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Environmental Microbiology (EM)  |  Biodegradation and Bioremediation

Microbiol. Biotechnol. Lett. 2024; 52(4): 397-415

https://doi.org/10.48022/mbl.2407.07011

Received: July 17, 2024; Revised: October 2, 2024; Accepted: October 14, 2024

Optimization and Depletion of Ammonia in the Liquid Phase Using Dried Bacillus subtilis Cells

Siti Baizura Mahat1,2, Syahanim Saidun1, Anis Amirah Ahmad Fuad1, Charles Ng Wai Chun1, Ramizah Kamaludin1, Azieyati Hani Hussain1, Muaz Mohd Zaini Makhtar1, and Husnul Azan Tajarudin1*

1Bioprocess Engineering Technology Division, School of Industrial Technology, Jalan Persiaran Sains, 11800, Universiti Sains Malaysia, Pulau Pinang, Malaysia
2Biomass Transportation Cluster, School of Industrial Technology, Jalan Persiaran Sains, 11800, Universiti Sains Malaysia, Pulau Pinang, Malaysia

Correspondence to :
Husnul Azan Tajarudin,    azan@usm.my

This study investigated the optimization and depletion of ammonia in the liquid phase using dried Bacillus subtilis cells. Parameters such as temperature, pH, agitation, inoculation concentration, and ammonia concentration were analyzed via OFAT analysis. Optimal conditions achieved significant reductions: 37℃ temperature, pH 7, 150 rpm agitation, 1.0 g/l inoculation concentration, and 4 ml/l ammonia concentration. One-way ANOVA was used to identify significant parameters influencing ammonia reduction and B. subtilis growth. The results showed that temperature, concentration of ammonia, and inoculation concentration significantly impacted ammonia reduction, while pH and agitation influenced B. subtilis growth. This study optimized the reduction of ammonia and biomass production of B. subtilis using response surface methodology (RSM) and central composite design (CCD), which achieved significant improvements. RSM and CCD enhanced the process, resulting in a 7.01 mg/l reduction in ammonia and a 1.07 g/l decrease in B. subtilis biomass. Model validation confirmed the efficacy of the optimized conditions. This underscores RSM and CCD's potential for environmental remediation and biomass production. The research highlights B. subtilis' role as a biocontrol agent for mitigating ammonia emissions, aiding sustainable environmental management and public health.

Keywords: Ammonia reduction, Bacillus subtilis, liquid phase, ANOVA, response surface methodology (RSM), central composite design (CCD)

Graphical Abstract


Ammonia, a compound commonly released during agricultural and industrial activities, poses significant environmental challenges when it contaminates water bodies and soil. Elevated ammonia levels can harm aquatic ecosystems, degrade soil quality, and pose risks to human health. Specifically, ammonia contributes to water pollution, respiratory issues, and soil acidification [1, 2]. Addressing ammonia pollution requires a comprehensive understanding of its sources, transport mechanisms, and environmental impacts. Ammonia is primarily released from agricultural activities, such as the application of fertilizers and animal waste management. Industrial processes, including chemical manufacturing and wastewater treatment, also contribute to ammonia emissions. Once released into the environment, ammonia can undergo various transformations, including nitrification and volatilization, leading to the formation of other nitrogenous compounds that further impact the environment.

In aquatic ecosystems, elevated ammonia levels can be toxic to fish and other aquatic organisms [1]. Ammonia interferes with the oxygen-carrying capacity of fish blood, leading to respiratory distress and, in severe cases, death. Additionally, ammonia can promote the growth of harmful algal blooms, which deplete oxygen levels in water bodies and create dead zones, further stressing aquatic life [3]. In soil, ammonia can contribute to soil acidification, which affects soil fertility and plant growth. Acidic soils can lead to the leaching of essential nutrients, such as calcium and magnesium, and increase the availability of toxic metals like aluminum. These changes can negatively impact crop yields and soil health, posing challenges for sustainable agriculture.

B. subtilis is a gram-positive aerobic bacterium with rod-shaped cells. B. subtilis is a facultative anaerobe that was once thought to be an obligatory aerobe. It can secrete a number of enzymes that breakdown in a wide range of substrates, which allows bacteria to thrive in an ever-changing environment. In addition, B. subtilis is easy and fast growing because its doubling time is as low as 20 min, and its optimal growth temperature is only between 30 and 35℃. In this research, B. subtilis was chosen for use as the reinforcing material because it has numerous practical applications across a wide range of industries [4]. In a study by Wang et al. [5], B. subtilis Ab03 was characterized for its efficacy in removing ammonia nitrogen. Among the various bacterial strains used for purifying water in aquaculture, B. subtilis is a highly effective microecological bacterium. Their investigation focused on independent variables such as pH and temperature. The results indicated that B. subtilis Ab03 exhibited a remarkable ability to degrade ammonia nitrogen, removing 91.67% of nitrate from the mixture, highlighting its potential as an efficient agent for ammonia removal.

Similarly, Kamaruddin et al. [6] explored the potential of the probiotic B. subtilis to reduce ammonia levels and improve the production performance of seaworms (Nereis sp.) in laboratory-scale cultivation. Their study investigated temperature, concentration of ammonia, and pH as independent variables. The findings revealed that the application of B. subtilis as a probiotic led to decreased ammonia concentrations, enhanced growth, and reduced abundance of Vibrio sp. These findings underscore the beneficial effects of B. subtilis in promoting production efficiency and maintaining water quality in seaworm cultivation systems. Another study by Santoso et al. [7] focused on the use of dried B. subtilis culture (DBSC) to mitigate ammonia gas release in poultry houses. The independent variables included pH, temperature, and time. Their findings demonstrated that feeding DBSC to chickens effectively reduced the amount of ammonia gas released in the poultry house environment. Moreover, the duration of DBSC feeding influenced the extent of ammonia reduction from both layer and broiler chicken feces, suggesting the consistent efficacy of dried B. subtilis in minimizing ammonia emissions in poultry farming operations.

