Scaling methane emissions in ruminants and global estimates in wild populations

Water sprinkling as a tool for heat abatement in farmed Iberian red deer: Effects on calf growth and behaviour

Climatic models predict scenarios in which ambient temperature will continue increasing worldwide. Under these climatic conditions, fitness and animal welfare of many populations are expected to suffer, especially those that live in captive or semi-natural conditions, where opportunities of heat abatement are limited. We undertook an experimental design to assess the effect of heat abatement that water sprinkling might have on Iberian red deer calf growth and behaviour from birth to weaning (135 days). One group of ten mother-calf pairs lived on plots with water sprinkling (treatment) available during summer’s hottest time of the day, while the control group (nine mother-calf pairs) occupied plots with no available water sprinkling. Treatment and control groups were fed ad libitum and swapped between plots every seven days to minimise any plot effect. Body weight was monitored weekly and individual behaviour was recorded once or twice a week at mid-day. We observed that calves had showers under the sprinklers and wallowed in mud puddles. The results clearly indicated that calves of the treatment group showed a significant increase in body weight at weaning in comparison with the control group, with no differences between sexes (treatment: male = 56.5 kg, female = 50.3 kg; control: male = 50.3 kg, female = 46.5 kg). Mother weight and mother age effects were negligible on calf body weight at weaning. The heavier the mother the faster was the rate of growth of its offspring, irrespective of calf sex. The model indicated that although males grew significantly slower than female calves in the control group, males grew faster than females when exposed to the treatment. Calves of the treatment group spent less time drinking, less time in the shade, similar time eating and more time in motion than calves of the control group. There were no behavioural differences between calf sexes of treatment and control groups. The results indicate the importance of providing animals with opportunities of heat abatement in hot environments to improve animal growth and welfare in farmed Iberian red deer.

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.

Heat stress reduces growth rate of red deer calf: Climate warming implications

Climate models agree in predicting scenarios of global warming. In endothermic species heat stress takes place when they are upper their thermal neutral zone. Any physiological or behavioural mechanism to mitigate heat stress is at the cost of diverting energy from other physiological functions, with negative repercussions for individual fitness. Tolerance to heat stress differs between species, age classes and sexes, those with the highest metabolic rates being the most sensitive to stressing thermal environments. This is especially important during the first months of life, when most growth takes place. Red deer (Cervus elaphus) is supposedly well adapted to a wide range of thermal environments, based on its worldwide distribution range, but little is known about the direct effect that heat stress may have on calf growth. We assessed the effect that heat stress, measured by heat stress indices and physical environment variables (air temperature, relative air humidity, wind speed and solar radiation), have on calf and mother body weights from calf´s birth to weaning. We used 9265 longitudinal weekly body weight records of calf and mother across 19 years in captive Iberian red deer. We hypothesised that (i) heat stress in hot environments has a negative effect on calf growth, especially in males, as they are more energetically demanding to produce than females; and that (ii) the body weight of the mother through lactation should be negatively affected by heat stress. Our results supported hypothesis (i) but not so clearly hypothesis (ii). By weaning (day 143) calves growing under low heat stress environment grew up to 1.2 kg heavier than those growing in high heat stress environment, and males were more affected by heat stress than females. The results have implications in animal welfare, geographical clines in body size and adaptation to climate change.

Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation

Rumen fermentation is known to be effective for lignocellulosic-wastes biodegradation to certain extent but it is still unclear if there exists a termination of the microorganisms' action to further degrade the bio-refractory fractions. In order to illuminate the related microbiological characteristics, experiments were conducted in a prolonged duration of rumen fermentation of mechanically ruptured wheat straw, with inoculation of cow rumen microorganisms in vitro. Although the organic wastes could not be biodegraded quickly, continuous conversion of the lignocellulosic contents to volatile fatty acids and biogas proceeded in the duration of more than three months, resulting in 96-97% cellulose and hemicellulose decomposition, and 42% lignin decomposition. X-ray diffraction and Fourier transform infrared spectroscopy further demonstrated the characteristics of lignocellulosic structure decomposition. Under the actions of cow rumen microorganisms, stable pH was maintained in the fermentation liquid, along with a steady NH₄⁺-N, volatile fatty acids accumulation, and a large buffering ability. It was identified by enzyme analysis and Illumina MiSeq sequencing that the rich core lignocellulolytic enzymes secreted by the abundant and diverse rumen bacteria and fungi contributed to the persistent degradation of lignocellulosic wastes. Members of the Clostridiales order and Basidiomycota phylum were found to be the dominant lignocellulolytic bacteria and fungi, respectively. It could thus be inferred that the main lignocellulose degradation processes were a series of catalytic reactions under the actions of lignocellulolytic enzymes secreted from bacteria and fungi. The dominant hydrogenotrophic methanogens (Methanomassiliicoccus, Methanobrevibacter, Methanosphaera, and Methanoculleus) in the rumen could also assist CH₄ production if the rumen fermentation was followed with anaerobic digestion.

