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Article

Tomato Production with Organic Fertilizer from Soluble Bonito Fish Waste in Hydroponic Cultivation Systems

by
Dannisa Fathiya Rachma
1,†,
Kazuya Maeda
1,†,
Yuta Yamanouchi
2,
Hiroshi Ueda
2,
Makoto Shinohara
3 and
Dong-Hyuk Ahn
1,*
1
Institute of Vegetable and Floriculture Science, Greenhouse Productivity Research Division, National Agricultural and Food Research Organization, Tsukuba 305-8519, Japan
2
Institute of Vegetable and Floriculture Science, Vegetable and Flower Breeding Research Division, National Agricultural and Food Research Organization, Tsu 514-2392, Japan
3
Institute of Vegetable and Floriculture Science, Greenhouse Productivity Research Division, National Agricultural and Food Research Organization, Tsu 514-2392, Japan
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Horticulturae 2025, 11(4), 381; https://doi.org/10.3390/horticulturae11040381
Submission received: 28 February 2025 / Revised: 31 March 2025 / Accepted: 31 March 2025 / Published: 2 April 2025
(This article belongs to the Special Issue Sustainable and Organic Farming of Vegetable Crops in Greenhouse and Open Field Systems)
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Versions Notes

Abstract

:
Using organic fertilizer made from waste materials is beneficial for both the economy and the environment, promoting sustainability and reducing pollution. In hydroponics, decomposition converts these materials into fertilizer, with multiple parallel mineralization (MPM) enabling efficient nutrient conversion by microorganisms. The tomato cultivar “Momotaro Next” was cultivated hydroponically in order to determine whether organic fertilizer derived from soluble bonito fish waste (OF) through MPM could be used in tomato hydroponic cultivation compared with a chemical nutrient solution treatment (CF). In this study, ammonium (NH4+) was generated through the OF decomposition process. During cultivation, the ammonium concentration tended to increase, while the nitrate (NO3−) concentration tended to decrease. The total yield (TY), total dry matter (TDM), and leaf area index (LAI) were lower after OF treatment than after CF treatment. Notably, the TY, TDM, and LAI were 5.4 kg m−2, 594 g plant−1, and 1.7 for OF and 6.8 kg m−2, 895 g plant−1, and 3.8 for CF, respectively. The results of the tomato fruit qualities show no significant differences for total soluble solids (TSS) (%Brix), lycopene, glucose, fructose, or sucrose. However, significant differences were observed for gamma-aminobutyric acid (GABA), glutamate, aspartate, and citric acid. The lower yield and quality of the tomato crop with the OF treatment were caused by the high concentration of NH4+ that occurred during cultivation due to a nonoptimal mineralization process. Therefore, a well-managed MPM process could improve crop quality by reducing the risk of high NH4+.

