Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations

Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances

Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane (CH₄). Research on methanogens in the rumen has attracted great interest in the last decade because CH₄ emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH₄ emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.

Oregano Extract Added into the Diet of Dairy Heifers Changes Feeding Behavior and Concentrate Intake

This experiment aimed to describe the effects of Oregano extract (OE) inclusion into the concentrate fed to dairy heifers on physiological parameters, feeding behavior, intake, and performance. Thirty-two Holstein heifers were randomly distributed into four treatments: C = control, without addition of OE; OE2.5 = 2.5 g; OE5.0 = 5.0 g and OE7.5 = 7.5 g of Oregano extract per heifer/day. Feeding behavior and concentrate intake were assessed individually every day and total dry matter intake (DMI) was determined on the last week of the trial. Compared to control group, OE7.5 reduced by 32% the latency time to approach the feed bunk but increased by 6% the time spent eating the concentrate. Each inclusion of 2.5 grams of OE into the concentrate increased the occurrence of postingestive licking the feed bunk with abundant saliva production 1.2 times (P < 0.01) and tended to increase the occurrence of sneeze events 1.2 times (P < 0.10). No statistical difference was detected between treatments for total DMI, but concentrate DMI was 9% lower for OE7.5 when compared to control and OE2.5. The inclusion of 7.5 grams/day of OE causes small but negative effects in feeding behavior and concentrate intake, without change on total dry matter intake.

Effects of purified lignin on in vitro rumen metabolism and growth performance of feedlot cattle

Objective

The objectives were to assess the effects of purified lignin from wheat straw (sodium hydroxide dehydrated lignin; SHDL) on in vitro ruminal fermentation and on the growth performance of feedlot cattle.

Methods

In vitro experiments were conducted by incubating a timothy-alfalfa (50:50) forage mixture (48 h) and barley grain (24 h) with 0, 0.25, 0.5, 1.0, and 2.0 mg/mL of rumen fluid (equivalent to 0, 2, 4, 8, and 16 g SHDL/kg diet). Productions of CH₄ and total gas, volatile fatty acids, ammonia, dry matter (DM) disappearance (DMD) and digestion of neutral detergent fiber (NDF) or starch were measured. Sixty Hereford-Angus cross weaned steer calves were individually fed a typical barley silage-barley grain based total mixed ration and supplemented with SHDL at 0, 4, 8, and 16 g/kg DM for 70 (growing), 28 (transition), and 121 d (finishing) period. Cattle were slaughtered at the end of the experiment and carcass traits were assessed.

Results

With forage, SHDL linearly (p<0.001) reduced 48-h in vitro DMD from 54.9% to 39.2%, NDF disappearance from 34.1% to 18.6% and the acetate: propionate ratio from 2.56 to 2.41, but linearly (p<0.001) increased CH₄ production from 9.5 to 12.4 mL/100 mg DMD. With barley grain, SHDL linearly increased (p<0.001) 24-h DMD from74.6% to 84.5%, but linearly (p<0.001) reduced CH₄ production from 5.6 to 4.2 mL/100 mg DMD and NH₃ accumulation from 9.15 to 4.49 μmol/mL. Supplementation of SHDL did not affect growth, but tended (p = 0.10) to linearly reduce feed intake, and quadratically increased (p = 0.059) feed efficiency during the finishing period. Addition of SHDL also tended (p = 0.098) to linearly increase the saleable meat yield of the carcass from 52.5% to 55.7%.

Conclusion

Purified lignin used as feed additive has potential to improve feed efficiency for finishing feedlot cattle and carcass quality.

Recent Advances in Measurement and Dietary Mitigation of Enteric Methane Emissions in Ruminants