Optimization techniques like one-factor-at-a-time (OFAT) and response surface methodology (RSM) are crucial for enhancing process efficiency. OFAT involves varying one factor at a time while keeping other factors constant, allowing for the identification of the effect of individual variables on the process outcome. However, this method can be time-consuming and may not account for interactions between variables. RSM, in particular, is advantageous for evaluating multiple variables simultaneously and determining optimal conditions [810]. It uses statistical and mathematical methods to design, enhance, and optimize processes, making it more efficient than traditional methods. RSM involves the use of experimental designs, such as central composite design (CCD) and Box-Behnken design (BBD), to systematically explore the effects of multiple factors and their interactions on the response variable [11]. Several studies have utilized RSM for optimizing various processes. Zhou et al. [12] and Yu et al. [13] used RSM to optimize conditions for ammonia removal, achieving high accuracy and efficiency. Behera et al. [14] and Mourabet et al. [15] also demonstrated the effectiveness of RSM in optimizing different chemical processes. The application of RSM in bioremediation processes, such as ammonia removal using B. subtilis, can lead to significant improvements in process performance and efficiency.

This study aims to optimize ammonia reduction in liquid phases using dried B. subtilis cells by investigating factors such as temperature, pH, agitation, inoculation concentration, and ammonia concentration to determine the optimal conditions for maximal ammonia reduction. Comprehensive analyses, including one-way ANOVA and RSM, were conducted to understand the interactions among these parameters and their effects on ammonia reduction and B. subtilis growth. The primary objectives are to evaluate the effectiveness of dried B. subtilis cells in reducing ammonia levels in liquid phases, identify the key factors influencing ammonia reduction and B. subtilis growth, optimize the conditions for maximal ammonia reduction using RSM, and analyze the interactions between different factors and their combined effects on the process outcome. The findings have significant implications for environmental management and sustainable agriculture, contributing to the development of efficient and cost-effective bioremediation strategies. The use of dried B. subtilis cells offers a practical and scalable solution for mitigating ammonia pollution in various settings, including agricultural runoff, industrial effluents, and wastewater treatment. Furthermore, the application of RSM highlights the importance of advanced optimization techniques in enhancing process efficiency, with insights that can be applied to other bioremediation processes, promoting the broader adoption of environmentally friendly technologies for pollution control.

Preparation of culture media and bacteria (B. subtilis)

Nutrient agar and broth preparation. Nutrient agar was prepared by dissolving 28 g of nutrient agar powder in 1 L of distilled water, followed by autoclaving at 121℃ for 15 min. The sterilized liquid was poured into Petri dishes to solidify. Nutrient broth was prepared similarly by dissolving 13 g of nutrient broth powder in 1 L of distilled water, autoclaving, and then transferring to a conical flask for bacterial growth.

Bacterial preparation and cultivation. B. subtilis ATCC 11774 was sourced from the Laboratory of Bioprocess Technology Division, Universiti Sains Malaysia. A stock culture was maintained at 37℃ and preserved in 40% glycerol at -20℃. Subculturing was performed using the streak plate method on nutrient agar, followed by incubation at 37℃ for 24 h.

For large-scale cultivation, a single colony was transferred to 1000 ml of autoclaved Penassay broth in a conical flask. The flask was incubated at 37℃ and 150 rpm for 24 h.

Harvesting and freeze-drying. Post-incubation, the culture was centrifuged at 5000 rpm for 6 min at 4℃. The bacterial pellet was collected, stored at -20℃, and then freeze-dried at -41℃ for 24 h. The dried bacteria were ground into a fine powder and stored in a desiccator as shown in Fig. 1.

Figure 1.Powdered form of Bacillus subtilis.

Preparation of ammonia liquid solution

The ammonia liquid solution was prepared with different volumes of ammonia solution (2, 4, 6, 8 and 10 ml of ammonia) and mixed with 150 ml of deionized water and 0.15 g of B. subtilis powder with different parameters. Five different parameters were investigated: temperature (30, 35, 37, and 40℃), pH (4, 5, 6, and 7), agitation (0, 50, 100, 150, and 200 rpm), inoculation concentration (0, 0.3, 0.5, and 1.0 g), and ammonia concentration (2, 4, 6, 8, and 10 ml/l). Each sample of each parameter was incubated for 8 h. The absorbance (OD600) was measured every hour for 8 h via a spectrophotometer. Then, 2 ml of each sample of each parameter was mixed with Nessler’s reagent (dH2O + polyvinyl alcohol + mineral stabilizer + dispersing agent + Nessler reagent) to determine the presence of ammonia in the sample. Triplicate readings of the ammonia concentration (mg/l) of the sample were taken via a spectrophotometer.

Optimization and validation process (OFAT → ANOVA → RSM → CCD)

The RSM optimization process consists of three steps: preliminary, experimental design selection, and model validation. The first preliminary stage will determine whether the independent variable has a statistically significant impact on the response variable. Then, experimental designs such as central composite design (CCD) or Box-Behnken design (BBD) with a series of tests will be selected. Moreover, CCD is the most prominent and often employed method for creating secondorder response surface models (Salehi et al., 2012). Finally, in the third stage, the model is assessed and validated, and the ideal value for each parameter is established.

Investigation of one factor at one time (OFAT) parameters for the reduction of ammonia in the liquid phase

In this study, ammonia reduction was observed in the liquid phase with different parameters, including temperature, pH, agitation, inoculation concentration and ammonia concentration. Each sample for each parameter was measured at 8-h intervals. As shown in Supplementary Fig. S1 is the standard curve of B. subtilis biomass production. The initial concentration of ammonia at 8 ml/l serves as a consistent baseline for comparing the effects of different conditions (temperature, pH, agitation, inoculation concentration) on the kinetic growth and ammonia reduction by B. subtilis.

Correlation of temperature with the reduction of Ammonia and the Growth of B. subtilis (OFAT for temperature)

Supplementary Fig. S2 shows the correlation of 8 ml/l ammonia at different temperatures (30, 35, 37, and 40℃) over 8 h, with data on ammonia concentration, reduction, and B. subtilis biomass production. The optimal conditions were a pH of 7, an ammonia concentration of 8 ml/l, 150 rpm agitation, and an inoculation concentration of 0.15 g/l. Chen et al. [16] reported that B. subtilis can grow at temperatures ranging from 25 to 37℃, demonstrating its resilience. However, higher temperatures can slow growth rates. The optimal temperature for B. subtilis growth and ammonia reduction was 37℃, with a biomass yield coefficient of 1.847 g/l/mg/l and a doubling time of 8.02 h. At 40℃, the bacteria’s growth and ammonia reduction efficiency decreased.

