‘Farm of the future’ project marries microbiology and machine learning

Science Daily – looking into how farms of the future will feed a projected 9.8 billion people by 2050 – reports on a “smart farm” project which marries microbiology and machine learning. The aim is to reduce the need for chemical fertilisers and enhance soil carbon uptake, thus improving the long-term viability of the land while increasing crop yields.

The report features a farm in Arkansas, growing soybeans, corn and rice, that is aiming to be the most scientifically advanced farm in the world.

Soil samples are run through powerful machines to have their microbes genetically sequenced, drones are flying overhead taking hyperspectral images of the crops, and soon supercomputers will be crunching the massive volumes of data collected.

Scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), working with the University of Arkansas and Glennoe Farms, hope this project, which brings together molecular biology, biogeochemistry, environmental sensing technologies, and machine learning, will revolutionise agriculture and create sustainable farming practices that benefit both the environment and farms.

If successful, the scientists envision being able to reduce the need for chemical fertilisers and enhance soil carbon uptake, thus improving the long-term viability of the land, while at the same time increasing crop yields.

Understanding the role of microbes in the health of the soil is a major focus of the research.

“Microbes are a critical component of soil health and productivity,” said scientist Ben Brown.

“By understanding how microbes work and modifying the environments where they function, we can eventually engineer microbial communities to enhance soil productivity. What’s more, Berkeley Lab’s research is showing that healthy soils are more resilient to system shocks such as climate change, drought, and insects.”

A key challenge for advancing these goals is the recognition of the significant spatial variability of soil properties within a single field and between fields.

The “AR1K Smart Farm” project has brought together a range of expertise to focus on a 1,000-acre farm near Stuttgart, Arkansas, as a test bed.

The project is co-led by Haruko Wainwright, an expert in environmental monitoring and estimation methodologies in Berkeley Lab’s Earth and Environmental Sciences Area, and Ben Brown, an expert in machine learning and microbial analysis in the Biosciences Area.

Science Daily notes the world’s population is forecast by the United Nations to grow to 9.8 billion by 2050. Feeding these people will require raising food production by more than 70 per cent.

Yet industrialised farming practices have depleted a majority of the USA’s agricultural land of active carbon and a balanced microbial ecosystem. This is reflected in measurements of organic matter that average only 1 to 2 per cent in most farmland, compared to historic levels of around 10 per cent.

“Our farmers are dependent on a heavy prescription of genetically modified seeds, fertiliser, chemical herbicides, and pesticides to render a profitable crop,” said Jay McEntire, manager of Glennoe Farms.

“For the farmer this dependency raises their input costs and increases their economic risk. For the landowner depleted soils and chemical regimes represent risks for both economic and environmental sustainability.”

Building on Berkeley Lab’s ENIGMA and Microbes to Biomes initiatives, the project scientists aim to develop and evaluate microbial amendments, which can be thought of as “probiotics for soil,” to replace the carbon, phosphorus, and other nutrients that have been lost.

As Science Daily points out, repeated use of bulk fertilisers and chemicals over the years have depleted the soils and caused other environmental damage, creating a vicious cycle that makes the current model of industrial agriculture potentially unsustainable — and increasingly expensive as more and more chemical and bulk salt-based fertiliser additives are required each year.

What’s more, the world’s supply of phosphorus is limited.

But Berkeley Lab is pursuing a microbial solution.

“The good news is, there are lots and lots of microbes that have enzymes called phytases that are capable of resolubilizing inorganic phosphorus,” which is essentially the “leftovers” in the ground after plants take up what they need from the rock phosphorus, says Brown.

While the concept of microbial amendments is not new — commercial products are on the market — a predictive understanding of how the soil microbiome interacts with and affects plant growth is lacking.

“There are millions of species of microbes per cubic centimeter of soil,” Brown said.

“As you approach the plant root and its interior tissues, you go from millions to dozens. So plants do an exceptional job of farming their microbiomes. They release materials, including antimicrobial compounds, to selectively kill undesirable microbes, and they release food to incentivise beneficial microbes. It’s a highly symbiotic and enormously complex interaction, and we understand almost nothing about it.”

The challenge will be in figuring out the cause-and-effect relationships between the microbial amendments and plant growth.

“You’re trying to connect events at timescales relevant to molecules to events that occur over the course of a six-month growing season,” said Brown. “You’re trying to bridge something like 18 orders of magnitude across spatiotemporal scales. That is seriously nontrivial.”