1. Introduction

Tomatoes (Solanum lycopersicum L.) are a globally significant crop, with an estimated production of 192.3 million tons in 2023, with China and India as the leading producers [1]. Tomato plays a crucial role in addressing food scarcity and enhancing food security [2]. As a major global fruit crop, they are a significant source of nutrition, rich in vitamin C, vitamin A, carotenoids, and essential minerals such as phosphorus, iron, and calcium [3]. Therefore, developing tomato production methods that enhance efficiency and quality while maintaining sustainability is essential to meet the growing demand.
Increasing amounts of solid waste from industries, commercial sites, agricultural lands, and households are often improperly disposed of in landfills, resulting in significant public health and environmental problems (such as air, water, and soil pollution) [4]. Sustainable strategies are essential for the effective management of solid waste. The global solid waste stream currently comprises approximately 46% organic waste [5], where a high amount of organic matter should be considered a major source for producing value-added products. The bioconversion of organic waste into value-added products (such as biogas and fertilizers) presents a viable solution to mitigate this issue [4]. This approach not only reduces the volume of waste but also minimizes the dependence on nonrenewable resources [6]. Organic wastes, derived from living organisms, often contain essential nutrients such as nitrogen, phosphorus, and potassium. These wastes are biodegradable and beneficial for plant growth, making them suitable for conversion into fertilizers [7,8].
In terms of the economy and environment, organic fertilizers are a favorable option since organic substances are more sustainable than chemical ones [9,10]. Organic matter can be converted into fertilizers through several common processes such as composting, vermicomposting, anaerobic digestion, and fermentation [5]. In soil-based cultivation, organic fertilizers are typically applied directly during the cultivation process. Once incorporated into the soil, these fertilizers undergo degradation by soil microorganisms, which convert organic nitrogen into nitrate through the processes of ammonification and nitrification [11]. However, the direct application of organic fertilizers in hydroponic culture systems carries the risk of the phytotoxic phenomenon, which inhibits plant growth and causes difficulties in balancing and providing the proper levels of nutrients [12]. Thus, the microbial preprocessing of the organic matters is required to provide ammonification and nitrification before using them as fertilizer in a hydroponic system [11].
Since nitrate is the preferred source of nitrogen for crop production, it is essential to effectively generate nitrate from organic fertilizer [11]. To enable the microbial decomposition of organic matter used in the hydroponic culture system efficiently without the accumulation of phytotoxins and dissolved oxygen deficiency, the multiple parallel mineralization (MPM) method was developed [11,13]. In the MPM method, the hydroponic nutrient solution must be under aerobic conditions, and the organic material must be applied continuously in small amounts combined with an inoculum (such as seawater, bark, and nursery soil) [11,14]. The use of organic fertilizer as a nutrient solution for hydroponic culture systems is a promising application for the future; in some of the previous studies conducted, organic fertilizer has been observed to achieve a similar yield, but of lower quality, as a commercial chemical fertilizer [15], and in one study, 90% of lettuce cultivated with an organic nutrient solution had a substantially higher shoot fresh weight than the marked weight of commercial lettuce head [16]. The difference in yield between the organic and chemical cultivations depends on the crops, organic sources, and management practices. Some research has been conducted using different organic materials for the organic fertilizer, such as aquaculture sludge, CSL (Corn Steep Liquor), waste from sugar production (waste molasses, distillery slop, and sugar cane leaves), fish-based soluble food waste, and biogas digestate from animal manure [11,14,15,16,17,18,19,20].
In Japan, 36% of the total waste generated is from food organic waste, where, in total, only 0.4% composting and 0.1% anaerobic digestion treatments have been applied [21]. One of the waste types generated is from the production of bonito fish flakes, which is a condimental food often found in Japanese cuisine. Here, bonito fish waste refers to the unused fish parts mixed with the water used during the production process. In an agricultural context, fish waste is rich in nutrients like nitrogen (N), phosphorus (P), and calcium (Ca) [22], making it a valuable raw material for fertilizer production. In hydroponically grown tomatoes, cultivation with organic-based fertilizer results in lower yield and fruit quality due to insufficient essential microelements [15]. Maintaining an optimal pH level (5.5–6.5) in the nutrient solution is crucial for nutrient availability in hydroponic tomato cultivation [23]. Nutrient imbalances can lead to diseases such as blossom-end rot (BER) in fruits, thereby reducing production [24]. Currently, the use of organic fertilizers, particularly those based on soluble bonito fish waste, in improving the yield and quality of hydroponically grown fruit and vegetable crops such as tomatoes has not been widely studied.
In a past study, a microbial culture solution from fish-based soluble waste with an additional inoculum was used with the nutrient film technique (NFT) in a closed, recirculating hydroponic system. No significant differences were observed in the fruit yield between the use of soluble fish waste, CSL, and chemical nutrient solution [11]. However, higher %Brix levels were found with the fish-based soluble treatment [11]. This demonstrated the potential of organic fertilizer derived from soluble bonito fish waste to be used in hydroponic systems. To determine whether organic fertilizer derived from soluble bonito fish waste (OF) through MPM can be used in hydroponic tomato cultivation, the current study comprehensively evaluated the yield and quality of tomatoes grown hydroponically using this organic fertilizer.