Fig. 2 shows the percentage reduction in ammonia at different temperatures over time, with the highest reduction (64.88%) at 37℃ and the lowest (53.25%) at 30℃. Table 1 summarizes the kinetic growth of B. subtilis, indicating that the sample at 37℃ had the highest biomass yield coefficient, meaning B. subtilis consumed the most ammonia. The maximum ammonia removal rate at 37℃ was 0.031 mg/l/h, highlighting the bacteria’s efficiency in rapidly reducing ammonia under optimal conditions. Temperatures exceeding 37℃ reduced the bacteria’s ability to lower ammonia levels effectively.

Table 1 . Summary of kinetic growth and ammonia reduction by B. subtilis under various conditions (OFAT analysis).

ConditionParameterμ (h-1)Doubling Time, Td (h)Max Removal (mg/l/h)Yx/s (g/l/mg/l)
Temperature (℃)300.024228.640.0201.139
350.09847.040.0251.367
370.08648.020.0311.847
400.022430.940.0221.586
pH40.0045154.030.0161.92
50.014149.160.0192.243
60.024428.410.0202.681
70.009870.730.0222.762
80.009374.530.0201.749
Agitation (rpm)00.0062111.800.0020.881
500.066410.440.0181.184
1000.0069100.460.0231.451
1500.046714.840.0262.733
2000.011659.750.0242.529
Inoculation Concentration (g/l)0.00.0024288.810.0001.178
0.30.009374.530.0381.386
0.50.048014.440.0461.487
1.00.29222.370.0541.934
Ammonia Concentration (ml/l)40.07149.710.0291.846
60.064910.680.0251.414
80.050613.700.0230.931
100.050313.780.0220.657

Figure 2.Comparison of the percentage reduction in ammonia at different temperatures against time.

Correlation of pH with the reduction of ammonia and the growth of B. subtilis (OFAT for pH)

Supplementary Fig. S3 shows the correlation of 8 ml/l ammonia at different pH values (4, 5, 6, 7, and 8) over time, with data on ammonia concentration, reduction, and B. subtilis biomass production. Each sample contained 0.15 g of B. subtilis and 8 ml/l of ammonia, maintained at 150 rpm and 37℃. The biomass of B. subtilis increased over 8 h, with the highest growth at pH 7. B. subtilis can grow across a pH range of 4 to 8, with optimal growth at pH 7. Gauvry et al. [17] reported that B. subtilis can grow at pH values from 4.8 to 9.2. However, growth rates varied with pH, with alkaline conditions (pH 8) reducing growth. Thus, B. subtilis grows better in acidic conditions than in alkaline ones.

Fig. 3 shows that ammonia reduction was greatest at pH 7 (73.42%) and lowest at pH 8 (65.75%). Different pH values affect B. subtilis growth and ammonia reduction. Table 1 shows the kinetic growth data, with pH 7 yielding the highest biomass production and ammonia reduction. The biomass yield coefficient (YX/S) at pH 7 was 2.762 g/l/mg/l. The doubling time for B. subtilis at pH 7 was 70.73 h, and the maximum ammonia removal rate was 0.022 mg/l/h, indicating the highest and most rapid ammonia removal from the liquid sample.

Figure 3.Comparison of the percentage of ammonia reduction at different pH values against time.

Correlation of agitation with the reduction in ammonia and the growth of B. subtilis (OFAT for agitation)

Supplementary Fig. S4 shows the correlation of different agitation conditions (0, 50, 100, 150, and 200 rpm) with ammonia concentration, reduction, and B. subtilis biomass production after 8 h. Each sample contained 8 ml/l of ammonia and 0.15 g/l of B. subtilis, with constant variables of 37℃ and pH 7. Agitation significantly impacts the growth cycle of bacterial populations by efficiently mixing oxygen, heat, and nutrients during fermentation [18]. It supplies necessary oxygen for cell growth and eliminates exhaust gases [19]. The biomass of B. subtilis increased under all agitation conditions, with the highest biomass observed at 150 rpm and 200 rpm, while the lowest was at 0 rpm. However, high agitation speeds can create shear forces that damage bacteria, and low speeds can increase broth viscosity, reducing mass transfer effectiveness or decrease the biomass production of B. subtilis [20].

Fig. 4 shows that the highest ammonia reduction occurred at 150 rpm (73.21%), followed by 200 rpm (71.67%) and 0 rpm (46.83%). Different agitation rates affect B. subtilis growth and ammonia reduction. Table 1 presents the kinetics of B. subtilis growth and ammonia reduction under various agitation conditions. Optimal agitation at 150 rpm provided the best balance for biomass production and ammonia reduction, while extreme conditions either too high or too low negatively impacted the bacteria’s efficiency.

Figure 4.Comparison of the percentage reduction in ammonia under different aeration conditions against time.

Correlation of inoculation concentration with the reduction in ammonia and growth of B. subtilis (OFAT for inoculation concentration)

Supplementary Fig. S5 illustrates the correlation between different concentrations of B. subtilis (0, 0.3, 0.5, and 1.0 g/l) and time, showing data on ammonia concentration, ammonia reduction, and biomass production of B. subtilis after 8 h. The experiment was conducted under constant conditions: a temperature of 37℃, agitation at 150 rpm, an 8 ml/l concentration of ammonia, and a pH of 7. The biomass production of B. subtilis increased gradually over 8 h for each dose, but at 0.3 g/l, 0.5 g/l, and 1.0 g/l, the bacteria were depleted by 5 h and continued to decrease until the end of the experiment. This depletion might be due to nutrient limitations as the amount of B. subtilis increased. Despite this, bacterial production continued as B. subtilis can grow well in the sample. Additionally, the concentration of ammonia decreased across all inoculation concentration over the 8-h period, with higher doses (1.0 g/l) leading to greater ammonia reduction. This is because a higher inoculation concentration can remove ammonia more rapidly and efficiently.

Fig. 5 shows the percentages of ammonia reduction with different inoculation concentrations (0, 0.3, 0.5, and 1.0 g/l). The highest reduction in ammonia was observed at the 1.0 g/l dose of B. subtilis, achieving 65.92%, while the lowest reduction was at 0 g/l, with 54.08%. Ammonia reduction still occurred at 0 g/l, likely due to the oxidation of ammonia in the sample. Therefore, higher inoculation concentration resulted in greater ammonia reduction and removal from the sample. Table 1 presents the kinetics of B. subtilis growth and ammonia reduction with various doses of B. subtilis.

