NZ-led rumen microbial genome work published in prestigious journal

A global scientific project led by New Zealand researchers, which has generated a reference set of genome sequences of microbes found in the stomachs of sheep and cattle, has been published in the respected international scientific journal Nature Biotechnology.

The project, called the Hungate1000, was led by former AgResearch scientist Dr Bill Kelly, and AgResearch scientist Dr Sinead Leahy. The pair brought together nearly 60 scientists from 14 research organisations across nine countries, who collaborated to generate a reference catalogue of 501 rumen microbial genomes—before Hungate1000, just 15 rumen microbial genomes were available to the scientific community.

Dr Kelly says the project was named after Bob Hungate, an American scientist who trained the first generation of New Zealand rumen microbiologists in the 1960s and 1970s.

“Bob Hungate developed the pioneering technique of growing anaerobic bacteria—that technique of culturing the microbes that then have their genomes sequenced has been the cornerstone of our project.”

Dr Kelly says the project gives a new understanding of what exactly is taking place inside a rumen.

“Hungate1000 means we can now start to reveal the intricacies of how the rumen microbial community functions, and provides a roadmap for where to take the science next,” he says.

“This data can be translated into interventions that are useful, such as identifying targets for vaccines and inhibitors to reduce methane emissions and improve productivity, among other things.”

Dr Leahy, who is currently seconded to the New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC) as its International Capability and Training Coordinator, says the project represents a major scientific advancement in the field of rumen microbiology, an area of science that up until recently had largely been unexplored.

“These microbes in the stomachs of ruminants are crucially important—they convert grass and other dietary components into smaller compounds that the sheep or cow uses to make meat and milk,” she says. “The data we’ve made available with Hungate1000 will underpin the development of technologies to target these microbes and aid productivity or reduce greenhouse gas emissions—you need to know what you’re targeting to make a specific impact on the rumen microbiome environment.”

Dr Andy Reisinger, the NZAGRC’s Deputy Director (International), says Hungate1000 is central to the work that the NZAGRC is managing.

“Hungate1000 shows what a powerhouse the rumen is in converting digestible plant material to energy, and gives us a much better understanding of how we might be able to use science to influence that process,” he says. “This will help us find ways not only to enhance productivity but also to achieve emissions reductions and deliver solutions to farmers—such as inhibitors and vaccines—that don’t affect their bottom lines.”

The Hungate1000 data is available as a community resource on the United States Department of Energy Joint Genome Institute website.

“We had an open release policy, which meant the data was made available as soon as we generated it,” explains Dr Leahy. “That aligns with the GRA’s ethos of science for the greater good—Hungate1000 is about coming together to advance global knowledge.”

The Hungate1000 was funded by the New Zealand Government through the Ministry for Primary Industries in support of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases (GRA), which is administered by the NZAGRC. The genome sequencing and analysis component of the project was supported by the United States Department of Energy’s Joint Genome Institute (JGI), via its Community Science Program.

Dr Harry Clark, the Director of the NZAGRC who also co-chairs the GRA’s Livestock Research Group, says Hungate1000 would not have come about without the financial support of the New Zealand government.

“The investment by MPI to support good science delivers multiple benefits, not just to New Zealand but globally too,” he says. “This project shows the power of international collaboration—we’ve been able to bring scientists together from around the world to create this resource that can benefit all countries, and New Zealand can be proud that we made it happen.”

Dr Kelly says he and the rest of the Hungate1000 team are delighted to see their work published in Nature Biotechnology.

The kudos of getting something published in a high-impact journal like Nature Biotechnology highlights the value of this work to a global audience, he says.

Source: AgResearch


Myrtle rust found for first time in Manawatu

Myrtle rust has been detected in Manawatu for the first time, the Ministry for Primary Industries confirmed today.

The fungus was found on a young ramarama (Lophomyrtus) in a planted area off Victoria Esplanade in Palmerston North.

Myrtle rust response spokesperson Dr Catherine Duthie says operational activity will start immediately to try to contain the disease.

“Hopefully, we have found it in this region early, which would give us a chance of trying to eliminate it or, at least, slow down the spread there. We are swinging straight into action. The infected plant will be removed and securely disposed of and one of our 7 field surveillance teams will begin an intensive inspection of myrtle plants on all properties within a200-metree radius.

“It is disheartening that myrtle rust has been detected in another region, but it is consistent with the expected infection pattern.

“Residents can help, by checking the myrtle plants in their garden. At this time of year, the fungus is still in its sporulation, or spreading, stage. This means it is very visible. Without touching the plant, you can look on either side of the leaves and new shoots for any sign of a bright yellow, powdery eruption. Some leaves could also be buckled or twisted, or look diseased with dry pustules that are grey or brown. It’s really important not to touch the plants or brush against them, as this can disrupt the spores and speed up its spread.”

Suspected cases of myrtle rust can be reported to the biosecurity freephone number – 0800 80 99 66.

The ministry will investigate suspected cases, track and monitor its spread, and collect information to help understand the disease’s impact on New Zealand.

