Rumen methanogens: a review

The Methanogens are a diverse group of organisms found in anaerobic environments such as anaerobic sludge digester, wet wood of trees, sewage, rumen, black mud, black sea sediments, etc which utilize carbon dioxide and hydrogen and produce methane. They are nutritionally fastidious anaerobes with the redox potential below −300 mV and usually grow at pH range of 6.0–8.0 [1]. Substrates utilized for growth and methane production include hydrogen, formate, methanol, methylamine, acetate, etc. They metabolize only restricted range of substrates and are poorly characterized with respect to other metabolic, biochemical and molecular properties.     

Some rumen ciliates have endosymbiotic methanogens

Abstract Most of the small ciliate protozoa, including Dasytricha ruminantium and Entodinium spp. living in the rumen of sheep, were found to have intracellular bacteria. These bacteria were not present in digestive vacuoles. They showed characteristic coenzyme F₄₂₀ autofluorescence and they were detected with a rhodamine-labelled Archaea-specific oligonucleotide probe. The measured volume percent of autofluorescing bacteria (1%) was close to the total volume of intracellular bacteria estimated from TEM stereology. Thus it is likely that all of the bacteria living in the cytoplasm of these ciliates were endosymbiotic methanogens, using H₂ evolved by the host ciliate to form methane. Intracellular methanogens appear to be much more numerous than those attached to the external cell surface of ciliates.     

A re-appraisal of the diversity of the methanogens associated with the rumen ciliates

The diversity of methanogenic archaea associated with different species of ciliated protozoa in the rumen was analysed. Partial fragments of archaeal SSU rRNA genes were amplified from DNA isolated from single cells from the rumen protozoal species Metadinium medium, Entodinium furca, Ophryoscolex caudatus and Diplodinium dentatum. Sequence analysis of these fragments indicated that although all of the new isolates clustered with sequences previously described for methanogens, there was a difference in the relative distribution of sequences detected here as compared to that of previous work. In addition, many of the novel sequences, although clearly of archaeal origin have relatively low identity to the sequences in database which are most closely related to them.     

The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review

Among different conversion processes for biomass, biological anaerobic digestion is one of the most economic ways to produce biogas from various biomass substrates. In addition to hydrolysis of polymeric substances, the activity and performance of the methanogenic bacteria is of paramount importance during methanogenesis. The aim of this paper is primarily to review the recent literature about the occurrence of both acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of particulate biomass to methane (not wastewater treatment), while this review does not cover the activity of the acetate oxidizing bacteria. Both acetotrophic and hydrogenotrophic methanogens are essential for the last step of methanogenesis, but the reports about their roles during this phase of the process are very limited. Despite, some conclusions can still be drawn. At low concentrations of acetate, normally filamentous Methanosaeta species dominate, e.g., often observed in sewage sludge. Apparently, high concentrations of toxic ionic agents, like ammonia, hydrogen sulfide (H₂S) and volatile fatty acids (VFA), inhibit preferably Methanosaetaceae and especially allow the growth of Methanosarcina species consisting of irregular cell clumps, e.g., in cattle manure. Thermophilic conditions can favour rod like or coccoid hydrogenotrophic methanogens. Thermophilic Methanosarcina species were also observed, but not thermophilic Methanosaetae. Other environmental factors could favour hydrogentrophic bacteria, e.g., short or low retention times in a biomass reactor. However, no general rules regarding process parameters could be derivated at the moment, which favours hydrogenotrophic methanogens. Presumably, it depends only on the hydrogen concentration, which is generally not mentioned in the literature.     

Effect of combined herbal feed additives on methane,total gas production and rumen fermentation

The present study was to evaluate effect of herbal feed additives on methane and total gas production during the rumen fermentation for environment and animal health concern. Different parts of the five medicinal plants were selected such as leaf and small stems of Ocimum sanctum (Tulsi), roots of Curcuma longa (Haldi), fruits of Emblica officinalis (Amla), leaves of Azadirachta indica (Neem) and leaves and small stem of Clerodendrum phlomidis (Arni) for our study. Addition of different herbal additive combinations did not influence IVDMD and total gas production however methane production (mg/g of substrate DM) was significantly (P<0.05) reduced in Amla: Neem and Neem: Arni combinations. Total nitrogen significantly (P<0.01) increased in the combinations of Tulsi: Haldi and Amla: Neem. TCA–ppt-N is significantly (P<0.01) increased in Tulsi: Haldi, Haldi: Amla, Amla: Neem and Neem: Arni however NH₃-N (mg/dl) significantly decreased in all treatments. We conclude that the screening of plant combinations, Amla: Neem and Neem: Arni have potential to decrease methane production and our herbal feed supplements have no side-effects on the ruminant in small amount.     

Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate

The evaluation of how the gut microbiota affects both methane emissions and animal production is necessary in order to achieve methane mitigation without production losses. Toward this goal, the aim of this study was to correlate the rumen microbial communities (bacteria, archaea, and fungi) of high (HP), medium (MP), and low milk producing (LP), as well as dry (DC), Holstein dairy cows in an actual tropical production system with methane emissions and animal production traits. Overall, DC cows emitted more methane, followed by MP, HP and LP cows, although HP and LP cow emissions were similar. Using next-generation sequencing, it was found that bacteria affiliated with Christensenellaceae, Mogibacteriaceae, S24-7, Butyrivibrio, Schwartzia, and Treponema were negatively correlated with methane emissions and showed positive correlations with digestible dry matter intake (dDMI) and digestible organic matter intake (dOMI). Similar findings were observed for archaea in the genus Methanosphaera. The bacterial groups Coriobacteriaceae, RFP12, and Clostridium were negatively correlated with methane, but did not correlate with dDMI and dOMI. For anaerobic fungal communities, no significant correlations with methane or animal production traits were found. Based on these findings, it is suggested that manipulation of the abundances of these microbial taxa may be useful for modulating methane emissions without negatively affecting animal production.     

The pterin lumazine inhibits growth of methanogens and methane formation

The pterin compound lumazine [2, 4-(1H, 3H)-pteridinedione] inhibited the growth of several methanogenic archaea completely at a concentration of ≤ 0.6 mM and was bacteriocidal for Methanobacterium thermoautotrophicum strain Marburg. In contrast, growth of two non-methanogenic archaea, several eubacteria, and one eukaryote was not strongly affected at much higher concentrations. In washed-cell suspensions, methanogenesis from H₂ and CO₂ by Mb. thermoautotrophicum or from H₂ and methanol by Methanosarcina barkeri was inhibited by addition of lumazine. In cell-free extracts of Mb. thermoautotrophicum, H₂-driven methane production from CO₂ or CH₃-S-CoM was completely inhibited by 0.6 mM lumazine. The results suggest that the compound may be useful in probing the methanogenesis pathway or in selecting against methanogens. Received: 30 January 1996 / Accepted 15 May 1996     

Butachlor inhibits production and oxidation of methane in tropical rice soils under flooded condition

In laboratory incubation experiments, application of a commercial formulation of the herbicide butachlor (N-butoxymethyl-2-chloro-2',6'-diethyl acetanilide) to three tropical rice soils, widely differing in their physicochemical characteristics, under flooded condition inhibited methane (CH4) production. The inhibitory effect was concentration dependent and most remarkable in the alluvial soil. Thus, following application of butachlor at 5, 10, 50 and 100 microg g(-1) soil, respectively, cumulative CH4 production in the alluvial soil was inhibited by 15%, 31%, 91% and 98% over unamended control. Since CH4 production was less pronounced in the sandy loam and acid sulfate soil, the impact of amendment with butchalor, albeit inhibitory, was less extensive than the alluvial soil. Inhibition of CH4 production in butachlor-amended alluvial soil was related to the prevention in the drop in redox potential as well as low methanogenic bacterial population especially at high concentrations of butachlor. CH4 oxidation was also inhibited in butachlor-amended alluvial soil with the inhibitory effect being more prevalent under flooded condition. Inhibition in CH4 oxidation was related to a reduction in the population of soluble methane monooxygenase producing methanotrophs. Results demonstrate that butachlor, a commonly used herbicide in rice cultivation, even at very low concentrations can affect CH4 production and its oxidation, thereby influencing the biogeochemical cycle of CH4 in flooded rice soils.     