Figure 5.Reduction percentage of ammonia at different dosages of B. subtilis over time.

Correlation of the concentration of ammonia with the reduction in ammonia and the growth of B. subtilis (OFAT for concentration of ammonia)

Supplementary Fig. S6 illustrates the correlation between different concentrations of ammonia (4, 6, 8, and 10 ml/l) and time, showing data on ammonia concentration, ammonia reduction, and biomass production of B. subtilis after 8 h. The experiment was conducted under constant conditions: pH 7, 37℃, 150 rpm, and 0.15 g of B. subtilis. The optimum concentration of ammonia was 4 ml/l, as B. subtilis was able to grow and remove ammonia most effectively at this concentration. Higher concentrations of ammonia led to a dramatic decrease in bacterial growth, which in turn lowered the reduction and removal of ammonia. Previous studies have shown that ammonia, rather than ammonium ions, is the main cause of growth inhibition in Bacillus species. Additionally, most Bacillus spp. ammonia-utilizing bacteria prefer 0.5 to 5 mg/ml ammonia for optimal growth.

Fig. 6 presents the percentage reduction in ammonia at different ammonia concentrations over time. The greatest reduction in ammonia occurred at the lowest concentration (4 ml/l), while the lowest reduction was observed at the highest concentration (10 ml/l). This indicates that ammonia can be reduced more rapidly and efficiently at lower concentrations. Although 0.15 g of B. subtilis can reduce ammonia in samples with 10 ml/l ammonia, the rate of reduction was still lower compared to samples with only 4 ml/l ammonia. Table 1 shows the kinetics of B. subtilis growth and ammonia reduction at various concentrations, with 4 ml/l ammonia resulting in the fastest bacterial growth and greatest ammonia removal.

Figure 6.Comparison of the percentage reduction in ammonia at different ammonia concentrations over time.

Optimum conditions in the OFAT study

Table 2 summarizes the optimum conditions identified in the OFAT study for maximizing ammonia removal and biomass yield by B. subtilis.

Table 2 . Summary of the optimum conditions in the OFAT study.

No.Optimum Condition (Variable)Fixed valueMaximum removal (mg/l/h)Yx/s (g/l/mg/l)
1Temperature – 37℃· 0.15 g/l – Inoculation concentration
· pH – 7
· Agitation – 150 rpm
· Concentration of ammonia - 8 ml/l
0.0311.847
2pH – 7· 0.15 g/l – Inoculation concentration
· Temperature 37℃
· Agitation – 150 rpm
· Concentration of ammonia - 8 ml/l
0.0222.762
3Agitation – 150 rpm· 0.15 g/l - Inoculation concentration
· pH – 7
· Temperature 37℃
· Concentration of ammonia - 8 ml/l
0.0262.733
4Inoculation concentration – 1.0 g/l· Temperature 37℃
· pH – 7
· Agitation – 150 rpm
· Concentration of ammonia - 8 ml/l
0.0541.934
5Concentration of ammonia – 4 ml/l· 0.15 g/l - Inoculation concentration
· pH – 7
· Agitation – 150 rpm
· Temperature 37℃
0.0291.846


Investigation of significant parameters reflecting ammonia reduction and the growth of B. subtilis in the liquid phase

The present study examined five parameters: temperature, pH, agitation, ammonia concentration, and inoculation concentration, to determine which provided the best reduction of ammonia and biomass production of B. subtilis in the liquid phase. Each parameter for the screening test was set to 37℃, pH 7, agitation at 150 rpm, ammonia concentration of 4 ml/l, and inoculation concentration of 1.0 g/l. Statistical analysis was performed using R 4.1.3 software, utilizing one-way analysis of variance (ANOVA) to determine the significance of the differences in the parameters at a significance level greater than 95%. The level of statistical significance (α value) was set at 0.05 for all analyses.

Screening ANOVA at various temperatures for ammonia reduction and the growth of B. subtilis

Temperature significantly affects B. subtilis biomass production and ammonia reduction. The study investigated temperatures of 30, 35, 37, and 40℃ under constant conditions. The highest ammonia reduction (64.88%) was at 37℃, while the lowest (53.25%) was at 30℃. The reduction increased from 30℃ to 37℃ but decreased at 40℃, likely due to the adverse effects of high temperatures on B. subtilis growth. ANOVA results depicted in Table 3 confirmed the significant impact of temperature on ammonia reduction with a p-value of 0.00322. Supplementary Fig. S7 shows the percentage reduction in ammonia yield at different temperatures, illustrating that optimal reduction occurs at 37℃, while extreme temperatures (30℃ and 40℃) are less effective. This finding aligns with previous studies that have shown B. subtilis performs optimally within a temperature range of 25 to 37℃ [4].

Table 3 . One-way ANOVA analysis of various parameters on ammonia reduction and B. subtilis biomass production.

ParameterDfSum SqMean SqF valuePr(>F)
TemperatureEffect of Temperature on Ammonia Reduction
Temperature31.7190.57315.6390.00322 **
Residuals323.2520.1016
Effect of Temperature on B. subtilis Biomass Production
Temperature30.00320.0010720.0460.987
Residuals320.75270.023522
Inoculation ConcentrationEffect of Inoculation concentration on Ammonia Reduction
Inoculation concentration329.7018.06714.41.32e-12***
Residuals323.1250.09764
Effect of Inoculation concentration on B. subtilis Biomass Production
Inoculation concentration325.9088.6362474<2e-16***
Residuals320.1120.003
Ammonia ConcentrationEffect of Ammonia Concentration on Ammonia Reduction
Concentration of Ammonia367.5022.49918.982.95e-07***
Residuals3237.921.185
Effect of Ammonia Concentration on B. subtilis Biomass Production
Concentration of Ammonia30.03440.011450.6280.602
Residuals320.58360.01824
AgitationEffect of Agitation on Ammonia Reduction
Agitation40.7570.18930.9380.452
Residuals408.0670.2017
Effect of Agitation on B. subtilis Biomass Production
Agitation43.2930.823440.241.62e-13***
Residuals400.8180.0205
pHEffect of pH on Ammonia Reduction
pH40.3630.090651.0720.383
Residuals403.3820.08454
Effect of pH on B. subtilis Biomass Production
pH40.102790.02569819.824.63e-09***
Residuals400.051870.001297

Significance codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1



Supplementary Fig. S8 shows that the highest biomass production of B. subtilis (0.251 g/l) was obtained at 37℃, while the lowest (0.159 g/l) was at 30℃. Growth increased from 30℃ to 37℃ but decreased at 40℃. Chen et al. [4] reported that B. subtilis can grow and synthesize within a temperature range of 25 to 37℃. High temperatures (40℃) may slow growth. However, the oneway ANOVA results shown in Table 3 confirmed that different temperatures did not significantly affect growth, with a p-value of 0.987, which is greater than 0.05. Therefore, temperature will not be further considered in the optimization process.

