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Minimise Methane through the Microbiome

Although it receives less attention as a greenhouse gas, methane is an extremely important target for climate change mitigation strategies. Reducing methane emissions is good for the environment, is cost-effective, and has follow-on effects on human health and crop yields. The methane produced by livestock is a major contributor to worldwide methane emissions. This methane is produced by microorganisms in ruminants, therefore microbiome-targeted approaches could help to mitigate increases in methane emissions.

What is methane and how is it formed?

Methane is a gas found in small quantities in the atmosphere. As the simplest hydrocarbon, it is highly flammable and a principle component of natural gas. Methane has a global warming potential several orders of magnitude larger than that of carbon dioxide because of its ability to efficiently trap heat. However, it only persists in the atmosphere for a relatively short period of time – up to 12 years. Methane emission control strategies are attractive because they have an effect that can be seen directly in terms of effects on climate, human health, and agriculture.

Globally, methane is produced naturally and from human-related activities. Human-related activities contribute to 60% of methane emissions. These activities can be broadly classified into those from the fossil fuel sector, from agriculture and from waste management. Approximately one third of man-made methane emissions are related to the extraction and transport of fossil fuels. A further 40% are from agriculture, particularly from enteric fermentation in cattle, and from rice wetlands. Additionally, 20% is produced by waste management operations.

Initiatives to reduce methane emissions

Globally, there are a number of measures that can be used to significantly reduce methane emissions. Measures that are currently available could reduce emissions by 45% in 2030 and also be cost-effective. A reduction of this magnitude is predicted to limit global warming to 1.5ºC.

Livestock-related methane emission reduction is an attractive target as it is a large contributor to overall emissions. Estimated potential methane reduction from livestock has a wide range, reducing methane from 4-42 Mt per year. There is also high variation in methane production: each head of cattle produces 150 to 400 litres of methane per day, and each sheep produces 25 to 55 litres of methane per day. The Climate and Clean Air Coalition highlights the potential of methane mitigation strategies by stating that “rapid and large scale implementation of improved livestock feeding strategies can reduce 20% of global methane emissions by 2030.”

An integrated approach to livestock management with capture the largest decreases in methane production in any agricultural enterprise. Sustainable farming practices such as maintaining a high level of animal health, managing waste streams and maximising the feed conversion ratio will increase the overall efficiency of production and therefore the methane production per head of livestock. A complementary approach could be used to modulate the microbiome and thereby reduce the enteric formation of methane via feed additives or the manipulation of the composition of the feed.

Methane production in the rumen

Methane is produced in the rumen as a hydrogen sink. Methanogenesis is part of complex process consisting conceptually of several steps that are performed primarily by different microbial kingdoms. Chewed plant matter is converted to monomers via primary anaerobic fermenters. Secondary anaerobic fermentation takes place that produces volatile fatty acids that are used by livestock for energy, with dihydrogen and carbon dioxide produced as by-products of this process. Methanogenic archaea convert these by-products to methane, which leaves the rumen via belching. Some methane is further metabolised by methanotrophic bacteria.

Regardless of its role as a hydrogen sink, methane loss to the atmosphere is considered a loss of energy of between 2% and 12% of total energy consumption (Ungerfeld, 2020). Efforts to reduce methane emissions from the rumen therefore have the potential to improve feed conversion ratios. Nevertheless, blunt approaches that reduce methane production in the rumen through various mechanisms tend to cause a reduction in feed intake, fermentation and unfavourable effects on digestive processes. The exact role of methanogens within the rumen ecosystem, in particular their symbiotic relationships with rumen protozoa, fungi, and bacteriophages, is being actively researched.

Can methane production in the rumen be influenced by the microbiome?

Various methods of reducing methane production in livestock have been explored, including animal management, dietary composition, use of anti-methanogenic agents, and directly influencing the methanogens themselves. Via these methods, the growth or metabolic activity of methanogens can be modulated, or the production of hydrogen gas can also be shifted towards greater production of volatile fatty acids.

The production of methane can be influenced by diet: higher feed fibre content directs volatile fatty acid production towards acetate and higher methane production, whilst a starch-rich feed tend to result in higher levels of propionate and lower methane (Janssen, 2010). Essentially, the changes in macronutrient concentrations cause alterations in the microbiome that effect methane production. Thus, metagenomic approaches can guide and complement research into reducing methane emissions.

In one example, publicly available 16S data from one thousand dairy cows was used to identify taxa and functional traits associated with low methane production (Cardinale and Kadarmideen, 2022). Various phyla and SNPs were found to play an important role in rumen methanogenesis, which could be used as targets for or biomarkers of methane emission reduction interventions.

Macroalgae (red seaweed) has been used successfully to reduce methane emission in cattle. Halogenated compounds produced by these plants inhibit the enzyme in the final step of methanogenesis by rumen archaea, thus causing a reduction in methane production. Research has shown a large, sustained reduction in methane emissions of beef cattle by up to 80% when red seaweed was added to feed, with no change in feed conversion or sensory qualities of the meat (Roque et al., 2021).

The Methane Metabolism Pipeline – Enabling Research into Feed Additives to Reduce Methane Emissions

The role of the ruminant microbiome on methane production was kept central in the development of the methane metabolism pipeline. In trials investigating the role of feed additives on methane emission, the pipeline can be used to:

  • Identify taxa, genes and enzymes affecting methane production.
  • Elucidate relationships across microbial kingdoms.
  • Assess the effectiveness of feed supplements.
  • Profile the relative abundance of both species and proteins in metagenome samples from rumen microbiomes.
  • Determine associations between functional and taxonomic abundance, and trial metadata, using powerful statistical tools.
  • Deliver custom analysis and reporting to the client.

The pipeline starts with using the shortBRED method to identify protein sequences of interest, which are fed into a marker sequences database, containing over 16,000 gene sequences in total. Deep shotgun metagenome samples from the rumen are then run in parallel: the abundance of genes of interest are quantified, and the taxonomic relative abundance is generated with the Shotgun Taxonomic Analysis pipeline using Kraken and Bracken. Relationships between the trial metadata and both taxonomic and functional profiles are computed, and an association analysis is performed to find relationships between taxonomic and functional abundances. Finally, tables and visualisations are produced according to client specifications.

Applications of the Methane Metabolism Pipeline

Metagenome analyses offered by the methane metabolism pipeline assist researchers in identifying taxa, genes and enzymes that influence methane production in livestock. The pipeline is tailored towards profiling the relative abundance of species and proteins in rumen metagenome samples that are associated with methane production. While the pipeline was set up with animal feeding trials in mind, the effects of other interventions in ruminants can also be tested.

The new pipeline offers a sophisticated tool to develop novel feed additives or research animal management practises to reduce methane production by enteric fermentation. The dedicated rumen microbiome database, parallel functional and taxonomic analyses, and integration with trial-related metadata provide robust insights into the microbial community involved in methane production and how it can be engineered to improve the sustainability of livestock production.

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