Strategies to reduce methane emissions from farmed ruminants grazing on pasture

Relationship between Dairy Cow Health and Intensity of Greenhouse Gas Emissions

The dairy industry is facing criticism for its role in exacerbating global GHG emissions, as climate change becomes an increasingly pressing issue. These emissions mostly originate from methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2). An optimal strategy involves the creation of an economical monitoring device to evaluate methane emissions from dairy animals. Livestock production systems encounter difficulties because of escalating food demand and environmental concerns. Enhancing animal productivity via nutrition, feeding management, reproduction, or genetics can result in a decrease in CH4 emissions per unit of meat or milk. This CH4 unit approach allows for a more accurate comparison of emissions across different animal production systems, considering variations in productivity. Expressing methane emissions per unit allows for easier comparison between different sources of emissions. Expressing emissions per unit (e.g., per cow) highlights the relative impact of these sources on the environment. By quantifying emissions on a per unit basis, it becomes easier to identify high-emission sources and target mitigation efforts accordingly. Many environmental policies and regulations focus on reducing emissions per unit of activity or output. By focusing on emissions per unit, policymakers and producers can work together to implement practices that lower emissions without sacrificing productivity. Expressing methane emissions in this way aligns with policy goals aimed at curbing overall greenhouse gas emissions. While it is true that total emissions affect the atmosphere globally, breaking down emissions per unit helps to understand the specific contributions of different activities and sectors to overall greenhouse gas emissions. Tackling cattle health issues can increase productivity, reduce GHG emissions, and improve animal welfare. Addressing livestock health issues can also provide favourable impacts on human health by reducing the prevalence of infectious illnesses in livestock, thereby mitigating the likelihood of zoonotic infections transmitting to humans. The progress in animal health offers the potential for a future in which the likelihood of animal diseases is reduced because of improved immunity, more effective preventative techniques, earlier identification, and innovative treatments. The primary objective of veterinary medicine is to eradicate clinical infectious diseases in small groups of animals. However, as the animal population grows, the emphasis shifts towards proactive treatment to tackle subclinical diseases and enhance production. Proactive treatment encompasses the consistent monitoring and implementation of preventive measures, such as vaccination and adherence to appropriate nutrition. Through the implementation of these measures, the livestock industry may enhance both animal well-being and mitigate the release of methane and nitrous oxide, thereby fostering environmental sustainability. In addition, advocating for sustainable farming methods and providing farmers with education on the significance of mitigating GHG emissions can bolster the industry's endeavours to tackle climate change and infectious illnesses. This will result in a more robust and environmentally sustainable agriculture industry. This review seeks to conduct a thorough examination of the correlation between the health condition of cattle, the composition of milk produced, and the emissions of methane gas. It aims to identify areas where research is lacking and to provide guidance for future scientific investigations, policy making, and industry practices. The goal is to address the difficulties associated with methane emissions in the cattle industry. The primary global health challenge is to identify the causative relationship between climate change and infectious illnesses. Reducing CH4 and N2O emissions from digestive fermentation and animal manure can be achieved by improving animal well-being and limiting disease and mortality.

- Invited Review - The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production

Ruminal methane production functions as the main sink for metabolic hydrogen generated through rumen fermentation and is recognized as a considerable source of greenhouse gas emissions. Methane production is a complex trait affected by dry matter intake, feed composition, rumen microbiota and their fermentation, lactation stage, host genetics, and environmental factors. Various mitigation approaches have been proposed. Because individual ruminants exhibit different methane conversion efficiencies, the microbial characteristics of low-methane-emitting animals can be essential for successful rumen manipulation and environment-friendly methane mitigation. Several bacterial species, including Sharpea, uncharacterized Succinivibrionaceae, and certain Prevotella phylotypes have been listed as key players in low-methane-emitting sheep and cows. The functional characteristics of the unclassified bacteria remain unclear, as they are yet to be cultured. Here, we review ruminal methane production and mitigation strategies, focusing on rumen fermentation and the functional role of rumen microbiota, and describe the phylogenetic and physiological characteristics of a novel Prevotella species recently isolated from low methane-emitting and high propionate-producing cows. This review may help to provide a better understanding of the ruminal digestion process and rumen function to identify holistic and environmentally friendly methane mitigation approaches for sustainable ruminant production.

The contemporary nexus of medicines security and bioprospecting: a future perspective for prioritizing the patient

Reacting to the challenges presented by the evolving nexus of environmental change, defossilization, and diversified natural product bioprospecting is vitally important for advancing global healthcare and placing patient benefit as the most important consideration. This overview emphasizes the importance of natural and synthetic medicines security and proposes areas for global research action to enhance the quality, safety, and effectiveness of sustainable natural medicines. Following a discussion of some contemporary factors influencing natural products, a rethinking of the paradigms in natural products research is presented in the interwoven contexts of the Fourth and Fifth Industrial Revolutions and based on the optimization of the valuable assets of Earth. Following COP28, bioprospecting is necessary to seek new classes of bioactive metabolites and enzymes for chemoenzymatic synthesis. Focus is placed on those performance and practice modifications which, in a sustainable manner, establish the patient, and the maintenance of their prophylactic and treatment needs, as the priority. Forty initiatives for natural products in healthcare are offered for the patient and the practitioner promoting global action to address issues of sustainability, environmental change, defossilization, quality control, product consistency, and neglected diseases to assure that quality natural medicinal agents will be accessible for future generations.

Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle

Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.

Relevance of sward structure and forage nutrient contents in explaining methane emissions from grazing beef cattle and sheep

Forage nutrient contents are an important factor explaining the dry matter intake (DMI), average daily gain (ADG), and methane emissions (CH₄) of ruminants fed indoors. However, for grazing animals, the forage nutrient contents might be limited in explaining such response variables. We aimed to verify the explanatory power of forage nutrient contents and sward structure on daily intake, performance, and CH₄ emissions by sheep and beef cattle grazing different grassland types in southern Brazil. We analyzed data from five grazing trials using sheep and beef cattle grazing on Italian ryegrass (Lolium multiflorum), mixed Italian ryegrass and black oat (Lolium multiflorum + Avena strigosa), pearl millet (Pennisetum americanum), and multispecies native grassland. We used mixed models, including the forage nutrient contents [crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF)], sward structure (sward height and herbage mass) and their interactions, as fixed effects and trial, season, methodologies, animal species, grassland type, and paddock, as random effects. The model for DMI (kg DM/LW^0.75) had an adjusted coefficient of determination (R²_adj) of 71.6 %, where 11.3, 23.1, and 37.2 % of the R²_adj were explained by the forage nutrient contents, sward structure, and their interaction, respectively. The ADG (kg/LW^0.75) model presented an R²_adj of 74.2 %, with 12.5 % explained by forage nutrient contents, 29.3 % by sward structure, and 32.4 % by their interaction. The daily CH₄ emission (g/LW^0.75) model had a lower adjusted coefficient of determination (R²_adj = 47.6 %), with 16.8 % explained by forage nutrient contents and 30.8 % explained by sward structure, but no effect of the interaction. Our results show that in grazing ecosystems, the forage nutrient contents explain a small fraction, and the greater explanatory power for DMI, ADG, and CH₄ emissions models is related to sward structure descriptors, such as sward height and herbage mass. Moreover, the interaction between these variables explains most of the variation. In conclusion, forage nutrient contents and sward structure have different influences on DMI, ADG, and CH₄ emissions by grazing ruminants. Because of its relevance to daily CH₄ emissions, offering an optimal sward structure to grazing animals is a major climate-smart strategy to improve animal production and mitigate CH₄ emissions in pastoral ecosystems.

