Analysis of Edaphic Factors on the Role of Probiotics in the Development of Sustainable and Productive Aquaculture

Abstract

The use of antibiotics in aquaculture is associated with significant environmental risks, including ecosystem disruption and the accumulation of antibiotics in reservoirs and soil cover, as well as the spread of antibiotic-resistant strains, which encourages the search for sustainable alternatives, such as probiotics. This review summarizes the research results on the use of probiotics in aquaculture systems. Special attention is paid to the action mechanisms and diverse effects on the health of aquatic animals, water quality and, most importantly, on the properties of soil in ponds. The research results show that certain strains of probiotics, in particular Bacillus spp., effectively decompose organic substances in sediments, reduce toxic metabolites’ concentration (ammonia, nitrites, hydrogen sulfide), stabilize soil structure, improve aeration and regulate sediments’ pH level and microbial diversity. However, the efficacy in field conditions can vary. Probiotics represent a science-based strategy to reduce dependence on antibiotics, increase system resilience by improving soil and water conditions, and increase productivity. In order to achieve maximum results, it is necessary to optimize the application methods, whilst taking into account local environmental factors.

1. Introduction

Parker [1] defined the original definition of the term “probiotic” as “organisms and substances contributing to the microbiological balance of the intestine. Then, Fuller [2] revised the term to mean “a living microbiological feed additive that has a beneficial effect on the body of the host animal, improving the microbiological balance of its intestines”. In their study, Verschuere et al. [3] take into account the deep integration of aquatic organisms into the aquatic environment, where exogenous factors (environment and nutrition patterns) determine their microbiological status. A probiotic was defined as a living microbial additive that modulates communities associated with the host or environment for a beneficial effect. The modern concept [4] expands the definition to include living, inactivated cells or their components that improve resistance, growth, feed digestibility, and host health through microbial balance in the body and environment. The key modes of action for probiotics have been established: (i) growth stimulation, (ii) synthesis of inhibitory compounds, (iii) improvement of nutrient absorption, (iv) optimization of water quality, (v) potentiation of the immune response, and (vi) competitive exclusion [5,6]. For probiotic status, microorganisms must meet the following criteria: (i) absence of pathogenicity, (ii) survival during transportation, (iii) ability to colonize and persist in the host, and (iv) absence of virulence genes and mobile antibiotic resistance genes. Lactobacillus spp., Bacillus spp., Bifidobacterium spp., Lactococcus spp., and Saccharomyces cerevisiae [7,8] are traditionally used. The potential of actinobacteria (producers of secondary metabolites) has not been sufficiently studied, despite the promise of Streptomyces spp. [9,10,11]. Research by Lazado et al. [12] has demonstrated that, in the context of disease control, probiotics inhibit pathogens’ growth and reproduction and stimulate the dominance of beneficial microbiota in a host and its growing environment.

The modes of action for probiotics in aquaculture systems include several aspects, and experimental studies confirm their ability to reduce fish morbidity due to direct antagonistic activity against pathogens [13,14], as well as to have a stimulating effect on the growth of aquatic organisms, which may be associated with both improved nutrient absorption and the direct provision of vitamins and other biologically active compounds [15,16]. Historically, the use of probiotics in aquaculture began relatively recently [17]. However, interest in these biological preparations has increased significantly in recent decades. For example, Biswas et al. [18] studied the effectiveness of commercial probiotics in Bangladesh, finding that a 60 day application led to only slight changes in sediment parameters: a pH increase of 0.1–0.2 units and stable organic matter content (3.8–4.2%). This result underscores the critical importance of accounting for local conditions—such as high salinity and erosion processes—when developing probiotic regimens. According to FAO [19], global aquaculture produces ~70 million tons of products and supplies 25% of global animal protein. Between 2000 and 2019, global aquaculture production demonstrated a sharp increase, rising by approximately 180%. However, the industry remains highly unevenly developed: Asia, as the main producer, accounted for 92% of production by 2019. Such significant dominance by a single region highlights the vast potential for the development of aquaculture outside Asia [20,21]. This critical industry requires urgent reform due to uncontrolled antimicrobial use, which has fueled resistant pathogen strains [12,22]. Consequently, developing alternative strategies—notably probiotics, prebiotics, and their synergies—has become essential [23,24,25]. Modern research confirms that probiotics are a multifunctional tool capable of simultaneously solving the tasks of biocontrol, improving productivity, and reducing environmental stress; however, to maximize their potential, it is necessary to develop adapted application methods that take into account both the specifics of cultivated species and the specifics of local environmental conditions.

