Partial replacement of inorganic fertilizer with organic inputs for enhanced nitrogen use efficiency, grain yield, and decreased nitrogen losses under rice-based systems of mid-latitudes

Abstract

In the rice-based system of mid-latitudes, mineral nitrogen (N) fertilizer serves as the largest source of the N cycle due to an insufficient supply of N from organic sources causing higher N losses due to varying soil and environmental factors. However, aiming to improve soil organic matter (OM) and nutrients availability using the best environmentally, socially, and economically sustainable cultural and agronomic management practices are necessary. This study aimed to enhance nitrogen use efficiency (NUE) and grain yield in rice-based systems of mid-latitudes by partially replacing inorganic N fertilizer with organic inputs. A randomized complete block design (RCBD) was employed to evaluate the effects of sole mineral N fertilizer (urea) and its combinations with organic sources—farmyard manure (FYM) and poultry compost—on different elite green super rice (GSR) genotypes and were named as NUYT-1, NUYT-2, NUYT-3, NUYT-4, NUYT-5, and NUYT-6. The study was conducted during the 2022 and 2023 rice growing seasons at the Rice Research Program, Crop Sciences Institute (CSI), National Agricultural Research Centre (NARC), Islamabad, one of the mid-latitudes of Pakistan. The key objective was to determine the most effective N management strategy for optimizing plant growth, N content in soil and plants, and overall crop productivity. The results revealed that the combined application of poultry compost and mineral urea significantly enhanced soil and leaf N content (1.36 g kg^− 1 and 3.06 mg cm^− 2, respectively) and plant morphophysiological traits compared to sole urea application. Maximum shoot dry weight (SDW) and root dry weight (RDW) were observed in compost-applied treatment with the values of 77.62 g hill^− 1 and 8.36 g hill^− 1, respectively. The two-year mean data indicated that applying 150 kg N ha⁻¹, with half provided by organic sources (10 tons ha⁻¹ FYM or poultry compost) and the remainder by mineral urea, resulted in the highest N uptake, utilization, and plant productivity. Thus, integrated management of organic carbon sources and inorganic fertilizers may sustain the productivity of rice-based systems more eco-efficiently. Further research is recommended to explore root and shoot morphophysiological, molecular, and biochemical responses under varying N regimes, aiming to develop N-efficient rice varieties through advanced breeding programs.

Introduction

Rice (Oryza sativa L.) is one of the staple food crops across the globe where 90% of its production is done in Asia, ensuring the dietary requirements of more than 60% of the world population while supporting the livelihoods of millions of small and marginal communities, especially in South Asia [1, 2]. In Pakistan, rice is the second main staple food crop after wheat as well as the second major exportable food commodity after cotton. It shares 1.9% of value addition in agriculture and 0.4% in gross domestic production (GDP) [3]. Traditional farming heavily reliant on chemical fertilizers generally produces higher yields but has also raised environmental issues such as soil degradation and biodiversity loss (microbial abundance and diversity) [4, 5]. With increasing global food demand, mineral nutrition has become one of the most critical factors limiting crop productivity worldwide [6]. Among these nutrients, nitrogen (N) plays a crucial role in crop growth and development, as it is required in large quantities for optimal crop production [7]. The evaluation of maximum yield per unit of N applied, absorbed, or utilized by crop plant is measured through NUE, which encompasses several aspects including agronomic efficiency, physiological efficiency, agro-physiological efficiency, apparent recovery efficiency, and utilization efficiency [8, 9].

