Impact of Organic and Inorganic Sources of Nitrogen on Soil Fertility, Nitrogen Use Efficiency, and Carbon Accumulation Potential Under Subtropical Rice-Based Cropping Patterns in Farmers’ Fields

Abstract

This study aimed to assess the effect of organic amendment-based integrated nitrogen (N) application on major soil macronutrients, carbon (C) accumulation, crop productivity and N use efficiency (NUE) of different rice-based cropping patterns. This experiment was composed of various organic amendments ((i): control (no organic amendment, application of 100% N from urea); (ii): 25% N from compost + 75% N from urea; (iii): 25% N from cowdung + 75% N from urea; iv: 25% N from vermicompost + 75% N from urea) and rice-based cropping patterns ((i) rice–rice–rice, (ii) rice–fallow–rice–mustard, and (iii) rice–vegetables–rice). Organic amendments and soils (0–20 cm) were collected from farmers’ fields and were analyzed for major nutrients: N and organic C (OC), phosphorus (P), potassium (K) and sulphur (S). Soil OC accumulation potential, system productivity and partial factor productivity of N were also calculated. The results indicate that organic amendment application significantly enhanced soil OC (0.957–1.604%) compared to control (0.916–1.292%), with vermicompost attaining the highest OC content and OC accumulation potential (up to 24.15%), especially in the rice–vegetables–rice pattern. Vermicompost also predominantly increased N (22–62%) and S (51–78%) level in soils, while cowdung significantly amended P levels (155–178%) and contributed steadily to improved K levels in soil. Overall, nutrient improvements and soil fertility were highest under the rice–vegetables–rice system, followed by rice–fallow–mustard–rice and rice–rice–rice. System productivity was maximum in the rice–vegetables–rice pattern (up to 85.7 t ha⁻¹), with remarkable enhancements in NUE when organic amendments were applied. Cowdung and vermicompost both matched or exceeded the performance of chemical fertilizer in these cases. These results demonstrate the advantages of integrated N management and diversified cropping to improve nutrient cycling, soil health and sustainable productivity in rice-based agroecosystems.

1. Introduction

Around the world, maintaining sustainable soil fertility has become increasingly important. Intensive agricultural practices can significantly contribute to the deteriorating fertility of soil [1]. Higher soil fertility typically indicates enhanced stored or sequestered carbon (C) content [2], greater nutrient availability for plants [3], and greater crop growth and yield [4]. Sequestered C is a vital sign of soil fertility, reflecting the soil’s capacity to support sustainable agricultural productivity [5]. However, in most cases, sequestered C declines because of some agricultural practices [6]. Farmers, particularly in South Asia, tend to prioritize crop yield to meet the food demands of a densely populated region over long-term soil health. They often rely heavily on chemical fertilizers, with less focus on organic amendments such as compost, cowdung, crop residue, etc., despite the recognized benefits (improve soil structure, increase nutrient accessibility, microbial biomass, and crop yield, etc.) of organic amendments for soil health [7,8]. Most of the rice farmers of Bangladesh, the fourth-largest rice-producing country in the world, practice blanket application of sole chemical fertilizer to supply nitrogen (N) [9]. Nitrogen is crucial for rice production as grain formation depends on N accumulation in plants [10]. So, proper management of N fertilizer is an important factor in productivity and profitability. Moreover, N fertilization also intensely effects the distribution, lability and stratification of soil C pools and stock in subtropical rice-based cropping systems [11]. However, this traditional system of fertilization causes losses of about 60–70% of the applied N [12], ultimately resulting in lower N use efficiency (NUE), which is typically about 20–50% in rice [13]. Lower NUE does not only indicate higher input cost or lower profitability; it also means loss of about 60–80% applied N to the environment, which contributes to greater greenhouse gas emissions and pollution [14]. Thus, an integrated approach (i.e., chemical fertilizer + organic amendments) to N application could be the best practice for enhancing sustainable crop production by optimizing NUE and improving soil health and C and N dynamics while minimizing environmental impact [15,16,17].

