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Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions

Received: 4 September 2025     Accepted: 17 September 2025     Published: 10 October 2025
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Abstract

A biofilm in aquaculture is a community of microorganisms, including bacteria, algae, fungi, and others, that forms a complex and structured layer attached to surfaces within water systems. Aquaculture bioreactors rely on biofilms as critical microbial consortia that drive water quality improvement through nutrient cycling and organic matter degradation. This review highlights the dynamic succession and diversity within biofilm microbial communities, particularly emphasizing key bacterial groups such as Planctomycetes, Bacteroidetes, nitrifiers, and denitrifies that mediate ammonia and nitrogen removal. Biofilms form robust structures through sequential attachment, growth, and maturation stages, influenced by physical and chemical parameters. Molecular tools like 16S rRNA gene sequencing have advanced our understanding of biofilm ecology, revealing community shifts responsive to environmental and operational conditions. Biofilms also contribute to pathogen suppression yet pose challenges through antimicrobial resistance, necessitating balanced management to optimize treatment efficiency without biomass overgrowth. Promising future directions include engineering microbial communities and incorporating probiotics to enhance functional biofilms tailored for sustainable aquaculture. This collective knowledge supports improved aquaculture sustainability by ensuring efficient water treatment, fish health, and environmental protection. Continued integration of molecular techniques and biofilm management strategies will enhance bioreactor design and operation for resilient, eco-friendly aquaculture systems. The aim of this review is to assess the role of biofilms and microbial community dynamics in aquaculture bioreactors for effective water quality control and sustainable aquaculture production.

Published in American Journal of Bioscience and Bioengineering (Volume 13, Issue 5)
DOI 10.11648/j.bio.20251305.12
Page(s) 99-105
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2025. Published by Science Publishing Group

Keywords

Biofilm, Aquaculture Bioreactors, Microbial Community Dynamics, Water Quality Control, Nitrification, Denitrification, Organic Matter Degradation

