Methyl-coenzyme M reductase A as an indicator to estimate methane production from dairy cows

The impact of twice daily 3-nitroxypropanol supplementation on enteric methane emissions in grazing dairy cows

Although 3-NOP has been proven to reduce enteric methane (CH4) by ∼30% in indoor systems of dairying when the additive is mixed throughout a total mixed ration (TMR), there has been very limited research to date in grazing systems in which the most convenient method of additive supplementation is at milking twice daily. To investigate the effect of twice daily 3-NOP supplementation on enteric CH4 emissions, a 12-week study was undertaken in which treatment cows (n = 26) were supplemented with 3-NOP (80 mg per kg dry matter intake; DMI) twice daily at morning and evening milking, while control cows (n = 26) received no additive supplementation. Enteric CH4, hydrogen (H2) and carbon dioxide (CO2) were measured using GreenFeed units, while milk production, body weight (BW), body condition score (BCS) and DMI were monitored to determine the effect of 3-NOP supplementation on productivity. There was no significant effect of 3-NOP supplementation on any of the aforementioned parameters with the exception of CH4 and H2 production, respectively. Cows supplemented with 3-NOP produced ∼36% more H2 (P < 0.001) across a 24-h period, with reductions in CH4 production of 28.5% recorded in the 3 h after additive consumption (P < 0.001), however, levels of CH4 production returned to that of the control group thereafter. When CH4 production was considered across the entire 24-h period, the cows offered 3-NOP produced ∼5% less CH4 than the control (P < 0.050). Future research should focus on methods to increase the efficacy of the additive throughout the day which would include the deployment of a slow-release form or an out of parlor feeding system that allows animals consume the product at additional time points.

Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).

Improving mesophilic anaerobic digestion of food waste by side-stream thermophilic reactor: Activation of methanogenic, key enzymes and metabolism

Anaerobic digestion (AD) is a favorable way to convert organic pollutants, such as food waste (FW), into clean energy through microbial action. This work adopted a side-stream thermophilic anaerobic digestion (STA) strategy to improve a digestive system's efficiency and stability. Results showed that the STA strategy brought higher methane production as well as higher system stability. It quickly adapted to thermal stimulation and increased the specific methane production from 359 mL CH₄/g·VS to 439 mL CH₄/g·VS, which was also higher than 317 mL CH₄/g·VS from single-stage thermophilic anaerobic digestion. Further exploration of the mechanism of STA using metagenomic and metaproteomic analysis revealed enhanced activity of key enzymes. The main metabolic pathway was up-regulated, while the dominant bacteria were concentrated, and the multifunctional Methanosarcina was enriched. These results indicate that STA optimized organic metabolism patterns, comprehensively promoted methane production pathways, and formed various energy conservation mechanisms. Further, the system's limited heating avoided adverse effects from thermal stimulation, and activated enzyme activity and heat shock proteins through circulating slurries, which improved the metabolic process, showing great application potential.

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

Physically effective neutral detergent fiber (peNDF) is a concept that accounts for the particle length of NDF in diets, sustaining the normal chewing behavior and rumen fermentation of ruminants. Specifically, peNDF>1.18 is the commonest one that is calculated from NDF and the percentage of feed dry matter left on the 1.18, 8.00, and 19.00 mm sieves. This study aimed to investigate the effects of different levels of peNDF>1.18 on the rumen microbiome and its correlation with nutrient digestibility and rumen fermentation in goats. A total of 30 Lezhi black goats were randomized and blocked to five dietary treatments (n = 6). All the diets were identical in composition but varied in hay lengths, leading to the different peNDF>1.18 content of the diets: 32.97, 29.93, 28.14, 26.48, and 24.75%. The results revealed that the nutrient digestibility increased when dietary peNDF>1.18 levels decreased from 32.97% to 28.14%, with the highest digestibility at 28.14% peNDF>1.18 treatment, after which nutrient digestibility decreased with the decreasing of dietary peNDF levels. Ruminal NH3-N concentrations in the 29.93% and 28.14% groups were higher than that in the 24.75% group (p < 0.05). Ruminal microbial protein concentration was the highest in the 32.97% group (p < 0.05). Daily CH4 production in the 32.97% and 24.75% peNDF>1.18 treatments was lower than that in the 26.48% group (p < 0.05) and no differences were observed among other groups. The relative abundance of rumen fungi at the phylum and genus levels and archaea at the species were affected by dietary peNDF>1.18 content. In conclusion, decreasing dietary peNDF>1.18 levels within a certain range can improve nutrient digestibility and change the rumen microbial community structure of goats. Dietary peNDF>1.18 level should be 28.14% (roughage length around 1 cm) among the five levels for 4 months Lezhi black goats with the purpose of optimal nutrient digestibility.

