Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions

BACKGROUND

Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.

RESULTS

Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization.

CONCLUSIONS

We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.

Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield

Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.

Roles of Essential Oils, Polyphenols, and Saponins of Medicinal Plants as Natural Additives and Anthelmintics in Ruminant Diets: A Systematic Review

Public awareness on health and safety issues in using antibiotics for livestock production has led many countries to ban the use of all growth-promoting antibiotics (GPA) for livestock feeding. The ban on the utilization of antibiotics in livestock, on the other hand, is an opportunity for researchers and livestock practitioners to develop alternative feed additives that are safe for both livestock and the consumers of animal derived foods. Many feed additives were developed from a number of plants that contain secondary metabolites, such as essential oils, polyphenols, and saponins. These secondary metabolites are extracted from various parts of many types of plants for their uses as feed additives and anthelmintics. Recent investigations on using essential oils, polyphenols, and saponins as dietary additives and anthelmintics demonstrate that they can increase not only the production and health of ruminants but also ensure the safety of the resulting foods. There are many publications on the advantageous impacts of dietary plant bioactive components on ruminants; however, a comprehensive review on individual bioactive constituents of each plant secondary metabolites along with their beneficial effects as feed additives and anthelmintics on ruminants is highly required. This current study reviewed the individual bioactive components of different plant secondary metabolites and their functions as additives and anthelmintics to improve ruminant production and health, with respect to safety, affordability and efficiency, using a systematic review procedure.

Feeding 3-nitrooxypropanol reduces methane emissions by feedlot cattle on tropical conditions

Our objective was to evaluate the effects of feeding 3-nitrooxypropanol (3-NOP; Bovaer, DSM Nutritional Products) at two levels on methane emissions, nitrogen balance, and performance by feedlot cattle. In experiment 1, a total of 138 Nellore bulls (initial body weight, 360 ± 37.3 kg) were housed in pens (27 pens with either 4 or 5 bulls per pen) and fed a high-concentrate diet for 96 d, containing 1) no addition of 3-NOP (control), 2) inclusion of 3-NOP at 100 mg/kg dry matter (DM), and 3) inclusion of 3-NOP at 150 mg/kg DM. No adverse effects of 3-NOP were observed on DM intake (DMI), animal performance, and gain:feed (P > 0.05). In addition, there was no effect (P > 0.05) of 3-NOP on carcass characteristics (subcutaneous fat thickness and rib eye area). In experiment 2, 24 bulls (initial BW, 366 ± 39.6 kg) housed in 12 pens (2 bulls/pen) from experiment 1 were used for CH4 measurements and nitrogen balance. Irrespective of the level, 3-NOP consistently decreased (P < 0.001) animals' CH4 emissions (g/d; ~49.3%), CH4 yield (CH4/DMI; ~40.7%) and CH4 intensity (CH4/average daily gain; ~38.6%). Moreover, 3-NOP significantly reduced the gross energy intake lost as CH4 by 42.5% (P < 0.001). The N retention: N intake ratio was not affected by 3-NOP (P = 0.19). We conclude that feeding 3-NOP is an effective strategy to reduce methane emissions, with no impairment on feedlot cattle performance.

Biochemical Properties of Black and Green Teas and Their Insoluble Residues as Natural Dietary Additives to Optimize In Vitro Rumen Degradability and Fermentation but Reduce Methane in Sheep

Black (BTL) or green (GTL) tea and their spent tea (STL) leaves can be used as natural dietary additives for ruminants. Experiment 1 used a 3 × 2 × 2 factorial arrangement, with four replicates (n = 4) to test the effects of three different inclusions of tea leaves at 0 (control), 50, and 100 g/kg DM of two different tea types (BTL and GTL) in two different total mixed diets containing either ryegrass hay (RH) or rice straw (RS) on in vitro rumen organic matter degradability (IVOMD), volatile fatty acids (VFA), pH, ammonia (NH3), and methane (CH4) outputs over a 24 h incubation time. Experiment 2 followed a 3 × 2 × 2 factorial arrangement, with eight replicates (n = 8) to study the impacts of three different STL inclusions at 0, 100, and 200 g/kg DM of two different STL types (black and green) into two different total mixed diets containing either RH or RS on the same in vitro measurements. Both types of tea leaves decreased NH3 (p < 0.001) and CH4 (p < 0.01) without affecting (p > 0.05) rumen degradability, but the effect of their STL was less remarkable. Tea leaves and their STL inclusions improved (p < 0.01 and p < 0.001, respectively) the acetate to propionate (A:P) ratio. Compared with BTL, GTL containing diets had higher IVOMD (p < 0.05) and A:P ratio (p < 0.05) but lower NH3 (p < 0.001). Reduced rumen NH3 and CH4 outputs can be useful for protein and energy use efficiency while an increased A:P ratio might lead to increased milk fat synthesis and reduced low-fat milk syndrome. The surplus or wasted tea leaf products could be used as sustainable sources of nutrients to optimize rumen function and minimize environmental impacts of feeding ruminant animals.

