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Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.
Microbiomas intestinales como indicadores clave de monitoreo para la reintroducción de animales cautivos Resumen Los programas de reintroducción buscan restaurar las poblaciones degradadas y revertir la pérdida de la biodiversidad. Realizamos un monitoreo metagenómico intensivo durante más de diez años para caracterizar la sucesión ecológica y la evolución adaptativa de los simbiontes intestinales de pandas reintroducidos en la naturaleza y así comprobar la hipótesis de que estos simbiontes pueden usarse como indicadores de una reintroducción exitosa. Recolectamos 63 muestras fecales de tres individuos reintroducidos y 22 de nueve individuos silvestres y usamos 96 muestras disponibles al público de otros tres individuos cautivos. Mediante el análisis de la composición microbiana identificamos tres grupos comunitarios del microbioma intestinal (denominados como enterotipos) con una sucesión entre enterotipos relacionada cercanamente al proceso de reintroducción. Identificamos cada uno de los tres enterotipos con base en la variación significativa en los niveles de uno de los tres géneros: Clostridium, Pseudomonas, y Escherichia. El enterotipo de los pandas cautivos fue Escherichia. A este enterotipo lo reemplazó gradualmente el enterotipo de Clostridium durante el proceso de adaptación a la naturaleza, y a su vez fue reemplazado por el enterotipo de Pseudomonas similar al de los pandas silvestres, un indicador de la conversión a la vida silvestre y de una reintroducción exitosa. También aislamos una cepa de Pseudomonas protegens del enterotipo silvestre, un microbio reportado previamente como de vida libre, y descubrimos que su evolución dentro del hospedero contribuyó a que este se adaptara a la naturaleza de la dieta. El monitoreo de la estructura microbiana intestinal proporciona una herramienta novedosa y no invasiva que puede usarse como indicador del éxito de la reintroducción de un individuo cautivo a la naturaleza.
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Microbioma Gastrointestinal , Ursidae , Humanos , Animales , Conservación de los Recursos Naturales , Biodiversidad , Heces , DietaRESUMEN
China announced the development of its first 5 national parks in 2021, the primary objective of which is to conserve the natural state and integrity of natural ecosystems. As such, ecosystem services and biodiversity levels are crucial assessment factors for the parks. For Giant Panda National Park (GPNP), we evaluated ecological sensitivity based on water and soil erosion and rocky desertification; ecosystem services based on headwater conservation, soil and water conservation, and biodiversity conservation; and presence of giant panda (Ailuropoda melanoleuca) and sympatric species (e.g., takin [Budorcas taxicolor], Asiatic black bear [Ursus thibetanus]) habitat suitability derived from niche modeling to identify the ecosystem status and assess ecological problems within the park. From our results, we proposed ecologically critical areas to target to meet the park's goals. The suitable habitat for pandas and sympatric species encompassed 62.98% of the park and occurred mainly in the Minshan Mountains. One quarter of the total area (25.67%) contained areas important for ecosystem services. Ecologically sensitive and extremely sensitive areas covered 88.78% of the park and were distributed mainly in Qionglaishan and Minshan Mountains. This coverage indicated that there was much habitat for pandas and sympatric species but that the ecosystems in GPNP are vulnerable. Therefore, ecologically critical areas encompassed all suitable habitats for all the species examined and areas important and extremely important to ecosystem service provision,ecologically sensitive and extremely sensitive areas, encompassed 15.17% of panda habitat, accounted for 16.37% of the GPNP area, and were distributed mainly in the Minshan Mountains. Our results indicated where conservation efforts should be focused in the park and that by identifying ecologically critical areas managers can provide targeted protection for wildlife habitat and ecosystems and effectively and efficiently protect the composite ecosystem. Additionally, our methods can be used to inform development of new national parks.
