Methane mitigation: Understanding the rumen microbiome

“Addressing these knowledge gaps has the potential to lead to the development of novel strategies or to complement existing strategies to effectively reduce CH₄ formation while also improving productivity in dairy cows,” they said.

Significance of the rumen microbiome

Dairy cows are dependent on rumen microbes to derive their energy and protein needs from the microbial fermentation of feeds. The rumen microbiome is predominated by anaerobic bacteria, followed by less abundant archaea (methanogens, protozoa, and fungi) that work collectively to digest feed. As fermentation increases following feed intake, VFA and gases (CO₂ and H₂) are produced. The VFAs are absorbed by the host as sources of energy but most of the H₂ is used by methanogenic archaea to reduce CO₂ leading to the formation of CH₄.

It has been postulated that individual methanogenic lineages form specific syntrophic (obligate metabolic mutualism) with certain cohorts of bacteria in the rumen and differences in these bacteria-archaea interactions may be linked to ruminant health and production. Understanding the different types of methanogens, how they interact with other microbes and their role in methanogenesis may enable the unveiling of mitigation strategies that can effectively reduce CH₄ formation without disturbing the ruminal environment.

Methanogenic diversity in the rumen

Methanogenic archaea are an ecologically diverse group of strictly anaerobic microorganisms with a distinct energy metabolism that results in the formation of CH₄ through different pathways that include the reduction of CO₂, formate, methanol, methylamines, and the cleavage of acetate. The advent of PCR has enabled the identification of specific marker genes such as 16S rRNA and mcrA (α subunit of MCR) that are conserved among methanogens. Using either the 16S rRNA gene or terminal-RFLP of the mcrA gene, ruminal methanogens have been broadly clustered into 3 distinct genera: Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales in dairy cows.

Notably, studies show that RNA-based approaches such as meta-transcriptomics are more discriminatory than those of DNA-based approaches such as metagenomics and that CH₄ formation is tightly linked to microbial gene expression. The researchers stated that although the use of marker genes combined with total and metabolically active components has provided new insights on the composition of individual methanogenic lineages in the rumen, better characterization of these lineages to the species level and a better understanding of their role in total CH₄ formation across multiple ruminant species are needed to fully understand methanogenesis in the rumen.

Hydrogen metabolism under normal and inhibited methanogenesis

In the rumen, feed fermentation represents a series of oxidation and reduction reactions involving the production and transfer of H₂ within and between microbes to allow re-oxidisation of reduced co-factors and prevent interruptions in microbial fermentation.

Therefore, understanding the production and utilisation of H₂ via determination of the distribution and role of hydrogenases under normal and modulated conditions such as inhibited methanogenesis will be pivotal to spare H₂ from forming CH₄ and redirect that H₂ to alternate sinks that lead to significant improvements in energy efficiency in the rumen. For example, some studies show that H₂ spared from forming CH₄ is redirected to alternate sinks such as butyrate-producing bacteria.

Ruminal methanogenesis pathways

Despite the common product, individual methanogens have distinct physiological and metabolic capabilities for their survival including substrate utilisation, H₂ thresholds, responses to the partial pressure of H₂, and structural differences. According to the researchers, several methanogenesis pathways use different substrates among methanogens. Knowledge of possible pathways to CH₄ formation may enable the identification of new targets to inhibit CH₄ formation or alter feeding strategies to reduce the supply of methanogenic substrates in the rumen.

Some of the pathways stated (as retrieved from the Kyoto Encyclopedia of Genes and Genomes databases and genomes of individual methanogens) are as follows:

• Acetoclastic pathway

• Glycine pathway

• CO2 + H2 pathway

• GTP pathway

• Methanol pathway

• Methyl amines pathway

• Phosphonate pathway

In addition to the different methanogenesis pathways, the researchers highlighted that there is constant interaction between bacteria, protozoa, fungi, and methanogenic archaea resulting in the exchange of metabolites such as H₂. A better understanding of these interactions may help to select cows with a natural tendency for higher ruminal efficiency. They stated that differences in microbial cohorts between high and low CH₄-yield phenotypes among ruminant hosts may be linked to several factors including, but not limited to, rumen size, passage rate, rumination, and VFA absorption.

Global approach for better mitigation strategies

Researchers believe that, on a global scale, focusing on the effect of different mitigation strategies such as feed supplements (including lipids, essential oils, tannins, and monensin), vaccines, and microbial modulators across different dietary and management styles and breeds on the rumen microbiome may enable a better understanding of ruminal methanogenesis.

They stated the importance of global research to identify factors that drive methanogen diversity to come up with better mitigation strategies to reduce CH₄ formation and improve ruminal efficiency. They emphasised the importance of optimising consistency in sampling strategies, temporal dynamics, sample storage, extraction of nucleic acids, and bioinformatics pipelines.

They concluded that genomic technologies may help determine the contribution of individual methanogenic lineages to total CH₄ formation and how they are inhibited by different mitigation strategies. And, overall, understanding the knowledge gaps in methanogenesis and how to divert H₂ to alternate sinks can lead to the development of novel strategies or complement existing strategies to effectively reduce CH₄ formation while also improving productivity in dairy cows.