Potatoes are in many countries one of the most common and simple foods. Have you ever
wondered how important potatoes really are in our diet?
There are thousands of potato varieties cultivated everywhere around the world, representing 300 million
metric tons of crops, or in other words the third most important food crop in the world (Potato Facts and
Figures, CIP International Potato Center). We can therefore consider potato crops as a major element for food
security. Potato is an essential food source: for instance, from 1845 to 1852, a massive destruction
of potato crops, from which the Irish population was relying on, caused a big famine, also called “The Irish
Potato Famine”. It was responsible for the death of a million people and the flee of two million people.
Ireland's global population decreased by one third (Gillissen, 2015).
In Switzerland, the blackleg disease is the first cause of removal of the market of potato lots (Rouffiange
et al. , 2014), by causing the loss of tens of hectares of crops. Climate change is exacerbating this issue:
the effects of increased greenhouse gasses concentrations, now more than ever, are being felt. 2021 is the
7th consecutive year (2015-2021) where global temperature has been over one celsius degree above pre-industrial temperature
(according to the World meteorological organization).
In Europe for that matter, “the major effects reported on Climate Change are reduced water availability and
a shorter suitable winter time slot for potato production” (Haverkort, A.J., Verhagen, 2008). Since there
will be longer heat waves and humidity, pathogens might also be more and more present (Romero et al, 2021).
Both insects and pests are the main explanation for crop damage and yield loss. Right now, the easiest way
to limit crop damage is by using pesticides: it is the most widely used form of crop protection. However,
these products are worsening environmental and human health problems. Among them, we can note a particularly
huge decline of insects, including pollinators. Non negligible amounts of greenhouse gasses are emitted
during pesticide manufacturing: carbon dioxide, methane and nitrous oxide (Heimpel GE, Yang Y, Hill JD,
Ragsdale DW 2013). For example, phosphate mining for pesticide production causes major damages to the
ecosystems and pollutes the environment (Wozniacka G. 2019).
Moreover, the rising heat of water due to climate change worsens pesticides damages on aquatic life (Folmar,
LC, Sanders HO, Julin AM. 1979). Indeed, the rate of animal and plant extinction tends to accelerate:
there’s more and more imbalances in natural systems creating larger outbreaks of pests and weeds. According
to soil scientists, regarding the current soil destruction, human health will be seriously endangered within
50 years. Food crops might also provide less and we will not have enough fertile arable land to feed
ourselves (Thiel T, Drossel B. 2018). Human health is at risk as long as pesticide use and climate change
coexist. Pesticides, even in small quantities can cause diverse health issues and diseases (Lau WKM, Kim KM.
2021). It becomes quite clear that we need to develop more sustainable solutions: here you can find a link to our sustainable
development page.
In a context of climate change, it is necessary to find new solutions that are more planet-friendly, in every sector but especially agriculture, a sector in which the stakes are crucial as it concerns a vital need endangered. New technologies need to be developed in order to be efficient quickly, and replace toxic products.
FIAT LUX’s goal is to help scientists develop new tools, such as biocontrol tools. Our tool helps create more precise technologies and thus helping develop the agriculture of precision. Making agriculture more precise will definitely help settle more respectful methods of production which are harder to apply than pesticides (highly effective but nocive for the environment) for example.
The dangers of pesticides on the environment are numerous. They contaminate and kill other actors in the food chain, they pollute the air we breathe, as well as water supplies to the point of making them undrinkable. They are harmful and the cause of many health problems in humans. We need to develop non-toxic methods to treat crops and maintain their quality.
By freeing crops from pesticides, or at least drastically lowering their usage, FIAT LUX has an impact on biodiversity, health of the soil but also the health of humans and animals in the surroundings. Its core concept is to be used conjointly with biocontrol methods, respecting the environment.
Nowadays, so many losses are due to diseases and phytopathogenic bacteria, that years or even dozens of years are sometimes needed to determine their mode of action and to develop a solution. Creating knowledge and finding out the mode of action of new pathogenic bacteria is essential, and time is of the essence.
