Seasonal diet composition of Pyrenean chamois is mainly shaped by primary production waves

"Get the best out of what comes in" - adaptation of the microbiota of chamois (Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps

As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.

Feeding Ecology of the Cuvier's Gazelle (Gazella cuvieri, Ogilby, 1841) in the Sahara Desert

Knowledge of the feeding ecology of ungulates in arid biomes offers an interesting model for understanding the drought resistance of large desert-adapted herbivores, a crucial issue in the face of increasing desertification due to climate change. To assess the feeding ecology of the endangered Cuvier's gazelle (Gazella cuvieri) in the Sahara desert, we used a multi-method approach combining faecal samples, direct observations, and the recording of indirect signs of feeding. We hypothesised that browser behaviour is the best foraging strategy for species living in hyper-arid environments, mainly due to long periods without grazing opportunities. Complementarily, we explored the effects of the main environmental descriptors (rainfalls and NDVI) on feeding patterns and diet quality. We found that Cuvier's diets are based mainly on acacias (Vachellia tortilis, V. flava) and occasionally on the annual forb Anastatica hierochuntica. In total, eighteen species (five trees, nine shrubs, three herbs, and one grass) belonging to fifteen families were recorded. Our result confirmed the browsers' characteristic of this species, reaffirming its ability to settle in a hostile environment. Acacias stand out as key species consumed at the southernmost limit of their range; hence, future conservation plans and strategies should take this into account for the survival of Cuvier's gazelle in desert environments.

Grazing influences biomass production and protein content of alpine meadows

Alpine grasslands are essential for carbon sequestration and food supply for domestic and wild herbivores inhabiting mountainous areas worldwide. These biomes, however, are alternatively threatened by the abandonment of agricultural and livestock practices leading to a fast-growing shrubification process while other mountain grasslands are suffering from the impacts of overgrazing. The functioning of alpine meadow ecosystems is primarily driven by climatic conditions, land-use legacies and grazing. However, although it is critically important, the role of large herbivores on the aboveground biomass and protein content of palatable plants is poorly understood for most alpine meadows. In this work, we explore the effects of grazing on grassland vegetation at two different spatial and temporal scales in the Eastern Pyrenees, Spain. Remote sensing was used to assess the effect of high and moderate grazing (HG and MG respectively) on grass biomass using the leaf area index (LAI) at the meso-scale (patches between 2.3 and 38.7 ha). We also explored the impact of null (NG), overgrazing (MO, mimicked overgrazing) and high (HG) grazing intensities at local scale setting eighteen 1 m² exclusion boxes in six meadows (three boxes each) commonly used by domestic and wild ungulates. Historical satellite data showed that LAI values are greater in high than in low grazed areas (HG, mean = 0.66, LG, mean = 0.55). Along the same lines, high and moderate grazing pressures improved biomass production at the local-scale (HG, mean = 590.3 g/m², MO, mean = 389.3 g/m² and NG, mean = 110.8 g/m²). Crude protein content reached higher values under MO pressure than under HG pressure. Our results confirm that grazing intensity exerts significant changes on the above-ground biomass production and the protein content of plants consumed by domestic (cattle and horses) and wild ungulates (Southern Chamois, Rupicapra pyrenaica). We can conclude that ungulates sustain biomass and nutritive values of grass exerting a negligible effect on biomass and protein content of woody vegetation. Our results will inform management guidelines to support profitable grazing activities and promote conservation of the open landscapes in the alpine ecosystems under the current global change scenario.

Seasonal Differences in Fecal Microbial Community Structure and Metabolism of House-Feeding Chinese Merino Fine-Wool Sheep

