Microbial Pathogens in Aquaculture: Emerging Threats Review

Review Article Published: 2025-07-18 https://doi.org/10.20935/AcadBiol7814 Microbial pathogens in aquaculture: a review of emerging threats Vijay A. K. B. Gundi1, *, Devi Bogireddy1 , Anil Kumar Vundru1 , Praveen Kumar Arthala1 , Manohar Babu Vadela2 , Satyanagalakshmi Karri2 , Uday Sankar Allam1 , Mary Sandeepa Gujjula1 , Vidya Prabhakar Kodali1 Academic Editors: César Marcial Escobedo Bonilla, Eric Lewallen Abstract Aquaculture, a rapidly growing sector of global food production, faces significant challenges from microbial pathogens, which can lead to substantial economic losses and pose risks to human health. Intensification of aquaculture practices, characterized by high stocking densities and poor water quality management, has created environments conducive to the emergence and spread of various bacterial, viral, fungal, and parasitic pathogens. Bacterial pathogens such as Vibrio spp., Aeromonas spp., and Streptococcus spp. are among the most significant threats, causing a range of diseases with high fish mortality rates. Viral pathogens, including tilapia lake viruses and megalocytiviruses, have also emerged as serious concerns, with limited control options available. The use of antibiotics to manage these diseases has led to the development of antimicrobial-resistant pathogens, which can spread to humans through horizontal gene transfer and the food chain. This has prompted the exploration of alternative disease management strategies such as probiotics, bacteriophages, and quorum-sensing inhibitors. Environmental factors, including water temperature and quality, play crucial roles in the dynamics of microbial pathogens, and climate change is expected to exacerbate disease outbreaks. Advances in metagenomics and genomic technologies have provided insights into the complex microbial interactions within aquaculture systems, guiding the development of targeted interventions and sustainable management practices. Effective biosecurity measures, vaccination, and adoption of a One Health approach are essential for mitigating the impacts of microbial pathogens in aquaculture. Collaborative efforts among researchers, policymakers, and industry stakeholders are necessary to address the multifaceted challenges posed by emerging microbial threats and to ensure the long-term sustainability of the aquaculture sector. Keywords: aquaculture, microbial pathogens, antimicrobial resistance, aquatic animals, disease outbreaks, food security Citation: Gundi VAKB, Bogireddy D, Vundru AK, Arthala PK, Vadela MB, Karri S, et al. Microbial pathogens in aquaculture: a review of emerging threats. Academia Biology 2025;3. https://doi.org/10.20935/AcadBiol7814 1. Introduction Aquaculture, the cultivation of aquatic organisms, has become an increasingly vital part of global food production, providing a substantial portion of the animal protein consumed worldwide [1]. Since the 1980s, aquaculture has experienced rapid expansion, particularly in Asian countries, which have contributed approximately 89% of global aquaculture production; as such, it has established itself as the fastest-growing food production sector [2]. This growth has been driven by several factors, including an increasing global population, rising demand for seafood, and declining wild fish stocks [3, 4]. The potential of aquaculture to enhance global food security is considerable, especially when considering its capacity to reduce agricultural land use compared to current food system trends [5]. Despite its potential, the rapid expansion of aquaculture has not been challenging. One of the primary constraints of aquaculture production is the susceptibility of farmed aquatic animals to infectious diseases [6–8]. The intensification of aquaculture practices, characterized by high stocking densities and monoculture systems, has created environments conducive to the emergence and spread of pathogens [9]. These conditions could weaken the immune system of aquatic animals, making them more vulnerable to infection. The reliance on antimicrobials in aquaculture, while aimed at controlling disease outbreaks, has contributed to the escalating problem of antimicrobial resistance, posing significant risks to the health of both aquatic animals and humans [10]. A comprehensive search was performed through 2025 from 2015 in the Medline via PubMed (https://pubmed.ncbi.nlm.nih.gov/ advanced/ accessed on 2025 May 5), Scopus (https://www.else vier.com/en-in/products/scopus/search/ accessed on 2025 May 12) and Web of Science (https://webofscience.help.clarivate.co m/en-us/Content/advanced-search.html/ accessed on 2025 May 9) electronic databases using specific search terms: “Aquaculture”, “Microbial pathogens”, “Antimicrobial resistance”, “Bacteria”, “Viruses”, “Fungi”, “Parasites”, “Aquatic animals”, “Disease outbreaks”, “Food security”. The reference lists of the selected articles were also searched for additional studies. 2. Current understanding of microbial pathogens Disease outbreaks in aquaculture have caused substantial economic losses, affecting farmers and the industry. Antimicrobials and chemical disinfectants are currently used to control disease 1 Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India. 