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There’s more to a belch than meets the eye

Belching is becoming an ever-increasing problem for the planet, not out of bashfulness, but out of cows.

November 23, 2017

But what are the organisms that lie behind a bovine belch, and what can methane tell us about the complex lives of microbial communities?

It’s a question of microbes. The guts of humans and ruminants alike are teeming with billions of tiny microbial cells, which work together in communities to break down organic matter which we, ourselves, would barely be able to handle.

There are more bacteria cells in the human body than human cells, and around one third of your poo is made up of dead bacteria, possible exhausted from digesting all your food (and making your vitamin K2).

But outside of the digestive tracts of mammals, anaerobic digestion plays an important role in many biotechnological processes, and a better knowledge of how communities of microorganisms function might increase efficiency of a whole swathe of industrial applications - from managing waste and producing fuel through to producing food and drinks for human consumption.

Methane and us.

Methane release from cattle is about as efficient at accelerating the balminess of our global greenhouse as the transport services that ship our prime cuts of beef from the other side of the globe.

We produce a fair amount of gas ourselves, too, about three pints a day (that’s 1.5 litres), although many people don’t produce methane. It perhaps depends on what methanogenic (methane-producing) microbes were passed down by your parents.

However, between 30-50% of adult humans do produce methane to some degree, which might even be linked to cases of chronic constipation, irritable bowel syndrome and others.

Heifers clearly do possess a hefty amount of these microbes, which thrive together in communities that share resources to efficiently break down the steady stream of chyme sent through a cow’s complicated bowels.

Among these, there are methanogenic archaea (cells that look like bacteria but are completely different, genetically). Indeed, the methanogenic archaea are responsible for most of the methane production on the planet, with over 50 described species helping to keep the cows belching.

Of course, methanogens are not limited to the intestinal tracts of mammals, but can be found in all sorts of environments, for example contributing to marsh gas in bogs and wetlands, as well as contributing significantly to wastewater treatment (methane release from which might even provide an alternative fuel source).

Indeed, microbes exist together in communities thriving in every nook and cranny of the globe. Sometimes, these communities are forced together, in the event of a flood, for example, or the tillage of soil, or even due to the release of a cow pat.

So, what happens during these community mixing events, and what does it mean for the community structure of the microbes involved? Using various communities of methanogens taken from a delectable range of anaerobic digesters in the South of England, lead researchers Angus Buckling and Pawel Sierocinski of the University of Exeter and including Earlham Institute’s Sarah Bastkowski, Mark Alston and David Swarbreck set out to answer these questions.

Methanogens can contribute to marsh gas in bogs and wetlands. Credit: Shutterstock

Wetlands

Community cohesion.

It had previously been expected that, among communities of microbes subjected to “community coalescence” (mixing, in English), a dominant community would become apparent after mixing - and this community would be the most efficient at using resources when grown in isolation.

How to test this theory? Methane seemed a good option. This product of resource use by microbial communities including methanogens is a pretty easy thing to measure, for one.

Another good reason is that, as part of a community, methanogens require cooperation with other organisms in a cohesive unit, as each constituent species contributes to a complex cross-feeding operation. The waste of one organism is the food for another, after all.

In this way, it’s likely that many of the species in these communities have evolved together, therefore looking at how the balance of communities plays out after mixing is both important and interesting, especially as it may hold applications for industrial biotechnology.

Thus, the research team collected microbial communities that had been growing on a variety of delicious substrates, comprising combinations of silage, slurry, sewage, food waste and manure.

These pungent cocktails were cooked up in laboratory-scale anaerobic digesters, and the community profiles of each microbial soup was established, using 16S rRNA sequencing at EI, a modern detection tool to quickly and accurately identify different microbes.

This technique is particularly useful when studying complex communities of microbes, which are hard to prize apart on an individual species basis.

Further information:

16s rRNA makes up part of the ribosome, which is a vital part of cell machinery that makes proteins.

RNA is the single-stranded sister of DNA, which helps cells to turn the genetic instructions into physical components, or even makes up the components themselves, as with the ribosome.

Most of the 16s rRNA is “highly conserved” between species, i.e. it is mostly the same. However, there are sections that are deemed “hypervariable” regions, which means that there are stretches of RNA sequence that can be used to identify species-specific markers, which can be used to split all of the different types of archaea or bacteria in a community.

Methane and maths.

The team then set to work mixing the various different communities of methane-generating microbes, sequencing the community make-up before and after mixing, and analysing their relative ability to generate methane.

It turns out that the mixing all ten communities of different microbes together produced a more efficient system, on average, than was observed in the individual populations.

However, in line with the predictions, even the high-performing mixtures could not out-produce the most efficient single community of methanogens. Indeed, the mixtures tended also to most resemble the same high performing individual microbial community.

Overall, it looks like there is indeed a dominant community that establishes itself within a mixture, and this contributes to increasing efficiency of the mixture as a whole.

It turns out that investigating precisely why this happens isn’t that easy, for many reasons, among them that cultivating isolated microbes often isn’t possible in a lab, which seems to support the idea that co-selection is probably why a strong population is able to contribute so much to a mixed community.

Indeed, mathematics is the best method we currently have of probing these mysteries, and the application of an optimisation approach (non-negative least squares (NNLS)) to the mixed microbial communities revealed that the best performing individual community (in terms of methane production) contributed upwards of 40% of its constituent varieties to the mixtures.

Dr. Sarah Bastkowski of Earlham Institute, a biomathematician, said, “Our approach seems to work really well and helps to detangle the sometimes complex interactions of individual community structures within a mixture. We will follow up this approach in further studies to establish its reliability.”

Dr. Mark Alston added that, “the application of NNLS to microbial communities is a fresh approach of the technique and although NNLS is a relatively simple idea it is reassuring to see its predictions backed up by what we see in the laboratory.”

Open quote marks

And, maybe, one day, armed with this knowledge, we can inoculate the stomachs of cows with microbes that produce something other than methane (or a little bit less of it), and do a little bit of good for the future of the planet.

Closing quote marks

Biotechnology applications.

Essentially, the team found that the more efficient an individual community is at resource usage, in an anaerobic environment, the more likely it is to dominate a mixed community after a mixing event.

The reason is relatively simple. Strong anaerobic communities of microbes are fostered through mutual coevolution, whereby feeding can only occur if certain species of bacteria or archaea are present together.

When these super-performing communities are inoculated into a mixture, co-selection then favours their dominance, which, usefully, boosts production of the mixture as a whole.

In terms of biotechnology these findings point to a simple trick: inoculate communities from many different sources, and the best performing addition will dominate anyway - boosting production of anaerobic digestion as a whole.

Considering the amount of industries that rely on microbial communities, many of them focussed on improving resource efficiency, these findings could prove very handy indeed.

And, maybe, one day, armed with this knowledge, we can inoculate the stomachs of cows with microbes that produce something other than methane (or a little bit less of it), and do a little bit of good for the future of the planet.

Article author

Peter Bickerton

Scientific Communications Officer (Part time)