Rumen sampling methods bias bacterial communities observed

The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.

Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle

Background

Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions.

Results

The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R² < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (P_adj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found to be differentially abundant between low- and high-emission animals and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals.

Conclusions

Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the relative abundance of Bacteria, Archaea, and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH₄ emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.

Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies

Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.

The relationship between methane emission and daytime-dependent fecal archaeol concentration in lactating dairy cows fed two different diets

Archaeol is a cell membrane lipid of methanogenic archaea excreted in feces and is therefore a potential biomarker for individual methane emission (MEM). The aims of this study were to examine the potential of the fecal archaeol concentration (fArch) to be a proxy for MEM prediction in cows fed different diets and determine if the time of fecal collection affected the archaeol concentration. Thus, we investigated (i) the variation of the fArch concentration in spot samples of feces taken thrice within 8 h during respiration chamber measurements and (ii) the effect of two diets differing in nutrient composition and net energy content on the relationship between fArch and MEM in lactating cows. Two consecutive respiration trials with four primiparous and six multiparous lactating Holstein cows were performed. In the first trial (T1) at 100±3 d in milk (IM), a diet moderate in starch and fat content was fed for ad libitum intake, whereas in the second trial (T2) at 135±3 d IM, cows received a diet lower in starch and fat. Individual MEM (g d-1) was measured for 24 h. Fecal samples were taken at 06:30, 10:00, and 14:30 LT and analyzed for fArch using Soxhlet lipid extraction and GC–MS. Cows produced less methane (364 g CH4 d-1) during T1 and had significantly lower fArch concentrations (37.1 µg g-1 dry matter; DM) compared to T2 (392 g CH4 d-1 and 47.6 µg g-1 DM). A significant positive relationship between fArch (µg g-1 fecal DM) and MEM, expressed on a dry matter intake (DMI) basis (g kg-1 DMI), was found (R2=0.53, n=20). Among samples collected over the day, those collected at 10:00 LT provided the best coefficient of determination for MEM (R2=0.23). In conclusion, fArch offers some potential in serving as a proxy for innovative breeding schemes to lower enteric methane when fecal samples are taken at a certain time of the day, but more data on the sources of variation of the MEM : fArch ratios are required.

Metaproteomic analysis of the relationship between microbial community phylogeny, function and metabolic activity during biohydrogen-methane coproduction under short-term hydrothermal pretreatment from food waste

Short-term hydrothermal pretreatment (SHP) is an attractive method for food waste anaerobic digestion, which facilitates the solubilisation of recalcitrant particles. This study employed metaproteomic method to evaluate the relationships among microbial community phylogeny, function, and metabolic activity during two-stage anaerobic digestion under SHP (SHPT) from food waste. The presence of 651 bacterial proteins and 477 archaeal protein has been detected by liquid chromatography online linked to mass spectrometry, revealing a high metabolic heterogeneity during SHPT. The different stages of SHPT highlighted important roles for the bacterial proteins from Gammaproteobacteria, Bacilli, and Clostridia and the archaeal proteins from Methanosarcinales. The identified proteins related to biohydrogen production come from pyruvic acid decarboxylase and formic acid decomposition pathway in carbohydrate metabolism and methanogenesis from acetate, CO₂ and a methylotrophic pathway during energy metabolism. This could provide functional evidence of the metabolic activities and biogas production during SHPT.