The role of seaweed as a potential dietary supplementation for enteric methane mitigation in ruminants: Challenges and opportunities

Seaweeds are macroalgae, which can be of many different morphologies, sizes, colors, and chemical profiles. They include brown, red, and green seaweeds. Brown seaweeds have been more investigated and exploited in comparison to other seaweed types for their use in animal feeding studies due to their large sizes and ease of harvesting. Recent in vitro and in vivo studies suggest that plant secondary compound-containing seaweeds (e.g., halogenated compounds, phlorotannins, etc.) have the potential to mitigate enteric methane (CH4) emissions from ruminants when added to the diets of beef and dairy cattle. Red seaweeds including Asparagopsis spp. are rich in crude protein and halogenated compounds compared to brown and green seaweeds. When halogenated-containing red seaweeds are used as the active ingredient in ruminant diets, bromoform concentration can be used as an indicator of anti-methanogenic properties. Phlorotannin-containing brown seaweed has also the potential to decrease CH4 production. However, numerous studies examined the possible anti-methanogenic effects of marine seaweeds with inconsistent results. This work reviews existing data associated with seaweeds and in vitro and in vivo rumen fermentation, animal performance, and enteric CH4 emissions in ruminants. Increased understanding of the seaweed supplementation related to rumen fermentation and its effect on animal performance and CH4 emissions in ruminants may lead to novel strategies aimed at reducing greenhouse gas emissions while improving animal productivity.

Increasing the Production of Volatile Fatty Acids from Corn Stover Using Bioaugmentation of a Mixed Rumen Culture with Homoacetogenic Bacteria

Volatile fatty acids (VFA) are industrially versatile chemicals and have a major market. Although currently produced from petrochemicals, chemical industries are moving towards more bio-based VFA produced from abundant, cheap and renewable sources such as lignocellulosic biomass. In this study, we examined the effect of bioaugmentation with homoacetogenic bacteria for increasing VFA production in lignocellulose fermentation process. The central hypothesis of this study was that inhibition of methanogenesis in an in vitro rumen bioreactor fed with lignocellulosic biomass hydrolysate increases the hydrogen partial pressure, which can be redirected towards increased VFA production, particularly acetic acid, through targeted bioaugmentation with known homoacetogenic bacteria. In this study, methanogenesis during ruminal fermentation of wet exploded corn stover was initially inhibited with 10 mM of 2-bromoethanesulfonate (BES), followed by bioaugmentation with either Acetitomaculum ruminis and Acetobacterium woodii in two separate bioreactors. During the inhibition phase, we found that addition of BES decreased the acetic acid yield by 24%, while increasing headspace hydrogen from 1% to 60%. After bioaugmentation, the headspace hydrogen was consumed in both bioreactors and the concentration of acetic acids increased 45% when A. ruminis was added and 70% with A. woodii added. This paper demonstrates that mixed microbial fermentation can be manipulated to increase VFA production through bioaugmentation.

New challenges for efficient usage of Sargassum fusiforme for ruminant production

Sargassum fusiforme, which is a type of brown algae, can provide fiber and minerals to ruminant diets. In this study, dried S. fusiforme was tested in vitro at four different doses 1, 3, 5, and 10% of the total ration for its effect on ruminal fermentation characteristics, and gas profiles when incubated for 72 h. At a level of 1 and 10%, S. fusiforme supplementation augmented total volatile fatty acid (VFA) concentrations compared to that with 0% supplementation. In addition, total gas, methane, and carbon dioxide emissions significantly decreased at 3 and 24 h of incubation at this dose. An in situ trial was performed for 72 h with S. fusiforme to evaluate it as a potential feed ingredient by comparing its degradation parameters with timothy hay (Phleum pretense). 1H nuclear magnetic resonance spectroscopy profiling was used to identify and quantify metabolites of S. fusiforme. Mannitol, guanidoacetate and ethylene glycol were largely accumulated in S. fusiforme. Moreover, nutritious minerals for feed ingredients were present in S. fusiforme. Whereas a high concentration of arsenic was found in S. fusiforme, it was within the allowable limit for ruminants. Our results suggest that S. fusiforme could represent an alternative, renewable feed ingredient for ruminant diets, with nutritional, as well as environmental, benefits.

