Factors affecting rumen methanogens and methane mitigation strategies

Comparative anti-methanogenic ability of green algae (C. reinhardtii) with/without nanoparticles: in vitro gas and methane production

Introduction

The purpose of this study was to investigate how in vitro gas production (GP) and ruminal fermentation characteristics were affected by increasing concentrations of green algae plant (C. reinhardtii) extracts in combination with nanoparticles MgO and MgS.

Methods

A solution containing 0.1 M MgCl2 was prepared in 300 mL for the green production of MgCl nanoparticles. The mixture was refluxed for two hours at 85°C using a reflux condenser after 10 mL of pomegranate plant extract was added. The green algal plant (C. reinhardtii), which has many non-toxic antioxidants, was used as a carbon source to produce carbon quantum dots (CQD). Chemical analysis was conducted in accordance with AOAC (2005) recommendations. Rumen fluid from recently slaughtered calves is used to produce in vitro gas immediately following slaughter. Analysis of variance (ANOVA) was performed on the obtained data from the in vitro study in a completely randomized design using the mixed model of SAS (version 9.4; Inc., Cary NC, USA).

Results and Discussion

The variance analysis results and the average values of the chemical compositions were significantly influenced by the extracts (all p < 0.0001). In this line, the values of net gas, pH, OMD, ME, NEl, and ME were found to be the highest for Algae + 50 MgO and the lowest for Algae + 50 MgS, respectively (all p < 0.0001). These promising results imply that extracts from C. Reinhardtii may be able to mitigate the adverse consequences of rumen fermentation. To precisely ascertain the impact particular Rhodophyta on greenhouse gas emissions, additional investigation is needed.

Application of propionate-producing bacterial consortium in ruminal methanogenesis inhibited environment with bromoethanesulfonate as a methanogen direct inhibitor

Methane production in ruminants is primarily due to the conversion of metabolic hydrogen (H2), produced during anaerobic microbial fermentation, into methane by ruminal methanogens. While this process plays a crucial role in efficiently disposes of H2, it also contributes to environmental pollution and eliminating methane production in the rumen has proven to be challenging. This study investigates the use of probiotics, specifically propionate-producing bacteria, to redirect accumulated H2 in a methane-mitigated environment. For this objective, we supplemented experimental groups with Lactiplantibacillus plantarum and Megasphaera elsdenii for the reinforced acrylate pathway (RA) and Selenomonas ruminantium and Acidipropionibacterium thoenii for the reinforced succinate pathway (RS), as well as a consortium of all four strains (CB), with the total microbial concentration at 1.0 × 1010 cells/mL. To create a methane-mitigated environment, 2-bromoethanesulfonate (BES) was added to all experimental groups at a dose of 15 mg/0.5 g of feed. BES reduced methane production by 85% in vitro, and the addition of propionate-producing bacteria with BES further decreased methane emission by up to 94% compared with the control (CON) group. Although BES did not affect the alpha diversity of the ruminal bacteriome, it reduced total volatile fatty acid production and altered beta diversity of ruminal bacteriota, indicating microbial metabolic adaptations to H2 accumulation. Despite using different bacterial strains targeting divergent metabolic pathways (RA and RS), a decrease in the dominance of the [Eubacterium] ruminantium group suggesting that both approaches may have a similar modulatory effect. An increase in the relative abundance of Succiniclasticum in the CB group suggests that propionate metabolism is enhanced by the addition of a propionate-producing bacterial consortium. These findings recommend using a consortium of propionate-producing bacteria to manage H2 accumulation by altering the rumen bacteriome, thus mitigating the negative effects of methane reduction strategies.

Effects of melatonin on rumen microorganisms and methane production in dairy cow: results from in vitro and in vivo studies

BACKGROUND

Methane (CH4) is a major greenhouse gas, and ruminants are one of the sources of CH4 which is produced by the rumen microbiota. Modification of the rumen microbiota compositions will impact the CH4 production. In this study, the effects of melatonin on methane production in cows were investigated both in the in vitro and in vivo studies.

RESULTS

Melatonin treatment significantly reduced methane production in both studies. The cows treated with melatonin reduced methane emission from their respiration by approximately 50%. The potential mechanisms are multiple. First, melatonin lowers the volatile fatty acids (VFAs) production in rumen and reduces the raw material for CH4 synthesis. Second, melatonin not only reduces the abundance of Methanobacterium which are responsible for generating methane but also inhibits the populations of protozoa to break the symbiotic relationship between Methanobacterium and protozoa in rumen to further lowers the CH4 production. The reduced VFA production is not associated with food intake, and it seems also not to jeopardize the nutritional status of the cows. This was reflected by the increased milk lipid and protein contents in melatonin treated compared to the control cows. It is likely that the energy used to synthesize methane is saved to compensate the reduced VFA production.