Effects of monolaurin on ruminal methanogens and selected bacterial species from cattle, as determined with the rumen simulation technique

Before being able to implement effective ruminal methane mitigation strategies via feed supplementation, the assessment of side effects on ruminal fermentation and rumen microbial populations is indispensable. In this respect we investigated the effects of monolaurin, a methane-mitigating lipid, on methanogens and important carbohydrate-degrading bacteria present in ruminal fluid of dairy cattle in continuous culture employing the rumen simulation technique. In six experimental runs, each lasting for 10 days, four diets with different carbohydrate composition, based on hay, maize, wheat and a maize-wheat mixture, either remained non-supplemented or were supplemented with monolaurin and incubated in a ruminal-fluid buffer mixture. Incubation liquid samples from days 6 to 10 of incubation were analyzed with relative quantitative polymerase chain reaction (qPCR) of 16S rRNA genes to assess monolaurin-induced shifts in specific rumen microbial populations in relation to the corresponding non-supplemented diets. Monolaurin completely inhibited Fibrobacter succinogenes in all diets while the response of the other cellulolytic bacteria varied in dependence of the diet. Megasphaera elsdenii remained unaffected by monolaurin in the two diets containing maize, but was slightly stimulated by monolaurin with the wheat and largely with the hay diet. The supply of monolaurin suppressed Methanomicrobiales below the detection limit with all diets, whereas relative 16S rRNA gene copy numbers of Methanobacteriales increased by 7-fold with monolaurin in case of the hay diet. Total Archaea were decreased by up to over 90%, but this was significant only for the wheat containing diets. Thus, monolaurin exerted variable effects mediated by unknown mechanisms on important ruminal microbes involved in carbohydrate degradation, along with its suppression of methane formation. The applicability of monolaurin for methane mitigation in ruminants thus depends on the extent to which adverse effects on carbohydrate-degrading bacteria actually impair the supply of digested carbohydrates to the animal.     

Effects of protozoa on Methane production in rumen and hindgut of calves around time of weaning

Effects of the presence or absence of ciliate protozoa on methanogenesis in the rumen and hindgut were investigated in young calves during a 7-week period. Ten Holstein calves, aged 7 days, were divided in two groups (n = 5) and fed an increasing amount of a commercial milk replacer and small amounts of a calves starter. One group was inoculated with ciliate fauna on two occasions, week 5 and 6, while the second remained ciliate-free. The absence of protozoa in the rumen decreased rumen empty weight ( ? 23%, P < 0.01), and rumen pool size of N ( ? 36%, P < 0.01) and crude fat ( ? 37%, P < 0.05). Rumen bacteria of non-faunated calves contained a higher proportion of total amino acid-N per 16 g N ( + 3%, P < 0.01) and D-alanine-N per 16 g N ( + 13%, P < 0.05) compared to faunated calves. Further results contain a reference for a higher bacterial mass in the ciliate-free rumen with an increased number of bacteria adherent to rumen mucosa. The CH₄ production in the rumen increased exponentially with the increase in protozoa population size (R² = 0.68). In presence of 46 · 10⁴ protozoa per ml rumen fluid, the in vitro CH₄ production of rumen fluid per mol total VFA was about 34% higher in faunated than in non-faunated calves (P < 0.001). Hydrogen (2H) recovery of rumen fermentation was positively correlated (R² = 0.55) to the CH₄ production rate. Methanogens were attached on rumen mucosa. Methanogenesis, induced by rumen mucosa attached bacteria, was stimulated by ruminal protozoa. In the absence of protozoa in the rumen, the acetate - propionate ratio and butyrate proportion of VFA were reduced. In vivo in the absence of protozoa not only the whole animal CH₄ production ( ? 30%, P < 0.05) but also the digestibility of carbohydrates ( ? 4%, P < 0.05) was reduced. Thereby no difference was observed in the intake of ME per kg DM between the groups. In conclusion, the methanogenesis in the rumen, but not in hindgut, is associated with the development of the ruminal protozoa population. The level of methanogenesis (mol/mol VFA) in the hindgut amounts to 20% of the ruminal methanogenesis.     

Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture

Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7 d intervals (21, 45 and 63 d, respectively) were established to enrich for plant fibre degrading co-cultures of anaerobic fungi and methanogens from rumen digesta. Microbial diversity and fermentation end-products were measured at appropriate intervals over each CBC time-course. While methanogenic populations remained diverse, anaerobic fungal diversity was related to transfer interval and appeared to decrease with increasing transfer number. Acetate was the principal aqueous fermentation end-product with minimal quantities of lactate and formate detected. Methane and carbon dioxide were detected in the gaseous head-space of all co-cultures and the total amounts of gas generated per transfer was greater with transfer intervals of 5 and 7 d compared with a 3 d interval, although the 3 d interval tended to be more efficient per unit time. In conclusion, rapidly growing, methane producing co-cultures of anaerobic fungi and methanogens from rumen digesta were easy to establish on lignocellulose (barley straw) and maintain over considerable time periods. These results suggest such co-cultures have potential in industrial scale anaerobic digestion (AD) of highly fibrous substrates, which are resistant to degradation in conventional AD plants.     