Models for predicting enteric methane emissions from dairy cows in North America, Europe, and Australia and New Zealand

There are several models in the literature for predicting enteric methane (CH4 ) emissions. These models were often developed on region or country-specific data and may not be able to predict the emissions successfully in every region. The majority of extant models require dry matter intake (DMI) of individual animals, which is not routinely measured. The objectives of this study were to (i) evaluate performance of extant models in predicting enteric CH4 emissions from dairy cows in North America (NA), Europe (EU), and Australia and New Zealand (AUNZ) and (ii) explore the performance using estimated DMI. Forty extant models were challenged on 55, 105, and 52 enteric CH4 measurements (g per lactating cow per day) from NA, EU, and AUNZ, respectively. The models were ranked using root mean square prediction error as a percentage of the average observed value (RMSPE) and concordance correlation coefficient (CCC). A modified model of Nielsen et al. (Acta Agriculturae Scand Section A, 63, 2013 and 126) using DMI, and dietary digestible neutral detergent fiber and fatty acid contents as predictor variables, were ranked highest in NA (RMSPE = 13.1% and CCC = 0.78). The gross energy intake-based model of Yan et al. (Livestock Production Science, 64, 2000 and 253) and the updated IPCC Tier 2 model were ranked highest in EU (RMSPE = 11.0% and CCC = 0.66) and AUNZ (RMSPE = 15.6% and CCC = 0.75), respectively. DMI of cows in NA and EU was estimated satisfactorily with body weight and fat-corrected milk yield data (RMSPE < 12.0% and CCC > 0.60). Using estimated DMI, the Nielsen et al. (2013) (RMSPE = 12.7 and CCC = 0.79) and Yan et al. (2000) (RMSPE = 13.7 and CCC = 0.50) models still predicted emissions in respective regions well. Enteric CH4 emissions from dairy cows can be predicted successfully (i.e., RMSPE < 15%), if DMI can be estimated with reasonable accuracy (i.e., RMSPE < 10%).

Methane and nitrous oxide emissions from Canadian dairy farms and mitigation options: An updated review

This review examined methane (CH4) and nitrous oxide (N2O) mitigation strategies for Canadian dairy farms. The primary focus was research conducted in Canada and cold climatic regions with similar dairy systems. Meta-analyses were conducted to assess the impact of a given strategy when sufficient data were available. Results indicated that options to reduce enteric CH4from dairy cows were increasing the dietary starch content and dietary lipid supplementation. Replacing barley or alfalfa silage with corn silage with higher starch content decreased enteric CH4per unit of milk by 6%. Increasing dietary lipids from 3% to 6% of dry matter (DM) reduced enteric CH4yield by 9%. Strategies such as nitrate supplementation and 3-nitrooxypropanol additive indicated potential for reducing enteric CH4by about 30% but require extensive research on toxicology and consumer acceptance. Strategies to reduce emissions from manure are anaerobic digestion, composting, solid–liquid separation, covering slurry storage and flaring CH4, and reducing methanogen inoculum by complete emptying of slurry storage at spring application. These strategies have potential to reduce emissions from manure by up to 50%. An integrated approach of combining strategies through diet and manure management is necessary for significant GHG mitigation and lowering carbon footprint of milk produced in Canada.