1. Introduction
Biofilms play a crucial role in aquaculture water treatment by forming attached communities of microorganisms on submerged surfaces that contribute to water quality improvement . These biofilms harbor nitrifying bacteria that convert toxic ammonia waste into less harmful compounds through nitrification, reducing the need for water exchange and minimizing harmful nitrogen accumulation in culture systems . Additionally, biofilms provide a nutritious food source for aquatic species and shelter, thus supporting growth and survival. Their role in trapping suspended solids, breaking down organic matter, and enhancing microbial activity further stabilizes the aquatic environment, making biofilm-based technology a sustainable and cost-effective tool for aquaculture production, especially benefiting resource-limited farmers .
Microbial communities within biofilms participate actively in critical biogeochemical cycles such as nitrogen cycling, including aerobic nitrification and anaerobic denitrification, with the presence of both aerobic and anaerobic microenvironments . These microbial processes not only improve water quality but also reduce the buildup of pathogenic bacteria by lowering nitrogenous compounds to safe levels . Moreover, biofilm microbial activity enhances the removal of phosphorus and organic matter, thus maintaining a balanced ecosystem conducive to healthy aquaculture practices. Microbial biofilms also contribute enzymes and bioactive compounds that promote immune function and growth in cultured organisms .
The integration of biofilm systems into aquaculture aligns closely with sustainable aquaculture practices by minimizing environmental impact, reducing the frequency of water exchange, and recycling nutrients naturally within the system . This promotes efficient resource use, decreases water pollution risk, and supports healthier and higher yields in fish and shellfish production. Biofilm-based technologies thus offer an eco-friendly approach to wastewater treatment and nutrient control in both small-scale and intensive aquaculture, advancing the goals of sustainability in food production .
2. Biofilm Formation and Structure
Biofilm formation on bioreactor surfaces in aquatic environments is a highly regulated, multi-stage process critical to water treatment applications in aquaculture . Initially, free-floating microbial cells attach reversibly to surfaces through physical interactions aided by bacterial appendages such as pili and flagella. This phase is characterized by weak and reversible binding. As cells transition to irreversible attachment, they produce adhesive substances and surface proteins, establishing strong adherence that enables resistance to physical and chemical shear forces . Subsequently, attached cells proliferate and produce extracellular polymeric substances (EPS), creating a protective matrix that encapsulates cells and forms microcolonies . The biofilm then matures into a complex, three-dimensional structure with differentiated microenvironments, including water channels that facilitate nutrient distribution and waste removal . Cell-to-cell communication through quorum sensing regulates the development and maintenance of this architecture . Finally, biofilms undergo dispersion where cells actively or passively detach, reverting to their planktonic state to colonize new surfaces . The physical and chemical properties of biofilms, such as EPS composition and surface hydrophobicity, as well as environmental factors like nutrient availability, temperature, and hydrodynamic forces, critically influence biofilm growth, stability, and functional performance in bioreactors . Understanding these biofilm dynamics is essential for optimizing water quality control and enhancing the sustainability of aquaculture bioreactor systems.
3. Microbial Community Dynamics
Microbial community dynamics within aquaculture bioreactors are central to the efficacy of biofilm-mediated water quality control. These microbial assemblages are typically diverse, comprising bacteria with functional roles in nutrient cycling critical to maintaining system health . Key bacterial groups commonly observed include nitrifying bacteria such as Nitrosomonas and Nitrospira, responsible for ammonia oxidation and nitrite oxidation, respectively, which are fundamental in biofilm-driven nitrification processes . Denitrifying bacteria, including members of genera such as Pseudomonas and Paracoccus, are also integral, facilitating the reduction of nitrate to nitrogen gas in anaerobic zones within the biofilm matrix. Other important bacterial taxa involved in organic matter degradation and sulfur cycling, such as Planctomycetes and Saprospiraceae, contribute to biofilm stability and ecosystem functioning .
Temporal changes and microbial succession within bioreactors reflect adaptations to shifting environmental and operational conditions such as nutrient availability, temperature, pH, and hydraulic regimes . Early biofilm stages often see colonization by fast-growing heterotrophs, followed by enrichment of specialized nitrifiers and denitrifiers as biofilm structure matures . Throughout production cycles, microbial community composition shifts can affect water treatment efficiency and biofilm resilience .
Environmental factors, including dissolved oxygen levels, organic carbon availability, and water flow patterns, strongly influence microbial population dynamics . Operational parameters such as feed rates, reactor design, and cleaning frequency also shape microbial assemblages by modifying habitat conditions and selective pressures . Understanding these complex microbial interactions and their temporal dynamics is key for optimizing biofilm bioreactor performance and ensuring sustained water quality control in aquaculture systems.
4. Role of Biofilms in Water Quality Control
Biofilms play a pivotal role in controlling water quality in aquaculture systems through multiple mechanisms . Primarily, biofilms contribute to nutrient removal by hosting microbial communities that perform nitrification, converting toxic ammonia to nitrite and nitrate, followed by denitrification, which reduces nitrate to nitrogen gas, effectively removing nitrogen from the system. Additionally, certain biofilm-associated microorganisms facilitate phosphorus removal by assimilating it into biomass or through chemical precipitation processes . Biofilms also play an essential role in the degradation of organic matter, breaking down complex organic compounds into simpler substances that are less harmful to the aquatic environment .
The interaction between biofilm microorganisms and aquaculture species is multifaceted. Biofilms provide a beneficial habitat that supports microbial processes vital for maintaining water quality, which in turn creates a healthier environment for cultured species . Additionally, biofilms can serve as a natural source of supplemental nutrition for some aquatic organisms. Importantly, biofilms contribute to controlling harmful microbial populations by outcompeting pathogenic bacteria for space and nutrients and by producing antimicrobial compounds, thereby reducing disease risks in aquaculture operations .