CONCLUSION

This study enlightens the potential mechanisms by which melatonin reduces rumen methane production in dairy cows. Considering the greenhouse effects of methane on global warming, these findings provide valuable information using different approaches to achieve low carbon dairy farming to reduce the methane emission. Video Abstract.

Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture

Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L-1), potassium (37-78 mg L-1), and zinc (8-17 mg L-1), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml-1). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm-1. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.

Enteric methane emission estimates for the Zimbabwean Sanga cattle breeds of Tuli and Mashona

The effectiveness of methane mitigation in ruminant livestock production systems depends on the accuracy of estimating methane emission factors and providing accurate emission inventories. Following the Paris Climate agreement, it is recommended that countries adopt the Tier-2 approach for estimating enteric methane emissions from ruminants instead of the Tier-1 approach currently used by most countries. This study sought to provide base line enteric methane emission estimates for the Tuli and Mashona Sanga cattle breeds in Zimbabwe using the IPCC Tier-2 model. Using animal characterization data collected from 412 cattle from Grasslands Research Institute and 406 cattle from Makoholi Research Institute, net energy requirements were estimated. From this and the estimate for digestibility, gross energy intake and dry matter intake were estimated. Gross energy intakes and the estimated methane conversion factor were used to estimate enteric methane emissions. Mean emission factors for Tuli were 45.1, 56, 28.5, 28.4 and 20.6 kg CH₄/head/year for cows, bulls, heifers, steers and calves, respectively. For Mashona, they were 47.8, 51.9, 29, 29.1 and 20.7 kgCH₄/head/year for cows, bulls, heifers, steers and calves, respectively. Generally, estimated Tier-2 emission factors were significantly different from the IPCC Tier-1 default emission factors. This study concluded that enteric methane emission factors estimated using the IPCC Tier-2 model offer insights into the controversial use of the default IPCC Tier-1 emission factors.

Thermo-physiological responses and oxidative status of West African dwarf rams fed diets containing supplemental Tetrapleura tetraptera fruit meal

Plant secondary metabolites in Tetrapleuratetraptera fruit meal (TTFM) could be exploited as natural safe feed additives alternative to non- nutritive chemical and antibiotics to enhance rumen fermentation and feed utilization efficiency with negative oxidative stress. The study investigated the responses of West African Dwarf (WAD) rams to the diets containing varying levels of supplemental Tetrapleura tetraptera fruit meal on the oxidative status and thermo-physiological parameters. Thirty five (35) WAD rams with an average live weight of 13.20±0.2 kg were used in a completely randomized design for 140 days. Five concentrate diets containing varying levels (0, 0.5, 1.0, 1.5 and 2.0 %) of TTFM were formulated while Panicum maximum was fed as a basal diet. The rectal temperature, pulse rate and respiratory rate were measured at two week intervals while blood was collected through jugular veins at the onset and at the end of feeding trial to determine oxidative status parameters in terms of superoxide dismutase (SOD), glutathione peroxidase, thiobarbituric acid reactive substance (TBARS).Data collected were subjected to one way Analysis of Variance (ANOVA). No significant difference observed (p>0.05) in the rectal temperature while the pulse rate and breathing rate increased significantly (p<0.05) till 12th week of the experiment. Increased glutathione peroxidase, superoxide dismutase and lowered thiobarbituric acid reactive substance were recorded on the rams at the end of the feeding trial. It was therefore concluded that inclusion of Tetrapleura tetraptera up to 2 % level reduced the oxidative stress in the experimental animals coupled with better thermo-physiological responses

Enteric Methane Emissions and Animal Performance in Dairy and Beef Cattle Production: Strategies, Opportunities, and Impact of Reducing Emissions

Enteric methane (CH4) emissions produced by microbial fermentation in the rumen resulting in the emission of greenhouse gases (GHG) into the atmosphere. The GHG emissions reduction from the livestock industry can be attained by increasing production efficiency and improving feed efficiency, by lowering the emission intensity of production, or by combining the two. In this work, information was compiled from peer-reviewed studies to analyze CH4 emissions calculated per unit of milk production, energy-corrected milk (ECM), average daily gain (ADG), dry matter intake (DMI), and gross energy intake (GEI), and related emissions to rumen fermentation profiles (volatile fatty acids [VFA], hydrogen [H2]) and microflora activities in the rumen of beef and dairy cattle. For dairy cattle, there was a positive correlation (p < 0.001) between CH4 emissions and DMI (R2 = 0.44), milk production (R2 = 0.37; p < 0.001), ECM (R2 = 0.46), GEI (R2 = 0.50), and acetate/propionate (A/P) ratio (R2 = 0.45). For beef cattle, CH4 emissions were positively correlated (p < 0.05−0.001) with DMI (R2 = 0.37) and GEI (R2 = 0.74). Additionally, the ADG (R2 = 0.19; p < 0.01) and A/P ratio (R2 = 0.15; p < 0.05) were significantly associated with CH4 emission in beef steers. This information may lead to cost-effective methods to reduce enteric CH4 production from cattle. We conclude that enteric CH4 emissions per unit of ECM, GEI, and ADG, as well as rumen fermentation profiles, show great potential for estimating enteric CH4 emissions.