By precisely analyzing the evolution of a pathogen inside the plant, FIAT LUX is literally a tool to create knowledge and allows us to develop solutions faster. The role of FIAT LUX, so soon in the food chain, impacts the whole food chain production by creating this knowledge and allowing new cures and solutions to be tested.
Creating innovation for scientists always has an ethical and moral side to it: science cannot be neutral. Especially in the 21st century at the heart of the anthropocene era, it is a responsibility to bring new tools which will improve the world we live in and not deteriorate it.
Our new tool, as well as its software and hardware combined, were designed to be responsible. The mere purpose of the tool is to improve agriculture conjointly with biocontrol tools, to create knowledge in order to cure crop diseases, without using harmful products as a default solution. Moreover, our software and hardware were designed to be complementary to our biological tool and be affordable to whoever will need the technology.
Nowadays, existing tools for bacteria tracking require destroying the organism in order to observe bacteria. Furthermore, being able to observe the evolution of bacteria in situ can give much more insight into its development and kinetics details.
By working without interfering with the plant’s normal function, and being easily observable, FIAT LUX allows us to recreate bacterial propagation in real conditions.
Ensuring a good level of food quality and safety is essential to provide adequate protection for consumers. Monitoring quality assurance will reduce food losses, which is especially important in those situations where food security is threatened.
FIAT LUX is part of actions that can keep food protected from hazards that can increase human health risks. We are responsible as a society, from the farmer to the consumer, to keep the food supply safe. Protecting crops and ensuring their quality of production benefits the whole food chain.
Food security is one of the major challenges of the century. The population is growing and food losses are more and more important. We need to find solutions to feed everyone.
Understanding new pathogenic bacteria faster will allow scientists to find cures or methods to avoid crop losses. Ensuring a quality crop is essential to feed the world.
FIAT LUX was born from our will to create a project for a more planet-friendly society, and the influence of several actors: we discovered Dickeya plant pathogens, because our PI teachers, at the MAP lab, worked on this genus, so we decided to investigate it. We contacted inov3PT, a research institute that studies Dickeya, amongst other potato plant pathogens, and they introduced us to the blackleg disease, caused by Dickeya solani. They were the ones who made us realize the huge food losses due to this disease. Our PI already had the ilux operon, so we came up with the idea of using bioluminescence to track pathogen bacteria in plants and help inov3PT and other research labs develop new treatments for crops diseases. That is how we decided, since the beginning, to use Dickeya solani as our proof of concept. With this idea in mind, we contacted and had talks with all of the following actors to truly grasp the issues, the stakes and the organization of this sector.
Understanding the context of
agriculture,
more specifically regarding
potatoes:
We tried to meet as many actors of the potato industry as we could, in order to
understand not only the sector, but also how our tool could help every single
stakeholder. Through our encounters, we were able to reconstruct the following
scheme of the organization of the potato sector in France.
Marine, a team member, on board of a potato tractor on Olivier Loridan's farm
Potato preservation box in Olivier Loridan's farm
Throughout the project, we were able to meet with the different professional institutions of the seed and potato production sector, law makers, plant research institutes, producers' and farmers' unions, different types of farmers with different visions and methods, as well as consumers. These meetings, as shown on this diagram, made us realize the importance of the production chains, and research process, from the conception of the variety to the sale in industry and in detail to the consumers. But above all, it showed us the importance of communicating on the difficulty of setting up new ways of producing that are satisfactory for the producers, for sanitary norms, for the final customers in terms of quality, price and aesthetics . These difficulties supported the need for our tool to help scientists to develop remedies more quickly as the turnover, of potato species in particular, is slow.
Food security is the challenge of the 21st century.
Throughout our work, we tried to understand the needs of the people in charge of
producing
and selling food to the population. The aim was to identify precisely
the
challenges they have to face, in order to design a tool in line with the
current
issues.