2 R & D Center, Sahasra Crop Science Pvt. Ltd., Hyderabad, Telangana, India. ∗ email: [email protected] ACADEMIA BIOLOGY 2025, 3 1 of 16 https://doi.org/10.20935/AcadBiol7814 outbreaks in fish species under crowded conditions [11]. Poor stocking density affects fish physiological conditions, including insulin levels that reduce immunity, predisposing them to pathogenic infections. This has led to the development of alternative disease control strategies [12]. Bacteria, viruses, fungi, and parasites are the main microbial pathogens affecting aquaculture. Bacterial pathogens like Vibrio spp., Aeromonas spp., and Flavobacterium columnare cause diseases in fish and shellfish, leading to high mortality. Viral pathogens, including infectious salmon anemia virus, white spot syndrome virus, and viral hemorrhagic septicemia virus, threaten aquaculture by causing widespread mortality, with limited control options [13]. Fungal infections like saprolegniasis affect freshwater fish species, particularly in their early life stages. Parasitic diseases from protozoa, helminths, and crustaceans compromise farmed aquatic animals’ health. The emergence of antimicrobial resistance in aquaculture is concerning, driven by antibiotic overuse in veterinary and human settings. Aquaculture systems, with high animal densities and frequent antibiotic use, enable the development of antimicrobialresistant bacteria [14]. Subtherapeutic antibiotic doses and exposure through consumption or environmental release contribute to resistance [15]. Resistance genes transfer between bacteria through mechanisms like horizontal gene transfer [16]. Antibiotic use can disrupt aquatic animals’ gut microbiome, compromising their health. Initial colonization begins in water and sediments, with microbiota structure depending on environmental conditions [17]. The dynamics of microbial pathogens in aquaculture represents a critical challenge for global fish farming sustainability. The aquaculture industry has grown significantly due to the rising demand for seafood and due to intensive farming practices. However, this expansion has increased disease outbreaks from pathogenic microorganisms, affecting economics and food security [18]. Diseases caused by pathogens like Aeromonas hydrophila, Vibrio harveyi, and Streptococcus iniae have increased due to overcrowded conditions, fish stress, and bacterial virulence evolution [19, 20]. Aquaculture environments enhance potentially pathogenic bacteria [21]. Vibrio species in marine environments cause diseases in aquatic organisms and humans through contaminated seafood [21, 22]. Fish farms act as pathogen reservoirs facilitating outbreaks, while biofilms harbor pathogens, increasing disease transmission risk [20, 23]. The use of antibiotics has created resistant bacteria, limiting treatment effectiveness and threatening human health through resistant strain transfer [24, 25]. Increasing resistance in bacteria like Streptococcus agalactiae has led to the exploration of alter- ACADEMIA BIOLOGY 2025, 3 natives such as probiotics, bacteriophages, and quorum-sensing inhibitors [26–28]. Probiotics offer promise as antibiotic alternatives by outcompeting pathogens, improving fish gut health, and enhancing immune responses [26–28]. Some probiotic strains show quorumquenching properties, disrupting pathogenic bacteria communication and reducing virulence [26, 29]. This approach provides sustainable microbial threat management aligned with the demand for antibiotic-free seafood [30]. The dynamic nature of ecosystems underscores microbial interactions in aquaculture systems. The interplay between bacterial populations can promote or inhibit pathogen growth, emphasizing the importance of balanced microbial communities [31]. Advances in metagenomics have provided us with an understanding of these communities, enabling the identification of key microbes that improve fish health and reduce disease outbreaks. Probiotic products from beneficial strains like Bacillus spp. have shown efficacy in reducing economically damaging diseases in aquaculture [26, 32]. Probiotics enhance fish health via competitive exclusion, immune modulation, and gut barrier reinforcement. Beneficial bacteria colonize the gastrointestinal tract and outcompete pathogens while stimulating protective mucus production [33–36]. Some probiotic strains exhibit quorum-quenching properties by secreting enzymes that degrade bacterial signaling molecules, disrupting pathogenic communication [37–40]. These mechanisms reduce disease outbreaks without promoting antibiotic resistance, offering sustainable disease management. Probiotic strains used in aquaculture are typically derived from fish microbiota or natural environments, minimizing ecological risks [41–43]. Bacillus subtilis is classified as Generally Recognized as Safe (GRAS) for humans [44–46]. Unlike antibiotics, probiotics do not contribute to resistance and quorum-quenching enzymes target bacterial signaling without affecting host cells [47, 48]. Environmental factors significantly influence microbial organisms in aquaculture systems. Elevated temperatures can enhance pathogen virulence, particularly in overcrowded farms [19, 49, 50]. Recent efforts to develop vaccines targeting specific pathogens have gained momentum [51, 52]. Vaccination can reduce antibiotic reliance, though challenges remain with regard to identifying suitable pathogens and ensuring vaccine efficacy in aquatic environments [51, 52]. Some examples of emerging microbial pathogens in aquaculture are listed in Table 1. Overall, the complexity of microbial pathogens in aquaculture necessitates a multifaceted approach combining improved management practices, use of probiotics, innovative vaccine development, and ongoing research into microbial interactions to ensure the sustainability of aquaculture operations and safeguard public health. 