Integrated Soil Fertility Management Enhances Soil Properties, Yield, and Nitrogen Use Efficiency of Rice Cultivation: Influence of Fertilizer Rate, Humic Acid, and Gypsum

Abstract

Integrated soil fertility management is essential for improving soil productivity, rice yield, and nitrogen use efficiency (NUE). This study investigated the combined effects of the chemical fertilizer rate, humic acid (HA), and flue gas desulfurization gypsum (FG) on the soil chemical properties, rice yield, NUE, and nitrogen agronomic efficiency (NAE) in acidic paddy soil. The following three factors were evaluated: (1) fertilization based on farmer practices and rice nutrient requirements; (2) HA at 0 and 975 kg ha⁻¹; and (3) FG at 0, 23, and 636 kg ha⁻¹. Fertilization based on rice requirements reduced the nitrogen (N) input by 14.5% compared to farmer practices while still maintaining similar grain yields. Under farmer practice, HA enhanced total N content, cation exchange capacity (CEC), rice yield, NUE, and NAE. HA with FG (636 kg ha⁻¹) increased total organic carbon (TOC) levels, total N levels, and exchangeable ammonium nitrogen (NH₄-N), but decreased the yield. In contrast, HA combined with FG at 23 kg ha⁻¹ enhanced the soil exchangeable Ca and S levels, as well as resulting in a high rice yield (7.7 t ha⁻¹), NUE (39%), and NAE (32 kg kg⁻¹). The findings suggest that to maintain farmer fertilization practices while improving soil properties and rice yield, HA should be applied with FG (23 kg ha⁻¹).

1. Introduction

Rice is a staple food and a major contributor to food security; this is particularly true in Asia, where it is not only widely cultivated and consumed but also supports millions of livelihoods [1]. Various nutrient and soil fertility management strategies have been employed to maximize rice yield and enhance fertilizer use efficiency. Generally, farmers in developed countries, such as those in Thailand, commonly rely on conventional nutrient management based on their personal experience, knowledge, or perception rather than scientifically informed approaches [2,3]. Consequently, these practices often fail to align with actual crop nutrient requirements, resulting in a low nitrogen use efficiency (NUE) and agronomic efficiency (NAE). To exemplify, the over-fertilization of N under farmer practices in China (205 N kg ha⁻¹) in late-season rice crops led to a reduced rice yield and a lower NUE (22%) and NAE (6 kg kg⁻¹) compared to a nutrient expert system, which achieved a higher NUE (33%) and NAE (20 kg kg⁻¹) [4]. This highlights the inefficiency of excessive fertilizer inputs, which contributed to both economic loss and environmental degradation [5]. The low yield and use efficiency of applied fertilizers under farmer practices have presented significant opportunities for improvement in order to enhance the NUE and NAE of farmer practices. The improvement strategies of NUE and NAE are vital for sustainable rice production, as they increase yield and decrease nutrient inputs, thereby enhancing the beneficial returns to farmers.

Aligning fertilizer application to crop nutrient requirements is the key to success in obtaining optimum nutrient application rates and achieving the targeted yield [6]. Previous studies have revealed that when the fertilizer input falls in line with crop nutrient requirements, targeted yields and optimized NUE values are achieved in numerous crops, including rice and maize [7,8]. The amounts of nutrients required to attain targeted yield vary among plant species and varieties [9,10]. For instance, producing 1 ton of grain requires approximately 14 kg N ha⁻¹ for Indica hybrid rice and 18 kg N ha⁻¹ for Japonica rice [9]. A study by Sukitprapanon et al. [11] reported that Sakon Nakhon glutinous rice in Thailand absorbs about 21 kg N ha⁻¹ per 1 ton of grain produced.

Integrated soil fertility management (ISFM) practice entails the integration of inorganic, organic, and natural nutrient resources and agronomic practices in order to enhance soil fertility and promote crop productivity and sustainability [12]. ISFM has been widely adopted to improve long-term soil health while minimizing environmental impact by reducing the chemical fertilizer input [13,14]. Its key components include inorganic fertilizers, organic amendments (e.g., compost, manure, green manure, and cover crops), and locally accessible soil amendments (e.g., biochar, humic acid (HA), gypsum, and lime). In principle, ISFM incorporates at least two of these components [15]. However, the use of organic amendments as one of the ISFM components possesses a slow onset effect since they initially undergo a decomposition process to produce humic substances [16]. This slow onset effect can be accelerated by adding a pre-made HA into the soil as a soil amendment.

HA is a major component of humic substances, which are formed after the decomposition of organic matter. The extraction of HA can be enhanced by sourcing it from various organic materials, which contain the following percentages of HA: sugarcane waste compost (49%), vermicompost (6–8%), farmyard manure (4%), chicken dung compost (5%), sewage sludge (31%), and leonardite (30–56%) [17,18]. Leonardite is mainly used for global HA production because of its natural abundance, cost-effectiveness, high HA content, and high amounts of plant nutrients, such as N [19]. HA also supplies additional carbon to promote total organic carbon (TOC) accumulation in soils [20]. In addition, HA improves soil structure, acting as a binding agent that binds soil particles to form microaggregates, which accelerate soil aggregate formation [21]. The functional groups of HA, such as carboxylic (R-COOH) and phenolic (R-OH) groups, form complexes and chelate more exchangeable cations, resulting in an enhanced cation exchange capacity (CEC), which is linked to a high nutrient retention in soils [22]. HA has a positive effect on N cycling by enhancing N availability and reducing its loss, as it delays the oxidation of ammonium (NH₄⁺) to nitrate (NO₃⁻) [23]. Therefore, the application of HA has been shown to boost soil nutrient turnover, nutrient uptake, yield, and the NUE of crops, such as maize, wheat, and rice [24,25,26].

Flue gas desulfurization gypsum (FG), which is a by-product of coal combustion in power plants, is locally accessible, abundant, and cost-effective as a soil amendment. The application of FG can improve the levels of extractable calcium (Ca) and sulfur (S) in soils, particularly acidic soils that are deficient in Ca [27,28]. The Ca released from FG displaces the exchangeable bases (e.g., Mg, K, and Na) in topsoil, allowing them to move downward in the soil profile [29]. The Ca, which is derived from FG, promotes soil aggregate formation and clay flocculation [30]; in addition, it plays a role in N translocation and enhances NUE in plants [31].