Medición de los servicios ambientales y la sensibilidad ecológica para una conservación integral en el Parque Nacional del Panda Gigante Resumen China anunció el crecimiento de sus primeros cinco parques nacionales en 2021, con el objetivo principal de conservar el estado natural y la integridad de los ecosistemas naturales. Para ello, los servicios ambientales y los niveles de biodiversidad son factores cruciales de evaluación para los parques. Para poder identificar el estado del ecosistema y evaluar los problemas ecológicos dentro del Parque Nacional del Panda Gigante (PNPG), analizamos la sensibilidad ecológica con base en la erosión del agua y del suelo y la desertificación rocosa; los servicios ambientales con base en el suministro de conservación del agua, del agua y del suelo y de la biodiversidad; y la idoneidad de hábitat del panda gigante (Ailuropoda melanoleuca) y de especies simpátricas (takín [Budorcas taxicolor], oso negro asiático [Ursus thibetanus]) derivada del modelo de nichos. A partir de nuestros resultados proponemos enfocarnos en áreas ecológicamente críticas para lograr los objetivos del parque. El hábitat idóneo para los pandas y las especies simpátricas englobó el 62.98% del parque y se ubicó principalmente en las montañas Minshan. Un cuarto del área total (25.67%) albergó áreas importantes para los servicios ambientales. Las áreas ecológicamente sensibles y extremadamente sensibles cubrieron el 88.78% del parque y se distribuyeron en las montañas Minshan y Qionglaishan. Esta cobertura indica que hay bastante hábitat para los pandas y las especies simpátricas pero que los ecosistemas en el PNPG son vulnerables. Por lo tanto, las áreas ecológicamente críticas englobaron todos los hábitats para todas las especies analizadas y todas las áreas importantes y extremadamente importantes para el suministro de servicios ambientales. Las áreas ecológicamente sensibles y extremadamente sensibles englobaron el 15.17% del hábitat del panda, representaron el 16.37% del área del PNPG y se localizaron principalmente en las montañas Minshan. Nuestros resultados indican en dónde se deben enfocar los esfuerzos de conservación dentro del parque y que, si identificamos las áreas ecológicamente críticas, los gestores pueden proporcionar una protección focalizada para el hábitat y los ecosistemas y así proteger efectiva y eficientemente el ecosistema compuesto. Además, nuestro método puede usarse para guiar el desarrollo de nuevos parques nacionales.
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Ecosistema , Ursidae , Animales , Parques Recreativos , Conservación de los Recursos Naturales/métodos , Biodiversidad , ChinaRESUMEN
The use of umbrella species to promote biodiversity conservation is practiced worldwide. The giant panda (Ailuropoda melanoleuca) an iconic species for world wildlife conservation, that inhabits regions with significant biodiversity. Given that the functions at wildlife of different trophic levels and in different body size groups are different within the ecosystem, it is unknown whether those groups of wildlife co-occurring with giant pandas are each likewise protected. To examine the umbrella effect of giant pandas on sympatric species, we used an extensive dataset of wildlife from more than 78% of giant panda habitats. We analysed the changes in distribution for four wildlife categories (large carnivores, large herbivores, medium carnivores and medium herbivores) using a generalized linear mixed model, and the underlying driving factors using binomial logistic regression models. Changes in forests in giant panda habitats were evaluated using Fragstats. The results have shown that the counts of herbivores and medium carnivores increased significantly during the decade. However, those of large carnivores significantly declined. Forest cover and nature reserves showed significant and positive effects on wildlife in 2001 and 2011, while the human population had significant and negative impacts on the herbivores and carnivores. Our results have also suggested that there has been a slight alleviation in forest fragmentation in areas unaffected by earthquakes. We concluded that the umbrella strategy of using the giant panda as an umbrella species achieved partial success by promoting the recovery of herbivores and medium carnivores. Meanwhile, this has indicated that the strategy was not sufficient for large carnivores, and therefore not enough for local ecosystems, given the critical role of large carnivores. We have suggested integrating habitat patches, controlling human disturbance, and preparing for potential human-wildlife conflict management in the Giant Panda National Park to restore large carnivore populations and maintain ecosystem functioning.
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Ursidae , Animales , Humanos , Ecosistema , Conservación de los Recursos Naturales/métodos , Simpatría , Biodiversidad , Animales Salvajes , ChinaRESUMEN
The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus "Chapparvovirus", and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
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Aves/virología , Heces/virología , Virus/genética , Virus/aislamiento & purificación , Animales , Genoma Viral , Metagenoma , Filogenia , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/veterinaria , Virus/clasificaciónRESUMEN
BACKGROUND: Polyomaviruses infect a wide variety of mammalian and avian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. METHODS: Viral metagenomics and general PCR methods were used to detected viral nucleic acid in the samples from a diseased and healthy giant pandas. RESULTS: A novel polyomavirus, the giant panda polyomavirus 1 (GPPyV1) from the nasal cavity of a dead giant panda (Ailuropoda melanoleuca) was characterized. The GPPyV1 genome is 5144 bp in size and reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. Phylogenetic analyses of the large T antigen of the GPPyV1 indicated GPPyV1 belonged to a putative new species within genus Deltapolyomavirus, clustering with four human polyomavirus species. The GPPyV1 VP1 and VP2 clustered with genus Alphapolyomavirus. Our epidemiologic study indicated that this novel polyomavirus was also detected in nasal swabs and fecal samples collected from captive healthy giant pandas. CONCLUSION: A novel polyomavirus was detected in giant pandas and its complete genome was characterized, which may cause latency infection in giant pandas.