Along with integrated nutrient management, land use, particularly cropping pattern, significantly influences soil C storage, overall soil fertility, resource utilization, agronomic production and profitability [15,18]. Rice-based cropping patterns are dominant in Southeast Asia, but intensive cultivation and improper management of nutrients are very common and often limit the system’s productivity. It is reported that the submerged conditions for growing rice, in turn, decelerate soil C mineralization, so that paddy soils, on average, store more C than adjacent sites under dry land cropping [19]. However, this same submerged environment can also hamper N availability for plants, leading to lower NUE [20]. It is uncertain whether fields under different rice-based cropping patterns would accumulate C or not, and how C and other nutrients’ levels would change with different nutrient management practices [21]. Thus, this study was conducted to assess the impact of various organic amendment applications on the soil fertility and C accumulation of soils with diverse cropping patterns. This research aims to (i) evaluate the effect of combined application of fertilizer and various organic amendments on the major soil nutrient contents, C accumulation potential, NUE and crop productivity of rice-based cropping patterns and (ii) determine the effect of various rice-based cropping patterns on soil fertility, C accumulation and productivity.

2. Materials and Methods

2.1. Description of the Experimental Site

Soil samples were collected from Bogir para village (24°86′66.74″ N 90°40′36.74″ E) located in Tarakanda upazila, Mymensingh district, Bangladesh (Figure 1). The area belongs to Agro-ecological Zone (AEZ)-9, Old Brahmaputra Floodplain, and has non-calcareous dark grey soil. Fields under three rice-based cropping patterns were chosen following an initial survey and farmer interviews in the area. The selected fields are located in a sub-tropical climate which is characterized by moderately high temperature and heavy rainfall during the summer season (April–September) and low rainfall with moderately low temperature during the winter season (October to March) (Figure 2).

2.2. Experimental Factors

The experiment was composed of two factors: (A) organic amendment-based integrated N management and (B) rice-based cropping patterns. For N management, there were four types of soil amendment practices: i. control (no organic amendment, application of 100% N from chemical fertilizer-urea), ii. 25% N from compost + 75% N from urea, iii. 25% N from cowdung + 75% N from urea, and iv. 25% N from vermicompost + 75% N from urea. Urea fertilizer was applied as per the rates typically used in local rice farming practices. The full amount (100% N dose) of urea was 247 kg ha⁻¹ for winter rice (boro) and 148 kg ha⁻¹ for both monsoon rice (aman) and summer rice (aus). Details of the fertilizer + organic amendment management and organic amendments’ preparation in farmers’ households are given in the Supplementary Information (Tables S1 and S2). For cropping patterns, there were three common rice-based patterns: i. rice–rice–rice (winter rice–summer rice–monsoon rice), ii. rice–fallow–rice–mustard (winter rice–fallow–monsoon rice–mustard) and iii. rice–vegetables–rice (winter rice–summer vegetables–monsoon rice).

