The evolution of phylogenetic differences in the efficiency of digestion in ruminants

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Faecal nutrient deposition of domestic and wild herbivores in an alpine grassland

The contribution of herbivores to ecosystem nutrient fluxes through dung deposition has the potential to, directly and indirectly, influence ecosystem functioning. This process can be particularly important in nutrient-limited ecosystems such as alpine systems. However, herbivore dung content (carbon, C; nitrogen, N; phosphorus, P; potassium, K) and stoichiometry (C/N) may differ among species due to differences in diet, seasonality, body type, feeding strategy, and/or digestive system with consequences for soil biogeochemistry. Here we explore how species, body size, and seasonality may result in differences in dung stoichiometry for four alpine herbivores (chamois, sheep, horse, and cattle). We found that herbivore dung nutrient content often varies among species as well as with body size, with the dung of small herbivores having larger C, N, and P faecal content. Seasonality also showed marked effects on faecal nutrient content, with a general pattern of decreasing levels of faecal P, N and an increase of C/N as the summer progresses following the loss of nutrient value of the vegetation. Moreover, we showed how herbivores play an important role as natural fertilizers of C, N, and P in our study area, especially cattle. Our study highlights the importance of considering the relative contribution of different herbivores to ecosystem nutrient fluxes in management practices, especially with ongoing changes in wild and domestic herbivore populations in alpine ecosystems.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

"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.

Periodontitis Disease in Farmed Ruminants-Current State of Research

Periodontal disease in ruminants is common and occurs in farmed and wild animals. Periodontal lesions can result from the secretion of endotoxins by pathogenic bacteria and as consequences of immune system activity. Three main types of periodontitis have been described. The first is chronic inflammation involving mainly premolars and molars-periodontitis (PD). The second type is an acute inflammatory reaction occurring with calcification of the periosteum of the jawbone and swelling of the surrounding soft tissues (Cara inchada, CI-"swollen face"). Finally, a third type, similar to the first but located in the incisor area, is called "broken mouth" (BM). Etiological variation between the different types of periodontitis is indicated. This particularly manifests in the composition of the microbiome, which is characteristic of the different forms of periodontitis. The widespread detection of lesions has drawn attention to the current nature of the problem.

Description of Gut Mycobiota Composition and Diversity of Caprinae Animals

The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.

A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota

Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.

Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency

Feed efficiency is one of the economically important traits for the cattle industry that affects profit (feed costs) and the environment (production of manure and methane). Due to that feed efficiency is driven by multi-factors, mechanisms contributing to the animal to animal variation in this trait have not been well defined, limiting the development of precision feeding strategies to improve the herd production efficiency. Rumen microbial fermentation and volatile fatty acids (VFA) production have been recently reported to be associated with cattle feed efficiency, however the roles of rumen epithelial function in feed efficiency are less studied although the rumen epithelium has an important function in VFA absorption and metabolism which can affect host feed efficiency. Rumen epithelium is colonized with a diverse microbial population, termed epimural microbiota, which has proposed functions in tissue development, barrier and inflammation, urea transport, and oxygen scavenging, suggesting that they can affect rumen epithelial functions and subsequently cattle feed efficiency. Especially, prospective functions of epimural microbiota, enhanced rumen immunity and increased rumen epithelial thickness, might contribute to less nutritional requirement for tissue recuperation. Thus, the understanding of the functions of rumen epithelium, epimural microbiota, and rumen epithelial host-microbe interactions is essential to identify their roles in contributing to feed efficiency. In this review, we will focus on to date research findings on the structure of rumen epithelium, epimural microbiota, and epithelial host-microbe interactions together with their functions and how these are associated with feed efficiency, aiming to provide insights on future directions to study rumen epithelial host-microbe interactions and improve the rumen functions in cattle.