2. Materials and Methods

2.1. Plant Materials and Seedling Preparation

This study used the Japanese tomato cultivar “Momotaro Next” (Takii Seeds Co., Ltd., Kyoto, Japan). This variety produces medium-to-large fruits and is resistant to multiple diseases, including tomato mosaic virus Tm-2a type, wilt races 1 and 2 (F1, F2), root rot wilt (J3), half-leaf wilt race 1 (V1), downy mildew (Cf9), spot (LS), and sweet potato cyst nematode (N). Its seeds were sown in seed trays filled with nursery soil and germinated in the dark at 28 °C for 3 days. Then, they were transferred to a seedling growth chamber with fluorescent light (Nae Terrace; Mitsubishi Chemical Agri Dream Co., Ltd., Tokyo, Japan) with a light period of 14 h per day, air temperature settings of 23 °C (daytime) and 16 °C (nighttime), and 1000 µmol mol−1 CO2. Seedlings were fertilized once every 2 days using commercial nutrient solution (High-Tempo; Sumitomo Chemicals, Tokyo, Japan); the solution consisted of 10.7 mM NO3−, 6.3 mM K+, 10.8 mM Ca2+, 3.8 mM Mg2+, 7.2 mM H2PO4−, 3.8 mM Fe, 0.38 mg L−1 Mn, 0.26 mg L−1 B, 0.15 mg L−1 Zn, 0.05 mg L−1 Cu, and 0.07 mg L−1 Mo, adjusted to an electrical conductivity of 1.8 dS m−1.

2.2. Growth Conditions in the Greenhouse

This experiment was conducted from September to December 2023 in a greenhouse (9 m wide × 21 m long × 6 m high, north–south orientation) with an environmental control system facility at the National Agriculture and Food Research Organization, Tsukuba, Ibaraki Prefecture, Japan (36°1′ N, 140°6′ E). After 3 weeks, seedlings were transplanted on 7.5 cm × 7.5 cm rockwool (The Grodan Delta NG 2.0 block; Grodan, Roermond, The Netherlands) and then moved to a greenhouse for 10 days. The seedlings were then transplanted into 1 m rockwool slabs (Grodan Vital NG 2.0; Grodan, Roermond, The Netherlands) in the greenhouse compartment, with a plant density of 2.5 plant m−2. Then, the treatments were started. Tomato plants were pinched at three leaves above the 3rd truss, old leaves were not pruned, flowers were pollinated with 4-Chlorophenoxyacetic acid (Ishihara Tomato tone, Ishihara Sangyo Kaisha, Ltd., Osaka, Japan), and gibberellin was sprayed after the blooming of 4 flowers in each truss according to the manufacturers’ protocols. The number of fruits per truss was adjusted by pruning 4 to 5 fruits per truss. The cultivation period lasted for approximately 90 days after transplanting.

2.3. Treatments and Measurements

The compositions of the nutrient solutions in each treatment are presented in Table 1: the control chemical nutrient solution (CF) comprised chemical fertilizer Otsuka SA formula (Otsuka Agri-Techno, Tokyo, Japan), and the organic nutrient solution from soluble bonito fish waste was processed with the multiple parallel mineralization (MPM) technique [11,13]. The soluble bonito fish waste was from Makurazaki, Kagoshima Prefecture, Japan. Natural potassium, blackstrap molasses, and OAT formula No.5 (Otsuka Agri-Techno, Tokyo, Japan) were added into the organic material to support the potassium level and micronutrients (such as K, Mn, B, Fe, Cu, Zn, and Mo). The total organic material of approximately 18 L consisted of approximately 480 g of soluble bonito fish waste, 624 mL of natural potassium, 33.6 g of blackstrap molasses, and the remainder was water. The inoculation of microorganisms in an MPM system was conducted in 3 separate tanks with continuous aeration, where the organic raw material was added continuously in small amounts. This allowed the ammonification and nitrification processes of organic nitrogen to occur separately. The ion compositions of each nutrient solution are listed in Table 1 (including the ion composition of the OF raw material, OF after the MPM process, and CF). The daily concentrations of ammonium (NH4+), nitrite (NO2−), and nitrate (NO3−) ions were analyzed with an RQ-Flex Plus Analyzer (Merck, Frankfurt, Germany).
In this research, 3 rows were used in the greenhouse, with 15 rockwool slabs in each row (in total, 15 m in length with 0.8 m between the rows). The first and third rows were guard plants, and in the second row, 2 slabs in the front and 1 slab in the back were plotted as guard plants. There were 3 replications and 8 plants per treatment in each replication. At the end of the cultivation period, four plants per treatment in each replication were destructively sampled to measure the leaf area and dry weight of each organ (stem, leaf, and fruit). Leaf area samples were measured using an LI-3100C leaf area meter (Li-Cor Inc, Lincoln, NE, USA). The aboveground TDM of each plant was obtained as the sum of the leaf, stem, and fruit dry weight. The photosynthetic rate was measured on the 3rd fully expanded leaf from the top. The measurements were carried out between 10:00 and 14:00, using an LI-6800 portable photosynthesis system (Li-Cor, Lincoln, NE, USA). Measurements were carried out at a leaf cuvette air temperature of 25 °C, PPFD of 1000 µmol m−2 s−1, CO2 concentration of 400 ppm, and relative humidity of 60–70%. The measurement was repeated three times in each treatment.