The effect of Macleaya cordata extract on in vitro ruminal fermentation and methanogenesis

Methane production is the main gas energy loss in ruminants and generates a powerful greenhouse gas that contributes to climate changes. Macleaya cordata is a plant commonly utilized additive in livestock diet as it contains various chemical compounds with beneficial health effects. This study aimed to explore the influence of M. cordata extract on in vitro methanogenesis and rumen fermentation. Three cannulated Jingjiang cattle were used as rumen fluid donors. The mixture of rumen fluid and a buffer (60 ml, 1:2 volume ratio) was treated with 6 different concentrations of M. cordata extract (0.01%, 0.11%, 0.21%, 0.31%, 0.41%, and 0.51%) and incubated for 12 and 24 hr. The control sample, with no addition of plant extract, was also analyzed. At each time point, pH, total gas, methane, dry matter (DM) digestibility, neutral detergent fiber (NDF), acid detergent fiber (ADF), ammonia nitrogen (NH3-N), microbial protein (MCP), and volatile fatty acids (VFA) concentrations were determined. Total gas production decreased with increasing the amount of M. cordata extract at all time points. Methane production also decreased dose-dependently with M. cordata extract after 3, 6, 9, and 12 hr of incubation, but increased after 24 hr. M. cordata extract decreased the concentration of NH3-N and VFA, and the amount of acetic, propionic, and butyric acid. M. cordata extract decreased the MCP concentration after 12 hr, but its level returned to the initial value after 24 hr. Supplementation with 0.01, 0.11, and 0.21% of M. cordata extract did not affect the DM digestibility. However, supplementation with 0.31, 0.41, and 0.51% of M. cordata extract significantly decreased the DM digestibility. Supplementation with 0.11% of M. cordata extract effectively reduced methane production without affecting the DM digestion in vitro. However, its effect on in vivo methane production, rumen fermentation, and ruminant production requires further investigation.

Impact of volatile fatty acids to alkalinity ratio and volatile solids on biogas production under thermophilic conditions

The study assessed the impact of volatile fatty acids (VFA) to total alkalinity (TA) ratio (VFA/TA), and percentage volatile solids (VS) reduction of batch and semi-continuous anaerobic co-digestion of palm nut paste waste (PNPW) and anaerobic-digested rumen waste (ADRW) on digester stability and biogas production under the environmental condition of 50 ± 1°C and hydraulic retention time of 21 days for the batch studies and 14 days for semi-continuous co-digestion. The co-digestion ratios were based on percentage digester volume corresponding to 90%:10%, 75%:25% and 50%:50%. During batch and semi-continuous anaerobic co-digestion, VFA/TA of 0.32-1.0 and VS reduction of 53-67% were observed as the stable range at which biogas production was maximum. In terms of semi-continuous anaerobic digestion (AD), except for the 50%:50% ratio where biogas production progressed steadily from the first to fourteenth days, biogas production initially dropped from 180.1 to 171.3 mL between the first and third days of the 90%:10% reaching a maximum of 184 mL on the fourteenth day. Biogas production declined from 198.8 to 187.5 mL on the second day and then increased to 198.8 ± 0.5 mL in the case of the 75%:25% with a significant difference between the treatment ratios at p < 0.05. Therefore, the study can confirm that the 50%:50% ratio (PNPW:ADRW) is a suitable option for managing crude fat-based waste under thermophilic AD due to its potential for rapid start-up and complete biodegradation of active biomass within a 21-day period. This presupposes that residual methane as greenhouse gas will be void in the effluent if disposed of.

Archaea: An Agro-Ecological Perspective

Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.

Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation

Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows

Background

Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows’ production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.

Results

HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH₃-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.

Conclusions

HC feeding significantly decreased ruminal pH and increased the content of NH₃-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH₃ content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine’s function in dairy cows and provided new strategies to improve dairy cows’ health under high-concentrate feeding regime.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1745-0) contains supplementary material, which is available to authorized users.

Effect of Caraway, Fennel and Melissa addition on in vitro Rumen Fermentation and Gas Production

BACKGROUND AND OBJECTIVE

Medicinal herbs and aromatic plants could be used to manipulate rumen fermentation. This study aimed to evaluate the effect of adding herbal and aromatic plants at 1, 3, 5, 7% of total ratio DM supplementation of the incubation media of an in vitro rumen model.

MATERIAL AND METHODS

About 400±4 mg of feed sample (roughage and concentrate ratio of 45:55%) with each level, weighted into 125 mL glass bottles (6 bottles for each treatment), rumen fluid injected into these bottles and incubated at 39°C, after 24 h incubation digestibility of dry matter (IVDMD) and organic matter digestibility (IVOMD), total gas production (TG) and metabolic energy (ME) were studied.

