NPEC: will a tiny country lead the next green revolution?

In April 2018, NWO awarded funding to ten proposals in the National Roadmap for Large-Scale Scientific Infrastructure. Among the lucky few is the Netherlands Plant Eco-phenotyping Centre (NPEC) of Utrecht University and Wageningen University & Research. Initiators George Kowalchuk and Mark Aarts describe the what, why, and how of NPEC.

George Kowalchuk is Professor of Ecology and Biodiversity at Utrecht University. He explains: “NPEC addresses a pressing societal challenge: to produce more food using fewer resources, while avoiding negative effects on our planet. Historically, the majority of farmers have aimed for high crop production, using large amounts of pesticides and fertilisers: ‘high input, high output’. People now realise that this is not sustainable in the long term, especially with the world population growing at its current rate. Hence, we will need a next green revolution: we require methods to feed the world without destroying it.”

Professor George Kowalchuk

Mark Aarts, Professor of the Genetics of Plant Environmental Adaptation at Wageningen University & Research, continues Kowalchuk’s story: “In parallel with this societal development, technological advances have introduced various high-end technologies into the field of plant science. As a result, sequencing plant genomes has become relatively easy; this is not a bottleneck anymore. Plant science has therefore shifted to the next step: unravelling how interactions between the genome and the environment determine plant characteristics and crop yield. To this end, we need systematic high-throughput studies. This is exactly what NPEC will make possible.”

Professor Mark Aarts

Six modules
NPEC will enable researchers to unravel the genetics of the interactions between plants and the environment. The facility will allow for systematic, high-throughput measurements of plant characteristics and the precise manipulation of environmental conditions. NPEC will include six modules, ranging from small climate chambers to precision greenhouses and an open-field study system (see Figure 1). Where the climate chambers allow researchers to precisely manipulate a variety of environmental conditions, the environment in the greenhouses and open fields is increasingly more difficult to regulate. Therefore, the outcomes of the research in the environmental chambers can be tested in more realistic situations in greenhouses and the open field.

NPEC will utilise advanced equipment to conduct automated, precise measurements on plants. For instance, plant growth, shape, and photosynthetic efficiency will be measured using regular and infrared cameras and fluorescence monitoring. The open field system will be equipped with drones and self-propelled tractors. Kowalchuk: “NPEC will obviously create enormous amounts of complex data. Storing, organising, accessing, and analysing these data properly is critical. The quality control, data management, and data access will thus be organised centrally, and we will adhere to the FAIR principles as much as possible. We plan to align this with ELIXIR-NL.”

Figure 1: The six modules of NPEC: 1. An Ecotron, where large containers of soil are transferred from an outdoor environment into an indoor environment. 2. A high-throughput plant-microbe interactions system with robots that allows researchers to manipulate plants and their associated microbes. 3. A large battery (30-36) of small precision climate chambers that allow researchers to accurately manipulate a variety of conditions such as the amount and colour of light, the amount and composition of nutrients, temperature, moisture level, and CO2 level. 4. A high-throughput climate chamber phenotyping system where robots measure a variety of plant physiological measures on many plants in a controlled environment. 5. Automated precision greenhouses for larger scale measurements using in situ monitoring technology to track plant growth and other traits, from the time of sowing or planting to harvest. 6. An open field study system equipped with monitoring technology on drones and tractors.


The researchers provide two examples of how NPEC may help realise the next green revolution. Kowalchuk: “In Utrecht, we are interested in numerous plant-microbe interactions. Millions of microbes inhabit plants and the direct vicinity of their roots, influencing plant growth and health. One way to increase crop production in a more sustainable way is to breed plants that have the capacity to efficiently recruit a strong microbiome. To do this, we will need a thorough understanding of the fundamental principles of plant-microbe interactions. NPEC’s high-throughput system with in situ monitoring technology will allow researchers to study this in a high-throughput, systematic way. Each plant can be examined in real time to track the impact of various environmental factors on visible plant traits, physiological and biochemical changes, and responses within the associated microbiome. Based on the data that is generated and theoretical models, we can make predictions that can be tested with crops in greenhouses and in the open field, using sophisticated cameras, sensors, and drones.”

Aarts: “In Wageningen, we are intrigued by photosynthesis. It is remarkable that centuries of plant breeding have hardly affected the efficiency of photosynthesis in the majority of crops. This efficiency is only 1% on average. We think that it should be possible to improve photosynthetic efficiency through breeding. This would constitute another approach to improve crop yield in a sustainable way. In particular, it seems that the plants’ photosynthetic acclimation to a suboptimal environment may be improved. This means that we will first need to discover which genetic variants affect this plant characteristic. So far, adequately measuring photosynthesis has been a bottleneck. At present, scientists measure photosynthesis parameters manually in open fields by sequentially measuring individual leaves. So, light conditions and other environmental factors are likely to change during the experiment, creating substantial variability in the data. NPEC will allow us to simultaneously measure photosynthetic capacity of whole plants, producing precise phenotypic data under a variety of environmental conditions. We expect that these phenotypic data with much less noise will enable us to pinpoint genetic loci that affect photosynthetic capacity.”

Originally, Utrecht and Wageningen had both prepared a Roadmap preproposal and the Roadmap Committee asked them to join forces. Kowalchuk: “This process went very smoothly; the collaboration made great sense from the start. NPEC will be one united facility, located at two physical locations. It is a fifty-fifty effort of Wageningen and Utrecht. The facility will be open to investigators from other universities, and we intend to create a simple procedure to evaluate requests to use the facility.”

The NPEC team at the presentation of the Roadmap certificates at Utrecht Science Park in April 2018. Front row,  left to right: René Klein Lankhorst (WUR), Rick van de Zedde (WUR), Mark Aarts (WUR), and George Kowalchuk (UU). In the back, left to right: Corné Pieterse (UU) and Roeland Berendsen (UU).

Aarts: “We are now in the process of selecting equipment suppliers. We will receive Roadmap funding for a ten-year period. After that, we will have to finance the infrastructure by other means. Receiving Roadmap funding has provided a major boost to the NPEC initiative and has substantially strengthened our international visibility.” Kowalchuk concludes: “The Netherlands is the perfect country to host NPEC. We have excellent plant scientists and ecologists, as well as a world-leading agricultural sector. Our hope is that NPEC will enable the Netherlands to lead the next revolution in agriculture.”

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