We first considered what type of research is done in the industry, in order to have a global idea of all the challenges that the stakeholders have to face. Arvalis, the plant institute, the main institute conducting applied agricultural research, focuses on 4 aspects:
While continuing our investigation, we tried to understand to what extent those
aspects were priorities to the field, and if others were at stake.
Olivier Loridan, a seed potato grower, being interviewed by our team
Loss of production due to current changes
Because of global warming, the agricultural field is facing changes at an unprecedented rate. It has never been so difficult to adapt agricultural behaviors to minimize the crops’ losses.
“Nowadays, we do not have a regular year anymore. This will generate huge problems”:
“Each year will be a new climatic record”
However, we decided to focus on a less known, yet equally devastating consequence of global warming on crops: the proliferation of new pathogens. According toContext of agricultural diseases
Most of the stakeholders we met (interprofessions, farmers, producers, law makers and scientists) understood the drastic consequences of climate change on production safety, especially on agricultural diseases. More and more efforts are put into research but there are many barriers : it is time consuming and even though “all the actors of the sector are aware of the problem, the answers to bring are not necessarily obvious”, reported to us
“Agriculture has developed thanks to mechanization, fertilizers and chemistry. There is a shift towards chemistry, but the shift is being taken a little abruptly”
“Agriculture has developed itself thanks to mechanization, fertilizers and chemistry. There is a shift towards chemistry, but the shift is being taken a little abruptly, and it is difficult to take the lead in this shift” said“There is no instruction sheet when it comes to biocontrol”
It seems important to notice that the implementation of such methods could be more time consuming: there could be some reluctance from the different actors.
“Between what is said and what is done, there are big differences”
We should however differentiate the expectations of the consumers, and their real behavior. According to
There is a serious lack of communication to the public: the production of potato plants is not an attractive topic for the media, and the occupation of agricultors lacks exposure. Only a few people ever wonder who is behind their potato dish. There is a need for an education to be done to the public, to explain the functioning of the field and the importance of the variety choice.
“It can take up to 10 years to generate a variety with a resistance, thanks to genetic crossbreeding. In the end it can take more than 20 years to fully implement a variety in the market.”
Scientists do not know how to highlight resistance factors to blackleg disease in new varieties.We realized that these solutions are rather long to test and implement, so they will not be usable in fields for a long time. That is why we still need diagnosis solutions, such as FIAT LUX, in order to characterize phytopathogens and to develop more specific and efficient treatments.
“These last few years, more criteria are taken into account during the re-examination of the product as new scientific knowledge influences evaluation criteria”
These last few years, more criteria are taken into account during the re-examination of the product as new scientific knowledge influences evaluation criteria. For instance, the EFSA guidance for the identification of endocrine disruptors has been approved only in 2018. The approval criteria to reach the European market at very restrictive in order to ensure a high level of protection of both human and animal health and the environment. Some companies are more likely to turn to other markets, which have less strict norms and rules. Trying to enter a product on Europe’s market can represent a lot of money and energy spent for an uncertain outcome even if it’s a guarantee of quality and safety. Those new prohibitions are becoming more and more an issue for producers who face a lack of alternative solutions to treat the crops. Hence anticipation plans are being launched to find solutions and anticipate the disappearance of certain products with institutes (like INRAE), farmers' unions, industrialists, and other stakeholders. We discovered that in order to promote the development of alternative solutions and especially biocontrol the government launched a specific plan “FRANCE 2030” : a program for energy transition containing 10 objectives. The 6th objective in particular is endowed with 2 billion euros which will be dedicated to the investment for healthier, more sustainable and traceable food."Alternative methods are much longer to implement and difficult to apply. We can’t afford to make mistakes: we have to strive for excellence"
Producers bear a huge responsibility, as they have to provide healthy and quality plants each year, while respecting those strict rules and reglementation , both on the plants they produce and on the means of fighting pathogens. Their occupation is thus in constant evolution. There is a constant need to find new solutions against phytopathogens, but in compliance with such regulations, that are becoming increasingly stricter. “Each year we have several solutions of treatment that are no longer approved”, explains
Team members with Jean-Claude Laversin, an expert seed potato inspector, in front of the North Committee
What is the blackleg disease?