RESULTS

The differences among plants, added at different levels, were significant. Significant differences were also observed between highest level added compared with control in ammonia (NH3) and volatile fatty acids (VFA), IVDMD and IVOMD compared with control. Total gas (TG) was significantly higher at level 7%, especially with added Melissa compared with other plants. Metabolic energy (ME), was significantly higher in all treatments compared with control.

CONCLUSION

It may be concluded that addition of different medicinal and aromatic herbal plants Caraway (Carum carvi), fennel (Foeniculum vulgare) and Melissa (Melissa officinali)), especially at highest levels tested has a great potential in manipulating rumen fermentation, which may be of benefit when applied in ruminant nutrition.

Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China

Background

Tibetan sheep (TS) and Gansu Alpine Finewool sheep (GS) are both important plateau sheep raised and fed on the harsh Qinghai–Tibetan Plateau, China. Rumen methanogen and protozoal communities of plateau sheep are affected by their hosts and living environments, and play important roles in ruminant nutrition and greenhouse gas production. However, the characteristics, differences, and associations of these communities remain largely uncharacterized.

Results

The rumen methanogen and protozoal communities of plateau sheep were investigated by 16S/18S rRNA gene clone libraries. The predominant methanogen order in both sheep species was Methanobacteriales followed by Methanomassiliicoccales, which is consistent with those seen in global ruminants. However, the most dominant species was Methanobrevibacter millerae rather than Methanobrevibacter gottschalkii seen in most ruminants. Compared with GS and other ruminants, TS have more exclusive operational taxonomic units and a lower proportion (64.5%) of Methanobrevibacter. The protozoa were divided into Entodiniomorphida and Vestibuliferida, including nine genera and 15 species. The proportion of holotrich protozoa was much lower (1.1%) in TS than ordinary sheep. The most predominant genus was Entodinium (70.0%) in TS and Enoploplastron (48.8%) in GS, while the most common species was Entodinium furca monolobum (43.9%) and Enoploplastron triloricatum (45.0%) in TS and GS, respectively; Entodinium longinucleatum (22.8%) was only observed in TS. LIBSHUFF analysis indicated that the methanogen communities of TS were significantly different from those of GS, but no significant differences were found in protozoal communities.

Conclusion

Plateau sheep have coevolved with unique rumen methanogen and protozoal communities to adapt to harsh plateau environments. Moreover, the host appears to have a greater influence on rumen methanogen communities than on rumen protozoal communities. The observed associations of methanogens and protozoa, together with the findings of previous studies on methane emissions from ruminant livestock, revealed that the lower proportion of Methanobrevibacter and holotrich protozoa may be responsible for the lower methane emission of TS. These findings facilitate our understanding of the rumen microbial ecosystem in plateau sheep, and could help the development of new strategies to manipulate rumen microbes to improve productivity and reduce the emission of greenhouse gases.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1351-0) contains supplementary material, which is available to authorized users.

Impact of the flour of Jerusalem artichoke on the production of methane and carbon dioxide and growth performance in calves

Aim:

The aim of the research was to evaluate the growth performance, to measure the amount of methane (CH₄) and carbon dioxide (CO₂) in calves’ rumen, and to compare the obtained results between the control group (CoG) and the experimental group (Pre12) which received the additional supplement of the prebiotic inulin.

Materials and Methods:

The research was conducted with ten Holstein Friesian (Bos taurus L.) crossbreed calves with an average age of 33±6 days. Calves were split into two groups: 5 calves that were fed with the control non-supplemented diet (CoG) and 5 calves that were fed with the same diet further supplemented with 12 g of flour of Jerusalem artichoke (Helianthus tuberosus L.) containing 6 g of prebiotic inulin per 0.5 kg of barley flour diet (Pre12). The duration of the experiment was 56 days. CH₄ and CO₂ were measured using cavity ringdown spectroscopy device Picarro G2508. The weight and samples from calves’ rumen were evaluated 3 times during the experimental period - on the 1^st, 28^th, and 56^th days. Samples were obtained by puncturing the calf rumen.

Results:

The weight gain (kg) during the whole experimental period was higher in the Pre12 (65.8±6.57) compared to CoG (36.8±7.98) calves (p<0.001). The daily weight gain was also increased in the Pre12 (1.2±0.12) than CoG (0.7±0.14) calves (p<0.001). There was no difference in the levels of CH₄ and CO₂ produced in the rumen of CoG and Pre12 calves (p>0.05).

Conclusion:

The main results showed that the prebiotic inulin can promote weight gain in calves, without affecting the mean concentration of CH₄ and CO₂ in calves’ rumen.

Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review

Methanobacterium formicicum (Methanobacteriaceae family) is an endosymbiotic methanogenic Archaean found in the digestive tracts of ruminants and elsewhere. It has been significantly implicated in global CH₄ emission during enteric fermentation processes. In this review, we discuss current genomic and metabolic aspects of this microorganism for the purpose of the discovery of novel veterinary therapeutics. This microorganism encompasses a typical H₂ scavenging system, which facilitates a metabolic symbiosis across the H₂ producing cellulolytic bacteria and fumarate reducing bacteria. To date, five genome-scale metabolic models (iAF692, iMG746, iMB745, iVS941 and iMM518) have been developed. These metabolic reconstructions revealed the cellular and metabolic behaviors of methanogenic archaea. The characteristics of its symbiotic behavior and metabolic crosstalk with competitive rumen anaerobes support understanding of the physiological function and metabolic fate of shared metabolites in the rumen ecosystem. Thus, systems biological characterization of this microorganism may provide a new insight to realize its metabolic significance for the development of a healthy microbiota in ruminants. An in-depth knowledge of this microorganism may allow us to ensure a long term sustainability of ruminant-based agriculture.

Use of probiotics and botanical extracts to improve ruminant production in the tropics: A review

Ruminant production, especially in the tropics and developing countries suffers a setback when compared with the temperate and developed countries, which is attributable to the kinds of available feed resources in the region of production. In the tropics, ruminants are restricted to grazing on low-quality forages, crop residues and agro-industrial by-products with very little or no concentrate diets, which adversely affect the animals in exhibiting their full production potential. Considering this fact, there is an increasing interest in improving the digestibility of these feed resources. In recent years, researchers have explored several methods to enhance the functions of rumen microflora, improve digestion and fermentation processes, as well as increase bioavailability and utilization of nutrients through feed supplementation. This review aims to explore the positive effects of supplementation of ruminant diets with probiotics or botanical extracts and their metabolites on the productivity of the animals. Moreover, the functions of these non-pathogenic and non-toxic live microorganisms (probiotics) and plant biologically active compounds (botanical extract) are explored because of the ban on non-therapeutic use of antibiotics as growth promoters coupled with the critical preference of consumers to high quality and safe animal products. It has been reported that these alternative supplemental products have a beneficial impact on both animal health and productivity, which is affecting stabilization of rumen environment, inhibition of pathogenic bacteria proliferation in gastro-intestinal tract, modulation of immune response, increase in fibre degradation and fermentation, nutrients availability and utilization, animal growth performance and milk production, among others. However, long-term in vivo studies are still required to determine the synergetic effects of these 2 safe supplemental products.

Comparative aspects of plant tannins on digestive physiology, nutrition and microbial community changes in sheep and goats: A review

Comparative aspects of plant tannins on digestive physiology, nutrition and microbial community in sheep and goats are discussed in the context of differences due to feed intake, digestibility, utilization of nutrients and microbial community. The purpose of this review was to present an overview of the potential benefits of tannin-containing diets for sheep and goats and specie differences in their response to tannins. It is well established that moderate level of tannins in the diet (3%-4% tannins DM) can precipitate with soluble proteins and increase protein supply to the sheep, but comparative aspects of tannin-containing diets in sheep and goats on animal performance, digestive physiology, rumen microbial changes and potential benefits to sustainable animal production by those compounds have received little attention. In addition, developing plant-based tannin-containing diets for control of rumen microbiota and rumen fermentation (e.g., methane gas) would be expected to have a greater impact on the ruminant health, productivity and emission of greenhouse gasses. The positive impacts of the plant tannin compounds mainly depend on their influence on the gut microbiome diversity and ability to generate fermentation end products (short-chain fatty acids) that have diverse biological roles. Diets which contain optimal levels of tannins have potential benefits for sustainability of small ruminant production systems. However, there is a need for an improved understanding of the utilization of tannin-containing forages to improve their management. This implies investigations of animal responses to tannin-containing forages or browse species and, in particular, a better understanding of the interactions that can arise between sheep and goats on digestion, DMD, rumen fermentation and microbial community changes. This knowledge could help to improve current feeding systems in terms of efficiency of feed use and environmental impacts (reduce methane gas production) and thus contribute to the development of a sustainable sheep and goat production.

Comparative diversity analysis of ruminal methanogens in Murrah buffaloes (Bubalus bubalis) in four states of North India

We compared the community structure of methanogens in Murrah breed of buffaloes of four states of north India using 16S rRNA gene clone library method. The results revealed the dominance of methanogens related to Methanobrevibacter in three states, while Methanomicrobium-related methanogens were abundant in one state.

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.