2.4. Fruit Quality Analysis

Fruits were harvested at the orange to red stage. Then, the fruit’s fresh weight was measured, and the fruits from the first bunch (10 samples from the OF and 11 samples from the CF) were qualitatively analyzed (including the weight, TSS, lycopene, GABA, glutamate, aspartate, acid, citric acid, glucose, fructose, and sucrose). The weight of each tomato and its lycopene content were measured using a visible–near-infrared (VIS-NIR) spectrometer (K-SS900LC, Kubota, Osaka, Japan). The detailed principles of lycopene measurements have been described in a previous review [25]. Tomatoes were cut into eight pieces, and two diagonal pieces were collected. Equal amounts of Milli-Q water were added and heated in a microwave oven until the tomato temperature reached 80 °C to inactivate endogenous enzymes. After homogenization using a mixer (IFM-800DGM, Iwatanani, Osaka, Japan) and centrifugation (15,000× g, 5 min), the supernatant was collected and used for the following analysis.
The TSSs were measured using a digital refractometer (PR-101α, ATAGO, Tokyo, Japan) and expressed as %Brix. Citric acid, fructose, glucose, and sucrose were measured using a capillary electrophoresis system (Model 7100, Agilent Technologies, Palo Alto, CA, USA) with a diode array detector [26]. An uncoated fused-silica capillary of 100 cm (91.5 cm effective length, 50 μm i.d.) was purchased from GL Sciences (Tokyo, Japan). In total, 20 µL of the supernatant mentioned in the previous paragraph, 80 µL of Milli-Q water, and 100 µL of 2 mg/mL fucose (Tokyo Chemical Industry, Tokyo, Japan) as an internal standard were mixed to prepare analysis samples for CE (the final concentration of fucose was 1 mg/mL). A running buffer was used: 20 mM 2,6-pyridinedicarboxylic acid and 0.5 mM hexadecyltrimethylammonium bromide (pH = 12.1). Samples were injected into the capillary with a pressure of 50 mbar for 5 s. The separation voltage applied was −30 kV, and detection was performed at 350 nm with a reference at 270 nm, and the capillary temperature was controlled at 25 °C, where the detailed analytical conditions were described in a previous study [27]. Amino acid contents (aspartate, glutamate, and GABA) were measured using the precolumn derivatization method with a high-performance liquid chromatography (HPLC) system (Model 1260 Infinity, Agilent Technologies). The analytical conditions were the same as those in previous studies [28], except that 3-aminobutyric acid (Tokyo Chemical Industry) was used as the internal standard. In total, 50 µL of the supernatant, 440 µL of Milli-Q water, and 10 µL of 1.0 mg/mL 3-aminobutyric acid were mixed to prepare an analysis sample for HPLC (the final concentration of 3-aminobutyric acid was 20 µg/mL). Then, 0.4 N Borate buffer (pH 10.2, 5 µL), analysis sample (1 µL), o-Phthalaldehyde reagent (Agilent Technologies, 0.5 µL), and 5 mM citrate buffer (pH 6.3, 8 µL) containing 2% phosphoric acid were mixed with an injector program and analyzed immediately. A representative electropherogram of the CE and chromatogram of the HPLC are shown in Figure S1.

2.5. Statistical Analysis

Statistical analysis was performed using Microsoft Excel software for Microsoft 365 MSO version 2408, and significant differences were analyzed via a t-test (p < 0.05, p < 0.01, and p < 0.001).

3. Results

The daily average environmental data during the cultivation are presented in Supplementary Figure S2. The daily average temperature data show a slight decrease at the beginning of cultivation and tend to be stable thereafter, with minimum, maximum, and daily average temperatures of 13.8 °C, 33.4 °C, and 19.9 °C, respectively, while the average values of outside radiation during cultivation and daytime CO2 concentration were 10.5 MJ m−2 d−1 and 413.4 ppm, respectively.

