Food sufficiency is one of the biggest global challenges of the 21st century (FAO 2022). The human population has continued to grow at an alarming rate, as global arable land per capita is shrinking (Roser 2013; FAO 2020). There is an alarming gap between theoretical productivity and the actual output (GAP Report 2018).
Global warming is aggravating the situation and hence threatening today’s
agriculture (The World Bank 2021). The Intergovernmental Panel on Climate Change (IPCC) report
has clearly stated that even though we may hope to prevent extreme heat for the future, the
+1.5°C threshold will most certainly be reached (IPCC 2022).
Figure 1 - Graph presenting the world’s arable land area (Ha/person) and histogram presenting the world population size, between 1960 and 2020 (FAO 2012)
Mankind needs to be ready for this inevitable increase in temperature and its consequences. Warmer temperatures will disrupt ecosystems and threaten diversity with floodings and severe droughts, leading to the loss of arable land. These conditions will also lead to the emergence of new threats: previously unknown pathogenic microorganisms that can proliferate in these unusual conditions (IPCC 2022; BioScience 2018). The reason: global warming provides pathogens with the optimal proliferation temperature. Indeed, an increasing number of virulent infectious diseases have been observed these past two decades (BioScience 2018; Velásquez et al. 2018). These pathogens affect major crops world-wide (potato, rice, wheat, etc.) (Velásquez et al. 2018).
Up to 40% of global crop production is lost to pests every year, and
plant diseases cause up to $220 billion of losses per year (FAO 2021).
The current solutions to fight off these pathogens are mostly based
on pesticides, which have a considerable impact on the environment and human health. They
contaminate and persist in soils and water, and can also be harmful to other organisms (Aktar et
al. 2009). Instead of simply fighting off the pathogen with chemicals, an ideal option would
be to understand the biological development of the pathogen, in order to prevent an
infection or to develop new biocontrol agents. More environmentally friendly
agricultural practices are needed: for this, it is necessary to monitor the pathogens in
situ (Mutka et al. 2016), to understand how they cause diseases, in order to protect
plants.
However, according to inov3PT (FN3PT research entity, the French
agricultural professional organization for potato seeds), the actual tools to understand
pathogens in situ are not efficient enough. Examples of existing techniques include:
This is why our team decided to create a novel in situ long-term tracking tool: FIAT LUX.
FIAT LUX is a biotechnological tool, that makes bacteria produce
luminescence, allowing us to observe their propagation on a plant in real time, in a
non-intrusive manner.
FIAT LUX therefore enables the propagation of pathogenic bacteria to
be monitored within the host, facilitating research in plant protection. FIAT LUX opens up the
possibility of finding targeted treatments against new threats to crops. Our turnkey invention
is thereby aimed at tackling the enormous food waste issue in agriculture, induced by pathogens
across the world.
To create this biosynthetic tool, our team focused on establishing
the following strategy described in our Experiments
page:
To achieve these goals, our team relied on a variety of skills,
resulting in multidisciplinary approaches. This enabled us to individually focus on a set of
different aspects of the project and accurately contribute to the goals we had planned. We also
drew on the expertise of our Primary Instructors (PIs), advisors and their laboratory. All of
this contributed to the development and perfection of our tool. The only goal we could not
successfully achieve is the biochemical characterization of the luciferase enzymatic reaction.
However, our project not only relies on synthetic biology. To allow access of this tool to as many people as possible, open-source software and hardware have also been developed by our team.
Figure 2 - Left: picture of the hardware we designed and constructed, allowing us to visualize the luminescence produced by FIAT LUX, on Petri dishes or in plants. Right: screenshot of the interface of the software we designed, allowing us to analyze the produced luminescence in plants.
The software was created to analyze the luminescence produced by our engineered bacteria. It is composed of a user-friendly interface, allowing anyone to use and understand it. Our software is described on our Software page.
The hardware we developed replaces the expensive machines that are
usually needed to analyze bioluminescence. Indeed, our fiatlux operon enables bacteria to
produce luminescence that is so strong that a simple smartphone is enough to detect it. The
prototype for less than $400 is made up of a wooden box and electrical components, creating a
pitch black space to detect the bioluminescence. Our hardware is described on our Hardware page.
Therefore, more than a plasmid, we have developed a turnkey tool
based on 5 key features.
FIAT LUX is:
Our solution will enable researchers to study the long-term
propagation of any type of bacteria on any living organism in situ, without farmers
having to resort to the use of pesticides, thus limiting the impact of agricultural practices on
the environment and biodiversity. Farmers could then be advised to use a given treatment or to
destroy whole or part of infected crops, to avoid the spread of the disease to the remaining non
infected plants… and disastrous losses could be avoided. It is important to note that this
tool will not be used directly on the crops, but in laboratory conditions. FIAT LUX, a
highly useful application, is a perfect example of how synthetic biology helps tackle world
issues. This tool has huge potential in addressing one of the biggest issues of the 21st
century: food security. We focused on one type of phytopathogenic bacteria in particular (D.solani),
with the intention of extending the use of our tool to many different hosts.
