Probiotics have been commonly practiced in commercial shrimp farms to increase pond production. However, these possibilities were based on the results of in vitro studies or laboratory in vivo trials. Here are the results of research that traced the composition and abundance of commercial probiotic species applied to commercial shrimp farms in an intensive aquaculture system using high-throughput sequencing.
Probiotics have been considered an eco-friendly approach to increase the yield of aquaculture production through several mechanisms, including maintaining water quality, growth performance, or the survival rate of aquatic organisms.
For example, studies have confirmed that probiotics application has enabled us to significantly reduce antibiotic use in aquaculture industries and avoid the occurrence of antibiotic resistance genes in microbes. Some probiotics have been documented to produce digestive enzymes such as protease, amylase, lipase, alginate lyase, and cellulase which help animal hosts to digest ingested diets.
Probiotic strains were documented to produce antimicrobial compounds active against bacterial pathogens. Also, some probiotic species have the capacity to degrade and prevent the accumulation of aquaculture waste in culture ponds, including solid organic waste or soluble toxic chemicals such as ion amonia (NH4+ ) or nitrite (NO2–).
Despite the benefits of the use of probiotics in aquaculture, most of these studies were based on in vitro studies or in vivo laboratory trials in very small-scale rearing systems where environmental conditions were easily controlled. Some studies have confirmed that the results of in vitro and in vivo studies are frequently uncorrelated.
Therefore, there is a question of whether probiotic strains can survive and significantly contribute to the quality of rearing water, digestibility, or disease resistance, as reported by many in vitro or laboratory-scale studies.
To address this question, here are the results of the research that traced the composition and abundance of commercial probiotics species applied in commercial shrimp farms (ponds and the intestinal tract of white shrimps) in an intensive aquaculture system using high-throughput sequencing.
Materials and methods
Four commercial probiotic species (Lactobacillus plantarum, Lactobacillus fermentum, Bacillus subtilis, and Pseudomonas putida) were applied to the commercial White shrimp, Litopenaeus vannamei ponds (@800 m2 area of high-density polyethene ponds) in the morning at a dose of 5 ppm once every 2 days in the first month, and once a week from the second month onward.
“The pond consisted of three plots with an area of 800 m2 and a stocking population of 220,000 individuals. Feeding of shrimps were done manually 1–5 times a day, according to the shrimp sizes.”
Water samples were collected from six ponds using a long pole sampling device and a 20 mL sterile plastic cup. The collected water was stored in a 50 mL falcon tube that had previously been filled with 30 mL of absolute ethanol for DNA preservation.
Samples were kept on ice until processed in the laboratory within the next 8 h. A total of 30 healthy shrimps showing no symptoms of the disease were collected from 3 shrimp ponds (10 shrimps per pond) on day 47. Then, the presence of the probiotic species was traced by collecting the rearing water and shrimp’s intestines on day of culture (DOC) 47 to monitor their composition and abundance using high-throughput sequencing.
Profiles of probiotic species in grow-out ponds
The results showed that the number of bacteria classified as Ordo Lactobacillales was quite abundant in the three ponds. A total of 4,704 bacterial sequences, or 5% of the total bacteria detected in pond 1, were assigned to Ordo Lactobacillales, of which 4,375 sequences (93%) were identified as genus Lactobacillus and belonged to 12 bacterial species (Table 1).
From pond 2, a total of 4,572 bacterial sequences (5% of the total identified bacteria in pond 2) were assigned to Ordo Lactobacillales, of which 3,795 sequences (83%) were classified as the genus Lactobacillus and belonged to 12 bacterial species (Table 1).
Both pond 1 and pond 2 appeared to be very similar in terms of Lactobacillales proportions (5%) and the number of Lactobacillus species (12 species).
From pond 3, a total of 2,986 sequences or 3% of the total identified bacteria in pond 3 were assigned to Ordo Lactobacillales, of which 65 sequences (2% of Lactobacillales) were identified as the genus Lactobacillus and belonged to three bacterial species, which are Lactobacillus sp (2 sequences), L. salivarius (60 sequences), and L. ruminis (3 sequences).
“However, none of the Lactobacillus species identified in the three ponds showed to be the introduced probiotic species, which were L. plantarum and L. fermentum.”
A member of the genus Bacillus was not found in ponds 2 and 3, but was found only in pond 1. A total of 441 bacterial sequences or 0.4% of the total detected bacterial sequences, were assigned to Ordo Bacillales. Of which 395 sequences or 99% were classified as Bacillus sp (OTU_160).
Other NGS results showed that Pseudomonas spp were detected only in two ponds with very low abundance. A total of 39 bacterial sequences or 0.04% of total bacterial sequences detected from the rearing water of pond 1 were assigned to the Ordo Pseudomonadales, but none of them belonged to Pseudomonas spp.
In pond 2, 35 bacterial sequences were assigned to Ordo Pseudomonadales, and only one sequence was identified as Pseudomonas azotoformans.