2.3. Crop Management at Farmers’ Field

After a base survey and interview with farmers of Bogir para village, Kakni union, Tarakanda upazila of Mymensingh district, Bangladesh, it was noticed that most of the rice-producing farmers of this village followed the most common nutrient management, i.e., use of only chemical fertilizers according to the local farming practice. There were also few promising contact farmers who showed interest in the idea of using organic amendment in the field after related training and demonstrations organized by the Department of Agricultural Extension (DAE), Government of the Peoples Republic of Bangladesh, at upazila level. Notably, female members of farming families started producing organic manures like cowdung, conventional compost, and vermicompost at home (Table S2) and used them in some of their fields along with chemical fertilizers for a number of years. One of the farmers’ fields from this group has been selected for this study. As stated earlier, the farmer generally grows rice following the three common rice-based cropping patterns using chemical fertilizers based on local farming practice in most of these fields (control, traditional field). They also have few adjacent fields under the same cropping patterns where they use both organic and chemical amendments (new field). These experimental sites were adjacent to each other and had been cultivated for more than thirty (traditional field) and five (new field) years, respectively. For combined use of organic and chemical fertilizers, the farmer followed the guidance of the DAE, applying about 75% N from urea and 25% N from organic amendments (source: DAE office personnel and farmer interviews). The doses of all the other fertilizers (triple super phosphate, muriate of potash, gypsum and zinc sulphate) were similar in all the fields. Fertilizers and organic amendments were used exclusively for rice, while no such inputs (chemical or organic) were reported for mustard or vegetables in the cropping patterns. Urea was applied in a split application and all the other fertilizers were applied basally, and the organic amendments were incorporated into the soils two weeks before transplanting of rice. The details on cultivated crops, the name and dose of fertilizers, and organic amendments used are given in Table S1.

2.4. Sample Collection and Preparation

Soil samples (0–20 cm) were collected from three fields, each representing one of the three-rice based cropping patterns at the end of the crop year (after harvesting winter rice). Each cropping pattern field was further subdivided into plots receiving one of four organic amendments including a control. Two adjacent plots were assigned to each organic amendment treatment as replications to reduce field variability and improve sampling reliability. Twelve random soil samples were taken from each plot, thoroughly mixed to form one composite sample per treatment per replication, air-dried, ground, then sieved through a 2 mm screen and kept in airtight containers. Cowdung, compost and vermicompost were collected from the contact farmers in three replicates. After air-drying, the organic amendments were crushed, passed through a 2 mm sieve, then sealed in airtight containers for subsequent analysis.

2.5. Sample Analysis

2.5.1. General Properties of Soil and Organic Amendment

Only soils from control plots were analyzed for pH, carbonate, electrical conductivity (EC), and texture to characterize the initial soil properties. Soil pH and EC (soil/water ratio: 1:5) were determined using a Multiparameter benchtop meter (InoLab® Multi 9310 IDS, Germany), as described by Jackson [22]. Soil texture determination was carried out using a hydrometer as outlined by Bouyoucos [23]. Carbonate and bicarbonate were analyzed through a titration method [24]. The collected soil samples did not have a considerable amount of carbonate or bicarbonate. All laboratory extractions and analytical measurements of individual soil and organic amendment samples were performed in triplicate.

2.5.2. Organic Carbon and Macronutrient Analyses

Organic C (OC) and macronutrient (N, phosphorus (P), potassium (K) and sulphur (S)) contents of organic amendments and soils were measured. For soil samples, OC and N contents were determined using the wet oxidation method [25] and Kjeldahl method [26], respectively. The dry ashing method was used to determine the organic matter content of the amendments [27]. Phosphorus concentration was determined by following the method of Olsen [28]. Potassium was measured by Warncke and Brown’s [29] method and S was determined by following Combs et al. [30].

2.5.3. Carbon Accumulation Potential Calculation

The percentage of OC accumulation potential was computed as [31]

$$\mathrm{OC}\mathrm{accumulation}\mathrm{potential}(\%)={\displaystyle \frac{{\mathrm{O}\mathrm{C}}_{\mathrm{i}}-{\mathrm{O}\mathrm{C}}_{\mathrm{c}}}{{\mathrm{O}\mathrm{C}}_{\mathrm{c}}}}\times 100$$

(1)

where OC_i = OC content of soil collected from plots under integrated N management and OC_c = OC content of soil collected from plots under traditional N management (control).

