IGEM Groningen 2020/21 - RootPatch

Motivation

Potatoes are one of the most common agricultural crops globally. Annually, a loss of est. €460 million worth of potato crop is incurred due to Potato Cyst Nematodes (PCNs), which induce the development of harmful syncytia on the roots by inserting genome altering chemicals. A syncytium is a single cell or a cytoplasmic mass that contains several nuclei. Formation of syncytia on potato roots results in the withdrawal of nutrients from the crop and dramatically reduced tuber size. Moreover, female nematodes form cysts that can survive in the soil for up to 20 years. When the environmental conditions are favourable for them to hatch, the cysts release 200 to 300 juvenile nematodes to invade the plant roots. In the north of the Netherlands (our local area), potato farming is negatively affected by the PCN, Globodera pallida (Been, T.H. and Schomaker, C.H. 1998).

The control of pathogens and pests using pesticides has substantially increased crop yields and helped to cope with the increasing food demand of the world’s population. However, the extensive use of broad-spectrum pesticides has had a detrimental impact on soil biodiversity which is critical for the maintenance of important environmental processes such as nutrient cycling and soil detoxification (Prashar, P.
and Shah, S. 2016).

RootPatch

In this project, we use synthetic biology to develop an innovative and sustainable alternative to the conventional broad-spectrum pesticides that harm ecologically important, soil-dwelling organisms. Our team aims to use the naturally occurring soil bacterium Bacillus mycoides (isolated from the potato root endosphere), which can form biofilms on the surface of potato roots. The potato tubers/seeds will be covered in the B. mycoides inoculant before they are planted. This way, the biofilm will develop along with the crop, and the grown potato plants will have their roots fully covered with our engineered B. mycoides.

To protect the potato plant from G. pallida, the B. mycoides will be genetically engineered to constitutively produce and secrete Neuropeptide-like Proteins (NLPs). NLPs are a class of nematode neuropeptides, which modulate the activity of the nematode’s neuronal network. In a recent study, specific NLPs were found to reverse the chemotactic attraction of PCNs towards the crop root exudates, thus reducing their infectivity. Interestingly, a subset of NLPs act specifically on G. pallida juveniles and didn’t show any effect on other nematode species, making the use of NLPs a high precision strategy.The NLPs we will be using induce a repellent behaviour of G. pallida juveniles towards the potato root exudates, thereby preventing the G. pallida juveniles from infiltrating the root system. Since survival of the parasitic G. pallida juveniles is dependent on root infection, they will eventually die of starvation (read more on NLPs: Nathoo, A.N, et al. 2001 and Warnock, N.D. et al. 2017).

Goal

Conventional pesticides against nematodes (nematicides) are often non-specific and have harmful side effects, which has led to their phase-out in many countries. The broad-spectrum fumigant methyl-bromide, for instance, is a gas highly toxic for humans and implicated in the depletion of the ozone layer which led to the stepwise abolishment of its use during the 2000s. Alternative nematicides and soil treatments, such as steam sterilization of soil or alternative chemical treatments have been proposed. However, these approaches harm many non-target organisms such as beneficial nematode species which promote the integrity of the soil ecosystem by nitrogen mineralization and the regulation of soil-populations (Ferris, H, 2010 and Curell, C, 2013). 

The goal of RootPatch is to prevent the loss of potato crops caused by the PCNs. With RootPatch we are hoping to create an innovative way of protecting the potato crop that is safe to the environment and just as efficient as common nematicides. Importantly, the biological solution we use is based on specific neuropeptides which are only active against PCNs and not against other beneficial nematodes found in soil. Eventually, RootPatch may abolish the need for broad-spectrum chemical pesticides for a wide variety of pests and consequently increase soil health and the biodiversity of soil-dwelling organisms.