Geometric morphometrics of mandibles for dietary differentiation of Bovidae (Mammalia: Artiodactyla)

The mammalian family Bovidae has been widely studied in ecomorphological research, with important applications to paleoecological and paleohabitat reconstructions. Most studies of bovid craniomandibular features in relation to diet have used linear measurements. In this study, we conduct landmark-based geometric-morphometric analyses to evaluate whether different dietary groups can be distinguished by mandibular morphology. Our analysis includes data for 100 species of extant bovids, covering all bovid tribes and 2 dietary classifications. For the first classification with 3 feeding categories, we found that browsers (including frugivores), mixed feeders, and grazers are moderately well separated using mandibular shape. A finer dietary classification (frugivore, browser, browser-grazer intermediate, generalist, variable grazer, and obligate grazer) proved to be more useful for differentiating dietary extremes (frugivores and obligate grazers) but performed equally or less well for other groups. Notably, frugivorous bovids, which belong in tribe Cephalophini, have a distinct mandibular shape that is readily distinguished from all other dietary groups, yielding a 100% correct classification rate from jackknife cross-validation. The main differences in mandibular shape found among dietary groups are related to the functional needs of species during forage prehension and mastication. Compared with browsers, both frugivores and grazers have mandibles that are adapted for higher biomechanical demand of chewing. Additionally, frugivore mandibles are adapted for selective cropping. Our results call for more work on the feeding ecology and functional morphology of frugivores and offer an approach for reconstructing the diet of extinct bovids.

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

BACKGROUND

Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.

RESULTS

Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.

CONCLUSIONS

Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.

Rewilding Lite: Using Traditional Domestic Livestock to Achieve Rewilding Outcomes

The vision of rewilding is to return ecosystems to a “natural” or “self-willed” state with trophic complexity, dispersal (and connectivity) and stochastic disturbance in place. The concept is gaining traction, particularly in Europe where significant land abandonment has taken place in recent years. However, in reality, the purest form of rewilding (Rewilding Max) is constrained by a number of context-specific factors whereby it may not be possible to restore the native species that form part of the trophic structure of the ecosystem if they are extinct (for example, mammoths, Mammuthus spp., aurochs, Bos taurus primigenius). In addition, populations/communities of native herbivores/predators may not be able to survive or be acceptable to the public in small scale rewilding projects close to areas of high human density or agricultural land. Therefore, the restoration of natural trophic complexity and disturbance regimes within rewilding projects requires careful consideration if the broader conservation needs of society are to be met. Here we highlight the importance of herbivory as a key factor in rewilding. We argue that the use of the suite of livestock species, and in particular traditional breeds, offers the opportunity, under both land sharing/sparing strategies, to reinstate a more “natural” form of herbivory but still retain the option for management interventions (Rewilding Lite). It will even be possible to gain economic returns (ecotourism, sale of livestock products) from these systems, which will make them more acceptable to state and private landowners. We develop our case based on the advantages of using landraces versus de-domestication strategies, and on the implementation of eco-shepherding herbivory as a restoration tool in fine mosaics of agriculture/natural patches. If this approach is adopted, then larger areas can be given over to conservation, because of the potential broader benefits to society from these spaces and the engagement of farmers in practices that are closer to their traditions.

Tail regeneration alters the digestive performance of lizards

Tissue regeneration is a fundamental evolutionary adaptation, which is well known in lizards that can regenerate their entire tail. However, numerous parameters of this process remain poorly understood. Lizard tail serves many functions. Thus, tail autotomy comes with many disadvantages and the need for quick regeneration is imperative. To provide the required energy and materials for caudal tissue building, lizards are expected to undergo a number of physiological and biochemical adjustments. Previous research showed that tail regeneration induces changes in the digestive process. Here, we investigated if and how tail regeneration affects the digestive performance in five wall lizard species deriving from mainland and island sites and questioned whether the association of tail regeneration and digestion is affected by species relationships or environmental features, including predation pressure. We expected that lizards from high predation environments would regenerate their tail faster and modify accordingly their digestive efficiency, prioritizing the digestion of proteins; the main building blocks for tissue repair. Second, we anticipated that the general food shortage on islands would inhibit the process. Our findings showed that all species shifted their digestive efficiency, as predicted. Elongation rate was higher in sites with stronger predation regime and this was also applied to the rate with which protein digestion raised. Gut passage time increases during regeneration so as to improve the nutrient absorbance, but among the islanders, the pace was more intense. The deviations between species should be attributed to the different ecological conditions prevailing on islands rather than to their phylogenetic relationships.

Seasonal dietary changes increase the abundances of savanna herbivore species

African savannas are home to the world's last great megafaunal communities, but despite ongoing population declines, we only poorly understand the constraints on savanna herbivore abundances. Seasonal diet shifts (except migration) have received little attention, despite a diversity of possible dietary strategies. Here, we first formulate two theoretical models that predict that both mixed feeding and migratory grazing increase population sizes. These predictions are borne out in comprehensive data across African savanna parks: Mixed feeders are the most abundant herbivores in Africa, alongside a few migratory grazer populations. Overall, clear mixed-feeder dominance may reflect a historical pattern or may instead mirror a general global decline in specialists. Regardless, mixed feeders dominate the savannas of the present and future.

