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Using Probiotics in Aquaculture: Farming Fish for a Sustainable Future

Every year the world eats more and more fish. In fact, according to the UN Food and Agriculture Organization, global fish consumption is increasing by over 3% annually. To meet the growing demand, the world’s aquaculture sector is also booming. In 2020, fish farming contributed almost 46% of global fish production.

Global demand for seafood is growing steadily. ©astrakanimages/envato
Global demand for seafood is growing steadily. ©astrakanimages/envato

As with other farming sectors, the aquaculture industry has faced concerns about its use of antibiotics and feed. Specifically, questions have been raised about whether intensive aquaculture is harmful to marine ecosystems and to seafood consumers. In response, the aquaculture industry is turning to the use of probiotics to lead its practices toward a more sustainable future.

Probiotics: A Boon for Health

In 1905, Bulgarian physician and microbiologist Stamen Grigorov discovered a probiotic in yogurt. Decades later, in 1953, German bacteriologist and food scientist Werner Kollath introduced the term, “probiotic,” referring to active, beneficial microorganisms that are “essential for a health development of life.” Today, consumers around the world view probiotics as “live” microorganisms that offer health benefits, especially in the digestive system when eaten or in other ways when applied to the body.

Probiotics have also found a purpose in a wide range of industries, including aquaculture. In fish farming, probiotics are mainly used as microbial fish feed supplements to benefit the intestinal microbial balance of the host fish as well as having other benefits.

Types of Probiotics: Bacterial and Non-Bacterial

In aquaculture, a wide range of bacteria are nurtured for use as probiotics, including gram-positive bacteria—bacteria with thick cell walls—(Bacillus, Carnobacterium, Enterococcus, Lactobacillus) and gram-negative bacteria (Vibrio and Pseudomonus).

Non-bacterial probiotics such as bacteriophages—viral parasites of bacteria—are also used in aquaculture. They can alleviate the need for antibiotics while doing no harm to the host.

Other non-bacterial probiotics include yeast (Saccharomyces cerevisiae and Yarrowialipolytica), various microalgae (Tetraselmissuecica, Isochrysisgalbana, and Dunaliella salina), and fungi (Debaryomyces), used primarily to supplement protein, lipids, and nutrients in fish feed.

These have all been produced and promoted to global markets as environmentally friendly choices for supplementation in aquaculture.

Probiotic Sources and Delivery Systems

The main source of probiotics for aquaculture is the gastrointestinal (GI) tract of aquatic animals where diversified types of microbes naturally live and colonize. These microbes can be cultured at an industrial scale using what is called batch fermentation in a growth media.

The end products are commercially available probiotics in liquid, powder, or microencapsulated form that can be administered as feed additives or added directly to the water in which aquatic species are cultured, or raised.

Probiotics are also available in combination with prebiotics—non-digestible beneficial nutritional additives—as well as with immunostimulants or natural plant products. Probiotic-enriched live aquaculture feed—brine shrimp, zooplankton, and small crustaceans—is also regarded as a viable option.

A high-density aquaculture system. ©ESchwartz/Pixabay
A high-density aquaculture system. ©ESchwartz/Pixabay

The Environmental Effects of Aquaculture Should Not Be Overlooked

The growing production of aquatic species, particularly in tightly packed conditions, can have substantial environmental impacts if not managed effectively. Excess and uneaten feed gradually deteriorate the surrounding water quality as microorganisms decompose the uneaten feed, removing oxygen from the water and releasing carbon dioxide in the process. Additionally, when other nutrients including phosphate are released into the water, detrimental algal growth can increase.

Antibiotic overuse is another growing problem in aquaculture which produces survivor pathogens that are increasingly difficult to control due to antibiotic resistance. Scientists have estimated that about 80% of the antibiotics applied in aquaculture remain active in the environment, including in waterway sediment.

To make matters worse, the guts of aquatic animals contribute to the spread of antibiotic resistant genes in water. The ease of horizontal gene transfer in water allows antibiotic resistant bacteria—the ones that are harmless to humans—to transfer their resistant genes to human pathogens.

Probiotics Clean Up Aquaculture in Many Ways

Waterways permeated with nitrogen pollution can also suffer from choking algal growth. Organic nitrogen is formed when excess fish feed, feces, and dead fish accumulate in bodies of water as waste from aquaculture. This organic nitrogen is converted by fungi or bacteria to ammonium and ammonia, which are then converted to nitrites, and subsequently from nitrites to nitrates. Through the process of denitrification, these nitrates are converted to nitrogen gas by probiotic fungi or bacteria, thereby returning nitrogen to the atmosphere.

Probiotic Bacillus species provide several key benefits for aquaculture. They play an especially important role in this nitrogen cycle through ammonification, nitrification, and denitrification, thereby effecting the elimination of various forms of nitrogen from aquaculture waste water. Additionally, Bacillus species use mineralization and nitrification to modulate pH and dissolved oxygen levels in water. They can even improve fish appetite by increasing the digestive enzymes of fish which results in less feed waste.