Previous studies have shown that the coapplication of HA and FG to salt-affected soils positively affected not only the soil properties (e.g., electrical conductivity (EC), TOC, water-stable macroaggregate, and available water content) but also the crop yield (e.g., rapeseed and rice) [32,33,34,35]. The coapplication of HA and FG can achieve better N retention [36]. The incorporation of HA with FG in coastal saline soil improved rice yield by 10%, mitigated greenhouse gas emissions by 32%, and enhanced NUE by 27% [35]. Previous studies have applied HA mixed with FG in salt-affected soils, where the Ca from FG was prominent in relation to sodium displacement. In contrast, under highly acidic paddy soil conditions such as those in Thailand, FG has been recognized as supplying Ca and promoting root development [28]. Although the coapplication of HA and FG has been shown to increase the levels of exchangeable Ca and S [28], its effect on N dynamics in acidic paddy soil systems remains poorly understood. Prior research has not addressed the coapplication of HA with FG in relation to the application rate being tailored to site-specific soil properties conditions (e.g., clay content and Ca deficiency) and the crop’s nutrient requirements (e.g., Ca demand per ton of rice yield), especially in strongly acidic paddy soil. Furthermore, to our knowledge, no study has examined the combined applications of fertilizer, HA, and FG on soil properties, yield, NUE, and NAE in highly acidic paddy soil with an inherent Ca deficiency.

Therefore, this study hypothesized that the interaction effect of soil fertilization based on crop nutrient requirement with HA and an optimal FG rate can effectively increase TOC, CEC, exchangeable forms of NH₄-N (NH₄-N), Ca, and S; NUE; and NAE for rice production in highly acidic paddy soil compared to farmer-based fertilization alone. This study aims to evaluate the individual and interactive effects of fertilizer, HA, and FG on soil properties, yield, NUE, and NAE in a highly acidic paddy soil with a Ca deficiency; identify the optimal combination of HA and FG in order to maximize NUE and NAE under different fertilization regimes; and assess the relationship between rice yield and NUE, as well as rice yield and NAE for rice cultivation in an acidic paddy soil. This study contributes to effective site-specific ISFM practices that enhance rice production while decreasing the use of chemical fertilizers, thus promoting sustainable agriculture and a healthier environment.

2. Materials and Methods

2.1. Site Characteristics

A pot experiment was conducted from August 2022 to January 2023 in a greenhouse at the Soil and Fertilizer Research Station, Khon Kaen University, Khon Kaen, Thailand. The initial soil used in this study was collected from a paddy field in Khon Kaen, Thailand (UTM: 48Q 256,751 E, 1,827,796 N), which is topographically 187 m above sea level. The study area was under a tropical savanna climate, with an average maximum temperature of 32 °C and a minimum temperature of 21 °C. The cumulative precipitation during the experiment totaled 412 mm [37]. The paddy soil used in this study was classified as Aeric Kandiaquult according to Soil Taxonomy [38]. The topsoil (0–15 cm) is a sandy loam with sand, silt, and clay contents of 583, 359, and 58 g kg⁻¹, respectively. The initial soil was acidic (pH 4.7) and had low levels of EC (0.08 mS cm⁻¹), TOC (1.6 g kg⁻¹), and CEC (2.6 cmol kg⁻¹), as well as a base saturation of 34.6%. The initial soil contained exchangeable ammonium nitrogen (NH₄-N) (23 mg kg⁻¹), exchangeable nitrate nitrogen (NO₃-N) (12 mg kg⁻¹), exchangeable Ca (95 mg kg⁻¹), and exchangeable S (37 mg kg⁻¹). Additionally, the soil had total N, Ca, and S concentrations of 0.56, 0.28, and 0.14 g kg⁻¹, respectively (

Table 1. Characteristics of soil, humic acid, and flue gas desulfurization gypsum used in this study [28].

Property	Initial Soil	Humic Acid	FG
Soil classification	Aeric Kandiaquult	-	-
Soil texture	Sandy loam	-	-
Sand (g kg−1)	583	-	-
Silt (g kg−1)	359	-	-
Clay (g kg−1)	58	-	-
pH	4.7	9.8	7.7
EC (mS cm−1)	0.08	8.3	3.3
TOC (g kg−1)	1.6	291	-
CEC (cmol kg−1)	2.6	57	-
Base saturation (%)	34.6	-	-
NH4-N (mg kg−1)	23	-	-
NO3-N (mg kg−1)	12	-	-
Exchangeable Ca (mg kg−1)	95	-	-
Exchangeable S (mg kg−1)	37	-	-
Water soluble Ca (g kg−1)	-	-	141
Total N (g kg−1)	0.56	11	0.12
Total Ca (g kg−1)	0.28	9.4	388
Total S (g kg−1)	0.14	6.7	199

HA = humic acid; FG = flue gas desulfurization gypsum; EC = electrical conductivity; TOC = total organic carbon; CEC = cation exchange capacity; NH₄-N = exchangeable ammonium nitrogen; NO₃-N = exchangeable nitrate nitrogen; Total N = total nitrogen; Total Ca = total calcium; Total S = total sulfur.

) [28].

2.2. Greenhouse Experiment

The experimental design was arranged in a 2 × 2 × 3 factorial in a randomized complete block design with three replications. Three factors for ISFM were employed. The first factor was chemical fertilizer at two application rates, including rates pertaining to farmer practices (FP) and those pertaining to rice nutrient requirements (NR). According to a study by Sukitprapanon et al. [11], the N, P₂O₅, and K₂O nutrient inputs pertaining to farmer practice were 75, 38, and 38 kg ha⁻¹, while those relating to rice nutrient requirements were 61, 25, and 12 kg ha⁻¹, respectively. The N input was set at 61 kg ha⁻¹, based on the targeted yield of 2.9 tons ha⁻¹. As previously reported by Sukitprapanon [11], rice (Sakhon Nakhon variety) grown in Thailand required 21 kg N ha⁻¹ for 1 ton of rice production. The applied chemical fertilizer was prepared from urea (46-0-0), diammonium phosphate (DAP) (18-46-0), and muriate of potash (MOP) (0-0-60) at a rate of 131, 81, and 63 kg ha⁻¹ for farmer practice and at a rate of 112, 53, and 19 kg ha⁻¹ for rice nutrient requirement, respectively. Compared to the nutrient input based on farmer practices, the chemical fertilizer applied based on rice requirement declined by 14.5, 34.6, and 69.8% for urea, DAP, and MOP, respectively.

The second factor was HA incorporation. The HA used in this study was produced from leonardite, which was obtained from Concurchem Co., Ltd., Bang Yai District, Nonthaburi, Thailand. The HA was strongly alkaline (pH 9.8) and contained an elevated level of EC (8.3 mS cm⁻¹), as well as elevated contents of TOC (291 g kg⁻¹), CEC (57 cmol kg⁻¹), total N (11 g kg⁻¹), total Ca (9.4 g kg⁻¹), and total S (6.7 g kg⁻¹) (Table 1). The HA application included two levels: no HA and HA applied at a rate of 975 kg ha⁻¹ (HA), which provided an input of 10.68 kg ha⁻¹ of N in organic form. This HA application rate was acquired from the optimum rate for rice production in paddy soils in Northeast Thailand, which was found in a previous study by Sukitprapanon et al. [11]. The HA was applied in a solid form (powder) and was thoroughly incorporated into the soil prior to rice transplantation.