To this day, there is no efficient treatment against the blackleg disease.
"Blackleg is our pet peeve!"
Most of all, all plants do not develop symptoms for the disease on the field. They can appear later on, during transportation, and therefore infect all the batch. This is a real issue for the producer, who does not have any control on his batch after harvest, and who could not check if his plants are infected or not.All along the design and the
development of our tool, we made sure
to
always be aware of what was at stake, to make our tool fit as much as possible the
needs
of the stakeholders. We developed our tool keeping in mind the reality of the field,
in
parallel to our work in the laboratory. We met many scientists to understand their
working method, but also farmers to observe the reality of work in the fields.
Whenever
we received feedback on how we designed our tool, we made sure to take it into
consideration.
Creating knowledge of precision
Finding out the concerns of the farmers about trying new uncertain methods that could jeopardize their yearly crop made us think about how our project would play a role within this situation. As we previously explained, even though many technologies are currently being developed to find new environmentally-friendly solutions, those technologies are still not efficient enough to replace pesticides. As it was reported to us by almost every actor, solutions such as biocontrol or even variety selection are not efficient for all pathogens, and especially not for blackleg disease. As we previously explained, producers need to lessen their use of pesticides to face climate change, new regulations, and consumers preferences but solutions that are not pesticides require a more precise and specific use. Especially for biocontrol, we understood that it is necessary to better characterize phytopathogens and biocontrol tools in order to make them easier to use.Providing non-destructive analysis
Dry lab
As far as the dry lab is concerned, the code was always designed with the idea of using less memory space, and optimizing the processing time for environmental reasons. Moreover, we always prioritized accessibility while coding our software. We decided to use Python, because this is an accessible and easy programming language, so that even non IT specialists could understand and appropriate our software. For the graphical user interface, we chose to use Tkinter, mostly used across the world, to increase the accessibility of our software. All along the development of our code, we thought about the easiest structure possible of the code, in order to make it readable for everyone who wants to use it. You can learn more about this on our software page!Adaptability
Bibliographical research
Accessibility
Timelapse (24h) of bioluminescence produced by our biological tool with the bacteria Dickeya solani in chicoree plants
Wet lab
How will scientists use our tool?
FIAT LUX cannot be used directly by producers, because it cannot be used in
fields.
However, it will be extremely helpful to scientists who work on diagnosis
and
treatments
for crop diseases. Especially, our tool brings new opportunities to the
research
field:
it enables us to follow a live infection throughout time without destroying
the
plant or
altering its development. This opens up the possibility to collect precious
data
about
the pathogen’s behavior.
It will especially be useful to inov3PT, research organism for potato seed
growers,
and
Arvalis, research organism for consumption potato producers.
"The fact that it is a real time monitoring enables us to see if our biocontrol agent is efficient to destroy the luminescent Dickeya solani"
Generally, our tool would be useful to study bacterias’ behavior under several circumstances. For example, it would be interesting to test our tool in a controlled environment: inoculate the bacterium in the soil, in water, to understand how they reach the plants. Of course, this would be done in isolated and secured field batches to ensure that our bacteria can not interact with the exterior environment. It is still a challenge to reproduce the environments in the labs. In vitro, we need to reproduce conditions such as contact, irrigation, different substrates, and lots of other factors in order to say that one soil is more likely to infect with blackleg than another. We could also study how the bacteria behave in the plants at different times and maturities to help know when to clear the plants. It would also help identify the means of contamination of the plants, such as how fast Dickeya contaminates, or study the propagation of bacteria with the humidity, the distance between plants, and the UV. It would also be interesting to know how long bacteria stay on the different surfaces: leafs, soils…
"Our tool can show directly which plants are more sensitive to the disease!"
