Science boost for Overseer farm management tool

The Coalition Government and the primary sector will work together to boost the science behind the valuable Overseer farm management tool, Agriculture Minister Damien O’Connor and Environment Minister David Parker announced in a Budget press statement.

Overseer is a tool used by a range of primary industries and regional councils to help measure nutrient use and greenhouse gas emissions.

“Well-used, it can assist farmers to minimise waste and maximise profits,” says Mr O’Connor.

The Budget includes an investment of $5 million of operating funding over the next four years to enhance it.

The extra funding for Overseer will enable:

• quicker adoption of environmentally friendly farm practices

• the inclusion of a wider range of land types and farming systems

• a more user-friendly interface.

“All farmers and growers want to keep their fertilisers on their paddocks and crops, and they want the best tools to manage their environmental responsibilities,” Mr O’Connor says.

Mr Parker says the extra funding in the Budget opens up opportunities for farmers to trial new technologies, techniques and tools that would otherwise be too risky or expensive to try.

“We need practical, science-backed tools to achieve this Government’s goals to improve land use, achieve a net-zero-emissions economy by 2050, and help clean up our rivers so our kids can swim in them without getting crook.”

The Ministry for Primary Industries, AgResearch and the Fertiliser Association of New Zealand each hold one-third stakes in the Overseer intellectual property.



Dr Kumar and the secrets of reducing methane emissions from sheep

Dr Sandeep Kumar has been looking at one of the world’s most pressing issues –  greenhouses gases – and one bacterium that might hold the key to reducing emissions.

Dr Kumar, who graduated at a Massey University ceremony in the Manawatū yesterday, arrived in New Zealand in the summer of 2011 as a LEARN scholar from India to work in AgResearch’s rumen microbiology team.

His journey from India to Palmerston North is told on the Massey University website (HERE).

He grew up in a village in the eastern part of India where he gained his initial understanding of agriculture and its impact on society. His eagerness to learn more about it brought him to Palmerston North.

He returned briefly to India, then came back to start a PhD in 2013 thanks to funding from the New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC) and a Walsh fellowship from Teagasc (Ireland).

For this PhD, Dr Kumar investigated sheep that naturally produce less methane, and the key bacteria associated with these sheep.

“Methane is a by-product of feed digestion that contributes about one-third of New Zealand’s anthropogenic greenhouse gases,” Dr Kumar says.

“In the rumen [the first stomach of a ruminant], nearly all bacteria exist by fermenting the plant material ingested by the animal. There is a rather large bacterium found to be abundant in the rumen of naturally low-methane emitting sheep called Quinella, I wanted to understand why large populations of Quinella are associated with the rumens of sheep producing less methane.

“The problem is that the few published attempts that define its metabolism were contradictory, so we needed to study it further to work out its role in low methane emissions.”

Quinella, a bacterium first seen in sheep rumen contents in 1913, cannot be cultured. Dr Kumar found a way to generate preparations of rumen contents highly enriched with Quinella by exploiting the physical size of this bacterium.

By analysing four Quinella genomes assembled from DNA extracted from rumen contents, he found that Quinella has all the genes needed to produce propionate and acetate as well as lactate.

Results showed it produced little or no hydrogen, a major precursor for methane, which explains why greater abundances of these bacteria leads to lower methane emissions.

Additionally, Dr Kumar found there were several species of the genus Quinella besides Quinella ovalis. 

“As a microbiologist it is quite challenging to work with unculturable bacteria but at the same time it is rewarding as well when you successfully answer the question,” he says.

” In my PhD that is what exactly happened, as even after an unsuccessful isolation attempt, with the help of molecular biology and bioinformatics tools and software, I was able to construct the physiology of Quinella.”

Dr Kumar conducted much of his research at the AgResearch Grasslands campus, supervised by Dr Peter Janssen (AgResearch), Dr Mark Patchett (Massey University) and Dr Sinead Waters (Teagasc).

Other interesting aspects of its metabolism were also found during Dr Kumar’s work, but those will be for others to investigate. He has now accepted a post-doctoral scientist position in AgResearch, where he will be applying his microbiological skills to study bacterial endophytes.

Source: Massey University

Applying maths to methane to learn more about rumen systems and how to reduce emissions

A research project combining the disciplines of biology and mathematics—funded by the New Zealand Agricultural Greenhouse Gas Research Centre—is set to boost scientific knowledge of methane, rumen systems and the mitigation of 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.

He developed a mathematical model that describes the interactions between microbes in the rumen and their food source.

“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 being prepared for publication in a science journal.

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.

Source: New Zealand Agricultural Greenhouse Gas Research Centre

Groundbreaking trial seeks links to GHG emissions

A ground-breaking trial at Landcorp’s Waikite farm will test the link between the administration of long-acting drench products in sheep, and greenhouse gas emissions.

Landcorp is working with staff from AgResearch’s Animal Health, Rumen Microbiology, Plant Functional Biology and Animal Genomics teams, along with a team from Landcare Research, to conduct the trial, which has financial support from AgResearch, Beef+Lamb NZ and the New Zealand Agricultural Greenhouse Gas Research Institute.

“The link with GHG emissions is just one of several questions the trial will hopefully answer”, says AgResearch principal scientist Dr Dave Leathwick.

“We have multiple objectives based around whether the administration of these long-acting drench products to sheep has unforeseen side-effects.

“Some of the active ingredients in these products have fungicidal and/or antibiotic activity. The trial will look for possible changes in the composition of the rumen microbiome and the production of greenhouse gases as a result of treating ewes with these products”.

In addition, all 300 ewes in the trial will be used to test for a possible relationship between sheep genotype, rumen microbiome and production characteristics.