The last factor was FG application rates. The FG used in this study was obtained from Mae Moh Power Plant, Electricity Generating Authority of Thailand, Mae Moh District, Lampang Province, Thailand. The FG used in the study was neutral (pH H₂O of 7.7) and rich in total concentrations of Ca (388 g kg⁻¹) and S (199 g kg⁻¹) (Table 1). Three rates of FG application were used: no FG; application based on the amount of Ca required by rice (23 kg FG ha⁻¹) (FG23); and an application rate based on gypsum requirements (GR) for high-acidity soil (636 kg ha⁻¹) (FG636). These rates lead to total N contents in the soil of 0, 0.003, and 0.08 kg ha⁻¹, respectively. The FG application rates were selected to compare different strategies of alleviating Ca deficiency in acidic paddy soil. The FG at 23 and 636 kg ha⁻¹ represent the crop requirement supply and soil-based correction strategies, respectively. The Ca required by rice was suggested by Sukitprapanon et al. [11]. Rice cultivated in Thailand required 3.19 kg Ca ha⁻¹ for a 2.9 ton total of grain production [11]. In this study, FG was applied at a rate of 23 kg ha⁻¹ based on water-soluble Ca concentration in the studied FG (141 g kg⁻¹) (Table 1) to meet Ca required by rice. Although the soil used in this experiment was collected from the 0 to 15 cm layer, the GR was calculated using the clay content (106 g kg⁻¹) at a depth of 20–40 cm [11], where the Ca deficiency is more pronounced and gypsum is expected to exert its primary effects on subsoil improvement. The GR was calculated by multiplying the clay content (g kg⁻¹) by 6 and dividing the result by 1000, as suggested in several previous studies [28,39,40]. Moreover, the GR method is typically applied to low-acidity soil [39,40]. This study adopted the GR method for the application of FG in high-acidity soil based on the regional soil clay content to increase the Ca concentration of acidic soils in Thailand.

A summary of the total N input from chemical fertilizer, HA, and FG is shown in

Table 2. The amounts of nutrient nitrogen input (kg ha⁻¹) from chemical fertilizer, humic acid, and flue gas desulfurization gypsum used in this study.

Treatment	Nitrogen Input (kg ha−1)
	Fertilizer	HA	FG	Total
FP	75	0	0	75
FP + FG23	75	0	0.003	75.003
FP + FG636	75	0	0.08	75.08
FP + HA	75	10.68	0	85.68
FP + HA + FG23	75	10.68	0.003	85.683
FP + HA + FG636	75	10.68	0.08	85.76
NR	61	0	0	61
NR + FG23	61	0	0.003	61.003
NR + FG636	61	0	0.08	61.08
NR + HA	61	10.68	0	71.68
NR + HA + FG23	61	10.68	0.003	71.683
NR + HA + FG636	61	10.68	0.08	71.76

HA = humic acid; FG = flue gas desulfurization gypsum; FP = fertilizer application rate based on farmer practices; NR = fertilizer application rate based on rice nutrient requirements; HA = HA application at 975 kg ha⁻¹; FG23 = FG application rate based on Ca required by rice at 23 kg ha⁻¹; FG636 = FG application rate followed gypsum requirement at 636 kg ha⁻¹.

. In this study, three pots without added fertilizer, HA, and FG were set aside for the analyses of NUE and NAE. Soil amendments were incorporated and incubated for 14 days before rice transplantation. Half a dose of N and a full dose of P₂O₅ and K₂O were applied 7 days after transplantation, while the remaining half of the N dose was applied at the panicle stage, which was approximately 65 days after planting (DAP).

The rice (Oryza sativa L.) (Sakon Nakhon variety) was sown in a plastic tray filled with soil. After 14 days, the seedlings demonstrating similar growth were selected and transplanted to a pot with dimensions of 30 cm length × 30 cm width × 39 cm height, at 20 cm spacings. The soil was kept under a waterlogged condition at 5 cm water height above the soil surface from the transplantation stage to 7 days before harvest. Crop management practices, including seed selection, seedling transplanting, weeding, pest and disease control, and harvesting, followed the recommendations of the Thai Department of Agriculture [41]. The grain yield, straw, and root biomass from each pot were recorded at harvest (128 DAP). The rice grain, straw, and root were cleaned with deionized water (DI water) and stored in sample paper bags, which were transported to the laboratory. All parts of the rice were oven-dried at 65 °C until they reached a constant weight. The oven-dried samples were then finely ground using a plant grinder for total N concentration analysis.

2.3. Soil Sampling

Soil samples were collected from the pot after rice was harvested (128 DAP) and were divided into two subsamples, including air-dried and field-moist soil samples. The air-dried soil samples were ground and sieved through a 2 mm sieve, while the field-moist soil samples were packed in plastic containers and immediately refrigerated at 4 °C to minimize microbial activity.

2.4. Laboratory Analyses

2.4.1. Humic Acid and Flue Gas Desulfurization Gypsum Analyses

The pH and EC of both HA and FG were determined using a 1:5 soil amendment-to-DI water ratio [42]. Total N and TOC analyses were performed using dry combustion with a CN analyzer (Multi N/C 2100s, Analytik Jena GmbH, Jena, Germany). The CEC of HA was determined using 1 M ammonium acetate (NH₄OAc) at pH 7 [43]. Water-soluble Ca in the FG was determined according to the method of Soil Survey Staff [44]. Briefly, 50 g of FG was mixed with 50 mL of DI water and shaken on an end-over-end for 1 h. The suspension was filtered through a Whatman No. 1 filter paper. The concentration of water-soluble Ca was measured using inductively coupled plasma–optical emission spectroscopy (ICP-OES) (Analytic Jena PQ 9000, Analytik Jena GmbH, Jena, Germany). Total Ca and S concentrations in HA were analyzed using hot acid digestion (7 mL of HClO₄ at 190 °C until the color of the suspension was clear) [42], while those for FG were determined using aqua regia (3:1 HCl:HNO₃ at 130 °C for 1 h) [45]. The concentrations of Ca and S were measured via ICP-OES (Analytic Jena PQ 9000, Analytik Jena GmbH, Jena, Germany).