2.5.4. Calculation of System Productivity and Nitrogen Use Efficiency

The overall efficiency of the cropping patterns in utilizing resources to produce crops is referred to as system productivity and is expressed as rice-equivalent yield here. So, rice-equivalent yield (system productivity) was calculated as

$$\mathrm{R}\mathrm{i}\mathrm{c}\mathrm{e}\mathrm{e}\mathrm{q}\mathrm{u}\mathrm{i}\mathrm{v}\mathrm{a}\mathrm{l}\mathrm{e}\mathrm{n}\mathrm{t}\mathrm{y}\mathrm{i}\mathrm{e}\mathrm{l}\mathrm{d}={\displaystyle \frac{(\mathrm{Y}\mathrm{i}\mathrm{e}\mathrm{l}\mathrm{d}\mathrm{o}\mathrm{f}\mathrm{i}\mathrm{n}\mathrm{d}\mathrm{i}\mathrm{v}\mathrm{i}\mathrm{d}\mathrm{u}\mathrm{a}\mathrm{l}\mathrm{n}\mathrm{o}\mathrm{n}\mathrm{r}\mathrm{i}\mathrm{c}\mathrm{e}\mathrm{c}\mathrm{r}\mathrm{o}\mathrm{p}\times \mathrm{L}\mathrm{o}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{m}\mathrm{a}\mathrm{r}\mathrm{k}\mathrm{e}\mathrm{t}\mathrm{p}\mathrm{r}\mathrm{i}\mathrm{c}\mathrm{e}\mathrm{o}\mathrm{f}\mathrm{t}\mathrm{h}\mathrm{a}\mathrm{t}\mathrm{n}\mathrm{o}\mathrm{n}\mathrm{r}\mathrm{i}\mathrm{c}\mathrm{e}\mathrm{c}\mathrm{r}\mathrm{o}\mathrm{p})}{\mathrm{L}\mathrm{o}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{m}\mathrm{a}\mathrm{r}\mathrm{k}\mathrm{e}\mathrm{t}\mathrm{p}\mathrm{r}\mathrm{i}\mathrm{c}\mathrm{e}\mathrm{o}\mathrm{f}\mathrm{r}\mathrm{i}\mathrm{c}\mathrm{e}}}$$

(2)

Partial factor productivity for N is a proxy to measure NUE and can be applied to evaluate the effectiveness of different N management practices. It was calculated as the ratio of crop yield to the total amount of N applied (from chemical and organic sources). This factor is also calculated for the cropping pattern or system as the ratio of total crop yield and total amount of N applied for all the crops included in the pattern. For patterns with non-rice crops, rice-equivalent yield was included in calculating total crop yield.

2.6. Statistical Analysis

Three analytical replicates for each soil parameter were averaged within each field replication, and subsequent statistical analyses were performed on the resulting mean values. Two-way analysis of variance (ANOVA) was used to look at the impacts of cropping pattern × organic amendment combinations on soil nutrient contents (OC, N, C:N ratio, P, K and S) and OC accumulation potential. One-way ANOVA was performed to find out the effect of amendments to a similar cropping pattern or the effect of cropping patterns of a similar organic amendment on the changes in soil nutrients after application of organic amendments. Comparisons of treatment means were performed using the Least Significant Difference (LSD) test. All the statistical analyses were performed using he R software package (version 4.4.0) [32].

3. Results

3.1. General Physicochemical Properties of Soil and Organic Amendments

The soils from control plots under all three cropping patterns demonstrated a neutral pH ranging from 7.2 to 7.4 and were classified as non-saline, with electrical conductivity values between 48.5 and 112.5 μS cm⁻¹ (

Table 1. General characteristics of soils (<2 mm) from control plots under various rice-based cropping patterns.

Cropping Pattern	pH	EC (µs cm−1)	Particle Sizes (%)			Texture
	(1:5 H2O)		Sand	Silt	Clay
Rice–rice–rice	7.4 ± 0.03	48.5 ± 0.50	34.0 ± 0.0	55.0 ± 1.0	11.0 ± 1.1	Silty loam
Rice–fallow–rice–mustard	7.2 ± 0.04	61.0 ± 1.00	35.0 ± 1.0	55.0 ± 1.0	10.0 ± 0.0
Rice–vegetables–rice	7.3 ± 0.00	112.5 ± 2.50	36.5 ± 0.5	54.5 ± 0.5	9.0 ± 0.0

EC = electrical conductivity. Values represent mean ± standard error (n = 2 field replicates).