The intensification of aquaculture exacerbates the problems of pollutants’ bioaccumulation: for example, heavy metals in Pangasius hypophthalmus as documented by Pragnya et al. [26], and issues including disease control, optimization of water quality, and degradation of sediments, as reported by Subasinghe et al. [27]. The organic matter accumulation, the development of anaerobic processes, and soil acidification directly reduce the health of aquatic animals and ecosystem stability [27,28]. Despite the widespread use of biological products (bacterial inoculates, enzymes, phytoextracts) to improve the aquatic and soil environment, their effectiveness remains ambiguous. Bazar et al. [29] demonstrate both the absence of a significant effect of bacterial inoculates and the limited effect of enzyme treatments, which enhance the mineralization of organic matter, but do not provide a steady increase in production. Probiotics represent an alternative that can improve the digestion and immune status of fish, as well as modulate key parameters of the aquatic environment and edaphic factors.

Outbreaks of diseases remain a limiting factor in the aquaculture industry [28,30]. In this context, probiotics offer a comprehensive solution. In addition to their main function of controlling pathogens, they demonstrate a multifunctional effect, including modulation of the immune response [3,28], optimization of digestive processes [31,32] and, most importantly, improvement of soil stratum characteristics, which is crucial for the stable state of aquaculture systems. However, the number of independent studies confirming the application efficacy in pond systems remains limited. Manufacturers’ statements, often exaggerated, are often based primarily on internal tests and feedback from farmers. Nevertheless, Boyd and Gross [33] demonstrated that farmers’ desire to improve water and soil quality, reduce morbidity, and increase productivity supports the active use of probiotics.

Studies on the bacterial probiotics’ effectiveness in pond aquaculture often do not reveal a significant effect on water quality. Studies by Boyd et al. [34] and Tucker and Lloyd, [35] demonstrated that a complex bacterial inoculum in ponds with channel catfish showed no statistically significant differences (p > 0.05) in key parameters (inorganic nitrogen, total phosphorus, chlorophyll, phytoplankton, proportion of cyanobacteria, and fish production) compared with the control, except for isolated cases of increased dissolved oxygen (p < 0.05). Similarly, Chiayvareesajja and Boyd [36] did not find a decrease in ammonia either in laboratory microcosms or in field ponds (p > 0.05). Although Queiroz and Boyd [37] noted an increase in survival and catfish production (p < 0.1) when using Bacillus spp., there were no differences in water quality or sediment composition, and the mechanism of the effect remained unclear.

A critical limitation is the discrepancy between laboratory conditions, including the modeling of mesocosms [38], and the heterogeneity of real ponds. The high variability of natural factors (water quality, soil, farm management) reduces the predictive value of laboratory data. Therefore, a reliable assessment of the effectiveness of probiotics requires mandatory field testing under specific operating conditions.

The overarching goal of this review is to dissect the complex mechanisms by which edaphic factors govern the performance and impact of probiotics in aquaculture ecosystems. By systematically examining the literature on soil-probiotic interactions, we aim to establish a robust conceptual framework that links specific soil parameters to probiotic functions in enhancing water quality, nutrient cycling, disease suppression, and overall system sustainability. This synthesis is crucial for informing the design and interpretation of future research, including our planned investigations into pond soil dynamics under probiotic application.

2. Effect of Probiotics on Aquaculture

2.1. Potential Applications of Probiotics

The search and testing of effective probiotic alternatives to antibiotics for disease control on pond farms is a priority area of modern research [39,40]. A reservoir with a high accumulation density, often located in a small area, has a limited ability to self-clean. To ensure good water quality and reduce diseases’ spread, it is necessary to use probiotics at various stages. The introduction of probiotics into a reservoir primarily promotes the reproduction of beneficial bacteria and the competitive inhibition of pathogens entering the aquatic system from various sources such as air, feed, feces, etc. [41,42,43,44]. Probiotics play an important role in the prevention and control of pathogens in aquaculture systems, due to their ecological properties [45]. Bioremediation using beneficial microorganisms, both individual strains and combinations thereof, helps to reduce the volume of wastewater from reservoirs in aquaculture systems and other industries. The advantages of bioremediation include the implementation of the process on site; the possibility of permanent disposal of excess waste; economic efficiency due to the biological nature of the process. The integration of probiotics into fish and shrimp feed complexes is an important component of the strategy for the transition to resource efficient and environmentally friendly aquaculture [46]. Probiotics have proven effective in improving the growth, survival, and health of aquatic animals [47]. Uncontrolled and indiscriminate use of antibiotics has led to the emergence of antibiotic-resistant bacteria in aquaculture [48,49,50,51]. In addition, it has been proven that aquaculture ponds are reservoirs of antibiotic resistance genes [52,53]. These genes can be acquired by human and animal pathogens through horizontal gene transfer [52], which makes it difficult to treat infectious diseases. In addition, recent evidence of the presence of residual antibiotics in grown organisms may pose a potential risk to consumer health [54,55,56,57]. Studies show that probiotics can be a promising alternative to antibiotics in aquaculture, demonstrating beneficial effects on the host body by fighting diseases, improving growth, and stimulating the host body’s immune response to infections [4,51].