Technical note: Analytical refinements of the methane indicator archaeol in bovine feces, rumen fluid, and feedstuffs

Archaeol (1,2-di-O-phytanyl-sn-glycerol) is a cell membrane lipid component of methanogens that has the potential to be used as a biomarker for methane production in ruminants. However, its analysis via gas chromatography-mass spectrometry (GC-MS) is challenging because of its molecular size and structure. In this study, 2 different sample preparation methods were tested, Soxhlet and sonication-aided extraction, and the methods were compared for extraction efficiency using the internal standard (IS; 1,2-di-o-hexadecyl-rac-glycerol). The extraction efficiency of the Soxhlet method for fecal archaeol was twice that of sonication. With the use of a high-temperature GC column, the retention times of IS and archaeol were 17.6 and 19.4 min, respectively, with a total run time of only 25 min. The molecule ions m/z 611.4 (IS) and m/z 725.8 (archaeol), or alternatively the fragment ion of the glycerol moiety m/z 130.0, were used for identification and quantification via GC-MS in positive chemical ionization mode. The intra-assay coefficients of variation for fecal archaeol measurements were 1.3% (m/z 725.8) and 2.1% (m/z 130.0) (n=3), respectively. Fecal archaeol quantifications did not differ between the use of the molecule or glycerol moiety ions (paired t-test, n=156). Archaeol concentrations tended to be 3.3% greater in samples stored at -20°C before drying compared with samples that were immediately dried after collection (paired t-test, n=5). The detection limit of archaeol was 0.5 µg/g of fecal dry matter (DM); no archaeol could be detected in feed samples. In different fractions of rumen fluid, archaeol levels ranged from 1.9 to 24.0 µg/g of DM. In 10 cows fed the same grass and corn silage/hay-based ration, diurnal variations of fecal archaeol levels (5 time points over 2 d) were cow dependent and ranged from 26.2 to 77.2 µg/g of DM (mean 48.4 µg/g of DM). Thus, within-animal variation in cows on the same diet was between 4 and 27%. We suggest that this finding is related to the amount and time of the latest feed intake event before the fecal sampling. Feeding pattern can determine the passage rate of digesta through the alimentary tract and thus the duration of contact time of archaea with their substrate.

Body fat mobilization in early lactation influences methane production of dairy cows

Long-chain fatty acids mobilized during early lactation of dairy cows are increasingly used as energy substrate at the expense of acetate. As the synthesis of acetate in the rumen is closely linked to methane (CH4) production, we hypothesized that decreased acetate utilization would result in lower ruminal acetate levels and thus CH4 production. Twenty heifers were sampled for blood, rumen fluid and milk, and CH4 production was measured in respiration chambers in week -4, +5, +13 and +42 relative to first parturition. Based on plasma non-esterified fatty acid (NEFA) concentration determined in week +5, animals were grouped to the ten highest (HM; NEFA > 580 μmol) and ten lowest (LM; NEFA < 580 μmol) mobilizing cows. Dry matter intake (DMI), milk yield and ruminal short-chain fatty acids did not differ between groups, but CH4/DMI was lower in HM cows in week +5. There was a negative regression between plasma NEFA and plasma acetate, between plasma NEFA and CH4/DMI and between plasma cholecystokinin and CH4/DMI in week +5. Our data show for the first time that fat mobilization of the host in early lactation is inversely related with ruminal CH4 production and that this effect is not attributed to different DMI.

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.

Methane is a highly potent greenhouse gas and ruminants are the major source of methane emissions from anthropogenic activities. Here we show in an experiment with cattle that genetic selection of low-emitting animals is a viable option based on a newly developed selection criterion. The experimental data provided a comprehensive insight into the host additive genetic influence on the microbiome, the impact of nutrition on genetics and the microbiome, and the effect of metagenomic microbial genes on the analysed traits. We developed a selection criterion to change those traits by evaluation of hosts based on the relative abundance of microbial genes. This criterion is shown to be highly informative and it is therefore suggested to be used in studies analysing different traits and species. This study provides a proof of principle that there is an additive genetic influence of the host on its microbiome and that selection for the desired host can be based on the abundance of a suite of genes in the ruminal metagenome associated with the trait. The use of this criterion will allow genetic analysis on a large number of hosts, previously a significant barrier to determination of host genetic effects on such traits.