). Soils were silt-loam-textured, consisting of approximately 55% silt, 34–36.5% sand, and 9–11% clay.

The chemical composition of the organic amendments varied considerably (

Table 2. General characteristics of the organic amendments.

Amendment Type	OC	N	C:N Ratio	P	K	S
	(%)			(ppm)	(meq 100 g−1)	(ppm)
Compost	12.2 ± 0.01 a	1.63 ± 0.03 b	7.5	303 ± 0.67 b	129 ± 0.47 a	122 ± 0.97 c
Cowdung	11.6 ± 0.15 b	2.10 ± 0.12 a	5.5	341 ± 0.75 a	54 ± 0.03 c	306 ± 0.50 a
Vermicompost	11.5 ± 0.02 b	1.50 ± 0.06 b	7.7	267 ± 0.61 c	67 ± 0.04 b	294 ± 0.80 b
Level of significance	**	**		***	***	***

OC = organic carbon, N = nitrogen, P = phosphorus, K = potassium and S = sulphur. Values represent mean ± standard error (n = 3 field replicates). Different letters within a column denote significant differences between organic matter amendments, ** = significant at probability level (p) 0.01, *** = significant at p 0.001.

). Compost had the highest OC content (12.2%), followed by vermicompost (11.5%) and cowdung (11.6%). Cowdung had the highest N concentration (2.10%), followed by compost (1.63%) and vermicompost (1.5%). The C:N ratios ranged from 5.5 to 7.7, with vermicompost having the widest and cowdung having the narrowest ratio. The concentration of P ranged from 267 to 341 ppm, K ranged from 54 to 129 meq 100 g⁻¹ and S ranged from 122 to 294 ppm. Overall, compost had the most K while cowdung had the highest P and S.

3.2. Influence of Organic Amendments on Soil Organic Carbon and Major Nutrients

Soil OC and the major macronutrients were significantly influenced by the application of soil organic amendments in all three cropping patterns (Figure 3,

Table 3. Content of major nutrient elements in soils after the application of organic amendments under diverse rice-based cropping patterns.

Cropping Pattern	Soil Amendments	P (ppm)	K (meq 100 g−1)	S (ppm)
Rice–rice–rice	Control	16.3 ± 0.6 gh	0.094 ± 0.004 d	5.7 ± 0.1 g
	Compost	34.0 ± 1.8 bc	0.102 ± 0.000 d	7.5 ± 0.1 f
	Cowdung	45.1 ± 0.3 a	0.136 ± 0.005 c	9.3 ± 0.3 de
	Vermicompost	29.0 ± 2.2 de	0.144 ± 0.001 c	10.0 ± 0.3 d
Rice–fallow–rice–mustard	Control	12.4 ± 0.1 i	0.099 ± 0.001 d	7.3 ± 0.2 f
	Compost	25.7 ± 0.6 ef	0.114 ± 0.002 d	8.5 ± 0.1 ef
	Cowdung	31.7 ± 1.2 cd	0.138 ± 0.006 c	12.3 ± 0.8 c
	Vermicompost	17.7 ± 1.9 g	0.153 ± 0.019 c	13.0 ± 0.9 c
Rice–vegetables–rice	Control	14.2 ± 0.0 hi	0.295 ± 0.004 b	13.4 ± 0.2 c
	Compost	30.1 ± 0.3 d	0.311 ± 0.001 b	18.8 ± 0.4 b
	Cowdung	36.0 ± 0.1 b	0.355 ± 0.009 a	21.1 ± 0.5 a
	Vermicompost	23.3 ± 0.2 f	0.356 ± 0.007 a	20.1 ± 0.4 a
Level of significance		*	*	**