However, biofilms can also harbor pathogens protected from disinfectants within their extracellular matrix, necessitating careful biofilm management to balance their positive and negative impacts . Effective biofilm-mediated water treatment in aquaculture relies on understanding these microbial dynamics and optimizing conditions that promote beneficial biofilm functions to sustain clean water and healthy aquatic species .
5. Advances in Understanding via Molecular Techniques
Advances in molecular techniques such as 16S rRNA gene sequencing and metagenomics have revolutionized the understanding of microbial communities within aquaculture biofilms . Targeted sequencing of the 16S rRNA gene allows for detailed taxonomic profiling by analyzing hypervariable regions that reveal bacterial diversity and composition in biofilms . This approach distinguishes both culturable and unculturable bacteria, providing insights into the complex microbial consortia involved in nutrient cycling and biofilm functions . Metagenomic analyses complement this by uncovering functional genes related to key bioprocesses such as nitrification, denitrification, and organic matter degradation, offering a functional perspective on microbial community roles .
Microbial community profiling through these molecular tools has elucidated succession patterns and shifts in community composition in response to environmental and operational changes, enabling targeted biofilm manipulation . For instance, case studies have demonstrated enhanced water quality outcomes by promoting beneficial bacterial groups involved in ammonia oxidation or denitrification through bioaugmentation or controlled reactor conditions . These molecular insights facilitate precision in designing and managing bioreactors to optimize biofilm performance, reduce pathogenic microbes, and improve overall aquaculture system sustainability . In sum, 16S rRNA gene sequencing combined with metagenomics provides a comprehensive framework to decode the microbial ecology of aquaculture biofilms, revealing both taxonomic diversity and functional potential, which is critical for advancing biofilm-based water treatment strategies .
6. Challenges and Management
Biofilms in aquaculture systems pose significant challenges due to their inherent resistance to antimicrobial agents, which complicates disease control and water treatment. The extracellular polymeric substance (EPS) matrix of biofilms acts as a physical barrier that restricts antibiotic penetration, while also chemically neutralizing or degrading antimicrobial compounds . This structural protection, combined with altered metabolic states of biofilm cells, leads to increased tolerance and survival against antibiotics . Another critical contributor to resistance is horizontal gene transfer, which occurs at elevated rates within biofilms, facilitating the spread of antibiotic resistance genes among bacterial populations . Studies in aquaculture have reported high prevalence of biofilm-associated resistance genes, such as beta-lactamases, highlighting the potential public health risks posed by biofilm-harbored multidrug-resistant bacteria .
Balancing biofilm growth in bioreactors is crucial to maximize treatment efficiency while minimizing negative impacts like clogging, excessive biomass accumulation, or pathogen persistence . Overgrown biofilms can impede mass transfer and reactor hydraulics, reducing system performance. Therefore, controlled biofilm management strategies such as periodic cleaning, hydraulic shear regulation, and selective microbial inoculation are employed . Optimization approaches include modulation of nutrient supply to favor beneficial biofilm communities, use of biofilm inhibitors or dispersants when necessary, and employing materials or coatings on reactor surfaces that support stable but manageable biofilm formation .
In sum, addressing biofilm antimicrobial resistance requires integrated strategies combining prevention of excessive biofilm formation with targeted interventions to disrupt resistance mechanisms . Advances in molecular diagnostics and engineered bioreactor designs are enhancing the ability to monitor and control biofilms for sustainable aquaculture water treatment .
7. Future Directions
Future directions in enhancing aquaculture bioreactor performance center on engineering microbial communities to optimize biofilm functions and water treatment efficacy. One promising approach is the integration of probiotics with biofilm management strategies . Probiotics, such as Bacillus, Lactobacillus, and Pseudomonas species, can form beneficial biofilms on surfaces including fish skin and intestinal tracts, creating protective barriers against pathogens while improving water quality through enhanced nutrient cycling and organic matter degradation . These beneficial biofilms produce extracellular polymeric substances with antimicrobial properties and modulate immune responses in cultured species, contributing to disease resistance and overall health . Moreover, probiotics can disrupt harmful biofilms formed by pathogens, limiting their colonization and biofilm development .
Advancements in sequencing technologies, including high-throughput 16S rRNA gene sequencing and metagenomics, are providing unprecedented resolution in mapping biofilm microbial ecology in aquaculture systems . These techniques allow detailed profiling of both taxonomic and functional aspects of microbial communities, enabling the identification of key strains and functional genes involved in nutrient removal, pathogen suppression, and biofilm stability . This knowledge supports precision engineering of microbial consortia tailored to specific aquaculture environments and operational conditions . Integration of probiogenomics further accelerates the discovery and application of effective probiotic strains by linking genomic traits to performance in aquaculture contexts . Overall, future innovations will hinge on combining microbial community engineering with molecular insights and probiotic applications to sustainably enhance bioreactor water treatment, disease control, and aquaculture productivity.
8. Conclusion
In conclusion, biofilms and their microbial community dynamics play a crucial role in enhancing water quality control within aquaculture bioreactors. The formation of complex biofilm structures enables efficient nutrient cycling through processes such as nitrification and denitrification, organic matter degradation, and phosphorus removal. Key bacterial groups dynamically shift in response to environmental and operational conditions, maintaining biofilm functionality essential for removing harmful substances and controlling pathogenic populations. Advances in molecular techniques, especially high-throughput 16S rRNA gene sequencing and metagenomics, have provided deeper insights into biofilm ecology, allowing targeted manipulation of microbial consortia to improve bioreactor performance.
These findings underscore the importance of optimizing biofilm growth and microbial interactions to sustain aquaculture productivity while minimizing environmental impacts. Through integrated approaches including probiotic application and engineering of microbial communities, sustainable management of biofilms holds significant promise for advancing water treatment and disease control in aquaculture. Overall, continued research and technological innovation in biofilm dynamics and microbial ecology are vital for improving sustainability and ensuring healthy, efficient aquaculture systems in the future.
Abbreviations