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Cavidad Nasal/virología , Poliomavirus/clasificación , Ursidae/virología , Animales , Genes Virales , Genoma Viral , Genómica/métodos , Filogenia , Poliomavirus/genética , Poliomavirus/aislamiento & purificación , Secuenciación Completa del GenomaRESUMEN
Giant panda (Ailuropoda melanoleuca) conservation is a possible success story in the making. If extinction of this iconic endangered species can be avoided, the species will become a showcase program for the Chinese government and its collaborators. We reviewed the major advancements in ecological science for the giant panda, examining how these advancements have contributed to panda conservation. Pandas' morphological and behavioral adaptations to a diet of bamboo, which bear strong influence on movement ecology, have been well studied, providing knowledge to guide management actions ranging from reserve design to climate change mitigation. Foraging ecology has also provided essential information used in the creation of landscape models of panda habitat. Because habitat loss and fragmentation are major drivers of the panda population decline, efforts have been made to help identify core habitat areas, establish where habitat corridors are needed, and prioritize areas for protection and restoration. Thus, habitat models have provided guidance for the Chinese governments' creation of 67 protected areas. Behavioral research has revealed a complex and efficient communication system and documented the need for protection of habitat that serves as a communication platform for bringing the sexes together for mating. Further research shows that den sites in old-growth forests may be a limiting resource, indicating potential value in providing alternative den sites for rearing offspring. Advancements in molecular ecology have been revolutionary and have been applied to population census, determining population structure and genetic diversity, evaluating connectivity following habitat fragmentation, and understanding dispersal patterns. These advancements form a foundation for increasing the application of adaptive management approaches to move panda conservation forward more rapidly. Although the Chinese government has made great progress in setting aside protected areas, future emphasis will be improved management of pandas and their habitat.
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Conservación de los Recursos Naturales , Especies en Peligro de Extinción , Ursidae/fisiología , Animales , ChinaRESUMEN
Scent marking sites served as a primary means of chemical communication for giant pandas, enabling intraspecific communication. We integrated metabolomics and high-throughput sequencing techniques to examine the non-targeted metabolome and microbial community structure of scent marking sites and feces in the field. Integrative analysis revealed a more comprehensive array of chemical compounds compared to previous investigations, including ketones, acids, heterocycles, alcohols, and aldehydes. Notably, specific compounds such as 2-decenal, (E)-, octanal, decanal, L-α-terpineol, vanillin, and nonanal emerged as potential key players in scent signaling. Intriguingly, our study of the microbial domain identified dominant bacterial species from the Actinobacteria, Bacteroidetes, and Proteobacteria phyla, likely orchestrating metabolic processes at scent marking sites. Comparative analyses showed, for the first time, that feces do not share the same functions as scent markers, indicating distinct functional roles. This research deepens scientific understanding of chemical communication in wild pandas.
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As human activities continue to expand, wildlife persistence faces escalating threats from roads. In Wolong area of Giant Panda National Park, the local giant pandas (Ailuropoda melanoleuca) are divided into two population groups along the National Highway G350 (NHG). Therefore, selecting suitable areas to help those giant pandas communicate across the NHG is necessary. In this research, we evaluated the presence of human activities and simulated their absence to analyze how they affect the giant panda's habitat in Wolong. Subsequently, based on the kernel density estimation (KDE) for giant pandas and the main human distribution locations, we selected suitable areas for the population link between the two road sections on the NHG. We simulated the absence of human activities on the two road sections to compare changes in the habitat suitability index (HSI) and connectivity value (CV) relative to their presence. We aimed to carefully select the area for future giant panda corridor plans and simulate whether eliminating human activities will significantly improve the HSI and CV of the area. Our results show that: (1) Human activities presence has led to subtle changes in the landscape pattern of suitable habitats and a decrease in Wolong by 78.76 km2 compared to their absence. (2) Human activities presence significantly reduced HSI and CV in the 1000 m buffer along the NHG compared to their absence. (3) The HSI and CV of the 1000 m buffer in the simulated absence of human activities for the two road sections were significantly higher than their presence. This research identified the optimal road section for crossing the NHG to link giant panda population groups and habitats in Wolong. These insights are significant for formulating conservation decisions and corridor plans and for promoting wildlife conservation in reserves amid high levels of human activity.