Dietary mitigation of enteric methane emissions from ruminants: A review of plant tannin mitigation options

Methane gas from livestock production activities is a significant source of greenhouse gas (GHG) emissions which have been shown to influence climate change. New technologies offer a potential to manipulate the rumen biome through genetic selection reducing CH4 production. Methane production may also be mitigated to varying degrees by various dietary intervention strategies. Strategies to reduce GHG emissions need to be developed which increase ruminant production efficiency whereas reducing production of CH4 from cattle, sheep, and goats. Methane emissions may be efficiently mitigated by manipulation of natural ruminal microbiota with various dietary interventions and animal production efficiency improved. Although some CH4 abatement strategies have shown efficacy in vivo, more research is required to make any of these approaches pertinent to modern animal production systems. The objective of this review is to explain how anti-methanogenic compounds (e.g., plant tannins) affect ruminal microbiota, reduce CH4 emission, and the effects on host responses. Thus, this review provides information relevant to understanding the impact of tannins on methanogenesis, which may provide a cost-effective means to reduce enteric CH4 production and the influence of ruminant animals on global GHG emissions.

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation

Ruminant methane production is a significant energy loss to the animal and major contributor to global greenhouse gas emissions. However, it also seems necessary for effective rumen function, so studies of anti-methanogenic treatments must also consider implications for feed efficiency. Between-animal variation in feed efficiency represents an alternative approach to reducing overall methane emissions intensity. Here we assess the effects of dietary additives designed to reduce methane emissions on the rumen microbiota, and explore relationships with feed efficiency within dietary treatment groups. Seventy-nine finishing steers were offered one of four diets (a forage/concentrate mixture supplemented with nitrate (NIT), lipid (MDDG) or a combination (COMB) compared to the control (CTL)). Rumen fluid samples were collected at the end of a 56 d feed efficiency measurement period. DNA was extracted, multiplexed 16s rRNA libraries sequenced (Illumina MiSeq) and taxonomic profiles were generated. The effect of dietary treatments and feed efficiency (within treatment groups) was conducted both overall (using non-metric multidimensional scaling (NMDS) and diversity indexes) and for individual taxa. Diet affected overall microbial populations but no overall difference in beta-diversity was observed. The relative abundance of Methanobacteriales (Methanobrevibacter and Methanosphaera) increased in MDDG relative to CTL, whilst VadinCA11 (Methanomassiliicoccales) was decreased. Trimethylamine precursors from rapeseed meal (only present in CTL) probably explain the differences in relative abundance of Methanomassiliicoccales. There were no differences in Shannon indexes between nominal low or high feed efficiency groups (expressed as feed conversion ratio or residual feed intake) within treatment groups. Relationships between the relative abundance of individual taxa and feed efficiency measures were observed, but were not consistent across dietary treatments.

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.

Thinking Outside the Cereal Box: Noncarbohydrate Routes for Dietary Manipulation of the Gut Microbiota

The gut microbiota is a diverse and dynamic ecological community that is increasingly recognized to play important roles in host metabolic, immunological, and behavioral functioning. As such, identifying new routes for manipulating the microbiota may provide valuable additional methods for improving host health. Dietary manipulations and prebiotic supplementation are active targets of research for altering the microbiota, but to date, this work has disproportionately focused on carbohydrates. However, many other resources can limit or shape microbial growth. Here, we provide a brief overview of the resource landscape in the mammalian gut and review relevant literature documenting associations between noncarbohydrate nutrients and the composition of the gut microbiota. To spur future work and accelerate translational applications, we propose that researchers take new approaches for studying the effects of diet on gut microbial communities, including more-careful consideration of media for in vitro experiments, measurement of absolute as well as relative abundances, concerted efforts to articulate how physiology may differ between humans and the animal models used in translational studies, and leveraging natural variation for additional insights. Finally, we close with a discussion of how to determine when or where to employ these potential dietary levers for manipulating the microbiota.

Effects of Tea Saponin Supplementation on Nutrient Digestibility, Methanogenesis, and Ruminal Microbial Flora in Dorper Crossbred Ewe

Simple Summary

Greenhouse gas emissions are a serious cause of global warming and climate change, and have become a common focus for all countries. Methane has been proven the second most commonly occurring greenhouse gas. Ruminants have been blamed for substantially contributing to methane emissions. Supplementation with tea saponin (TS) effectively decreased methane emissions and nitrogen emissions. It is not only beneficial for environmental protection, but also has potential economic benefits.