EPS

Extracellular Polymeric Substance

rRNA

Ribosomal Ribonucleic Acid

Author Contributions
Alebachew Molla is the sole author. The author read and approved the final manuscript.
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Not applicable.
Data Availability Statement
No new data were created or analyzed in this review.
Funding
This review received no external funding.
Conflicts of Interest
The author declares no conflicts of interest.
References
[1] Z. Li et al., “Water Treatment Effect, Microbial Community Structure, and Metabolic Characteristics in a Field-Scale Aquaculture Wastewater Treatment System,” Front. Microbiol., vol. 11, no. June, pp. 1–13, 2020,
[2] Z. Li et al., “Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds,” FEMS Microbiol. Lett., vol. 364, no. 4, pp. 1–7, 2017,
[3] F. Fahruddin, M. Tuwo, M. F. Samawi, A. Abdullah, G. F. T. Putri, and E. Ibrahim, “Potential of Biofilm Bacteria for Ammonia Degradation in Shrimp Pond,” Egypt. J. Aquat. Biol. Fish., vol. 29, no. 1, pp. 413–429, 2025,
[4] S. Navada, M. F. Knutsen, I. Bakke, and O. Vadstein, “Nitrifying biofilms deprived of organic carbon show higher functional resilience to increases in carbon supply,” Sci. Rep., vol. 10, no. 1, pp. 1–11, 2020,
[5] R. N. Rasheed, A. Pourbakhtiar, M. M. Allaf, M. Baharlooeian, N. Ra, and F. V. Winck, “Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges,” no. September, pp. 1–25, 2023,
[6] S. Martínez-Moreno, E. Leon-Palmero, H. J. Pula, A. M. Cabello, I. Ferrera, and I. Reche, “Subcuticular and biofilm microbiomes in Holothuria tubulosa and their potential for denitrification,” Mar. Ecol. Prog. Ser., vol. 736, pp. 81–92, 2024,
[7] A. Emmanuel, Y. Wei, M. N. Ramzan, W. Yang, and Z. Zheng, “Dynamics of Bacterial Communities and Their Relationship with Nutrients in a Full-Scale Shrimp Recirculating Aquaculture System in Brackish Water,” Animals, vol. 15, no. 10, 2025,
[8] S. Li, C. Peng, T. Cheng, C. Wang, L. Guo, and D. Li, “Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability,” J. Environ. Sci. (China), vol. 76, no. Dunhai Li, pp. 89–99, 2019,
[9] X. Ma et al., “Application of a biofilm-enhanced A2O system in the treatment of wastewater from mariculture,” Front. Mar. Sci., vol. 11, no. May, pp. 1–9, 2024,
[10] S. Ende, J. Henjes, M. Spiller, M. Elshobary, D. Hanelt, and A. Abomohra, “Recent advances in recirculating aquaculture systems and role of microalgae to close system loop,” Bioresour. Technol., vol. 407, no. July, p. 131107, 2024,
[11] K. Sauer et al., “The biofilm life cycle: expanding the conceptual model of biofilm formation,” Nat. Rev. Microbiol., vol. 20, no. 10, pp. 608–620, 2022,
[12] M. A. Rather, K. Gupta, and M. Mandal, “Microbial biofilm: formation, architecture, antibiotic resistance, and control strategies,” Brazilian J. Microbiol., vol. 52, no. 4, pp. 1701–1718, 2021,
[13] S. Yu, X. Lu, and H. Lu, “Marine microbial biofilms on diverse abiotic surfaces,” Front. Mar. Sci., vol. 12, no. February, pp. 1–18, 2025,
[14] M. H. Muhammad et al., “Beyond Risk: Bacterial Biofilms and Their Regulating Approaches,” Front. Microbiol., vol. 11, no. May, pp. 1–20, 2020,
[15] S. Saini, S. Tewari, J. Dwivedi, and V. Sharma, “Biofilm-mediated wastewater treatment: a comprehensive review,” Mater. Adv., vol. 4, no. 6, pp. 1415–1443, 2023,