In vitro screening of anti-methanogenic additives for use in Australian grazing systems

Despite considerable effort to develop and optimise additives to reduce methane emissions from cattle, little information on additive effectiveness exists for cattle under grazing scenarios. As the majority of Australian cattle production occurs on grazing land it is pertinent to report on the use of additives under simulated conditions. The current study evaluated the addition of nine additives to Rhodes grass hay under in vitro conditions, to estimate their impact on methane (CH4), gas production, and rumen fermentation parameters (volatile fatty acids, rumen pH and in vitro dry matter digestibility [IVDMD]). Citral extract at 0.1% of rumen media decreased all CH4 production parameters, but reduced gas production and digestibility, compared to a 100% hay control. Similarly, Sandalwood essential oil decreased CH4 production at 48 h, IVDMD and gas production, compared to the control. Biochar + nitrates at 5 and 8% DM, and Biochar + Asparagopsis at 5% DM decreased cumulative CH4 production (15.6%, 25.9%, 23.8%, respectively; P < 0.01), compared to the control. No changes in IVDMD and gas production were observed. As such, the biochar additives were considered the most promising additives from those evaluated with a substrate designed to replicate Australian grazing systems.

Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems

Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH₄), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H₂ and CO₂), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH₄-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH₄ mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.

GHG Emissions from Dairy Small Ruminants in Castilla-La Mancha (Spain), Using the ManleCO2 Simulation Model

Simple Summary

Greenhouse gas emissions from ruminants contribute to global warming. “ManleCO₂” is an empirical model that simulates different management aspects in dairy sheep and goat farming, linking milk production to farming and environmental health. The carbon footprint of 1 L of fat- and protein-corrected milk varied from 2.01 to 5.62 kg CO₂e. Simulation scenarios showed a higher reduction in GHG emissions associated with animal feeding strategies and a lower reduction associated with farming management strategies. ManleCO₂ may provide useful information for planning and developing different strategies that might support the reduction of GHG emissions at the dairy sheep and goat farm level.

Abstract

The first goal of this work was the description of a model addressed to quantify the carbon footprint in Spanish autochthonous dairy sheep farms (Manchega group), foreign dairy sheep farms (foreigners group: Lacaune and Assaf breeds), and Spanish autochthonous dairy goat farms (Florida group). The second objective was to analyze the GHG emission mitigation potential of 17 different livestock farming practices that were implemented by 36 different livestock farms, in terms of CO₂e per hectare (ha), CO₂e per livestock unit (LU), and CO₂e per liter of fat- and protein-corrected milk (FPCM). The study showed the following results: 1.655 kg CO₂e per ha, 6.397 kg CO₂e per LU, and 3.78 kg CO₂e per liter of FPCM in the Manchega group; 12.634 kg CO₂e per ha, 7.810 CO₂e kg per LU, and 2.77 kg CO₂e per liter of FPCM in the Foreigners group and 1.198 kg CO₂e per ha, 6.507 kg CO₂e per LU, and 3.06 kg CO₂e per liter of FPCM in Florida group. In summary, purchasing off-farm animal feed would increase emissions by up to 3.86%. Conversely, forage management, livestock inventory, electrical supply, and animal genetic improvement would reduce emissions by up to 6.29%, 4.3%, 3.52%, and 0.8%, respectively; finally, an average rise of 2 °C in room temperature would increase emissions by up to 0.62%.

Predicting metabolizable energy from digestible energy for growing and finishing beef cattle and relationships to the prediction of methane

Reliable predictions of metabolizable energy (ME) from digestible energy (DE) are necessary to prescribe nutrient requirements of beef cattle accurately. A previously developed database that included 87 treatment means from 23 respiration calorimetry studies has been updated to evaluate the efficiency of converting DE to ME by adding 47 treatment means from 11 additional studies. Diets were fed to growing-finishing cattle under individual feeding conditions. A citation-adjusted linear regression equation was developed where dietary ME concentration (Mcal/kg of dry matter [DM]) was the dependent variable and dietary DE concentration (Mcal/kg) was the independent variable: ME = 1.0001 × DE - 0.3926; r2 = 0.99, root mean square prediction error [RMSPE] = 0.04, and P < 0.01 for the intercept and slope. The slope did not differ from unity (95% CI = 0.936 to 1.065); therefore, the intercept (95% CI = -0.567 to -0.218) defines the value of ME predicted from DE. For practical use, we recommend ME = DE - 0.39. Based on the relationship between DE and ME, we calculated the citation-adjusted loss of methane, which yielded a value of 0.2433 Mcal/kg of dry matter intake (DMI; SE = 0.0134). This value was also adjusted for the effects of DMI above maintenance, yielding a citation-adjusted relationship: CH4, Mcal/kg = 0.3344 - 0.05639 × multiple of maintenance; r2 = 0.536, RMSPE = 0.0245, and P < 0.01 for the intercept and slope. Both the 0.2433 value and the result of the intake-adjusted equation can be multiplied by DMI to yield an estimate of methane production. These two approaches were evaluated using a second, independent database comprising 129 data points from 29 published studies. Four equations in the literature that used DMI or intake energy to predict methane production also were evaluated with the second database. The mean bias was substantially greater for the two new equations, but slope bias was substantially less than noted for the other DMI-based equations. Our results suggest that ME for growing and finishing cattle can be predicted from DE across a wide range of diets, cattle types, and intake levels by simply subtracting a constant from DE. Mean bias associated with our two new methane emission equations suggests that further research is needed to determine whether coefficients to predict methane from DMI could be developed for specific diet types, levels of DMI relative to body weight, or other variables that affect the emission of methane.

Sodium nitrate has no detrimental effect on milk fatty acid profile and rumen bacterial population in water buffaloes

This study evaluated the influence of dietary sodium nitrate on ruminal fermentation profiles, milk production and composition, microbial populations and diversity in water buffaloes. Twenty-four female water buffaloes were randomly divided into four groups and fed with 0, 0.11, 0.22, 044 g sodium nitrate per kg body weight diets, respectively. Results showed that the concentration of acetate, propionate, butyrate and total VFA in all sodium nitrate–adapted water buffaloes were greater than the control group (P  < 0.05). Although the milk fatty acids value at 0.11 g sodium nitrate/kg/d were slightly lower than other treatments, no significant differences were observed among different treatments (P  > 0.05). Compared to the control group, the archaea richness (ace and chao1) and diversity (Shannon index) indices were increased by nitrate supplementation (P  < 0.05). Compared with the control group, sodium nitrate did not affect bacterial abundance at the phylum and genus level, but the relative abundance of the methanogen genera was greatly changed. There was a tendency for Methanobrevibacter to decrease in the sodium nitrate group (P  = 0.091). Comparisons of archaea communities by PCoA analysis showed significant separation between the control group and nitrate treatments (P  = 0.025). It was concluded that added 0.11–0.44 g sodium nitrate/kg of body weight increased the rumen VFA production and archaeal diversity of water buffaloes but had no detrimental effect on milk yield or composition, fatty acids profile, rumen methanogen or Butyrivibrio group population related to biohydrogenation.