2 of 16 https://doi.org/10.20935/AcadBiol7814 Table 1 • Emerging microbial pathogens in aquaculture. Pathogen Type Primary hosts Disease/impact Notable characteristics Reference Tilapia Lake Virus (TiLV) Virus Tilapia High mortality (>80%), neurological and hepatic lesions, global spread since 2014 Segmented RNA virus; lacks effective vaccine; significant threat to tilapia aquaculture [53] Aquatic Circoviruses Virus Turbot, shrimp, clams, snails Acute hemorrhagic syndrome in turbot; high mortality in laboratory settings Small ssDNA viruses; broad host range; challenges in diagnosis and control [54] Vibrio anguillarum Bacteria Marine and freshwater fish, crustaceans, mollusks Vibriosis: hemorrhagic septicemia, skin ulcers, systemic infections Produces siderophores; biofilm formation; antibiotic resistance concerns [55] Vibrio coralliilyticus Bacteria Corals, oyster larvae, rainbow trout Coral bleaching; high mortality in oyster hatcheries; tissue lesions in fish Temperature-dependent virulence; multiple secretion systems; impacts both invertebrates and fish [56] Streptococcus spp. Bacteria Tilapia, other freshwater fish Streptococcosis: septicemia, meningoencephalitis; significant economic losses Zoonotic potential; high re-infection rates; challenges with antibiotic resistance [57] Ranavirus Virus Amphibians, various fish species Systemic infections; mass mortality events; ecological and economic impacts Double-stranded DNA virus; affects both wild and cultured species; linked to amphibian declines [58] Flavobacterium columnare Bacteria Freshwater fish Columnaris disease: skin lesions, gill necrosis, high mortality in young fish Forms biofilms; thrives in warm water; significant in recirculating aquaculture systems [59] Sphaerospora molnari Parasite Common carp (Cyprinus carpio) Gill and skin sphaerosporosis; tissue necrosis; respiratory failure Myxozoan parasite; proliferates in gill and skin tissues; linked to warmer pond temperatures [60] Kudoa thyrsites Parasite Marine fish (e.g., salmon, mackerel) Post-mortem myoliquefaction; flesh softening leading to unmarketable fish Myxosporean parasite; forms pseudocysts in muscle fibers; broad host range [61] Streptococcus iniae Bacteria Tilapia, red drum, hybrid striped bass, rainbow trout Meningoencephalitis, skin lesions, septicemia; zoonotic infections in humans Gram-positive bacterium; significant economic impact; challenges in identification [62] Amoebic Gill Disease (AGD) Parasite Atlantic salmon, turbot, bass, bream Gill lesions, respiratory distress, mortality; significant economic losses in salmon aquaculture Caused by Neoparamoeba perurans; proliferates in gill tissues; linked to warmer water temperatures [63] Bacterial Cold Water Disease (BCWD) Bacteria Salmonid fish (e.g., rainbow trout, salmon) Tissue erosion, fin rot, systemic infections; high mortality in fry Caused by Flavobacterium psychrophilum; thrives in cold water; challenges in control [64] Scuticociliatosis Parasite Marine fish (e.g., flounder, seahorses, sharks) Skin ulceration, haemorrhage, necrosis; high mortality rates Caused by Scuticociliates; opportunistic parasites; outbreaks linked to warmer temperatures [65] Piscine Orthoreovirus (PRV) Virus Atlantic and Pacific salmon Heart and skeletal muscle inflammation (HSMI); jaundice/anaemia RNA virus; high prevalence in net pen salmon; concerns over transmission to wild populations [66] Megalocytivirus (e.g., ISKNV) Virus Various fish species Systemic infections; high mortality; significant economic losses DNA virus; affects a wide range of fish; challenges in diagnosis and control [67] ACADEMIA BIOLOGY 2025, 3 3 of 16 https://doi.org/10.20935/AcadBiol7814 3. Emerging microbial threats in aquaculture The intensification of aquaculture practices, including increased stocking densities and poor water quality, raises disease outbreak risks [14]. Poor environmental conditions and inadequate management have been linked to the spread of disease in aquaculture [2]. The movement of live aquatic animals can spread pathogens to new regions with susceptible populations. Climate change threatens aquaculture as rising temperatures and altered precipitation patterns affect pathogen distribution and virulence, creating favorable conditions for pathogen growth while increasing host susceptibility. Aquatic environments face antibiotic contamination risks from eutrophication and antibiotic overuse [68]. These factors necessitate proactive measures against emerging microbial threats. Inter-species transfer of antibiotic residues shows the broad impact of antimicrobial use in aquaculture [2]. These residues pose human health risks through the food chain [69] and