2.2. Soil in Aquaculture

The economic and environmental sustainability of the aquaculture sector is fundamentally dependent on three critical pillars: maintaining optimal water and soil quality, effective disease prevention and control, and the continuous improvement of growth and production efficiency [58]. A soil type is determined by a combination of physical, chemical and biological factors directly affecting formation methods and operational characteristics of aquaculture reservoirs [59]. Soil quality is a critical factor in productivity, regulating bottom sediments’ stability and physicochemical parameters. Organic soils and acid sulfate soils or their associations dominate shrimp ponds [47]. Bottom sediment management through tillage at a depth of 10–20 cm, drainage, subsequent soaking, and washing helps to reduce the concentration of toxic compounds and increase productivity [60]. Soil improvement technologies demonstrate an increase in productivity, mainly through the water quality optimization [47]. Mehmood et al. [61] explore the interaction between aquaculture and agriculture, specifically the potential for reusing fishpond sediment (aquaculture) to improve the health of degraded soils (soil cover). The study demonstrates that aquaculture waste, particularly when combined with biochar, can be transformed from a disposal problem into a valuable resource for restoring soil fertility and ecological functions. Thus, the research confirms a positive synergy between these two sectors: aquaculture can serve as a sustainable source of organic amendments for enhancing soil quality, which in turn supports safer crop production. The authors emphasize the need for further field studies to explore this interaction and develop sustainable agro-aquaculture systems.

The accumulation of organically enriched sediments provokes the development of anaerobic conditions, leading to the generation of compounds that are toxic to aquatic organisms: ammonia, nitrites, and hydrogen sulfide. The probiotic application has been recognized as an effective strategy for maintaining the quality of the aquatic environment in the field of aquaculture [62,63,64], which in turn contributes to optimizing the growth and survival conditions of tiger shrimps [65,66,67]. Probiotics demonstrate a multifunctional effect, including the control of pathogens, improvement of the physiological state of growing plants, enzymatic activity, and immunomodulation [12,68]. Pantjara and Kristanto [69] have confirmed the effectiveness of a combined approach combining bottom treatment and the use of probiotics to suppress pathogenic microflora experimentally.

The study by Kamilya and Devi [70] highlights the potential of Bacillus strains as probiotics for aquaculture, capable of not only optimizing the microbial balance in the gastrointestinal tract of aquatic organisms but also performing a key bioremediation function in the aquatic environment through the combination of heterotrophic nitrification and aerobic denitrification processes. This mechanism, particularly effective under conditions of high organic load, enables probiotic strains to directly utilize toxic forms of nitrogen (ammonium nitrogen), converting them into gaseous compounds, thereby maintaining water quality and reducing the risk of eutrophication: thus, comprehensively enhancing the sustainability of aquaculture systems.

In intensive aquaculture systems with a high stocking density, the organic sludge accumulation in bottom sediments creates a substrate for the development of opportunistic microorganisms (Vibrio, Pseudomonas, Aeromonas) and the formation of toxic metabolites, which leads to a deterioration in water quality and reduced productivity [71]. Traditional processing methods (drying, mechanical treatment, liming) are aimed at intensifying organic degradation and suppressing pathogens [72] but require optimization. As shown by Ninawe and Selvin [73], antagonistic probiotics are considered to be a comprehensive solution for epizootic regulation, maintenance of growth rates, and control of water and soil parameters. Representatives of the genus Pseudomonas, which produce biologically active secondary metabolites, demonstrate the potential to suppress the activity of pathogenic bacteria [74].

Bacillus (PS1, PS2, PS5, and PS6 strains) efficiently process organic sludge components, which is confirmed by a decrease in the total suspended solids content and the secretion of extracellular hydrolytic enzymes [75]. These strains reduce nitrogen compounds in aquaculture wastewater [76] and improve aquatic environment parameters (reducing concentrations of ammonium nitrogen, nitrites, total nitrogen, and phosphorus) [77]. Probiotics play a significant role in improving the quality of water and soil cover, which correlates with increased productivity [78]. A serious study of the processes in aquaculture facilities’ soil matrix is necessary to develop sustainable environmental quality management strategies.

2.3. Effects of Probiotics on Pond Soils

The mechanism of probiotics’ positive effects on sediments includes three main aspects. Firstly, they promote bioremediation by degrading organic matter and reducing the concentration of toxic metabolites such as ammonia and hydrogen sulfide [79]. Secondly, probiotics stabilize the soil structure, preventing siltation processes and improving aeration through the aerobic microflora stimulation [80]. Thirdly, they normalize key biochemical parameters, including a decrease in acidity and the content of oxidizable carbon in bottom sediments. The complex effect makes probiotics a promising tool for solving both microbiological and edaphic problems in modern aquaculture. The criteria for effective strains are supplemented by the requirement of soil competence: the ability to colonize bottom substrates and exhibit metabolic activity in anoxic/low pH conditions [2]. It is known that probiotics used in pond farms have several mechanisms of action, as shown in Figure 1. These include the competitive displacement of pathogenic bacteria through the production of inhibitory compounds; improved water and soil quality; and the improved nutrition of host species through the production of additional digestive enzymes [3].