Review: Comparative methane production in mammalian herbivores

Methane (CH4) production is a ubiquitous, apparently unavoidable side effect of fermentative fibre digestion by symbiotic microbiota in mammalian herbivores. Here, a data compilation is presented of in vivo CH4 measurements in individuals of 37 mammalian herbivore species fed forage-only diets, from the literature and from hitherto unpublished measurements. In contrast to previous claims, absolute CH4 emissions scaled linearly to DM intake, and CH4 yields (per DM or gross energy intake) did not vary significantly with body mass. CH4 physiology hence cannot be construed to represent an intrinsic ruminant or herbivore body size limitation. The dataset does not support traditional dichotomies of CH4 emission intensity between ruminants and nonruminants, or between foregut and hindgut fermenters. Several rodent hindgut fermenters and nonruminant foregut fermenters emit CH4 of a magnitude as high as ruminants of similar size, intake level, digesta retention or gut capacity. By contrast, equids, macropods (kangaroos) and rabbits produce few CH4 and have low CH4 : CO2 ratios for their size, intake level, digesta retention or gut capacity, ruling out these factors as explanation for interspecific variation. These findings lead to the conclusion that still unidentified host-specific factors other than digesta retention characteristics, or the presence of rumination or a foregut, influence CH4 production. Measurements of CH4 yield per digested fibre indicate that the amount of CH4 produced during fibre digestion varies not only across but also within species, possibly pointing towards variation in microbiota functionality. Recent findings on the genetic control of microbiome composition, including methanogens, raise the question about the benefits methanogens provide for many (but apparently not to the same extent for all) species, which possibly prevented the evolution of the hosting of low-methanogenic microbiota across mammals.

Ericaceous species reduce methane emissions in sheep and red deer: Respiration chamber measurements and predictions at the scale of European heathlands

Despite the importance of atmospheric methane as a potent greenhouse gas and the significant contribution from ruminant enteric fermentation on methane emissions at a global scale, little effort has been made to consider the influence that different plant-based natural diets have on methane emissions in grazing systems. Heathland is an ericaceous dwarf-shrub-dominated habitat widespread across the northern hemisphere, in Europe, provides valuable ecosystem services in areas with poor soils, such as water flow regulation, land-based carbon skin, energy reservoir and habitat of key game species. We (i) measured methane emissions from red deer (Cervus elaphus) and sheep (Ovis aries) fed mixed diets of natural grass plus ericaceous species (either Calluna vulgaris or Vaccinium myrtillus) using open-circuit respiration chambers; and (ii) modelled the results to estimate methane emissions from red deer and sheep populations inhabiting heathland habitats across Europe under different scenarios of grass-based mixed diets with varying proportions of ericaceous species. Our results indicated that methane emissions per unit of digestible organic matter intake decreased as the proportion of ericaceous species in diet increased, but this relationship was complex because of the significant interaction between the proportion of ericaceous species in the diet and digestible organic matter intake. According to our estimates red deer and sheep populations across European heathlands produce 129.7 kt·y^-1 methane (se = 1.79) based on a hypothetical grass-ericaceous species mixed diet containing 30% of ericaceous species; this is 0.5% of total methane emissions from human activity across Europe (24,755 kt·y^-1), and a reduction in methane emissions of 63.8 kt·y^-1 against the same deer and sheep populations, if assumed to consume a grass-only diet. We suggest the implementation of carbon credits as a measure to value the relevance of heathland systems to promote biodiversity and its potential contribution to reduce methane emissions in ruminant grazing systems.

Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance

BACKGROUND

Enteric methane from the ruminant livestock is a significant source in global greenhouse gas emissions, which is mainly generated by the methanogens inhabiting the rumen and cecum. Sika deer (Cervus nippon) not only produces less methane than bovine, but they also harbor a distinct methanogen community. Whereas, knowledge of methanogens colonization in the rumen and cecum of sika deer is relatively still unknown, which could provide more insights to the manipulation of gut microbiota during early life.

RESULTS

Here, we examined the development of bacteria and methanogens in the rumen and cecum of juvenile sika deer from birth to post-weaning (1 day, 42 days and 70 days, respectively) based on next generation sequencing. The results showed that the facultative anaerobic bacteria were decreased and the cellulolytic bacteria were increased. However, methanogens established soon after birth thrived through the whole developmental period, indicating a different succession process than bacteria in the GIT, and the limited role of age and dietary change on GIT methanogens. We also found Methanobrevibacter spp. (Mean relative abundance = 44.2%) and Methanocorpusculum spp. (Mean relative abundance = 57.5%) were dominated in the rumen and cecum, respectively. The methanogens also formed specific correlations with bacteria under different niches, suggesting a role of ecology niche on methanogen community.