Although substantial amounts of N fertilizers are applied to sustain rice yields to ensure food security goals, however, the utilization efficiency of nitrogenous fertilizer is low, typically ranging from 30 to 35%, leading towards considerable losses [9, 10]. In South Asian countries, N is applied at 140–150 kg N ha^− 1 season^− 1 utilizing different sources, which is around double the applied rate of Japan (≈ 80 kg N ha^− 1 season^− 1) and marginally higher than in the United States (≈ 140 kg N ha^− 1 season^− 1) [11, 12]. Amongst N losses, ammonia (NH₃) stands out as a crucial byproduct resulting from applied N in rice, with higher volatilization representing the main pathway for soil N losses [13]. Due to higher rice production, Asian countries rank top globally in air pollution due to elevated concentrations of greenhouse gase (GHG) emissions [14]. Volatilized N serves as a secondary source for nitrous oxide (N₂O) and nitric oxide (NO), contributing to approximately 30% of N deposition [15]. In Asia, agricultural gaseous N losses mainly N volatilization, are projected to reach 18.8 Tg N yr^− 1 by 2030 [16, 17].

Reducing N losses from rice cultivation will improve the eco-efficiency and economic stability associated with N fertilizers while enhancing air and water quality. To enhance nitrogen use efficiency (NUE) by managing the N-cycle, various strategies have been proposed [18], including the application of nitrification inhibitors (NI) [19], urease inhibitors (UI) [20], elemental sulfur (S) [21], and polymers [16]. Additionally, effective management of crop residues and the incorporation of organic amendments have been recognized as important practices for improving [22, 23]. The impact of organic amendments such as poultry manure, farmyard manure (FYM), biochar, and compost on NUE from wetland rice fields of mid-latitudes remains inconclusive and uncertain, as certain studies have indicated positive effects [24,25,26,27], while others reported negative effects [28,29,30]. The reduced NUE correlates with N fertilizer rates and types, indicating that utilizing organic amendments could allow for a reduction in N fertilizer application rates, thereby lowering both economic and environmental burdens while preserving soil and environmental quality.

Scientific literature often distinguishes between food loss and food waste; the former refers to waste occurring from post-harvest to pre-consumption by humans and animals, while the latter pertains to food loss at the retail and final consumption stages [31, 32]. According to the FAO report, approximately 32% of all food produced worldwide was categorized as loss and waste [33]. Compost, a nutrient-rich material derived from the decomposition of organic matter, has shown promise in reducing N losses and enhancing soil and crop productivity [34,35,36]. To achieve both promising crop yield and enhanced NUE simultaneously, there is a need to develop a practical approach with an optimal combination of chemical fertilizers and organic composts necessarily for long-term soil and environmental sustainability [37]. However, the effectiveness of these organic amendments in improving NUE, crop and soil productivity, and particularly environmental sustainability in rice-based systems, requires further investigation. Therefore, this study hypothesizes that the partial replacement of inorganic N fertilizers with organic inputs will enhance NUE, improve soil and plant nutrient content, and increase rice yields in mid-latitude rice-based systems. This study aims to provide insights into integrated N management practices that could sustainably enhance rice productivity in mid-latitude regions, contributing to both food security and environmental sustainability. The specific objectives of this study are: to evaluate the impact of combined applications of organic (FYM, poultry compost) and inorganic (urea) N fertilizers on soil and plant N content; to assess the effects of these combined N management strategies on the growth, morphophysiological traits, and grain yield of GSR genotypes; and to determine the optimal ratio of organic to inorganic N fertilizers that maximizes NUE and crop productivity while minimizing nutrient losses.

Materials and methods

Study area description and rationale of the study

A comprehensive field was designed on the farm at Rice Research Program, Crop Sciences Institute (CSI), National Agricultural Research Centre (NARC), Islamabad located at 33.67°N and 73.13°E during the rice-growing season in 2022 and 2023. The city is situated in the northern part of the country, on the Potohar Plateau, at an altitude of approximately 500 m (1,650 feet). Winters are mild, with temperatures typically ranging from 5 °C to 20 °C and moderate rainfall. Summers are hot and humid, with temperatures often soaring above 35 °C. The city receives most of its annual rainfall, averaging around 1,100 mm (43 inches), during the monsoon season from July to September. The mean weather conditions prevailed during the rice growth seasons of 2022 and 2023 are presented in Table 1.