P = phosphorus, K = potassium and S = sulphur. Values represent mean ± standard error (n = 2 field replicates). Here, control = only urea application (100% N based on farmer’s practice); compost, cowdung and vermicompost applied @ 25% N + 75% N from urea. Different letters indicate significant differences between cropping pattern × amendment combinations, * = significant at probability level (p) 0.05, ** = significant at p 0.01.

and Tables S3 and S4). The OC level in traditionally (control) managed plots ranged from 0.916% to 1.292%, whereas the values were between 0.957% and 1.604% for the amended plots irrespective of the cropping patterns (Figure 3A). Overall, the OC content was higher in vermicompost-amended plots followed by cowdung and compost. Considering the cropping pattern, rice–vegetables–rice showed the highest OC in soil, followed by rice–fallow–mustard–rice and rice–rice–rice (Figure 3 and Table S3). The N content in soil varied between 0.081% and 0.179% among the different amendment types and cropping patterns, with the consistent lowest in the control and the highest in the case of cowdung application (Figure 3B). The impact of cropping pattern on soil N was similar to that of soil OC. The C:N ratio ranged between 7.6 and 11.4 for all the amendment types and cropping patterns (Figure 3C). The ratio was relatively narrower in vermicompost- and cowdung-amended soils under rice–vegetables–rice and rice–fallow–mustard–rice patterns compared to the compost-amended and control soils under the three rice cropping patterns.

Application of organic amendments significantly increased the concentration of the major nutrients in soils across various rice-based cropping patterns (Table 3 and Tables S3 and S4). The content of P, K and S varied between 12.4 ppm and 45.1 ppm, 0.094 meq 100 g⁻¹ and 0.356 meq 100 g⁻¹ and 5.7 ppm and 18.8 ppm, respectively. In the case of P, cowdung-amended soils yielded the highest values, followed by vermicompost, cowdung and control. For S, the highest values were found with vermicompost applications, which were statistically similar to cowdung-applied plots, with an exception in rice–vegetables–rice. However, the K content trend was vermicompost > cowdung > compost > control. These nutrient contents (particularly K and S) were the highest in the rice–vegetables–rice pattern followed by rice–fallow–rice–mustard and rice–rice–rice.

Notable increases in soil OC (Figure 4) and other nutrient levels (Figure 4) were observed following the use of organic amendments compared to the control. Soil OC accumulation potential reflects the enhancement of OC following a shift in nutrient management from traditional chemical-only N application to an integrated N management approach (Figure 4). In general, OC accumulation potential in comparison to the control is the lowest under compost application (3.23–7.66%), medium under cowdung application (4.43–9.10%) and the highest with vermicompost use (7.09–24.15%), particularly in the rice–vegetables–rice pattern.

Vermicompost application resulted in the highest N increase (22–62%), followed by cowdung (13–45%) and compost (7–39%) (Figure 5A). Across the cropping patterns, rice–vegetables–rice consistently delivered the highest N gain followed by the by rice–fallow–rice–mustard and rice–rice–rice patterns. A remarkable increase in P levels was also evident in all cases of organic amendments and cropping patterns (Figure 5B). Phosphorus concentration increased from 43% to 178%, with the highest value in cowdung amendments (155–178%) followed by compost (107–112%) and vermicompost (43–78%). Potassium levels were most enhanced by cowdung use (20% to 45%), followed by compost (9% to 15%), while vermicompost application caused both a decrease (−19%) and increase (21–54%) in K levels in soils (Figure 5C). Sulphur contents in soils increased up to 78%, with the maximum increment from vermicompost use (51% to 78%), followed by cowdung (58–69%) and compost application (16–41%) (Figure 5D).

3.3. System Productivity and Nitrogen Use Efficiency

System productivity and partial factor productivity of N were notably influenced by both cropping pattern and type of organic amendment (

Table 4. System productivity and partial factor productivity of nitrogen in different rice-based cropping patterns after application of organic amendments.