[16] A. Y. H. Al-ethari, S. D. Khalaf, and Z. H. Abbas, “Regulation of Biofilm Formation By Quorum Sensing: Implications For Pathogenesis and Antibiotics Resistance,” no. 1, 2025.
[17] K. P. Rumbaugh and K. Sauer, “Biofilm dispersion,” Nat. Rev. Microbiol., vol. 18, no. 10, pp. 571–586, 2020,
[18] Y. Li, X. Li, Y. Hao, Y. Liu, Z. L. Dong, and K. Li, “Biological and physiochemical methods of biofilm adhesion resistance control of medical-context surface,” Int. J. Biol. Sci., vol. 17, no. 7, pp. 1769–1781, 2021,
[19] N. S. de Oliveira et al., “Advantages of using biofilms to obtain high-value molecules by microbial biotransformations,” Explor. Drug Sci., pp. 1–14, 2025,
[20] C. Selvam, D. Mutisyab, and and R. T. Prakashc Sandhya, Kasturi Rangannaa, “乳鼠心肌提取 HHS Public Access,” Physiol. Behav., vol. 176, no. 1, pp. 139–148, 2017,
[21] Z. Su, T. Liu, J. Guo, and M. Zheng, “Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges,” Environ. Sci. Technol., vol. 57, no. 34, pp. 12557–12570, 2023,
[22] D. Bastos Almeida, M. Semedo, C. Magalhães, I. Blanquet, and A. P. Mucha, “The network of nitrifying and pathogenic prokaryotic interactions in a recirculating aquaculture system of a sole (Solea senegalensis) hatchery,” Front. Mar. Sci., vol. 9, no. December, pp. 1–11, 2022,
[23] K. Morinaga, K. Yoshida, K. Takahashi, N. Nomura, and M. Toyofuku, “Peculiarities of biofilm formation by Paracoccus denitrificans,” Appl. Microbiol. Biotechnol., vol. 104, no. 6, pp. 2427–2433, 2020,
[24] M. S. Islam, A. Alatishe, C. C. Lee-Lopez, F. Serrano, and E. T. Yukl, “H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing in Paracoccus denitrificans,” J. Proteome Res., vol. 23, no. 11, pp. 4988–5000, 2024,
[25] H.-P. Lu, Y.-H. Shao, J.-H. Wu, and C. Hsieh, “System Performance Corresponding to Bacterial Community Succession after a Disturbance in an Autotrophic Nitrogen Removal Bioreactor,” mSystems, vol. 5, no. 4, pp. 1–12, 2020,
[26] J. Huang et al., “Deciphering nitrogen-driven microbial succession in an anaerobic membrane bioreactor-coupled A2/O ecological system for the remediation of industrial swine wastewater,” Sci. Rep., vol. 15, no. 1, pp. 1–13, 2025,
[27] D. Zhou et al., “Comparative analysis of bacterial communities and environmental interactions in seawater and saline-alkali aquaculture ponds for Scylla paramamosain in northern China,” Front. Microbiol., vol. 16, no. May, pp. 1–15, 2025,
[28] D. Hou et al., “Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems,” Front. Microbiol., vol. 8, no. NOV, pp. 1–12, 2017,
[29] B. O. Johansen, S. O. Mikalsen, E. Magnussen, E. J. Patursson, G. á Norði, and A. Djurhuus, “Impacts on microbial communities in sediments by aquaculture farming during one salmon cycle,” Front. Mar. Sci., vol. 11, no. August, pp. 1–11, 2024,
[30] Q. Zhang, “Research on The Application of Microorganisms in The Ecological Health of Water Bodies,” vol. 28, no. 3, pp. 1–10, 2024,
[31] S. Rahayu et al., “Probiotics application in aquaculture: its potential effects, current status in China and future prospects,” Front. Mar. Sci., vol. 11, no. September, pp. 1–23, 2024,
[32] R. Funari and A. Q. Shen, “Detection and Characterization of Bacterial Biofilms and Biofilm-Based Sensors,” ACS Sensors, vol. 7, no. 2, pp. 347–357, 2022,