Abstract

Two experiments were conducted using Dorper × thin-tailed Han crossbred ewes. In experiment 1, eighteen ewes were randomly assigned to two dietary treatments (a basal diet, or the same basal diet supplemented with 2.0 g tea saponin (TS)/head/day) to investigate the effects of TS supplementation on nutrient digestibility and methane emissions. In experiment 2, six ewes with ruminal cannulae were assigned to the same two dietary treatments as in experiment 1 to investigate the effects of TS supplementation on rumen fermentation and microbial flora. TS supplementation increased the apparent digestibility of organic matter (OM) (p = 0.001), nitrogen (N) (p = 0.036), neutral detergent fibre (NDF) (p = 0.001), and acid detergent fibre (ADF) (p < 0.001). Urinary N (p = 0.001) and fecal N (p = 0.036) output were reduced, and N retention (p = 0.001) and nitrogen retention/nitrogen intake (p = 0.001) were increased. Supplementary TS did not decrease absolute methane emissions (p = 0.519) but decreased methane emissions scaled to metabolic bodyweight by 8.80% (p = 0.006). Ammonia levels decreased (p < 0.001) and total volatile fatty acid levels increased (p = 0.018) in response to TS supplementation. The molar proportion of propionate increased (p = 0.007), whereas the acetate:propionate ratio decreased (p = 0.035). Supplementation with TS increased the population of Fibrobacter succinogenes (p = 0.019), but the population of protozoans tended to decrease (p = 0.054). Supplementation with TS effectively enhanced the apparent digestibility of OM, N, NDF, and ADF, and decreased methane emissions scaled to metabolic bodyweight.

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production

The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber. pH in the sheep rumen was more than 1 unit higher than that in the rabbit cecum. The acetate to propionate ratio in the rabbit cecum was more than threefold greater than that in the sheep rumen. Comparative analysis of 16S rRNA gene amplicon libraries revealed distinct microbiota between the rumen of sheep and the cecum of rabbits. Hydrogen-producing fibrolytic bacteria, especially Butyrivibrio, Succiniclastium, Mogibacterium, Prevotella, and Christensenellaceae, were more predominant in the sheep rumen, whereas non-hydrogen producing fibrolytic bacteria, such as Bacteroides, were more predominant in the rabbit cecum. The rabbit cecum had a greater predominance of acetogens, such as those in the genus Blautia, order Clostridiales, and family Ruminococcaceae. The differences in the occurrence of hydrogen-metabolizing bacteria probably explain much of the differential methane outputs from the rumen and the cecum. Future research using metatranscriptomics and metabolomics shall help confirm this premise and understand the factors that shape the differential microbiota between the two digestive organs. Furthermore, our present study strongly suggests the presence of new fibrolytic bacteria in the rabbit cecum, which may explain the stronger fibrolytic activities therein.

Dietary sources and their effects on animal production and environmental sustainability

Animal agriculture has been an important component in the integrated farming systems in developing countries. It serves in a paramount diversified role in producing animal protein food, draft power, farm manure as well as ensuring social status-quo and enriching livelihood. Ruminants are importantly contributable to the well-being and the livelihood of the global population. Ruminant production systems can vary from subsistence to intensive type of farming depending on locality, resource availability, infrastructure accessibility, food demand and market potentials. The growing demand for sustainable animal production is compelling to researchers exploring the potential approaches to reduce greenhouse gases (GHG) emissions from livestock. Global warming has been an issue of concern and importance for all especially those engaged in animal agriculture. Methane (CH₄) is one of the major GHG accounted for at least 14% of the total GHG with a global warming potential 25-fold of carbon dioxide and a 12-year atmospheric lifetime. Agricultural sector has a contribution of 50 to 60% methane emission and ruminants are the major source of methane contribution (15 to 33%). Methane emission by enteric fermentation of ruminants represents a loss of energy intake (5 to 15% of total) and is produced by methanogens (archae) as a result of fermentation end-products. Ruminants׳ digestive fermentation results in fermentation end-products of volatile fatty acids (VFA), microbial protein and methane production in the rumen. Rumen microorganisms including bacteria, protozoa and fungal zoospores are closely associated with the rumen fermentation efficiency. Besides using feed formulation and feeding management, local feed resources have been used as alternative feed additives for manipulation of rumen ecology with promising results for replacement in ruminant feeding. Those potential feed additive practices are as follows: 1) the use of plant extracts or plants containing secondary compounds (e.g., condensed tannins and saponins) such as mangosteen peel powder, rain tree pod; 2) plants rich in minerals, e.g., banana flower powder; and 3) plant essential oils, e.g., garlic, eucalyptus leaf powder, etc. Implementation of the -feed-system using cash crop and leguminous shrubs or fodder trees are of promising results.

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach

Background

Forestomach fermentation in Australian marsupials such as wallabies and kangaroos, though analogous to rumen fermentation, results in lower methane emissions. Insights into hydrogenotrophy in these systems could help in devising strategies to reduce ruminal methanogenesis. Reductive acetogenesis may be a significant hydrogen sink in these systems and previous molecular analyses have revealed a novel diversity of putative acetogens in the tammar wallaby forestomach.