2.4.2. Soil Analyses

The soil pH and redox potential (Eh) under field conditions were measured at the harvesting stage (128 DAP) using a portable pH meter (HI 98103, Hanna Instruments, Woonsocket, RI, USA) and an oxidation-reduction potential (ORP) meter (HI 8424, Hanna Instruments, Woonsocket, RI, USA), respectively. Both soil pH and Eh were measured by inserting the electrode of the respective instrument directly into the moist soil at a depth of approximately 5 cm. The pH value was recorded once the reading stabilized. The Eh was recorded directly in millivolts (mV). Air-dried soil samples were analyzed for particle size distribution, total N, TOC, exchangeable Ca, and CEC. The particle size distribution of the initial soil was determined using the pipette method [46]. Total N and TOC were determined using dry combustion with a CN analyzer (Multi N/C 2100s, Analytik Jena GmbH, Jena, Germany). Exchangeable Ca and CEC were analyzed using 1 M NH₄OAc at pH 7 [43]. The total Ca and S concentrations were determined using aqua regia digestion (1:3 HNO₃:HCl at 130 °C for 1 h) [45], and their concentrations were determined using ICP-OES (Analytic Jena PQ 9000, Analytik Jena GmbH, Jena, Germany).

Field-moist soil samples were prepared for exchangeable S, NH₄-N (NH₄-N), and NO₃-N (NO₃-N) analysis. The exchangeable S concentration was extracted with Mehlich-3 solution and quantified using ICP-OES (Analytic Jena PQ 9000, Analytik Jena GmbH, Jena, Germany) [43]. NH₄-N and NO₃-N were extracted using 2 M KCl and 0.5 M K₂SO₄, respectively. The NH₄-N concentration was determined using salicylate–sodium hypochlorite, while NO₃-N was determined using salicylic acid–sodium hydroxide [47]. The concentration of NH₄-N and NO₃-N was determined using the colorimetric method using a spectrophotometer (SP-UV 300, PerkinElmer Inc., Waltham, MA, USA) at 650 and 410 nm, respectively [47].

2.4.3. Plant Analyses

The plant samples, including grain, straw, and root biomass, were digested using hot acid digestion with 7 mL of HClO₄ at 190 °C until the color of the suspension became clear [42]. The N concentration in the solution was determined using the Kjeldahl distillation method [47]. The total N uptake in rice was computed by multiplying the N concentration in grain, straw, and root by the oven-dried biomass.

The NUE was determined by the difference in total N uptake, which was derived from grain, straw, and root biomass, between pots that received fertilizer and soil amendments and those that did not receive any fertilizers and soil amendments, as explained in Equation (1) [28].

$$\mathrm{NUE} (\%)={\displaystyle \frac{\mathrm{Nf}-\mathrm{Nu}}{\mathrm{Total} \mathrm{amount} \mathrm{of} \mathrm{N} \mathrm{applied} (\mathrm{kg} {\mathrm{ha}}^{-1})}}\times 100$$

(1)

Here, Nf is the amount (kg ha⁻¹) of total N uptake of rice in the pot with fertilizer and soil amendments. Nu is the amount (kg ha⁻¹) of total N uptake of rice in the pot without fertilizer and soil amendments.

The NAE, i.e., the grain production per unit of fertilizer applied, was calculated according to the ratio of the difference in the grain yield of the fertilized pot and unfertilized pot compared to the total amount of N applied, as shown in Equation (2) [28].

$$\mathrm{NAE} (\mathrm{kg} {\mathrm{kg}}^{-1})={\displaystyle \frac{\mathrm{Gf}-\mathrm{Gu}}{\mathrm{Total} \mathrm{amount} \mathrm{of} \mathrm{N} \mathrm{applied} (\mathrm{kg} {\mathrm{ha}}^{-1})}}$$

(2)

Here, Gf is the amount (kg ha⁻¹) of grain yield of the pot with fertilizer and soil amendments. Gu is the amount (kg ha⁻¹) of grain yield of the pot without fertilizer and soil amendments.

2.5. Statistical Analyses

All data were analyzed using a three-way analysis of variance (ANOVA) along with mean comparisons using the least significant difference (LSD) test (p < 0.05) to determine the effect of fertilizer, HA, FG, and their interactions on soil properties and rice yields. The data describing the relationship between yield components and agronomic attributes were analyzed using principal component analysis (PCA) and regression analysis at p < 0.05. Data analyses were conducted using Statistica software version 8.0, while graphical visualizations were created using SigmaPlot version 11 and OriginPro 2018 version 9.5.

3. Results and Discussion

3.1. Effects of Fertilizer, Humic Acid, and Gypsum Application on Soil Properties

The effects of fertilizer, HA, and FG application on paddy soil properties are shown in

Table 3. Soil properties influenced by applications of fertilizer, humic acid, and flue gas desulfurization gypsum under rice cultivation in an acidic paddy soil.

Soil Properties	Soil pH	Eh	TOC	CEC	Total N	Total Ca	Total S	NH4-N	NO3-N	Exc. Ca	Exc. S
		(mV)	(g kg−1)	(cmol kg−1)	(g kg−1)	(mg kg−1)
Fertilizer (F)
FP	6.8	−100	2.3	3.1 a	1.5 a	409 b	686	16 b	5.2 a	280	57
NR	6.9	−110	2.3	2.2 b	1.4 b	514 a	718	19 a	4.4 b	295	63
p value	0.448	0.217	0.168	<0.001	0.052	<0.001	0.442	0.013	0.023	0.173	0.167
Humic acid (HA)
No HA	6.8	−97	2.2 b	2.3 b	1.4 b	423 b	653 b	17	5.2 a	286	60
HA	6.8	−113	2.3 a	3.0 a	1.6 a	500 a	751 a	19	4.4 b	290	60
p value	0.913	0.064	0.003	<0.001	<0.001	0.004	0.023	0.109	0.038	0.741	0.928
Gypsum (FG)
No FG	7	−104	2.3	2.7 ab	1.4	450	645 b	18 ab	4.2 b	284 b	54 b
FG23	6.8	−101	2.2	2.4 b	1.5	442	683 ab	15 b	5.7 a	329 a	77 a
FG636	6.8	−111	2.3	2.8 a	1.5	492	779 a	20 a	4.6 b	250 c	50 c
p value	0.122	0.514	0.136	0.023	0.404	0.211	0.037	0.001	0.012	<0.001	<0.001
Interactions (p value)
F × HA	0.238	0.343	0.32	0.099	0.01	<0.001	0.008	0.089	0.362	<0.001	0.751
F × FG	0.721	0.577	0.143	0.45	0.696	0.388	<0.001	0.116	0.028	0.085	0.352
HA × FG	0.802	0.174	0.319	0.006	0.003	0.005	0.043	0.004	0.024	<0.001	0.158
F × HA × FG	0.313	0.697	0.379	<0.001	<0.001	0.008	0.141	0.267	0.681	0.018	0.682

HA = humic acid; FG = flue gas desulfurization gypsum; FP = fertilizer application rate based on farmer practices; NR = fertilizer application rate based on rice nutrient requirements; HA = HA application at 975 kg ha⁻¹; FG23 = FG application rate based on Ca required by rice at 23 kg ha⁻¹; FG636 = FG application rate based on gypsum requirement at 636 kg ha⁻¹. Eh = field redox potential; TOC = total organic carbon; CEC = cation exchange capacity; Total N = total nitrogen; Total Ca = total calcium; Total S = total sulfur; NH₄-N = exchangeable ammonium nitrogen; NO₃-N = exchangeable nitrate nitrogen; Exc. Ca = exchangeable calcium; Exc. S = exchangeable sulfur. Mean values followed by different letters show significant differences at p < 0.05.

and Figure 1 and Figure 2.