Gentiana straminea supplementation improves feed intake, nitrogen and energy utilization, and methane emission among Simmental calves in northwest China

Objective

Native plants can be used as additives to replace antibiotics to improve ruminant feed utilization and animal health. An experiment was conducted to evaluate the effects of Gentiana straminea (GS) on nutrient digestibility, methane emissions, and energy metabolism of Simmental calves.

Methods

Thirty-two (5-week-old) male Simmental clves, with initial body weight (BW) of 155±12 kg were fed the same basal diet of concentrates (26%), alfalfa hay (37%), and oat hay (37%) and were randomly separated into four treatment groups according to the amount of GS that was added to their basal diet. The four different groups received different amounts of GS as a supplement to their basal diet during whole experiment: (0 GS) 0 mg/kg BW, the control; (100 GS) 100 mg/kg BW; (200 GS) 200 mg/kg BW; and (300 GS) 300 mg/kg BW.

Results

For calves in the 200 GS and 300 GS treatment groups, there was a significant increase in dry matter (DM) intake (p<0.01), average daily gain (ADG) (p<0.05), organic matter intake (p<0.05), DM digestibility (p<0.05), neutral detergent fibre (NDF) digestibility (p<0.05), and acid detergent fibre (ADF) digestibility (p<0.05). Dietary GS supplementation result in quadratic increases of DM intake (p<0.01), ADG (p<0.05), NDF intake (p<0.05), and ADF intake (p<0.05). Supplementing the basal diet with GS significantly increased nitrogen (N) retention (p<0.001) and the ratio of retention N to N intake (p<0.001). Supplementing the basal diet with GS significantly decreased methane (CH₄) emissions (p<0.01), CH₄/BW^0.75 (p<0.05) and CH₄ energy (CH₄-E) (p<0.05). Dietary GS supplementation result in quadratic increases of CH₄ (p<0.01) and CH₄/DM intake (p<0.01). Compared with 0 GS, GS-supplemented diets significantly improved their gross energy intake (p<0.05). The metabolizable energy and digestive energy intake were significantly greater for calves in the 100 GS and 200 GS calves than for 0 GS calves (p<0.05).

Conclusion

From this study, we conclude that supplementing calf diets with GS could improve utilization of feed, energy, and N, and may reduce CH₄ emissions without having any negative effects on animal health.

Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors

Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.

In Vitro Screening of East Asian Plant Extracts for Potential Use in Reducing Ruminal Methane Production

Indiscriminate use of antibiotics can result in antibiotic residues in animal products; thus, plant compounds may be better alternative sources for mitigating methane (CH₄) production. An in vitro screening experiment was conducted to evaluate the potential application of 152 dry methanolic or ethanolic extracts from 137 plant species distributed in East Asian countries as anti-methanogenic additives in ruminant feed. The experimental material consisted of 200 mg total mixed ration, 20 mg plant extract, and 30 mL diluted ruminal fluid-buffer mixture in 60 mL serum bottles that were sealed with rubber stoppers and incubated at 39 °C for 24 h. Among the tested extracts, eight extracts decreased CH₄ production by >20%, compared to the corresponding controls: stems of Vitex negundo var. incisa, stems of Amelanchier asiatica, fruit of Reynoutria sachalinensis, seeds of Tribulus terrestris, seeds of Pharbitis nil, leaves of Alnus japonica, stem and bark of Carpinus tschonoskii, and stems of Acer truncatum. A confirmation assay of the eight plant extracts at a dosage of 10 mg with four replications repeated on 3 different days revealed that the extracts decreased CH₄ concentration in the total gas (7-15%) and total CH₄ production (17-37%), compared to the control. This is the first report to identify the anti-methanogenic activities of eight potential plant extracts. All extracts decreased ammonia (NH₃-N) concentrations. Negative effects on total gas and volatile fatty acid (VFA) production were also noted for all extracts that were rich in hydrolysable tannins and total saponins or fatty acids. The underlying modes of action differed among plants: extracts from P. nil, V. negundo var. incisa, A. asiatica, and R. sachalinensis resulted in a decrease in total methanogen or the protozoan population (p < 0.05) but extracts from other plants did not. Furthermore, extracts from P. nil decreased the population of total protozoa and increased the proportion of propionate among VFAs (p < 0.05). Identifying bioactive compounds in seeds of P. nil by gas chromatography-mass spectrometry analysis revealed enrichment of linoleic acid (18:2). Overall, seeds of P. nil could be a possible alternative to ionophores or oil seeds to mitigate ruminal CH₄ production.

Does grazing management provide opportunities to mitigate methane emissions by ruminants in pastoral ecosystems?

Agriculture, and livestock production in particular, is criticized for being a contributor to global environmental change, including emissions of greenhouse gases (GHG). Methane (CH₄) from grazing ruminants accounts for most of livestock's carbon footprint because a large share of them are reared under suboptimal grazing conditions, usually resulting in both low herbage intake and animal performance. Consequently, the CH₄ quota attributed to animal maintenance is spread across few or no animal outputs, increasing the CH₄ intensity [g CH₄/kg live weight (LW) gain or g CH₄/kg milk yield]. In this review, the generalized idea relating tropical pastures with low quality and intrinsically higher CH₄ intensity is challenged by showing evidence that emissions from animals grazing tropical pastures can equal those of temperate grasses. We demonstrate the medium-to-high mitigation potential of some grazing management strategies to mitigate CH₄ emissions from grazing ruminants and stress the predominant role that sward canopy structure (e.g., height) has over animal behavioral responses (e.g., intake rate), daily forage intake and resulting CH₄ emissions. From this ecological perspective, we identify a grazing management concept aiming to offer the best sward structure that allows animals to optimize their daily herbage intake, creating opportunities to reduce CH₄ intensity. We show the trade-off between animal performance and CH₄ intensity, stressing that mitigation is substantial when grazing management is conducted under light-to-moderate intensities and optimize herbage intake and animal performance. We conclude that optimizing LW gain of grazing sheep and cattle to a threshold of 0.14 and 0.7 kg/day, respectively, would dramatically reduce CH₄ intensity to approximately 0.2 kg CH₄/kg LW gain, as observed in some intensive feeding systems. This could represent a mitigation potential of around 55% for livestock commodities in pasture-based systems. Our results offer new insights to the debate concerning mitigation of environmental impacts of pastoral ecosystems.