Modern research demonstrates the positive effects of probiotics on pond soil. For instance, the study de Oliveira et al. [81] undertook on the effect of the probiotic BioPlus^® PS application to the pond soil for polyculture of shrimp and tilapia showed that a single application (150–2000 g ha⁻¹) after 15 days led to a significant decrease in the content of organic matter, oxidized carbon, and potential acidity. Metagenomic analysis revealed an increase in the alpha diversity of the microbiome and a decrease in the relative abundance of Vibrio parahaemolyticus. Pfeiffer’s chromatography indicated an improvement in soil quality and enzymatic activity at high doses (1000 and 2000 g ha⁻¹). These results indicate the biological mediation potential of the probiotic and its ability to positively modulate the soil microbiome.

Permanent toxicity caused by the accumulation of ammonia (NH₃/NH₄⁺), nitrites (NO₂⁻), and hydrogen sulfide (H₂S) in the water column and sediments is one of the important processes requiring detailed study. The source of these toxicants is excess feed, feces, and degradable biomass (including microalgae). The resulting eutrophication, oxidative stress in cultivated organisms, and subsequent immunosuppression create conditions for outbreaks of infectious diseases and high mortality [82].

Another common problem in aquaculture is the silt accumulation at the bottom of ponds. Sludge consists of uneaten food, shrimp excrement, dead plankton, and other organic waste generated in shrimp ponds, which settle in a thick layer at the bottom of the pond [72]. Increased silt accumulation poses a threat to water quality and the productivity of fish farms, as it serves as a food source for pathogens and produces undesirable toxic substances such as ammonia (NH₃), nitrites (NO₂⁻) and hydrogen sulfide (H₂S) [83]. This causes stress during shrimp farming and increases susceptibility to disease and mortality.

2.4. Effect of Probiotics on Physicochemical Soil Properties

One of the ways to apply probiotics is to directly introduce them into ponds to improve water and soil quality, and modulate the microbiota of the environment, as proposed by Dittmann et al. [84]. In the case of shrimp farming, due to the fact that these animals live on the border of soil and water, the conditions at the bottom are of particular importance. Often during the growing cycle, due to excessive intensification and improper management methods, the bottom of the pond deteriorates because of the accumulation of organic substances, and anaerobic and acidic conditions. As a result, this practice can lead to immunosuppression and the proliferation of potentially pathogenic bacteria, as concluded by Avnimelech and Ritvo [85]. Species of the genus Bacillus are among the most used probiotics, due to their ability to inhibit pathogenic bacteria and bioremediation of water and pond sediments [86,87]. The effect of their use in pond soils was assessed by analyzing physicochemical parameters [88,89,90] and microbiological methods based on cultivation [88,91], while metagenomic approaches were used to evaluate the use of environmental probiotics only for water in culture [92,93]. The number of bacterial species found in a single soil sample may exceed the number of known cultured bacteria [94]. This fact highlights the importance of using cultivation-independent methods in assessing the soil microbiome. Imaging methods traditionally used in agricultural soils, such as Pfeiffer’s circular chromatography—validated by Fritz et al. [95] as a complementary approach to chemical analysis—can provide additional insights into soil states post-probiotic application. In a study by Lemonnier et al. [96], it was demonstrated that acidic conditions, measured by sediment pH, negatively correlate with osmotic hemolymph pressure, an indicator of stress in shrimps, i.e., increased acidity was associated with increased stress in shrimps.

McGuire and Treseder [97] demonstrated that different soil microbiological communities vary in their capacity to decompose organic substances. Thus, probiotics may accelerate organic matter decomposition by introducing communities that outperform autochthonous microbiota. Such nutrient-poor conditions are ecologically advantageous, as nutrient-rich environments favor fast-growing r-strategists (e.g., opportunistic pathogens), which is a framework articulated by De Schryver and Vadstein [98]. In the study by de Oliveira et al. [81], significantly lower levels of organic matter were observed in soils treated with probiotics, followed by significantly lower values of oxidized carbon, which indicates the potential of bioremediation when using Bacillus spp. in the soils of ponds. In addition to organic substances, nitrogen and phosphorus enrichment is a concern in aquaculture because of their potential for eutrophication [99]. Although Li and Boyd [100] question the effectiveness of using environmental probiotics, there are many studies confirming both bioremediation and modulation of the environmental microbiome [72,79,88,93,101].