After harvest, the soil pH ranged from 6.6 to 7.2 and was not influenced by the applications of chemical fertilizer, HA, and FG, or their combinations (Table 3) (Figure 1a). However, the soil pH values increased by approximately 40% to 53%, compared to the initial soil pH (4.7) (Table 1). The alteration in soil pH is related to the reduction in elements, particularly ferric iron (Fe³⁺) to ferrous iron (Fe²⁺); manganic (Mn⁴⁺) to manganous (Mn²⁺); sulfate (SO₄²⁻) to hydrogen sulfide (H₂S); and carbon dioxide (CO₂) to methane (CH₄), under waterlogged conditions, which consume protons and raise pH levels [48,49,50]. In this study, the soil pH was not responsive to the sole addition of HA or FG or the co-application of HA + FG due to the negative charges of HA being more likely to form a complex and increase soil CEC rather than altering the soil pH (Table 3). FG is a neutral salt (pH 7.7) (Table 1), which does not neutralize the soil pH. Similarly, the coapplication of HA + FG did not alter soil pH in acidic paddy soil [28]. In contrast, previous studies reported that the coapplication of HA + FG in salt-affected soil led to a reduction in the soil pH [33]. Under these conditions, FG releases sulfate (SO₄), while HA induces microbial activity in order to produce organic acid or sulfate transformation, which leads to acidification [33]. The contrast in the soil pH response highlights that the effect of the coapplication of HA + FG on soil pH is dependent on the soil conditions.

The soil Eh was also unaffected by chemical fertilizer, HA, and FG. The soil Eh ranged from −141 to −85 (Figure 1b). These values indicate that the studied soils are under reducing conditions, commonly observed under anaerobic conditions where soil microbes utilize alternative electron acceptors to compensate for the lack of oxygen [51].

TOC was neither affected by fertilizer nor FG. However, the TOC was affected by HA addition (Table 3). The TOC in soil treated with HA (2.3 g kg⁻¹) was higher compared to those without HA (2.2 g kg⁻¹). The integrated use of FP + HA + FG636 achieved the highest TOC (2.4 g kg⁻¹) (Figure 1c), likely due to HA being rich in stable organic carbon, which enhanced the TOC in the soil (Table 1). Additionally, FG-released Ca plays an important role in TOC stabilization and accumulation, as Ca—being a polyvalent cation—acts as a bridge between the negative charge of the clay particle and the organic colloids during the deprotonation of the carboxylic (COOH) and phenolic OH functional groups [52]. Likewise, a previous study has demonstrated that HA + FG promoted the TOC under both acid- and salt-affected soil conditions, primarily through their contribution to the retention of organic carbon [28,32].

The CEC was significantly improved by chemical fertilizer, HA, and FG application. Soil treated with FP, HA, and FG636 had higher CEC values (3.1, 3.0, and 2.8 cmol kg⁻¹, respectively) (Table 3). The interaction effect of FP + HA and HA + FG636 significantly elevated CEC to 3.3 and 3.4 cmol kg⁻¹, respectively (Figure 2a,b). The highest CEC was recorded under NR + HA + FG636 (3.5 cmol kg⁻¹) (Figure 1d). Chemical fertilizer indirectly raises soil CEC by promoting plant growth (e.g., root biomass) (

Table 4. Yield, total N uptake, and nitrogen use efficiency as influenced by applications of fertilizer, humic acid, and flue gas desulfurization gypsum under rice cultivation in acidic paddy soil.

Treatment	Straw Biomass	Root Biomass	Grain Yield	Total N Uptake	NUE	NAE
	(t ha−1)			(kg ha−1)	(%)	(kg kg−1)
Fertilizer (F)
FP	15.4	9.5 a	7.3	68	31 b	28
NR	14.7	8.1 b	7.1	67	36 a	30
p value	0.099	<0.001	0.23	0.657	0.008	0.234
Humic acid (HA)
No HA	14.9	9.3 a	7.0 b	65 b	30 b	25 b
HA	15.1	8.3 b	7.4 a	70 a	36 a	33 a
p value	0.73	0.014	0.004	0.013	0.004	<0.001
Gypsum (FG)
No FG	15.3	8.5 b	7.3	69	36	31 a
FG23	15.4	9.7 a	7.3	68	33	30 a
FG636	14.5	8.3 b	6.9	66	31	26 b
p value	0.12	0.011	0.094	0.429	0.101	0.034
Interactions (p-value)
F × HA	0.499	0.008	0.903	0.177	0.161	0.073
F × FG	0.243	0.257	0.368	0.334	0.853	0.631
HA × FG	0.662	0.027	0.768	0.053	<0.001	0.001
F × HA × FG	0.709	0.218	0.184	0.073	<0.001	0.012

HA = humic acid; FG = flue gas desulfurization gypsum; FP = fertilizer application rate based on farmer practices; NR = fertilizer application rate based on rice nutrient requirements; HA = HA application at 975 kg ha⁻¹; FG23 = FG application rate based on Ca required by rice at 23 kg ha⁻¹; FG636 = FG application rate based on gypsum requirement at 636 kg ha⁻¹. Total N uptake = total nitrogen uptake; NUE = nitrogen use efficiency; NAE = nitrogen agronomic efficiency. Mean values followed by different letters show significant differences at p < 0.05.

), which can contribute to an increased organic carbon input from the decaying of plant residues to the soil, as the soil was collected before the root biomass collection. Brar et al. [53] reported that the application of chemical fertilizer can contribute to a higher soil organic carbon pool due to higher root biomass. In addition, chemical fertilizer, particularly N, indirectly led to higher CEC values by stimulating microbial activity and consequently increasing microbial products (necromass and stable organic matter) accumulation [54]. Higher CEC values under HA + FG application are related to the increase in soil TOC. Our study has reported that CEC was positively related to TOC (R² = 0.13) (p < 0.05) (Figure 3a), indicating that the addition of organic matter, particularly HA, can increase CEC in the soils by providing negative charges, which are derived from its functional groups such as carboxylic and phenolic groups [11,22,55]. FG application helps to increase CEC in soils because Ca released from FG favors soil aggregate formation, which increases the surface area for cation exchange, thereby indirectly benefiting CEC [30]. This finding aligned with a previous study, which reported that the increase in CEC in highly acidic paddy soil following the co-application of HA + FG is attributed to the enhancement of the TOC level, which is due to their combined effects [28].