Methane (CH4) emission, which is mainly produced during normal fermentation of feeds by the rumen microorganisms, represents a major contributor to the greenhouse gas (GHG) emissions. Several enteric CH4 mitigation technologies have been explored recently. A number of new techniques have also been developed and existing techniques have been improved in order to evaluate CH4 mitigation technologies and prepare an inventory of GHG emissions precisely. The aim of this review is to discuss different CH4 measuring and mitigation technologies, which have been recently developed. Respiration chamber technique is still considered as a gold standard technique due to its greater precision and reproducibility in CH4 measurements. With the adoption of recent recommendations for improving the technique, the SF6 method can be used with a high level of precision similar to the chamber technique. Short-term measurement techniques of CH4 measurements generally invite considerable within- and between-animal variations. Among the short-term measuring techniques, Greenfeed and methane hood systems are likely more suitable for evaluation of CH4 mitigation studies, if measurements could be obtained at different times of the day relative to the diurnal cycle of the CH4 production. Carbon dioxide and CH4 ratio, sniffer, and other short-term breath analysis techniques are more suitable for on farm screening of large number of animals to generate the data of low CH4-producing animals for genetic selection purposes. Different indirect measuring techniques are also investigated in recent years. Several new dietary CH4 mitigation technologies have been explored, but only a few of them are practical and cost-effective. Future research should be directed toward both the medium- and long-term mitigation strategies, which could be utilized on farms to accomplish substantial reductions of CH4 emissions and to profitably reduce carbon footprint of livestock production systems. This review presents recent developments and critical analysis on different measurements and dietary mitigation of enteric CH4 emissions technologies.

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations

BACKGROUND

Rumen microbiome has a great influence on ruminant health and productivity. Different plant extracts have been tested for their ability to modulate the rumen microbiome to improve feed digestion and fermentation. Among the evaluated plant extracts, essential oils, tannins, and saponins appeared to have positive effects on rumen protein metabolism, volatile fatty acids production, and methane and ammonia production.

METHODS

The objective of this study was to evaluate the effect of rosemary (Rosmarinus officinalis L.) leaves and essential oils on rumen microbial populations. Four ruminally cannulated sheep were used in a 4×4 Latin square design fed (21 d/period): 1) a control diet composed of alfalfa hay and concentrate pellet (CTR), 2) CTR supplemented with 7 g/d/sheep of rosemary essential oil adsorbed on an inert support (EO), 3) CTR with 10 g/d/sheep of dried and ground rosemary leaves (RL), and 4) CTR with 10 g/d of dried and ground rosemary leaves pelleted into concentrate (RL pellet). Abundance of total bacteria, archaea, protozoa, and some select bacterial species or groups was quantified using qPCR, while the community of bacteria and archaea was profiled using denaturing gradient gel electrophoresis.

RESULTS

No difference in abundance was noted for total bacteria, protozoa, or Ruminococcus flavefaciens between the control and the treatments, but the rosemary leaves, either in loose form or in pellet, decreased the abundance of archaea and the genus Prevotella (P < 0.001). The rosemary leaves in loose form also decreased (P < 0.001) the abundance of Ruminococcus albus and Clostridium aminophilum, while the EO increased (P < 0.001) the abundance of Fibrobacter succinogenes. The community of bacteria and archaea was not affected by any of the supplements.

CONCLUSIONS

Being able to affect the abundance of several groups of rumen microbes that are known to be involved in degradation of protein and fiber and production of methane and ammonia, rosemary leaves may be used to modulate rumen microbiome and its function.

Effects of Medicinal Herb Extracts on In vitro Ruminal Methanogenesis, Microbe Diversity and Fermentation System

This study was aimed to evaluate the in vitro effects of medicinal herb extracts (MHEs) on ruminal fermentation characteristics and the inhibition of protozoa to reduce methane production in the rumen. A fistulated Hanwoo was used as a donor of rumen fluid. The MHEs (T1, Veratrum patulum; T2, Iris ensata var. spontanea; T3, Arisaema ringens; T4, Carduus crispus; T5, Pueraria thunbergiana) were added to the in vitro fermentation bottles containing the rumen fluid and medium. Total volatile fatty acid (tVFA), total gas production, gas profiles, and the ruminal microbe communities were measured. The tVFA concentration was increased or decreased as compared to the control, and there was a significant (p<0.05) difference after 24 h incubation. pH and ruminal disappearance of dry matter did not show significant difference. As the in vitro ruminal fermentation progressed, total gas production in added MHEs was increased, while the methane production was decreased compared to the control. In particular, Arisaema ringens extract led to decrease methane production by more than 43%. In addition, the result of real-time polymerase chain reaction indicted that the protozoa population in all added MHEs decreased more than that of the control. In conclusion, the results of this study indicated that MHEs could have properties that decrease ruminal methanogenesis by inhibiting protozoa species and might be promising feed additives for ruminants.

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.

Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock

Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal’s circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock.