Are there phylogenetic differences in salivary tannin-binding proteins between browsers and grazers, and ruminants and hindgut fermenters?

While feeding, mammalian browsers (primarily eat woody plants) encounter secondary metabolites such as tannins. Browsers may bind these tannins using salivary proteins, whereas mammalian grazers (primarily eat grasses that generally lack tannins) likely would not. Ruminant browsers rechew their food (ruminate) to increase the effectiveness of digestion, which may make them more effective at binding tannins than nonruminants. Few studies have included a sufficient number of species to consider possible scaling with body mass or phylogenetic effects on salivary proteins. Controlling for phylogeny, we ran inhibition radial diffusion assays of the saliva of 28 species of African herbivores that varied in size, feeding strategy, and digestive system. We could not detect the presence of salivary proline-rich proteins that bind tannins in any of these species. However, using the inhibition radial diffusion assay, we found considerable abilities to cope with tannins in all species, albeit to varying degrees. We found no differences between browsers and grazers in the effectiveness of their salivary proteins to bind to and precipitate tannins, nor between ruminants and nonruminants, or scaling with body mass. Three species bound all tannins, but their feeding niches included one browser (gray duiker), one mixed feeder (bush pig), and one grazer (red hartebeest). Five closely related species of small ruminant browsers were very effective in binding tannins. Megaherbivores, considered generalists on account of their large body size, were capable of binding tannins. However, the grazing white rhinoceros was almost as effective at binding tannins as the megaherbivore browsers. We conclude, contrary to earlier predictions, that there were no differences in the relative salivary tannin-binding capability that was related to common ancestry (phylogeny) or to differences in body size.

Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.

Drivers of diet selection of critically endangered Western Derby eland during the food shortage period within conservation breeding in Senegal

Browsers represent a challenge for breeding facilities because of their sensitivity to nutritional management. Western Derby eland (Tautrotragus derbianus derbianus, WDE) is a large browsing antelope with a very diverse diet. Because of its critically endangered status, a small WDE population is kept for conservation purposes in the fenced Fathala reserve (Senegal) and during the critical, hot dry season, the animals are offered supplementary Acacia albida pods. We aimed to identify which woody plant species were preferentially selected/avoided by WDE during the period of food shortage, which plant nutritional properties were drivers of animals’ diet selection, and how this selectivity was affected by supplemental feed. The animals were selective for certain plant species, most for Piliostigma thonningi pods. Preferences decreased with a feed supplement, while avoidances remained intact. Diet selection was connected with chemical traits, mostly by negative correlations to N, Mg, Ca and hemicellulose, which disappeared or were weaker when supplemental feed was offered. Our findings indicate that large browsers during periods of food shortage must cope with inappropriate chemical composition in regard to nutrition and seek to alleviate them not only by diversification of plant species in the diet, but also by adjusting chemical diet quality as a whole.

Effects of intrinsic and extrinsic factors on ruminating, grazing, and bedding time in bighorn sheep (Ovis canadensis)

Rumination is the repeated process of regurgitation of a food bolus, followed by chewing, swallowing, and regurgitation, which enhance nutrient assimilation. Time spent in lateral recumbency (i.e., bedded, lying) has often been used as a proxy for time spent ruminating due to difficulties of observing detailed rumination behavior in the field. The actual proportion of time spent ruminating, or other activities, will in turn be affected by the age and sex of an individual but also with changes in food quality. We studied the effects of intrinsic and extrinsic factors on time spent ruminating, bedding, proportion of bedding time spent ruminating, and grazing of individually marked bighorn sheep (Ovis canadensis). Our results show that bighorn sheep spent more time ruminating and less time grazing in summer and autumn. Overall, females spent less time ruminating, and more time grazing than males. Bighorn sheep decreased their time spent ruminating with increasing acid detergent fiber (ADF) content in the forage. Age influenced the time spent grazing, bedded and proportion of bedded time spent ruminating. Older sheep not only increased their bedding time but also their time spent bedded without ruminating compared to younger individuals. The proportion of time spent grazing was also affected by age, with a decrease in the proportion of time spent grazing with increasing age. Our results suggest that these four behaviors are plastic and variable. We thus conclude that bedding time does not reflect time spent ruminating but that the latter is affected by both intrinsic and extrinsic factors.