Results

Methanogen-inhibited enrichment cultures prepared from tammar wallaby forestomach contents consumed hydrogen and produced primarily acetate. Functional gene (formyltetrahydrofolate synthetase and acetyl-CoA synthase) analyses revealed a restricted diversity of Clostridiales species as the putative acetogens in the cultures. A new acetogen (growth on H₂/CO₂ with acetate as primary end product) designated isolate TWA4, was obtained from the cultures. Isolate TWA4 classified within the Lachnospiraceae and demonstrated >97% rrs identity to previously isolated kangaroo acetogens. Isolate TWA4 was a potent hydrogenotroph and demonstrated excellent mixotrophic growth (concomitant consumption of hydrogen during heterotrophic growth) with glycerol. Mixotrophic growth of isolate TWA4 on glycerol resulted in increased cell densities and acetate production compared to autotrophic growth. Co-cultures with an autotrophic methanogen Methanobrevibacter smithii revealed that isolate TWA4 performed reductive acetogenesis under high hydrogen concentration (>5 mM), but not at low concentrations. Under heterotrophic growth conditions, isolate TWA4 did not significantly stimulate methanogenesis in a co-culture with M. smithii contrary to the expectation for organisms growing fermentatively.

Conclusions

The unique properties of tammar wallaby acetogens might be contributing factors to reduced methanogen numbers and methane emissions from tammar wallaby forestomach fermentation, compared to ruminal fermentation. The macropod forestomach may be a useful source of acetogens for future strategies to reduce methane emissions from ruminants, particularly if these strategies also include some level of methane suppression and/or acetogen stimulation, for example by harnessing mixotrophic growth capabilities

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0314-3) contains supplementary material, which is available to authorized users.

Effect ofPropionibacterium freudenreichiion ruminal fermentation patterns, methane production and lipid biohydrogenation of beef finishing diets containing flaxseed oil in a rumen simulation technique

Meale, S. J., Ding, S., He, M. L., Dugan, M. E. R., Ribeiro Jr. G. O., Alazzeh, A. Y., Holo, H., Harstad, O. M., McAllister, T. A. and Chaves, A. V. 2014. Effect of Propionibacterium freudenreichii on ruminal fermentation patterns, methane production and lipid biohydrogenation of beef finishing diets containing flaxseed oil in a rumen simulation technique. Can. J. Anim. Sci. 94: 685–695. The objectives of this study were to examine the effects of Propionibacterium freudenreichii (strain T54; PB) and flaxseed oil (FO) in a total mixed ration on ruminal fermentation, CH4production and fatty acid biohydrogenation in two artificial rumens (RUSITEC). The experiment consisted of 8 d of adaptation and 12 d of sample collection with four replicate fermenters per treatment. Treatments were: (1) CON; (2) PB; (3) FO (60 g kg−1DM with autoclaved PB); (4) FOPB (60 g kg−1DM with PB). Disappearance of DM (g kg−1DM) and gas production (mL g−1DM) were not affected by treatment (P>0.05). Inclusion of FOPB increased (P=0.01) total volatile fatty acid (VFA) production (mmol d−1), compared with CON and PB. The acetate:propionate ratio was reduced (P<0.001) in all treatments, compared with CON. Methane production (mL g−1DM or mL g−1DMD) was lowest (P<0.001) with PB (27.1%); however, FO (14.3%) and FOPB (19.3%) also reduced CH4compared with CON. Fatty acid profiles for PB were similar (P>0.05) to CON for most fatty acids. Concentrations of 18:3n-3 were greater (P<0.001) in FO and FOPB in both digesta and effluent, compared with CON. Propionibacterium freudenreichii had very little effect on ruminal biohydrogenation, but reduced CH4production under the current conditions as a result of increasing propionate production.

An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea

The aim of this work was to study whether feeding a methanogen inhibitor from birth of goat kids and their does has an impact on the archaeal population colonizing the rumen and to what extent the impact persists later in life. Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with bromochloromethane after giving birth and over 2 months. The other 8 goats were not treated (D−). One kid per doe in both groups was treated with bromochloromethane (k+) for 3 months while the other was untreated (k−), resulting in four experimental groups: D+/k+, D+/k−, D−/k+, and D−/k−. Rumen samples were collected from kids at weaning and 1 and 4 months after (3 and 6 months after birth) and from does at the end of the treating period (2 months). Pyrosequencing analyses showed a modified archaeal community composition colonizing the rumen of kids, although such effect did not persist entirely 4 months after; however, some less abundant groups remained different in treated and control animals. The different response on the archaeal community composition observed between offspring and adult goats suggests that the competition occurring in the developing rumen to occupy different niches offer potential for intervention.

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.