De Mello Júnior et al. [101] proved that the application of B. subtilis and B. licheniformis (BioPlusR PS) to soils in laboratory conditions reduced the levels of organic matter, oxidized carbon and potential acidity, which indicates the potential of the probiotic in the field of bioremediation. It also modulated the soil microbiome, increasing α-diversity and decreasing the relative abundance of Vibrio spp. and V. parahaemolyticus, an important opportunistic microorganism for shrimp. The commercial soil probiotic “Super-PS”, containing strains of Rhodobacter spp. and Rhodococcus spp., demonstrates a complex impact on aquaculture ecosystems, where improving soil characteristics is a key factor in sustainability. Studies confirm that these microorganisms carry out bioremediation of bottom sediments due to the degradation of organic waste (feed residues and excrement) through the activation of hydrolytic enzymes, which reduces the concentration of toxic metabolites, including ammonia and hydrogen sulfide, by 25–42%, and also reduces the content of oxidized carbon [29,81]. In parallel, structural stabilization of the soil is observed, and stimulation of aerobic mineralization prevents anaerobic siltation and improves pore aeration [86,91], which is critically important for maintaining the redox potential of the bottom layers.

Soil parameters’ optimization is closely related to the improvement of growing conditions for aquatic organisms. Normalization of the C/N ratio and the acidity (pH) of bottom sediments [29,81] creates prerequisites for increased productivity, which is confirmed by field testing on Pangasius hypophthalmus. When applying “Super-PS” to water (100–200 kg/ha) and feed (2–5% by weight), there was not only a 42% decrease in ammonia in the soil (p < 0.01), but also a statistically significant correlation between an improvement in soil characteristics and an increase in fish biomass (r = 0.87, p < 0.05). This synergistic effect is described by Rengpipat et al. [32] and explained by the fact that colonization of fish intestines with probiotic strains enhances nutrient uptake by 12–18% and provides immunomodulation, while suppression of pathogenic microflora in the soil due to competitive exclusion reduces the overall microbiological burden on aquatic organisms [2,3].

Comprehensive Improvement of the Pond Ecosystem

The study by Soltani et al. [102] highlights the key role of Bacillus spp. Lactobacillus spp. and probiotics in bioremediation of aquaculture systems, targeting degradation of toxic compounds (ammonia, nitrites, nitrates, CO₂) in water and sediments. The authors note that intensive aquaculture coupled with anthropogenic pressure leads to the accumulation of harmful substances that reduce productivity. Probiotics not only neutralize toxins but also compete with pathogens, improving microbial balance in water and soil. The technology is characterized as a cost-effective and environmentally friendly alternative for sustainable aquaculture development, though its efficacy varies across conditions.

The results of Biswas et al.’s [18] study on fish farms in Bangladesh demonstrate the pronounced effectiveness of probiotics based on Bacillus spp. strains. in optimizing the parameters of the aquatic environment and increasing the productivity of aquaculture. Probiotics’ application led to a statistically significant (p < 0.05) improvement in key indicators: the proportion of reservoirs with optimal pH levels (7.5–8.4) increased from 63% to 77%, due to three main mechanisms of action: activation of nitrification (NH₄⁺ → NO₃⁻ + OH⁻), mineralization of organic matter with the release of carbonate buffer systems, and suppression of acid-forming microflora through competitive exclusion. At the same time, other critical parameters improved: the dissolved oxygen content in the optimal range (5–10 mg/L) increased from 74% to 87% of farms, and the safe ammonia level (0.00–0.50 mg/L) increased from 24% to 89%. Significant changes were recorded in the indicators of transparency and the color of the water—the light green water proportion (an indicator of a productive phytoplankton community) increased from 47% to 78%, which indicates the formation of a favorable food supply. The temperature regime has also been optimized—the number of farms with an optimal range of 31–35 °C has increased from 54% to 76%. These improvements in environmental parameters directly correlated with increased productivity: the maximum weight gains were observed in groups using probiotics—for shrimp, 21–25 g; tilapia, 451–600 g; freshwater fish, 700–1000 g and over 1000 g. The data obtained confirm that probiotics are an effective bioremediation tool that acts through the stimulation of beneficial bacterial processes (nitrification, mineralization), transformation of the structure of the microbial community, and an indirect effect on the development of phytoplankton, which together leads to reliable optimization of the parameters of the soil and aquatic environment (pH, dissolved oxygen, ammonia, transparency, and temperature) and a significant increase in the productivity of fish farms.

An important aspect is the indirect effect of soil bioremediation on the aquatic environment. Bazar et al. [29] found that an improvement in the oxygen regime in the bottom layers (an increase in dissolved O₂ by 28%) is a direct consequence of optimizing biochemical processes in the soil, which reduces operating costs for aeration by 17–23%. Thus, the probiotic implements a systematic approach, where the transformation of soil characteristics serves as the basis for improving the environmental and economic efficiency of aquaculture. A promising area of further research is the adaptation of dosages to the specifics of different types of bottom sediments and the assessment of the long-term dynamics of soil microbiomes.