At 19 March, there has been a total of 409 properties affected by myrtle rust on mainland New Zealand: Northland (4 properties), Auckland (63), Waikato (33), Bay of Plenty (92), Taranaki (200), Manawatu (1) and Wellington (16). In the last couple of weeks, most detections have been in Taranaki and Auckland.

There have been no detections in the South Island to date, although north-western areas were identified in climate modelling of being at a high risk from spores carried on the wind from Australia.

Source: Ministry for Primary Industries

MPI reminds consumers of the risks when they drink raw milk

The Ministry for Primary Industries is reminding consumers to take care when drinking raw unpasteurised milk because raw milk is a high-risk food.

The ministry was aware of several recent recalls of raw milk,  the ministry’s director animal and animal products, Dr Paul Dansted, said.

It was important that consumers remember and understand the risks with drinking raw milk, which is milk that has not been pasteurised (heat treated) to kill harmful bacteria such as CampylobacterListeria and toxin-producing strains of E. coli (STECs) which  potentially are present in the milk.

In 2014, the ministry introduced rules which require farmers selling raw milk to meet food safety requirements.

But consumers still needed to take care when drinking raw milk, Dr Dansted said.

“Some people who drink raw milk may not always fully understand the risks and don’t realise that there is the possibility of getting sick from the harmful bacteria in the milk.

“Pregnant women, young children (particularly babies), the elderly, and people with weakened immune systems should not drink raw milk as they are at greatest risk of getting sick and the consequences for them can be more severe, and in some cases can lead to death,” says Dr Dansted.

“No matter how carefully the animals are milked, there is always a risk that harmful bacteria can get into the milk. There is no way of telling by taste, sight or smell if the milk you are drinking contains harmful bacteria, so we recommend that people heat their raw milk until just boiling (or to 70°C for one minute) before drinking it.”

Keeping raw milk refrigerated (4°C or less) also reduces the risk of any harmful bacteria in the milk growing to levels which make people sick when they drink it.

Consumers are advised to discard the milk if it has been left out of the fridge for two hours or more and drink it by its use-by date.

People who choose to drink raw milk should make sure they are getting their milk directly from the farmer and are only buying it for personal and household consumption, Dr Dansted said.

Source: Ministry for Primary Industries.

Annual bee colony survey finds losses comparatively low

Bee colony losses in New Zealand continue to be significantly lower than many other countries, according to the Ministry for Primary Industries’ third annual survey on bee colony losses.

Annual hive losses were reported at 9.84% overall.

Dr Michael Taylor, the ministry’s biosecurity surveillance and incursion investigation (aquatic and environment health) manager, says this loss rate is low, compared to international results, which consistently show rates well over 10%.

“Many of the pests and diseases that negatively impact beehives overseas are not present in New Zealand, and we have a robust biosecurity system to prevent them from coming into the country and deal with them if they do,” Dr Taylor said.

The ministry contracted Manaaki Whenua – Landcare Research to conduct the New Zealand Colony Loss Survey,  which looks at the state of New Zealand’s honey bee colonies and the challenges beekeepers face.

More than 2,060 beekeepers completed the 2017 survey, representing 30% of production colonies in New Zealand.

The reported rate of losses in this country has stayed relatively stable from 2016, when the survey recorded 9.78% of beehive losses but this was down from 2015, when the loss rate was 10.73%.

The leading reported causes of hive loss in 2017 included:

  • Queen problems (such as death, disappearance, or not laying eggs).
  • Suspected varroa mite.
  • Suspected starvation of bees (weather and other causes).
  • Wasps (killing bees, eat pupae and steal honey).

Losses to American foulbrood disease, natural disasters, Argentine ants, and theft were also contributing factors, but these were less commonly reported.

Dr Taylor says the Bee Colony Loss Survey provides baseline information for monitoring managed honey bee colony loss and survival over time.

He said the information from the survey was a valued resource for ongoing work the ministry undertakes with the beekeeping industry to promote good colony health and bee-keeping practice as well as the Bee Pathogen Programme, which addresses the prevalence of honey bee diseases and parasites already in New Zealand.

Find out more

Source: Ministry for Primary Industries



Government and industry unite on Mycoplasma bovis

Agriculture and Biosecurity Minister Damien O’Connor today had more to say about the Mycoplasma bovis outbreak response – and came up with costs.

These include the sums which private industry will chip in.

Funding of $85 million for operational and compensation costs for the outbreak response, beginning 1 July 2017 to the end of the current financial year, was approved by Cabinet today, Mr O’Connor said.

In December last year, $10 million was approved.

The Ministry for Primary Industries estimates that total operational costs of $35 million and compensation liabilities of $60 million will be required until a decision on whether or not to eradicate the disease is made.

Since Mycoplasma bovis was found in July last year, the ministry has spent $10 million on the operational response and $2.5 million on compensation claims.

Industry bodies DairyNZ, Beef + Lamb New Zealand and the Meat Industry Association have committed $11.2 million. towards operational costs.

