There are over 90, 000 types of pollutants on our planet, which are distributed in the air, soil, and water bodies. According to the WHO report in 2016, 1.3 million people die each year from exposure to pollutants. Fortunately, there are some microorganisms in the natural environment that can grow on pollutants as nutrients. They "eat" pollutants and convert them into carbon dioxide, water, or other harmless components— this process is known as "biodegradation". Scientists can use microorganisms to degrade pollutants in the environment. But in real-world pollution scenarios, such as industrial wastewater and marine oil spills, multiple toxic organic pollutants are mixed with each other, and microorganisms can degrade only one or a few of the pollutants, making it difficult to biodegrade complex organic pollutants in practice.

To address this problem, researchers from Shanghai Jiao Tong University, Shenzhen Institute of Advanced Technology， Chinese Academy of Sciences, and Chinese Academy of Agricultural Sciences applied synthetic biology to construct an engineered bacterial strain to remediate five organic pollutants in industrial wastewater and soil. This project has resulted in significant progress and was published on May 7, 2025.

The researchers used Vibrio natriegens, a fast-growing bacterium with high salinity tolerance, as the chassis cell. To enhance genome editing, researchers optimized the efficient natural transformation method and subsequently developed an iterative genome editing method named INTIMATE, which can accurately insert long DNA fragments into a specific site of the genome of V. natriegens, and repeatedly insert new DNA fragments into the previously constructed engineered bacterial strain. This method enabled continuous expansion and modification of the same strain. After multiple rounds of iterative editing, the researchers obtained the final strain, VCOD-15, which was capable of degrading five organic pollutants at the same time. The results of simulated application tests showed that VCOD-15 could remediate all of the five organic pollutants in saline wastewater samples from oil refinery and chemical plants in 2 days.

This research successfully developed a technical platform for the construction of complex organic pollutant degradation bacterial strains, which realized the entire process from the designing and synthesizing of metabolic pathways to the construction, testing, and application of pollutant degrading strains in real-world scenarios. It provides a cheap and environmentally friendly solution for global challenges such as saline industrial wastewater emission, offshore oil spills, and microplastic pollution. At the same time, INTIMATE provides a universal technical platform to integrate multiple metabolic pathways within a single strain and expand the functions of engineered strains. It can be extended to the construction of other pollutant degradation bacterial systems, as well as other applications such as natural product synthesis and high-value chemical cell engineering construction.

Dr. Su Cong from the Shenzhen Institute of Advanced Technology， Chinese Academy of Sciences, Cui Haotian and Dr. Wang Weiwei from Shanghai Jiao Tong University are the co first authors of the article. Prof. Dai Junbiao and Prof. Tang Hongzhi are co-corresponding authors of the article. The collaborators of the article include Cheng Zhenyu, Yang Mengqiao, Li Ye, and He Siyang from Shanghai Jiao Tong University, Dr. Liu Yong, Wang Chen, and Qu Liwen from Shenzhen Institute of Advanced Technology， Chinese Academy of Sciences, and Cai Yuejin, Zheng Jiaxin, and Zhao Pingping from Chinese Academy of Agricultural Sciences. Prof. Xu Ping and Prof. Li Yuehui from Shanghai Jiao Tong University and Prof. Wang Qinhong from Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences provided important help for this research work.