Pasture intensification in beef cattle production can affect methane emission intensity

Increasing greenhouse gas (GHG) emissions from anthropogenic activities have contributed to global warming and consequently to climate change. Among all sources of emissions, the agricultural sector accounts for just under a quarter, mainly because of the intensification of food production systems necessary to supply the growing demand of the population. As ruminal fermentation is the largest source of methane emission in the livestock industry, emission by cattle has become the focus of studies. The aim of this study was to evaluate enteric methane emission and emission intensities of Nellore cattle at different ages submitted to levels of intensification of the grazing system. Twenty-four animals per cycle (age of 21.8 and 13.1 mo in cycles 1 and 2, respectively) were randomly distributed across different grazing systems: irrigated pasture with a high stocking rate (IHS), dryland pasture with a high stocking rate (DHS), recovering dryland pasture with a moderate stocking rate (DMS), and degraded pasture with a low stocking rate (DP). Methane emission was measured using the sulfur hexafluoride technique in each season of the cycle. Intensive systems provided higher yields of good-quality forage as well as superior animal performance when compared with DP. Methane yields were different between seasons and cycles. Methane emissions per average daily weight gain and dry matter digestible intake were different between treatments. Differences in the results were observed when they were analyzed per hectare, with the highest gain yield (P = 0.0134), stocking rate, weight gain, carcass production, and total methane emission (P < 0.0001) being found for the intensive systems. There were no differences in emissions per weight gain or carcass production between production systems, while a difference was observed between cycles (P = 0.0189 and P = 0.0255, respectively), resulting in lower emission intensities for younger animals. We conclude that more intensive systems resulted in a higher kilograms production of carcass per hectare; however, animals at 19 mo of age raised in the IHS and DMS systems had a lower emission intensity in kilogram of CO2-eq. per kilogram of carcass. Moderate intensification (DMS) using animals at about 19 mo of age might be an effective strategy to mitigate GHG emissions from Brazilian tropical pastures. Further studies are needed to understand the relationship between increasing productivity and decreasing environmental impacts, especially methane emission from ruminants.

Distinct Stage Changes in Early-Life Colonization and Acquisition of the Gut Microbiota and Its Correlations With Volatile Fatty Acids in Goat Kids

In livestock, a comprehensive understanding of the early-life establishment and acquisition of commensal gut microbiota allow us to develop better husbandry management operations and manipulate the gut microbiota for young animals, improving the efficiency of animal production. Here, we collected 123 microbial samples of 11 healthy goat kids and their mothers to investigate the colonization and acquisition of the gut microbiota and their correlations with volatile fatty acids (VFAs) in goat kids from birth to day 56. An age-dependent increasing and more homogeneous diversity were observed for the feces of goat kids. Overall, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla in the fecal microbiota of goat kids, but their relative abundance varied considerably with age. Accordingly, the colonization of the fecal microbiota in goat kids was divided into three distinct stages: newborn (day 0), non-rumination stage (days 7–21), and transition stages (days 28–56). LEfSe analysis revealed a total of 49 bacterial biomarkers that are stage-specific (LDA score > 3, P < 0.05). Significant Spearman correlations (P < 0.05) were observed between the abundances of several bacterial biomarkers and the VFA concentrations. Furthermore, a substantial difference in the fecal microbiota composition was present between 56-day-old goat kids and mothers, whereas there was a moderate difference in the rumen microbiota between them. Among four body sites (i.e., feces, oral cavity, vagina, and breast milk) of mothers, the maternal vaginal and breast milk microbiota were the major source of the fecal microbiota of goat kids in the first 56 days after birth, although their contributions decreased with age and unknown sources increased after day 28. In summary, we concluded that the gut bacterial community in goat kids after birth was mainly acquired from the maternal vagina and breast milk. Its colonization showed three distinct phases with dramatic shifts of composition mainly driven by age and diet changes. Our results provide a framework for a better understanding of the roles of the gut microbiota in young ruminants.

Animal, feed and rumen fermentation attributes associated with methane emissions from sheep fed brassica crops

Methane emissions from ruminants enhance global warming and lead to a loss of feed energy. The emissions are low when fed brassica crops, but the factors contributing to low emissions are unknown. A meta-analysis was conducted with individual animal data collected from seven experiments. In these experiments, methane emissions were measured using respiration chambers. Animal characteristics, feed chemical composition and rumen fermentation parameters were included for the analysis using multiple regression models. Feed intake level, animal live weight and age were animal factors that were weakly and negatively related to methane yield (g/dry matter intake). The duration in which sheep were fed brassica crops was a significant contributor in the model, suggesting that the effect on emissions diminishes with time. Among a range of feed chemical composition characters, acid detergent fibre and hot-water-soluble carbohydrate contributed significantly to the model, suggesting that both structural and soluble carbohydrates affect methane formation in the rumen. There was no significant correlation between the concentration of sulphate in brassicas and emissions, but nitrate was moderately and negatively correlated with methane yield (r = -.53). Short-chain fatty acid profiles in the rumen of animals fed brassicas were different from those fed pasture, but these parameters only moderately correlated to methane emissions (r = .42). Feeding forage rape resulted in low rumen pH. The pH before morning feeding was strongly correlated to methane yield (r = .90). Rumen pH, together with microbial communities mediated by pH, might lead to low emissions. Bacteria known to produce hydrogen were relatively less abundant in the rumen contents of brassica-fed animals than pasture-fed animals. In conclusion, animal and feed factors, rumen fermentation and microbial communities all affect methane emissions to some extent. The interactions of these factors with each other thus contribute to methane emissions from brassica-fed sheep.

Are Vaccines the Solution for Methane Emissions from Ruminants? A Systematic Review

Ruminants produce considerable amounts of methane during their digestive process, which makes the livestock industry as one of the largest sources of anthropogenic greenhouse gases. To tackle this situation, several solutions have been proposed, including vaccination of ruminants against microorganisms responsible for methane synthesis in the rumen. In this review, we summarize the research done on this topic and describe the state of the art of this strategy. The different steps implied in this approach are described: experimental design, animal model (species, age), antigen (whole cells, cell parts, recombinant proteins, peptides), adjuvant (Freund's, Montanide, saponin, among others), vaccination schedule (booster intervals and numbers) and measurements of treatment success (immunoglobulin titers and/or effects on methanogens and methane production). Highlighting both the advances made and knowledge gaps in the use of vaccines to inhibit ruminant methanogen activity, this research review opens the door to future studies. This will enable improvements in the methodology and systemic approaches so as to ensure the success of this proposal for the sustainable mitigation of methane emission.

Methane production and estimation from livestock husbandry: A mechanistic understanding and emerging mitigation options

Globally, livestock is an important contributor to methane (CH₄) emissions. This paper reviewed the various CH₄ measurement and estimation techniques and mitigation approaches for the livestock sector. Two approaches for enteric livestock CH₄ emission estimation are the top-down and bottom-up. The combination of both could further improve our understanding of enteric CH₄ emission and possible mitigation measures. We discuss three mitigation approaches: reducing emissions, avoiding emissions, and enhancing the removal of emissions from livestock. Dietary management, livestock management, and breeding management are viable reducing emissions pathways. Dietary manipulation is easily applicable and can bring an immediate response. Economic incentive policies can help the livestock farmers to opt for diet, breeding, and livestock management mitigation approaches. Carbon pricing creates a better option to achieve reduction targets in a given period. A combination of carbon pricing, feeding management, breeding management, and livestock management is more feasible and sustainable CH₄ emissions mitigation strategy rather than a single approach.