Screening ANOVA at various inoculation concentration for ammonia reduction and the growth of B. subtilis

The effect of inoculation concentration (0, 0.3, 0.5, and 1.0 g/l) on ammonia reduction was studied under constant conditions: temperature 37℃, 4 ml/l ammonia, 150 rpm agitation, and pH 7. The highest reduction (65.92%) was at 1.0 g/l. Increasing the inoculation concentration from 0 to 1.0 g/l enhanced ammonia reduction, indicating that higher inoculation concentration improves the reduction process. ANOVA results depicted in Table 3 showed a significant effect of inoculation concentration on ammonia reduction with a p-value of 1.32e-12. Supplementary Fig. S9 shows the percentage reduction in ammonia yield at different inoculation concentrations, highlighting that the maximum inoculation concentration (1.0 g/l) achieves the greatest reduction, while lower inoculation concentration is less effective. Similar results were observed in studies where higher concentrations of B. subtilis led to more efficient ammonia reduction [21].

The effect of inoculation concentration (0, 0.3, 0.5, and 1.0 g/l) on the growth of B. subtilis was investigated under constant conditions. Supplementary Fig. S10 shows that the inoculation concentration significantly increased biomass production. The highest biomass production (0.433 g/l) was obtained at a 1.0 g/l dose. This indicates that the number of bacteria affects biomass production in the liquid sample. The ANOVA results shown in Table 3 indicate that different doses of B. subtilis had a statistically significant impact on growth, with a p-value of < 2e-16, which is less than 0.05 (Table 3).

Screening ANOVA at various concentrations of ammonia for ammonia reduction and the growth of B. subtilis

The study examined ammonia concentrations of 4, 6, 8, and 10 ml/l under constant conditions: inoculation concentration of 1.0 g/l, pH 7, agitation at 150 rpm, and temperature 37℃. The highest reduction (64.87%) was at 4 ml/l. As the concentration increased, the reduction decreased, suggesting that higher ammonia concentrations hinder the reduction process. ANOVA results depicted in Table 3 confirmed the significant impact of ammonia concentration on reduction with a p-value of 2.95e-07. Supplementary Fig. S11 shows the percentage reduction in ammonia yield at different concentrations of ammonia, demonstrating that lower concentrations (4 ml/l) are more effectively reduced by B. subtilis compared to higher concentrations (10 ml/l). This trend is consistent with findings that higher ammonia concentrations can inhibit microbial activity [22].

The effect of ammonia concentration (4, 6, 8, and 10 ml/l) on the biomass production of B. subtilis was investigated under constant conditions. Supplementary Fig. S12 shows the yield of B. subtilis biomass at different ammonia concentrations. The highest growth (0.231 g/l) was obtained at 4 ml/l. Increasing ammonia concentration from 4 to 10 ml/l decreased biomass production, likely due to higher ammonia levels inhibiting growth. The one-way ANOVA results shown in Table 3 confirmed that different ammonia concentrations did not have a statistically significant impact on biomass production, with a p-value of 0.602, which is greater than 0.05 (Table 3).

Screening ANOVA at various agitation conditions for ammonia reduction and the growth of B. subtilis

Agitation speeds (0, 50, 100, 150, and 200 rpm) were tested under constant conditions: an inoculation concentration of 1.0 g/l, ammonia concentration of 4 ml/l, pH 7, and temperature 37℃. The highest ammonia reduction (73.21%) was at 150 rpm. Increasing the speed to 200 rpm decreased the ammonia reduction due to excessive shear forces and heterogeneous mixing. ANOVA results indicated that agitation did not significantly affect ammonia reduction, with a p-value of 0.452, which is greater than 0.05 (Table 3). Hence, the agitation variable is not further used in the optimization process. Supplementary Fig. S13 shows the percentage reduction in ammonia yield at different agitation speeds, indicating that moderate agitation (150 rpm) is optimal, while very low (0 rpm) and very high (200 rpm) speeds are less effective.

The effect of agitation (0, 50, 100, 150, and 200 rpm) on the biomass production of B. subtilis was investigated under constant conditions. Supplementary Fig. S14 shows the yield of B. subtilis (g/l) biomass produced under different agitation conditions. The highest biomass production (0.217 g/l) was obtained at 150 rpm. At 0 rpm, the second highest biomass production was observed (0.204 g/l), while the lowest was at 200 rpm (0.022 g/l). As agitation increases, bacterial production increases due to better circulation of oxygen and nutrients. However, bacterial production decreased at 200 rpm, likely due to excessive agitation eliminating necessary gases. The one-way ANOVA results shown in Table 3 confirmed that different agitation levels had a statistically significant effect on the reduction in ammonia yield (%), with a p-value of 1.62e-13*** (Table 3).

Screening ANOVA at various pH values for ammonia reduction and the growth of B. subtilis

The effect of pH (4, 5, 6, 7, and 8) on ammonia reduction was investigated under constant conditions: inoculation concentration (1.0 g/l), ammonia concentration (4 ml/l), agitation (150 rpm), and temperature (37℃). The highest reduction (73.42%) was at pH 7. Increasing the pH to 8 decreased the reduction. ANOVA results showed that pH did not significantly affect ammonia reduction, with a p-value of 0.383, which is greater than 0.05 (Table 3). Hence, this pH parameter will not be further used for the optimization process. Supplementary Fig. S15 shows the percentage reduction in ammonia yield at different pH values, illustrating that neutral pH (7) is optimal for ammonia reduction, while more acidic (pH 4) or more alkaline (pH 8) conditions are less effective. This observation is supported by studies indicating that B. subtilis thrives in neutral pH environments.