Effect of supplementation of allicin on methanogenesis and ruminal microbial flora in Dorper crossbred ewes

Background

Garlic extracts have been reported to be effective in reducing methanogenesis. Related mechanisms are not well illustrated, however, and most studies have been conducted in vitro. This study investigates the effects of supplementary allicin (AL) in sheep diet on in vivo digestibility, rumen fermentation, and shifts of microbial flora.

Methods

Two experiments were conducted using Dorper × thin-tailed Han crossbred ewes. In experiment 1, eighteen ewes (60.0 ± 1.73 kg BW) were randomly assigned for 29 days to either of two dietary treatments: a basal diet or the basal diet supplemented with 2.0 g AL/head·day to investigate supplementary AL on nutrient digestibility and methane emissions. In experiment 2, six ewes (65.2 ± 2.0 kg BW) with ruminal canulas were assigned to the same two dietary treatments as in experiment 1 for 42 days to investigate supplementary AL on ruminal fermentation and microbial flora. The methane emissions were determined using an open-circuit respirometry system and microbial assessment was done by qPCR of 16S rRNA genes.

Results

Supplementary AL increased the apparent digestibility of organic matter (P < 0.001), nitrogen (P = 0.006), neutral detergent fiber (P < 0.001), and acid detergent fiber (P = 0.002). Fecal nitrogen output was reduced (P = 0.001) but urinary nitrogen output was unaffected (P = 0.691), while nitrogen retention (P = 0.077) and nitrogen retention/nitrogen intake (P = 0.077) tended to increase. Supplementary AL decreased methane emissions scaled to metabolic bodyweight by 5.95 % (P = 0.007) and to digestible organic matter intake by 8.36 % (P = 0.009). Ruminal pH was unaffected (P = 0.601) while ammonia decreased (P = 0.024) and total volatile fatty acids increased (P = 0.024) in response to supplementary AL. Supplementary AL decreased the population of methanogens (P = 0.001) and tended to decrease that of protozoans (P = 0.097), but increased the populations of F. succinogenes (P < 0.001), R. flavefaciens (P = 0.001), and B. fibrisolvens (P = 0.001).

Conclusions

Supplementation of AL at 2.0 g/head·day effectively enhanced OM, N, NDF, and ADF digestibility and reduced daily methane emissions (L/kg BW^0.75) in ewes, probably by decreasing the population of ruminal protozoans and methanogens.

Soybean oil suppresses ruminal methane production and reduces content of coenzyme F420 in vitro fermentation

This experiment examined which type of oils was a superior suppressor to methane mitigation in ruminants. Four oils, peanut, rapeseed, corn and soybean oils, varying in the contents of unsaturated fatty acids as indicated by their iodine values, were used to investigate their effects on methane production and on the content of the F420 enzyme of ruminal methanogens in an in vitro fermentation. The control group was added with calcium palmitate (100% saturated 16C fatty acid). The results showed that the total gas production over a period of 36 h varied from 20.61 mL to 39.67 mL, and were lower in rapeseed, corn and soybean oil treatments than the control (P < 0.05), but not in the peanut oil treatment. The methane concentration in the total gas differed significantly among groups (P < 0.05), and decreased with the increases of unsaturation degree of the oils. The coenzyme F420 content, as indicated by F420 fluorescence intensity in supernatant of the medium, was significantly lower in the oil treatments than in the control (P < 0.05), and the intensity values decreased with the increases of unsaturation degree of the oils, except for the rapeseed oil treatment. Furthermore, there was a close correlation between F420 content and methane production (r = 0.916). By comparison, soybean oil treatment had higher dehydrogenase activity and bacteria density than the other groups (P < 0.05); but was lower in methanogens and genus entodinium (P < 0.05), except for the rapeseed oil treatment. Overall, soybean oil contained a high level of unsaturated fatty acids, and could be used as an ingredient of ruminant diets for methane suppression.

Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time.

Greenhouse gases, short-chain fatty acids and ruminal pH in vitro of biodiesel byproducts to replace corn silage