can increase antibiotic resistance even at subtherapeutic levels [70]. Antimicrobial-resistant bacteria and resistance genes in aquatic environments can lead to “superbugs,” threatening environmental and human health [71]. Antimicrobials consistently enter the environment, accelerating resistance development. Antibiotic consumption in aquaculture is increasing globally to combat microbial pathogens. Antibiotic residues are found in waters, sediments, and aquatic organisms’ muscles. Common antibiotics used in aquaculture have been reviewed by Yuan et al. [72], as listed in Table 2. Table 2 • The commonly found antibiotics in aquaculture environment (modified [72]). Antibiotics Major family Macrolide Example Roxithromycin (ROM) Erythromycin (ERM) Ciprofloxacin (CIP) Quinolones Enrofloxacin (ENR) Norfloxacin (NOR) Sulfadiazine (SDZ) Sulfonamides Sulfadimethoxine (SDM) Sulfamethoxazole (SMX) Methicillin (TMP) Chlortetracycline (CTC) Tetracyclines Oxytetracycline (OTC) Tetracycline (TC) ACADEMIA BIOLOGY 2025, 3 Emerging microbial threats in aquaculture are extensively researched due to microbial communities’ critical role. These threats include antibiotic resistance, environmental contaminants, and changing microbial populations. Understanding microbial dynamics is crucial for developing effective management strategies. Antibiotic resistance poses a significant threat to aquaculture. The intensive use of antibiotics to manage disease outbreaks leads to selective pressure, fostering resistant bacterial strains. According to Watts et al. [14], indiscriminate antibiotic use has contributed to antibiotic-resistant bacteria (ARB) in aquaculture environments, compromising therapeutics and affecting human health through the food chain. Lee et al. [73] noted that drugresistant bacteria emergence highlights the urgency of exploring alternatives like probiotics or phage therapy. Pepi and Focardi [74] emphasized that antibiotic resistance pervades entire microbial communities. Horizontal gene transfer among bacteria facilitates resistance genes’ dissemination across ecosystems, including terrestrial environments. The microbial composition of aquaculture systems is altered by untreated wastewater, organic feed inputs, and sediment dynamics. Chen et al. [75] found that aquaculture effluents affect microbial diversity and community structure, leading to pathogenic species proliferation. These shifts correlate with altered water parameters, affecting aquatic organisms’ health [76]. Freshwater aquaculture systems are susceptible to microbial community changes during intensive practices. Mohsen et al. [77] showed that microbial saturation on plastic substrates can lead to pathogen dominance. Maintaining diverse microbial ecosystems is crucial for resilience against pathogens [31]. Researchers advocate using metagenomics to understand microbial dynamics in aquaculture. Rajeev et al. [78] demonstrated that genomic approaches reveal core microbial communities in biofloc systems, enabling better probiotic management. Environmental changes from climatic factors can drive pathogenic microbe emergence. Climate change impacts disease susceptibility, potentially shifting microbial communities and affecting aquaculture sustainability [79]. Emerging viral pathogens represent another dimension of microbial threats in aquaculture. Stachnik et al. [80] identified viruses affecting sturgeon aquaculture, emphasizing the need to monitor these pathogens due to their potential to cause acute outbreaks. Adaptation of management practices to include viral surveillance and pathogen identification is essential for protecting aquaculture investments. Viral infections share common risk factors with bacterial diseases, such as environmental stressors and high stocking densities, but present unique challenges in transmission dynamics and host interactions. Unlike bacteria, viruses rely on host cellular machinery for replication, making stressed fish particularly vulnerable. Vertical transmission and a lack of effective antiviral treatments complicate viral disease management compared to the management of bacterial infections that can be treated with antibiotics [81]. Proactive management is essential for addressing viral pathogen risks in aquaculture. While bacterial infections can often be treated through water quality management, viral diseases require comprehensive approaches, including quarantine protocols and genetic selection for disease-resistant breeds. The persistence of viruses in carrier hosts and rapid spread in dense 4 of 16 https://doi.org/10.20935/AcadBiol7814 populations highlight the importance of early detection. Integrating these strategies helps aquaculture operations reduce viral outbreaks and ensure sustainable production, complementing bacterial disease control measures [82]. Microbial interactions in aquaculture systems refer to dynamic relationships among diverse microbial communities, including beneficial microbes, opportunistic pathogens, and environmental microorganisms. These interactions occur in the water column, sediment, and host-associated microbiomes of aquatic animals. These microbial communities engage in competition, mutualism, commensalism, predation, and quorum sensing, which influence the health and disease resistance