Fishponds’ water quality depends on a soil type, water source, and the pond’s location [103,104]. Strategies have been developed in various countries to improve water quality and fish growth. Probiotics as a tool for optimizing aquaculture systems demonstrate a complex effect on water–soil parameters and productivity. Being active agents, they inhibit pathogens through competition for nutrient substrates [16,105,106,107,108,109,110] and stimulate the growth of aquatic organisms. According to Sreenivasulu et al. [15] and Abasaliand Mohmad [111], the use of soil probiotics provided a statistically significant improvement in key indicators compared to the control data. Sambasivam et al. [112] note that key effects include optimization of the hydro-chemical regime, maintaining a stable pH in a physiologically acceptable range, as well as a decrease in ammonia and nitrite concentrations by 30–42%, an increase in dissolved oxygen content, a decrease in organic load by 25–35%, and accelerated mineralization of organic matter, which is confirmed by the stabilization of soil parameters: total phosphorus (2.65–3.2%), organic carbon (1.15–1.36%), calcium (0.13–0.20%) and magnesium (0.07–0.12%). An increase in survival rates leads to an increase in biomass and fish yield, which correlates with an improvement in environmental quality. The mechanisms of action are associated with the stimulation of nitrifying bacteria consuming dissolved organic matter and the induction of photosynthetic activity of phytoplankton. This explains the negative correlation between water transparency and oxygen content (due to the development of phytoplankton) [113,114,115,116] and the positive relationship between pH and dissolved oxygen [117]. The results of the research Suhendra et al. [118] performed indicate the ability of probiotics to reduce the accumulation of organic matter and stabilize environmental conditions. The soil cover and other components of aquaculture are inextricably linked. Ahmed et al. [119] have been made attempts to isolate beneficial bacteria from various sources, such as soil, water, and animal intestines, to combat pathogens in aquaculture systems.

Aquatic probiotics contain several strains of bacteria, such as Bacillus acidophilus, B. subtilis, B. licheniformis, Nitrobacter sp., and Aerobacter. These probiotics in tanks and ponds play an important role in maintaining fish health by improving water quality by changing the bacterial composition of water and sediments. The decomposition of organic substances by microbes determines the water quality in aquaculture systems [120,121], which in turn affects the quality of bottom sediments. However, tiger shrimp production has declined due to the deterioration of environmental quality, especially with regard to pond water and soil [122].

2.5. Soil Investigation Methods in Aquaculture

Boyd and Gross’ [33] research emphasizes that the study of soils in aquaculture mainly focuses on the analysis of physicochemical properties and nutrient content (

Table 1. Studies of soil quality affecting processes in aquaculture.

Parameters	Processes Affected in Pond	References
Particle size and texture	erosion and sedimentation, embankment stability, seepage, suitability of bottom habitat	[69,72,85,99,130,131,132]
pH (acidity)	nutrient availability, microbial activity, benthic productivity, hydrogen ion toxicity	[42,69,85,96,100,132]
Organic matter	embankment stability, oxygen demand, nutrient supply, suitability of bottom habitat	[42,85,90,99,120,130,133]
Nitrogen concentration and C:N ratio	decomposition of organic matter, nutrient availability	[42,69,85,120,134,135,136]
Redox potential	toxin production, mineral solubility	[69,85,90,99,130,132,135]
Sediment depth	reduction in pond volume, suitability of bottom habitat	[69,72,85,99,130,132,133]
Nutrient concentration	nutrient availability and productivity	[69,85,90,99,115,132,136]

), which are critically important for environmental sustainability [123,124,125,126,127]. Changes in land use, such as the creation of aquaculture ponds, significantly affect the soil microenvironment, including humidity, density, electrical conductivity, and pH [128,129], and irrational use methods can lead to soil degradation.

Rocha et al. [137] propose a novel methodological framework for assessing benthic soil quality in cultivation ponds of Litopenaeus vannamei. Conventional monitoring practices, reliant on single-point sampling at the pond centroid, are considered methodologically insufficient, due to their inability to account for spatial heterogeneity in sediment chemical parameters. The authors advocate for a systematic transect-based sampling protocol, wherein samples are collected along radials extending from the perimeter to the hydrographic center of the pond. This approach facilitates the generation of a spatially resolved representation of critical sediment variables, including organic matter content, available phosphorus, and redox-related acidity.

Implementation of this protocol in Brazilian aquaculture systems revealed significant geochemical differentiations: pronounced centripetal accumulation of organic matter and nutrients was observed, with intensive culture systems exhibiting substantially elevated sedimentary loads relative to extensive systems. These findings validate the proposed methodology as a superior tool for informing management decisions on water quality control, aerator deployment optimization, and benthic substrate remediation. Consequently, this technique supports enhanced production outcomes and promotes long-term operational sustainability in commercial aquaculture.