Tea saponin reduced methanogenesis in vitro but increased methane yield in lactating dairy cows

The effect of tea saponin supplementation in the ruminant diet on methane emissions, rumen fermentation, and digestive processes is still under debate. The objective of this study was to assess the effect of this plant extract on methanogenesis, total-tract digestibility, and lactating performances of dairy cows. The work included 2 independent and successive experiments. First, the effect of 7 tea saponin doses (from 0 to 0.50 g/L) on methane emissions and protozoa concentrations was tested in 2 repeated in vitro batch culture incubations using bovine rumen contents as inoculum and a cereal mixture as substrate. After 18 h of incubation, total gas production and composition as well as rumen fermentation parameters and protozoa concentration were analyzed. Increasing dosage of the plant extract reduced methane production and protozoa concentration, with a maximum reduction of 29% for CH₄ (mL/g of substrate) and 51% for protozoa (10⁵/mL). Tea saponin did not affect volatile fatty acids concentration, but marginally decreased total gas production by 5% at the highest dose. Second, a 2-period crossover design experiment was carried out with 8 lactating dairy cows fed a basal diet (54% corn silage, 6% hay, and 40% pelleted concentrates on a dry matter basis) without (control) or with 0.52% tea saponin (TSP). Each experimental period lasted 5 wk. Animals were fed ad libitum during the first 3 wk of the period (wk 1, 2, and 3) and restricted (95% of ad libitum intake) during the last 2 wk (wk 4 and 5). Intake and milk production were recorded daily. Methane emissions were quantified using open chambers (2 d, wk 4). Total-tract digestibility and nitrogen balance were determined from total feces and urine collected separately (5 d, wk 5). Rumen fermentation parameters and protozoa concentration were analyzed from samples taken after morning feeding (1 d, wk 5). Milk production, dry matter intake, and feed efficiency were reduced with TSP (-18, -12, and -8%, respectively). As daily methane production (g/d) was not affected, methane emissions (g/kg of dry matter intake) increased by 14% with TSP. Total-tract digestibility and nitrogen balance were similar between diets, except for acid detergent fiber digestibility, which tended to be improved with TSP (+4 percentage units). Rumen fermentation parameters and protozoa concentration were relatively unchanged by diets. Under the conditions of this experiment, tea saponin is not efficient to reduce methane emissions from dairy cows.

Critical evaluation of essential oils as rumen modifiers in ruminant nutrition: A review

Ruminant livestock systems contribute significantly to emission of methane, a potent greenhouse gas as they waste a portion of the ingested energy (2-15%) as methane and a large proportion (75-95%) of the ingested nitrogen as ammonia. Recently, numerous researches have been conducted to evaluate plant secondary metabolites, including essential oils (EO), as natural feed additives in ruminant nutrition and to exploit their potential to improve rumen fermentation efficiency. Essential oils appeared to be very promising compounds as they selectively reduced methane production and protein breakdown in both in vitro and in vivo studies. However, in some studies, the use of EO as feed additives was accompanied with decreased feed degradability and lowered volatile fatty acid. These adverse effects could be attributed to their broad and often non-specific antimicrobial activities within the rumen. Future research should be directed to identification of the active and useful EO compounds, optimization of EO doses, and use of a whole-farm approach with a focus on animal welfare, performance and economic benefits.

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus

Svalbard reindeer (Rangifer tarandus platyrhynchus) is a non-migratory subspecies of reindeer inhabiting the high-arctic archipelago of Svalbard. In contrast to other Rangifer tarandus subspecies, Svalbard reindeer graze exclusively on natural sources of food and have no chance of ingestion of any crops. We report the use of a non-invasive method for analysis of fecal microbiome by means of sequencing the 16S rDNA extracted from the fecal microbiota of R. tarandus platyrhynchus from a small, isolated population in Hornsund, South Spitsbergen National Park. Analyses of all samples showed that 99% of the total reads were represented by Bacteria. Taxonomy-based analysis showed that fecal bacterial communities consisted of 14 phyla. The most abundant phyla across the population were Firmicutes and Bacteroidetes, and those phyla jointly accounted for more than 95% of total bacterial sequences (ranging between 90.14 and 98.19%). Specifically, Firmicutes comprised 56.53% (42.98–63.64%) and Bacteroidetes comprised 39.17% (34.56–47.16%) of the total reads. The remaining 5% of the population reads comprised of Tenericutes, Cyanobacteria, TM7, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia, Planctomycetes, Fibrobacteres, Spirochaetes, Chloroflexi, and Deferribacteres. Differences in the fecal bacteria composition between particular reindeer were not statistically significant which may reflect the restricted location and similar diet of all members of the local population.

RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis

Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that are key to using these tools to further define the science of ruminal methanogenesis.

Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows

The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.