[33] V. Vanessa, D. E. Waturangi, A. Yulandi, P. G. S. Julyantoro, and N. Papuangan, “Antibiofilm activity of Morganella morganii JB8F and Pseudomonas fluorescens JB3B compound to control single and multi-species of aquaculture pathogens,” BMC Microbiol., vol. 24, no. 1, 2024,
[34] T. Miller, D. E. Waturangi, and Yogiara, “Antibiofilm properties of bioactive compounds from Actinomycetes against foodborne and fish pathogens,” Sci. Rep., vol. 12, no. 1, p. 18614, 2022,
[35] H. Y. Liu, E. L. Prentice, and M. A. Webber, “Mechanisms of antimicrobial resistance in biofilms,” npj Antimicrob. Resist., vol. 2, no. 1, pp. 1–10, 2024,
[36] S. D. Goodman and L. O. Bakaletz, “Bacterial Biofilms Utilize an Underlying Extracellular DNA Matrix Structure That Can Be Targeted for Biofilm Resolution,” Microorganisms, vol. 10, no. 2, 2022,
[37] L. R. Martínez-Córdova et al., “Taxonomic profile of bacterial communities detected with 16S-rRNA in mature phototrophic and heterotrophic marine biofilms used for aquaculture,” Ciencias Mar., vol. 44, no. 4, pp. 251–266, 2018,
[38] T. Yamada et al., “16S rRNA Gene Amplicon Sequencing of Microbiota in Polybutylene Succinate Adipate-Packed Denitrification Reactors Used for Water Treatment of Land-Based Recirculating Aquaculture Systems,” Microbiol. Resour. Announc., vol. 8, no. 47, pp. 14–16, 2019,
[39] J. S. Johnson et al., “Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis,” Nat. Commun., vol. 10, no. 1, pp. 1–11, 2019,
[40] I. Butler et al., “Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections,” Front. Cell. Infect. Microbiol., vol. 15, no. March, pp. 1–15, 2025,
[41] D. Kneis, T. U. Berendonk, S. K. Forslund, and S. Hess, “Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts,” Environ. Sci. Technol., vol. 56, no. 21, pp. 14913–14922, 2022,
[42] M. Rajeev, I. Jung, I. Kang, and J.-C. Cho, “Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture,” mSystems, vol. 9, no. 10, pp. 1–19, 2024,
[43] P. K. Bech, S. A. Jarmusch, J. A. Rasmussen, M. T. Limborg, L. Gram, and N. N. S. E. Henriksen, “Succession of microbial community composition and secondary metabolism during marine biofilm development,” ISME Commun., vol. 4, no. 1, 2024,
[44] W. Qi, S. L. Aalto, P. V. Skov, K. J. de Jesus Gregersen, and L. F. Pedersen, “Diverse reactions of aquaculture biofilter biofilms following acute high-dose peracetic acid,” Biofilm, vol. 9, no. December 2024, pp. 22–27, 2025,
[45] I. Roalkvam, K. Drønen, H. Dahle, and H. I. Wergeland, “A case study of biofilter activation and microbial nitrification in a marine recirculation aquaculture system for rearing Atlantic salmon (Salmo salar L.), Aquac. Res., vol. 52, no. 1, pp. 94–104, 2021,
[46] W. Taylor et al., “Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons, J. Water Health, vol. 22, no. 8, pp. 1429–1443, 2024,
[47] C. Uruén, G. Chopo-Escuin, J. Tommassen, R. C. Mainar-Jaime, and J. Arenas, “Biofilms as promoters of bacterial antibiotic resistance and tolerance,” Antibiotics, vol. 10, no. 1, pp. 1–36, 2021,
[48] K. E. Grooters et al., “Strategies for combating antibiotic resistance in bacterial biofilms,” Front. Cell. Infect. Microbiol., vol. 14, no. January, pp. 1–7, 2024,
[49] C. Michaelis and E. Grohmann, “Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms,” Antibiotics, vol. 12, no. 2, 2023,
[50] N. Puvača et al., “Microbial Resistance to Antibiotics and Biofilm Formation of Bacterial Isolates from Different Carp Species and Risk Assessment for Public Health,” 2023.