Hyperspectral sensors on the drones will be able to detect light reflectance from the plants and see hundreds of channels of spectra, from the visible to near infrared.

“The human eye has only three channels — red, green, and blue,” said Wainwright. “You can see if a leaf looks yellow or green. But with hundreds of channels you can measure carbon and nitrogen content, and you can tell a lot about plant health, plant disease, or leaf chemistry, all of which affect crop yield.”

In addition, surface geophysical techniques are used to map soil electrical properties in 3-D, which greatly controls soil microbial activities.

Machine learning is the tool that will tie all the data together.

“The team science approach pioneered at Berkeley Lab is being put to use to integrate all the information within the machine learning context,” said Wainwright. “Our ultimate goal is to provide actionable intelligence to the farming community.”

Currently farmers have no such information, even though services and products have sprung up providing various “big data” solutions.

“All the private companies have a big incentive to lock their own data sets, so they can’t be used in conjunction with other data sets,” Wainwright said. “That’s where the public sector, like Berkeley Lab, can step in. We’re not incentivised by profit.”

The scientific challenge is formidable but not insurmountable.

“We think it’s a tractable problem, and we’re hoping to prove it in the next year,” Brown said.

The Berkeley Lab team is collaborating with the University of Arkansas with support from Laboratory Directed Research and Development funding and collaboration with Glennoe Farms, the landowners, and M2Capital Partners LLC.

Source: Science Daily. 


New research centre announced as Massey Agriculture sets sights on future

College of Sciences Pro-Vice Chancellor Professor Ray Geor, Head of the School of Agriculture and Environment Professor Peter Kemp, and Massey University Vice-Chancellor Professor Jan Thomas.

Massey University’s School of Agriculture and Environment has given stakeholder’s a glimpse into its future plans, including the announcement of a new research centre.

It began with a bus tour showcasing some of the University’s operations, including the new Apple Innovation Orchard, BioLumic’s work with ultra-violet light at the Plant Growth Unit, and the Dairy 4 Plantain Programme. It ended with speeches at the Sir Geoffrey Peren building, where the plans for the school were unveiled.

Massey University Vice-Chancellor Professor Jan Thomas spoke about the school’s past and how it aims to make further history. She said:

“We believe we are a significant university in the global scene, we intend to grow that, we intend to make a difference to New Zealand, we intend to make a difference working in partnership with our stakeholders, our businesses, our communities and our governments. We aim to help drive the primary sector to being something we can all be proud of now and in years to come.”

Among the announcements were commitments to refresh the agriculture, horticulture and animal science degrees, as well as brokering further community engagement across all that the school does.

College of Sciences Pro-Vice Chancellor Professor Ray Geor announced the Massey Agritech Partnership, a new Massey research centre.

“We have a reputation for innovative agritech developments and we plan to build on these with our latest research centre, Massey Agritech Partnership,” Professor Geor said.

“The centre is about partnerships both within Massey and in working alongside industry. It brings together engineers, technologists, programmers and business analysts who generate ideas and work with businesses to find solutions.”

Professor Ian Yule leads the new centre and he is joined by post-harvest engineer Professor Andrew East, robotics expert Professor Johan Potgieter, and their respective teams.

Initial projects will be in the areas of sensing and imaging, rapid data processing and modeling and simulation. The centre will focus on harnessing data for real-time decision making to predict pasture growth, yield and quality at proposed harvest times and to direct products to appropriate markets.

Head of school, Professor Peter Kemp, spoke about Massey Agriculture and Massey Horticulture better working together to be more productive and to improve people’s well-being through innovation, but also through community engagement at all levels.

“Massey Agriculture has a long and proud history of excellence in advancing knowledge in the primary industries and developing leaders, but it’s like all organisations, you can’t rest on your laurels. You have to move forward, there’s plenty of new challenges and to respond to those you have to change.”

Massey believed innovation in how things are done would help create greater value and working together both within Massey and with its partners would make a difference.

Source: Massey University.

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



Maori company teams up with Crown to breed unique berries for global markets

A joint venture company has been established to breed and develop new unique berry varieties to be marketed exclusively by a Māori-owned firm, Miro Limited Partnership (Miro).

Government-owned Plant & Food Research and Miro signed a 50:50 joint venture agreement today at an event hosted by Ngati Haua at the iwi’s Rukumoana Marae in Morrinsville.

The agreement provides the new company with access to Plant & Food Research berry genetics for the development of proprietary new varieties. The joint venture partners will create a breeding programme for new high-value berry varieties.