The total N levels ranged from 1.1 to 2.0 g kg⁻¹ (Figure 1e), with significant increases observed under farmer practice (1.5 g kg⁻¹) and HA (1.6 g kg⁻¹) (Table 3). The interaction effect of FP + HA and HA + FG636 significantly increased total N to 1.7 g kg⁻¹ and 1.8 g kg⁻¹, respectively (Figure 2c,d). The highest total N level was achieved by integrating FP + HA + FG636 (2.0 g kg⁻¹) (Figure 1e). The increase in total N in farmer practice and HA was due to FP supplying higher total N levels to the soil (Table 2) and HA containing a high N content (Table 1), respectively. The highest total N in FP + HA + FG636 was attributed to the fact that N was supplied by fertilizer, HA, and FG, with a total N input of 85.76 kg N ha⁻¹ to the soil (Table 2).

NH₄-N was significantly increased by the application of fertilizer, FG, and the combination of HA and FG (Table 3 and Figure 2e). NR and HA showed similar NH₄-N concentrations (19 mg kg⁻¹ for both), while the FG636 increased NH₄-N to 20 mg kg⁻¹ (Table 3). The HA + FG636 significantly elevated NH₄-N to 23 mg kg⁻¹ (Figure 2e).

NO₃-N was significantly affected by fertilizer, HA, FG, fertilizer × FG, and HA × FG (Table 3). The NO₃-N concentrations were notably increased either by FP (5.2 mg kg⁻¹) or FG23 (5.7 mg kg⁻¹) (Table 3). The FP + FG23 treatment slightly increases NO₃-N to 6.0 mg kg⁻¹ (Figure 2f). Both the sole HA (4.4 mg kg⁻¹) and FG636 (4.6 mg kg⁻¹) treatments, as well as their interactions in the HA + FG636 treatment, significantly reduced NO₃-N to 3.8 mg kg⁻¹ (Table 3) (Figure 2g), which is lower than in the initial soil (12 mg kg⁻¹) (Table 1). The bivariate relationship revealed that NH₄-N had a negative relationship with NO₃-N (R² = 0.11) (p < 0.05) (Figure 3b), indicating that when the HA and FG are incorporated into the soil, NH₄-N is adsorbed onto the soil surface of TOC, thereby preventing nitrification and resulting in NH₄-N accumulation in soils. The S derived from FG hindered NH₄-N transformation to NO₃-N by forming complexes with NH₄⁺ in order to form ammonium sulfate ((NH₄)₂SO₄) [56]. The HA can also adsorb NH₄-N due to its negative charge, which slows the transformation of NH₄-N to NO₃-N through nitrification, leading to a decrease in nitrogen losses through leaching, volatilization, and denitrification [23].

Although FG636 supplied 30-fold higher total Ca (492 mg kg⁻¹) levels in the soil, it did not increase the soil exchangeable Ca. Conversely, the application of FG23 increased the concentrations of exchangeable Ca to 329 mg kg⁻¹, which was 1.3-fold higher than that in FG636 (250 mg kg⁻¹) (Table 3). The HA + FG23 treatment significantly enhanced exchangeable Ca levels to 350 mg kg⁻¹ (Figure 2h). Exchangeable Ca concentrations after applying FG, especially FG23, increased by 1.6- to 2.5-fold (Table 3) higher than the initial soil (95 mg kg⁻¹) (Table 1). A higher amount of exchangeable Ca was achieved using the FP + HA + FG23 (355 mg kg⁻¹) treatment, which is not significantly different from that of the NR + HA + FG23 (345 mg kg⁻¹) treatment (Figure 1f). The low concentration of exchangeable Ca in the FG636 treatment is attributed to the excessive Ca supply inducing a chemical reaction in the soil; i.e., exchangeable Ca reacts with P to form calcium phosphate minerals such as brushite (Ca(PO₃OH)·2H₂O), which is not available to the plant [57,58]. Thus, this study suggested that a suitable FG application rate in paddy field conditions should be considered based on the Ca required by rice.

The total S levels were significantly improved by HA (751 mg kg⁻¹) and FG636 (779 mg kg⁻¹) application. However, despite FG636 inputting higher levels of S to the soil, the exchangeable S did not increase proportionally in FG636 (50 mg kg⁻¹). Exchangeable S levels were recorded to be higher under FG23-treated soil (77 mg kg⁻¹) (Table 3). The FG used in this study contained 19.9% of S (Table 1) and supplied 4.6 and 127 kg ha⁻¹ of S for FG23 and FG636, respectively, contributing to the increase in both total S and exchangeable S concentrations (Table 3). However, FG636 maximizes the total S concentration but results in a lower concentration of exchangeable S compared to that of FG23 due to the lower Eh value in FG636 (−111 mV) (Table 3). A higher FG application rate supplied more sulfate ions (SO₄²⁻) to the soil and served as an electron acceptor, producing hydrogen sulfide (H₂S), which led to a lower Eh. A higher reduction state transforms SO₄²⁻ to H₂S, which is prone to volatilization. Eventually, the exchangeable S depleted [59]. A study from Fuentes-Lara et al. [60] revealed that the excessive S addition under anaerobic conditions can be microbially reduced to H₂S, which is a phytotoxic substance that contributes to atmospheric pollution. Furthermore, the optimum S application for rice crop requirements is 10–30 kg ha⁻¹ of S per year [61]. In this study, FG636 supplied approximately 127 kg S ha⁻¹, which exceeded the S required by rice. This underscores the risk of environmental pollution through H₂S volatilization if excessive S is applied under flooded conditions. Therefore, this study highlights the importance of considering the FG application rate with soil redox condition in acidic paddy soil to minimize S losses and environmental risks.

3.2. Yield, Nitrogen Uptake, Nitrogen Use Efficiency, and Nitrogen Agronomic Efficiency of Rice

Straw biomass was not affected by fertilizer, HA, and FG, or their interactions (Table 4). Straw biomass ranged between 14 and 16 t ha⁻¹ (Figure 4). The highest straw biomass (16 t ha⁻¹) was observed under the FP, FP + HA, and FP + HA + FG23 treatments, whereas the lowest straw biomass was reported under the FP + FG636 and NR + FG636 (14 t ha⁻¹) treatments (Figure 4).

