Kaleidoscope Of An Urban Farm Microbiome: Sustainable Crop Production

Image sourced from NUS faculty of science

Image sourced from NUS faculty of science



NUS researchers have reconstructed nearly a thousand microbial genomes from green leafy vegetables commonly consumed in Singapore to improve the quality of urban farmed crops. This study is a first step towards uncovering the microbiomes associated with urban farmed vegetables. It also marks progress in developing bio-based solutions for local food production. The microbiomes refer to the microbial community that typically interacts extensively with a plant, performing various plant beneficial activities.

Although our understanding about microbiomes and their ability to promote plant growth is advancing, most of this knowledge comes from non-crop plants or model species in controlled environments. Lately, microbiomes have garnered a lot of interest and diverse stakeholders in this domain are working together to create lucrative bio-based solutions to pave the way for sustainable crop production. To achieve this goal, in-depth understanding of crop-specific microbiomes is important. Cataloguing crop-specific microbial genomes is an important research priority as a first step to reach this goal. Surprisingly, high-quality crop-specific microbial genome collections have been lacking.

Through this paper, the research team led by Prof Sanjay SWARUP from the Department of Biological Sciences, NUS plan to fill this gap at least partly by creating a valuable resource of microbial genomes from urban farmed vegetables (see Figure). This resource will enable a wide range of comparative studies that seek to understand the different functional aspects of vegetable crop-associated microbiomes and for devising new strategies for microbial cultivation in the future.

This initiative is a part of a cross-disciplinary project in collaboration with a local urban farm over the last four years. This study is timely and unique, given that green leafy vegetables are suitable for a variety of farming formats that are being adopted by diverse stakeholders as part of Singapore’s “30 by 30” goal of having one-third of the food that the nation needs to be grown locally by 2030. The wealth of information generated from this resource will aid in cultivating high quality green leafy vegetables with reduced chemical inputs.

From the assembled microbial genomes, the researchers have identified the functional potential for nutrient provisioning, biocontrol and phytostimulation which will be validated further in a series of systematic studies aimed at specific crop trait enhancement. Outcomes from these studies will be instrumental for selecting and screening microbial strains for developing bio-based solutions to improve crop production.

Dr PAVAGADHI Shruti, the senior manager of the research team said, “As the world grapples with the COVID-19 pandemic which, adversely impacts food supply-chains, we need urgent reformative actions to build greater food resilience and security. Through this study, we are taking the first step towards building innovative solutions to boost local production in a highly sustainable manner.

Prof Swarup added, “Green-leafy vegetables are nutrient-dense and packed with bioactive compounds known for promoting human health. These leafy greens are short-cycle crops suitable for adoption in various farming formats. Focusing our research priorities on this food group will address food and nutritional security and cater to both quantity and quality aspects of food production.”


Illustration depicts the experimental design for the study.  Three commonly consumed green-leafy vegetables were sampled at two growth stages and their associated microbiomes were harvested for metagenome sequencing and analyses. The phylogenetic tree on the right side represents the maximum likelihood tree of all bacterial species-level MAGs (Metagenome Assembled Genomes) associated with the green-leafy vegetables.  Concentric rings moving outward from the tree show the detection of assembled microbial genomes across the three vegetable crops computed globally, its genome completeness, and genome redundancy, respectively. The outermost bar plot shows the size of the assembled microbial genomes. 


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