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Physiological indexes like blood parameters have been widely used to monitor the health of free-roaming animals. Attempts to reintroduce one of China's most endangered species, the giant panda (Ailuropoda melanoleuca), have been hampered by a lack of data on its ecology and physiology. We examined three giant pandas' hematological and blood chemistry parameters in a soft release program and 30 captive giant pandas as controls and determined the reference intervals (RIs) for those blood parameters in the captive animals. Elevation, captivity status and the interaction of those factors were statistically significant for hematologic measures. Release pandas had significantly higher hemoglobin and hematocrit values after they moved to high elevation locations. We also found significant difference in the enzyme parameters between high and low elevation pandas such as higher aspartate aminotransferase, alanine aminotransferase, creatinine kinase, amylase and lower lactate dehydrogenase and alkaline phosphatase. Release pandas also had higher nutrition parameter values such as higher albumin, globulin and creatinine. The RI for blood parameters in our study provides a baseline to monitor the health of captive animals and forms the basis for assessing the health of free-roaming giant pandas in future reintroduction efforts.
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The giant panda (Ailuropoda melanoleuca) was taken to the brink of extinction in the 1980s through a combination of deforestation, large-scale loss of bamboo in the core of its range, poaching, and zoo collection, causing over 1000 deaths from the 1950s. It was thought that the drastic population decline was likely to impose a severe impact on population viability. Here, based on temporal genotyping of individuals, we show that this rapid decline did not significantly reduce the overall effective population size and genetic variation of this species, or of the two focal populations (Minshan and Qionglai) that declined the most. These results are contrary to previously assumptions, probably because the population decline has not produced the expected negative impact due to the short time scale involved (at most 10 generations), or because previous surveys underestimated the population size at the time of decline. However, if present-day habitat fragmentation and limited migration of giant pandas remains, we predict a loss of genetic diversity across the giant pandas' range in the near future. Thus, our findings highlight the substantial resilience of this species when facing demographic and environmental stochasticity, but key conservation strategies, such as enhancing habitat connectivity and habitat restoration should be immediately implemented to retain the extant genetic variation and maintain long-term evolutionary potential of this endangered species.
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Ecosistema , Actividades Humanas , Ursidae/genética , Ursidae/fisiología , Animales , ADN Mitocondrial/genética , Demografía , Variación Genética , Humanos , Repeticiones de Microsatélite , Factores de TiempoRESUMEN
Fat storage and weight gain are dominant traits for hibernating mammals. However, excessive fat accumulation may cause liver damage. Here, we explore the lipid accumulation and metabolic processes of the Himalayan marmot (Marmota himalayana), a hibernating rodent species. We find that the unsaturated fatty acid (UFA) content in food was consistent with a large increase in the body mass of Himalayan marmots. Metagenomic analysis shows that Firmicutes Bacterium CAG:110 plays a synergistic role by synthesizing UFAs, which is demonstrated by fecal transplantation experiments, indicating that the gut microbiome promotes fat storage in Himalayan marmots for hibernation. Microscopic examination results indicate that the risk of fatty liver appears at maximum weight; however, liver function is not affected. Upregulations of UFA catabolism and insulin-like growth factor binding protein genes provide an entry point for avoiding liver injury.