Miro will grow, market and sell the berries in New Zealand and globally with support from BerryCo NZ Limited.

The joint venture is a milestone in horticultural entrepreneur Steve Saunders’ vision for Miro, to create a step-change in both the New Zealand berry industry and the regional Māori economy for current and future generations.

Miro chair Rukumoana Schaafhausen said Miro is owned by over 20 Māori trusts, iwi and entities from the top of the north to the top of the South Island, from the East Coast to Taranaki.

“We came together because we wanted jobs for our people, higher returns on our land, and to own IP and a global business that would secure a future for our mokopuna. We’re so excited about the opportunities ahead of us and we would love for more Māori landowners to join in.

“In simple terms, Miro is aiming to build a business every bit as successful as Zespri. It represents a high-value, market-led, vertically integrated berry export business. There’s no reason why berries can’t be the next billion dollar New Zealand horticulture industry, and we’re proud to partner with Plant & Food Research to create that future.”

Plant & Food Research chief executive David Hughes says the joint venture is aligned with the science company’s mandate to use research innovation to add value to fruit, vegetable, crop and food products and their industries.

“In Miro we have a partner with global ambitions matched by scale and capability in New Zealand,” said David Hughes.

He expects the deal to open up fresh innovation challenges for the Crown research institute’s scientists and described it as a welcome addition to its diverse range of commercial activity.

Source: Plant & Food Research.

AI farm assistant and plant proteins go on show at field days

Massey University is showcasing a prototype of a virtual farm assistant at Central Districts Field Days this year and wants the public to put it through its paces.

Field Days crowds can also try some plant-based proteins that Massey is developing, with some meat patties that look and taste like meat, but are made from soy.

Yoghurt made from coconut milk and bread made from nut and cricket flour will be available, too.

The three-days field days – New Zealand’s largest regional agricultural event – kicked off at Manfeild Park, Feilding, today with over 550 exhibitors.

Artificially intelligent systems that can clean the house, manage heating for cheaper power and provide surveillance of the family home are developing every day.

Massey engineers have been developing a screen-based prototype to help on the farm that could be used from anywhere – the home, the ute, even on an overseas holiday.

Still in its early stages of development, the system involves users speaking to a computer-generated avatar, who answers farm-related questions and puts forward data-driven solutions based on the information it has.

The system is designed to tap into sensors on the farm that give real-time information to farm managers about what is happening. It can compare that to what has happened in the past, and recommend options for what to do next, based on the data available.

The questions can be wide-ranging – from the levels of milk solids in the cow shed vats, how that compares to the same time last year, what’s the pasture cover and where everyone is currently located on the farm.

Professor Johan Potgieter, of the Massey Agritech Partnership, is leading the project with Massey master’s student Hayden Wilson doing the development.

The development team wants to know from farmers what they would use it for and how it could help them. They are keen to have farmers involved with the development.

The system will be able to absorb historical data from the farm and be capable of linking with on-farm systems to analyse data to help farmers make better informed decisions, as well as helping with the day-to-day running of the farm.

The tool is not just designed to optimise productivity, but every aspect of farm life, for example in the identification of animal illness. These may include spore count data on certain paddocks to let farmers know which paddocks might be contributing to facial eczema. The system would automatically flag these paddocks and let the farmer know so they can efficiently manage the farm based on the information the system provides.

Source: Massey University.

New partnership to drive innovation in perennial fruits

Agtech solutions company Autogrow and Plant & Food Research have signed a Memorandum of Understanding confirming their intention to collaborate in the development of protocols to maximise yield and enable continuous production of perennial fruits.

The agreement was signed in Auckland by Autogrow chief executive Darryn Keiller and Dr Kieran Elborough, General Manager Science – New Cultivar Innovation for Plant & Food Research.

“We are incredibly excited to be working with Plant & Food Research and see collaborations like this as fundamental to furthering our industry, ultimately benefiting both growers and consumers,” said Mr Keiller.

“Plant & Food Research are responsible for some of the best cultivars to come on to the global market and their science expertise combined with our knowledge of controlled environment agriculture will take perennial fruits to the next level.”

Autogrow’s Director of Plant Science and Agronomy, Dr Tharindu Weeraratne, will head Autogrow’s team as part of the arrangement.

Speaking at the signing, Dr Elborough said working with a global company like Autogrow had the potential for Plant & Food Research to match new breeding strategies with future growing systems that deal with numerous horticultural challenges such as climate change, sustainable food production and reducing land availability.

Source: Plant & Food Research.