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)

The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.

Do body size, diet type or residence time explain habitat use in a vertebrate herbivore community?

Many theories attempt to explain patterns of community organisation among large herbivores. We explored the role of body size, diet type and residence time on habitat use in a community comprising four metatherians (western grey kangaroo, Macropus fuliginosus; eastern grey kangaroo, M. giganteus; red-necked wallaby, Notamacropus rufogriseus; swamp wallaby, Wallabia bicolor) and two eutherians (red deer, Cervus elaphus; European rabbit, Oryctolagus cuniculus) in south-eastern Australia. We used camera traps to estimate habitat occupancy, quantified habitat specialisation using relative entropy, and ran regressions using percentage grass consumed, log(mass) and log(time at site) as predictor variables and relative entropy as the response. If body size influenced habitat use, we predicted smaller species would occupy fewer habitats. If diet type influenced habitat use, we predicted intermediate feeders would use more habitats. If the time that a species had been present at a site predicted community organisation, newer species would use more habitats. None of these theories explained habitat use in our community. Red deer used a narrower range of habitats than expected, perhaps due to the poor suitability of habitats available in the Grampians. While interactions between our hypotheses are likely to be important, the body size model deserves further attention in this community.

A continent-wide assessment of the form and intensity of large mammal herbivory in Africa

Megafaunal extinctions and a lack of suitable remote sensing technology impede our understanding of both the ecological legacy and current impacts of large mammal herbivores in the Earth system. To address this, we reconstructed the form and intensity of herbivory pressure across sub-Saharan Africa ~1000 years ago. Specifically, we modeled and mapped species-level biomass for 92 large mammal herbivores using census data, species distributions, and environmental covariates. Trait-based classifications of these species into herbivore functional types, and analyses of their biomass surfaces, reveal four ecologically distinct continental-scale herbivory regimes, characterized by internally similar forms and intensities of herbivory pressure. Associations between herbivory regimes, fire prevalence, soil nutrient status, and rainfall provide important insights into African ecology and pave the way for integrating herbivores into global-scale studies.

Climate and species richness predict the phylogenetic structure of African mammal communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.

An integrative assay to quantify the nutritional quality of the selected diet of two Mediterranean free-living deer by faecal-FT-NIRS

Integrating the interaction between cell wall components through a lignin and neutral detergent fibre ratio as a cell wall digestibility (CWD) index may provide a suitable method for diet quality and fibre digestibility estimation. Predictive faecal-Fourier-transform (FT)-near infrared reflectance spectroscopy (NIRS) equations useful for CWD determination were developed as an integrative assessment of the digestibility and quality of the diet selected by red (Cervus elaphus hispanicus) and fallow (Dama dama) deer in southern Spain. A chemometric regression was used from spectra of faeces and wet chemical rumen contents analysis as reference data coupled with partial least-squares. The accuracy and feasibility of the equations obtained for red and fallow deer samples separately were evaluated, as well as after pooling all samples for both species. The predictive equations had a high linearity with correlation coefficients (r) ranging between 0.89 and 0.99, as well as a reliable accuracy considering the errors of prediction (RMSEP 0.57–0.87), calibration (RMS 0.04–0.45) and cross-calibration (RMSECV 0.80–1.12) in relation to the range of values for which the NIRS calibration was set for each parameter, giving very good RER (residual error value) indices (7.44–13.23). The ability of the calibration equations to predict new samples from the same deer populations was also assessed through an external validation. Equations obtained for the red deer data were successfully applied not only to red deer but also to fallow deer, and vice versa. Feasible CWD simultaneous determination in red and fallow deer was also obtained by using the broad-based equations. There was variation of the CWD index throughout the year and differences between the two deer species. A lower CWD of the forage was recorded in red deer, while a lower CWD ratio was detected at the end of winter coinciding with the highest browsing levels in both species. This technique has potential to enable closer examination of the non-grass variables and distinguish between browse and herbage feeding behaviour. The faecal-NIRS method of CWD ratio determination is a useful, non-invasive tool for monitoring variations in the diet quality of Mediterranean deer in their natural environment.