The root biomass was higher in the FP (9.5 t ha⁻¹) and no HA (9.3 t ha⁻¹) treatments compared to their corresponding counterparts at different rates (Table 4). Meanwhile, FG23 had the highest root biomass of 9.7 t ha⁻¹, compared to those treated with FG636 (8.3 t ha⁻¹) and no FG (8.5 t ha⁻¹) (Table 4). The interaction of fertilizer × HA and HA × FG significantly affected root biomass (Table 4). The FP + no HA and no HA + FG23 treatments significantly increased root biomass to 11 t ha⁻¹ (Figure 5a,b), while the FP + FG23 treatment showed the highest root biomass (13 t ha⁻¹) (Figure 4).

For grain yield, although fertilizer application showed a non-significant effect on grain yield, the requirement-based approach can reduce the amounts of N input by 14.5% without a significant decline in grain yield compared to farmer practice. Grain yield significantly increased with the addition of HA (7.4 t ha⁻¹) (Table 4). Although the rice grain yield was not responsive to the interaction of fertilizer, HA, and FG, this study found that both the FP + HA and FP + HA + FG23 treatments achieved the maximum grain yield (7.7 t ha⁻¹), whereas both FP + FG636 (6.8 t ha⁻¹) and NR + FG636 (6.6 t ha⁻¹) gained the minimum grain yield (Figure 4). Therefore, this study highlighted the fact that the application of FG at a high rate based on the gypsum requirement at 636 kg ha⁻¹ (FG636) restricts straw biomass and grain yield in the acidic paddy soil.

The total N uptake was significantly increased by HA (70 kg ha⁻¹) (Table 4). NUE was significantly influenced by both fertilizer application rates and HA. NR and HA increased NUE to 36% (Table 4), while the FP + HA + FG23 treatment resulted in the highest NUE (39%) under farmer practices (Figure 6a). Under rice nutrient requirement-based fertilization, the NR + HA + FG636 treatment maximizes the NUE to 46% (Figure 6a). NAE was significantly improved by HA and further enhanced by multiple interactions (fertilizer × HA, fertilizer × HA × FG, and HA × FG) (Table 4). Applying NR (30 kg kg⁻¹) tended to give higher NAE values than FP (28 kg kg⁻¹) and were significantly increased by HA addition (33 kg kg⁻¹) (Table 4). Both the FP + HA and FP + HA + FG23 treatments produced an optimal NAE (32 kg kg⁻¹) under farmer practices, whereas the NR + HA + FG636 practice maximized the NAE to 41 kg kg⁻¹ for rice grown under rice nutrient requirement-based fertilization (Figure 6b).

The application of fertilizer according to rice nutrient requirements reduces the use of chemical fertilizers without adversely affecting rice yield. NR provided an appropriate nutrient supply to achieve the optimum rice yield. Therefore, this study advocates nutrient applications based on crop nutrient requirements, such as rice, for its crucial role in achieving precision nutrient management and sustainability. The increase in grain yield in both the FP + HA and FP + HA + FG23 treatments is primarily due to the fact that HA application contributed to a higher grain yield, NUE, and NAE, primarily by stimulating the nutrient uptake (Table 4), as the HA incorporation increases the accumulation of soil nutrient availability like NH₄-N (Table 3).

Conversely, the FP + HA + FG636, FP + FG636, and NR + FG636 practices, where the FG was applied at a higher rate (636 kg ha⁻¹), tended to reduce rice yield. Previous studies reported the crop response to FG application at different rates to slightly acidic soil (pH 6.3–6.5) and revealed that FG applied at a higher rate led to a yield reduction because Ca, released from FG, induced nutrient imbalance and lower nutrient levels of P, K, and Mg uptake [28,62]. According to the current study, the decline in rice yield is related to FG636 releasing a large amount of Ca to the soil, which potentially inhibits N uptake, as was found in previous work, whereby Ca released from FG plays a crucial role in regulating N absorption [31,63]. In contrast, HA + FG incorporation into salt-affected soil increases rice yield by 10%, but these conditions differ from acidic paddy soil systems [35]. Our findings fill the knowledge gap by demonstrating that a similar effect can be achieved in acidic paddy soil if the FG rate is based on rice Ca demand rather than soil GR. Therefore, this finding suggests that careful consideration should be made when considering FG application. Additionally, the FG should be applied based on the Ca needed by the rice (23 kg ha⁻¹) as it increased soil exchangeable Ca and S levels. This finding can be applied to other types of gypsum to be applied to paddy soils.

The NR + HA + FG636 practice did not achieve a higher rice yield like FP + HA and FP + HA + FG23 did, but this practice achieves maximum NUE and NAE. This finding indicates that higher NUE and NAE under the NR + HA + FG636 practice are mainly attributed to lower total nutrient input (71.76 kg ha⁻¹) to the soil. i.e., 19% lower than FP + HA (85.68 kg ha⁻¹) and FP + HA + FG23 (85.683 kg ha⁻¹) (Table 2). Both the coapplication of FP + HA + FG23 and NR + HA + FG636 increased NUE and NAE in acidic paddy soil (Table 4). Similarly, the coapplication of HA + FG promoted NUE by 27% in salt-affected soil [35]. Our results extend these findings to highly acidic paddy soil conditions, where there is a Ca deficiency rather than Na toxicity. Furthermore, this study reported that NUE was under 50% across treatments, indicating that a substantial proportion of the applied N was not taken up by rice. The remaining N has probably been lost through nitrate leaching, ammonia volatilization, and denitrification [64,65]. A previous study has revealed that the coapplication of HA + FG can mitigate greenhouse gas emissions by 32% in salt-affected paddy soil [35]. HA can reduce N losses via leaching by stabilizing NH₄-N through adsorption and delaying NH₄-N conversion to NO₃-N [23], while FG releases SO₄, which can form complexes with NH₄-N to reduce N loss pathways [56]. Additionally, our study observed an increase in NH₄-N and a decrease in NO₃-N in HA + FG-treated soil (Table 3). This suggests that the coapplication of HA + FG will potentially retain N in its available form and minimize the N losses. While this study focused on NUE, future studies should determine the N loss pathways under field conditions, particularly in high acidity conditions, in order to comprehensively assess and confirm whether such environmental benefits of this ISFM practice extend to acidic paddy soil. Furthermore, the N dynamics observed in the controlled pot experiment, which is filled with sandy loam topsoil (0–15 cm), may not fully represent those under typical field conditions, where an underlying clayey horizon is present. In the paddy fields, clayey subsoil layers can influence N behavior by affecting retention, leaching, volatilization, and gaseous emissions. Therefore, the differences in the nutrient input and dynamics should be considered when extrapolating these findings to field applications.

3.3. Relationship Between Soil Properties, Rice Yield, Nitrogen Uptake, Nitrogen Use Efficiency, and Nitrogen Agronomic Efficiency

Principal component analysis (PCA), performed using the basis of the standardized average values of soil properties (including soil pH, Eh, TOC, CEC, total N, total Ca, total S, NH₄-N, NO₃-N, exchangeable Ca, and exchangeable S), rice grain, straw biomass, root biomass, total N uptake, NUE, and NAE, is presented in Figure 7.

