5. Methods of Applying Prebiotics and Probiotics in Marine Species

5.1. Microencapsulation

Marine species can benefit from the microencapsulation of probiotics and prebiotics to enhance their health and growth performance. In this method, beneficial microorganisms and substrates are encapsulated to protect them from harsh environmental conditions and to improve their delivery and efficacy within the host. The integration of probiotics and prebiotics, often referred to as synbiotics, has shown significant potential to improve the health, immune response, and disease resistance of marine species such as shrimp and fish [145]. Several applications and benefits of microencapsulation in marine aquaculture are discussed in the following sections. Pacific white shrimp larvae were fed microencapsulated Pseudoalteromonas piscicida (1Ub) combined with MOS, a prebiotic, via enrichment with Artemia sp. This method reduced the Vibrio harveyi population while enhancing the growth performance, immune responses, and disease resistance. Microencapsulation preserved probiotics from degradation, ensuring their viability during storage and application and thereby optimizing their effects in the shrimp digestive tract. Synbiotic treatment yielded the best results in this study [92]. Pangasianodon hypophthalmus was microencapsulated with the probiotic Bacillus sp. NP5 and the prebiotic MOS. Probiotics are protected during digestion and storage by microencapsulation, which makes them more effective [146]. Microencapsulation enhances the application of probiotics and prebiotics in marine species by protecting them during processing, storage, and digestion. By minimizing degradation, this technique ensures that beneficial bacteria, such as Bacillus subtilis E20, can effectively modulate the gut microbiota. In marine species such as white shrimp (Penaeus vannamei), microencapsulation promotes the proliferation of beneficial bacterial strains while reducing harmful bacteria such as Vibrio, thereby improving health, immune response, and metabolic functions [147]. To promote digestive health, microencapsulation can enhance the survival of probiotics and prebiotics, enabling effective colonization of the gut microbiota and modulation. By ensuring adequate delivery of beneficial microorganisms, this method can potentially improve gut health in various species [148].

5.2. Bio‐Carrier Inoculation

Bio‐carrier inoculation involves using carriers to deliver beneficial microorganisms to marine organisms, thereby enhancing their resilience and health. This approach has been explored in various marine species, including corals, sponges, and aquaculture‐reared fish and shellfish, to improve stress tolerance and the microbiome composition. Carriers, such as rotifers, alginate beads, and biofilm‐coated substrates, have shown promise in effectively delivering probiotics to target organisms, facilitating microbiome manipulation and environmental remediation. The following sections delve into specific applications and findings related to bio‐carrier inoculation in marine species [149].

5.2.1. Rotifers as Bio‐Carriers for Coral Probiotic Delivery

Rotifers, specifically Brachionus plicatilis, have been used as biocarriers for delivering Beneficial Microorganisms for Corals (BMCs) to corals such as Pocillopora damicornis. In this method, rotifers consume and accumulate probiotics, after which they were then consumed by corals. This dual‐delivery system offers several ecological implications: it enhances coral resistance to environmental stressors, improves coral health, and provides additional nutritional benefits through the rotifers themselves. Collectively, these effects contribute to the resilience of the overall marine ecosystems [149].

5.2.2. Sponge Extracts as a Bio‐Carrier Strategy for Cyanobacterial Cultivation

In another application, sponge extracts from Sigmodocia carnosa have been investigated as a bio‐carrier approach to enhance the growth of sponge‐associated cyanobacterial symbionts. Extracts were incorporated into culture media, resulting in significantly improved biomass production and biochemical constituents in cyanobacteria. This technique not only promotes the cultivation of previously uncultivable marine microorganisms but also reduces sponge waste accumulation along coastal areas, thereby contributing to the health and sustainability of marine ecosystems [150].

5.2.3. Bio‐Carrier Inoculation in Recirculating Aquaculture Systems

Beyond direct delivery to marine organisms, bio‐carrier inoculation has also been applied in recirculatory aquaculture systems (RAS) to improve water quality and system performance [151]. In a study evaluating moving bed biofilm reactors (MBBRs), bio‐carriers were inoculated with mature biofilm (MBI) to accelerate nitrification and stabilize water quality parameters. This approach reduced system start‐up time by 26 days and achieved a stable total ammonia nitrogen (TAN) concentration below 0.5 mg/L within 132 days post‐inoculation. Furthermore, MBI‐treated systems exhibited the highest microbial richness compared to other treatments and the control group, indicating a more robust and resilient biofilter [152]. In summary, bio‐carrier inoculation offers a versatile and effective strategy for delivering beneficial microorganisms to marine species and aquaculture systems. Whether through live carriers such as rotifers, biochemical carriers such as sponge extracts, or engineered carriers such as biofilm‐coated substrates, this approach enhances host health, promotes beneficial microbial interactions, and improves system‐level performance. Future research should focus on optimizing carrier materials, evaluating their long‐term effects on host microbiomes, and scaling up these methods for commercial aquaculture and marine conservation applications.

5.3. Artificial Reef Biofilms

Biofilms that develop on artificial biological reef structures, typically composed of concrete and bioactive materials derived from marine algae, are referred to as artificial reef biofilms. These biofilms play a critical role in marine habitat restoration by fulfilling biochemical requirements and supporting the settlement of eukaryotic larvae and algal spores. Compared to natural reefs and control models, artificial reef biofilms exhibit higher microbial diversity and richness, particularly with dominant phyla such as Cyanobacteria, Proteobacteria, and Planctomycetota [153]. Marine biofilms serve as the biological foundation for artificial reefs, transforming submerged structures into a functioning reef ecosystem. Biofilm formation begins when microorganisms adhere to submerged surfaces and release extracellular polymeric substances (EPS), which attract additional microbial colonizers and facilitate community development. However, environmental contaminants such as crude oil and chemical dispersants can disrupt biofilm diversity and function, with cascading effects on higher trophic levels. Understanding the response of these biofilms to environmental disturbances is therefore crucial for mitigating the impacts of oil spills and preserving marine infrastructure [154]. The formation of biofilms on artificial reefs is also essential for the initial recruitment of marine organisms. A study comparing two coral reef sites found that biofilm compositions differed significantly due to environmental factors and anthropogenic impacts. These biofilms, composed of both prokaryotic and eukaryotic organisms, are critically important for coral recruitment and overall reef community health. By creating favorable conditions for reef organism settlement, understanding biofilms can significantly enhance restoration efforts [155]. Submerged structures like historic shipwrecks can also support artificial reef biofilms, providing substrates for microorganisms to attach and form diverse communities. Over time, these biofilms mature through continued EPS deposition, supporting the settlement of both microbes and macrobes and improving corrosion resistance. Nevertheless, environmental disruptions, including oil spills, can alter the biofilm composition and function, potentially affecting the biodiversity and ecological value of these artificial reefs [156]. In summary, artificial reef biofilms are dynamic and ecologically significant communities that underpin the success of artificial reef structures. Their high microbial diversity, recruitment functions, and sensitivity to environmental disturbances make them both valuable tools for habitat restoration and important indicators of ecosystem health.