Snout shape in extant ruminants

Snout shape is a prominent aspect of herbivore feeding ecology, interacting with both forage selectivity and intake rate. Previous investigations have suggested ruminant feeding styles can be discriminated via snout shape, with grazing and browsing species characterised by ‘blunt’ and ‘pointed’ snouts respectively, often with specification of an ‘intermediate’ sub-grouping to represent ambiguous feeding styles and/or morphologies. Snout shape morphology is analysed here using a geometric morphometric approach to compare the two-dimensional profiles of the premaxilla in ventral aspect for a large sample of modern ruminant species, for which feeding modes are known from secondary criteria. Results suggest that, when browsing and grazing ruminants are classified ecologically based on a range of feeding style indicators, they cannot be discriminated unambiguously on the basis of snout profile shape alone. Profile shapes in our sample form a continuum with substantial overlap between groupings and a diverse range of morphologies. Nevertheless, we obtained an 83.8 percent ratio of correct post hoc feeding style categorisations based on the proximity of projected profile shapes to group centroids in the discriminant space. Accordingly, this procedure for identifying species whose feeding strategy is ‘unknown’ can be used with a reasonable degree of confidence, especially if backed-up by additional information. Based on these results we also refine the definitions of snout shape varieties, taking advantage of the descriptive power that geometric morphometrics offers to characterize the morphological disparities observed. The shape variance exhibited by both browsing and grazing ruminants corresponds strongly to body mass, providing further evidence for an interaction between snout shape, feeding style, and body size evolution. Finally, by exploring the role of phylogenetic similarity in snout shape, we find a slight increase in successful categorisation when repeating the analysis with phylogenetic control on the geometric profiles.

Robustness and management adaptability in tropical rangelands: a viability-based assessment under the non-equilibrium paradigm

Rangelands provide the main forage resource for livestock in many parts of the world, but maintaining long-term productivity and providing sufficient income for the rancher remains a challenge. One key issue is to maintain the rangeland in conditions where the rancher has the greatest possibility to adapt his/her management choices to a highly fluctuating and uncertain environment. In this study, we address management robustness and adaptability, which increase the resilience of a rangeland. After reviewing how the concept of resilience evolved in parallel to modelling views on rangelands, we present a dynamic model of rangelands to which we applied the mathematical framework of viability theory to quantify the management adaptability of the system in a stochastic environment. This quantification is based on an index that combines the robustness of the system to rainfall variability and the ability of the rancher to adjust his/her management through time. We evaluated the adaptability for four possible scenarios combining two rainfall regimes (high or low) with two herding strategies (grazers only or mixed herd). Results show that pure grazing is viable only for high-rainfall regimes, and that the use of mixed-feeder herds increases the adaptability of the management. The management is the most adaptive with mixed herds and in rangelands composed of an intermediate density of trees and grasses. In such situations, grass provides high quantities of biomass and woody plants ensure robustness to droughts. Beyond the implications for management, our results illustrate the relevance of viability theory for addressing the issue of robustness and adaptability in non-equilibrium environments.

Herbivory and body size: allometries of diet quality and gastrointestinal physiology, and implications for herbivore ecology and dinosaur gigantism

Digestive physiology has played a prominent role in explanations for terrestrial herbivore body size evolution and size-driven diversification and niche differentiation. This is based on the association of increasing body mass (BM) with diets of lower quality, and with putative mechanisms by which a higher BM could translate into a higher digestive efficiency. Such concepts, however, often do not match empirical data. Here, we review concepts and data on terrestrial herbivore BM, diet quality, digestive physiology and metabolism, and in doing so give examples for problems in using allometric analyses and extrapolations. A digestive advantage of larger BM is not corroborated by conceptual or empirical approaches. We suggest that explanatory models should shift from physiological to ecological scenarios based on the association of forage quality and biomass availability, and the association between BM and feeding selectivity. These associations mostly (but not exclusively) allow large herbivores to use low quality forage only, whereas they allow small herbivores the use of any forage they can physically manage. Examples of small herbivores able to subsist on lower quality diets are rare but exist. We speculate that this could be explained by evolutionary adaptations to the ecological opportunity of selective feeding in smaller animals, rather than by a physiologic or metabolic necessity linked to BM. For gigantic herbivores such as sauropod dinosaurs, other factors than digestive physiology appear more promising candidates to explain evolutionary drives towards extreme BM.