3.1. Microbial Preprocessing of Organic Materials

The microbial preprocessing of organic matter from soluble bonito fish waste using the MPM method not only generated nitrate but also ammonium (Figure 1). As for other components (Table 1), the OF solution showed high concentrations of Na+ and Cl− even after the dilution in the MPM process and lower concentrations of Ca2+ and Mg2+ than the CF. Although it continuously generates nitrate during cultivation, the daily ion concentration in the OF solution was not stable. Figure 1 shows the concentration of NO3−, NO2−, and NH4+ ions during cultivation; note that NO2− was not detected during the cultivation. In the early stage of cultivation, the mineralization process could generate approximately 217 mg L−1 of nitrate, which decreased during the cultivation and reached approximately 106 mg L−1 at the end. Again, in this study, the decomposition process of soluble fish waste fertilizer using the MPM method not only produced nitrate but also ammonium. The concentration of ammonium (NH4+) tended to increase at the end of cultivation, where the highest NH4+ ion concentration in the OF treatment reached 90 mg L−1.

3.2. Aboveground Plant Biomass

The aboveground plant biomass was measured. Figure 2 shows the results of the TY, TDM, LAI, and maximum photosynthesis rate (Pmax) in each of the treatments. The TY was significantly lower with the organic fertilizer (OF) treatment than with the chemical fertilizer (CF) treatment, with values of 5.4 kg m−2 and 6.8 kg m−2, respectively. The results show that the dry matter of the stem, leaf, and fruit was significantly higher in the CF treatment, which led to higher TDM (Figure 2B). However, the fruit’s dry matter distribution rate was higher in the OF treatment than the CF treatment, 66% and 55%, respectively. Furthermore, the LAI was lower in the OF treatment than in the CF treatment, with average values of 1.7 and 3.8, respectively. Additionally, the maximum photosynthetic rate (Pmax) was significantly higher in the CF treatment compared to the OF treatment.

3.3. Fruit Quality

The quality of the tomato fruit in both treatments was analyzed, as shown in Figure 3. No significant differences were found in the average individual fruit weight, TSS, or lycopene of fruits between treatments. However, significant differences were observed in the average GABA, glutamate, aspartate, and citric acid content between treatments, where the OF treatment showed lower levels of these parameters than the CF treatment. The values were as follows: GABA content: 87 mg 100g FW−1 for OF and 114.2 mg 100g FW−1 for CF; glutamate: 177.7 mg 100g FW−1 for OF and 244.5 mg 100g FW−1 for CF; aspartate: 40.9 mg 100g FW−1 for OF and 70.2 mg 100g FW−1 for CF; and citric acid: 427.5 mg 100g FW−1 for OF and 541.3 mg 100g FW−1 for CF.