The effect of pH (4, 5, 6, 7, and 8) on the biomass production of B. subtilis was investigated under constant conditions. Supplementary Fig. S16 shows the yield of B. subtilis (g/l) biomass produced at different pH values. The highest biomass production (0.189 g/l) was obtained at pH 7. As the pH increased from 4 to 7, bacterial growth also increased, but production decreased at an alkaline pH of 8. Some researchers have stated that an alkaline pH may slow the growth of bacteria. B. subtilis grows within a pH range of 5.4 to 8.5, with optimum growth occurring at pH 7.0 [16]. The one-way ANOVA results shown in Table 3 confirmed that different pH levels had a significant effect on the reduction in ammonia yield (%), with a p-value of 4.63e-09***, which is less than 0.05 (Table 3).

Based on the one-way ANOVA for all parameters shown in Table 3, it was found that temperature, ammonia concentration, and inoculation concentration had significant effects on the reduction of ammonia, as their p values were less than 0.05. Consequently, these three parameters will be further investigated in the next stage of optimization using the R software program. Similarly, pH and agitation were found to have a significant effect on the biomass production of B. subtilis, with p values lower than 0.05, and will also be further investigated in the next stage of optimization using the R software program.

Reduction of ammonia

These three parameters, ammonia concentration, temperature and inoculation concentration, had p values less than 0.05 for the reduction of ammonia based on the above discussion. These parameters show that the reduction of ammonia in the liquid phase was significant when the p value was less than 0.05. These parameters were further optimized using response surface methodology (RSM) in R software, with central composite design (CCD) in the RSM step. Moreover, the RSM package in R enables the analysis of parameter relationships and their impact on response variables.

According to the results obtained for the reduction of ammonia, the conditions for the optimization process were chosen based on their significant factors and suitable values for low and high ammonia concentrations: 3.0−5.0 ml/l (±1.0 ml/l), 0.8−1.2 g/l (±0.2 g/l), and 36.0− 38.0℃ (±1.0℃), which are summarized in Supplementary Fig. S17. Supplementary Fig. S18 summarizes the results of 18 experiments with randomized concentrations of ammonia, concentrations of B. subtilis and temperatures at a constant pH (7), and agitation (150 rpm) throughout the experiment. The greatest reduction in ammonia (7.42 mg/l) was obtained in run 15 when the concentration of ammonia was 4.0 ml/l, the inoculation concentration was 1.0 g/l, and the temperature was 37℃ . Moreover, the lowest reduction in ammonia (6.04 mg/l) was obtained in run 18 when the concentration of ammonia was 2.2 ml/l, the inoculation concentration was 1.0 g/l, and the temperature was 37℃.

Moreover, the RSM is also capable of assessing the influence of several independent variables at a time and selecting the optimal operating parameters for the process [23]. Through multiple regression analysis, an enhanced model is produced, and the equation can be used to plot the response surface. Zhou et al. [12] investigated the recovery percentage of NH4+-N (R(N)) and Cr loading (L(Cr)) as dependent variables, focusing on the independent variables of pH, the molar ratio of magnesium to nitrogen (Mg/N), and the molar ratio of phosphorus to nitrogen (P/N). Using Design-Expert 12.0 software and Box-Behnken design (BBD), they achieved a high R2 value of 0.9877. The optimal conditions for NH4+-N recovery were determined to be pH = 9.16, Mg/N = 1.3, and P/N = 1.165, resulting in an impressive R(N) of 98.944% and an L(Cr) of 0.116%.

Similarly, Yu et al. [13] explored the removal rate of NH4+ as the dependent variable, considering contact time, initial concentration, temperature, and pH as independent variables. Design-Expert 12.0 software and Box-Behnken design (BBD) were used to obtain a robust R2 value of 0.9762. Their optimization revealed that a contact time of 899.41 min, initial concentration of 17.35 mg/l, temperature of 15℃, and pH of 6.98 led to an NH4+ removal rate of 63.74%, with a negligible relative error of 0.87%. Behera et al. [14] studied the percentage of ash reduction as the dependent variable and investigated hydrofluoric acid (HF) concentration, temperature, and leaching time as independent variables. Using Design- Expert 8.0.7.1 software and central composite design (CCD), they achieved an impressive R2 value of 0.9909. The optimal conditions were determined to be an HF concentration of 18 vol.%, a temperature of 92℃, and a leaching time of 162 min. Mourabet et al. [15] investigated the adsorption capacity of fluoride as the dependent variable, considering pH, adsorbent mass, and temperature as independent variables. Design-Expert 7.0.0 software and Box-Behnken design (BBD) were used to obtain a satisfactory R2 value of 0.927. Their optimization revealed that a pH of 7.5, adsorbent mass of 0.1 g, and temperature of 30℃ resulted in an adsorption capacity of fluoride of 60 mg/l.

Biomass production of B. subtilis

Five parameters were evaluated: temperature, pH, ammonia concentration, inoculation concentration and agitation. However, only two parameters, pH and agitation, had p values lower than 0.05 for the biomass production of B. subtilis. These parameters show that a p value lower than 0.05 had a significant effect on the biomass of B. subtilis in the liquid phase. These parameters were further optimized using response surface methodology (RSM) in R software, with central composite design (CCD) in the RSM step. Moreover, the RSM package in R enables the analysis of parameter relationships and their impact on response variables.

According to the results obtained from the biomass production of B. subtilis, the conditions for the optimization process were chosen based on their significance and suitable values for low and high levels for every parameter: pH, 6.5−7.5 (±0.5); agitation, 140−160 rpm (±10 rpm); these conditions are summarized in Supplementary Fig. S19. Supplementary Fig. S20 summarizes 12 experiments with randomized pH and agitation at a constant concentration of ammonia (4 ml/l), inoculation concentration (1.0 g/l) and temperature (37℃) throughout the experiment. Based on the results of the experiment, the highest biomass production of B. subtilis (0.328 g/l) was obtained in run 7 when the pH was 7 and agitation occurred at 150 rpm. Moreover, the lowest biomass production of B. subtilis (0.132 g/l) was obtained in run 5 when the pH was 6.5 and agitation at 140 rpm.