Data Build-up for the Construction of Korean Specific Greenhouse Gas Emission Inventory in Livestock Categories

Many studies on methane (CH₄) and nitrous oxide (N₂O) emissions from livestock industries have revealed that livestock production directly contributes to greenhouse gas (GHG) emissions through enteric fermentation and manure management, which causes negative impacts on animal environment sustainability. In the present study, three essential values for GHG emission were measured; i.e., i) maximum CH₄ producing capacity at mesophilic temperature (37°C) from anaerobically stored manure in livestock category (B_0,KM, Korean livestock manure for B₀), ii) EF_3(s) value representing an emission factor for direct N₂O emissions from manure management system S in the country, kg N₂O-N kg N⁻¹, at mesophilic (37°C) and thermophilic (55°C) temperatures, and iii) N_ex(T) emissions showing annual N excretion for livestock category T, kg N animal⁻¹ yr⁻¹, from different livestock manure. Static incubation with and without aeration was performed to obtain the N₂O and CH₄ emissions from each sample, respectively. Chemical compositions of pre- and post-incubated manure were analyzed. Contents of total solids (% TS) and volatile solid (% VS), and the ratio of carbon to nitrogen (C/N) decrease significantly in all the samples by C-containing biogas generation, whereas moisture content (%) and pH increased after incubation. A big difference of total nitrogen content was not observed in pre- and post-incubation during CH₄ and N₂O emissions. CH₄ emissions (g CH₄ kg VS⁻¹) from all the three manures (sows, layers and Korean cattle) were different and high C/N ratio resulted in high CH₄ emission. Similarly, N₂O emission was found to be affected by % VS, pH, and temperature. The B_0,KM values for sows, layers, and Korean cattle obtained at 37°C are 0.0579, 0.0006, and 0.0828 m³ CH₄ kg VS⁻¹, respectively, which are much less than the default values in IPCC guideline (GL) except the value from Korean cattle. For sows and Korean cattle, N_ex(T) values of 7.67 and 28.19 kg N yr⁻¹, respectively, are 2.5 fold less than those values in IPCC GL as well. However, N_ex(T) value of layers 0.63 kg N yr⁻¹ is very similar to the default value of 0.6 kg N yr⁻¹ in IPCC GLs for National greenhouse gas inventories for countries such as South Korea/Asia. The EF_3(s) value obtained at 37°C and 55°C were found to be far less than the default value.

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

Three strictly anaerobic, methanogenic strains JH1(T), JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales, and Methanobrevibacter wolinii SH(T) was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1(T), JH4 and JH8 and M. wolinii SH(T) were 96.2 and 89.0 % respectively, and DNA-DNA hybridization of the isolates and M. wolinii DSM 11976(T) showed a 20 % reassociation. Strain JH1(T) exhibited 92 % DNA-DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5-1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37-40 °C and pH 6.5-7.0. The DNA G+C content of strain JH1(T) was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter, for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1(T) ( = KCTC 4102(T) = JCM 18376(T)).

Genome sequence of Methanobrevibacter sp. strain jh1, isolated from rumen of Korean native cattle

The Methanobrevibacter sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo; Bos taurus coreanae). Here, we provide a 2.06-Mb draft genome sequence of strain JH1 that might provide more information about the lifestyle of rumen methanogens and about the genes and proteins that can be targeted to curb methane emissions.

Changes in methane emission, rumen fermentation in response to diet and microbial interactions

To evaluate relative contributions of different microbial groups in rumen, the mono-culture (i.e. bacteria, protozoa and fungi) and co-cultures (i.e. bacterial-protozoal, fungal-protozoal and bacterial-fungal) were tested in vitro using high and low roughage diets. Total gas and methane were higher in bacterial-fungal and bacterial-protozoal co-cultures, while lower in fungal-protozoal than controls (high and low roughage with complete rumen consortia; control 1 and 2, respectively). Digestibility and total volatile fatty acids were lower in bacterial-fungal co-culture with both high and low roughage diets. Methanogens decreased in bacterial-fungal co-culture with high roughage. With high roughage, counts were lower for bacteria with bacterial-protozoal, protozoa with fungal-protozoal, and fungi with the bacterial-fungal co-cultures. Total gas was higher in bacterial mono-culture with low roughage, but methane was not detected in any mono-culture. Digestibility and total volatile fatty acids were significantly lowered with protozoal mono-culture. Methanogens reduced significantly in mono-cultures with high roughage diet than control 1. Defaunation reduced methanogens without significantly affecting rumen fermentation.

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.

Methanogenic population and CH₄ production in swedish dairy cows fed different levels of forage