The highest abundance sequences of Ordo Pseudomonadales were detected from pond 3 which contained 6,325 bacterial sequences, of which 303 sequences belonged to the genus Pseudomonas and were assigned to 3 species: Pseudomonas psychrotolerans, Pseudomonas azotoformans, and Pseudomonas sp.
These results indicated that Pseudomonas putida which came from commercial probiotics had difficulties adapting and proliferating in the rearing water of shrimp ponds. Based on NGS results, the most abundant species was P. psychrotolerans (213 sequences) followed by Pseudomonas azotoformans (81 sequences) and Pseudomonas sp with 9 sequences.
Profile of probiotic strains in intestinal trats
From the shrimp intestines collected in pond 1, a total of 172 bacterial sequences or 0.2% of the total identified bacteria, were assigned to Ordo Lactobacillales. Of these sequences, 90 sequences (52% of Lactobacillales) belonged to the genus Streptococcus, 33 sequences (19% of Lactobacillales) belonged to the genus Enterococcus, 17 sequences (10% of Lactobacillales) belonged to the genus Lactobacillus, 9% (16 OTUs) belonged to the genus Weisella, 5% (9 sequences) belonged to the genus Lactococcus, and 4% (7 sequences) belonged to the genus Leuconostoc.
The 17 sequences of the genus Lactobacillus were identified as 3 species: L. ruminis (12 sequences), L. aviaries (4 sequences), and Lactobacillus sp (1 sequence) (Table 2).
From the shrimp intestines collected in pond 2, a total of 1,669 bacterial sequences, or 2% of the total identified bacteria, were assigned to Ordo Lactobacillales. 1,569 sequences (94% of Lactobacillales) belonged to the genus Lactobacillus, 84 sequences (5% of Lactobacillales) belonged to Streptococcus, 11 sequences (0.7% of Lactobacillales) belonged to Enterococcus, and one sequence belonged to Weisella. 1,569 Lactobacillus were identified as 12 species and the three most abundant species were Lactobacillus sp (469 sequences), followed by L. pentosus (339 sequences), and L. reuteri (287 sequences).
While the species with the lowest abundance were L. agilis and L. acidipiscis with a single sequence each. Furthermore, a total of 1,265 bacterial sequences were assigned to Ordo Lactobacillales from the shrimp intestines collected from pond 3. Of these sequences, 945 (75% of Lactobacillales) were identified as belonging to the genus Lactobacillus.
“Lower taxonomic annotation indicated that the sequences were classified into 12 bacterial species. The three most abundant species were Lactobacillus sp (216 sequences), followed by L. pentosus (209 sequences) and L. reuteri (101 sequences).”
From the shrimp intestines collected in pond 1, 48 sequences or 0.05% of the total identified bacteria, were classified as Bacillaceae. Of the sequence, 18 sequences were identified as Bacillus badius, 24 sequences as Bacillus sp, and 6 sequences were identified as B. thermoamylovorans (Figure 1).
From the shrimp intestines collected in pond 2, 43 sequences or 0.05% of the total identified bacteria, were assigned to Bacillaceae (Figure 1). Of these, 36 sequences (84% of Bacillaceae) belonged to the genus Oceano bacillus. Six sequences (14% of Bacillaceae) belonged to genus Bacillus, and were identified as four species, which were B. thermoamylovorans (2 sequences), B. badius (2 sequences), Bacillus coagulans (1 sequence), and Bacillus sp (1 sequence).
In addition, from the shrimp intestines collected in pond 3, 12 bacterial sequences or 0.01% of the total identified bacterial sequences, were assigned into Family Bacillaceae (Figure 1). Of these, 7 sequences (58%) were identified as B. thermoamylovorans, while the other 5 sequences (42% of Bacillaceae) were “unclassified.”
Pseudomonas spp also appeared to be in very low abundance in the intestinal tract of white shrimp reared in commercial ponds. In pond 1, a total of 106 sequences or 0.1% of the total identified bacterial sequences, were assigned to Ordo Psedomonadales, of which only 4 sequences (4% of Pseudomonadales) were identified as Pseduomonas sp.
While in pond 2, 28 sequences or 0.03% of total bacterial sequences, were assigned to Ordo Pseudomonadales. Seven sequences (25% of Pseudomonadales) belonged to genus Pseudomonas, five sequences of P. geniculata and two sequences of Pseudomonas sp.
Furthermore, 13 sequences were assigned to Ordo Psedomonadales but none belonged to Pseudomonas spp in pond 3.
The application of probiotics has been considered the eco-friendliest method to boost aquaculture production through several mechanisms, including maintaining water quality, improving growth rates, and enhancing disease resistance.
However, positive results from probiotic applications are mostly based on in vitro studies or small-scale in vivo trials in which all environmental conditions are easily managed and controlled. Meanwhile, the application of probiotics on large scales, such as commercial shrimp farms are still less investigated.