Probiotics, such as Lactobacillus, have been shown to effectively protect aquatic species against heavy metals.

Probiotic Bacillus also converts organic matter effectively into carbon dioxide. The carbon dioxide is then utilized by β- and γ-proteobacteria—a type of gram-negative bacteria—as a carbon source. Whereas other bacteria convert organic matter into slime or bacterial biomass, probiotic Bacillus, in removing organic matter from aquaculture, reduces sludge accumulation.

Additionally, as microorganisms decompose excess feed and fish waste and release phosphate that fuels eutrophication, probiotic Bacillus, Saccharomyces, Nitrosomonus, and Nitrobactor reduce phosphate levels in water bodies.

Probiotics, such as Lactobacillus, have also been shown to effectively protect aquatic species against heavy metals.

Probiotics and Their Contribution to Fish Health

The health benefits of probiotics begin in the fish gut, where give-and-take occurs between probiotics, epithelial cells, and the gut immune system.

Probiotics actively safeguard against pathogens in the gut by competing for pathogen food sources and by changing the pH in the gut to reduce pathogen growth. Moreover, probiotics enhance the immune system of fish by modulating different immune cells in the fish, including B lymphocytes (a type of white blood cell that produces antibodies), T lymphocytes, and natural killer-cells that kill cancerous tumors and viruses.

Probiotics also activate phagocytic cells, types of immune cells that can kill microorganisms, eat foreign material, remove dead cells, and boost immune response.

Respiratory burst—an important immune response—can be increased by probiotics. Probiotics can also raise levels of lysosomal enzymes (proteases, amylases, and lipases), thereby removing cell-ingested biomolecular waste and debris from the serum and skin mucosa of fish and allowing nutrients to be absorbed more easily.

Traditional fish farm in a purpose-built tank in Moyna, India. ©Srinibas Das
Traditional fish farm in a purpose-built tank in Moyna, India. ©Srinibas Das

Probiotic supplementation promotes fish health by producing essential nutrients—like Vitamin B12, biotin, and fatty acids, and may also improve nutrient availability to the fish by increasing the villi size populating the absorptive area of the gut. Furthermore, probiotics have been shown to increase muscle development and growth rate in fish by upregulating growth-related genes and key metabolic enzymes.

In addition, probiotics like B.circulans improve flesh quality in fish and increase their protein and beneficial oil content.

Probiotic Benefits Far Outweigh the Cons

As with any supplement, the benefits of probiotics depend upon dose, duration of feeding, mode of supplementation and environmental conditions. A prolonged or excessive application of probiotics could create immune suppression in fish, making them more susceptible to disease.

For instance, recurrent usage of Bacillus subtilis in shrimp aquaculture has been linked to the development of bacterial white spot syndrome (BWSS). Although it is a rather harmless phenomenon, BWSS is difficult to distinguish from white spot viral syndrome, a deadly disease that afflicts shrimp.

Having the right knowledge and awareness about the use of probiotics in aquaculture is crucial for probiotics to have the desired effects. Mislabeling or misreading of labels on probiotic products may lead to misuse. Further clarification through research as well as better guidance for producers, middlemen, and farmers is essential; this includes proper instructions for probiotic storage and the monitoring of results.

In the long term, whether trying to destroy or encourage microbes via probiotic use, it is important to achieve overall microbial homeostasis, while keeping in mind human, animal, and plant ecosystem health.

Future Projections for Probiotics in Fish Farming

RAS aquaculture system at Virginia Tech University ©Narek75/Wikimedia Commons
RAS aquaculture system at Virginia Tech University ©Narek75/Wikimedia Commons

The ultimate destiny of probiotics is still unknown and requires more study. Ongoing research is working to establish the proper combinations of microbes for the trending aquaculture production systems of today, such as recirculating aquaculture systems and biofloc systems.

Specific probiotics are under development to include higher levels of plant materials in aqua feed which may help fish feed more efficiently, grow larger, and stay healthier.

Going forward, researchers will need to better classify probiotic strains according to their specific actions, thus permitting a fuller range of products for use. One cutting-edge technique would be to develop specific probiotics or a “cocktail” of probiotics to use with a particular fish species.

Finally, having real-time data on pathogen adhesion and colonization in the fish gut as well as applying next-generation sequencing to identify microbes would be helpful in discovering more viable aquaculture probiotics for sustainable food production.


*Indrajit Kar, Ph.D., is an assistant professor at West Bengal University of Animal & Fishery Sciences in Kolkata, India. His areas of professional interest include heavy metals in environments, pathology, use of probiotics, and phytomedicinal plants, especially mint.

Srinibas Das is an assistant professor in the Department of Fish Nutrition at West Bengal University of Animal & Fishery Sciences in Kolkata, India. He works mainly in areas related to Animal and Fish Nutrition.


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