4. Discussion

In hydroponic tomato crop production, nitrate is the desired form of nitrogen over the ammonium form [11]. Although ammonium is important for cultivation, when ammonium is the main source of nitrogen, it often causes crop failure (such as leaf chlorosis, reduced net photosynthesis, and reduced crop production through the appearance of blossom end-rot fruits) [29,30,31]. In the present study, nitrate was generated through multiple parallel mineralization (MPM), which included the microbial processes of ammonification and nitrification. However, during the cultivation, the concentration of nitrate (NO3−) was unstable and decreased over time, while the concentration of ammonium (NH4+) tended to increase at the end of cultivation (Figure 1). Thus, the ratio of nitrate to ammonium decreased. Although the optimal ratio of nitrate to ammonium in nutrient solutions for hydroponic cultivation depends on the plant species and growth stage, a study found that without stress, a nitrate-to-ammonium ratio of 3:1 results in a higher growth parameter, photosynthetic rate, and chlorophyll concentration; soluble protein in roots; and the presence of leaf nitrates of tomato seedlings [32].
An unstable nitrate concentration can be caused by the denitrification process that occurs during the microbial mineralization process. In addition, high concentrations of Na+ and Cl− were found in the OF solution, which were not found in the CF, and the OF solution had lower concentrations of Ca2+ and Mg2+ than the CF solution (Table 1). According to this study’s results, denitrification may occur due to low dissolved oxygen levels, which could lead to the disruption of the nitrification process by aerobic nitrifiers [14], resulting in decreases in nitrate (NO3−) (Figure 1). It may be possible for anaerobic conditions and a supply of organic matter as an energy source for denitrifying microbes to cause the denitrification process, which would also enhance anaerobic ammonia oxidation (anammox) [33,34]. Denitrification and/or anammox were found in the thick biofilm and sediment on the bottom of the tank, as evidenced by the decrease in nitrate and the increase in ammonium ions. The unstable concentration of nitrate and high concentration of ammonium could lead to NH4+ toxicity and affect the production of tomato fruits.
As shown in Figure 2A,B, tomatoes grown using OF produced a fresh yield 11.7% lower than that of the CF treatment, and TDM 33.7% lower than that with the CF. According to the hierarchy of yield components, the lower fresh fruit yield is caused by a lower dry weight yield and/or by an increase in the fruit dry matter content, and a lower dry weight is caused by lower TDM and/or an increase in the fraction going to the fruit [35]. Both conditions occur with the OF treatment: the OF treatment has lower TDM and a higher fruit dry matter distribution rate than the CF treatment (Figure 2B), where the fruit dry matter distribution is 66% and 55% with the OF and CF treatments, respectively. TDM is determined based on the light use efficiency (LUE) and the amount of light intercepted by the plants. Furthermore, LUE is determined using the light extinction coefficient and photosynthetic rate on the leaf [35]. The leaf photosynthetic rate differed significantly between treatments, where the OF treatment showed a lower photosynthesis rate than the CF treatment (Figure 2D). On the other hand, light intercepted by plants is affected by the LAI. In this study, there was a significant difference in the LAI between the treatments, where the OF treatment had a significantly lower LAI than the CF treatment (1.7 and 3.8, respectively). Thus, lower TDM in the OF treatment was correlated to both a lower photosynthetic rate and lower LAI.
A past study observed that the net photosynthesis of tomato seedlings was greatest when a nitrate-to-ammonium ratio of 3:1 was used, which decreased as the NH4+ concentration increased [32]. High concentrations of ammonium can lower the pH in the root zone, increasing acidity and disrupting the pH gradient required for efficient photosynthesis enzyme activity. This also causes photoinhibition and damage to PSII, leading to a decreased photosynthesis rate under NH4+ toxicity [36,37,38,39]. Moreover, this condition leads to decreases in the accumulation of N and results in a decreased root and leaf area as well as dry biomass in tomato plants [40]. Another factor that should not be forgotten is that the generation of Na+ and Cl− in the OF solution alongside the low concentrations of Ca2+ and Mg2+ in the current study may have contributed to the occurrence of salt stress, which inhibits plant growth. Generally, the concentration of NaCl in nutrient solutions is maintained at low levels to prevent salt stress, as a previous study observed significant decreases in the growth parameters of tomato seedlings when the concentration of NaCl was higher than 50 ppm [41]. As shown in Table 1, the concentrations of Na and Cl were 30 ppm and 79 ppm, respectively, in the OF solution; this equals approximately 206 ppm of NaCl, which has great potential for salt stress to happen.
In the present study, there were no significant differences in the quality of tomatoes between the OF and CF treatments, except for some amino acids (glutamate, aspartate, and GABA) and organic acids (citric acid), where they were lower with the OF (Figure 3). The lower results in some fruit quality parameters with the OF treatment could be due to the high concentration of NH4+ and salt stress caused by elevated NaCl levels, which altered metabolite levels in the plant, such as amino acids and organic acids [31]. In the case of NH4+ toxicity, it has been reported in several plant species (such as Arabidopsis, tomato, Brachy podium, wheat, tobacco, or rapeseed) that a reduction in organic acid content (malate, citrate, fumarate, and 2-OG) and an increase in total amino acids occur when there is a high concentration of NH4+ or exclusively NH4+ [42,43,44,45,46,47]. In tomato leaves, under a high concentration of ammonium, the significant enrichment was linked to three genes that produce the malate synthase enzyme (MS), which were downregulated [48]. Notably, gene Solyc03g111140, which produces a type of MS, and gene Solyc07g052480, which produces the isocitrate lyase (ICL) enzyme, were among the genes exhibiting the highest reductions in activity due to the high concentration of ammonium supplied [48]. These two enzymes complete the glyoxylate cycle, a special version of the TCA (tricarboxylic acid) cycle found in plants [48]. However, the lower expression of both genes does not seem to support the activation of the glyoxylate cycle, which may affect tomato fruit quality in the end. This is supported by the results of tomato plants grown with the NH4-N form in solution culture media, exhibiting symptoms of NH4+ toxicity and resulting in lower concentrations of glutamate acid, aspartate acid, and GABA in the shoots [49].
Moreover, plants grown under salinity conditions could experience stress due to the phototoxicity of ions such as Na+ and Cl− [50]. In previous studies, salt stress in tomato decreased plant growth and fruit yield but increased fructose, glucose, total soluble solids (%Brix), amino acids, and organic acids [51,52,53]. However, these changes in fruit quality were not observed in the current study. These results suggest that decreases in yield and fruit quality (citric acid, glutamate, aspartate, and GABA) are caused by high concentrations of NH4+ in the OF solution.
In order to prevent an excessive increase in the concentration of NH4+ in organic hydroponic cultivation, the decomposition of organic material such as soluble bonito fish waste through the MPM method should be carefully managed. It is important to maintain the required conditions (such as a continuous aeration and small additions of organic matters) in each reaction tank as they also affect the microbial mineralization during the decomposition process. In addition, the calcium carbonate present in oyster shells facilitates the nitrification of NH4+ into NO3− [54]. Therefore, soaking oyster shells during the MPM decomposition process or incorporating them at the base of tomato plants to enhance the nitrification process may help prevent an excessive increase in NH4+ concentration. Another option is an external treatment that could increase the plant tolerance to NH4+ toxicity. As in the previous study, feeding enhanced CO2 to the plant is suggested to maintain appropriate photosynthetic C assimilation to cope with the NH4+ accumulated in plant tissue [48]; although it does not improve tomato NH4+ tolerance, it notably regulates plant metabolism depending on the nitrogen source and dose [55].