The digestive tract microorganisms play a very important role in the host's nutrient intake, environmental suitability, and affect the host's physiological mechanism. Previous studies showed that in different seasons, mammalian gut microbes would be different. However, most of them are concentrated in wild animals. It remains unclear how seasonal change affects the gut microbes of Chinese merino fine-wool Sheep. Therefore, in this experiment, we continuously collected blood and feces samples of 50 Chinese merino fine-wool sheep in different seasons, measured the physiological indicators of blood, and passed 16S rRNA amplicon sequencing, determined the microbial community structure of fecal microorganisms and predicted flora function by PICRUSt. The results of blood physiological indicators showed that WBC, Neu and Bas in spring were significantly higher than those of other seasons. Fecal microbial sequencing revealed seasonal changes in gut microbial diversity and richness. Among them, Chinese merino fine-wool sheep had the highest gut microbes in summer. Firmicutes and Bacteroidetes were the dominant phyla, and they were unaffected by seasonal fluctuations. LEfSE analysis was used to analyze representative microorganisms in different seasons. The Lachnospiraceae and its genera (Lachnospiraceae_NK4A136_group, Lachnospiraceae_AC2044_group, g_unclassified_f_ Lachnospiraceae) were representative microorganisms in the three seasons of spring, summer and winter with harsh environmental conditions; while in autumn with better environmental conditions, the Ruminococcaceae and its genus (Ruminococcaceae_UCG-009 and Ruminococcaceae_UCG-005) were the representative microorganism. In autumn, the ABC transporter and the pyruvate metabolic pathway were significantly higher than other seasons. Correlation analysis results showed that Lachnospiraceae participated in the ABC transporters metabolic pathway, which caused changes in the blood physiological indicators. Overall, our results showed that, in response to seasonal changes, Chinese merino fine-wool sheep under house-feeding have adjusted their own gut microbial community structure, causing changes in the metabolism, and thus changing the physiological conditions of the blood. In the cold season, producers should focus on regulating the nutritional level of feed, enhancing the level of butyric acid in young animals to increase the ABC transporter, resist the external harsh environment, and improve the survival rate.

Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

Positive effect of spring advance on the diet quality of an alpine herbivore

Changes in vegetation phenology related to global warming are having alarming effects on the life history traits of many herbivore species. Such changes are particularly critical in alpine ecosystems, where strong climate limitations on plant growth make seasonal synchronization imperative for the growth, reproduction and survival of herbivores. However, despite the pivotal role of resource-use strategies on the performances of such species, few studies have explicitly assessed the mechanistic impact of climate change on their diets. We aimed to fill this gap by studying the effect of spring onset on the dietary composition and quality of a medium-size alpine herbivore while considering density-dependent processes and age- and sex-specific differences in foraging behavior. Using an exceptional, long-term (24 years) direct individual-based dietary monitoring of a Pyrenean chamois population (Rupicapra pyrenaica pyrenaica), we showed that ongoing earlier onsets of spring are leading to an earlier access to high-quality forage and therefore a higher diet quality at a fixed date, without apparent changes in diet composition. We also showed that at high densities, intraspecific competition reduced diet quality by driving animals to feed more on woody plants and less on nutritious forbs and graminoids. By assessing the mechanistic effects of global warming on the dietary patterns of species at the center of trophic networks, this study is an essential step for predictive models aiming at understanding the ongoing ecosystem consequences of the global climatic crisis.

Antimicrobial Resistance in Pasteurellaceae Isolates from Pyrenean Chamois (Rupicapra pyrenaica) and Domestic Sheep in an Alpine Ecosystem

Antimicrobial resistance (AMR) has spread worldwide due to the inappropriate use of antimicrobial drugs in human and veterinary medicine, becoming a public health problem. However, little is known about its occurrence and maintenance in wild animals, and very few studies have been carried out in ecosystems subjected to low human pressure. In our study, nasal and lung swabs were collected from hunted Pyrenean chamois (Rupicapra pyrenaica), and nasal swabs from sympatric domestic sheep were also collected. The swabs were cultured in agar plates to obtain bacterial isolates from the Pasteurellaceae family. The presence of AMR was assessed in a total of 28 Pasteurellaceae isolates from 45 Pyrenean chamois, and 9 isolates from sympatric domestic sheep found in the National Hunting Reserve of Freser-Setcases (Northeastern Pyrenees, Spain). The isolates belonged to one of the following three species: Pasteurella multocida, Mannheimia haemolytica and Bibersteinia trehalosi. Some P. multocida and M. haemolytica isolates tested positive for AMR. The statistical analysis revealed no differences between the AMR levels from chamois and domestic sheep isolates. However, one P. multocida of chamois origin presented resistance to cephalosporins and fluoroquinolones, which are antibiotics of critical importance for human health. Further studies are required to elucidate potential routes of dissemination of AMR genes in natural environments and assess any significant persistence in wildlife to design risk mitigation actions.