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences (p < 0.05) in the concentrations of total VFA and the proportions of acetate and butyrate in the rumen fluid among the three groups, whereas the proportions of propionate and the acetate/propionate ratio did not differ substantially. Alpha diversity of the rumen bacterial and archaeal populations in the GR and SF kids was significantly higher (p < 0.05) than that in the IF goat kids, and significant differences (p < 0.05) in similarity were observed in the comparisons of GR vs. IF and SF vs. IF. The most predominant bacterial phyla were Bacteroidetes and Firmicutes across the three groups, and the archaeal community was mainly composed of Euryarchaeota. At the genus and species levels, the cellulose-degrading bacteria, including Lachnospiraceae, Ruminococcaceae and Butyrivibrio fibrisolvens, were abundant in the GR and SF groups. Furthermore, 27 bacterial and 11 unique archaeal taxa, such as Lachnospiraceae, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium, were identified as biomarkers, and showed significantly different (p < 0.05) abundances among the three groups. Significant Spearman correlations (p < 0.05), between the abundances of several microbial biomarkers and the concentrations of VFAs, were further observed. In summary, our results demonstrated that the adaptation to grazing required more rumen bacterial populations due to complex forage types in shrub-grassland, although the rumen fermentation pattern did not change substantially among the three feeding systems. Some microbial taxa could be used as biomarkers for different feeding systems, particularly cellulose-degrading bacteria associated with grazing.

Effect of altering ruminal pH by dietary buffer supplementation on methane emissions from sheep fed forage rape

Low methane (CH4) emissions from sheep fed forage rape (Brassica napus) might be related to low ruminal pH value. In this study, sodium carbonate (Na2CO3: SC) was supplemented to the diet to alter ruminal pH for evaluation of its role in CH4 emissions from sheep fed forage rape. Fourteen intact and eight fistulated Romney sheep were adapted to forage rape over 32 days and then randomly allocated to one of two groups: diets supplemented with SC or not (control). Methane emissions were measured from intact sheep in seven experimental periods. In parallel, ruminal pH and fermentation characteristics were assessed using the fistulated sheep. In the first (P01) and the second (P02) periods, none of the sheep received SC to examine the baseline CH4 emissions. The P01 period was used as a covariate for analysis of gas emission measurements in subsequent measurement periods. Sodium carbonate was offered at 5% of the forage DM in P03 and P04, increased to 8% in P05 and P06 to assess the effect of pH increase on CH4 emissions and stopped in P07 to assess if the CH4 emissions reverted to values similar to those measured before the supplementation started. Methane yield (g/kg forage DM intake) was similar for the sheep in both groups during P02 and P03, but sheep supplemented with SC in the diet emitted 36%, 49% and 30% more CH4 per unit of forage DM intake than those in the control group during P04, P05 and P06, respectively. Emissions returned to similar levels when SC supplementation was ceased in P07. Ruminal pH was 0.412 to 0.565 units higher in SC supplemented sheep than for the control group during the SC treatment periods. Based on the lack of an immediate response in CH4 emissions to the supplementation of SC in P03, the positive responses in P04 to P06 and the rapid disappearance of the response after supplementation with SC stopped in P07, we propose a new hypothesis that ruminal pH effects on CH4 emissions are possibly through medium-term changes in microbial and methanogenic communities in the rumen, rather than a direct, short-term impact on methanogens per se. In conclusion, SC supplemented to the forage rape diet of sheep increased rumen pH, leading to an increase in CH4 emissions. Low ruminal pH in sheep fed forage rape explains, at least partially, the reported low CH4 emissions from sheep fed with this forage crop.

Diverse hydrogen production and consumption pathways influence methane production in ruminants

Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H₂), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H₂ metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H₂ production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H₂ uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H₂ metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H₂. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H₂ uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.

The influence of copper levels on in vitro ruminal fermentation, bacterial growth and methane production

BACKGROUND

Copper (Cu) is an essential microelement to the health and proper functioning of metabolic processes in animals, but the particular function of Cu in fermentation processes and the formation of methane (CH₄ ) in the rumen have been poorly analyzed. The innovative aspect of this study was to investigate the effects of high doses of Cu as copper sulfate on in vitro ruminal degradation, fermentation patterns, and CH₄ production.

RESULTS

There was a decrease (P < 0.04) on in vitro dry matter (DM) and organic matter degradability from 60 to 100 µg Cu/g DM. Ammonia concentration decreased drastically with increasing Cu levels (linear effect, P < 0.01). Total bacteria and volatile fatty acids (quadratic effect, P < 0.02) were reduced with 80 and 100 µg Cu/g DM. Methane production (milliliters per gram digestible organic matter) was decreased when dosages of Cu were increased (linear effect, P < 0.003).

CONCLUSION

Overall, the addition of increasing levels of Cu to 40 µg Cu/g DM did not have an adverse impact on ruminal bacteria growth and decreased CH₄ production, without affecting the ruminal kinetics. © 2018 Society of Chemical Industry.

Variation in methane production over time and physiological state in sheep

Livestock produce 10% of the total CO2-equivalent greenhouse gases in Australia, predominantly as methane from rumen fermentation. Genetic selection has the potential to reduce emissions and be adopted in Australian grazing systems. Developing a breeding objective for reduced methane emissions requires information about heritability, genetic relationships, when best to measure the trait and knowledge of the annual production of methane. Among- and within-animal variation in methane production, methane yield and associated traits were investigated, so as to determine the optimal time of measurement and the relationship between that measurement and the total production of methane. The present study measured 96 ewes for methane production, liveweight, feed intake, rumen volume and components, and volatile fatty acid (VFA) production and composition. Measurements were recorded at three ages and different physiological states, including growing (12 months), dry and pregnant (21 months) and dry (non-pregnant, non-lactating; 28 months of age). The single biggest determinant of methane production was feed intake, but there were additional effects of age, proportion of propionate to (acetate+butyrate) in rumen VFA, total VFA concentration and CO2 flux. Rumen volume and pregnancy status also significantly affected methane production. Methane production, CO2 flux, liveweight, feed intake and rumen volume had high repeatability (&gt;65%), but repeatability of methane yield and VFA traits were low (&lt;20%). There were no interactions between sire and age (or pregnancy status) for methane traits. This suggests that methane could be measured at any time in the production cycle. However, because MY is reduced during pregnancy, it might be best to measure methane traits in dry ewes (neither pregnant nor lactating).

Methanogenesis in animals with foregut and hindgut fermentation: a review

Methane is the main greenhouse-gas contributor to global warming in the livestock sector; it is generated by anaerobic fermentation in the different sections of the gut, and the methane concentration differs significantly among species. Methane is produced only by certain types of microorganisms called methanogens. The species composition of methanogenic archaea population is largely affected by the diet, geographical location, host and the section of the gut. Consequently, methane production, either measured as total grams emitted per day or per bodyweight mass, differs greatly among animal species. The main difference in methanogenic activity among different gut sections and animal species is the substrate fermented and the metabolic pathway to complete anaerobic fermentation of plant material. The three main substrates used by methanogens are CO2, acetate and compounds containing methyl groups. The three dominant orders of methanogens in gut environments are Methanomicrobiales, Methanobacteriales and Methanosarcinales. They normally are present in low numbers (below 3% of total microbiome). The present review will describe the main metabolic pathways and methanogens involved in CH4 production in the gut of different host-animal species, as well as discuss general trends that influence such emissions, such as geographical distribution, feed composition, section of the gut, host age and diurnal and season variation. Finally, the review will describe animal species (large and small domestic ruminants, wild ruminants, camelids, pigs, rabbits, horses, macropods, termites and humans) specificities in the methanogen diversity and their effects on methane emission.

