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Natural Products Produced by Fermentation Hold Potential to Help Singapore’s Farming Economy Grow

SMART team’s genetic breakthrough set to improve crop yields in urban farms.

by Dr Sarojam Rajani and Dr Kang Zhou

Fast-forward a decade, to a time when Singapore grows a third of the food it consumes. Imagine the scenario.

This tiny speck of just 724.2 square kilometres, most of which by 2030 will be given over to an even denser urban sprawl than it is today, will by then be home to thriving and bustling farmers’ markets in every district, full of fresh, locally grown produce.

Supermarket shelves will be brimming with fruit and vegetables that just a day before had been growing on trees and in the ground. Even stores in agriculture-rich parts of the world would struggle to compete with Singapore for freshness.

The country will become less beholden to imports, as it is today. Though the world will have almost a billion more mouths to feed by 2030, according to the United Nations, Singapore will not be one of those countries that do not grow their own food.

Given that more than nine-tenths of the food Singaporeans currently consume arrives from overseas, this scenario may easily be dismissed as a pipe dream. But it is also the government’s goal, and a realistic one too, in part through some of the breakthroughs we have been making at Singapore-MIT Alliance for Research and Technology (SMART), Massachusetts Institute of Technology’s research enterprise in Singapore.

A tiny, highly urbanised country like Singapore must approach farming very differently to a nation with vast tracts of fertile land and an age-old agricultural tradition. We need to force across new techniques onto urban farming by developing practices and materials to get the most out of the limited space that is available.

At SMART, our goal is to introduce disruptive and sustainable technologies for agricultural precision, which we refer to by an acronym of these words, DiSTAP – one of our six interdisciplinary research groups. Among these are ways we can contribute to the transformation of agriculture, alongside other players in the industry, on an island that would otherwise have little going for it in this regard.

As part of our investigations, we have been exploring new ways that microbial fermentation can create non-synthetic pesticides for urban farms, in the form of small volatile organic molecules (VOCs).

VOCs are lipophilic compounds derived from plant metabolic pathways with low molecular weight, low boiling point and high vapour pressure that allow them to act as signal molecules over short and long distances.

Some VOCs have been shown to stimulate plant growth while modulating growth, stress, nutrition, and health processes, while some others can repel pathogenic insects and microbes to defend crops. By doing so, they can not only encourage increased biomass, they also prompt a preservative effect, so produce can be stored for longer while maintaining quality.

But these compounds do not come without their challenges. They are extracted from plants in the form of essential oils and due to their volatility, they may evaporate quickly into the environment. In this way, their use is often in the hands of regulators who must adjudicate on their wider use.

Some VOCs by their nature are not very stable and they can be seen to react with air to form inactive or toxic by-products. There may not be an issue with storing them, as this can be done while they are in an anaerobic condition, but oxidation can occur while they are being used in farms.

In January 2018 , we began looking at how we can take genes from plants and place them into microbes. By achieving this, we would be able to produce VOCs from cheap substrates and even waste materials, such as food leftovers. Since it is time-consuming to genetically fine-tune the microbes, we have developed a standard to speed up the process.


Guanine/Thymine DNA Assembly Technology

Our research, recently published in Nature Communications, has led us to a solution that will result in faster, cheaper, more accurate and near-scarless plasmid construction, using standard and reusable parts, that is compatible with most popular DNA assembly methods. This work is essential because current methods to construct plasmids, which are an essential tool used in the genetic editing of microbes, are as expensive as they are laborious. We saw this step as a hold-up for the whole genetic engineering process.

To accommodate research into genetic engineering, laboratories must traditionally source custom-made genetic material from third-party suppliers, though we would use only a fraction of it—sometimes as little as one percent of what we have available. As each material is customised for research, we have to re-order more each time, which causes delays and adds further costs to the production.

Our new Guanine/Thymine (GT) DNA assembly technology, significantly changes things by enabling genetic engineers to reuse their materials. It provides a simple method to define the biological parts as standard DNA parts by efficiently adding any two barcodes to both ends of almost any fragment without leaving scars in most cases.

Moreover, unlike previous attempts at creating standardised materials which have an accuracy of up to 50 percent, the GT technology is close to 90 percent precise. As a near-scarless plasmid construction, the technology is substantially faster, being able to stitch up to seven parts to a DNA, as opposed to just two parts for other methods of similar accuracy.

Under GT technology, the microbial production of VOCs can further alleviate the challenges we face in using these compounds by offering ways to simplify their composition and to reduce their production cost.

By achieving such a high level of exactness, we expect that the huge cost and time savings that stem from it will help us uncover new fermentation processes for the manufacture of environmentally friendly chemicals to make urban farming in Singapore more efficient and safer. This technology can also be applicable to all genetic engineering fields, and we are actively looking at means to deploy it, even outside of agriculture.

Our work is motivated by the challenges faced by Singapore and other cities that need to import much of their food. And in the next few decades, as the world’s population increases, this problem is bound to worsen.


Volatile Organic Chemicals in Urban Farming

DiSTAP has been working to improve farming so we can make food more plentiful, safe and cost-effective in an urban setting. To this end, we are using this new class of VOCs emitted by plants to enhance this process.

There is also legitimate concern by consumers worldwide about the pesticide residue in foods. Hopefully through this approach we can get rid of some of the toxic synthetic chemicals that are commonplace in pesticides and fertilisers and replace them with wholly natural compounds, such as those that are naturally created by plants to protect themselves from predators.

For the VOC products our research looks to develop, we hope that small facilities could be established in Singapore that could manufacture these for use in urban farms in the country. This will, of course, deliver further economic value from our work to Singapore’s economy.

It is still in its early days, however, in terms of research into VOCs in agriculture across the world. We have yet to see many breakthroughs in this field, but by having a cost-effective and plentiful supply of the materials we need to take our studies forward, we now have a workable foundation.

In doing so, Singapore’s dream of bringing a degree of agricultural sustainability to its urban landscape is bound to come closer to reality. Our work is now being shown to open up a whole range of possibilities for VOCs to be employed in sustainable agriculture. [APBN]


  1. Ma, X., Liang, H., Cui, X., Liu, Y., Lu, H., Ning, W., Poon, N. Y., Ho, B., and Zhou, K. (2019). A standard for near-scarless plasmid construction using reusable DNA parts. Nature communications, 10(1), 3294. doi:10.1038/s41467-019-11263-0

About the Authors

Dr. Sarojam Rajani, Principal Investigator, DiSTAP, SMART, MIT’s Research Enterprise in Singapore, and Temasek Life Sciences Laboratory Ltd.



Dr. Kang Zhou, Principal Investigator, DiSTAP, SMART, MIT’s Research Enterprise in Singapore, and Assistant Professor at NUS