Carbon precursors of methane synthesis in the rumen of sheep dosed with ionophores

Rates of methane (CH4) production and the sources of carbon (C) for its synthesis were studied in four mature ewes when dosed with a CH4-mitigating ionophore ICI-111075, or monensin, or when untreated. The sheep were given 700 g/day of chaffed lucerne hay in equal portions every hour, before and during experiments in which 14C-labelled NaHCO3–, acetate, propionate, lactate and formate were infused intraruminally over 12 h and the specific radioactivity of C (SR) in each of these substrates was determined. During these infusions, the SR of material in the primary pool (the tracer infusion site) and in secondary metabolites of this material (secondary pools) approached asymptotic or ‘plateau’ values. The rate of infusion of 14CH4 (kBq/day) divided by the plateau SR value (kBq/g C) gave estimates of the rate of irreversible loss of CH4 (g C/day). These calculations indicated that CH4 production rate was reduced by 72% when sheep were dosed with ICI-111075 and by 58% when dosed with monensin. With monensin, the reduction in CH4 production was not associated with hydrogen (H2) accumulation in the rumen headspace gases whereas with ICI-111075, the decrease in CH4 production was associated with marked H2 accumulation in the headspace gases. When plateau SR were attained during the tracer infusions, the percentage ratio, (SR in any secondary pool: SR in the primary pool) gave an estimate of the fraction of C in that secondary pool derived from material of the primary pool. Calculated in this way, the percentage of CH4-C derived from rumen fluid carbon dioxide (CO2) averaged 59% in untreated sheep, and when sheep were dosed with ICI-111075, the corresponding percentage averaged 12%. These findings indicate there are sources of C for rumen CH4 synthesis other than rumen fluid CO2. However, there was no evidence that C from acetate, propionate, lactate or formate in rumen fluid were direct sources of the unidentified CH4-C. One plausible explanation for these findings is that CH4 is synthesised within naturally occurring microbial biofilms (attached to feed particles or the rumen wall) from CO2 that is produced locally by fermentation of unlabelled substrates within the biofilms. It is postulated that such pools of CO2 would be kinetically distinct and, during the infusion of 14C-labelled substrates, would exhibit a lower SR than the CO2 in the surrounding rumen fluid.

Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem

Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.

Enteric methane mitigation technologies for ruminant livestock: a synthesis of current research and future directions

Enteric methane (CH(4)) emission in ruminants, which is produced via fermentation of feeds in the rumen and lower digestive tract by methanogenic archaea, represents a loss of 2% to 12% of gross energy of feeds and contributes to global greenhouse effects. Globally, about 80 million tonnes of CH(4) is produced annually from enteric fermentation mainly from ruminants. Therefore, CH(4) mitigation strategies in ruminants have focused to obtain economic as well as environmental benefits. Some mitigation options such as chemical inhibitors, defaunation, and ionophores inhibit methanogenesis directly or indirectly in the rumen, but they have not confirmed consistent effects for practical use. A variety of nutritional amendments such as increasing the amount of grains, inclusion of some leguminous forages containing condensed tannins and ionophore compounds in diets, supplementation of low-quality roughages with protein and readily fermentable carbohydrates, and addition of fats show promise for CH(4) mitigation. These nutritional amendments also increase the efficiency of feed utilization and, therefore, are most likely to be adopted by farmers. Several new potential technologies such as use of plant secondary metabolites, probiotics and propionate enhancers, stimulation of acetogens, immunization, CH(4) oxidation by methylotrophs, and genetic selection of low CH(4)-producing animals have emerged to decrease CH(4) production, but these require extensive research before they can be recommended to livestock producers. The use of bacteriocins, bacteriophages, and development of recombinant vaccines targeting archaeal-specific genes and cell surface proteins may be areas worthy of investigation for CH(4) mitigation as well. A combination of different CH(4) mitigation strategies should be adopted in farm levels to substantially decrease methane emission from ruminants. Evidently, comprehensive research is needed to explore proven and reliable CH(4) mitigation technologies that would be practically feasible and economically viable while improving ruminant production.

Feeding of tropical trees and shrub foliages as a strategy to reduce ruminal methanogenesis: studies conducted in Cuba