Inhibition of Rumen Methanogens by a Novel Archaeal Lytic Enzyme Displayed on Tailored Bionanoparticles

Methane is a potent greenhouse gas, 25 times more efficient at trapping heat than carbon dioxide. Ruminant methane emissions contribute almost 30% to anthropogenic sources of global atmospheric methane levels and a reduction in methane emissions would significantly contribute to slowing global temperature rises. Here we demonstrate the use of a lytic enyzme, PeiR, from a methanogen virus that infects Methanobrevibacter ruminantium M1 as an effective agent inhibiting a range of rumen methanogen strains in pure culture. We determined the substrate specificity of soluble PeiR and demonstrated that the enzyme is capable of hydrolysing the pseudomurein cell walls of methanogens. Subsequently, peiR was fused to the polyhydroxyalkanoate (PHA) synthase gene phaC and displayed on the surface of PHA bionanoparticles (BNPs) expressed in Eschericia coli via one-step biosynthesis. These tailored BNPs were capable of lysing not only the original methanogen host strain, but a wide range of other rumen methanogen strains in vitro. Methane production was reduced by up to 97% for 5 days post-inoculation in the in vitro assay. We propose that tailored BNPs carrying anti-methanogen enzymes represent a new class of methane inhibitors. Tailored BNPs can be rapidly developed and may be able to modulate the methanogen community in vivo with the aim to lower ruminant methane emissions without impacting animal productivity.

Enteric methane emissions from low- and high-residual feed intake beef heifers measured using GreenFeed and respiration chamber techniques

The objectives of this study were to evaluate the relationship between residual feed intake (RFI; g/d) and enteric methane (CH) production (g/kg DM) and to compare CH and carbon dioxide (CO) emissions measured using respiration chambers (RC) and the GreenFeed emission monitoring (GEM) system (C-Lock Inc., Rapid City, SD). A total of 98 crossbred replacement heifers were group housed in 2 pens and fed barley silage ad libitum and their individual feed intakes were recorded by 16 automated feeding bunks (GrowSafe, Airdrie, AB, Canada) for a period of 72 d to determine their phenotypic RFI. Heifers were ranked on the basis of phenotypic RFI, and 16 heifers (8 with low RFI and 8 with high RFI) were randomly selected for enteric CH and CO emissions measurement. Enteric CH and CO emissions of individual animals were measured over two 25-d periods using RC (2 d/period) and GEM systems (all days when not in chambers). During gas measurements metabolic BW tended to be greater ( ≤ 0.09) for high-RFI heifers but ADG tended ( = 0.09) to be greater for low-RFI heifers. As expected, high-RFI heifers consumed 6.9% more feed ( = 0.03) compared to their more efficient counterparts (7.1 vs. 6.6 kg DM/d). Average CH emissions were 202 and 222 g/d ( = 0.02) with the GEM system and 156 and 164 g/d ( = 0.40) with RC for the low- and high-RFI heifers, respectively. When adjusted for feed intake, CH yield (g/kg DMI) was similar for high- and low-RFI heifers (GEM: 27.7 and 28.5, = 0.25; RC: 26.5 and 26.5, = 0.99). However, CH yield differed between the 2 measurement techniques only for the high-RFI group ( = 0.01). Estimates of CO yield (g/kg DMI) also differed between the 2 techniques ( ≤ 0.03). Our study found that high- and low-efficiency cattle produce similar CH yield but different daily CH emissions. The 2 measurement techniques differ in estimating CH and CO emissions, partially because of differences in conditions (lower feed intakes of cattle while in chambers, fewer days measured in chambers) during measurement. We conclude that when intake of animals is known, the GEM system offers a robust and accurate means of estimating CH emissions from animals under field conditions.

Changes in feed intake during isolation stress in respiration chambers may impact methane emissions assessment

Respiration chambers are considered the ‘gold standard’ technique for measuring in vivo methane (CH4) emissions in live animals. However, the imposed isolation required may alter feeding behaviour and intake, which ultimately impact CH4 emissions. The aim of this study was to assess the impact of isolation within respiration chambers on feed intake and CH4 emissions with two different diets and breeds of beef cattle. In addition, a routine stressor (transport) was used to examine the relationship between individual stress responsiveness and changes in feed intake during isolation. Eighty-four steers (castrated males) (569 ± 5.7 kg bodyweight, BW) were divided into two groups and each group fed with one of two basal diets consisting of (g/kg dry matter, DM) either 50 : 50 (Mixed) or 8 : 92 (Concentrate) forage to concentrate ratios. Within each basal diet there were three supplementation treatments: (1) control, (2) calcium nitrate, and (3) rapeseed cake. The stress biomarkers plasma cortisol, creatine kinase (CK), and free fatty acids (FFA) were determined before (0 h) and after (30 min, 3 h, 6 h and 9 h) a 30-min journey, when steers were transported to the respiration chamber facilities. Methane emissions were measured over a 3-day period using individual respiration chambers. Dry matter intake (DMI) was assessed within the group-housed pens (4 weeks before entry to training pen), in the training pens and the chambers. Cortisol, FFA and CK increased (P < 0.05) after transport confirming a stress response. DMI (g/kg BW) decreased (P < 0.001) during isolation in the training pens (14.7 ± 0.28) and the chambers (14.3 ± 0.26) compared with that of the same animals in the group pens (16.8 ± 0.23). DMI during isolation decreased more in those animals which had an increased (P < 0.05) stress response during transport as measured by cortisol, FFA and CK. With the Mixed diet, the decline in DMI was estimated to result in an increase in CH4 (g/kg DMI) (r = 0.25, P = 0.001), which did not occur with the Concentrate diet. According to the results of this experiment, the stress associated with isolation reduces the DMI resulting in an increase in g CH4/kg DMI in fibrous diets. Habituation to isolation needs refinement in order to reduce the impact of stress on intake and therefore achieve more accurate estimates of CH4 emissions. Alternatively, modelling CH4 estimations according to behavioural and physiological changes associated with isolation stress would improve accuracy of CH4 estimations.

Enzyme- and gene-based approaches for developing methanogen-specific compounds to control ruminant methane emissions: a review

Methane emissions from ruminants are of worldwide concern due to their potential to adversely affect climate patterns. Methane emissions can be mitigated in several ways, including dietary manipulation, the use of alternative hydrogen sinks, and by the direct inhibition of methanogens. In the present review, we summarise and emphasise studies where defined chemically synthesised compounds have been used to mitigate ruminant methane emissions by direct targeting of methanogens and discuss the future potential of such inhibitors. We also discuss experiments, where methanogen-specific enzymes and pure cultures of methanobacterial species have been used to aid development of inhibitors. Application of certain compounds can result in dramatic reductions of methane emissions from ruminant livestock, demonstrating ‘proof of principle’ of chemical inhibitors of methanogenesis. More recently, genome sequencing of rumen methanogens has enabled an in-depth analysis of the enzymatic pathways required for methane formation. Chemogenomic methods, similar to those used in the fight against cancer and infectious diseases, can now be used to specifically target a pathway or enzyme in rumen methanogens. However, few rumen methanogen enzymes have been structurally or biochemically characterised. Any compound, whether natural or man-made, that is used as a mitigation strategy will need to be non-toxic to the host animal (and humans), cost-effective, environmentally friendly, and not accumulate in host tissues or milk products. Chemically synthesised inhibitors offer potentially significant advantages, including high levels of sustained inhibition, the ability to be easily and rapidly produced for global markets, and have the potential to be incorporated into slow-release vehicles for grazing animals.