Thus, questions such as whether introduced probiotics could cope with or compete with native bacteria and contribute to the culture of organisms in commercial farms remained to be answered. The objective of the presented study was to trace and identifies four commercial probiotic species (L. plantarum, L. fermentum, B. subtilis, and P. putida) that were applied in three commercial shrimp ponds.
The result of the study indicated that none of the four commercial probiotics was able to be detected in the shrimp ponds or the intestinal tracts of white shrimp sampled on DOC 47. Each shrimp pond appeared to develop specific microbial communities in both the rearing water and the shrimp intestines.
Ponds 1 and 2, for instance, had 12 Lactobacillus species and the most dominant species was L. aviarius, but pond 3 had only two species of Lactobacillus and was dominated by L. salivarius.
Similarly, the genus Bacillus that developed in rearing water was different from commercial bacillus. A similar result was reported by Huerta-Rábago et al. (2019), where three commercial probiotics (Bacillus sp, Lactobacillus sp, and Saccharomyces sp) introduced into white shrimp ponds at nursery stages could not be detected on DOC 7, 21, and 42.
“These results may suggest that the introduced probiotics were unable to cope with their new environments and failed to proliferate and grow in the target sites (the intestinal tracts of white shrimps or rearing water).”
Based on previous studies, there were several possibilities as to why the commercial bacteria were unable to survive. First, the probiotic species were isolated from significantly different environmental conditions and therefore had difficulty adapting to the environmental condition in the shrimp ponds or intestines of shrimps.
A large loss of viability has been frequently attributed to the high acid and bile salt concentrations in the stomach and intestines. Conditions of rearing water that are different from conditions in culture, including dissolved oxygen, pH, salinity, temperature, and nutrient sources, will affect the growth rate of probiotic bacteria and total cell yields.
Another possibility is that native bacteria outcompete the introduced probiotics for the same organic substrate, such as carbon. This result might explain the inconsistent results concerning the efficacy of probiotic treatments on the survival and growth performance of white shrimps.
Since introducing probiotics were not viable in the target sites, a question to be answered is “are these commercial probiotics able to contribute to the aquaculture species? According to Chauhan and Singh (2019), probiotic viability is a very important factor in aquaculture species and serves as one of the prerequisites in screening probiotics for aquaculture.
Less viable probiotics may not contribute well because the commercial probiotics are not viable in the target sites; thus, they may not contribute to shrimp farms. This might be the reason why do studies report that the probiotic application does not have a significant effect on production yields.
“A study by Huerta-Rábago et al. (2019) reported that the addition of commercial probiotics did not affect the dominant bacteria in both phyla and genus levels in rearing ponds. All these facts suggest that methods and strategies for applying probiotics to aquaculture species should still be carefully restudied in order to increase their efficacy.”
Then, what is the effect of probiotics in the present study on microbial composition in general? The results of the present study showed that probiotic supplementation appeared not to change the structure of microbial compositions in the GITs of shrimps, as indicated by no significant difference in the top three bacterial phyla in both the probiotic treatment and the controls, which were Proteobacteria, Bacteroidetes and Planctomycetes.
Acknowledging these issues, the probiotic application in commercial outdoor shrimp farms should be evaluated. More studies are still required in order to develop more effective strategies, especially in the commercial outdoor system. Applying probiotics directly, as practiced in the present study, should be avoided.
Some factors such as time and frequency of administration, probiotic species, administration (encapsulation) method, and supplementation of prebiotics to support the nutrient requirements for probiotic species should be considered.
Four commercial probiotic species applied in the commercial grow-out shrimp ponds could not be detected in the rearing water or intestinal tracts of the white shrimps. These facts might explain why commercial ponds applying probiotics had high yield variations.
The characteristics of probiotic species and environmental conditions on commercial outdoor farms may explain these results.
Thus, more studies on selecting proper probiotic strains with good tolerance in a wide range of environmental conditions or strategies on how probiotics are applied in commercial outdoor farms should be done in the future in order to increase the probiotic efficacy in white shrimp production.
This article is sponsored by: REEF INDUSTRIES INC.
This is a summarized version developed by the editorial team of Aquaculture Magazine based on the review article titled “THE FATE OF PROBIOTIC SPECIES APPLIED IN INTENSIVE GROW-OUT PONDS IN REARING WATER AND INTESTINAL TRACTS OF WHITE SHRIMP, LITOPENAEUS VANNAMEI” developed by: Muhamad Amin, Yoga Pramujisunu, Mirni Lamid, and Yudi Cahyoko- Universitas Airlangga; Olumide A.
Odeyemi – University of Tasmania; Muhamad Ali – University of Mataram; Awik P. D. Nurhayati – Institut Teknologi Sepuluh Nopember.
The original article, including tables and figures, was published on NOVEMBER, 2022, through OPEN AGRICULTURE.
The full version can be accessed online through this link: https://doi.org/10.1515/opag-2022-0152