ANOVA of the second-order polynomial model and regression fitting

A test for the significance of the regression model and each model coefficient with a lack of fit test was carried out to fit a good model. Typically, the ranking of the significant factors is based on the F value or P value (probability value) with a 95% confidence level. To construct the statistical models, the experimental results were subjected to multivariable linear regression models: (1) first order, (2) two-way interaction, and (3) pure quadratic, which are outlined for the reduction of ammonia and for the biomass production of B. subtilis. To decide whether to accept or reject the null hypothesis, the probability >F (p value) values for each coefficient were calculated at the 95% confidence level.

Reduction of ammonia

As shown in Table 4 below, ANOVA revealed that the model was able to represent the actual relationship between the reduction in ammonia and the three significant variables. The F value of the first order of the model (16.3969) with Pr(>F) = 0.0008879 and the pure quadratic 0.0036551 interactions indicated that the model was significant at the 95% confidence level, as the pvalue was lower than 0.05, while the two-way interaction was not significant (0.3523553). A lack of fit of a model is essential for assessing its fit. The lack of fit of the F value of 6.4118 reveals that the “lack of fit” is not as significant as the p value (for ‘‘lack of fit” > 0.05), which is 0.0785444. In particular, there is a 7.85% chance that the lack of fit of the F value is due to noise [14]. As a result, the model is suitable for the experimental data because the lack of fit is not significant

Table 4 . ANOVA of the second-order polynomial model for the reduction of ammonia.

DfSum SqMean SqF valuePr(>F)
First Order32.515020.8383416.39690.0008879
Two-way interaction30.192750.064251.25670.3523553
Pure Quadratic30.590410.196803.84920.0036551
Residuals80.409020.05113
Lack of fits50.374020.074806.41180.0785444
Pure error30.035000.01167


Table 4 below shows the results of the reduction in ammonia in response to the combination of input variables (concentration of ammonia, inoculation concentration and temperature) according to the experimental design. According to the negative polynomial coefficient values for the variables, the response variables increase as the independent variables decrease. Despite the negative coefficients, a p value less than 0.05 demonstrated that the intercept and all factors and interactions had a significant impact on the reduction in ammonia. A second- order polynomial model was fitted to these relevant factors from the multiple regression analysis of CCD experiments (Equation (1)). The model showed how the independent variables (concentration of ammonia, inoculation concentration and temperature) related to one another and how they affected the response variables. The reduction in ammonia was represented by the second- order model shown below in terms of coded factors:

Y=7.006333+0.250000X10.153750X2+0.091250X3+0.115000X12+0.017500X130.035000X23

Y indicates the reduction in ammonia (mg/l), X1 is the concentration of ammonia (ml/l), X2 is the inoculation concentration (g/l) and X3 is the temperature (℃). A high correlation between the independent variables is shown by a high R2 value, which implies a good formula for determining the ideal conditions for maximizing the dependent variable.

The precision of the model can be checked by the coefficient of determination for both the predicted R2 and adjusted R2, as shown in Supplementary Fig. S21. The predicted R2 value was 0.9358, and the adjusted R2 value was 0.8635, which were closer to 1.00. Additionally, the model will represent more than 94% of the variance in the response, and no unaccounted for more than 6% of the total uncertainty. As a result, this quadratic model predicts a maximal value due to the significant correlation between the independent variables (concentration of ammonia, inoculation concentration and temperature), and the model has a high goodness of fit for predicting the reduction of ammonia. Moreover, when the value of Pr(>|t|) is smaller than 0.05, the model terms are significant. The individual terms (CAMM, CSUB and TEMP), interaction between different variable terms (CAMM: CSUB), and square terms (CAMM^2) were found to have significant effects on the reduction of ammonia.

Biomass production of B. subtilis

For Table 5 below, the first-order (0.49010) and twoway interaction (0.40251) interactions are not significant when the p value is greater than 0.05, while only the pure quadratic interaction is significant when the p value is less than 0.05, which is 0.01246. The lack of fit of a model is essential for assessing its fit. The lack of fit of the F value (1.19) reveals that the “lack of fit” is not significant as the p values (for ‘‘lack of fit” > 0.05). In particular, there is a 44.58% chance that the lack of fit of the F value is due to noise [14]. As a result, the model is suitable for the experimental data because the lack of fit is not significant.

Table 5 . ANOVA of the second-order polynomial model for the biomass production of B. subtilis.

DfSum SqMean SqF valuePr(>F)
First Order20.0108710.0054350.80510.49010
Two-way interaction10.0054760.0054760.81110.40251
Pure Quadratic20.1342100.0671059.93910.01246
Residuals60.0405100.006752
Lack of fits30.0219820.0073271.18640.44579
Pure error30.0185280.006176


Table 5 shows the results of the biomass production of B. subtilis in response to the combination of input variables (pH and agitation) according to the experimental design. Only the intercept and pH have positive polynomial coefficient values, implying that the response variable increases as the values of these parameters increase. Apart from the interaction between variables, all other variables except for the intercept do not have a significant impact on the response variable since their p value is greater than 0.05. The significant variables were then fitted to the following second-order polynomial model for optimal B. subtilis biomass production conversion (Eq. (2)):

Y=1.071417+0.039167X10.01667X20.037000X12

Y is the biomass production of B. subtilis, X1 is the pH, and X2 is the agitation (rpm). A high correlation between the independent variables is shown by a high R2 value, which implies a good formula for determining the ideal conditions for maximizing the dependent variable. The R2 value of 0.788 for the second-order model. Supplementary Fig. S22 shows that the model will represent more than 78% of the variance in the response, and there will not be any unaccounted for more than 22% of the total uncertainty. As a result, this quadratic model predicts a maximal value due to the significant correlation between the independent variables (pH and agitation) and the biomass of B. subtilis.

Validation

Response surface methodology (RSM) is also being used to construct three-dimensional (3D) response surface plots and contour plots by graphically presenting a polynomial equation, which is generated between independent and dependent variables.