Methanogenic community structure, methane production (CH(4)), and volatile fatty acid (VFA) profiles were investigated in Swedish dairy cows fed a diet with a forage/concentrate ratio of 500/500 or 900/100 g/kg of dry matter (DM) of total DM intake (DMI). The rumen methanogenic population was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR (qRT-PCR). Mean CH(4) yields did not differ (P > 0.05) between diets, being 16.9 and 20.2 g/kg DMI for the 500/500 and 900/100 diets, respectively. The T-RFLP analysis revealed that populations differed between individual cows and that each individual population responded differently to the diets. The 16S rRNA gene libraries revealed that Methanobrevibacter spp. dominated for both diets. CH(4) production was positively correlated with a dominance of sequences representing T-RFs related to Methanobrevibacter thaueri, Methanobrevibacter millerae, and Methanobrevibacter smithii relative to Methanobrevibacter ruminantium and Methanobrevibacter olleyae. Total numbers of methanogens and total numbers of Methanobacteriales were significantly higher with the 500/500 diet (P < 0.0004 and P < 0.002, respectively). However, no relationship was found between CH(4) production and total number of methanogens. No differences were seen in total VFA, propionic acid, or acetic acid contents, but the molar proportion of butyric acid in the rumen was higher for the 500/500 diet than for the 900/100 diet (P < 0.05). Interestingly, the results also revealed that a division of the identified methanogenic species into two groups, suggested in the work of King et al. (E. E. King, R. P. Smith, B. St-Pierre, and A. D. G. Wright, Appl. Environ. Microbiol. 77:5682-5687, 2011), increased the understanding of the variation in CH(4) production between different cows.

Review of methane mitigation technologies with application to rapid release of methane from the Arctic

Methane is the most important greenhouse gas after carbon dioxide, with particular influence on near-term climate change. It poses increasing risk in the future from both direct anthropogenic sources and potential rapid release from the Arctic. A range of mitigation (emissions control) technologies have been developed for anthropogenic sources that can be developed for further application, including to Arctic sources. Significant gaps in understanding remain of the mechanisms, magnitude, and likelihood of rapid methane release from the Arctic. Methane may be released by several pathways, including lakes, wetlands, and oceans, and may be either uniform over large areas or concentrated in patches. Across Arctic sources, bubbles originating in the sediment are the most important mechanism for methane to reach the atmosphere. Most known technologies operate on confined gas streams of 0.1% methane or more, and may be applicable to limited Arctic sources where methane is concentrated in pockets. However, some mitigation strategies developed for rice paddies and agricultural soils are promising for Arctic wetlands and thawing permafrost. Other mitigation strategies specific to the Arctic have been proposed but have yet to be studied. Overall, we identify four avenues of research and development that can serve the dual purposes of addressing current methane sources and potential Arctic sources: (1) methane release detection and quantification, (2) mitigation units for small and remote methane streams, (3) mitigation methods for dilute (<1000 ppm) methane streams, and (4) understanding methanotroph and methanogen ecology.

Indirect Estimation of CH4 from Livestock Feeds through TOCs Evaluation

Thirty-five available feeds were fermented in vitro in order to investigate their soluble total organic carbon (TOCs) and methane (CH₄) production rate. A fermentation reactor was designed to capture the CH₄ gas emitted and to collect liquor from the reactor during in vitro fermentation. The results showed that CH₄ production rate greatly varied among feeds with different ingredients. The lowest CH₄-producing feeds were corn gluten feed, brewer’s grain, and orchard grass among the energy, protein, and forage feed groups, respectively. Significant differences (p<0.05) were found in digestibility, soluble total organic carbon (TOCs), and CH₄ emissions among feeds, during 48 h of in vitro fermentation. Digestibility and TOCs was not found to be related due to different fermentation pattern of each but TOCs production was directly proportional to CH₄ production (y = 0.0076x, r² = 0.83). From this in vitro study, TOCs production could be used as an indirect index for estimation of CH₄ emission from feed ingredients.

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.

Analysis of methanogenic archaeal communities of rumen fluid and rumen particles from Korean black goats

Molecular diversity of methanogens in the rumen of Korean black goats was investigated with 16S rRNA gene clone libraries using methanogen-specific primers. The libraries were composed of rumen fluid-associated methanogens (FAM) and rumen particle-associated methanogens (PAM) from rumen-fistulated Korean black goats. Among the 141 clones of the FAM library, the sequences were mostly related to two phyla, the Methanobacteriaceae family (77.3%) and the Thermoplasmatales family (22.7%); and among the 68 clones of the PAM library, sequences were also mainly clustered in the two phyla, the Thermoplasmatales family (63.24%) and the Methanobacteriaceae family (35.29%). Most of the sequenced clones in the two libraries were closely related to uncultured methanogenic archaeon. Quantitative real-time PCR revealed that PAM (8.97 log 10) had significantly higher (P < 0.01) density of methanogens by the methanogenic 16S rRNA gene copies than FAM (7.57 log 10). The two clone libraries also showed difference in Shannon index (FAM library 1.70 and PAM library 1.59) and Chao 1 estimator (FAM library 18 and PAM library 17 operational taxonomic units). Apparent differences found in the microbial community from the two 16S rRNA gene libraries could be a result of such factors as the chemical and physical nature of the target material surface, types or component of diets, the interaction between the methanogens and other microbes, and age of the experimental goats.

Enumeration of methanogens with a focus on fluorescence in situ hybridization

Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

Methanogens: methane producers of the rumen and mitigation strategies

Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.