The aim of this paper was to present the main results obtained in Cuba on the effects of feeding tropical trees and shrubs on rumen methanogenesis in animals fed with low quality fibrous diets. More than 20 tree and shrub foliages were screened for phytochemicals and analyzed for chemical constituents. From these samples, seven promising plants (Samanea saman, Albizia lebbeck, Tithonia diversifolia, Leucaena leucocephala, Trichantera gigantea, Sapindus saponaria, and Morus alba) were evaluated for methane reduction using an in vitro rumen fermentation system. Results indicated that the inclusion levels of 25% of Sapindo, Morus, or Trichantera foliages in the foliages/grass mixtures (grass being Pennisetum purpureum) reduced (P < 0.01) methane production in vitro when compared to Pennisetum alone (17.0, 19.1, and 18.0 versus 26.2 mL CH(4)/g fermented dry matter, respectively). It was demonstrated that S. saman, A. lebbeck, or T. diversifolia accession 23 foliages when mixed at the rate of 30% in Cynodon nlemfuensis grass produced lower methane compared to the grass alone. Inclusion levels of 15% and 25% of a ruminal activator supplement containing 29% of L. leucocehala foliage meal reduced methane by 37% and 42% when compared to the treatment without supplementation. In vivo experiment with sheep showed that inclusion of 27% of L. leucocephala in the diet increased the DM intake but did not show significant difference in methane production compared to control diet without this foliage. The results of these experiments suggest that the feeding of tropical tree and shrub foliages could be an attractive strategy for reduction of ruminal methanogenesis from animals fed with low-quality forage diets and for improving their productivity.

The effect of dietary concentrate and soya oil inclusion on microbial diversity in the rumen of cattle

AIMS

Methane emissions from ruminants are a significant contributor to global greenhouse gas production. The aim of this study was to examine the effect of diet on microbial communities in the rumen of steers.

METHODS AND RESULTS

The effects of dietary alteration (50 : 50 vs 90 : 10 concentrate-forage ratio, and inclusion of soya oil) on methanogenic and bacterial communities in the rumen of steers were examined using molecular fingerprinting techniques (T-RFLP and automated ribosomal intergenic spacer analysis) and real-time PCR. Bacterial diversity was greatly affected by diet, whereas methanogen diversity was not. However, methanogen abundance was significantly reduced (P = 0.009) in high concentrate-forage diets and in the presence of soya oil (6%). In a parallel study, reduced methane emissions were observed with these diets.

CONCLUSIONS

The greater effect of dietary alteration on bacterial community in the rumen compared with the methanogen community may reflect the impact of substrate availability on the rumen bacterial community. This resulted in altered rumen volatile fatty acid profiles and had a downstream effect on methanogen abundance, but not diversity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Understanding how rumen microbial communities contribute to methane production and how these microbes are influenced by diet is essential for the rational design of methane mitigation strategies from livestock.

Ruminant enteric methane mitigation: a review

In Australia, agriculture is responsible for ~17% of total greenhouse gas emissions with ruminants being the largest single source. However, agriculture is likely to be shielded from the full impact of any future price on carbon. In this review, strategies for reducing ruminant methane output are considered in relation to rumen ecology and biochemistry, animal breeding and management options at an animal, farm, or national level. Nutritional management strategies have the greatest short-term impact. Methanogenic microorganisms remove H2 produced during fermentation of organic matter in the rumen and hind gut. Cost-effective ways to change the microbial ecology to reduce H2 production, to re-partition H2 into products other than methane, or to promote methanotrophic microbes with the ability to oxidise methane still need to be found. Methods of inhibiting methanogens include: use of antibiotics; promoting viruses/bacteriophages; use of feed additives such as fats and oils, or nitrate salts, or dicarboxylic acids; defaunation; and vaccination against methanogens. Methods of enhancing alternative H2 using microbial species include: inoculating with acetogenic species; feeding highly digestible feed components favouring ‘propionate fermentations’; and modifying rumen conditions. Conditions that sustain acetogen populations in kangaroos and termites, for example, are poorly understood but might be extended to ruminants. Mitigation strategies are not in common use in extensive grazing systems but dietary management or use of growth promotants can reduce methane output per unit of product. New, natural compounds that reduce rumen methane output may yet be found. Smaller but more permanent benefits are possible using genetic approaches. The indirect selection criterion, residual feed intake, when measured on ad libitum grain diets, has limited relevance for grazing cattle. There are few published estimates of genetic parameters for feed intake and methane production. Methane-related single nucleotide polymorphisms have yet to be used commercially. As a breeding objective, the use of methane/kg product rather than methane/head is recommended. Indirect selection via feed intake may be more cost-effective than via direct measurement of methane emissions. Life cycle analyses indicate that intensification is likely to reduce total greenhouse gas output but emissions and sequestration from vegetation and soil need to be addressed. Bio-economic modelling suggests most mitigation options are currently not cost-effective.

Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach

Reductive acetogenesis via the acetyl coenzyme A (acetyl-CoA) pathway is an alternative hydrogen sink to methanogenesis in the rumen. Functional gene-based analysis is the ideal approach for investigating organisms capable of this metabolism (acetogens). However, existing tools targeting the formyltetrahydrofolate synthetase gene (fhs) are compromised by lack of specificity due to the involvement of formyltetrahydrofolate synthetase (FTHFS) in other pathways. Acetyl-CoA synthase (ACS) is unique to the acetyl-CoA pathway and, in the present study, acetyl-CoA synthase genes (acsB) were recovered from a range of acetogens to facilitate the design of acsB-specific PCR primers. fhs and acsB libraries were used to examine acetogen diversity in the bovine rumen and forestomach of the tammar wallaby (Macropus eugenii), a native Australian marsupial demonstrating foregut fermentation analogous to rumen fermentation but resulting in lower methane emissions. Novel, deduced amino acid sequences of acsB and fhs affiliated with the Lachnospiraceae in both ecosystems and the Ruminococcaeae/Blautia group in the rumen. FTHFS sequences that probably originated from nonacetogens were identified by low "homoacetogen similarity" scores based on analysis of FTHFS residues, and comprised a large proportion of FTHFS sequences from the tammar wallaby forestomach. A diversity of FTHFS and ACS sequences in both ecosystems clustered between the Lachnospiraceae and Clostridiaceae acetogens but without close sequences from cultured isolates. These sequences probably originated from novel acetogens. The community structures of the acsB and fhs libraries from the rumen and the tammar wallaby forestomach were different (LIBSHUFF, P < 0.001), and these differences may have significance for overall hydrogenotrophy in both ecosystems.

Decrease of ruminal methane production in Rusitec fermenters through the addition of plant material from rhubarb (Rheum spp.) and alder buckthorn (Frangula alnus)

Roots of rhubarb (Rheum spp.) and bark of alder buckthorn (Frangula alnus) were tested as feed additives for decreasing ruminal methane production released from anaerobic fermentation of a forage-based diet in a rumen-simulating fermenter (Rusitec). Sixteen fermentation units (vessels) were set up for the experiment lasting 19 d. Treated vessels were supplied with 1g/d of rhubarb or alder buckthorn (4 vessels per plant species); another 4 vessels received 12 microM sodium monensin (positive control), and the remaining 4 vessels were controls (no additive). Upon termination of the experimental period, batch cultures were inoculated with the liquid contents of the vessels for examining in vitro fermentation kinetics of cellulose, starch, barley straw, and the same substrate used in the Rusitec cultures. Monensin induced changes in fermentation in agreement with those reported in the literature, and inocula from those cultures decreased the fermentation rate and total gas produced in the gas kinetics study. Rhubarb decreased methane production, associated with limited changes in the profile of volatile fatty acids throughout the duration of the study, whereas digestibility and total volatile fatty acids production were not affected. Rhubarb inocula did not affect gas production kinetics except for cellulose. Alder buckthorn decreased only methane concentration in fermentation gas, and this effect was not always significant. The use of rhubarb (milled rhizomes of Rheum spp.) in the diets of ruminants may effectively modulate ruminal fermentation by abating methane production, thus potentially involving productive and environmental benefits.

Strategies to reduce methane emissions from farmed ruminants grazing on pasture

Methane emissions from livestock are a significant contributor to greenhouse gas emissions and have become a focus of research activities, especially in countries where agriculture is a major economic sector. Understanding the complexity of the rumen microbiota, including methane-producing Archaea, is in its infancy. There are currently no robust, reproducible and economically viable methods for reducing methane emissions from ruminants grazing on pasture and novel innovative strategies to diminish methane output from livestock are required. In this review, current approaches towards mitigation of methane in pastoral farming are summarised. Research strategies based on vaccination, enzyme inhibitors, phage, homoacetogens, defaunation, feed supplements, and animal selection are reviewed. Many approaches are currently being investigated, and it is likely that more than one strategy will be required to enable pastoral farming to lower its emissions of methane significantly. Different strategies may be suitable for different farming practices and systems.

Application of rumen microbial genome information to livestock systems in the postgenomic era

Sequencing the genomes of individual rumen microbes and determining the function of their encoded genes promises to transform our understanding of the microbiology of the rumen. The diversity and density of microbes in the rumen, and our inability to culture the majority of rumen microbes, limit current genome studies to only a small fraction of the microbes present in this environment. Nevertheless, genomes of fibre-degrading organisms are beginning to reveal a previously unexpected abundance of genes encoding glycosyl hydrolases and carbohydrate esterases, which could be used to enhance fibre digestion in the rumen. Additionally, genome sequencing of a rumen methanogen is identifying conserved genes within the methanogenic archaea that may serve as targets for their inhibition and therefore reduction of methane emissions from ruminants. The problem of rumen microbe culturability can be overcome by a new approach called metagenomics, in which microbial DNAs are extracted from rumen samples and sequenced independent of cultivation. In the future, sequencing individual genomes and metagenomic libraries is likely to capture much more of the microbial DNA in the rumen and, coupled with postgenomic studies on gene and protein expression, is likely to enhance our knowledge of the microbial component of ruminant digestion.