瘤胃甲烷菌及甲烷生成的调控

甲烷菌属于古细菌 ,参与有机物的厌氧降解 ,生成甲烷。反刍动物瘤胃内甲烷的生成损耗 2 %～ 12 %的饲料能量 ,并且通过嗳气排入大气。甲烷不仅是温室气体之一 ,而且还会破坏大气臭氧层。每年全球反刍动物排放大量的甲烷 ,减少瘤胃内甲烷的生成对提高饲料能量利用率和改善环境具有重要意义。近年来 ,有关瘤胃甲烷菌及甲烷生成调控的报道日益增多。概述甲烷菌的特性以及瘤胃内甲烷生成的途径 ,综述甲烷生成的调控手段 ,主要包括去原虫、日粮配合、添加电子受体、增加乙酸生成菌等方法     

Effects of nitrate on methane production, fermentation, and microbial populations in in vitro ruminal cultures

The objective of this study was to examine the effects of nitrate on methane production, important fermentation characteristics, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, total bacteria, and methanogens using in vitro ruminal cultures. Potential adaptation of the above microbes and persistency of nitrate to mitigate CH₄ production were also evaluated. Methane production was reduced by 70% at 12 μmol ml⁻¹ and nearly completely at ?24 μmol ml⁻¹ nitrate. Production of volatile fatty acids (VFAs) was affected to different extents at different nitrate concentrations. Over a series of six consecutive cultures receiving 12 μmol ml⁻¹nitrate, production of CH₄ and VFA did not change significantly. R. albus and R. flavefaciens seemed to adapt to nitrate, while F. succinogenes and methanogens did not. Nitrate may be used in achieving persistent mitigation of CH4 production by ruminants.     

Isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane

This study aimed to obtain natural cultures of anaerobic fungi and their indigenously associated methanogens from herbivores and investigate their ability to degrade lignocelluloses to methane. Eight natural cultures were obtained by Hungate roll tube technique. The fungi were identified as belonging to Piromyces, Anaeromyces and Neocallimastix respectively by microscopy, and the methanogens as Methanobrevibacter spp. by 16S rRNA gene sequencing. In vitro studies with rice straw showed that these cultures degraded 33.5-48.3% substrate and produced 0.33-0.84 mmol/(100 ml culture) methane. Two cultures were further selected for their ability to degrade different lignocellulosic materials and could produce 0.38-1.27 mmol/(100 ml culture) methane. When methanogens were inhibited, the lignocellulose-degrading ability of cultures significantly reduced. In conclusion, natural cultures of anaerobic fungi with indigenously associated methanogens with high fiber degradation ability were obtained, and these cultures may have the potential in industrial use in lignocelluloses degradation and methane production.     

Microbial colonisation of tannin-rich tropical plants: Interplay between degradability,methane production and tannin disappearance in the rumen

Condensed tannins in plants are found free and attached to protein and fibre but it is not known whether these fractions influence rumen degradation and microbial colonisation. This study explored the rumen degradation of tropical tannin-rich plants and the relationship between the disappearance of free and bound condensed tannin fractions and microbial communities colonising plant particles using in situ and in vitro experiments. Leaves from Calliandra calothyrsus, Gliricidia sepium, and Leucaena leucocephala, pods from Acacia nilotica and the leaves of two agricultural by-products: Manihot esculenta and Musa spp. were incubated in situ in the rumen of three dairy cows to determine their degradability for up to 96 h. Tannin disappearance was determined at 24 h of incubation, and adherent microbial communities were examined at 3 and 12 h of incubation using a metataxonomic approach. An in vitro approach was also used to assess the effects of these plants on rumen fermentation parameters. All plants contained more than 100 g/kg of condensed tannins with a large proportion (32–61%) bound to proteins. Calliandra calothyrsus had the highest concentration of condensed tannins at 361 g/kg, whereas Acacia nilotica was particularly rich in hydrolysable tannins (350 g/kg). Free condensed tannins from all plants completely disappeared after 24-h incubation in the rumen. Disappearance of protein-bound condensed tannins was variable with values ranging from 93% for Gliricidia sepium to 21% for Acacia nilotica. In contrast, fibre-bound condensed tannin disappearance averaged ～ 82% and did not vary between plants. Disappearance of bound fractions of condensed tannins was not associated with the degradability of plant fractions. The presence of tannins interfered with the microbial colonisation of plants. Each plant had distinct bacterial and archaeal communities after 3 and 12 h of incubation in the rumen and distinct protozoal communities at 3 h. Adherent communities in tannin-rich plants had a lower relative abundance of fibrolytic microbes, notably Fibrobacter spp. whereas, archaea diversity was reduced in high-tannin-containing Calliandra calothyrsus and Acacia nilotica at 12 h of incubation. Concurrently, in vitro methane production was lower for Calliandra calothyrsus, Acacia nilotica and Leucaena leucocephala although for the latter total volatile fatty acids production was not affected and was similar to control. Here, we show that the total amount of hydrolysable and condensed tannins contained in a plant govern the interaction with rumen microbes affecting degradability and fermentation. The effect of protein- and fibre-bound condensed tannins on degradability is less important.     