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Hígado Graso , Hibernación , Animales , Marmota/genética , Insulina , Ácidos Grasos , Hibernación/fisiologíaRESUMEN
The giant panda (Ailuropoda melanoleuca) and the Chinese red panda (Ailurus styani) are distributed in the same region in the mountain forest ecosystem on the eastern edge of the Qinghai Tibet Plateau and share the same food sources. In order to understand how sympatric giant pandas and Chinese red pandas maintain interspecific relationships to achieve stable coexistence, we used species distribution models and diurnal activity rhythms to analyze the spatial and temporal niche characteristics of giant pandas and Chinese red pandas in the Daxiangling Mountain system based on 187 camera traps data. The results show that: (1) In the Daxiangling Mountains, the total area of suitable habitats for giant pandas and Chinese red pandas is 717.61 km2 and 730.00 km2, respectively, accounting for 17.78% and 18.25%, respectively, of the study area. (2) The top five environmental factors contributing to the model of giant panda and Chinese red panda are precipitation seasonality, temperature seasonality, distance to the road, and elevation and vegetation type. (3) The total overlapping area of suitable habitats for giant pandas and Chinese red pandas is 342.23 km2, of which the overlapping area of highly suitable habitats is 98.91 km2. The overlapping index of suitable habitats is 0.472, and the overlapping index of highly suitable habitats is 0.348, which indicates that the two achieve spatial niches are separated to achieve stable coexistence. (4) The overlapping index of the daily activity rhythm of giant panda and Chinese red panda is 0.87, which is significantly different (p < .05). The existence of Chinese red panda will significantly affect the daily activity rhythm of giant panda (p < .001). This research can provide scientific reference for the researches about population and habitat protection of giant pandas and Chinese red pandas, so as to understand the driving mechanism of resource allocation and population dynamics of sympatric species.
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Ticks and tick-borne diseases have negative impacts on the health of wild animals including endangered and vulnerable species. The giant panda (Ailuropoda melanoleuca), a vulnerable and iconic flagship species, is threatened by tick infestation as well. Not only can ticks cause anemia and immunosuppression in the giant panda, but also bacterial and viral diseases. However, previous studies regarding tick infestation on giant pandas were limited in scope as case reports from sick or dead animals. In this study, an investigation focusing on the tick infestation of a reintroduced giant panda at the Daxiangling Reintroduction Base in Sichuan, China was conducted. Ticks were routinely collected and identified from the ears of the giant panda from March to September in 2021. A linear model was used to test the correlation between tick abundance and climate factors. All ticks were identified as Ixodes ovatus. Tick abundance was significantly different among months. Results from the linear model showed temperature positively correlated to tick abundance, while air pressure had a negative correlation with tick abundance. To the best of our knowledge, this study is the first reported investigation of tick species and abundance on a healthy giant panda living in the natural environment, and provides important information for the conservation of giant pandas and other species sharing the same habitat.
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Historically, giant panda conservation in China has been compromised by disparate management of protected areas. It is thus crucial to address how giant panda populations can be managed cohesively on a landscape scale, an opportunity offered by China's newly established Giant Panda National Park. Here, we evaluated giant panda populations in a metapopulation context, based on range-wide data from the Fourth National Giant Panda Survey. We delineated metapopulations by geographic range, relative abundance, and relative density and assessed the extent of human disturbance each metapopulation faced. We found density-dependent and disturbance-influenced effects on habitat selection across metapopulations. We determined the main effects faced by each metapopulation regarding area sensitivity, population size, intraspecific competition, and disturbance. To enhance the landscape-scale conservation of giant pandas and various other wildlife across China's national park system, we propose that metapopulation management incorporates population status along with density-dependent and disturbance-related effects on habitat selection.
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Cross-species transmission events were commonplace, with numerous cases of host-switching during the viral evolutionary history, but relatively little evidence for onward transmission in different species living in the same ecosystem. For understanding the communications of viruses in giant pandas (Ailuropoda melanoleuca) and their associated organisms, based on a large size of samples (N = 2305) collected between 2015 and 2020 from giant panda (N = 776) and other four giant panda-associated organisms in the same ecosystem, red pandas (N = 700), stray cats (N = 32), wild rats (N = 42), and mosquitoes (N = 755), viromics was used for the virus identification and subsequent virus traceability. The results showed that a feline panleukopenia virus (FPV) was found in giant pandas with clinical signs of vomiting and mild diarrhea. Meanwhile, the same FPV strain was also prevalent in the healthy red panda (Ailurus fulgens) population. From the viromes of the five different organisms, 250 virus genomes were determined. Our data revealed that besides FPV, other putative pathogenic viruses, such as red panda amdoparvoviruses (RPAVs) and Getah viruses (GETVs) were responsible for previous disease or death of some red pandas. We also demonstrated that a number of viruses were involved in potential interspecies jumping events between giant pandas and their associated species. Collectively, our results shed light on the genetic diversity and relationship of diverse viral pathogens in 'Giant pandas-Associated animals-Arthropods' and report some cases of possible viral host-switching among these host species living in the same ecosystem.
