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PGgRc is a research consortium that aims to decrease total agricultural emissions of greenhouse gases by 10% per unit of output in 2013 relative to 2004. PGgRc has formed excellent links between the agriculture sector and GHG mitigation research.
What does maths have to do with methane? Quite a lot, it turns out, with a research project combining the disciplines of biology and mathematics—funded by the New Zealand Agricultural Greenhouse Gas Research Centre—set to boost scientific knowledge of rumen systems and how to mitigate greenhouse gases.
Yuancheng (James) Wang is graduating from Massey University this month with a PhD in mathematics. His multidisciplinary thesis saw him apply his mathematical knowledge to a topic that was entirely new to him: rumen microbiology.
“For my project I developed a mathematical model that describes the interactions between microbes in the rumen and their food source,” explains James. “My model was also able to take into account the impact of the rumen environment on those interactions, which existing models designed to estimate methane production did not consider.”
He says the results provided by his mathematical model were consistent with biological expectations, and the model could be expanded to include other factors influencing methane production, such as feeding level and frequency.
While James’ project focused on methane-producing microbes (methanogens), he says his model will be able to be used in conjunction with models describing other parts of the rumen system, which will provide the full picture of rumen function.
James says there are real benefits of applying mathematical modelling to biological systems. “Modelling means you can explore interactions that occur in the rumen system in ways you cannot do in experiments, and you can test your knowledge to uncover any gaps,” he says. “It’s also very cost-effective as it allows you to perform multiple experiments to understand what might happen in rumen systems, before designing and carrying out much more expensive animal trials.”
His PhD was supervised by Drs Peter Janssen and David Pacheco from AgResearch, who provided guidance on the how the rumen functions, along with Dr Tammy Lynch and Associate Professor Bruce Van Brunt from Massey’s Institute of Fundamental Science who supervised the mathematical component of the research.
James says he never thought his background in mathematics would see him end up working in agricultural science.
“I’ve always been aware that mathematics can be applied to virtually any discipline, and it just happened that I got into this one which I’ve found extremely interesting,” he says. “I’ve really enjoyed learning about greenhouse gases—at the moment it’s a very critical topic for New Zealand, so it’s been great to be at the forefront of this science to help boost the knowledge a little.”
His work is currently being prepared for publication in a science journal in the near future.
James has moved back to Qingdao, China, to look for work and to be closer to family after more than a decade away from home. “I’ll certainly miss New Zealand though, and will always be grateful for the support provided by the NZAGRC for my project.”
A major force behind many ground breaking advances in animal genetics is being recognised with a Science NZ Lifetime Achievement award this month.
John McEwan, a principal scientist at AgResearch Invermay, has devoted his career to genomic research with the aim of improving the genetic merit of livestock—particularly sheep—in New Zealand and around the world. Up until recently he was also co-leading the low methane emitting sheep breeding programme, jointly funded by the New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC) and the Pastoral Greenhouse Gas Research Consortium (PGgRc).
The youngest son of Southland Romney stud breeders, John decided to pursue a career in science instead of following in the family farming footsteps, and studied chemistry and biochemistry at Otago University.
He describes the early part of his career as “chasing sheep around paddocks to estimate their breeding value”, and for a year was a secondary school teacher in Invercargill. For the past 20 years John’s work has been more laboratory-based, focusing on genetics.
In 1999 John was one of a number of people who helped establish Sheep Improvement Limited (SIL; now part of Beef+Lamb NZ Genetics). He designed its computational framework and with Sheryl Anne Newman wrote much of the genetic evaluation code that helped the organisation get off the ground.
“I’d say SIL brought some significant financial benefits to the sheep farming industry,” says John. “There’s pretty good evidence that the changes that were implemented as a result have made a major impact on the animals that we now have in New Zealand.”
Some of his other achievements include managing New Zealand’s contribution to sequencing the cattle genome, and being part of a similar international effort to map the sheep genome. John and other AgResearch staff were co-authors on a series of 3 papers published in the prestigious international journal, Science, about this work.
The sequencing of sheep and subsequent work helped identify more than 30 million DNA variants and has led to some very valuable spin-offs for New Zealand agriculture, including the development of a number of commercial tests that are now available to the sheep industry.
“We were able to create low, medium and high density ovine SNP (single nucleotide polymorphism) chips, which have allowed us to quickly and cheaply screen sheep for useful genes,” explains John.
