Inhibition of methyl-CoM Reductase from Methanobrevibacter ruminantium by 2-bromoethanesulfonate

In-Silico and in vitro Studies Revealed that Rosmarinic Acid Inhibited Methanogenesis via Regulating Composition and Function of Rumen Microbiota

Inhibition of methyl-coenzyme M reductase can suppress the activity of ruminal methanogens, thereby reducing enteric methane emissions of ruminants. However, developing specific and environmentally friendly inhibitors is a challenging endeavor. To identify a natural and effective methane inhibitor that specifically targets methyl-coenzyme M reductase, molecular docking technology was employed to screen a library of phytogenic compounds. A total of 52 candidate compounds were obtained through molecular docking technique. Rosmarinic acid (RA) was one of the compounds that could traverse a narrow channel and bind to the active sites of methyl-coenzyme M reductase, with a calculated binding free energy of -9.355 kcal/mol. Furthermore, the effects of rosmarinic acid supplementation on methane production, rumen fermentation, and the microorganism's community in dairy cows were investigated through in vitro rumen fermentation simulations according to a random design. Supplementation of RA resulted in a 15% decrease in methane production compared with the control. In addition, RA increased the molar proportion of acetate and propionate, whereas the sum of acetate and butyrate divided by propionate was decreased. At the bacterial level, the relative abundance of Rikenellaceae RC9 gut group, Christensenellaceae R7 group, Candidatus Saccharimonas, Desulfovibrio, and Lachnospiraceae FE2018 group decreased with RA supplementation. Conversely, the addition of RA significantly increased the relative abundance of DNF00809 (a genus from Eggerthellaceae), Denitrobacterium, an unclassified genus from Eggerthellaceae, an unclassified genus from Bacteroidales, and an unclassified genus from Atopobiaceae. At the archaeal level, the relative abundance of Methanobrevibacter decreased, while that of Methanosphaera increased with the RA supplementation. These findings suggested that RA has the potential to be used as a novel natural additive for inhibiting ruminal methane production.

Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways

Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.

Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment

Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.

Mitigating methane emission from oil sands tailings using enzymatic and lime treatments

Engineering strategies to reduce greenhouse gases (GHGs) emissions by inhibiting methanogenesis in oil sands tailings have rarely been examined. In this study, we explored the potential impact of chemical treatment (lime) and biological treatment using enzymes (lysozyme and protease) on inhibiting methane emissions from tailings. Overall, treatment with protease 3%, lysozyme 3%, and lime 5000 ppm reduced CH₄ production (by 52%, 28%, and 25%, respectively) and were weakly associated with the archaeal abundance. Enzymes treatment resulted in a higher reduction in CH₄ production compared with lime treatment. A 3% lysozyme treatment suppressed CH₄ production (the change in methane was 0.48 mmol) and reduced the degradation of hexane throughout the experiment. Similarly, 3% protease suppressed CH₄ production throughout the experiment (the change in methane was 0.78 mmol), which could be attributed to the pH reduction to pH 4.9 at week 23 resulting from the formation of volatile fatty acids. Another possible mechanism could be the formation of toxic compounds, such as high nitrogen content, after protease treatment that inhibited the microbial community. The toxicity effect to Vibrio fischeri was greater with lysozyme 3% and protease 3% treatment than with lime treatment (124 TU and 76 TU, respectively). Lime treatment resulted in the highest reduction in 16S rRNA gene copies from 5.7 × 10⁶ cells g^-1 (control) to 2.7 × 10⁵, 1.71 × 10⁵, and 1.4 × 10⁵ cells g^-1 for 1600, 3500, and 5000 ppm treatments, respectively. This study supports further work to examine and determine the optimum conditions (e.g., enzyme and lime dosages) for CH₄ inhibition.

Insights into the methanogenic degradation of N, N-dimethylformamide: The functional microorganisms and their ecological relationships

The methanogenic degradation of N, N-dimethylformamide (DMF) was investigated using anaerobic digested sludge (ADS), aerobic activated sludge (AAS) and co-cultured sludge (CCS), respectively. Both the metabolic pathway and the corresponding microorganisms which function in the methanogenic degradation of DMF were elucidated. DMF was unable to be degraded anaerobically by ADS due to the lack of DMF-hydrolyzing bacteria. DMF can be effectively degraded by AAS, however, no methane was recovered under the aerobic condition. The co-culture of DMF-hydrolyzing bacteria and methanogens in the CCS allowed for both hydrolysis of DMF and methane production to proceed successfully under the anaerobic condition, realizing the complete conversion from DMF to methane. However, a niche overlap due to the competition for the intermediates lowered the abundance of DMF-hydrolyzing bacteria. The introduction of nitrate, timely replenishment of AAS, micro-aeration and co-digestion were likely to maintain a high abundance of DMF-hydrolyzing bacteria to ensure an effective hydrolysis.

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

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

Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol

Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere. Along with the methane, up to 12% of the gross energy content of the feedstock is lost. Therefore, our recent report has raised interest in 3-nitrooxypropanol (3-NOP), which when added to the feed of ruminants in milligram amounts persistently reduces enteric methane emissions from livestock without apparent negative side effects [Hristov AN, et al. (2015) Proc Natl Acad Sci USA 112(34):10663-10668]. We now show with the aid of in silico, in vitro, and in vivo experiments that 3-NOP specifically targets methyl-coenzyme M reductase (MCR). The nickel enzyme, which is only active when its Ni ion is in the +1 oxidation state, catalyzes the methane-forming step in the rumen fermentation. Molecular docking suggested that 3-NOP preferably binds into the active site of MCR in a pose that places its reducible nitrate group in electron transfer distance to Ni(I). With purified MCR, we found that 3-NOP indeed inactivates MCR at micromolar concentrations by oxidation of its active site Ni(I). Concomitantly, the nitrate ester is reduced to nitrite, which also inactivates MCR at micromolar concentrations by oxidation of Ni(I). Using pure cultures, 3-NOP is demonstrated to inhibit growth of methanogenic archaea at concentrations that do not affect the growth of nonmethanogenic bacteria in the rumen.