Greenhouse potato plants for certification testing at the Nord Plant Committee
P3 level analytical laboratory at the North Plant Committee
Some varietal phenotypes are more likely to develop blackleg or other infections than others: it does not only depend on genes but also on phenotypes. In other words, within the same variety, phenotype differences in leaf size or color, for example, could be a criterion for disease development or not. Some phenotypes could also worsen the symptoms. If varieties have an odd phenotype, they should be removed or monitored to avoid the risk. Our tool could help identify risky phenotypes. This would especially be an advantage for variety selection researchers such as
We started with an idea: make a detection tool that would allow scientists to create cures and diagnoses more efficiently and not involve pesticides in those processes. We did not really know precisely how labs could use it for biocontrol methods, thought about how to make it adaptable, construct a device to observe our results, or even how it could be useful to future iGEM teams. Looking back at the entirety of our work and all the ethical and human reflection that was conducted, thanks to every single person we met, every trail they led us to follow and every adaptation it led us to think of, we managed to close the loop between what was needed and what was actually designed.
Even though we are very proud of our tool, we must recognize that there are still some
limitations that need to be kept in mind while using the tool.
It is not possible to use FIAT LUX directly in the “regular” field because it is
constituted
of engineered bacteria, so it would neither be safe nor allowed to place those directly in
the
environment. Our tool needs to be used in the lab, under the careful control of
scientists,
which requires to recreate a realistic context. In order to recreate the real soil
conditions, with all its bacteria and fungi, there are a lot of interactions to take
into
account. To do so, some methods already exist, based on the sequencing of all the DNA
present in the soil to have an overview on the flora present.
Another limitation is the compromises that we needed to make in order to produce the
best
tool possible, while keeping up with our timeline and our values. We could have pushed
the
tool further with a system called pDawn which is a light-inducible promoter (an idea we
had,
to make a switch on/off button and make the tool work only in the dark so FIAT LUX would
not
impact the behavior of the bacteria when we do not want to study the luminescence).
After
our investigations and meeting with all these actors of the field, we chose to
prioritize
accessibility and adaptability. In the end we decided to keep a constitutive expression
of
fiatlux in order to offer a qualitative characterization and especially to leave room
for
future reworkings and improvements of projects for future iGEM teams.
Right now, it’s only possible to implement our tool in cultivable bacteria. Non-cultivable and difficult to culture bacteria are rather difficult to exploit, and we cannot add our plasmid in a bacteria that we can not control in vitro. After some research, we found out that the phytopathogens that are responsible for most of the crop losses are cultivable. (Mansfield et al. 2012). Hence, while we hope that one day all bacteria will be cultivable in the lab, it does not influence so much the repercussions of our project on phytopathogenic bacteria.
The last limitation that we considered is an ethical limitation. Indeed, even though we conducted our project with the goal to help create more planet-friendly technologies, especially biocontrol tools, we do not have any control on how people will use our project. FIAT LUX was made to create knowledge, however we can not control what this knowledge will lead to. Our tool might as well be used for example to create toxic products for the environment, even though that is absolutely not its purpose. Science can never be neutral, and innovation can always be diverted from its original intention.
Throughout all of our project, we aimed at meeting with as many actors of the sector as possible, which allowed us to take a step back and realize how our tool could possibly impact the current challenges in the agricultural field and how its implementation could be influenced by all the factors inherent to this field. Having an upstream vision on the whole chain made us realize one thing: our tool intervenes at the basis of the chain, as a fundamental research project, and thus makes it possible to affect, in some ways, all the actors with whom we engaged.
Communicating with all these different interlocutors enabled us to understand how this field works, and to confront different points of view. The strong human interactions we had made us realize the reality of the field and the difficulties faced by these stakeholders. We were able to meet passionate people, who communicated their interest in their expertise field, and led us towards new ways of thinking. Such exchanges pushed us to improve our tool and to make it as complete and functional as possible. This communication process allowed us to design a tool that reflects the existing needs of stakeholders and ultimately consumers, but also brought us enriching human contacts, which is essential to integrate when it comes to scientific innovation. As we previously stated, science cannot remain neutral. It is true in the choice and conception of an idea as well as in its final application: we truly strived to incorporate this human aspect into our work.
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