Methane – one of the key greenhouse gases (GHGs) – is a natural product of the digestion process undertaken by microbes in the gut of ruminants. One of the challenges facing researchers in the field is how little is actually known about these rumen microbes, and what the potential implications of their manipulation could be.
As well as producing methane, those rumen microbes also produce volatile fatty acids (VFA). Those VFAs – propionate, butyrate, and acetate – provide some of the building blocks for milk protein and fat, as well as affecting milk volume. They also provide energy for other biophysical processes in the cow’s tissues (see page 108 for more).
Attempting to manipulate those microbes in the rumen in the search for reducing GHG emissions could lead to undesirable impacts on production factors.
The Pastoral Greenhouse Gas Research Consortium (PGgRC) was set up in 2002 to understand, and provide mitigation solutions for, greenhouse gases produced by grazing animals. PGgRC is made up of AgResearch, DairyNZ, Beef + Lamb NZ, DEEResearch, the Fertiliser Association of NZ, Fonterra, and PGG Wrightson.
AgResearch scientist Dr Peter Janssen summarised some of PGgRC’s progress at the NZ Society of Animal Production conference earlier this year.
He described the microbes in the rumen as a community. That community was made up of thousands of micro-organisms including bacterial, ciliate protozoa (organisms made of a single cell), and fungi.
“The microbial community reacts to the (feed) inputs and the environment of the rumen, and then in the long term if you make a change, there will be a change in the microbial community to reflect the changing conditions. The microbes, the mix of species that is best adapted to those conditions comes to dominate in that rumen.”
Different feeds or animals that were naturally low- or high-GHG emitters would have different microbial communities in the rumen.
One of the challenges of the research has been the need to essentially start from scratch. Most of the microbes in the rumen were unidentified and even the techniques for analysing the samples needed to be developed.
There was a need to develop a project pipeline, starting from zero – simply identifying and naming the microbes – right through to figuring out the impacts of manipulating the rumen microbial community.
“There are not a lot of tools for rumen work,” Janssen said.
“This work has been done in the human gut and looked at in the mouse, but once you go beyond that you don’t really have that many tools – so you have to devise all of your own tools.”
Even collecting a sample from the rumen required research into deciding the best technique, particularly when taking into account the large number of production animals that would need to be sampled in the course of the research. The team concluded stomach tubing would be acceptable, and moved on to the next challenge.
‘You couldn’t do these types of studies the way we were doing it three years ago.’
From a sample collected from the rumen, the DNA from everything in that sample is extracted. Marker genes linked with specific microbe families are checked against a reference database, mostly developed by the team, and a picture developed of the proportional representation of all the different groups in the rumen sample.
An innovation developed by the team allows multiple rumen samples to be analysed in the same testing run. The team developed a technique that allowed them to introduce an extra piece of DNA sequence to the mix that is unique to each sample – a “barcode”. That made the sample analysis process – a key step in any animal GHG research – much quicker.
“These pipelines we’ve developed, we’ve been able to handle large numbers of samples. You couldn’t do these types of studies the way we were doing it three years ago.”
The PGgRC has six key areas it is focusing on to find solutions that will reduce methane emissions – finding low methane animals, determining low-methane feeds, developing a vaccine that will inhibit methane production, identifying inhibitors of methane-generating microbes, reducing nitrous oxide and nitrogen leaching, and increasing soil carbon.
What they’re researching
Brassica effects
Research has shown that sheep fed brassicas consistently produce less methane than those fed pasture.
One NZ trial showed sheep fed forage rape emitted 20-30% less methane than those on pasture. The rumen microbial communities of the sheep on the two types of forage were found to be fundamentally different.
The forage rape-fed sheep had greater proportions of bacteria that are thought to ferment carbohydrates to lactate and propionate, while the rumens of the grass-fed sheep favoured bacteria that produced more hydrogen, a building block of methane.
More research is required to determine what mechanism governs this effect, but one of the theories put forward is that the lower rumen pH brought about by the high starch/sugar diet under forage rape grazing inhibits the methane-forming microbes (methanogens).
Natural variation
Some animals naturally emit less methane than their cohorts – there is between-animal variation. Research in sheep has shown this trait to be both heritable and consistent over time.
There are two microbial communities associated with low methane emissions. One – Q-type – is characterised by a bacterium favouring the production of propionate, the other – S-type – by a bacteria that produces lactate. Neither produce much hydrogen in their digestion process.
The sheep that produce relatively more methane – H-type – have a mix of bacteria, all known to be hydrogen-producing species.
‘This work has been done in the human gut and looked at in the mouse, but once you go beyond that you don’t really have that many tools.’
The question remains what factors determine which microbial community develops. The mechanism is still not well understood.
There have been observations that suggest low methane emitters have smaller rumen volumes, which could tie in with faster passage rates for material through the rumen, selecting for low hydrogen-producing communities. However, why there should be two different types of communities with similar impacts on methane emissions is not known.
These different communities could also have impacts on levels of production. The Q-type community, producing more propionate, could outperform the S-type, producing more lactate, giving one animal an advantage over the other, despite both being relatively low emitters of methane.
Feed efficiency, as measured by residual feed intake (RFI), has also been shown to be a heritable trait. RFI is the difference between the actual amount of feed eaten by the animal and the amount of feed you would expect it to eat for a given level of production.
Some studies have shown that the rumen microbial communities differ between high and low RFI animals although the reasons for this have not yet been examined.
Janssen said preliminary analysis of samples taken from animals involved in DairyNZ’s feed conversion efficiency research programme showed there were differences between microbial communities in low, medium, and high RFI animals, while there were similar communities within the RFI groups.
“This presents two opportunities. One, this could actually be quite a nice screening tool … And the second opportunity is that if it is something to do with the rumen, and we can find out what microbes they are and … using the other information about those animals, maybe we can piece together a hypothesis as to the mechanism behind it.”