This tool will also encourage more responsible and sustainable agricultural
practices, like biocontrol. All crops need to be protected against their natural aggressors. To
effectively protect plants, biocontrol is becoming increasingly important, used alone or with
environmentally friendly chemicals (CABI 2021). Biocontrol is based on the use of living
organisms or natural substances to prevent or reduce damage caused by harmful organisms (Busson
et al. 2016). It contributes to reducing the use of plant protection products and building the
agriculture of tomorrow.
Figure 3 - Diagram explaining how to use FIAT LUX. This workflow includes transformation of bacteria, infection of a plant, in situ and in real-time visualization of luminescence in our hardware and analysis with our software.
However, our tool is also a simple but highly efficient reporter gene. Along with our software and hardware, we are providing the field of research and future iGEM teams with a complete all-round tool that is affordable for and accessible to anyone.
Figure 4 - Diagram explaining the use of fiatlux as a reporter gene. This includes using the FIAT LUX operon to test the activity of a promoter for example.
More in-depth explanation of the implementation of our tool is
described on our Implementation
page.
As we have developed a proof of concept on the phytopathogenic
bacteria Dickeya solani, this has allowed us to demonstrate that the concept works and is
feasible. We have also successfully transformed two other strains (Citrobacter rodentium
and Pseudomonas putida), which emitted luminescence.
In just a few weeks, farmers could get an accurate diagnosis of the
pathogen destroying the crops that are sustaining our nutrition. After receiving a sample of an
infected plant, researchers would first identify the pathogen using traditional methods, and
then efficiently study its propagation in different conditions and under different treatments
using FIAT LUX. This would allow rapid identification of a solution to fight off the
phytopathogen.
Figure 5 - FIAT LUX will be of benefit to scientists, and researchers, to
companies in their R&D activities, to farmers and consumers.
During the brainstorming regarding the choice of the subject, we
quickly realized that the increasingly grave and unaddressed consequences of climate disruption
were a serious concern for all of us. We also realized the extent of food resource mismanagement
and overproduction. In addition, excessive pesticide use and increased trade have made the
situation worse.
Furthermore, the collaboration with our university’s MAP laboratory
made us aware of the growing risk linked to the emergence of the phytopathogenic bacterium Dickeya
solani. After several discussions, we realized that this subject was within our reach
and that it was of great interest and need to several companies in the industry. The urgency of
the situation and the huge potential our project could have, as well as the issues it will
attempt to tackle, confirmed our choice of subject. This new in situ study technique
seems to meet the needs of several companies in the agricultural sector and is optimized to
understand the interactions between plants and their pathogens. Our team drew on the work
already done in the field for inspiration and for developing protocols.
These 3 promising papers encouraged us in our research and we built upon them to create the future of the field. To further develop our project, our team also relied on the work done by previous iGEM teams, for inspiration.
To go beyond the creation of a bioluminescent system similar to that
of other teams, we planned to take their research one step further, and proposed an application
of this system as a tracking tool in agriculture.
This new tool, FIAT LUX, is based on the ilux operon, placed
on a vector with a transfer capacity.
ilux is the operon in charge of producing light. It is a modified lux operon from
Photorhabdus luminescens described in the Gregor et al. publication in 2018. The
ilux operon came from coexpression of an additional FMN reductase and subsequent
error-prone mutagenesis of the complete lux operon. This ilux operon has an
approximately sevenfold increase in brightness when expressed in Escherichia coli, thus
allowing single E. coli cell imaging with enhanced spatiotemporal resolution over several
days (Gregor et al. 2018). It is composed of the following genes: iluxC, iluxD,
iluxA, iluxB, iluxE and ilux-frp. Each of these genes has a specific
role:
Figure 6 - Diagram explaining the biochemical pathways generated by the ilux operon. Left: ilux operon coding for the proteins below (luciferase, fatty acid reductase, FMN reductase). Right: enzymatic reaction behind the ilux operon
Our team started working with the ilux operon, and transformed it into fiatlux: a standardized and customisable Biobrick. A more detailed description of our tool is provided on the Experiments page.
Our core ambition, as a team of highly motivated students, was to change today’s agricultural practices, by providing a non-intrusive in situ tracking tool, allowing a long-term study of bacterial propagation within a living organism. On a wider scale, this tool enables progress to be made in solving worldwide problems such as agricultural food waste and environmental issues, and will be valuable for the scientific community, for farmers all over the world, and for consumers, thereby helping to achieve the overall goal of "Local people solving local problems, using synthetic biology, everywhere around the world".
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