According to Bazar et al. [29], key soil properties including pH (measured electrochemically with a pH-meter electrode at a soil/water ratio of 1:2.5), electrical conductivity (EC-meter), organic carbon content (wet oxidation method), and levels of Ca and Mg (titrimetric method after NH₄OAc extraction) were quantified [138,139]. These fundamental properties (pH, EC, organic matter, cations) are critical determinants of microbial habitat suitability. The pH directly influences probiotic survival and enzymatic activity, while organic carbon and cation levels affect nutrient availability for both native microbiota and introduced probiotics, ultimately impacting their efficacy in waste decomposition and nutrient cycling within aquaculture ponds.

Research by Lin et al. [130] employed standardized methods to assess a comprehensive suite of soil parameters: pH and salinity (via pH- and EC-meters), bulk density (BD, from undisturbed samples), soil water content (SWC [140], gravimetrically), total and available nitrogen and phosphorus (dry combustion, acid mineralization, KCl extraction, Mehlich III), alongside key stoichiometric ratios (C:N, C:P, N:P, AN:AP). Statistical rigor was ensured through replication, normality/homogeneity tests (Shapiro–Wilk, Bartlett), two-factor ANOVA, t-tests, and correlation/RDA analyses. This holistic approach is vital for understanding the complex interplay between soil physical conditions (BD, SWC), nutrient pools (N, P forms), and microbial processes. Probiotics aimed at enhancing nutrient utilization or mitigating waste impacts must function within these specific physicochemical constraints; understanding these relationships through rigorous statistics is paramount for predicting probiotic performance in diverse aquaculture soil environments.

The methodology detailed by Shafi et al. [131] involved analyzing air-dried, sieved (<2 mm) soils. Granulometric composition was determined via the hydrometric method [134] using Calgon dispersion, while pH [141] and EC were measured in a 1:2 soil/water suspension [142]. Statistical analysis relied on SPSS 22, employing t-tests and ANOVA. Soil texture (sand, silt, clay percentages) [143], revealed by granulometry, profoundly affects water retention, aeration, and the adsorption of nutrients and microorganisms like probiotics. Understanding texture alongside pH and EC is essential for tailoring probiotic applications to specific soil types encountered in aquaculture, optimizing their retention and activity where needed most.

Data presented by Al-Wabel et al. [132] were derived from soils prepared by air-drying and sieving (<2 mm). Analyses included EC and pH (1:2.5 suspension), soil organic matter (Walkley-Black [139]), cation exchange capacity (CEC), major nutrients (Na, K, Mg, Ca, P, N forms via flame photometry [144], spectrophotometry [145], standard methods), available trace elements (AB-DTPA extraction, ICP-OES), and Sodium Adsorption Ratio (SAR). Statistics were performed using Statistix 8.01 (LSD test) [146]. Parameters like CEC, SAR, and nutrient availability are crucial indicators of soil fertility and stability. Probiotics can influence these directly (e.g., through organic acid production affecting CEC, nutrient solubilization) or indirectly, via altered microbial processing of organic matter and ions. Monitoring parameters helps evaluate how probiotics contribute to maintaining soil health and prevent salinization or nutrient imbalances in aquaculture systems.

The investigation described Hou et al. [133] measured critical soil carbon fractions alongside physical properties. The BD and SWC were determined via the cutting-ring method. The pH and EC were measured potentiometrically and conductometrically (1:2.5 suspension). Carbon pools analyzed included Soil Organic Carbon (SOC—elemental analyzer), Labile Oxidizable Carbon (LOC—KMnO₄ oxidation) [147], Dissolved Organic Carbon (DOC), and Microbial Biomass Carbon (MBC—TOC analyzer after specific extractions) [148,149]. Quantifying different carbon pools (SOC, LOC, DOC, MBC) is particularly relevant for probiotic applications. Probiotics directly contribute to and interact with the labile carbon pool (LOC, DOC) and MBC. Their effectiveness in enhancing microbial activity and organic matter turnover can be gauged by changes in these specific fractions, linking probiotic function to soil organic matter dynamics and overall carbon sequestration potential in aquaculture soils.

Analyses conducted by Yang et al. [150] on air-dried, sieved (<0.25 mm) soil/substrate samples encompassed pH (potentiometrically, 2:1 suspension), major nutrients (TOC, TN, AHN, TP, AP, TK, AK), available trace metals (A-Cu, A-Zn, A-Fe, A-Mn—standard methods [72,151,152]), and enzyme activities (invertase, urease, protease, catalase—spectrophotometry with commercial kits). The inclusion of enzyme activities provides a direct functional proxy for soil microbial health and biogeochemical cycling rates. Probiotics are often intended to stimulate specific enzymatic pathways (e.g., urease for nitrogen cycling, protease for organic matter breakdown). Measuring these activities alongside nutrient pools allows for a direct assessment of probiotic impact on key soil processes, governing water quality, and productivity in aquaculture.

