The development of synthetic biology and gene editing technology has led to the integration of nonconventional microorganisms into industrial biotechnology, aiming to unlock their robust potential. It has fostered the ‘Next Generation of Industrial Biotechnology’ (NGIB), with extremophilic microorganisms serving as the foundational chassis. Due to their unique salt tolerance and robustness, halophilic microorganisms are regarded as promising candidate chassis cells for NGIB (Chen and Jiang, 2018). Halophiles are salt-loving microorganisms that require certain concentration of salts to grow best, including bacteria, archaea and eukaryotes (Oren, 2008). Depending on their salt requirement, halophiles are broadly classified into four categories. Moderate and borderline extreme halophiles grow at a salt concentration of 0.5–2.5 M and 1.5–4.0 M, respectively. Extreme halophiles require a salt concentration of 2.5–5.2 M for their growth while halotolerant microorganisms do not require salt for growth but can thrive at high salt concentrations (Kushner, 1978). Currently, a range of halophilic microorganisms are being utilized in various industrial production processes.

For example, fast-growing haloalkaliphilic Halomonas species have been used for the industrial production of polyhydroxyalkanoates (PHA) and ectoine (Chen et al., 2022). Its haloalkaliphilic nature confers Halomonas with fitness and less susceptibility towards contamination for open fermentation under non-sterile conditions (Tan et al., 2011). Additionally, Halomonas exhibits excellent tolerance to high concentration of acetate and efficiently produce polyhydroxybutyrate (PHB) from it, which is a more cost-effective carbon source compared to glucose (Zhang et al., 2022). Thioalkalivibrio species are also a type of haloalkaliphilic, sulfur-oxidizing and chemolithotrophic bacteria that has been applied in the biological desulfurization of high-alkali and high-sulfate waste water (Sharshar et al., 2020). On the other hand, Dunaliella salina is a photoautotrophic unicellular microalga that can survive at 0.05 M to 5.0 M of NaCl. It can accumulate significant amounts of β-carotene, currently being considered as the foremost natural and commercial source of β-carotene (Lamers et al., 2008). In addition, when D. salina is cultivated under high-salinity conditions, it achieves an intracellular glycerol content exceeding over 50%, thus positioning it as a viable glycerol producer (Hosseini Tafreshi and Shariati, 2009). Additionally, solvent stable halophilic proteases are being applied in the detergent and textile industries to enhance the washing performance (Mokashe et al., 2018). For example, an alkaline protease secreted by Salinicoccus sp. UN-12 exhibits tolerance to high alkalinity, high salinity and high temperature. The proteolytic activity remained unaffected in the presence of various organic solvents, cyclodextrin, disodium cocoamphodiacetate, ionic liquids, hydrotropes, and even under ultrasound condition. These properties made this protease highly suitable for mixing with detergent formulations (Mokashe et al., 2017).

To enhance the efficient and energy-conscious utilization of halophilic chassis cells in industrial application, it is crucial to develop or refine genetic manipulation systems swiftly. The genetic manipulation platform comprises genetic transformation methods, plasmids along with essential genetic components, and gene editing systems. Extensive studies have been performed to develop feasible genetic toolkits in halophiles. This manuscript provides a comprehensive overview of genetic manipulation techniques applied to diverse halophilic microorganisms, including bacteria, archaea, and microalga contributing to biotechnological advancements (Fig. 1). These genetic toolkits aid the development of halophilic microbial chassis with desirable features and thus significantly contributes to the yield of bioproducts. The present review will definitely help to address the concerning challenges and present new opportunities in the engineering field of halophiles.