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Concepts of Bioremediation and its Application in Aquaculture

Ph. Lakshmi Chanu & Sagar C. Mandal*

College of Fisheries, Central Agricultural University, Lembucherra, Tripura (W), India

*Correspondence:, +919402169213 (M), +913812865291 (Fax)



Aquaculture production has increased steadily in recent years and is the fastest growing food production sector and has become a valuable component of national development and poverty reduction plans in many areas of the world. At a time when capture fisheries are leveling off, aquaculture production continues to increase. The increase in production is greatest in developing countries where about 93 percent of aquaculture production originates. It was once considered an environmentally sound practice because of its polyculture and integrated system of farming based on optimum utilization of farm resource, including farm wastes. Increased fish production is being achieved by the expansion of land and water under culture and the use of more intensive and modern farming technologies that involve higher usage of inputs such as water, feed, fertilizer and chemicals. As a result, aquaculture is now considered as a potential polluter of the aquatic environment and a cause of degradation of wetland areas.

What is Bioremediation?

Bioremediation consists of using living organisms (bacteria, fungi, actinomycetes, cyanobacteria and to a lesser extent, plants) to reduce or eliminate toxic pollutants. These organisms may be naturally occurring or laboratory cultivated. The physical, chemical and biological conditions of the culture environment have an influence on the shrimp to toxins like hydrogen sulphide, ammonia and carbon dioxide leads to stress and ultimately disease. Wastes produced in aquaculture farms differ in quality and quantity of components depending on the species farmed and the farming practices adopted. The wastes in aquaculture farms can be categorized as residual food and fecal matter, metabolic by-product, residues of biocides and biostats, fertilizer derived wastes and wastes produced during moulting and collapsing algal blooms. The current approach to improving water quality in aquaculture is the application of microbes/enzymes to the ponds known as 'bioremediation'. When macro and micro organisms and/or their products are used as additives to improve water quality, they are referred to as bioremediators or bioremediating agents. The newest attempt being made to improve water quality in aquaculture is the application of probiotics and enzymes to the ponds is known as bioremediation, which involves manipulation of microorganisms in ponds to enhance mineralization of organic matter and get rid of undesirable waste compounds.

Organic Detritus & Bioremediation

The dissolved and suspended organic matter contains mainly carbon chains and is abundantly available to microbes and algae. A good bioremediation must contain microbes that are capable of effectively clearing carbonaceous wastes from water. Further it would be very supportive, when these microbes multiply rapidly and have good enzymatic capability. Members of the genus Bacillus like Bacillus subtilis, B. licheniformes, B. cereus, B. coagulans and species Phenibacillus polymyxa are good examples of bacteria suitable for bioremediation of organic detritus. However, they are not normally present in the required quantities in the water column, their natural habitat being the sediment. When certain Bacillus strains are added to the water in sufficient quantities, they can make an impact. They compete with the bacterial flora naturally present for the available organic matter, like leached or excess feed and shrimp faeces. As a part of bio-augmentation, the Bacillus can be produced, mixed with sand or clay and broadcast to be deposited in the pond bottom. Lactobacillus is also used along with Bacillus to break down the organic detritus. These bacteria produce a variety of enzymes that break down proteins and starch to small molecules, which are then taken up as energy sources by other organisms. The removal of large organic compounds reduces water turbidity.

Nitrogenous Compounds & Bioremediation

Nitrogen applications in excess of pond assimilatory capacity can lead to deterioration of water quality through the accumulation of nitrogenous compounds (ammonia and nitrite) causing toxicity to fish and shrimp. The principal sources of ammonia are excretion and sediment flux derived from the mineralization of organic matter and molecular diffusion from reduced sediment. Bacteriological nitrification is the most practical method for the removal of ammonia from closed aquaculture systems and it is commonly achieved by the setting of sand and gravel bio-filters through which water is allowed to circulate. The ammonia oxidizers are placed under five genera Nitrosomonas, Nitrosovibrio, Nitrosococcus, Nitrolobus and Nitrospira. Nitrification not only produces nitrate but also alters pH towards the acidic range, facilitating the availability of soluble materials. The vast majority of aquaculture ponds accumulate nitrate, as they do not contain a denitrifying filter. Denitrifying filters help to convert nitrate to nitrogen. It creates an anaerobic region where anaerobic bacteria can grow and reduce nitrate to nitrogen gas. Nitrate may follow several biochemical pathways following production by nitrification.

Phosphorous & Bioremediation

Phosphorus normally has limitations in a freshwater environment. Any deviation from the normal NO3/PO4 ratio is believed to be dependent on which influence the rate of nitrification or bacterial regeneration of phosphorous, is available in organisms mainly as phospholipids and neucleoprotiens. Phosphorous is generated from organic compound as PO4 by certain bacteria that produce enzymes such as phosphotases and phytases. The solubility of inorganic phosphotases is primarily a function of pH. Bacteria are capable of liberating PO4 from these compounds through the production of organic and mineral acids.