SUMMARY The aim of the study was evaluate the production potential for methane (CH4) and carbon dioxide (CO2), short-chain fatty acids, ammonia nitrogen (N-NH3) and pH by semi-automated techniquein vitro from biodiesel byproducts cottonseed cake (Gossypium hirsutum), castor bean (Ricinus communis), moringa cake (Moringa oleifera), jatropha cake (Jatropha curcas) and sunflower cake (Helianthus annuus) substituting corn silage in increasing levels, 0, 30, 50 and 70%. The experimental design used was completely randomized in a 5 x 4 factorial arrangement (byproducts and substitution levels). The inoculum for the in vitro incubations was obtained from three Holstein cows with rumen fistulas. In the experiment, the conditions were verified for the differences in potential gas production among the ingredients. The byproduct of cotton was the ingredient with the greatest potential to produce acetate, butyrate, CO2 and CH4. The byproduct of moringa had the lowest potential for the production of acetate, butyrate, CO2 and CH4 from in vitro degraded dry matter and a greater potential for the production of propionate. Among the byproducts studied, moringa was distinguished for promoting mitigation of CH4 and obtaining levels of pH and N-NH3 satisfactory for maximum rumen fermentation; thus, it is recommended the byproduct of moringa to replace corn silage because reduces environmental impact without impairingin vitro rumen fermentation.

In vitro Screening of Essential Oil Active Compounds for Manipulation of Rumen Fermentation and Methane Mitigation

The objective of this study was to investigate the effects of 11 active compounds of essential oils (ACEO) on rumen fermentation characteristics and methane production. Two trials were conducted. In trial 1, ACEO (eugenol, carvacrol, citral, limonene, 1,4-cineole, p-cymene, linalool, bornyl acetate, α-pinene, and β-pinene) at a dose of 1,000 μL/L were incubated for 24 h in diluted rumen fluid with a 70:30 forage:concentrate substrate (16.2% crude protein; 36.6% neutral detergent fiber). Three fistulated Holstein cows were used as donors of rumen fluid. The reduction in methane production was observed with nine ACEO (up to 86% reduction) compared with the control (p<0.05). Among these, only limonene, 1,4-cineole, bornyl acetate, and α-pinene did not inhibit volatile fatty acid (VFA) production, and only bornyl acetate produced less methane per mol of VFA compared with the control (p<0.05). In a subsequent trial, the effects on rumen fermentation and methane production of two concentrations (500 and 2,000 μL/L) of bornyl acetate, the most promising ACEO from the first trial, were evaluated using the same in vitro incubation method that was used in the first trial. In trial 2, monensin was used as a positive control. Both doses of bornyl acetate decreased (p<0.05) methane production and did not inhibit VFA production. Positive effects of bornyl acetate on methane and VFA production were more pronounced than the effects of monensin. These results confirm the ability of bornyl acetate to decrease methane production, which may help to improve the efficiency of energy use in the rumen.

Effects of essential oils from African basil on fermentation ofAndropogon gayanusgrass in the Artificial Rumen (RUSITEC)

Kouazounde, J. B., Gbenou, J. D., He, M., Jardim, T., Jin, L., Wang, Y., Beauchemin, K. A. and McAllister, T. A. 2015. Effects of essential oils from African basil on fermentation of Andropogon gayanus grass in the Artificial Rumen (RUSITEC). Can. J. Anim. Sci. 95: 425–431. Essential oils (EO) from African basil (Ocimum gratissimum) have shown the potential to modify rumen microbial fermentation and reduce ruminal methane production from grass forages in in vitro batch cultures. However, it is not known whether the effects of EO on rumen microbial fermentation attenuate over time. The objective of this study was to examine the effects of African basil EO at 0 (control), 100, 200 and 400 mg L−1incubation medium on microbial fermentation and methane production in the Rumen Simulation Technique (RUSITEC) using Andropogon gayanus grass as a substrate. African basil EO quadratically affected (P<0.05) methane production gas production and the pH of fermenter liquid. Total volatile fatty acid (VFA) production was linearly decreased (P<0.05) by African basil EO along with a shift in VFA profile towards less propionate and more acetate and butyrate. African basil EO quadratically altered (P<0.05) apparent dry matter, neutral detergent fiber digestibility,15N incorporation into total microbial protein and the total production of microbial protein. This study confirms that EO from African basil quadratically affected methane emissions arising from the ruminal fermentation of A. gayanus grass mainly by reducing overall digestibility of the forage.

Effects of garlic oil, nitrate, saponin and their combinations supplemented to different substrates on in vitro fermentation, ruminal methanogenesis, and abundance and diversity of microbial populations

AIMS

To investigate the effect of garlic oil (G), nitrate (N), saponin (S) and their combinations supplemented to different forage to concentrate substrates on methanogenesis, fermentation, diversity and abundances of bacteria and Archaea in vitro.