Near Infrared Reflectance Spectroscopy Analysis to Predict Diet Composition of a Mountain Ungulate Species

Simple Summary

Ungulates are characterized by their ability to modify or maintain habitats through their impact on plant species composition and the structure of vegetation. Assessing the diet composition of ungulates is therefore important to understand their role in the ecosystem integrity and to develop monitoring and population management plans. The diet composition of free-ranging ungulates has most often been assessed by time-consuming and cost-intensive approaches such as the direct observation of animals, chemical analysis, molecular approaches or microhistological analysis of fecal samples. Near infrared reflectance spectroscopy analysis would be a quick, economic and non-destructive alternative to assess diet composition using fecal samples. In this work, we evaluated the use of this spectroscopy method to assess the diet composition of the Pyrenean chamois (Rupicapra pyrenaica pyrenaica), a medium-size subalpine ungulate with a broad dietary niche. Our results support the reliability of the fecal spectroscopy analysis to monitor diet composition of free-ranging ungulates.

Abstract

The diet composition of ungulates is important to understand not only their impact on vegetation, but also to understand the consequences of natural and human-driven environmental changes on the foraging behavior of these mammals. In this work, we evaluated the use of near infrared reflectance spectroscopy analysis (NIRS), a quick, economic and non-destructive method, to assess the diet composition of the Pyrenean chamois Rupicapra pyrenaica pyrenaica. Fecal samples (n = 192) were collected from two chamois populations in the French and Spanish Pyrenees. Diet composition was initially assessed by fecal cuticle microhistological analysis (CMA) and categorized into four functional groups, namely: woody, herbaceous, graminoid and Fabaceae plants. Regressions of modified partial least squares and several combinations of scattering correction and derivative treatments were tested. The results showed that models based on the second derivative processing obtained the higher determination coefficient for woody, herbaceous and graminoid plants (R²_CAL, coefficient of determination in calibration, ranged from 0.86 to 0.91). The Fabaceae group, however, was predicted with lower accuracy (R²_CAL = 0.71). Even though an agreement between NIRS and CMA methods was confirmed by a Bland–Altman analysis, confidence limits of agreement differed by up to 25%. Our results support the viability of fecal NIRS analysis to study spatial and temporal variations of the Pyrenean chamois’ diets in summer and winter when differences in the consumption of woody and annual plants are the greatest. This new use for the NIRS technique would be useful to assess the consequences of global change on the feeding behavior of this mountain ungulate and also in other ungulate counterparts.

Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores

Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.

Seasonal Variation and Sexual Dimorphism of the Microbiota in Wild Blue Sheep (Pseudois nayaur)

Microbiota of the wild blue sheep (Pseudois nayaur) presents a seasonal variation due to different dietary selection and feeding strategies from different ecological niches chosen by different sex in summer. To address those issues, we analyzed the variation of gut microbiota based on the material from the feces, with 16S rRNA and meta-genome aimed to explore seasonal and gender differences. The results indicate that seasonal dietary changes and gender differentiation, as expected, cause the variation in sheep's gut microbiota structure. The variation of the former is more significant than the latter. Dominant Firmicutes exists a significantly higher abundance in summer than that in winter. Subordinate Bacteroides expresses no seasonal difference between the two seasons. Compared with the winter group, the summer group is featured by abundant enzymes digesting cellulose and generating short-chain fatty acids (SCFAs), such as beta-glucosidase (EC: 3.2.1.21) for cellulose digestion, and butyrate kinase (EC:2.7.2.7) in butyrate metabolism, implying that the changes of the composition in intestinal flora allow the sheep to adapt to the seasonalized dietary selection through alternated microbial functions to reach the goal of facilitating the efficiency of energy harvesting. The results also show that the blue sheep expresses a prominent sexual dimorphism in the components of gut microbiota, indicating that the two sexes have different adaptations to the dietary selection, and demands for physical and psychological purposes. Thus, this study provides an example of demonstrating the principles and regulations of natural selection and environmental adaptation.