Safety

When working with genetically modified organisms (GMOs) in the environment, safety concerns are critical. To prevent the spread of our genetically modified soil bacteria into the surrounding environment, we are therefore developing a kill switch which makes the survival of the bacteria dependent on substances secreted by the potato plant into the rhizosphere (e.g. the potato root exudate). That is, only GMOs that stay in the rhizosphere will survive, but not those who escape and spread. This ensures safe use of the GMO only at the sites needed.

Current regulations on the use of GMOs in the EU are very strict. The EU has had a precedent of risk-averse regulations which means precautionary principles are the thumb rules for using GMOs in food crop protection, since the potential risks of GM foods is not known completely. Decisions tip on the side of vigilance and need a high level of proof for product safety (more information here).

Outlook

The eventual long-term goal of RootPatch is to provide potato farmers with a cheap, robust and environmentally friendly way of combating potato cyst nematodes. Our project aims to reduce pesticide use and protect crops by engaging them in a symbiotic relationship with genetically modified soil bacteria in a safe and responsible way. Excessive pesticide use has dramatically impacted soil ecosystems and finding a sustainable alternative to pesticides will protect biodiversity all over the world. The bacterial inoculant could be used in the form of an easy to use liquid which is sprayed onto the potato tubers prior to seeding in a sowing machine. Due to the modular design of RootPatch, this strategy could potentially be used for other pathogens and crops by swapping one or more parts of the genetic circuit. If this could be realized then RootPatch may not be just a single solution to an individual problem, but the start of a new paradigm for crop protection. This versatility opens up a lot of possible applications for RootPatch-like technologies in the future.

Due to the changes to iGEM related to COVID-19, our team will presumably not be able to perform laboratory experiments. Instead we follow the two-phase iGEM project in which we design and plan the project for the actual implementation by next year’s iGEM team. We will develop in silico models and do profound experimental planning of our project to lay ground for next year’s team. The models will focus on the efficiency of RootPatch in nature. Using population dynamics, we can investigate the robustness of RootPatch in repelling nematodes and discover weaknesses we should be able to see in the lab. In the end, we believe that the COVID-19 situation has also given opportunities to put time into aspects of synthetic biology that would normally not get the attention they deserve.

Network and iGEM community

We do not have any collaborations with other iGEM teams at the moment but we would certainly hope to establish many fruitful collaborations in the future. In parallel with our Rootpatch project, we are developing a Massive Online Open Course (MOOC) on the ethics of genetic modification. The learner is encouraged to think about what defines a GMO and if the usage of GMOs is desirable in varying scenarios. To realize this project we are working together with several companies and institutions like the University of Groningen ScienceLinx, science museum NEMO Amsterdam and online educational platform FutureLearn. As participants in the iGEM competition, our team would like to inform a broad public about genetic engineering principles and let them build a more educated opinion on the use of GMOs. We feel that if we can educate a broad public, synthetic biology will help resolve the debate surrounding the application of GMOs by taking away the prejudices and building a support base for its use.

The team

We are team iGEM Groningen from University of Groningen, Netherlands. Our PI is Prof. Dr. Jan Kok, Professor of Molecular Genetics, Prof. Dr. Sonja Billerbeck, Assistant Professor of Molecular Microbiology and Rianne Prins, PhD student of Molecular Microbiology. Our team consists of 12 members.

Team iGEM Groningen 2020 has members from 6 countries (Netherlands, India, Russia, Romania, Canada and Germany). Our university has been an active participant at the iGEM competition. Team Groningen 2012 even won the Grand Prize for their Food Warden project! So, having iGEM alumni has been useful in gaining an in-depth understanding of this competition and has allowed us to build on a pre-existing community. Our team is interdisciplinary with members studying/having prior experiences on subjects like Biomolecular Sciences, Zoology, Chemistry, Biotechnology, Molecular Neurosciences and Biomedical Engineering.

You can follow the iGEM Groningen 2020 team on instagram, Facebook and Twitter or if you want to contact them directly, you can write an email to igemgroningen2020@gmail.com.

You can also support their crowdfunding campaign.