“This is a sign of a healthy Government-industry relationship and allows us to continue to contain the disease to determine its full spread, keeping the option of eradication open until that decision is made in a few weeks,” says Mr O’Connor.

“This has been a particularly challenging time for everyone and in particular those caught up in this disease. The animal tracing to determine the spread is ongoing and poor uptake of NAIT, especially for farm-to-farm animal movements, has slowed this work considerably.

“I am heartened by the industry contribution as we work together to give ourselves the best possible shot of getting rid of this disease.”

The ministry’s work programme is driving to a decision on eradication being made in late March to early April, understanding the extent of the spread through the bulk milk testing and animal tracing is key to this, Mr O’Connor said.

A significant piece of work is under way to look at the technical feasibility of eradication and cost benefit of eradication versus long-term management. Either option will require additional funding.

Mr O’Connor has also asked officials to explore the feasibility and implications of making the North Island Mycoplasma bovis-free, because the large majority of infected properties are in the South Island.

There are currently 24 active infected properties (which are under movement restrictions). There have been 29 properties confirmed with infection since the response began but some have been amalgamated into one unit, or had restrictions lifted following depopulation and cleaning.

A total of 42 properties are under Restricted Place notices (includes the infected properties), 54 on Notice of Direction and 741 under surveillance. A total of 51 compensation claims have been received with 10 paid in part or in full.



Biosecurity Minister is further questioned about stink bugs from Japan

Damien O’Connor … committed to keeping  out the brown marmorated stink bug.

Biosecurity Minister Damien O’Connor was questioned in Parliament this week about assurances he had given  last week about stink bugs. He had said no vehicles were unloaded off ships carrying brown marmorated stink bugs from Japan recently.

But National’s Nathan Guy challenged him, saying around half the vehicles were unloaded from the Courageous Ace before loading was halted. Those cars, trucks, and buses sat on the wharf for several days before being reloaded back on to the vessel.

In reply, Mr O’Connor said he had been informed none had been unloaded.

“I will follow up on that.

“The important thing to know here — regardless of the actions that took place —is that we are absolutely committed to keeping out the brown marmorated stink bug, something that that member failed to do because he failed to resource the Ministry for Primary Industries (MPI) and their biosecurity responsibilities properly.”

Mr Guy wasn’t finished and called for the Minister to explain how he could say the biosecurity net is working well when, in November last year, “15 live stink bugs — nine of them female — went on a 1,000-kilometre road trip to Christchurch having already passed MPI’s inspection in Auckland?”

Mr O’Connor conceded this had happened but said the biosecurity system taken over by the Labour-New Zealand First Government “had huge holes in it”.

As those holes have been discovered “we have moved immediately to shut them down”.

Very few of the 1,200 import health standards that the previous Minister was responsible for had been reviewed and upgraded.

“That’s why we are having to move through every part of the biosecurity system to give security to those New Zealand producers in the country—because we desperately need them.”

Next, Mr Guy noted the Minister had said “We cannot afford to let … in [stink bugs] and we will shut down the pathways [whenever] we find them.” He asked how this could be reconciled with large construction equipment being left on the wharf for days prior to it being eventually fumigated.

Mr O’Connor replied:

“Once again, I can’t explain the protocols and systems left to us by the previous Government. But I can tell you that we’re working through every one of those, and every member of the biosecurity system in this country knows that they’ve got a new Government with a new focus on biosecurity; they don’t have the same lazy old lax one that they had in the past.”

Finally, Mr Guy asked if the Minister has requested new urgent funding for extra resources in Japan after stating that his ministry does not have enough people offshore to inspect every vehicle; if not, why not?

Mr O’Connor replied “we don’t have enough people to inspect every single car being loaded on to a ship, but I can tell you that the protocols around that will be upgraded and offer us security that was never there under the hundreds of thousands of cars that that member let into this country.”

Stink bug alert: a fourth bulk carrier is ordered to leave New Zealand

The Ministry for Primary Industries has directed a fourth bulk carrier from Japan to leave New Zealand waters following the discovery of brown marmorated stink bug aboard the vessel.

The Glovis Caravel was ordered to leave New Zealand yesterday evening after the crew reported finding nearly 600 stink bugs, 12 of them alive, while the vessel was anchored near Auckland.

“Even though the vessel was sealed, we assessed the risk was too high for it to remain in New Zealand waters. It will now have to be treated off shore before it can return,” says Steve Gilbert, MPI Border Clearance Services Director.

The ministry has increased its border inspection and verification of bulk carriers arriving from Japan following a recent jump in detections of brown marmorated stink bug.

“Some of the carriers arriving New Zealand require no further action, but where there is contamination we have the option of denying entry,” said Mr Gilbert.

“We firmly believe our actions to date have prevented stink bugs from getting past the New Zealand border and welcome the support we have been getting from a range of industries.

Mr Gilbert said everyone appreciates a brown marmorated stink bug incursion could have a devastating impact on New Zealand agriculture.