SNP chips have helped transform the future selection and breeding of sheep. “This technology is useful for identifying hard-to-measure traits that aren’t normally recorded until later in the animal’s life, such as longevity, disease resistance, meat quality and reproduction.” The low and medium density SNP chips are predicted to generate around $200 million for the New Zealand sheep farming industry over the next decade.
Similar genomic tools, but using DNA sequencing, developed more recently by the group are now commercially available for breeders and researchers in over 50 species and are being used in a range of other production industries including deer, goat and salmon as well as ryegrass and clover seed production.
John’s expertise on genomic selection also proved very useful for the NZAGRC-PGgRc low methane sheep breeding programme. His research involves determining whether the amount of methane emitted by individual animals can be changed through selective breeding, and what impact that would have on other productive traits.
“It had been known for some time that some individual animals produced more or less methane than others, so the first question was, can we breed for this? And the other was, how did they produce more or less methane?” says John. “We were able to establish that low methane production is a heritable and repeatable trait, and that the low emitting sheep have similar or higher productivity, have rumens that are around 20 percent smaller, have different rumen microbial communities and have different volatile fatty acid (VFA) concentrations in the rumen.”
John is currently investigating ways to make the rumen microbial sequencing process cheaper.
“Historically it would probably cost a couple of hundred dollars per animal, which is never going to be practical, so over the past six months our group has been coming up with ways to modify our low cost genotyping by sequencing process so that it can be used on the bacteria in rumen,” explains John. “It’s looking pretty promising—it’ll hopefully help us get a better handle on exactly how the animals produce less methane, which will make the selection process a lot easier than putting animals in a plastic box to measure their emissions.”
John says he feels very lucky that just about everything he’s worked on in his career has ended up being implemented in industry.
“You start to get a feel for what works and what doesn’t work. You might have a fancy, glitzy idea but you’ve actually got to convince people that it works. It might be something that’s good for the industry as a whole but farmers have got to be convinced of the benefits—they’ve got to know that they’ll get paid for it. Seeing money in their pockets is a great motivator, so that is our challenge as scientists—especially for solutions to low methane emissions.”
He says the reality of working in breeding is that it’s quite slow.
“You’ve got to be pretty cautious and pretty sure that you’re going in the right direction, because you don’t want to be 10 or 15 years down the track and realise it hasn’t worked out how you wanted it to.”
The award, which will be presented to John at a ceremony on November 9 at Te Papa in Wellington, is part of a Science NZ celebration marking 25 years of Crown Research Institutes (CRIs) in New Zealand. He’ll be one of three award recipients from AgResearch, and says it’s an honour.
“It’s pretty nice to get that recognition. I look at it as acknowledgement of the whole team of people behind this work, and the impact it’s had on industry,” he says. “The award’s probably just got my name on it because I’ve been around longer than everybody else!”
This publication provides an overview of how we may be able to use compounds that suppress an animal's methanogen population effectively without causing unwanted side effects in their health, welfare or production. It covers some of the commonly asked questions regarding sources of methane, enteric methane formation, the role of methanogens, what the NZAGRC and PGgRc research programme on methane inhibitors is investigating and, importantly, the timeline for an inhibitor's commercial availability.
Kelly WJ, Li D, Lambie SC, Jeyanathan J, Cox F, Li Y, Attwood GT, Altermann E, Leahy SC. 2016. Complete genome sequence of methanogenic archaeon ISO4-G1, a member of the Methanomassiliicoccales, isolated from a sheep rumen. Genome Announc 4(2):e00221-16. doi:10.1128/genomeA.00221-16.
Methanogenic archaeon ISO4-G1 is a methylotrophic methanogen belonging to the order Methanomassiliicoccales that was isolated from a sheep rumen. Its genome has been sequenced to provide information on the genetic diversity of rumen methanogens in order to develop technologies for ruminant methane mitigation.
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Kelly WJ, Li D, Lambie SC, Cox F, Attwood GT, Altermann E, Leahy SC. 2016. Draft genome sequence of the rumen methanogen Methanobrevibacter olleyae YLM1. Genome Announc 4(2):e00232-16. doi:10.1128/genomeA.00232-16.
Methanobrevibacter olleyae YLM1 is a hydrogenotrophic methanogen, isolated from the rumen of a lamb. Its genome has been sequenced to provide information on the genomic diversity of rumen methanogens and support the development of approaches to reduce methane formation by ruminants.
Kelly, W. J., G. Henderson, et al. (2016). "The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen." Standards in Genomic Sciences 11(1): 26.