METHODS AND RESULTS

The study was conducted in an 8 × 2 factorial design with eight treatments and two substrates using mixed ruminal batch cultures obtained. Quillaja S (0·6 g l(-1) ), N (5 mmol l(-1) ) and G (0·27 g l(-1) ) were used separately or in binary and tertiary combinations. The two substrates contained grass hay and a dairy concentrate mixture at a 70 : 30 (high-forage substrate) ratio or a 30 : 70 (high-concentrate substrate) ratio. Ruminal fermentation and cellulolytic bacterial populations were affected by interaction between substrate and anti-methanogenic compounds. The inhibitor combinations decreased the methane production additively regardless of substrate. For the high-concentrate substrate, S decreased methane production to a greater extent, so did G and N individually for the high-forage substrate. Feed degradability and total volatile fatty acid (VFA) concentrations were not decreased by any of the treatments. Fibre degradability was actually improved by N+S for the high-forage substrate. VFA concentrations and profiles were affected differently by different anti-methanogenic inhibitors and their combinations. All treatments inhibited the growth of Archaea, but the effect on Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens varied.

CONCLUSIONS

The results suggest that substrate influences the efficacy of these inhibitors when they are used separately, but in combinations, they can lower methanogenesis additively without much influence from the substrate.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presented research provided evidence that binary and tertiary combination of garlic oil, nitrate and saponin can lower the methane production additively without adversely impacting rumen fermentation and degradability, and forage to concentrate ratio does not change the above effects. These anti-methanogenic inhibitors in combination may have practical application to mitigate methane emission from ruminants.

Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis

In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs) in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P ≤ 0.05) in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P ≤ 0.05) correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae, and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria.

Effects of essential oils from medicinal plants acclimated to Benin on in vitro ruminal fermentation of Andropogon gayanus grass

BACKGROUND

Plants from West Africa commonly used in both human and veterinary medicine contain various secondary metabolites. However, their potential in mitigating ruminal methane production has not been explored. This study examined the effects of seven essential oils (EOs) from plants acclimated to Benin at four dosages (100, 200, 300 and 400 mg L(-1)), on in vitro rumen microbial fermentation and methane production using Andropogon gayanus grass as a substrate.

RESULTS

Compared to control, Laurus nobilis (300-400 mg L(-1) ), Citrus aurantifolia (300-400 mg L(-1)) and Ocimum gratissimum (200-400 mg L(-1)) decreased (P < 0.05) methane production (mL g(-1) DM) by 8.1-11.8%, 11.9-17.8% and 7.9-30.6%, respectively. Relative to the control, reductions in methane (mL g(-1) DM) of 11.4%, 13.5% and 14.2% were only observed at 400 mg L(-1) for Eucalyptus citriodora, Ocimum basilicum and Cymbopogon citratus, respectively. These EOs lowered methane without reducing concentrations of total volatile fatty acids or causing a shift from acetate to propionate production. All EOs (except M. piperita) reduced (P < 0.05) apparent dry matter (DM) disappearance of A. gayanus.

CONCLUSIONS

The current study demonstrated that EOs from plants grown in Benin inhibited in vitro methane production mainly through a reduction in apparent DM digestibility.

Evaluating in vitro dose-response effects of Lavandula officinalis essential oil on rumen fermentation characteristics, methane production and ruminal acidosis

Four in vitro experiments (Exp.) were conducted to evaluate lavender essential oil (LEO) effects at 0 (control), 250 (low dose), 500 (medium dose), 750 and 1000 µL per L (high doses) of incubation medium on rumen gas production kinetics (Exp.1), ruminal digestibility and fermentation (Exp.2), methane production (Exp.3) and rumen acidosis (Exp.4). The asymptote of gas production (A) increased quadratically (p < 0.001), but the lag phase (L) increased (p = 0.003), and gas production rate (µ) decreased linearly (p = 0.031) with increasing dose of LEO. A linear and quadratic effect (p < 0.01) was observed for the gas produced after 24 hr of incubation (GP24). In vitro true dry matter degradability (IVTDMD) and in vitro true organic matter degradability (IVTOMD) both decreased linearly (p < 0.01), but microbial biomass (MB) and partitioning factor (PF) changed quadratically with increasing doses of LEO (p < 0.05). A cubic effect was observed for total volatile fatty acid (TVFA) and ammonia (NH3) concentrations (p < 0.05). Acetate molar percentage decreased (p = 0.004), whereas those of butyrate and valerate increased linearly (p < 0.05) with LEO dosage. The molar percentage of propionate increased by 10.60 and 12.00% at low and medium doses of LEO, respectively. Methane production decreased by 11.00 and 44.00 to 60.00% at medium and high doses of LEO (p < 0.05), respectively. Lavender essential oil decreased also ruminal pH at all included doses (p < 0.05), intensifying rumen acidosis. These results revealed a dose-dependent selective effect (stimulatory at low and medium, and inhibitory at high doses) of LEO on rumen fermentation.

Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.

Bioaugmentation as a solution to increase methane production from an ammonia-rich substrate

Ammonia-rich substrates inhibit the anaerobic digestion (AD) process and constitute the main reason for low energy recovery in full-scale reactors. It is estimated that many full-scale AD reactors are operating in ammonia induced "inhibited steady-state" with significant losses of the potential biogas production yield. To date there are not any reliable methods to alleviate the ammonia toxicity effect or to efficiently digest ammonia-rich waste. In the current study, bioaugmentation as a possible method to alleviate ammonia toxicity effect in a mesophilic continuously stirred-tank reactor (CSTR) operating under "inhibited steady state" was tested. A fast growing hydrogenotrophic methanogen (i.e., Methanoculleus bourgensis MS2(T)) was bioaugmented in the CSTR reactor at high ammonia levels (5 g NH4(+)-N L(-1)). A second CSTR reactor was used as control with no bioaugmentation. The results derived from this study clearly demonstrated a 31.3% increase in methane production yield in the CSTR reactor, at steady-state, after bioaugmentation. Additionally, high-throughput 16S rRNA gene sequencing analysis showed a 5-fold increase in relative abundance of Methanoculleus spp. after bioaugmentation. On the contrary to all methods used today to alleviate ammonia toxicity effect, the tested bioaugmentation process performed without interrupting the continuous operation of the reactor and without replacing the ammonia-rich feedstock.

Combinations of nitrate, saponin, and sulfate additively reduce methane production by rumen cultures in vitro while not adversely affecting feed digestion, fermentation or microbial communities

This study investigated the effects of saponin (0.6g/L), nitrate (5mM) and sulfate (5mM), alone and in combinations, on methanogenesis, rumen fermentation, microbial community, and abundances of select microbial populations using in vitro rumen culture. Combinations of nitrate with saponin and/or sulfate additively suppressed methane production, with the lowest reduction (nearly 46%) observed for the combination of all the three inhibitors. None of the treatments adversely affected feed digestion or rumen fermentation. All the inhibitors, either alone or in combinations, did not alter the abundances of total bacteria, Ruminococcus albus, or archaea. However, saponin, alone and together with nitrate and/or sulfate, increased the abundance of Fibrobacter succinogenes and Ruminococcus flavefaciens, but decreased that of protozoa. DGGE analyses revealed limited changes in both bacterial and archaeal communities by the treatments. The nitrate-saponin-sulfate combination may be an effective and practical strategy to mitigate methane emission from ruminants.

The effect of essential oils of Zataria multiflora and Mentha spicata on the in vitro rumen fermentation, and growth and deaminative activity of amino acid-fermenting bacteria isolated from Mehraban sheep

Gas (CO2 and CH4) and ammonia production in the rumen represent major sources of lost carbon and nitrogen, respectively. The essential oils of some plants have been shown to decrease gas and ammonia production by selectively inhibiting rumen microbes. Particularly, those of Zataria multiflora (ZEO; thymol 21%, carvacrol 32%) and Mentha spicata (SEO; carvone 55%) were evaluated in vitro as ruminant-feed additives. The experiments employed mixed rumen microbes and a hyper-ammonia-producing bacterium (HAP) isolated from the rumen of a Mehraban sheep. Both ZEO and SEO decreased in vitro fibre digestibility and also gas production by mixed rumen microbes that were fermenting a typical growing-lamb diet. ZEO decreased ammonia concentration in mixed culture of rumen microbes, but SEO exerted the opposite effect. A bacterial isolate (MT8) was obtained from the rumen of a Mehraban sheep, and the 16S rRNA gene sequence indicated that it was most closely related to Clostridium bifermentans. Isolate MT8 exhibited rapid ammonia production when peptides were the growth substrate, which indicated that MT8 was a HAP. Both oils inhibited the growth and ammonia production of isolate MT8. However, ZEO decreased ammonia production at lower doses, and to a greater degree, than did SEO. These results indicated that both essential oils could potentially be used to modulate rumen fermentation. The detrimental effects on fibre digestion could be problematic in high-forage diets, and this requires further investigation. Isolate MT8 is the first described HAP from the Mehraban sheep rumen. Results on ammonia production by isolate MT8 and mixed rumen microbes indicate differential mode of action of each oil on this parameter.

