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Mapping microbial populations in grazing cattle – Lindsey Perry

My original plan after graduating with a degree in Equine Science was to work with horses, but as is common in life my plan took a U-turn after an internship at the William H. Miner Agricultural Research Institute in the USA. This internship was part of my university work placement and after helping out with a few dairy research trials I knew Agricultural research was the only place to be. Agriculture has an immediate relevance to life that no other sector can offer.

Modern Agriculture faces one of the biggest challenges in recent times, how to feed an ever increasing population with an estimated 9 billion mouths to feed by 2050. Perhaps the most useful role for ruminant agriculture (raising sheep and cattle) is a return to using forages otherwise unsuitable for human consumption – converting them into meat and milk.

Much of the beef herd in northern Australia is extensively grazed on arid land that is classed as not receiving enough rainfall for other food production (such as growing crops). Like similar climate zones in South America and Africa, the northern Australian rangelands have a rainy season followed by a variable dry period. This creates a feast and famine cycle, which presents nutritional constraints for animal health and growth. Cattle have a large stomach made up of four compartments, the microbial populations present in the largest of these, known as the rumen, excrete powerful enzymes, which are responsible for the conversion of plant fibre into energy to produce meat and milk for human use.  Microbial fermentation is also indirectly responsible for methane production from livestock. Methane is a potent greenhouse gas that may contribute to climate change. Therefore, increasing our understanding of this complex micro system is important to help make decisions affecting the environment and animal health and productivity.

The aim of my project is to map the change in microbial populations as grazing cattle transition from wet season to dry season pasture. To fully explore this question we are utilising new wave DNA sequencing technologies and metagenomics to monitor the population change. This technology extracts microbial DNA in the rumen fluid we collect from the cattle. Then, computer software is used to determine the genetic sequence of each organism, resulting in thousands of sequences. The software crunches the data down to tell us what populations of microorganisms are present and in what proportions.

A secondary part of my project is to measure methane production between seasons, both in the field using laser technology, and in the lab using gas production systems. We incubate a little of the seasonal forage cut with some rumen fluid and measure the gas produced from different feeds. Ultimately, this project will provide information on the micro biotic populations in the cow’s rumen and monitor how these populations change when nutrition is poor during the dry period. In addition, we will measure methane production from the cattle between wet and dry seasons.

The metagenomics field is exceptionally dynamic at the moment. The technology for sequencing the genetic code present in each individual species, and the software to crunch all those sequences into useful information about types of organisms are developing at a rapid rate. It is exciting being part of it. We are only beginning to realise the complexity of the microbial system, and can only guess at the meaning of the interactions, but as we move forward molecular information will help inform practical strategies for animal nutrition, health and productivity. This research will help provide information from which to base strategic decisions about supplementation and pasture management in northern Australian beef communities in an effort to improve production and maintain animal health.

In addition, knowledge of the seasonal change in methane emissions will help Australia to fine tune our national greenhouse gas accounting system. There are opportunities both for research scientists (animal and environmental), R&D managers, biotechnologists, animal nutritionists and of course microbiologists in this field. There are also critical openings for farmers and managers in applying this kind of research to management strategy.

My PhD project spans some niche areas around extensive livestock management, microbiology and nutrition. In the future I am interested in working in development of sustainable rangeland livestock programs in developing countries, and furthering our understanding of the metagenomic microbial world. Research was, and still is, incredibly exciting to me. No day is the same, and every day is full of problems to solve!


About Lindsey

Lindsey Perry graduated from the University of Limerick, Ireland in 2008 with a Bachelor of Science in Equine science. After graduating she spent 18 months working in equine and dairy nutrition research in the USA and she arrived in Australia in 2011 with the aim of completing a PhD in ruminant nutrition and microbiology. Lindsey enrolled at the University of Queensland in 2012.