[51] M. L. Rana, M. A. Ullah, M. N. Hoque, J. Hassan, M. P. Siddique, and M. T. Rahman, “Preliminary survey of biofilm forming, antibiotic resistant Escherichia coli in fishes from land based aquaculture systems and open water bodies in Bangladesh,” Sci. Rep., vol. 15, no. 1, pp. 1–11, 2025,
[52] E. J. Espinosa-Ortiz, R. Gerlach, B. M. Peyton, L. Roberson, and D. H. Yeh, “Biofilm reactors for the treatment of used water in space: potential, challenges, and future perspectives,” Biofilm, vol. 6, no. October 2022, p. 100140, 2023,
[53] M. Mathur, P. Choudhary, S. Sujathan, F. Naaz, C. Trenado-Yuste, and A. Malik, “A biologically driven model for rural wastewater management: feasibility and efficiency of algal-bacterial biofilm reactors for combined treatment and algae farming,” Front. Water, vol. 6, no. 3, pp. 1–14, 2024,
[54] R. Mishra, A. K. Panda, S. De Mandal, M. Shakeel, S. S. Bisht, and J. Khan, “Natural Anti-biofilm Agents: Strategies to Control Biofilm-Forming Pathogens,” Front. Microbiol., vol. 11, no. October, 2020,
[55] H. Hu, J. He, H. Yu, J. Liu, and J. Zhang, “A strategy to speed up formation and strengthen activity of biofilms at low temperature,” RSC Adv., vol. 7, no. 37, pp. 22788–22796, 2017,
[56] A. Barbosa, S. Miranda, N. F. Azevedo, L. Cerqueira, and A. S. Azevedo, “Imaging biofilms using fluorescence in situ hybridization: seeing is believing,” Front. Cell. Infect. Microbiol., vol. 13, no. May, pp. 1–16, 2023,
[57] J. Gao, F. A. Sadiq, Y. Zheng, J. Zhao, G. He, and Y. Sang, “Biofilm-based delivery approaches and specific enrichment strategies of probiotics in the human gut,” Gut Microbes, vol. 14, no. 1, pp. 1–22, 2022,
[58] M. Fachri et al., “Probiotics and paraprobiotics in aquaculture: a sustainable strategy for enhancing fish growth, health and disease prevention-a review,” Front. Mar. Sci., vol. 11, no. December, pp. 1–28, 2024,
[59] A. W. Decho and T. Gutierrez, “Microbial extracellular polymeric substances (EPSs) in ocean systems,” Front. Microbiol., vol. 8, no. MAY, pp. 1–28, 2017,
[60] A. Barzegari et al., “The battle of probiotics and their derivatives against biofilms,” Infect. Drug Resist., vol. 13, pp. 659–672, 2020,
[61] K. Janssen, S. L. Low, Y. Wang, Q. Y. Mu, G. Bierbaum, and C. T. Gee, “Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits,” Appl. Plant Sci., vol. 9, no. 8, pp. 1–15, 2021,
[62] X. Chen et al., “Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments,” Front. Mar. Sci., vol. 8, no. January, pp. 1–13, 2022,
[63] M. S. Chithira, P. V. Aishwarya, A. S. Mohan, and S. P. Antony, “Metagenomic analysis of microbial communities in the sediments of a semi-intensive penaeid shrimp culture system,” J. Genet. Eng. Biotechnol., vol. 19, no. 1, pp. 0–3, 2021,
[64] J. C. Boath, “Bioremediation, Waste Treatment and Carbon Capture Using Bioengineered Microbes for Sustainable Aquaculture,” J. Environ. Sci. Agric. Res., vol. 3, no. 4, pp. 1–8, 2025,
[65] S. K. Nayak, “Multifaceted applications of probiotic Bacillus species in aquaculture with special reference to Bacillus subtilis,” Rev. Aquac., vol. 13, no. 2, pp. 862–906, 2021,
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    Molla, A. (2025). Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions. American Journal of Bioscience and Bioengineering, 13(5), 99-105. https://doi.org/10.11648/j.bio.20251305.12