“We will also investigate possible cases of ill thrift (low body condition score) in the ewes, and particularly the role that parasites play in this,” Dr Leathwick says

Landcorp’s Waikite Farm Manager, Peter Strawbridge, says his staff found the experience of working with a big team of scientists and technicians an interesting diversion from everyday farm work.

“We aren’t scientists, but working with the AgResearch team was a fascinating insight into the role science plays in our sector,” Mr Strawbridge says.

The Waikite team are no strangers to research work, with previous AgResearch collaboration on anthelmintic drenches over the years. Chris Miller is one of the AgResearch team who is back on Waikite, 30 years after starting Grass Grub research on the farm.

The trial will continue to collect data from the 300 ewes, and their lambs, until weaning in December 2018.

Waikite Station is a 1578 hectatre property south of Rotorua, which is busy enough at the best of times. Peter Strawbridge the Farm Manager and the team are a Genetic Breeding Partner for Focus Genetics, breeding and growing Simmental, FocusPrime and Texel sires for Pāmu and the industry.

The team at Waikite produce over 50 of Australasia’s top ranking Simmental bulls every year and over 300 rams. This year’s ram sires are 85kg at 8 months old and the 18 month old bulls are already over 700kg and getting ready for the bull auction on May 18th.

Demand for the stud stock is growing, so Waikite is increasing the size of both the sheep and cattle studs this year, which means more mobs and more work.

Source: Landcorp

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 to New Zealand where, , 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 KandleriaQuinella 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 received valuable mentorship from several 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 under embargo while papers detailing some of his findings are being finalised and will be published in scientific journals.

He would 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.”

Source: New Zealand Agricultural Greenhouse Gas Research Centre

Study aims to to find if drinking a2 Milk™ helps lactose-intolerant people

The Liggins Institute needs lactose-intolerant Aucklanders for a study that researchers hope will make them better able to tolerate dairy.

The study participants will consume conventional cheese and milk for two weeks and a2 Milk cheese and milk for two weeks (with a recovery break between), to see if benefits of a2 Milk identified in an earlier study by the same researchers persist over a longer period.

That 2017 study, a collaboration between the Liggins Institute and AgResearch, found that a2 Milk prevents some symptoms of lactose intolerance and eases others, even though it contains the same amount of lactose as conventional milk.

Researchers showed a2 Milk was at least as effective as lactose-free milk at preventing or reducing some symptoms including nausea, stomach pain and bloating, but didn’t improve ratings of “overall digestive comfort”. It also produced the same levels of flatulence and gastric reflux as regular milk.

Globally, about 70 per cent of adults consider themselves lactose-intolerant and experience bloating, nausea or other unpleasant symptoms after consuming dairy products.

The study lead, Dr Amber Milan, a research fellow at the Liggins Institute, says:

“We already know that lactose-intolerant people can sometimes build up their tolerance to lactose over time by including lactose or milk in their diet.

“If we can help that process along, hopefully we can improve digestion of lactose after just a few weeks. We’re hopeful that consuming dairy with only the A2 protein will reduce symptoms by avoiding inflammation that might make intolerance worse.”

Regular milk contains both the A1 and A2 types of beta-casein protein, a major milk protein, while a2 Milkcomes from cows that naturally produce only the A2 type.

AgResearch scientist Matthew Barnett explains:

“There is evidence from animal studies that a breakdown product of the A1 protein causes inflammation in the small intestine, which could make lactose intolerance symptoms worse.”

The new study, dubbed Los aMiGoS, has been designed to minimise uncomfortable symptoms by limiting daily lactose to the equivalent of two glasses of milk – an amount that is usually tolerable for people with lactose intolerance.

To spare participants unnecessary discomfort, researchers will top up their protein consumption with daily servings of cheese, which is nearly lactose-free. Cheese from a2 Milk has been especially created for the study. Neither the participants nor researchers will know which kind of dairy they’re consuming for each fortnight stretch.

Participants need to be aged 20-40, believe they are lactose-intolerant, and be willing to give this study a go. People interested in joining the study can find out more here.

The study is funded through High Value Nutrition to AgResearch and in partnership with the a2 Milk™ Company.

Source: Liggins Institute


Professor Rich McDowell gives thoughts on new land report

AgResearch has posted comments from Professor Rich McDowell, its principal scientist and Chief Scientist for the Our Land and Water national science challenge, on the just-released report on the state of land in New Zealand.

The report can be read HERE.

Professor McDowell writes:

While this report does provide a snapshot of the state of the land as far as impacts, it is important to note that it does not provide insights into the trends in relation to phosphorus in the soil, and macroporosity of the soil – and how land use, and intensity of that use, contributes. Phosphorus in the soil is one measure, but there are other variables at play such as compaction of the soil, that will dictate whether there is phosphorus run-off into waterways to do damage.

What we do know is that the data for water quality (in regard to phosphorus) and sediment concentrations indicate that far more sites are showing improvements now (2004-2013) than before (1994-2003). This is despite changes in land use, land use intensity and indications that phosphorus under dairying is enriched, and macroporosity of the soil is impaired. These improvements may be due to greater awareness, farmers being more proactive or policy changes. Efforts include the isolation of critical source areas that contribute most phosphorus and sediment loss from farms or catchments, and targeting critical source areas with measures to mitigate these losses.

The question is always whether these efforts are enough to meet community aspirations of water quality. This is why the Our Land and Water National Science Challenge (hosted by AgResearch) is supporting work examining land use suitability, and providing indicators on what a parcel of land can produce, the potential of these land parcels to lose contaminants, and the effect of these contaminants on water according to a water quality objective. This work will also be expanded to examine objectives for soil.

You can read more about work in regard to land use suitability, and sources and flows of contaminants, at pages 17 and 18 HERE. 

Source: AgResearch