of the host. Beneficial bacteria may outcompete pathogens for nutrients and adhesion sites, or produce antimicrobial compounds. An imbalance in microbial communities due to stress, pollution, or antibiotic use can lead to harmful bacteria dominance, increasing disease susceptibility [83–85]. These interactions are critical under conditions of high organic load, poor water quality, fluctuating temperatures, and high stocking densities in intensive aquaculture operations. Such environments can destabilize microbial homeostasis, allowing pathogens to proliferate. Mitigation strategies focus on manipulating microbial interactions through probiotics, prebiotics, synbiotics, and quorum-quenching agents to promote healthy microbiomes. By understanding these microbial networks, it is possible to improve aquaculture sustainability [86]. Jun [87] highlighted bacteriophages that target bacterial pathogens, providing an alternative to antibiotics. The application of beneficial microbes is critical during periods of heightened disease risk, such as early developmental stages, high-density stocking, or stressful environmental conditions [88–90]. Introducing probiotics helps establish beneficial microbiota that can outcompete pathogens through competitive exclusion, nutrient depletion, and antimicrobial compounds [48, 91, 92]. Bacteriophages operate through specific lytic activity, targeting particular bacterial pathogens without affecting beneficial microbes. Their application is effective during bacterial outbreaks, where phage therapy reduces pathogen load without antibiotic resistance. Bacteriophages attach to bacterial cells, inject genetic material and replicate, causing bacterial lysis [93, 94]. This method is valuable in closed aquaculture systems or recirculating aquaculture systems (RASs), where water reuse can concentrate bacterial pathogens. Probiotics and phages offer a synergistic disease management approach that aligns with efforts to reduce antibiotic dependence in aquaculture [95–97]. Biofloc technology utilizes microbial communities to convert waste into high-protein feed for aquatic organisms, enhancing sustainability and creating a diverse microbial environment that suppresses pathogens. As outlined by Jamal et al. [98], biofloc systems enhance nutrient recycling for healthier aquaculture. Biofloc technology (BFT) promotes microbial aggregates of bacteria, algae, protozoa, rotifers and detritus that metabolize nitrogenous waste products like ammonia (NH3 ), nitrite (NO2 − ), and nitrate (NO3 − ). Heterotrophic bacteria, including Bacillus, Pseudomonas and Acinetobacter, assimilate ammonia into microbial biomass when carbon sources adjust the carbonto-nitrogen ratio [99, 100]. Nitrifying bacteria convert ammonia to nitrite and nitrate, though this pathway is less favorable in high-carbon systems [101]. Microalgae like Chlorella vulgaris, Scenedesmus spp. and Oscillatoria spp. assimilate nitrogen while ACADEMIA BIOLOGY 2025, 3 producing oxygen [102]. Bioflocs provide nutrient-rich feed containing proteins, lipids, vitamins, and immunostimulatory compounds for species like tilapia and Pacific white shrimp, improving growth performance [98, 103]. Genetic tools enhance our understanding of microbial communities, allowing harmful taxa to be identified through metagenomic analyses to maintain microbial health [104]. The emergence of microbial threats requires coordinated responses through sustainable practices, innovative technologies, and monitoring. As aquaculture expands, addressing these challenges remains vital for long-term sector viability. 4. Impact of pathogens on aquaculture practices Pathogens in aquaculture environments can transmit resistance genes horizontally among microbes, leading to ineffective treatment of aquatic diseases [105]. The extensive use of antibiotics in aquaculture may not be fully metabolized, leading to their environmental release via excretion [106]. This results from low expression of specific metabolic enzymes, which is indicative of the presence of under-expressed or inactive genes. The resulting metabolites can be more reactive and toxic than the parent compound due to exposed functional groups. These antibiotics exert selective pressure on microbial communities, favoring antibioticresistant bacteria and resistance genes (ARGs), such as bla, tet, sul, and erm. These genes transfer among microbes via horizontal gene transfer mechanisms, including conjugation, transduction, and transformation. Mobile genetic elements facilitate ARGs’ dissemination across bacterial populations in aquaculture systems, increasing the risk of the spread of resistance to human and animal pathogens [107–109]. Imprudent antimicrobial use in human health contributes to resistance in human pathogens [110]. The transfer of resistance genes from aquaculture to human pathogens is concerning, particularly in areas with concentrated aquaculture activity. These areas can harbor resistance genes and microbes that contaminate water, air, and sediments [111]. A One Health approach is essential when addressing antimicrobial resistance, recognizing the interdependence between animals, the environment, and humans [112]. Using antimicrobials instead of cleanliness can spread multidrug-resistant pathogens [113]. Implementing strategies to reduce antibiotic use in aquaculture and developing alternative disease management is crucial [114, 115]. Excessive antibiotic use in agriculture promotes antimicrobial resistance [116]. Antibiotics have reduced mortality and morbidity in humans, animals, and microorganisms [117], and effective antibiotics remain critical for combating infectious diseases [118]. Information resources should be strengthened in developing countries to support health professionals, animal keepers, patients, and the public [119]. This will help build the capacity for and understanding of antimicrobial use and resistance. The World Health Organization (WHO) has launched guidelines urging farmers and the food industry to cease routine antimicrobial use for growth promotion in healthy animals [112]. The rise in multidrugresistant strains has prompted legislative actions to restrict antibiotic usage, as highlighted by EU Regulation 2019/6 [120]. Collaboration among stakeholders is needed to develop strategies for managing antimicrobial resistance in aquaculture. 5 of 16 https://doi.org/10.20935/AcadBiol7814 Microbial pathogens pose a significant challenge to aquaculture practices worldwide. As production has increased to meet the global seafood demand, diseases from microbial pathogens have become a leading cause of production loss, affecting farmed species and human health [121, 122]. These pathogens proliferate in high-density farming environments, and this is particularly true of opportunistic bacteria like Vibrio and Aeromonas [31, 123]. Water quality management significantly influences microbial communities in aquaculture systems. These communities shift in response to nutrient loading from waste and feed, which can promote pathogenic bacteria [124]. Studies show that increased nitrogen loads alter bacterial community structure, leading to disease outbreaks [125, 126]. This highlights the importance of water management and microbial monitoring [31, 126, 127]. The use of probiotics to enhance stock health is becoming increasingly common in aquaculture. Probiotics improve gut microbiota in fish, enhancing immune responses [128, 129]. This represents a shift toward biocontrol methods as alternatives to antibiotics [26, 74]. Probiotic supplementation has been linked to improved feed conversion ratios and growth performance [129, 130]. Bioremediation technologies using specific microorganisms like sponge species can mitigate effluents from aquaculture systems [121]. These organisms purify water by breaking down organic substances and removing pathogenic bacteria, enhancing aquaculture ecosystem health [131, 132]. The integration of bioremediation addresses water quality issues and promotes sustainable aquaculture systems resilient to microbial infections. Microbial pathogens affect fish health and human populations through contaminated seafood consumption. The transmission of pathogens like Vibrio parahaemolyticus demonstrates the connection between aquatic ecosystems and human health [133, 134]. Surveillance of these pathogens in aquaculture environments and seafood products is essential for public health and consumer confidence [135]. Environmental variables like seasonal changes, salinity, and temperature influence microbial community composition and pathogen prevalence [136, 137]. Seasonal patterns in microbial diversity affect disease susceptibility, requiring continuous monitoring and management adaptability [21, 138]. Metagenomics and high-throughput sequencing have improved our understanding of microbial diversity and functions in aquaculture systems [104, 139]. These technologies help identify microbial population shifts and develop effective management strategies [140]. An overview of microbial pathogens and their impact on aquaculture is shown in Figure 1. The integration of advanced microbial management strategies presents promising solutions for pathogen mitigation in aquaculture. Success requires effective water quality management, microbial monitoring, and sustainable practices to ensure longterm industry viability amid environmental and health concerns [8, 141, 142]. 5. Strategies for prevention and control The aquaculture sector requires sustainable solutions to mitigate antimicrobial resistance and minimize novel pathogens. These solutions should help to reduce the use of antimicrobial agents in agriculture and aquaculture [143]. Better management and farmer ACADEMIA BIOLOGY 2025, 3 education are key to reducing antimicrobial use [70]. Vaccines against prevalent aquaculture pathogens offer a promising avenue for disease prevention. The implementation of biosecurity measures like quarantine and disinfection can prevent pathogen spread in aquaculture facilities. Immunostimulants, probiotics, and prebiotics in feeds can enhance aquatic animals’ immune response [144]. Antimicrobial stewardship programs in veterinary settings are necessary to minimize resistance [145]. These programs should educate veterinarians and farmers on appropriate antibiotic use and promote diagnostic testing. Research efforts must focus on understanding resistance mechanisms in aquaculture pathogens and developing countermeasures. Understanding resistance factors is critical for effective interventions [146]. The WHO Global Action Plan aims to improve surveillance, lower infection rates, and optimize antimicrobials [147]. The One Health approach, which recognizes the connection between human, animal, and environmental health, is essential for addressing resistance in aquaculture [148]. This requires collaboration among stakeholders to develop comprehensive control strategies [149]. Phytochemicals with antibacterial and antiviral properties can improve animal health [150]. Probiotics are being used to treat diseases as antibiotic alternatives [151]. The prevention of microbial pathogens in aquaculture is critical for sustainability and biosecurity. As the industry expands due to the rising demand for seafood, pathogen challenges require integrated strategies that combine biosecurity measures and effective management practices. One of the primary areas of focus is implementing effective biosecurity measures to minimize pathogen introduction and spread. High antimicrobial usage in aquaculture can lead to increased antimicrobial resistance (AMR), exacerbating the health threats posed by pathogens like Aeromonas veronii, which threatens tilapia farming through mortality events linked to poor water quality and intensive farming [152, 153]. Biosecurity includes water quality management, quarantine protocols, and hygiene practices within farming systems [152, 154]. Inadequate biosecurity can cause devastating concurrent infections in hatcheries, as seen in European seabass [154]. These measures must be tailored to local conditions and specific pathogens [155]. Systematic implementation of biosecurity policies significantly reduces disease outbreaks and improves fish health management [156]. The judicious use of antibiotics is crucial, as overreliance leads to AMR and risks to consumer safety [152, 157]. Alternative treatments like probiotics, prebiotics, and medicinal plants offer sustainable approaches to bacterial infections [158, 159]. Vaccination can prevent specific infections while reducing antibiotic dependence [160, 161]. Environmental DNA (eDNA) analysis enables noninvasive pathogen monitoring, allowing timely interventions [162]. For effective implementation, adequate training and resources must be provided to aquaculture workers [163]. Environmental management practices, including proper organic waste management and optimal water quality maintenance, are fundamental in reducing pathogen proliferation. Water quality parameters like nitrite and ammonia levels significantly affect disease prevalence in aquatic species, requiring regular monitoring [164]. Biofloc technology can support microbial communities for waste assimilation while improving water quality, reducing disease risks [165]. 6 of 16 https://doi.org/10.20935/AcadBiol7814 Figure 1 • Overview of microbial pathogens in aquaculture. A multifaceted strategy of biosecurity measures, antimicrobial alternatives, diagnostic tools, and environmental management forms the backbone of countering microbial pathogens in aquaculture. Continuous education of stakeholders is essential for sustainable aquaculture systems that meet global seafood demands while protecting animal health. 6. Challenges and future directions Despite the progress made in understanding microbial threats to aquaculture, significant challenges remain. A major challenge is the limited availability of effective treatments for many aquaculture diseases [166]. The emergence of antimicrobial resistance threatens aquaculture production sustainability [167]. The lack of standardized diagnostic methods and surveillance programs hinders outbreak control. Limited awareness of biosecurity practices among farmers, particularly in developing countries, poses another challenge. Several areas require attention to enhance microbial threat management. Advancements in production and detection technologies are needed for industry sustainability [168]. Research is needed to develop vaccines, diagnostic tools, and treatment strategies. Emphasis must be placed on identifying ecology-friendly substances, such as natural probiotics, that align with cultured organisms’ physiology. Efforts should improve biosecurity practices, including quarantine measures and water quality management. Understanding pathogen ecology and antimicrobial resistance factors is crucial. Collaboration among researchers, policymakers, and stakeholders is essential for effective management strategies. The intensification of aquaculture has increased species’ vulnerability to pathogens [169]. Strategies that enhance immunity are important, as the gut plays a vital role in nutrient absorption and pathogen resistance [170]. ACADEMIA BIOLOGY 2025, 3 There is promising research focused on monitoring and manipulating the gut microbiome [168]. Aquaculture development is crucial as population growth challenges food systems [171]. The industry must select species and feed to boost nutritional components [172]. Novel technologies can improve efficiency and optimize feeding protocols for fish health [173]. The management of microbial pathogens in aquaculture remains critical as the industry balances productivity with sustainability and animal health. The increase in aquaculture production faces challenges from infectious diseases caused by