The escalating expansion of industrial and food sectors is a significant source of waste, including traditional solid waste, agricultural by-products, processing residues, and biomass waste (Singh et al., 2021). Based on statistical projections, it is anticipated that global food waste will escalate to 2.6 billion tons by the year 2025, consequently leading to an annual economic loss estimated at $400 billion (Singh et al., 2023). Traditionally, waste disposal methods have mainly involved landfilling, incineration, and physical adsorption, all of which are costly and environmentally polluting (Fig. 1). For instance, incineration costs between $40 to $100 per ton of waste processed (Mukherjee et al., 2020). Moreover, the incineration not only generates carbon dioxide, hindering the achievement of global carbon neutrality goals, but also releases harmful substances such as sulfur dioxide, dioxins, and heavy metal vapors (Wen et al., 2023). In contrast, bioconversion pathways aligned with the principles of the 3Rs (reduce, recycle, and reuse) have become the current focus (Barnett et al., 2023). By pretreating waste and selecting suitable microorganisms, it is possible to achieve the precise degradation of waste, transforming it into valuable resources (Fig. 1).

Among the tens of thousands of microbial species, oleaginous microorganisms (lipids >20% of dry weight) can effectively utilize low-cost raw materials and wastes to produce microbial oils for renewable and sustainable energy sources as well as high-value chemicals (Jin et al., 2015). For example, filamentous fungi like Mucor circinelloides and Mortierella alpina are often utilized for the production of polyunsaturated fatty acids (PUFAs) such as γ-linolenic acid (GLA) and arachidonic acid (ARA) (Khot et al., 2020). Various microalgae species, including Nannochloropsis sp., Crypthecodinium cohnii, and Chlorella sp., are utilized for the production of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and biodiesel (Kumar et al., 2022). oleaginous yeast like Yarrowia lipolytica can produce citric acid, linoleic acid (LA), and biofuels among other lipid chemicals (Lopes et al., 2022). Indeed, in the process of turning waste into treasure, the key criteria for selecting oleaginous microbial species include their high robustness, environmental tolerance, ability to efficiently utilize various carbon/nitrogen/phosphorus sources in complex substrate fermentation environments, and high-yield performance under simple production processes. Therefore, researchers have shifted their focus to Thraustochytrids, a type of heterotrophic microorganism originating from the marine. They combine the advantages of microalgae and other oleaginous microorganisms, exhibiting high growth rates and robust lipid accumulation capabilities. Unlike microalgae, they can achieve high-density fermentation without the need for light and CO2, and possess the ability to produce various lipid chemicals, including biodiesel, PUFAs, and lipophilic terpenoids (Leyland et al., 2017; Song et al., 2023).

It is worth emphasizing that Thraustochytrids demonstrate significant advantages in converting waste into treasure within the scope of oleaginous microorganisms. Firstly, Thraustochytrids have been identified to encompass nine genera, each with unique production characteristics (Marchan et al., 2018). Aurantiochytrium and Schizochytrium typically employ the polyketide synthase pathway (PKS pathway) for synthesizing docosapentaenoic acid (DPA, n-6 type) and DHA, accumulating them in lipids by over 60% (Guo et al., 2020; Wang et al., 2023). In contrast, Parietichytrium utilizes the elongase-desaturase pathway (ELO/DES pathway) to achieve the synthesis of various types of PUFAs, including ARA, docosatetraenoic acid (DTA), DPA (n-6 and n-3 types) and DHA (Ishibashi et al., 2021). In addition, it also possesses the industrial production potential of various lipid chemicals such as biodiesel, squalene and carotenoids. These characteristics lay the foundation for customized production based on waste characteristics. Secondly, Thraustochytrids exhibit excellent environmental resilience. As marine microorganisms, they can thrive within a wide salinity range of 20% to 34%. They are frequently found in surface sediments, salt marshes, and various wastewater environments (Song et al., 2023). Their inherent ability to express extracellular hydrolytic enzymes (cellulases, pectinases, lipases, and proteases) enables them to degrade substances detrimental to their growth environment, hydrolyzing them into carbon/nitrogen sources for utilization (Marchan et al., 2018). These features alleviate concerns about the growth conditions of Thraustochytrids when utilizing waste, thereby reducing waste treatment procedures and costs. Furthermore, as a class of hosts that have obtained safety certification from the United States Food and Drug Administration (FDA), widespread commercial use has endowed Thraustochytrids with mature industrial production processes (Wang et al., 2021). Compared to other oleaginous microorganisms, their cell walls are easily treated, eliminating the need for enzyme treatment or organic solvent extraction during downstream lipid extraction. High lipid recovery can be achieved with just a three-phase centrifuge (Huang et al., 2023). Currently, the main limiting factor for its widespread application is the contradiction between production costs and value. For instance, DHA, the flagship product derived from Thraustochytrids, commands a production and selling price that is more than twice that of fish oil (Xu et al., 2020; Jesionowska et al., 2023). However, this drawback has paradoxically propelled research into utilizing Thraustochytrids for production using waste materials, achieving a win-win situation for waste management and low-cost fermentation.

In this review, the organic integration of efficient waste utilization and Thraustochytrids fermentation will be the primary focus. This encompasses strategies revolving around the efficient utilization of different waste types, fermentation regulation, genetic engineering and strain evolution to enhance waste utilization. Additionally, appropriate circular economic analysis will also be discussed. The aim of this review is to emphasize the value of Thraustochytrids in converting waste into valuable products and provide insights into precise cost reduction for future commercial production.