5. Conclusions

Organic fertilizer derived from soluble bonito fish waste through the MPM method could be used in tomato hydroponic cultivation as it continuously generates nitrate during cultivation. However, it was found that the fresh yield produced with OF was 11.7% lower than that with the CF treatment, and TDM was 33.7% lower than that with the CF. The difference in growth and yield is due to a decrease in TDM, which is caused by reduced light interception resulting from a lower LAI. Given the concerns of high NH4+ concentrations reducing yield and quality in tomatoes using organic fertilizer derived from soluble bonito fish waste, it is necessary to improve the management of MPM methods that can suppress increases in this concentration. This can be achieved by maintaining the required conditions, for example, via continuous aeration and the addition of small amounts of organic matter, and/or by adding oyster shells to the decomposition tank to enhance the nitrification process.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/horticulturae11040381/s1, Figure S1. (A) A representative electropherogram obtained from CE by measuring the content of citric acid and sugar (glucose, fructose, and sucrose). (B) A representative chromatogram obtained from HPLC by measuring the content of amino acids (aspartate, glutamate, and GABA). Figure S2. The daily average environment data (temperature inside the greenhouse, outside radiation, and CO2 concentration) during the cultivation.

Author Contributions

Conceptualization: D.F.R., K.M. and D.-H.A.; methodology: D.F.R., K.M. and M.S.; software: D.F.R. and K.M.; validation: D.F.R. and K.M.; formal analysis: D.F.R., K.M., Y.Y. and H.U.; investigation: D.F.R. and K.M.; resources: D.F.R., K.M., M.S. and D.-H.A.; data curation: D.F.R.; writing—original draft preparation, D.F.R.; writing—review and editing: D.F.R., K.M., Y.Y., H.U. and D.-H.A.; visualization, D.F.R. and K.M.; supervision: D.F.R., K.M. and D.-H.A. All authors have read and agreed to the published version of the manuscript.

Funding

This research is supported by a collaboration project of the National Agriculture and Food Research (NARO) with Asahi Kasei Corporation, Japan.

Data Availability Statement

Data is contained within the article and Supplementary Materials.

Conflicts of Interest

The authors declare no conflicts of interest.