A review on comparative mechanistic studies of antimicrobial peptides against archaea

Archaea was until recently considered as a third domain of life in addition to bacteria and eukarya but recent studies support the existence of only two superphyla (bacteria and archaea). The fundamental differences between archaeal, bacterial, and eukaryal cells are probably the main reasons for the comparatively lower susceptibility of archaeal strains to current antimicrobial agents. The possible emerging pathogenicity of archaea and the role of archaeal methanogens in methane emissions, a potent greenhouse gas, has led many researchers to examine the sensitivity patterns of archaea and make attempts to find agents that have significant anti-archaeal activity. Even though antimicrobial peptides (AMPs) are well known with several published reviews concerning their mode of action against bacteria and eukarya, to our knowledge, to date no reviews are available that focus on the action of these peptides against archaea. Herein, we present a review on all the peptides that have been tested against archaea. In addition, in an attempt to shed more light on possible future work that needs to be performed we have included a brief overview of the chemical characteristics, spectrum of activity, and the known mechanism of action of each of these peptides against bacteria and/or fungi. We also discuss the nature of and key physiological differences between Archaea, Bacteria, and Eukarya that are relevant to the development of anti-archaeal peptides. Despite our relatively limited knowledge about archaea, available data suggest that AMPs have an even broader spectrum of activity than currently recognized.

Comparative community structure of archaea in rumen of buffaloes and cattle

BACKGROUND

Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank.

RESULTS

Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes.

CONCLUSION

This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry.

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H₂ and CO₂ that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions.IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions.

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics

In vitro fermentation systems such as the rumen simulation technique (RUSITEC) are frequently used to assess dietary manipulations in livestock, thereby limiting the use of live animals. Despite being in use for nearly 40 years, improvements are continually sought in these systems to better reflect and mimic natural processes in ruminants. The aim of this study was to evaluate the effect of forage preparation, i.e., frozen minced (FM) and freeze-dried and ground (FDG), on the ruminal microbiota and on fermentation characteristics when included as a substrate in a RUSITEC system. A completely randomized design experiment was performed over a 15-day period, with 7 days of adaptation and an 8-day experimental period. Fermentation parameters (total gas, CH₄, and volatile fatty acid production) were analyzed on a daily basis over the experimental period and the archaeal and bacterial microbiota (liquid-associated microbes [LAM] and solid-associated microbes [SAM] was assessed at 0, 5, 10, and 15 days using high-throughput sequencing of the 16S rRNA gene. Results from this study suggested a tendency (P = 0.09) of FM treatment to increase daily CH₄ (mg/d) production by 16.7% when compared with FDG treatment. Of the major volatile fatty acids (acetate, propionate, and butyrate), only butyrate production was greater (P = 0.01) with FM treatment compared with FDG substrate. The archaeal and bacterial diversity and richness did not differ between the forage preparations, although feed particle size of the forage had a significant effect on microbial community structure in the SAM and LAM samples. The Bacteroidetes phylum was more relatively abundant in the FM substrate treatment, while Proteobacteria was enriched in the FDG treatment. At the genus-level, Butyrivibrio, Prevotella, and Roseburia were enriched in the FM substrate treatment and Campylobacter and Lactobacillus in the FDG substrate treatment. Evidence from this study suggests that forage preparation affects CH₄ production, butyrate production, and the structure of the rumen microbiota during in vitro fermentation.

Review: Sugar beets as a substitute for grain for lactating dairy cattle

Dairy cows are customarily given grains and highly digestible byproduct ingredients as additions to forage to support milk production. In many parts of the world growing seasons are short, and the grain crops that can be grown may not provide adequate yields. Sugar beets, on the other hand are relatively hardy, and dry matter yields surpass the yields of most grain crops. There are however, perceptions that beets may not be suitable as a feed ingredient due to the fact that the storage form of carbohydrate is sugar rather than starch. With little analytical support, sugar has been rejected in many feeding programs with the view that sugar reduces rumen pH, fiber digestion and microbial yield. This review explores available facts revolving around these concerns. Information regarding the feeding of sugar beets is provided and the use of sugar beets as a partial replacement for grain is proposed.

Vaccination of Sheep with a Methanogen Protein Provides Insight into Levels of Antibody in Saliva Needed to Target Ruminal Methanogens

Methane is produced in the rumen of ruminant livestock by methanogens and is a major contributor to agricultural greenhouse gases. Vaccination against ruminal methanogens could reduce methane emissions by inducing antibodies in saliva which enter the rumen and impair ability of methanogens to produce methane. Presently, it is not known if vaccination can induce sufficient amounts of antibody in the saliva to target methanogen populations in the rumen and little is known about how long antibody in the rumen remains active. In the current study, sheep were vaccinated twice at a 3-week interval with a model methanogen antigen, recombinant glycosyl transferase protein (rGT2) formulated with one of four adjuvants: saponin, Montanide ISA61, a chitosan thermogel, or a lipid nanoparticle/cationic liposome adjuvant (n = 6/formulation). A control group of sheep (n = 6) was not vaccinated. The highest antigen-specific IgA and IgG responses in both saliva and serum were observed with Montanide ISA61, which promoted levels of salivary antibodies that were five-fold higher than the second most potent adjuvant, saponin. A rGT2-specific IgG standard was used to determine the level of rGT2-specific IgG in serum and saliva. Vaccination with GT2/Montanide ISA61 produced a peak antibody concentration of 7 × 10¹⁶ molecules of antigen-specific IgG per litre of saliva, and it was estimated that in the rumen there would be more than 10⁴ molecules of antigen-specific IgG for each methanogen cell. Both IgG and IgA in saliva were shown to be relatively stable in the rumen. Salivary antibody exposed for 1–2 hours to an in vitro simulated rumen environment retained approximately 50% of antigen-binding activity. Collectively, the results from measuring antibody levels and stablility suggest a vaccination-based mitigation strategy for livestock generated methane is in theory feasible.