Reduction of ammonia

The plots display the effects of the three variables on the ammonia concentration, inoculation concentration and temperature. Fig. 7(A) shows a plot of the predicted yield versus the actual yield of ammonia reduction. Based on the model, the actual ammonia reduction yield was generated from the experimental data, and the predicted ammonia reduction yield was evaluated from the models. Since the R2 value is 0.9358, there is a very good correlation between the experimental and expected values, as the value is near 1. This showed that the model was aligned and fit with the experimental data. Fig. 7(B) is a quantile-quantile plot (Q-Q plot), which is used to determine the data distribution. Fig. 7(C) and (D) clearly show the reciprocal influence of these three variables. The saddle shape of the 3D plot demonstrates the presence of correlations between the independent variables and ammonia reduction [24]. Based on the 3D plot in Fig. 7(C), an increase in both the inoculation concentration and temperature tended to lead to an increase in the concentration of ammonia, while the other variables remained constant. This suggests a positive correlation between these variables and the concentration of ammonia.

Figure 7.(A) Plot of the predicted yield versus the actual yield of ammonia reduction, (B) quantile-quantile plot (Q-Q plot), and (C) and (D) 3D plot correlations between the independent variables and ammonia reduction.

Biomass production of B. subtilis

The plots below display the effects of the two variables of pH and agitation. Fig. 8(A) shows a plot of the predicted yield versus the actual yield of B. subtilis biomass. Based on the model, the actual biomass production yield was generated from the experimental data, and the predicted biomass production yield was evaluated from the models. Since the R2 value is 0.788, there is a good correlation between the experimental and expected values. This showed that the model aligned with the experimental data. Fig. 8(B) is a quantile-quantile plot (Q-Q plot), where it is used to determine the data distribution. Fig. 8(C) and (D) clearly show the reciprocal influence of these two variables. The saddle shape of the 3D plot demonstrates the presence of correlations between the independent variables and biomass production [24]. Based on the 3D plot in Fig. 8(C), an increase in both pH and agitation tended to lead to an increase in the bio-mass production of B. subtilis, while the other variables remained constant. This suggests a positive correlation between these variable and the biomass production of B. subtilis.

Figure 8.(A) Plot of the predicted yield versus the actual yield of Bacillus subtilis biomass; (B) quantile-quantile plot (Q-Q plot); (C) and (D) 3D plot of the correlations between the independent variables and Bacillus subtilis biomass production.

Reduction of ammonia

The optimum conditions for the reduction of ammonia were determined to be 0.7789% of the desirability value obtained by R 4.1.3 software. The experiment was carried out in triplicate according to the optimized conditions listed in Table 6 below. Since the R2 value is 0.9358, the R2 value shows the accuracy of the predicted value with respect to the experimental/actual value. The experimental value of the response (reduction of ammonia %) showed that at 37℃, 4.17 ml/l ammonia, and 1.03 g/l B. subtilis, the ammonia yield decreased to 7.01. The difference between the actual value (7.006333) and the predicted value (7.114832) of ammonia reduction was only 0.108499; thus, the model indicated good agreement, and the model validation was also proven. A good model will produce similar values with lower standard deviations between the expected and actual values for the answers and responses.

Table 6 . Predicted values for the reduction in ammonia concentration, independent variables and desirability values.

Optimum conditionReduction of ammonia (%)
Test variables valueActual valuePredicted valueDesirabilityDifferences
Temperature (37℃)
Concentration of ammonia (4.17 ml/l)7.0063337.11483210.108499
Inoculation concentration (1.03 g/l)


Biomass production of B. subtilis

The experiment was carried out again in triplicate according to the optimized conditions listed in Table 7 below. The optimum conditions for the reduction of ammonia were determined by the 0.4607287 desirability value obtained by R 4.1.3 software. This indicated that the response was 46%, which is close to the optimal value. The experimental results of the response (biomass production of B. subtilis) showed that at pH 7.02 and agitation at 150 rpm, a B. subtilis yield of 1.07 g/l was obtained. The difference between the actual (1.071417) and predicted (0.928917) values of B. subtilis biomass production was only 0.1425; thus, the results showed that the model indicated good agreement, and the model validation was also proven.

Table 7 . Predicted values for the biomass production of B. subtilis, independent variables and desirability values.

Optimum conditionBiomass production of B. subtilis
Test variables valueActual valuePredicted valueDesirabilityDifferences
pH (7.02)1.0714170.9289170.46072870.1425
Agitation (150 rpm)

This study successfully determined the optimal conditions for mitigating ammonia emissions in the liquid phase through a thorough investigation. By analyzing the impact of various factors, such as temperature, pH, agitation, inoculation concentration, and ammonia concentration, we identified significant parameters influencing ammonia reduction in the liquid phase. The optimal conditions for maximal ammonia reduction were a temperature of 37℃, a pH of 7, agitation at 150 rpm, inoculation concentration of 1.0 g/l, and an ammonia concentration of 4 ml/l. The findings emphasized the crucial roles of temperature, ammonia concentration, and inoculation concentration in effectively reducing ammonia emissions, while pH and agitation were observed to affect the growth of B. subtilis. Through the application of response surface methodology (RSM) and central composite design (CCD), notable enhancements were achieved in both ammonia reduction and biomass production by B. subtilis. The optimized conditions resulted in a substantial reduction in ammonia (7.01 mg/l) and a decrease in the biomass of B. subtilis (1.07 g/l). Model validation confirmed the accuracy of the predicted values, validating the efficacy of the optimized conditions. In conclusion, this study sheds light on the effectiveness of utilizing dried B. subtilis cells as a means to reduce ammonia emissions in liquid environments, offering promising avenues for sustainable environmental stewardship and improved public health outcomes.

· Optimized conditions, including a temperature of 37℃ and a pH of 7, lead to significant reductions in ammonia concentration.

· RSM and CCD enhanced the process, resulting in a 7.01 mg/l reduction in ammonia and a 1.07 g/l decrease in B. subtilis biomass

· Findings support B. subtilis as a biocontrol agent, promoting sustainable environmental management.

All authors contributed to the study conception and design. A.A.A.F., S.S., S.B.M. and C.N.W.C. prepared all the materials needed in the experiment, performed all the data collection and analysis, and was a major contributor to the writing of the manuscript. H.A.T. supervised the whole process of the experiment and provided all the resources needed for this research. A.A.A.F., S.S., C.N.W.C. and H.A.T. aided and guided the experiments, especially all the analyses. S.B.M., A.A.A.H., S.S., A.H.H. and R.K. performed and aided parts of the experiments. M.M.Z.M. and R.K. provided parts of the technical support needed for the experiments. All the authors have read and approved the final manuscript.

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