Cropping Pattern	Soil Amendments	System Productivity (t ha−1)	Partial Factor Productivity of N
			Summer Rice	Monsoon Rice	Winter Rice	System
Rice–rice–rice	Control	12.91	24.9	24.9	48.5	31.5
	Compost	10.14	18.7	18.7	40.4	24.7
	Cowdung	11.98	21.8	21.8	48.5	29.2
	Vermicompost	11.98	21.8	24.9	44.5	29.2
Rice–fallow–rice–mustard	Control	15.06	-	31.1	64.7	29.2
	Compost	12.44	-	24.9	56.6	24.7
	Cowdung	15.98	-	34.3	68.7	31.5
	Vermicompost	14.13	-	28.0	60.6	27.0
Rice–vegetables–rice	Control	73.44	-	31.1	64.7	29.4
	Compost	66.37	-	28.0	60.6	27.1
	Cowdung	85.73	-	31.1	64.7	29.4
	Vermicompost	85.73	-	31.1	64.7	29.4

Cropping pattern: rice–rice–rice (winter rice–summer rice–monsoon rice), rice–fallow–rice–mustard (winter rice–fallow–monsoon rice–mustard) and rice–vegetables–rice (winter rice–summer vegetables–monsoon rice). Control = only urea application (100% N based on farmer’s practice); compost, cowdung and vermicompost applied @ 25% N + 75% N from urea.

). System productivity ranged from 10.14 t ha⁻¹ to 85.73 t ha⁻¹ among the cropping patterns. Overall, the rice–vegetables–rice system recorded the highest productivity, reaching 85.73 t ha⁻¹, followed by rice–fallow–rice–mustard (12.44–15.06 t ha⁻¹) and rice–rice–rice (10.14–12.91 t ha⁻¹).

Since there was no external N applied as fertilizer or manure for mustard and vegetable cultivation, partial factor productivity of N is only calculated for individual rice crops, and also for the whole pattern considering the rice-equivalent yield of non-rice crops (Table 4). Considering the rice crop, this factor is lower in summer and monsoon rice (18.7–24.9) compared to winter rice (40.4–48.5) in the rice–rice–rice pattern. This trend was similar for the other two patterns but with higher factor values: 28–34.3 for monsoon rice and 56.6–68.7 for winter rice. Partial factor productivity of N for the system ranged from 27.0 to 31.5. Overall, cowdung and vermicompost application in all the cropping patterns enhanced the partial factor productivity of N or was sometimes equal to the value of the sole chemical fertilizer application (control). Compared to the rice–rice–rice pattern, the inclusion of mustard and vegetable crops in the pattern improved the NUE, with few exceptions.

4. Discussion

The findings of this study revealed that the integration of organic and inorganic N sources significantly enhanced soil nutrient status and soil OC accumulation and improved NUE without yield penalty or sometimes with enhanced yield compared to sole application of chemical fertilizers [33]. Among the organic amendments applied, vermicompost application showed the highest soil OC, K and S overall compared to cowdung and compost (Figure 3 and Table 3), whereas cowdung-amended soil had the maximum N and P. Thus, the accumulation of OC or other major macronutrients in the soil after applying organic amendments is most likely to be regulated by the amendments’ biochemical composition and rates of decomposition [18,34,35]. Therefore, blind application of any available organic amendments may not always confer beneficial effects on the soil.

Considering the relative changes in the soil nutrients in amended soils versus control, again the largest consistent positive changes happened in vermicompost-amended soils followed by cowdung and compost, except for P and K. Cowdung application led to higher P content than compost and vermicompost application. These results concur with the earlier studies by Das et al. [36], where livestock compost use increased P availability and microbial-facilitated P cycling in submerged paddy soils. Potassium level consistently increased from cowdung amendment, while it enhanced variably from vermicompost use with some notable depletion. Composts usually release more stable K, while vermicompost can both mobilize and possibly leach K, reliant on soil nutrient status and cropping pattern [37].