Common solutions to resolve different dietary challenges in the ruminant dentition: the functionality of bovid postcanine teeth as a masticatory unit

Plasticity of tooth shape in mammals is of great adaptive value for the efficient exploitation of specific feeding niches and is a crucial mechanism for ecological diversification. In this study, we aimed to infer chewing effectiveness from the functional shape of different postcanine teeth within bovids, the most diverse extant group of large herbivorous mammals. We consider the postcanine dentition as a masticatory unit and test for differences related to food biomechanical properties, dietary abrasiveness, and chewing dynamics. We compare functional properties of the postcanine tooth row among species with well-known dietary strategies by integrating digitalization of high-resolution occlusal surface 3D-models of upper postcanine dentitions and quantification of the indentation index (D), a structural parameter representing enamel complexity. We test for differences in the occlusal shape among tooth positions in the postcanine dentition using robust, heteroscedastic tests in a one-way analysis of variance. Our results show three distinct patterns of enamel complexity along the tooth row: (1) D is more homogeneously distributed among tooth positions; (2) D increases gradually in the mesiodistal axis along the tooth row; and (3) D increases abruptly only at the transition between premolars and molars. We interpreted these patterns as different adaptive configurations of the postcanine tooth row relating to diet. Grass- and fruit-eating bovids show the same abrupt increase in enamel complexity at the transition from premolars to molars. Intermediate feeding and leaf-browsing species show the same gradual, mesiodistal increase in complexity along the tooth row. The absolute physical dietary resistance (biomechanical properties plus abrasiveness) and its relation to mechanical constraints of the chewing stroke are the likely selective factors leading to convergence of enamel complexity patterns along the tooth row among taxa with different diets.

Fibre digestibility in large herbivores as related to digestion type and body mass--an in vitro approach

The coexistence of different ungulate species in a given ecosystem has been the focus of many studies. Differences between ruminant foregut fermenters and hindgut fermenters were remarkable for example in the way they ingest and digest high fibre diets. Digestion trials based on total collections are difficult to conduct or are sometimes even not possible for wild animals in the field or in zoos. To gain information on the fibre digestion achieved by these animals and the influence of body mass (BM) thereon, a method using spot sampling is desirable. In this study, in vitro fermentation of faecal neutral detergent fibre (NDF) was used as a measure of fibre digestion in large ungulates. Food and faecal samples of 10 ruminant foregut fermenting and 7 hindgut fermenting species/breeds were collected. All animals received 100% grass hay with ad libitum access. The NDF of food and faeces was fermented in vitro in a Hohenheim gas test (HGT) for 96 h. The digestion type generally had an effect on the gas production (GP) of faecal NDF in the HGT with hindgut fermenters showing higher values than ruminant foregut fermenters. At any time interval of incubation, BM had no influence on GP. The results are in accordance with both findings that ruminant foregut fermenters have longer mean retention times and more comprehensive particle reduction and findings of a lack of influence of BM on digesta mean retention time. It can be stated that the HGT (96 h) is a useful and quick method to show also small differences within groups in fibre digestion.

Assessing the Jarman-Bell Principle: Scaling of intake, digestibility, retention time and gut fill with body mass in mammalian herbivores

Differences in allometric scaling of physiological characters have the appeal to explain species diversification and niche differentiation along a body mass (BM) gradient - because they lead to different combinations of physiological properties, and thus may facilitate different adaptive strategies. An important argument in physiological ecology is built on the allometries of gut fill (assumed to scale to BM(1.0)) and energy requirements/intake (assumed to scale to BM(0.75)) in mammalian herbivores. From the difference in exponents, it has been postulated that the mean retention time (MRT) of digesta should scale to BM(1.0-0.75)=BM(0.25). This has been used to argue that larger animals have an advantage in digestive efficiency and hence can tolerate lower-quality diets. However, empirical data does not support the BM(0.25) scaling of MRT, and the deduction of MRT scaling implies, according to physical principles, no scaling of digestibility; basing assumptions on digestive efficiency on the thus-derived MRT scaling amounts to circular reasoning. An alternative explanation considers a higher scaling exponent for food intake than for metabolism, allowing larger animals to eat more of a lower quality food without having to increase digestive efficiency; to date, this concept has only been explored in ruminants. Here, using data for 77 species in which intake, digestibility and MRT were measured (allowing the calculation of the dry matter gut contents (DMC)), we show that the unexpected shallow scaling of MRT is common in herbivores and may result from deviations of other scaling exponents from expectations. Notably, DMC have a lower scaling exponent than 1.0, and the 95% confidence intervals of the scaling exponents for intake and DMC generally overlap. Differences in the scaling of wet gut contents and dry matter gut contents confirm a previous finding that the dry matter concentration of gut contents decreases with body mass, possibly compensating for the less favorable volume-surface ratio in the guts of larger organisms. These findings suggest that traditional explanations for herbivore niche differentiation along a BM gradient should not be based on allometries of digestive physiology. In contrast, they support the recent interpretation that larger species can tolerate lower-quality diets because their intake has a higher allometric scaling than their basal metabolism, allowing them to eat relatively more of a lower quality food without having to increase digestive efficiency.