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    Molla, A. Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions. Am. J. BioSci. Bioeng. 2025, 13(5), 99-105. doi: 10.11648/j.bio.20251305.12

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    Molla A. Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions. Am J BioSci Bioeng. 2025;13(5):99-105. doi: 10.11648/j.bio.20251305.12

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  • @article{10.11648/j.bio.20251305.12,
      author = {Alebachew Molla},
      title = {Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions
    },
      journal = {American Journal of Bioscience and Bioengineering},
      volume = {13},
      number = {5},
      pages = {99-105},
      doi = {10.11648/j.bio.20251305.12},
      url = {https://doi.org/10.11648/j.bio.20251305.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bio.20251305.12},
      abstract = {A biofilm in aquaculture is a community of microorganisms, including bacteria, algae, fungi, and others, that forms a complex and structured layer attached to surfaces within water systems. Aquaculture bioreactors rely on biofilms as critical microbial consortia that drive water quality improvement through nutrient cycling and organic matter degradation. This review highlights the dynamic succession and diversity within biofilm microbial communities, particularly emphasizing key bacterial groups such as Planctomycetes, Bacteroidetes, nitrifiers, and denitrifies that mediate ammonia and nitrogen removal. Biofilms form robust structures through sequential attachment, growth, and maturation stages, influenced by physical and chemical parameters. Molecular tools like 16S rRNA gene sequencing have advanced our understanding of biofilm ecology, revealing community shifts responsive to environmental and operational conditions. Biofilms also contribute to pathogen suppression yet pose challenges through antimicrobial resistance, necessitating balanced management to optimize treatment efficiency without biomass overgrowth. Promising future directions include engineering microbial communities and incorporating probiotics to enhance functional biofilms tailored for sustainable aquaculture. This collective knowledge supports improved aquaculture sustainability by ensuring efficient water treatment, fish health, and environmental protection. Continued integration of molecular techniques and biofilm management strategies will enhance bioreactor design and operation for resilient, eco-friendly aquaculture systems. The aim of this review is to assess the role of biofilms and microbial community dynamics in aquaculture bioreactors for effective water quality control and sustainable aquaculture production.
    },
     year = {2025}
    }
    

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  • TY  - JOUR
    T1  - Biofilm and Microbial Community Dynamics in Aquaculture Bioreactors for Water Quality Control: Current Status and Future Directions
    
    AU  - Alebachew Molla
    Y1  - 2025/10/10
    PY  - 2025
    N1  - https://doi.org/10.11648/j.bio.20251305.12
    DO  - 10.11648/j.bio.20251305.12
    T2  - American Journal of Bioscience and Bioengineering
    JF  - American Journal of Bioscience and Bioengineering
    JO  - American Journal of Bioscience and Bioengineering
    SP  - 99
    EP  - 105
    PB  - Science Publishing Group
    SN  - 2328-5893
    UR  - https://doi.org/10.11648/j.bio.20251305.12
    AB  - A biofilm in aquaculture is a community of microorganisms, including bacteria, algae, fungi, and others, that forms a complex and structured layer attached to surfaces within water systems. Aquaculture bioreactors rely on biofilms as critical microbial consortia that drive water quality improvement through nutrient cycling and organic matter degradation. This review highlights the dynamic succession and diversity within biofilm microbial communities, particularly emphasizing key bacterial groups such as Planctomycetes, Bacteroidetes, nitrifiers, and denitrifies that mediate ammonia and nitrogen removal. Biofilms form robust structures through sequential attachment, growth, and maturation stages, influenced by physical and chemical parameters. Molecular tools like 16S rRNA gene sequencing have advanced our understanding of biofilm ecology, revealing community shifts responsive to environmental and operational conditions. Biofilms also contribute to pathogen suppression yet pose challenges through antimicrobial resistance, necessitating balanced management to optimize treatment efficiency without biomass overgrowth. Promising future directions include engineering microbial communities and incorporating probiotics to enhance functional biofilms tailored for sustainable aquaculture. This collective knowledge supports improved aquaculture sustainability by ensuring efficient water treatment, fish health, and environmental protection. Continued integration of molecular techniques and biofilm management strategies will enhance bioreactor design and operation for resilient, eco-friendly aquaculture systems. The aim of this review is to assess the role of biofilms and microbial community dynamics in aquaculture bioreactors for effective water quality control and sustainable aquaculture production.
    
    VL  - 13
    IS  - 5
    ER  - 

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