Simple method for cryopreservation of an anaerobic rumen fungus using ethylene glycol and rumen fluid

Abstract The cryopreservation of an anaerobic rumen fungus, Piromyces communis OTS1, was examined at −84 °C using dimethyl sulfoxide, propylene glycol or ethylene glycol as cryoprotectants. Ethylene glycol was the most effective agent, combining high survival and low toxicity, followed by dimethyl sulfoxide and propylene glycol. Cell-free rumen fluid in the cryopreservation medium decreased the toxicity of the cryoprotectant agents and also had a protective action per se. A survival of 80% after 1 year storage was obtained when samples with an initial zoospore density of 5 × 10⁴ zoospores/ml were equilibrated for 15 min in medium containing 0.64 M ethylene glycol and 5% cell-free rumen fluid, then frozen with dry ice and stored at −84 °C.     

Relationship between rumen methanogens and methane production in dairy cows fed diets supplemented with a feed enzyme additive

Aims: To investigate the relationship between ruminal methanogen community and host enteric methane (CH₄) production in lactating dairy cows fed diets supplemented with an exogenous fibrolytic enzyme additive. Methods and Results: Ecology of ruminal methanogens from dairy cows fed with or without exogenous fibrolytic enzymes was examined using PCR–denaturing gradient gel electrophoresis (PCR–DGGE) analyses and quantitative real‐time PCR (qRT‐PCR). The density of methanogens was not affected by the enzyme additive or sampling times, and no relationship was observed between the total methanogen population and CH₄ yield (as g per head per day or g kg^?1 DMI). The PCR–DGGE profiles consisted of 26 distinctive bands, with two bands similar to Methanogenic archaeon CH1270 negatively correlated, and one band similar to Methanobrevibacter gottschalkii strain HO positively correlated, with CH₄ yield. Three bands similar to Methanogenic archaeon CH1270 or Methanobrevibacter smithii ATCC 35061 appeared after enzyme was added. Conclusions: Supplementing a dairy cow diet with an exogenous fibrolytic enzyme additive increased CH₄ yield and altered the composition of the rumen methanogen community, but not the overall density of methanogens. Significance and Impact of the Study: This is the first study to identify the correlation between methanogen ecology and host CH₄ yield from lactating dairy cows.     

Tannins determined by various methods as predictors of methane production reduction potential of plants by an in vitro rumen fermentation system

Relationships between chemical constituents, including values obtained with tannin assays (i.e., total phenols, total tannins, condensed tannins and tannin activity using a tannin bioassay) for plant materials (n = 17), and methane production parameters at 24 h of incubation in the in vitro Hohenheim gas method were established. The methane production reduction potential (MRP) was calculated by assuming net methane concentration for the control hay as 100%. The MRP of Bergenia crassifolia leaves and roots, and Peltiphyllum peltatum leaves, was >40%. Amongst the chemical constituents, neutral detergent fibre had a high correlation (r = 0.86) with methane concentration. There was negative relationship between total phenol, total tannins or tannin activity and methane concentration. However, a positive relationship existed between these tannin assays and the MRP, with r-values ranging from 0.54 to 0.79 (P<0.05). A very weak relationship (r = 0.09) occurred between condensed tannins and MRP. Similar results to those with MRP were obtained with the percent increase in methane on addition of polyethylene glycol. The highest correlations, 0.79 and 0.92 (P<0.001), were between tannin activity determined using the tannin bioassay and the MRP, or the percent increase in methane on addition of polyethylene glycol, respectively, suggesting that this tannin assay could be used to identify plants possessing antimethanogenic properties. Leaves of Rheum undulatum, Vaccinium vitis-idaea, B. crassifolia, Rhus typhina and P. peltatum, and roots of B. crassifolia have considerable potential (i.e., >25%) to decrease enteric methane production from ruminants.