Resource partitioning among African savanna herbivores in North Cameroon: the importance of diet composition, food quality and body mass

The relationship between herbivore diet quality, and diet composition (the range of food plants consumed) and body mass on resource partitioning of herbivores remains the subject of an ongoing scientific debate. In this study we investigated the importance of diet composition and diet quality on resource partitioning among eight species of savanna herbivore in north Cameroon, with different body mass. Dung samples of four to seven wild herbivore and one domesticated species were collected in the field during the dry and wet period. Diet composition was based on microhistological examination of herbivore droppings, epidermis fragments were identified to genus or family level. In addition, the quality of the faecal droppings was determined in terms of phosphorus, nitrogen and fibre concentrations. The results showed that there was no significant correlation between body mass and (differences in) diet composition for wet and dry season. When all species are considered, only significant relationships are found by the Spearman rank correlation analyses during the wet season between body mass and phosphorus and nitrogen, but this relationship did not exist during the dry season. When the analyses focuses on ruminants only (thus leaving out hippo), none of the relationships between body mass and diet quality was significant in either season. During the dry season the proportion of graminoids ranged between 10% (small unidentified herbivore species) to 90% (hippopotamus), during the wet season this proportion ranged from 60% (zebu) to 90% (hippopotamus). All species but zebu had more graminoids in their dung during wet season compared with dry season. However all species but hartebeest had more graminoids old stems in their dung during the dry season, compared with the wet season. The niche breadth for food categories consumed by kob (0.300), hippo (0.090), hartebeest (0.350), roan (0.510) and zebu (0.300) was much greater in the dry season than in the wet season for kob (0.120), hippo (0.020), hartebeest (0.190), roan (0.090) and zebu (0.200). When looking at grass taxa consumed, the niche breadth of kob (0.220), hartebeest (0.140), and roan (0.250) was also greater in the dry season when compared with the wet season for kob (0.050), hartebeest (0.120) and roan (0.120). The opposite was found for zebu and hippo. Comparison of the species’ diet compositions with randomized data showed that dietary overlap between different herbivore species was much higher than what would be expected on the basis of chance, demonstrating surprisingly limited niche separation between species. This offers potential for competition, but it is more likely that the high niche overlap indicates absence of competition, due to low herbivore densities and abundant food resources, permitting species to share non-limiting resources. With increasing herbivore densities and subsequent increasing scarcity of resources, the relationship between diet quality and body mass in combination with increased niche separation is expected to become more visible.

The effect of tannins on Mediterranean ruminant ingestive behavior: the role of the oral cavity

Sheep, cattle and goat are domestic ruminants of significant economic interest in the Mediterranean region. Although sharing the same pasture ranges, they ingest different plants and plant parts and, consequently different levels of tannins. This suggests an ability to detect and adapt ingestion according to animal physiological limits of tolerance for plant secondary metabolites. This review will detail the effects of dietary tannins on feeding behavior, and the role of the oral cavity in this process, with focus on such ruminant species. The role of salivary protein profile in tannin perception in the oral cavity, and as a defense mechanism, will be discussed.

Methane output of tortoises: its contribution to energy loss related to herbivore body mass

An increase in body mass (M) is traditionally considered advantageous for herbivores in terms of digestive efficiency. However, recently increasing methane losses with increasing M were described in mammals. To test this pattern in non-mammal herbivores, we conducted feeding trails with 24 tortoises of various species (M range 0.52–180 kg) fed a diet of grass hay ad libitum and salad. Mean daily dry matter and gross energy intake measured over 30 consecutive days scaled to M^{0.75 (95%CI 0.64–0.87)} and M^{0.77 (95%CI 0.66–0.88)}, respectively. Methane production was measured over two consecutive days in respiration chambers and scaled to M^{1.03 (95%CI 0.84–1.22)}. When expressed as energy loss per gross energy intake, methane losses scaled to 0.70 (95%CI 0.47–1.05) M^{0.29 (95%CI 0.14–0.45)}. This scaling overlaps in its confidence intervals to that calculated for nonruminant mammals 0.79 (95%CI 0.63–0.99) M^{0.15 (95%CI 0.09–0.20)}, but is lower than that for ruminants. The similarity between nonruminant mammals and tortoises suggest a common evolution of the gut fauna in ectotherms and endotherms, and that the increase in energetic losses due to methane production with increasing body mass is a general allometric principle in herbivores. These findings add evidence to the view that large body size itself does not necessarily convey a digestive advantage.