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Ursidae , Virus , Animales , Gatos , Ecosistema , Metagenómica , Filogenia , RatasRESUMEN
Dental caries severely hinders efficient access to adequate energy in wildlife. Different food supplies will develop characteristic plaque, and the microorganisms of these plaque are closely related to dental health. Here, plaque samples from panda cubs with caries and caries-free were collected for 16S rRNA high-throughput sequencing. All sequences clustered into 337 operational taxonomic units (OTUs; 97% identity), representing 268 independent species belonging to 189 genera, 98 families, 51 orders, 24 classes, and 13 phyla. Two groups shared 218 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in plaques with caries exceeded that of caries-free. The dominant phyla of plaque microbiota included Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. The dominant genera included unclassified Neisseriaceae, Actinobacillus, Lautropia, Neisseria, Porhyromonas, unclassified Pasteurellaceae, Moraxella, Streptococcus, Bergeywlla and Capnocytophaga. ß diversity analysis showed that the plaque microbial community structure was different between two groups. Using LEfSe analysis, 19 differentially abundant taxa were identified as potential biomarkers. Finally, function predictions analysis showed All the energy related metabolic pathways on KEGG level 2 were enriched in caries-active group. Consistent with the mainstream caries-causing narrative, our results illuminate the lack of information regarding the oral microflora composition and function within giant panda cubs.
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Caries Dental , Microbiota , Ursidae , Animales , Bacterias/genética , Humanos , Microbiota/genética , ARN Ribosómico 16S/genética , Ursidae/genéticaRESUMEN
To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.
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Tick infestations have been reported as one of the factors threatening the health of giant pandas, but studies of viral pathogens carried by ticks feeding on the blood of giant pandas are limited. To assess whether blood-sucking ticks of giant pandas can carry viral pathogens and if so, whether the viruses in ticks are associated with those previously detected in giant panda hosts, we determined the viromes of ticks detached from giant pandas in a field stocking area in Sichuan Province, southwest China. Using viral metagenomics we identified 32 viral species in ticks, half of which (including anellovirus [n = 9], circovirus [n = 3], and gemycircularvirus [n = 4]) showed homology to viruses carried by giant pandas and their associated host species (such as red pandas and mosquitoes) in the same living domain. Remarkably, several viruses in this study phylogenetically assigned as bunyavirus, hepe-like virus, and circovirus were detected with relatively high abundance, but whether these newly identified tick-associated viruses can replicate in ticks and then transmit to host animals during a blood meal will require further investigation. These findings further expand our understanding of the role of giant panda-infesting ticks in the local ecosystem, especially related to viral acquisition and transmission, and lay a foundation to assess the risk for giant panda exposure to tick-borne viruses. IMPORTANCE Ticks rank only second to mosquitoes as blood-feeding arthropods, capable of spreading pathogens (including viruses, bacteria, and parasites) to hosts during a blood meal. To better understand the relationship between viruses carried by ticks and viruses that have been reported in giant pandas, it is necessary to analyze the viromes of giant panda-parasitic blood-sucking ticks. This study collected 421 ticks on the body surface of giant pandas in Sichuan Province, China. We characterized the extensive genetic diversity of viruses harbored by these ticks and reported frequent communication of viruses between giant pandas and their ticks. While most of the virome discovered here are nonpathogenic viruses from giant pandas and potentially tick-specific viruses, we revealed some possible tick-borne viruses, represented by novel bunyaviruses. This research contributes to the literature because currently there are few studies on the virome of giant panda-infesting ticks.
Asunto(s)
Orthobunyavirus , Garrapatas , Ursidae , Virus , Animales , Ecosistema , Viroma/genética , Virus/genéticaRESUMEN
Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above-mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite-based Bayesian clustering clearly identified three groups (Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant isolation-by-distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large-scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai-Tibetan Plateau, subspecies classification and conservation of red pandas are discussed.
Asunto(s)
Ailuridae/genética , ADN Mitocondrial/genética , Variación Genética/genética , Genética de Población , Repeticiones de Microsatélite/genética , Ailuridae/clasificación , Animales , Secuencia de Bases , Teorema de Bayes , Conservación de los Recursos Naturales , ADN Mitocondrial/química , Ecosistema , Especies en Peligro de Extinción , Flujo Génico , Haplotipos , Humanos , Modelos Biológicos , Datos de Secuencia Molecular , Filogeografía , Análisis de Secuencia de ADN , TibetRESUMEN
The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.