Acetogens are a specialized group of anaerobic bacteria able to produce acetate from CO2 and H2 via the Wood–Ljungdahl pathway. In some gut environments acetogens can compete with methanogens for H2, and as a result rumen acetogens are of interest in the development of microbial approaches for methane mitigation. The acetogen Eubacterium limosum SA11 was isolated from the rumen of a New Zealand sheep and its genome has been sequenced to examine its potential application in methane mitigation strategies, particularly in situations where hydrogenotrophic methanogens are inhibited resulting in increased H2 levels in the rumen. The 4.15 Mb chromosome of SA11 has an average G + C content of 47 %, and encodes 3805 protein-coding genes. There is a single prophage inserted in the chromosome, and several other gene clusters appear to have been acquired by horizontal transfer. These include genes for cell wall glycopolymers, a type VII secretion system, cell surface proteins and chemotaxis. SA11 is able to use a variety of organic substrates in addition to H2/CO2, with acetate and butyrate as the principal fermentation end-products, and genes involved in these metabolic pathways have been identified. An unusual feature is the presence of 39 genes encoding trimethylamine methyltransferase family proteins, more than any other bacterial genome. Overall, SA11 is a metabolically versatile organism, but its ability to grow on such a wide range of substrates suggests it may not be a suitable candidate to take the place of hydrogen-utilizing methanogens in the rumen.
Sun Xuezhao, Pacheco David, Luo Dongwen (2016) Forage brassica: a feed to mitigate enteric methane emissions?. Animal Production Science 56, 451-456.
A series of experiments was conducted in New Zealand to evaluate the potential of forage brassicas for mitigation of enteric methane emissions. Experiments involved sheep and cattle fed winter and summer varieties of brassica forage crops. In the sheep-feeding trials, it was demonstrated that several species of forage brassicas can result, to a varying degree, in a lower methane yield (g methane per kg of DM intake) than does ryegrass pasture. Pure forage rape fed as a winter crop resulted in 37% lower methane yields than did pasture. Increasing the proportion of forage rape in the diet of sheep fed pasture linearly decreased methane yield. Feeding forage rape to cattle also resulted in 44% lower methane yield than did feeding pasture. In conclusion, reductions in methane emission are achievable by feeding forage brassicas, especially winter forage rape, to sheep and cattle. Investigating other aspects of these crops is warranted to establish their value as a viable mitigation tool in pastoral farming.
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Kittelmann, S., M. R. Kirk, et al. (2015). "Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen." Applied and Environmental Microbiology 81(21): 7470-7483.
Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.
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Vetharaniam, I., R. E. Vibart, et al. (2015). "A modified version of the Molly rumen model to quantify methane emissions from sheep1." Journal of Animal Science 93(7): 3551-3563.
We modified the rumen submodel of the Molly dairy cow model to simulate the rumen of a sheep and predict its methane emissions. We introduced a rumen hydrogen (H2) pool as a dynamic variable, which (together with the microbial pool in Molly) was used to predict methane production, to facilitate future consideration of thermodynamic control of methanogenesis. The new model corrected a misspecification of the equation of microbial H2 utilization in Molly95, which could potentially give rise to unrealistic predictions under conditions of low intake rates. The new model included a function to correct biases in the estimation of net H2 production based on the default stoichiometric relationships in Molly95, with this function specified in terms of level of intake. Model parameters for H2 and methane production were fitted to experimental data that included fresh temperate forages offered to sheep at a wide range of intake levels and then tested against independent data. The new model provided reasonable estimates relative to the calibration data set, but a different parameterization was needed to improve its predicted ability relative to the validation data set. Our results indicate that, although feedback inhibition on H2 production and methanogen activity increased with feeding level, other feedback effects that vary with diet composition need to be considered in future work on modeling rumen digestion in Molly.
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Pacheco, D., G. Waghorn, et al. (2014). "Decreasing methane emissions from ruminants grazing forages: a fit with productive and financial realities?" Animal Production Science 54(9): 1141-1154.
