strategy, the novel in vitro fertilization program in SWR and - for the first-time NWR - regarding health effects, donor-related, and procedural factors. Over the past 8 years, we performed 65 procedures in 22 white rhinoceros females (20 SWR and 2 NWR) comprising hormonal ovarian stimulation, ovum pick-up (OPU), in vitro oocyte maturation, fertilization, embryo culture, and blastocyst cryopreservation, at an efficiency of 1.0 ± 1.3 blastocysts per OPU, generating 22 NWR, 19 SWR and 10 SWR/NWR hybrid blastocysts for the future generation of live offspring.

Performance of a manually operated salad spinner centrifuge for serum separation in the healthy domestic horse (Equus caballus) and southern white rhinoceros (Ceratotherium simum).

Field veterinarians and researchers studying wild species, such as the southern white rhinoceros, often work in remote areas with limited access to standard laboratory equipment, hindering the ability to measure serum analytes. The first objective was to produce an inexpensive, manually operated centrifuge that could accept standard laboratory tubes by modifying a consumer-grade salad spinner with low-cost materials. The second objective was to compare biochemistry analysis results obtained from equine and southern white rhinoceros serum separated by traditional laboratory and manual salad spinner centrifugation. We optimized the design and serum separation protocol using non-anticoagulated equine blood. Equine and rhinoceros serum samples were separated by manual salad spinner or traditional laboratory centrifugation. Measured analytes included sodium, potassium, chloride, urea nitrogen, creatinine, phosphorous, total calcium, magnesium, glucose, total protein, albumin, globulin, creatinine kinase, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma-glutamyl transferase, total bilirubin, bicarbonate, sorbitol dehydrogenase, and triglycerides. Results obtained from serum separated by each centrifugation technique were compared by Deming regression and Bland-Altman analyses. A tube adaptor insert modeled after a swing angle rotor and a two-step salad spinner centrifugation yielded serum comparable to traditional laboratory centrifugation. For the majority of analytes, no proportional or constant biases were detected between centrifugation methods. A positive proportional bias in the measurement of ALP in serum separated by manual centrifugation was detected in both equine and rhinoceros samples. Manual centrifugation with a modified salad spinner yields diagnostic quality serum suitable for the measurement of most standard biochemistry analytes.

Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo

BackgroundManaged southern white rhinoceros (Ceratotherium simum simum) serve as assurance populations for wild conspecifics threatened by poaching and other anthropocentric effects, though many managed populations experience subfertility and reproductive failure. Gut microbiome and host health are inextricably linked, and reproductive outcomes in managed southern white rhinoceros may be mediated in part by their diet and gut microbial diversity. Thus, understanding microbial dynamics within managed populations may help improve conservation efforts. We characterized the taxonomic composition of the gut microbiome in the managed population of female southern white rhinoceros (n = 8) at the North Carolina Zoo and investigated the effects of seasonality (summer vs. winter) and age classes (juveniles (n = 2; 0–2 years), subadults (n = 2; 3–7 years), and adults (n = 4; >7 years)) on microbial richness and community structure. Collection of a fecal sample was attempted for each individual once per month from July-September 2020 and January-March 2021 resulting in a total of 41 samples analyzed. Microbial DNA was extracted and sequenced using the V3-V4 region of the 16S rRNA bacterial gene. Total operational taxonomic units (OTUs), alpha diversity (species richness, Shannon diversity), and beta diversity (Bray-Curtis dissimilarity, linear discriminant analysis effect size) indices were examined, and differentially enriched taxa were identified.ResultsThere were differences (p < 0.05) in alpha and beta diversity indices across individuals, age groups, and sampling months. Subadult females had higher levels of Shannon diversity (Wilcoxon, p < 0.05) compared to adult females and harbored a community cluster distinct from both juveniles and adults. Samples collected during winter months (January-March 2021) possessed higher species richness and statistically distinct communities compared to summer months (July-September 2020) (PERMANOVA, p < 0.05). Reproductively active (n = 2) and currently nonreproductive adult females (n = 2) harbored differentially enriched taxa, with the gut microbiome of nonreproductive females significantly enriched (p = 0.001) in unclassified members of Mobiluncus, a genus which possesses species associated with poor reproductive outcomes in other animal species when identified in the cervicovaginal microbiome.ConclusionTogether, our results increase the understanding of age and season related microbial variation in southern white rhinoceros at the North Carolina Zoo and have identified a potential microbial biomarker for reproductive concern within managed female southern white rhinoceros.

Evolutionarily Young African Rhinoceros Gammaretroviruses.

High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses. IMPORTANCE Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.