As reported by Tan et al. [136], surface soil samples (0–20 cm) were taken with a steel sampler (inner diameter 5 cm). The samples were transported in refrigerated containers and stored at 4 °C until the sample preparation process. Samples underwent analysis for pH, salinity, texture, SWC, BD, Cl⁻, SO₄²⁻, total carbon, and microbial genetic diversity using standard methods [153]. Samples were prepared by root/particle >2 mm removal, air-drying, grinding, and specific extractions for nitrogen forms, differentiating SIN and SON. The aliquot was dried in air, crushed (<0.149 mm), and total nitrogen (TN) was analyzed using a Vario MAX CN elemental analyzer (Elementar, Germany) [154,155]. Another aliquot was extracted with 2 M KCl to determine nitrate (NO₃⁻–N) and ammonium nitrogen (NH₄⁺–N) [156], followed by measurement on a SAN++ flow analyzer (Skalar, the Netherlands). Inorganic nitrogen (SIN) was calculated as the sum of NO₃⁻–N and NH₄⁺–N, and organic nitrogen (SON) as the difference between STN and SIN. The focus on nitrogen speciation (SIN vs. SON) and microbial diversity is highly pertinent. Probiotics can alter nitrogen transformation rates (mineralization, nitrification), affecting SIN availability and SON storage. Concurrent analysis of microbial diversity helps discern whether probiotics induce shifts in the native community, potentially enhancing or disrupting the ecosystem functions that are crucial for sustainable aquaculture soil management.

The study by Tian et al. [136] assessed physicochemical properties of mangrove soils. The granulometric composition was analyzed via laser diffraction. The remaining physicochemical parameters were evaluated according to established methods [134,157]. The pH value was measured potentiometrically (pH-meter PHS-2F) in a suspension of soil and deionized water in a ratio of 1:5. The volume density was calculated as the ratio of the mass of an absolutely dry sample to its volume. Soil moisture was determined by weight loss after drying the samples at 60 °C until a constant weight was reached within a week after sampling. The total organic carbon (TOC) content was measured on a Vario EL Cube element analyzer (Elementar, Germany). The concentrations of total nitrogen (TN) and total phosphorus (TP) were determined using the Futura II flow analyzer (Alliance Instruments, France). Understanding these properties (texture, moisture, TOC) under probiotic influence is key for sustainable practices like integrated shrimp farming. Probiotics must function effectively in these often organic-rich, waterlogged, and saline environments; characterizing the soil matrix is fundamental to evaluating their potential role in maintaining the health of these sensitive ecosystems.

The utility of these methods for assessing probiotic effects lies in their ability to detect changes in key soil properties modulated by microbial activity. Probiotics influence soil ecosystems by altering enzymatic rates, shifting microbial community composition and biomass, modifying nutrient bioavailability, and affecting soil structure/stability (e.g., aggregate stability, BD). Consequently, tracking these parameters before, during, and after probiotic application provides direct and indirect evidence of probiotic establishment, functional activity, and their resulting impact on soil processes that are essential for sustainable aquaculture productivity and environmental balance.

3. Conclusions

Thus, based on the conducted review, it can be concluded that probiotics have a positive complex effect on pond farms. This fact is confirmed by data indicating the provision of sustainable and productive aquaculture through exposure to environmental factors. However, the effectiveness of use in laboratory conditions is not always comparable with the results obtained in pond farms, and it is necessary to take into account the environmental factors of a particular region and farm. A complex of interacting and dynamic factors (temperature, water quality, soil and microbiome composition, feeding regime, and stressors) that cannot be fully replicated in the laboratory characterizes the field conditions. Laboratory studies, often constrained by scale (microcosms/mesocosms) and short time frames, fail to capture the long-term dynamics and spatial heterogeneity of natural pond ecosystems. In the field, probiotics interact with a more diverse and competitive autochthonous microbial community than in sterile or simplified laboratory models. Precise dosing, uniform application, environmental control, and monitoring are significantly more challenging in large ponds than under laboratory conditions. Consequently, reliable assessment of probiotic efficacy necessitates mandatory field trials under specific application conditions. Future research should prioritize closing critical knowledge gaps, such as: (1) long-term field studies quantifying the persistence and functional impact of probiotics on soil health, nutrient cycling, and microbiome resilience under real-world aquaculture pressures; (2) a mechanistic understanding of how specific soil properties (e.g., texture, SOM, salinity) modulate probiotic establishment and activity across different systems; (3) economic and environmental impact assessments of large-scale probiotic use; and (4) developing region-specific probiotic formulations and application protocols informed by local edaphic and water conditions.