Remote mapping of foodscapes using sUAS and a low cost BG-NIR sensor

The assessment of landscape condition for large herbivores, also known as foodscapes, is fast gaining interest in conservation and landscape management programs worldwide. Although traditional approaches are now being replaced by satellite imagery, several technical issues still need to be addressed before full standardization of remote sensing methods for these purposes. We present a low-cost method, based on the use of a modified blue/green/near-infrared (BG-NIR) camera housed on a small-Unmanned Aircraft System (sUAS), to create foodscapes for a generalist Mediterranean ungulate: the Iberian Ibex (Capra pyrenaica) in Northeast Spain. Faecal cuticle micro-histological analyses were used to assess the dietary preferences of ibexes and then individuals of the most common plant species (n = 19) were georeferenced to use as test samples. Because of the seasonal pattern in vegetation activity, based on the NDVI (Smooth term _Month = 21.5, p-value < .01, R² = 43%, from a GAM), images were recorded in winter and spring to represent contrasting vegetation phenology using two flight heights above ground level (30 and 60 m). Additionally, the range of image pixel sizes was 3.5-30 cm with the smallest pixel size representing the highest resolution. Boosted Trees were used to classify plant taxa based on spectral reflectance and create a foodscape of the study area. The number of target species, the sampling season, the height of flight and the image resolution were analysed to determine the accuracy of mapping the foodscape. The highest classification error (70.66%) was present when classifying all plant species using a 30 cm pixel size from acquisitions at 30 m height. The lowest error (18.7%), however, was present when predicting plants preferred by ibexes, at 3.5 cm pixel size acquired at 60 m height. This methodology can help to successfully monitor food availability and seasonality and to identify individual species.

Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates: A case study with Pyrenean chamois

The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) and emerging DNA-based methods being the most relevant. In this work, we refined and optimized a qualitative DNA-based approach combining PCR amplification of long trnL(UAA) and ITS2 fragments and capillary electrophoresis (PCR-CE), instead of short trnL(UAA) fragments and massive sequencing technologies commonly reported. To do so, we developed a controlled diet assay using a stabled Pyrenean chamois specimen (Rupicapra pyrenaica pyrenaica), which included representative herbaceous and shrubby plant species. We also assessed the impact of sample freshness on the diet determination of this mountain caprinae by exposing faecal samples to the outdoor environment for three weeks. Faecal samples from both experiments were analysed by qualitative PCR-CE and semi-quantitative CMA in order to compare the pros and cons of both approaches. Our results show that all of the offered plant species were detected by both methodologies although CMA over-detected shrubs compared to herbaceous species. At the same time, sample degradation due to sustained climate exposure is a limiting factor for molecular analysis, but not for CMA. Taken all together, our results suggest that the qualitative information obtained by CMA and PCR-CE can be interchangeable when faecal samples are fresh (less than one week after deposition) but, afterwards, molecular analysis underestimates diet composition probably due to DNA degradation. CMA, however, can accurately be used at least three weeks after defecation. Moreover, by combining the results of simultaneous PCR amplification of two complementary genes, this optimized PCR-CE methodology provides a reliable, feasible and more affordable alternative for multiple and routine analyses of complex samples. Neither CMA nor PCR-CE seems to solve comprehensively the quatification of herbivore diets and thus further research needs to be done.

Different effects of alpine woody plant expansion on domestic and wild ungulates

Changes in land-use and climate affect the distribution and diversity of plant and animal species at different spatiotemporal scales. The extent to which species-specific phenotypic plasticity and biotic interactions mediate organismal adaptation to changing environments, however, remains poorly understood. Woody plant expansion is threatening the extent of alpine grasslands worldwide, and evaluating and predicting its effects on herbivores is of crucial importance. Here, we explore the impact of shrubification on the feeding efficiency of Pyrenean chamois (Rupicapra p. pyrenaica), as well as on the three most abundant coexisting domestic ungulate species: cattle, sheep and horses. We use observational diet composition from May to October and model different scenarios of vegetation availability where shrubland and woodland proliferate at the expense of grassland. We then predicted if the four ungulate species could efficiently utilize their food landscapes with their current dietary specificities measuring their niche breath in each scenario. We observed that the wild counterpart, due to a higher trophic plasticity, is less disturbed by shrubification compared to livestock, which rely primarily on herbaceous plants and will be affected 3.6 times more. Our results suggest that mixed feeders, such as chamois, could benefit from fallow landscapes, and that mountain farmers are at a growing economic risk worldwide due to changing land-use practices and climate conditions.