The greatest soil OC accumulation potential (up to % over control) (Figure 4) and greatest relative N increase (Figure 5A) were also observed in vermicompost-applied plots, which aligns with the findings showing the positive impact of vermicompost use on soil OC stock, microbial biomass and N cycling compared to compost use [38]. This indicates the higher mineralization capacity, larger microbial population, and greater nutrient availability of vermicompost for plants over conventional compost [39,40]. These attributes of vermicompost cumulatively improve soil physical, chemical and biological properties and increase nutrient uptake by crop plants, which eventually enhance crop growth and productivity [41,42]. Overall, a similar productivity scenario was also observed in this study (Table 4). Organic amendments, particularly vermicompost and cowdung application, enhanced the system productivity as well as NUE in rice–vegetables–rice and rice–fallow–mustard–rice systems, while productivity was higher in the case of sole chemical fertilizer use for the rice–rice–rice system. This might suggest that such organic amendment-based nutrient management is not sufficient to fulfil the prompt demands of the triple-rice monocropping system. Continuous monocropping of rice, particularly under conventional management (frequently puddled tillage) with sole chemical N inputs, degrades soil structure, accelerates organic matter mineralization, and increases losses of C and N and other nutrient concentrations [43,44]. In this situation, readily available nutrients from heavy doses of chemical fertilizers currently lead to higher yields, which might not be sustainable in the long term considering potential soil health degradation. Moreover, the notable positive impact of organic amendments on system productivity and N utilization for the other two cropping patterns can be explained by the reduced tillage and crop residue management.

Soils under diversified cropping systems such as rice–vegetables–rice and rice–fallow–rice–mustard retained significantly higher soil OC than rice–rice–rice monoculture (Figure 3 and Figure 4). Reduced tillage disturbance during cultivation of upland crops (mustard or vegetables) likely contributes to OC preservation, consistent with findings by Zhang et al. [45], who reported improved C stabilization under less intensive cultivation. Furthermore, the practice of incorporating vegetable crop residue in the field by farmers might also have led to enhancements in soil organic matter, C and other nutrients in soil, which ultimately results in higher productivity and improved N utilization [46,47,48]. Additionally, improved NUE in integrated N management corroborates to slow and synchronized N release from organic sources, reducing leaching and gaseous losses like ammonia and N₂O emissions [44]. Thus, balanced application of organic and inorganic N not only ensures crop productivity but also contributes to mitigating climate change and maintaining soil sustainability over the long run.

5. Conclusions

This study reveals that the organic amendment-based integrated N management significantly enhances soil OC and macronutrient content (N, P, K, and S) across rice-based cropping systems. We acknowledge that, since this study was conducted under real on-farm conditions, various inherent cofounding factors such as soil properties, historical management, topography, and microclimates may have influenced the results to some extent. However, their impacts were expected to be minimized by careful selection of farmers’ fields, incorporation of field-level replicates and conducting multiple analytical replications.

Among the evaluated amendments, vermicompost steadily outperformed compost and cowdung in improving soil OC, N content, and S availability, predominantly under the rice–vegetables–rice cropping pattern, which evidenced to be the utmost productive and nutrient-efficient system. However, the cowdung amendment performed better in raising P levels in the soil. The inclusion of diversified cropping systems, particularly those integrating vegetables or mustard, improved both nutrient availability and system productivity while improving NUE compared to continuous rice cultivation. Remarkably, organic amendments like vermicompost and cowdung are not only on par with but often better than sole chemical fertilization in terms of crop productivity and NUE.

These findings highlight how integrated nutrient management and crop diversification can potentially optimize nutrient cycling, sustain crop production, and improve soil health in rice-based agroecosystems. In farmers’ fields, future research should place emphasis on optimizing amendment combinations and evaluating long-term effects on soil microbial dynamics, carbon sequestration, and greenhouse gas mitigation.