An Overview of the Structure, Metabolism, Applications, and Implications of Aerobic Microbial Biofilms

Subject Areas : Biotechnological Journal of Environmental Microbiology

Robab Bayrami ¹ , Aram Ebadati ² , Fatemeh Babaei ³ , Zeynab Moradi ⁴ , Mohammad Faezi Ghasemi ⁵

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Received: 2025-01-14 Accepted : 2025-02-10 Published : 2025-01-15

Keywords: Biofilm, Metabolism, Metagenomics, Microscopy, Microorganism,

Abstract :

Aerobic microbial biofilms are complex communities of microorganisms embedded within a self-produced extracellular polymeric substance(EPS) matrix and adhered to biotic or abiotic surfaces. In aerobic environments, these structures form a unique layered arrangement due to oxygen and nutrient gradients, leading to metabolic division of labor, cross-feeding, and a significant increase in resistance to antimicrobial agents. Studying these communities is essential for understanding their biological applications and addressing associated clinical and industrial challenges. This review was conducted by integrating findings from multiple studies.The methodologies employed included:Advanced Microscopy Techniques such as Confocal Laser Scanning Microscopy (CLSM) for 3D imaging and Scanning Electron Microscopy (SEM) for surface morphology examination.Molecular Analyses including metagenomics and metatranscriptomics to identify microbial composition and metabolic pathways.Mathematical Modeling and Computer Simulation, notably using an Active Fluid Model to simulate vertical growth dynamics and predict biofilm height using software like MATLAB and Python.Laboratory Systems and Bioreactors to simulate environmental conditions and assess biofilm performance in pollutant removal.The findings revealed that aerobic biofilms possess a multilayered structure with distinct metabolic zones.The surface layer, with high oxygen access, activates oxidative pathways like glycolysis and the TCA cycle. The middle and deep layers, with progressively decreasing oxygen, rely on the glyoxylate pathway and fermentative metabolism, respectively. This metabolic stratification enhances structural stability and increases drug resistance by up to 1000-fold compared to planktonic cells. From an application perspective, these biofilms were highly effective in bioremediation of pollutants, wastewater treatment, heavy metal recovery, and energy generation in microbial fuel cells. The active fluid model accurately predicted vertical biofilm growth and the impact of factors such as cell death rate.Due to their layered structure and flexible metabolism,aerobic biofilms present both valuable opportunities for biotechnological and environmental technologies and major challenges in healthcare and industry. Their beneficial applications in water and soil treatment are undeniable; however, their high resistance to antibiotics poses a serious public health threat. Future strategies should focus on developing green technologies for the targeted exploitation of these structures, alongside their effective control by interfering with specific metabolic pathways (e.g., c-di-GMP signaling) and EPS matrix enzymes.

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