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Horticulturae 11 00381 g001
Figure 1. Concentration of nitrate (NO3−), nitrite (NO2−), and ammonium (NH4+) ions in the organic nutrient solution derived from soluble bonito fish waste supplied during tomato cultivation.
Figure 1. Concentration of nitrate (NO3−), nitrite (NO2−), and ammonium (NH4+) ions in the organic nutrient solution derived from soluble bonito fish waste supplied during tomato cultivation.
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Figure 2. Aboveground plant biomass and photosynthetic rate. TY (A), TDM (B), LAI (C), and maximum photosynthesis rate (Pmax) (D) in each treatment (OF and CF). The (*/***) symbols mean that the average values are significantly different between treatments with p values < 0.05 and <0.001, respectively. The (NS) letters mean that the values are not significantly different. The horizontal line inside the boxes represents the median, the (◦) symbol represents each sample, and the whiskers above and below the boxes represent the lower and upper values.
Figure 2. Aboveground plant biomass and photosynthetic rate. TY (A), TDM (B), LAI (C), and maximum photosynthesis rate (Pmax) (D) in each treatment (OF and CF). The (*/***) symbols mean that the average values are significantly different between treatments with p values < 0.05 and <0.001, respectively. The (NS) letters mean that the values are not significantly different. The horizontal line inside the boxes represents the median, the (◦) symbol represents each sample, and the whiskers above and below the boxes represent the lower and upper values.
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Figure 3. Tomato fruit quality in each treatment (CF and OF). The green color represents the OF treatment while the blue color represents the CF treatment. The (***) symbols shown mean that the values are significantly different between treatments with a p value < 0.001. The (NS) letters shown mean that the values are not significantly different between treatments. The horizontal line inside the boxes represents the median, the (◦) symbol represents each sample, and the whiskers above and below the boxes represent the lower and upper values.
Figure 3. Tomato fruit quality in each treatment (CF and OF). The green color represents the OF treatment while the blue color represents the CF treatment. The (***) symbols shown mean that the values are significantly different between treatments with a p value < 0.001. The (NS) letters shown mean that the values are not significantly different between treatments. The horizontal line inside the boxes represents the median, the (◦) symbol represents each sample, and the whiskers above and below the boxes represent the lower and upper values.
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Table 1. Nutrient solution composition.
Table 1. Nutrient solution composition.
CompositionUnitOF RawOF (MPM)CF
ECmS cm−115.40.662.4
Cl−mg L−1360079-
NO3−-Nmg L−1<0.2220.71239
SO42−-Smg L−11305.47-
PO43−-Pmg L−1300048.8670.25
NH4+-Nmg L−112020.436
K+mg L−1180043.43398.45
Na+mg L−1110037.71-
Ca2+mg L−177022.14164.22
Mg2+mg L−1608.0636.18
Femg L−1400.282.3
Mnmg L−1100.110.58
Momg L−10.11<0.05-
Znmg L−13.80.280.09
Cumg L−10.940.10<0.05
Bmg L−14.90.130.34
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Rachma, D.F.; Maeda, K.; Yamanouchi, Y.; Ueda, H.; Shinohara, M.; Ahn, D.-H. Tomato Production with Organic Fertilizer from Soluble Bonito Fish Waste in Hydroponic Cultivation Systems. Horticulturae 2025, 11, 381. https://doi.org/10.3390/horticulturae11040381

AMA Style

Rachma DF, Maeda K, Yamanouchi Y, Ueda H, Shinohara M, Ahn D-H. Tomato Production with Organic Fertilizer from Soluble Bonito Fish Waste in Hydroponic Cultivation Systems. Horticulturae. 2025; 11(4):381. https://doi.org/10.3390/horticulturae11040381

Chicago/Turabian Style

Rachma, Dannisa Fathiya, Kazuya Maeda, Yuta Yamanouchi, Hiroshi Ueda, Makoto Shinohara, and Dong-Hyuk Ahn. 2025. "Tomato Production with Organic Fertilizer from Soluble Bonito Fish Waste in Hydroponic Cultivation Systems" Horticulturae 11, no. 4: 381. https://doi.org/10.3390/horticulturae11040381

APA Style

Rachma, D. F., Maeda, K., Yamanouchi, Y., Ueda, H., Shinohara, M., & Ahn, D.-H. (2025). Tomato Production with Organic Fertilizer from Soluble Bonito Fish Waste in Hydroponic Cultivation Systems. Horticulturae, 11(4), 381. https://doi.org/10.3390/horticulturae11040381

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