Biology of the sauropod dinosaurs: the evolution of gigantism

The herbivorous sauropod dinosaurs of the Jurassic and Cretaceous periods were the largest terrestrial animals ever, surpassing the largest herbivorous mammals by an order of magnitude in body mass. Several evolutionary lineages among Sauropoda produced giants with body masses in excess of 50 metric tonnes by conservative estimates. With body mass increase driven by the selective advantages of large body size, animal lineages will increase in body size until they reach the limit determined by the interplay of bauplan, biology, and resource availability. There is no evidence, however, that resource availability and global physicochemical parameters were different enough in the Mesozoic to have led to sauropod gigantism. We review the biology of sauropod dinosaurs in detail and posit that sauropod gigantism was made possible by a specific combination of plesiomorphic characters (phylogenetic heritage) and evolutionary innovations at different levels which triggered a remarkable evolutionary cascade. Of these key innovations, the most important probably was the very long neck, the most conspicuous feature of the sauropod bauplan. Compared to other herbivores, the long neck allowed more efficient food uptake than in other large herbivores by covering a much larger feeding envelope and making food accessible that was out of the reach of other herbivores. Sauropods thus must have been able to take up more energy from their environment than other herbivores. The long neck, in turn, could only evolve because of the small head and the extensive pneumatization of the sauropod axial skeleton, lightening the neck. The small head was possible because food was ingested without mastication. Both mastication and a gastric mill would have limited food uptake rate. Scaling relationships between gastrointestinal tract size and basal metabolic rate (BMR) suggest that sauropods compensated for the lack of particle reduction with long retention times, even at high uptake rates. The extensive pneumatization of the axial skeleton resulted from the evolution of an avian-style respiratory system, presumably at the base of Saurischia. An avian-style respiratory system would also have lowered the cost of breathing, reduced specific gravity, and may have been important in removing excess body heat. Another crucial innovation inherited from basal dinosaurs was a high BMR. This is required for fueling the high growth rate necessary for a multi-tonne animal to survive to reproductive maturity. The retention of the plesiomorphic oviparous mode of reproduction appears to have been critical as well, allowing much faster population recovery than in megaherbivore mammals. Sauropods produced numerous but small offspring each season while land mammals show a negative correlation of reproductive output to body size. This permitted lower population densities in sauropods than in megaherbivore mammals but larger individuals. Our work on sauropod dinosaurs thus informs us about evolutionary limits to body size in other groups of herbivorous terrestrial tetrapods. Ectothermic reptiles are strongly limited by their low BMR, remaining small. Mammals are limited by their extensive mastication and their vivipary, while ornithsichian dinosaurs were only limited by their extensive mastication, having greater average body sizes than mammals.

Rumen physiology constrains diet niche: linking digestive physiology and food selection across wild ruminant species

We propose a hypothesis for digestive constraints on the browsing and grazing options available to ruminants: that the diet-niche range (maximum and minimum grass intake) of a species is dependent upon its predisposition to stratified rumen contents, based on observations that this characteristic is a critical step towards enhanced fibre digestion and greater fluid throughput. We compare a physiological (heterogeneity of ingesta fluid content) and an anatomical (the intraruminal papillation pattern) measure with dietary evidence for a range of African and temperate species. Both measures are strongly related to the mean percentage of grass in species’ natural diets, as well as to the maximum and minimum levels of grass intake, respectively. The nature of these effects implies a stratification-level threshold, below which a species will not use a grass-based diet, but above which grass consumption can increase exponentially. However, above this threshold, a minimum percentage of grass in the diet is a prerequisite for optimal performance. We argue that this second constraint is crucial, as it depicts how a greater fluid throughput reduces potential for detoxification of plant secondary compounds, and therefore limits the maximum amount of browse a stratifying species will consume.