Effective reduction of enteric methane production by a combination of nitrate and saponin without adverse effect on feed degradability, fermentation, or bacterial and archaeal communities of the rumen

This study evaluated the effects of Quillaja saponin (0.6 and 1.2g/L), propynoate (4 and 8mM), and nitrate (5 and 10mM), alone or in combinations, on methanogenesis, fermentation, bacterial and archaeal communities, and abundances of select ruminal microbial populations. All treatment decreased methane production, but combination of all three inhibitors at high dose achieved the greatest inhibition (85%). Propynoate, alone or in combination with nitrate or saponin, decreased feed degradability and total volatile fatty acid (TVFA) concentrations. However, saponin and nitrate alone at high dose and in combination at low dose inhibited methanogenesis substantially while increasing feed degradability and TVFA concentrations. The abundances of methanogens were lowered by all inhibitors except saponin alone. Fibrobacter succinogenes and Ruminococcus flavefaciens were increased by saponin, both alone and in combination with nitrate, but inhibited by propynoate. Combination of saponin and nitrate may have practical application in mitigating methane emission from ruminants.

A novel production process for optically pure L-lactic acid from kitchen refuse using a bacterial consortium at high temperatures

We investigated L-lactic acid production in static batch fermentation of kitchen refuse using a bacterial consortium from marine-animal-resource (MAR) composts at temperatures ranging from 30 to 65 °C. At relatively low temperatures butyric acid accumulated, whereas at higher temperatures L-lactic acid was produced. In particular, fermentation at 50 °C produced 34.5 g L(-1) L-lactic acid with 90% lactic acid selectivity and 100% optical purity. Denaturing gradient gel electrophoresis indicated that dominant bacteria present in the original MAR composts diminished rapidly and Bacillus coagulans strains became the dominant contributors to L-lactic acid production at 45, 50 and 55 °C. This is the first report of the achievement of 100% optical purity of L-lactic acid using a bacterial consortium.

Evaluation of system performances and microbial communities of two temperature-phased anaerobic digestion systems treating dairy manure

Two temperature-phased anaerobic digestion (TPAD) systems, with the thermophilic digesters acidified by acidogenesis products (AT-TPAD) or operated at neutral pH and balanced hydrolysis/acidogenesis and methanogenesis (NT-TPAD), were evaluated to treat high-strength dairy cattle manure. Despite similar methane productions (about 0.22 L/g VS fed), the NT-TPAD system removed significantly more VS (36%) than the AT-TPAD system (31%) and needed no pH adjustments. The thermophilic digester of the NT-TPAD system dominated the system performance and performed significantly better than that of the AT-TPAD system. The opposite held true for the mesophilic digesters. Differences of the thermophilic digesters between two TPAD systems affected the microbial communities of both local and downstream digesters. Each digester harbored distinctive microbial populations, some of which were significantly correlated with system performance. Methanosarcina was the most important methanogenic genus in both TPAD systems, while Methanosaeta only in the NT-TPAD system. Their populations were inversely related to VFA concentrations.

Evaluation of system performance and microbial communities of a temperature-phased anaerobic digestion system treating dairy manure: thermophilic digester operated at acidic pH

A temperature-phased anaerobic digestion system with the thermophilic digester acidified by acidogenesis products (referred to as AT-TPAD) was evaluated to treat high-strength dairy cattle manure at a 15-day retention time. Three temperatures (50, 55, and 60°C) were tested on the thermophilic digester, and 50°C was found to be the optimal temperature for overall performance of the AT-TPAD system, achieving 31% VS removal and 0.22 L methane/g VS fed. The mesophilic digester contributed significantly more to the overall system performance than the thermophilic digester. The thermophilic and the mesophilic digesters had different microbial communities under all conditions, and both microbial communities exhibited dynamic changes in response to different conditions. Certain microbial groups were found significantly correlated with the system performance. Methanosarcina was the most important methanogen genus of the AT-TPAD system and its population abundance was inversely correlated with high concentrations of volatile fatty acids (VFA).

Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities

Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable enough to reflect changes in ruminal methanogenesis. A more robust technique to characterize changes in archaeal community structures will help to better understand the microbial process involved in ruminal methanogenesis and, hence, enabling the development of more effective dietary CH4 mitigation strategies.

Effects of gas composition in headspace and bicarbonate concentrations in media on gas and methane production, degradability, and rumen fermentation using in vitro gas production techniques

Headspace gas composition and bicarbonate concentrations in media can affect methane production and other characteristics of rumen fermentation in in vitro gas production systems, but these 2 important factors have not been evaluated systematically. In this study, these 2 factors were investigated with respect to gas and methane production, in vitro digestibility of feed substrate, and volatile fatty acid (VFA) profile using in vitro gas production techniques. Three headspace gas compositions (N2+ CO2+ H2 in the ratio of 90:5:5, CO2, and N2) with 2 substrate types (alfalfa hay only, and alfalfa hay and a concentrate mixture in a 50:50 ratio) in a 3×2 factorial design (experiment 1) and 3 headspace compositions (N2, N2 + CO2 in a 50:50 ratio, and CO2) with 3 bicarbonate concentrations (80, 100, and 120 mM) in a 3×3 factorial design (experiment 2) were evaluated. In experiment 1, total gas production (TGP) and net gas production (NGP) was the lowest for CO2, followed by N2, and then the gas mixture. Methane concentration in headspace gas after fermentation was greater for CO2 than for N2 and the gas mixture, whereas total methane production (TMP) and net methane production (NMP) were the greatest for CO2, followed by the gas mixture, and then N2. Headspace composition did not affect in vitro digestibility or the VFA profile, except molar percentages of propionate, which were greater for CO2 and N2 than for the gas mixture. Methane concentration in headspace gas, TGP, and NGP were affected by the interaction of headspace gas composition and substrate type. In experiment 2, increasing concentrations of CO2 in the headspace decreased TGP and NGP quadratically, but increased the concentrations of methane, NMP, and in vitro fiber digestibility linearly, and TMP quadratically. Fiber digestibility, TGP, and NGP increased linearly with increasing bicarbonate concentrations in the medium. Concentrations of methane and NMP were unaffected by bicarbonate concentration, but TMP tended to increase due to increasing bicarbonate concentration. Although total VFA concentration and molar percentage of butyrate were unchanged, the molar percentage of acetate, and acetate-to-propionate ratio decreased, whereas the molar percentage of propionate increased quadratically with increasing bicarbonate concentration. This study demonstrated for the first time that headspace composition, especially CO2 content, and bicarbonate concentration in media could significantly influence gas and methane production, and rumen fermentation in gas production techniques.

Effects of quillaja and yucca saponins on communities and select populations of rumen bacteria and archaea, and fermentation in vitro

AIMS

The objective of this study was to comprehensively evaluate quillaja (QSP) and yucca saponin (YSP) products with respect to their effects on diversity of rumen bacteria and archaea, abundance of selected microbes, and feed degradability and fermentation.

METHODS AND RESULTS

Both QSP and YSP at doses 0-0.6 g l(-1) tended to increase degradability of feed substrate in in vitro rumen cultures, but to different extents. Neither one of the saponins affected the concentrations of ammonia, total volatile fatty acids, or molar proportion of acetate. However, QSP increased molar proportion of propionate and decreased that of butyrate, whereas YSP tended to decrease that of butyrate. As determined by qPCR, QSP and YSP did not affect the abundance of total bacteria or Ruminococcus albus. The QSP did not affect the abundances of Fibrobacter succinogenes or genus Prevotella, but tended to decrease that of Ruminococcus flavefaciens, whereas YSP significantly increased the abundance of R. flavefaciens and Prevotella, and numerically increased that of F. succinogenes. Both saponins increased archaeal abundance, although to small magnitudes (0.3-0.4 log). The protozoal populations were decreased significantly by QSP, but not by YSP. Based on DGGE and T-RFLP analysis, both saponins altered the bacterial community and species organization, but less so the archaeal community.

CONCLUSIONS

This study demonstrated that saponins, although not effective in mitigating methane emission, may improve feed utilization at low doses, and modulate ruminal microbial communities in a dose-dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study suggest that saponins at low doses may directly stimulate the growth of some rumen bacteria including cellulolytic bacteria, thus improving digestibility of feeds, independent of their defaunation activity. In contrast, saponins at high doses modulate rumen fermentation characteristically similar to defaunation.