Advances in automated enrichment and directed domestication technologies and their applications in the development of environmental functional microorganisms

Abstract:

Environmental functional microorganisms play a key role in environmental engineering processes such as pollutant degradation, wastewater treatment, and resource utilization. Conventional enrichment and directed domestication technologies often have limitations such as long operational cycles and low throughput, being difficult to meet the demands for rapid screening, enhancement, and engineering application of functional microorganisms under complex environmental conditions. In recent years, advances in continuous cultivation, high-throughput cultivation, microfluidic chips, intelligent bioreactors, and automated adaptive laboratory evolution (ALE) have provided new approaches for the precise screening, targeted enhancement, and feedback-based process control of environmental functional microorganisms. This review systematically summarizes the basic principles and key platforms of automated enrichment and directed domestication technologies, as well as their application progress in the development of microorganisms for petroleum hydrocarbon and polycyclic aromatic hydrocarbon degradation, wastewater denitrification, heavy metal tolerance, and emerging contaminant degradation. In addition, by integrating our research group’s work on targeted environmental microorganism isolation devices, programmable logic controller (PLC)-driven ALE systems, and the screening of functional strains for halogenated organic pollutant degradation, this review analyzes the current limitations of these technologies in in situ simulation, maintenance of mixed microbial community interactions, screening of non-growth-coupled phenotypes, and engineering scale-up. Finally, future directions are proposed for the application of automated enrichment and directed acclimation technologies in the exploration, functional enhancement, and engineering application of environmental functional microbial resources. This review is expected to provide theoretical and methodological support for improving the technological framework of environmental functional microorganism development and facilitating its translation into engineering practice.