Researchers from California have discovered a possible mechanism for much of the methane blamed on cows and goats
Goats are known to have a highly diverse community of microbes in their gut and can break down the toughest of plants.
Understanding this unique microbiome could lead to the development of new biotechnologies to extract sugar and nutrients from plants and produce sustainable products such as fuels, commodity chemicals, and other materials.
While studying the goat’s gut, scientists at the University of California, Santa Barbara, have documented more than 700 previously unknown microbial genomes and thousands of new enzymes as well as a possible mechanism for much of the methane blamed on cows and goats.
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Michelle O’Malley, professor of chemical engineering at the university’s College of Engineering, said the aim of the study was to learn about the microbes that do the difficult job of breaking down fibres.
Anaerobic fungi constitute just a tiny fraction of the bacteria-rich microbe community in a goat’s gut yet they do the heavy lifting when it comes to breaking down plant biomass. They are able to physically penetrate plant cell walls, exposing surfaces for their enzymes to act on.
“(Despite their low number), they produce the lion’s share of the biomass-degrading enzymes that the community relies on to function,” said O’Malley.
At first it might seem that the fungi are technically non-essential since there are anaerobic bacteria in the gut that do the same thing and produce powerful enzymes.
“However, we have uncovered some evidence that the fungal population produces unique enzyme complexes that aid in their ability to deconstruct plant matter,” she said. “Also, they likely have unique enzymes that make it possible for them to break up lignin, which the gut bacteria cannot do.”
Anaerobic fungi are also hard to culture for laboratory study, which is likely why many science studies have overlooked their microbial contribution.
“Nobody had really looked at the effects of these rare members,” she said.
Helping with the research was Elway, a San Clemente Island goat and resident at the Santa Barbara Zoo. His fecal contributions consisted of four types of biomass (alfalfa, bagasse, reed canarygrass and xylan found in the cell walls of plants) and two antibiotic treatments. The material was used for over 400 parallel enrichment experiments to study biomass degrading.
The researchers extracted plant-degrading microbes using different biomass samples. They also altered the composition of some of the populations by using antibiotics to stop bacteria growth and allow rare microbes like fungi to dominate.
“We reconstructed hundreds of genomes of goat gut microbes from tiny pieces, and then scanned those genomes for metabolic pathways and enzymes that would be helpful in the community’s function,” she said. “It’s important to note that these are presumed functions only. We would need RNA sequencing and/or proteomic data (protein studies) to verify that these jobs are in fact true.”
They sequenced all the cultures and put the fragmented DNA back together again to reconstruct high-quality genomes. That gave them a clearer picture of what exactly was there.
“Then we scanned these genomes for enzymes and pathways that gave us a clue as to what each microbe was doing in the microbiome.”
During the sequencing, the team discovered more than 700 new microbial genomes unique to the species level. O’Malley said it was the first time they could see them in action within their community.
Alongside the increased rate of plant degradation came an increase in methane production.
A news release stated while both gut bacteria and gut fungi form partnerships with methanogens (micro-organisms that reduce carbon to methane), fungi are more efficient at it.
“Our data suggest that the fungi are more efficient in converting sugar-based carbon to methane,” said O’Malley. “By eliminating or reducing their population in ruminant herbivores, that might be one route to mitigating methane release.”
The insights from the research are expected to help direct further studies to develop technologies using microbes to make industrially important chemicals from cellulose, the most abundant organic compound of green plants on the planet.
O’Malley and her team are continuing to understand the roles and interactions between these members of ruminant communities with a vision for a future where designed microbial communities can create value-added chemicals.
“For example, by identifying the microbes that work most effectively together to break down lignocellulose, we can use those microbes (or microbes like them) in large-scale bioreactors to break down plant and agricultural waste into value-added products,” she said.
However, she added it is difficult to mimic the goat gut microbiome synthetically because a better picture is needed of the dynamics of the microbes in culture together.
The study was published recently in the journal Nature Microbiology.
