Getting to the bottom of a beneficial bacterium
Growing up in a remote village in India gave Dr Sandeep Kumar a first-hand understanding of the significant impact that farming can have on a society. Even the small-scale farms of his tiny hometown, where families might each have one or two cows in their backyard, made a big impression on the young Sandeep and fostered a desire to learn more about the very building blocks of agriculture.
That fascination led Sandeep all the way to New Zealand, and with the help of the New Zealand Agricultural Greenhouse Gas Research Centre, he is graduating this month from Massey University with a PhD on the physiology of rumen bacteria associated with low-methane emitting sheep.
After graduating with a Master’s degree in microbiology in India, Sandeep worked for the Indian Veterinary Research Institute as a rumen microbiologist. It was there he first made contact with a fellow rumen microbiologist on the other side of the world: AgResearch’s Dr Peter Janssen, who is the Principal Investigator of the jointly-funded PGgRc-NZAGRC methane mitigation programme.
“Like India, New Zealand also places a lot of value on agriculture, and I was quite fascinated by the dairy farming systems in New Zealand too, which are highly organised and very productive,” he says. “I had some conversations with Peter Janssen and we figured out that I could come to New Zealand on a LEARN (Livestock Emissions and Abatement Research Network) Fellowship, which I was lucky enough to do in 2011.”
Sandeep worked as a technician with Dr Janssen and Dr Gemma Henderson at AgResearch for six months, then returned to India for a year. However, he felt he had unfinished business in New Zealand, and came back to AgResearch to study what’s known in rumen microbiology circles as an historically iconic rumen bacteria, Quinella ovalis.
Along with Sharpea and Kandleria, Quinella ovalis has been found to be abundant in low-methane emitting sheep, and Sandeep wanted to understand why.
“This bacterium was first identified in 1913, more than a century ago, but it had never been cultured in the lab or studied in depth. In fact, the only two papers that had previously been written about how Quinella works appeared to contradict each other,” he says.
Sandeep received a Walsh fellowship from Teagasc (Ireland), along with research funding from the NZAGRC, which allowed him to enrol at Massey University to do his PhD. He was based mainly at AgResearch’s Grasslands campus in Palmerston North, and his research was supervised by Dr Janssen, Dr Mark Patchett (Massey) and Dr Sinead Waters (Teagasc). He also received valuable mentorship from a number of other current and former AgResearch scientists.
Because Quinella could not be cultured, Sandeep worked on developing different ways to analyse its metabolism to gain a better understanding of why it is more abundant in sheep that produce less methane and how it might be cultured. He worked out how to concentrate cells of Quinella from rumen contents and extracted their DNA. He discovered there were multiple Quinella species—he sequenced the genomes of four different species. He then analysed the proteins encoded by those genomes, and the key enzymes involved in the metabolic processes of this bacterium.
“This was the first time anyone had studied the physiology of Quinella,” says Sandeep. “Reconstructing its metabolic pathways showed that it creates a range of different products during the fermentation process: propionate, acetate and lactate. These products appeared in both of the previous studies, which shows they weren’t contradictory after all but actually demonstrated the different pathways that Quinella has.”
Sandeep’s research also showed Quinella either produces no hydrogen or much less hydrogen (which is the main precursor of methane in the rumen) than other bacteria.
“I think my work will be helpful for any future research in low-methane emitting animals, especially for things like breeding programmes, as well as a number of other research areas that the NZAGRC is supporting.”
Sandeep’s PhD thesis is currently under embargo while papers detailing some of his findings are being finalised and will be published in scientific journals.
He would one day like to take his knowledge back to India, but for now has accepted a position with AgResearch’s forage science group. “This will allow me to research the plant part of the digestive process, which is eaten by the animal and which ultimately contributes towards methane emissions,” Sandeep says.
“AgResearch are really among the world leaders in the field of rumen microbiology—the work they’re doing and the international recognition they’re receiving is amazing, so it’s been a real privilege to work with Peter Janssen and the other scientists there.”
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