Association of Temperament and Acute Stress Responsiveness with Productivity, Feed Efficiency, and Methane Emissions in Beef Cattle: An Observational Study

The aim of this study was to assess individual differences in temperament and stress response and quantify their impact on feed efficiency, performance, and methane (CH₄) emissions in beef cattle. Eighty-four steers (castrated males) (Charolais or Luing) were used. Temperament was assessed using two standardized tests: restlessness when restrained [crush score (CS)] and flight speed (FS) on release from restraint. Over a 56-day period individual animal dry matter intake (DMI) and weekly body weight was measured. Ultrasound fat depth was measured at the end of 56 days. Average daily gain (ADG), feed conversion ratio (FCR), and residual feed intake (RFI) were calculated. After the 56-day test period, animals were transported in groups of six/week to respiration chamber facilities. Blood samples were taken before and 0, 3, 6, and 9 h after transport. Plasma cortisol, creatine kinase (CK), glucose, and free fatty acids (FFA) were determined to assess physiological stress response. Subsequently, CH₄ emissions were measured over a 3-day period in individual respiration chambers. CS (1.7 ± 0.09) and FS (1.6 ± 0.60 m/s) were repeatable (0.63 and 0.51, respectively) and correlated (r = 0.36, P < 0.001). Plasma cortisol, CK, and FFA concentrations increased after transport (P = 0.038, P = 0.006, and P < 0.001, respectively). Temperament (CS) and CK concentration were correlated (r = 0.29; P = 0.015). The extreme group analysis reveals that excitable animals (FS; P = 0.032) and higher stress response (cortisol, P = 0.007; FFA, P = 0.007; and CK, P = 0.003) were associated with lower DMI. ADG was lower in more temperamental animals (CS, P = 0.097, and FS, P = 0.030). Fat depth was greater in steers showing calmer CS (P = 0.026) and lower plasma CK (P = 0.058). Temperament did not show any relationship with RFI or CH₄ emissions. However, steers with higher cortisol showed improved feed efficiency (lower FCR and RFI) (P < 0.05) and greater CH₄ emissions (P = 0.017). In conclusion, agitated temperament and higher stress responsiveness is detrimental to productivity. A greater stress response is associated with a reduction in feed intake that may both increase the efficiency of consumed feed and the ratio of CH₄ emissions/unit of feed. Therefore, temperament and stress response should be considered when designing strategies to improve efficiency and mitigate CH₄ emissions in beef cattle.

Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions

5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.

Correlations of methane and carbon dioxide concentrations from feedlot cattle as a predictor of methane emissions

Accurate measurements of methane (CH4) emissions from feedlot cattle are required for verifying greenhouse gas (GHG) accounting and mitigation strategies. We investigate a new method for estimating CH4 emissions by examining the correlation between CH4 and carbon dioxide (CO2) concentrations from two beef cattle feedlots in Australia representing southern temperate and northern subtropical locations. Concentrations of CH4 and CO2 were measured at the two feedlots during summer and winter, using open-path Fourier transform infrared spectroscopy. There was a strong correlation for the concentrations above background of CH4 and CO2 with concentration ratios of 0.008 to 0.044 ppm/ppm (R2 >0.90). The CH4/CO2 concentration ratio varied with animal diet and ambient temperature. The CH4/CO2 concentration ratio provides an alternative method to estimate CH4 emissions from feedlots when combined with CO2 production derived from metabolisable energy or heat production.

Reducing the carbon footprint of Australian milk production by mitigation of enteric methane emissions

This review examines research aimed at reducing enteric methane emissions from the Australian dairy industry. Calorimeter measurements of 220 forage-fed cows indicate an average methane yield of 21.1 g methane (CH4)/kg dry matter intake. Adoption of this empirical methane yield, rather than the equation currently used in the Australian greenhouse gas inventory, would reduce the methane emissions attributed to the Australian dairy industry by ~10%. Research also indicates that dietary lipid supplements and feeding high amounts of wheat substantially reduce methane emissions. It is estimated that, in 1980, the Australian dairy industry produced ~185 000 t of enteric methane and total enteric methane intensity was ~33.6 g CH4/kg milk. In 2010, the estimated production of enteric methane was 182 000 t, but total enteric methane intensity had declined ~40% to 19.9 g CH4/kg milk. This remarkable decline in methane intensity and the resultant improvement in the carbon footprint of Australian milk production was mainly achieved by increased per-cow milk yield, brought about by the on-farm adoption of research findings related to the feeding and breeding of dairy cows. Options currently available to further reduce the carbon footprint of Australian milk production include the feeding of lipid-rich supplements such as cottonseed, brewers grains, cold-pressed canola, hominy meal and grape marc, as well as feeding of higher rates of wheat. Future technologies for further reducing methane emissions include genetic selection of cows for improved feed conversion to milk or low methane intensity, vaccines to reduce ruminal methanogens and chemical inhibitors of methanogenesis.

Estimates of repeatability and heritability of methane production in sheep using portable accumulation chambers

This study was designed to screen a large number of sheep to identify individuals with high and low methane (CH4) production, and to estimate repeatability and heritability of CH4 emissions in sheep, utilising portable accumulation chambers (PAC) designed for in-field use. Mature ewes (n = 710) selected from a research flock with known sires had their CH4 production over 1 h measured in PAC [CH4 (g1h)]. Individuals with High (n = 103) or Low (n = 104) CH4 (g1h), adjusted for liveweight (LW), were selected and re-measured on three occasions 1–4 months later, at another site with more abundant and better quality pasture. Mean of the selected (207) ewes CH4 (g1h) emissions were ~50% higher than at the first measurement site (0.66 g vs 0.42 g). LW was a significant correlate of CH4 production (r = 0.47). Correlations between CH4 (g1h) for the three PAC measurements at Site 2, before adjusting for LW ranged from 0.44 to 0.55. After adjusting for the effect of LW, repeatability was 0.33 at the first and 0.43 at the second site. The correlation between estimates of an animal’s emissions at the first and second sites, adjusted for LW, was 0.24. Initial CH4 production of the selected High group was 32% greater than the Low group (P < 0.0001). On re-measurement there was still a significant difference (9–15%, P < 0.006) between Low and High groups. The initial estimate of heritability of CH4 (g1h), based on variation between the ewes’ sires (0.13), was not maintained across the two sites. This may be due to genotype × environment interactions. We postulate that aspects of rumen physiology, which modulate CH4 production, could be expressed differently in different nutritional environments. Our results indicate that field use of PAC to screen sheep populations for CH4 production is both robust and repeatable. However, further investigations are required into the relationship between CH4 output of individual animals in PAC compared with the more controlled conditions in respiration chambers.

Immunization against Rumen Methanogenesis by Vaccination with a New Recombinant Protein

Vaccination through recombinant proteins against rumen methanogenesis provides a mitigation approach to reduce enteric methane (CH₄) emissions in ruminants. The objective of present study was to evaluate the in vivo efficacy of a new vaccine candidate protein (EhaF) on methanogenesis and microbial population in the rumen of goats. We amplified the gene mru 1407 encoding protein EhaF using fresh rumen fluid samples of mature goats and successfully expressed recombinant protein (EhaF) in Escherichia coli Rosetta. This product was evaluated using 12 mature goats with half for control and other half injected with 400ug/goat the purified recombinant protein in day 1 and two subsequent booster immunizations in day 35 and 49. All measurements were undertaken from 63 to 68 days after the initial vaccination, with CH₄ emissions determined using respiration calorimeter chambers. The results showed that the vaccination caused intensive immune responses in serum and saliva, although it had no significant effect on total enteric CH₄ emissions and methanogen population in the rumen, when compared with the control goats. However, the vaccination altered the composition of rumen bacteria, especially the abundance of main phylum Firmicutes and genus Prevotella. The results indicate that protein EhaF might not be an effective vaccine to reduce enteric CH4 emissions but our vaccine have potential to influence the rumen ecosystem of goats.

Exploring the sheep rumen microbiome for carbohydrate-active enzymes

The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.