Hydrogen Sulphide (H2S) & Bioremediation

Sulphur is of some interest in aquaculture because of its importance in anoxic sediments. In aerobic conditions, organic sulphur decomposes to sulphide, which in turn gets oxidized to sulphate. Sulphate is highly soluble in water and so gradually disperses from sediments. Sulphide oxidation is mediated by micro organisms in the sediment, though it can occur by purely chemical processes. Organic loading can stimulate H2S production and reduction in the diversity of benthic fauna. Hydrogen Sulphide is soluble in water and has been suggested as the cause of gill damage and other ailments in fish. Unionised H2S is extremely toxic to fish that may occur in natural waters as well as in aquaculture farms. Bioassays of several species of fish suggest that any detectable concentration of H2S should be considered detrimental to fish production.

The photosynthetic benthic bacteria that break H2S at pond bottom have been widely used in aquaculture to maintain a favorable environment. These bacteria contain bacterio-chlorophyll that absorb light and perform photosynthesis under anaerobic conditions. They are purple and green sulphur bacteria that grow at the anaerobic portion of the sediment-water interface. Photosynthetic purple non-sulphur bacteria can decompose organic matter, H2S, NO2 and harmful wastes of ponds. The green and purple sulphur bacteria split H2S to utilize the wavelength of light not absorbed by the overlying phytoplankton. The purple and green sulphur bacteria obtain reducing electrons from H2S at a lower energy cost than H2O splitting photoautotrophs and thus require lower light intensities for carrying out photosynthesis.

Chromatiaceae and Chlorobiaceae are the two families of photosynthetic sulphur bacteria that favour anaerobic conditions for growth while utilizing solar energy and sulphide. Chromatiaceae contain sulphur particles in cells but Chlorobiaceae precipitate them out. The family Rhodospirillaceae is not of any use for H2S removal, can be used as efficient mineralizes at pond bottom as they grow in both aerobic and anaerobic conditions as heterotrophic bacteria even in the dark without utilizing solar energy. The common examples of photosynthetic bacteria of importance in aquaculture are Rhodospirillum, Rhodopseudomonas, Chromatium, Thiocystis, Thiospirillum, Thiocapsa, Lamprocystis, Thiodictyon, Thiopedia, Amoebobacter, Chlorobium, Prosthecochloris, Pelodictyon and Clathrochloris.

For bioremediation of H2S toxicity, the bacterium that belongs to Chromatiaceae and Chlorobiaceae can be mass cultured and can be applied as pond probiotic. Being autotrophic and photosynthetic, mass culture is less expensive and the cultured organisms can be adsorbed on to the sand grains and applied so that they may reach the pond bottom to enrich the hypolimnion and ameliorate H2S toxicity.

Screening of Microbes for Utilization as Bioremediators

Microorganisms both gram positive and gram negative have been tested for their efficacy as bioremediators in aquaculture by various workers. Bacillus is the most commonly used organism followed by Aeromonas and Pseudomonas. Bioremediators commercially available in the market mainly include Nitrifiers, Sulphur bacteria, Bacillus sp. and Pseudomonas sp.

Advantages of Bioremediation

  • It works on a variety of organic and inorganic compounds

  • Can be done either on-site or off-site, easy to implement and maintain

  • Low-cost compared to other treatment methods

  • Environmentally-friendly and aesthetically pleasing

  • Reduces the amount of wastes to be land filled

Disadvantages of Bioremediation

  • It may take several years to remediate and depends on climatic conditions

  • Restricted to sites with contamination near the roots

  • Harvested plants may be classified as hazardous waste

  • Consumption of contaminated plants may be harmful

  • There may be harmful effects on the food chain

Beneficial effects of Probiotics

  1. Neutralization of toxin and suppression of viable count

  2. Production of antibacterial compounds and competition for adhesion sites

  3. Alternation of microbial metabolism, stimulation of immunity in the host

  4. Accelerate the sediment decomposition by producing organic acids

  5. Production of hydrogen peroxide and enzymes

Application of Probiotics in Aquaculture

  1. To regulate the microflora of aquaculture water and pathogenic microorganisms.

  2. To enhance decomposition of the undesirable organic substances in aquaculture water and improve ecological environment of aquaculture by minimizing the toxic gases like ammonia, nitrite, hydrogen sulfide, methane etc.

  3. To increase the population of food organisms improves the nutrition level of aquaculture animals and improve immunity of cultured animals to pathogenic microorganisms.

  4. The frequent outbreaks of diseases can be prevented.


Constant efforts are being made to address the negative impacts food production systems including aquaculture have on the environment. The role of beneficial bacteria to control pathogens will become important in aquaculture, especially in the light of the increasing number of antibiotic resistant strains of bacteria. The management of pond microbial ecology is an area where applied research can lead to important findings for improving the productivity and environmental friendliness of the shrimp farming industry worldwide. The use of bioremediators will gradually increase and the success of aquaculture in future may be synonymous with the success of bioremediators that, if validated through rigorous scientific investigation and used wisely, may prove to be a boon for the aquaculture industry.


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