Ruminants contribute to human food supply and also anthropogenic greenhouse gas (GHG) emissions. An understanding of production systems and information on animal populations has enabled global inventories of ruminant GHG emissions (methane and nitrous oxide), and dietary strategies are being developed to reduce GHG emissions from ruminants. Mitigation strategies need to consider the management/feeding systems used to ensure that these strategies will be readily accepted and adopted by farmers. Housed systems allow diets to be formulated in ways that may reduce GHG production, but the challenge is much greater for systems where animals graze outdoors for long periods. A methane mitigation option in the form of fresh forage would be desirable in livestock production systems with high reliance on grazing. A brief summary of New Zealand research, carried out on fresh grasses, legumes, herbs and crops, suggest that we have an incomplete understanding of the feed characteristics that define a ‘high’ or a ‘low’ methane feed. The variation in methane emissions measured between feeds, individual animals and experiment is large, even in controlled conditions, and the dynamic nature of sward-animal interactions will only exacerbate this variation, creating challenges beyond the identification of mitigants. Furthermore, implementation of knowledge gained from controlled studies requires validation under grazing systems to identify any trade-offs between methane reduction and animal productivity or emission of other pollutants. Therefore, investment and research should be targeted at mitigation options that can and will be adopted on-farm, and the characteristics of temperate grasslands farming suggest that these options may differ from those for intensive (high input/output) or extensive (low input/output) systems.
Pastoral Greenhouse Gas Research Consortium release their 5 year science progress report for 2007-2012: Developing solutions to reduce New Zealand agricultural emissions.
To download the full document visit www.pggrc.co.nz
Morgavi, D., Kelly, W., Janssen, P., & Attwood, G. (2013). Rumen microbial (meta)genomics and its application to ruminant production. Animal, 7(S1), 184-201
Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.
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G.T. Attwood, E. Altermann, W.J. Kelly, S.C. Leahy, L. Zhang, M. Morrison, Exploring rumen methanogen genomes to identify targets for methane mitigation strategies, Animal Feed Science and Technology, Volume 166, 2011, Pages 65-75, ISSN 0377-8401,
Methane emissions from ruminant livestock is generated by the action of methanogenic archaea, mainly in the rumen. A variety of methanogen genera are responsible for CH4 production, including a large group that lacks cultivated representatives. To be generally effective, technologies for reducing ruminant CH4 emissions must target all rumen methanogens to prevent any unaffected methanogen from expanding to occupy the vacated niche. Interventions must also be specific for methanogens so that other rumen microbes can continue normal digestive functions. Thus a detailed knowledge of the diversity and physiology of rumen methanogens is required to define conserved features that can be targeted for methanogen inhibition. Genome sequencing projects are underway in New Zealand and Australia on several ruminal methanogen groups, including representatives of the genera Methanobrevibacter, Methanobacterium, Methanosphaera, Methanosarcina, and the uncultured group, Rumen Cluster C. The completed Methanobrevibacter ruminantium genome and draft sequences from other rumen methanogen species are beginning to allow identification of underlying cellular processes that define these organisms, and is leading to a better understanding of their lifestyles within the rumen. Although the research is mainly at the explorative stage, two types of opportunities for inhibiting methanogens are emerging, being inactivation of conserved methanogen enzymes by screening for, or designing, small inhibitors via a chemogenomics approach, and identifying surface proteins shared among rumen methanogens that can be used as antigens in an anti-methanogen vaccine. Many of the conserved enzyme targets are involved in energy generation via the methanogenesis pathway, while the majority of the conserved surface protein targets are of unknown function. An understanding of the expression and accessibility of these targets within methanogen cells and/or microbial biofilms under ruminal conditions will be required for their development as CH4 production mitigations.
This paper is part of the special issue entitled: Greenhouse Gases in Animal Agriculture – Finding a Balance Between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors: K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson.
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Bryce M. Buddle, Michel Denis, Graeme T. Attwood, Eric Altermann, Peter H. Janssen, Ron S. Ronimus, Cesar S. Pinares-Patiño, Stefan Muetzel, D. Neil Wedlock, Strategies to reduce methane emissions from farmed ruminants grazing on pasture, The Veterinary Journal, Volume 188, Issue 1, 2011, Pages 11-17, ISSN 1090-0233
Methane emissions from livestock are a significant contributor to greenhouse gas emissions and have become a focus of research activities, especially in countries where agriculture is a major economic sector. Understanding the complexity of the rumen microbiota, including methane-producing Archaea, is in its infancy. There are currently no robust, reproducible and economically viable methods for reducing methane emissions from ruminants grazing on pasture and novel innovative strategies to diminish methane output from livestock are required. In this review, current approaches towards mitigation of methane in pastoral farming are summarised. Research strategies based on vaccination, enzyme inhibitors, phage, homoacetogens, defaunation, feed supplements, and animal selection are reviewed. Many approaches are currently being investigated, and it is likely that more than one strategy will be required to enable pastoral farming to lower its emissions of methane significantly. Different strategies may be suitable for different farming practices and systems
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