bacteria, viruses, and parasites, exacerbated by farming intensification and climate change effects that increase pathogen virulence and disease outbreaks [18, 19]. To address these challenges, strategies including advances in biotechnology, improved management practices, and sustainable methods are essential for the industry’s future. A major challenge is antibiotic resistance emergence from antimicrobial overuse in fish farming [18, 174]. This poses risks to fish and public health through resistant bacteria transmission [74, 175]. As traditional treatments become less effective, alternatives like probiotics and bacteriocins show promise in enhancing fish health [130, 176]. Probiotics help establish protective intestinal flora against pathogens [130, 177]. Environmental factors significantly influence pathogen dynamics. Nutrient loading and sediment quality affect microbial communities in aquaculture systems [131, 135]. Robust biosecurity measures and environmental management are required to maintain water quality. Advanced monitoring systems, including machine learning and IoT, can help detect early signs of disease [9, 178]. Climate change poses challenges to aquaculture sustainability. Increased water temperatures enhance pathogen growth and alter host–pathogen interactions, increasing farmed species’ vulnerab- 7 of 16 https://doi.org/10.20935/AcadBiol7814 ility to diseases [19, 179]. Adaptive strategies considering climate variability are paramount. The development of resilient aquaculture systems integrating species with varying stress tolerance can help mitigate climate-induced disease susceptibility [31, 180]. Integrated multi-trophic aquaculture (IMTA) systems may enhance resilience and reduce pathogen load [181]. Funding Vaccine development is crucial in combating aquaculture diseases. Vaccination strategies can reduce fish mortality rates when targeting high-risk pathogens [28, 182]. However, vaccine efficacy and adaptation to evolving pathogens remain challenging. Genetic approaches to enhance disease resistance could provide long-term solutions to infectious outbreaks [179, 183]. Conceptualization, V.A.K.B.G. and A.K.V.; methodology, D.B. and P.K.A. and M.B.V. and S.K.; data curation, U.S.A. and M.S.G. and V.P.K.; writing—original draft preparation, V.A.K.B.G. and A.K.V.; writing—review and editing, V.A.K.B.G. and A.K.V. All authors have read and agreed to the published version of the manuscript. Proactive management using bioremediation techniques can control pathogen levels [121]. Natural remedies and alternative practices, including phytobiotics and essential oils, combat infections without the drawbacks of chemical treatment [184–186]. Collaborative efforts among researchers, practitioners, and policymakers are essential. Sharing knowledge strengthens biosecurity frameworks and enhances system resilience [118, 187]. This research received no external funding. Author contributions Conflict of interest The authors declare no conflicts of interest. Data availability statement The future of managing aquaculture pathogens requires a multidisciplinary approach that incorporates innovative technologies and sustainable practices. Ongoing research and methodology integration remain critical for maintaining healthy aquatic ecosystems while meeting the global seafood demand. Not applicable. 7. Conclusions Accepted: 2025-07-14 Microbial pathogens pose a significant challenge to aquaculture sustainability worldwide. The expansion of aquaculture, driven by the growing global seafood demand, has led to increased disease outbreaks from pathogenic microorganisms, including bacteria, viruses, fungi, and parasites. Intensive farming practices with high stocking densities and poor water quality have created environments conducive to pathogen spread. Antibiotic resistance is a major concern, as antibiotic overuse in aquaculture has led to resistant strains, risking animal and human health. The interactions among microbial communities, environmental factors, and host immunity complicate threat management. Solutions like probiotics, vaccines, and improved biosecurity are being developed to mitigate pathogens’ impact. However, an integrated approach combining research, policy, and industry collaboration is needed to address these challenges effectively. Farmers must adopt science-based practices, including health monitoring, water quality management, and responsible antimicrobial use. Implementation of vaccination programs, probiotic supplementation, and biosecurity protocols should be prioritized. Policymakers should regulate antibiotic usage, invest in disease surveillance, and support research into alternative control strategies. Collaborative training programs on disease prevention and sustainable farming practices are essential for minimizing pathogen risks in aquaculture. Acknowledgments The authors thank the anonymous reviewers for their critical comments that helped the authors to improve the manuscript. ACADEMIA BIOLOGY 2025, 3 Additional information Received: 2025-05-31 Published: 2025-07-18 Academia Biology papers should be cited as Academia Biology 2025, ISSN 2837-4010, https://doi.org/10.20935/AcadBiol7814. The journal’s official abbreviation is Acad. Biol. 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