PCA showed that Eh, exchangeable Ca, exchangeable S, NO₃-N, and root biomass were mainly associated with FP + FG23, NR + FG23, and NR + HA + FG23 (Figure 7). This is attributed to FG-enhanced root development due to the supply of exchangeable S (Table 3) [66]. Higher concentrations of exchangeable S in the soil treated by FG23 are discussed in Section 3.1.

Furthermore, total Ca, CEC, straw biomass, grain yield, total N uptake, NUE, and NAE were associated with FP + HA and FP + HA + FG23 (Figure 7). The bivariate relationship was positive between rice grain yield and straw biomass (R² = 0.48) (p < 0.05) (Figure 8a). In addition, grain yield was positively associated with total N uptake (R² = 0.38) (p < 0.05) (Figure 8b), indicating that increased straw biomass contributes to increased grain production because a higher straw biomass supports a higher photosynthesis rate and nutrient reserves, which are essential for grain development [67]. Furthermore, this study suggested that the total N uptake is critical for rice grain yield since N is a fundamental component of chlorophyll, which facilitates photosynthesis and carbohydrate synthesis for grain filling [68].

Straw biomass was positively associated with both total N uptake (R² = 0.21) (p < 0.05) and root biomass (R² = 0.13) (p < 0.05) (Figure 8c,d), indicating that total N uptake contributes more to increasing straw biomass as N is required for cell division and growth [69,70]. Improving underground biomass contributes to a higher straw biomass, as an extensive root system absorbs more nutrients and water that can be transported to the aboveground biomass [71].

NUE was positively correlated with total N uptake and grain yield (R² = 0.38 and 0.13, respectively) (p < 0.05) (Figure 8e,f). These findings underscore the importance of enhancing total N uptake in improving NUE, as total N uptake is a key component for NUE computation [72]. Moreover, grain yield, total N uptake, and straw biomass were associated with NAE (R² = 0.48, 0.20, and 0.18, respectively) (p < 0.05) (Figure 8g–i). The NAE is defined as the grain yield produced per unit of N applied [72]. Therefore, this study indicates that improving grain yield leads to achieving a higher NAE, which is a crucial component of ISFM [73]. A study by Vanlauwe et al. [73] revealed that a higher NAE can enhance economic returns for farmers. Therefore, the current study proposes that the ISFM of fertilizer application based on FP combined with HA (FP + HA) or with HA and FG based on rice Ca requirement (FP + HA + FG23) are optimal soil management practices to adopt in relation to acidic paddy soil because these practices potentially sustain rice production and NAE. While the FP + HA + FG23 treatment in this study offers promising agronomic results, further study evaluating the economic benefit of adopting FP + HA + FG23 under field conditions is required to support practical adaptation on a farm scale.

The increase in rice yield in soil treated with HA is due to the HA increasing the CEC, TOC, and NH₄-N, all of which, in turn, promote nutrient uptake and rice productivity. This is consistent with previous studies showing that HA applications (e.g., 1500 kg ha⁻¹ and 20 mg carbon L⁻¹) promoted crop growth and yield (e.g., rice and maize) in black soil in a typical cold region and hydroponic system, respectively [74,75]. Furthermore, the positive interactive effect of HA and FG in the FP + HA + FG23 treatment results in a higher grain yield, straw biomass, and NAE compared to the other treatments. Therefore, this study proposes that the integration of fertilizer application based on farmer practice, either with HA alone or combined with FG based on rice need at 23 kg ha⁻¹, is an effective strategy for improving grain yield and NAE in acidic paddy soil.

Other ISFM strategies, such as FP + HA + FG636, NR, NR + HA, and NR + HA + FG636, were associated with soil pH, TOC, total N, total S, and NH₄-N. Additionally, the NR + HA + FG636 treatment was associated with NUE, total N uptake, and NAE, which was situated along the factor 1 axis (Figure 7). The increase in TOC under the combined application of HA and FG (636 kg ha⁻¹) is attributed to TOC input from HA (Table 1) as well as TOC stabilization by Ca released from FG, as previously discussed in Section 3.1. Higher total N and total S in HA + FG (636 kg ha⁻¹) are related to higher input derived from both HA and FG (Table 1 and Table 2). This showed that the coapplication of HA and FG applied following gypsum requirements (636 kg ha⁻¹) under both fertilizer regimes of soils fertilized pertaining to farmer practice and rice requirements can improve the properties of the studied acidic paddy soil, but they did not bring about additional benefits to crop performance, i.e., NUE and NAE. In contrast, FG application according to gypsum requirements, along with fertilizer application rates based on rice’s needs, enhances total N uptake, NUE, and NAE. However, FG application at 636 kg ha⁻¹ led to excessive Ca and S input to paddy soil as it induces nutrient imbalance (e.g., Ca-P precipitation and low exchangeable Ca and S levels) and can produce H₂S, which potentially pollutes the atmosphere, as previously discussed in Section 3.1.

4. Conclusions

This study determines the effects of integrated soil fertility management (ISFM) involving the coapplication of chemical fertilizer, humic acid (HA), and flue gas desulfurization gypsum (FG) on soil properties, rice yield, nitrogen (N) use efficiency (NUE), and N agronomic efficiency (NAE) in a tropical acidic paddy soil. Fertilizer primarily enhances total N and exchangeable NO₃-N (NO₃-N) levels. HA incorporation improves soil TOC, CEC, total N, and exchangeable NH₄-N (NH₄-N). FG incorporation improves exchangeable Ca but requires careful management when it is applied alone. The coapplication of HA and FG based on gypsum requirement (636 kg ha⁻¹) in the acidic paddy soils improves total N, TOC, and NH₄-N. However, integrating FG at this rate with the application of chemical fertilizer based on farmer practices adversely affects rice yield and total N uptake. On the other hand, applying FG at 23 kg ha⁻¹, whether alone or with HA, improves exchangeable Ca and S concentrations under farmer practices. The optimal ISFM strategy combining the application of HA (975 kg ha⁻¹) and FG (23 kg ha⁻¹) significantly enhances soil properties and rice agronomic performance. The findings of this study highlight the optimum application rate of FG, which should be at 23 kg ha⁻¹, particularly in combination with HA, in order to maximize NUE, NAE, and rice yield. The higher FG application rates based on gypsum requirements should be avoided when paddy soils are fertilized using farmer practice, owing to the negative impacts on yield, total N uptake, and NUE. While this pot experiment demonstrated the agronomic benefits of the FP + HA + FG23 application on soil properties, yield, and NUE, further studies are needed to assess the effectiveness and applicability of this practice under field conditions, as well as to evaluate their economic and environmental benefits. This will support the practical adoption of ISFM strategies by farmers.