CONCLUSIONS

This study contributes to our knowledge about the microbial succession in GIT of sika deer, that may facilitate the development of targeted strategies to improve GIT function of sika deer.

Inferring symmetric and asymmetric interactions between animals and groups from positional data

Interactions between domestic and wild species has become a global problem of growing interest. Global Position Systems (GPS) allow collection of vast records of time series of animal spatial movement, but there is need for developing analytical methods to efficiently use this information to unravel species interactions. This study assesses different methods to infer interactions and their symmetry between individual animals, social groups or species. We used two data sets, (i) a simulated one of the movement of two grazing species under different interaction scenarios by-species and by-individual, and (ii) a real time series of GPS data on the movements of sheep and deer grazing a large moorland plot. Different time series transformations were applied to capture the behaviour of the data (convex hull area, k^th nearest neighbour distance, distance to centre of mass, Voronoi tessellation area, distance to past position) to assess their efficiency in inferring the interactions using different techniques (cross correlation, Granger causality, network properties). The results indicate that the methods are more efficient assessing by-group interaction than by-individual interaction, and different transformations produce different outputs of the nature of the interaction. Both species maintained a consistent by-species grouping structure. The results do not provide clear evidence of inter-species interaction based on the traditional framework of niche partitioning in the guild of large herbivores. In view of the transformation-dependent results, it seems that in our experimental framework both species co-exist showing complex interactions. We provide guidelines for the use of the different transformations with respect to study aims and data quality. The study attempts to provide behavioural ecologists with tools to infer animal interactions and their symmetry based on positional data recorded by visual observation, conventional telemetry or GPS technology.

Archaea: forgotten players in the microbiome

Archaea, the third domain of life containing unique membrane composition and highly diverse cell wall structures, were only recognized 40 years ago. Initially identified in extreme environments, they are currently recognized as organisms ubiquitously present in most, if not all, microbiomes associated with eukaryotic hosts. However, they have been mostly overseen in microbiome studies due to the lack of standardized detection protocols and to the fact that no archaeal pathogen is currently known. Recent years clearly showed that (i) archaea are part of the microbiomes associated with plants, animals and humans, (ii) form biofilms and (iii) interact and activate the human immune system. Future studies will not only define the host-associated diversity of archaea (referred to as 'archaeome') but also contribute to our understanding of the comprehensive metabolic interplay between archaea and bacteria and the long-term gain insights into their role in human health and their potential role(s) during disease development.

Review: Livestock production increasingly influences wildlife across the globe

With the growing human population, and their improving wealth, it is predicted that there will be significant increases in demand for livestock products (mainly meat and milk). Recent years have demonstrated that the growth in livestock production has generally had significant impacts on wildlife worldwide; and these are, usually, negative. Here I review the interactions between livestock and wildlife and assess the mechanisms through which these interactions occur. The review is framed within the context of the socio-ecological system whereby people are as much a part of the interaction between livestock and wildlife as the animal species themselves. I highlight areas of interaction that are mediated through effects on the forage supply (vegetation) - neutral, positive and negative - however, the review broadly analyses the impacts of livestock production activities. The evidence suggests that it is not the interaction between the species themselves but the ancillary activities associated with livestock production (e.g. land use change, removal of predators, provision of water points) that are the major factors affecting the outcome for wildlife. So in future, there are two key issues that need to be addressed - first, we need to intensify livestock production in areas of 'intensive' livestock production in order to reduce the pressure for land use change to meet the demand for meat (land sparing). And second, if wildlife is to survive in areas where livestock production dominates, it will have to be the people part of the socio-ecological system that sees the benefits of having wildlife co-exist with livestock on farming lands (land sharing and win-win).

Microbial technology with major potentials for the urgent environmental needs of the next decades

Several needs in the context of the water-energy-food nexus will become more prominent in the next decades. It is crucial to delineate these challenges and to find opportunities for innovative microbial technologies in the framework of sustainability and climate change. Here, we focus on four key issues, that is the imbalance in the nitrogen cycle, the diffuse emission of methane, the necessity for carbon capture and the deterioration of freshwater reserves. We suggest a set of microbial technologies to deal with each of these issues, such as (i) the production of microbial protein as food and feed, (ii) the control of methanogenic archaea and better use of methanotrophic consortia, (iii) the avoidance of nitrification and (iv) the upgrading of CO2 to microbial bioproducts. The central message is that instead of using crude methods to exploit microorganisms for degradations, the potentials of the microbiomes should be used to create processes and products that fit the demands of the cyclic market economy.

Archaea Are Interactive Components of Complex Microbiomes

Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.