Table 1 Mean weather conditions were prevalent during the experiment duration of 2022 and 2023

Chinese scientists initiated the Green Super Rice (GSR) project to address resource scarcity, environmental pollution, and ecological damage. The project was developed aiming to develop rice strains with traits such as pest and disease resistance, efficient fertilizer use, and drought tolerance. Beyond creating eco-friendly rice varieties, the GSR initiative focuses on sustainable crop management practices and high-yield techniques. It encompasses five main goals: developing whole-genome selection platforms, combining beneficial genes, creating novel germplasms with improved tolerance to biotic and abiotic stresses, producing high-yielding GSR cultivars, and formulating field management strategies for enhanced production. Conventional practices often result in significant N losses, reducing N use efficiency (NUE) and causing environmental harm. This study aims to assess the effectiveness of integrated management strategies, combining organic and inorganic sources, to optimize NUE and improve grain yield by reducing N losses in GSR-based system. The findings will contribute to developing sustainable rice cultivation practices that balance productivity and environmental protection.

Experimental design

In 2005, a group of Chinese scientists designed and executed the Green Super Rice (GSR) project against the continuous rise in scarcity of resources, environmental concerns, and ecological degradation. The GSR project was designed with five key objectives for rice breeding: developing selection platforms for rice whole-genome, incorporating environmentally beneficial genes, creating novel germplasms with enhanced tolerance to biotic stresses and improved resistance to various abiotic challenges, producing sustainable GSR cultivars—both hybrid and inbred types—to increase grain yield and quality, and finally, establishing field management strategies tailored to optimize production for GSR varieties.

Current GSR-based study was conducted in a completely randomized block design (RCBD) with three replications. Sowing of the nursery was done on 23rd May 2022 and 28th May 2023. Rice seedlings at the four-leaf heart stage comprising similar growth were selected and transplantation was done on 16th June 2022 and 20th June 2023 at a hill spacing of 15 × 20 cm, with two seedlings per hill. The plot size was managed at 6 m × 3 m in both study years. Treated plots were separated from each other at their perimeters by a polyvinyl chloride partition with 0.20 cm thickness, 50.0 cm aboveground height, and 20 cm belowground depth to restrict the exchange of irrigation water and fertilizer between plots. The elite GSR genotypes developed by undergoing a breeding program at Rice Research Program, CSI, NARC were selected for the assessment of the impacts of N management techniques on the grain yield, grain quality, and overall NUE. The germplasm was originally collected from the International Rice Research Institute (IRRI) Philippines and kept at the Plant Genetic Resource Institute (PGRI), Islamabad, Pakistan. Utilizing this germplasm, generation advancement was executed through a breeding program and elite genotypes were developed in terms of yield and environmental sustainability where the necessary details are presented in Table 2. The elite six genotypes involved in this study were named NUYT-1, NUYT-2, NUYT-3, NUYT-4, NUYT-5, and NUYT-6. The treatments involved 4 integrated N applications via co-application of inorganic and organic fertilizers which involved i) T₀ (control); T₁ (Urea application); T₂ (Urea + FYM); and T₄ (Urea + Compost). Macronutrient management for N, P, and K was done at the recommended dosage of 150, 90, and 60 kg ha^− 1, respectively. Different inorganic and organic fertilizer sources were included i.e., synthetic urea (46% N), FYM (nearly 1.0% N), and compost manufactured from poultry manure (nearly 2% N). Organic inputs were incorporated as basal doses during land preparation (one month before transplanting) at 10 t ha^− 1. The available percentages of N, P, and K accompanied by FYM and compost were calculated, while the remaining was satisfied by synthetic urea, diammonium phosphate (DAP; 46% P₂O₅ and 18% N), and Muriate of Potash (MOP; 60% K₂O), respectively. The remaining N after treatment and DAP application was calculated and applied as urea in three equal splits: at the basal stage, tillering, and panicle initiation. Except for the varying N fertilizer application rates, all other cultivation practices were consistent across all plots in both years. Manual weeding methods and chemicals were employed to manage weeds, diseases, and insects to prevent yield losses [38]. Avermectin, applied at a rate of 1.0 l per hectare, was used as an insecticide, sprayed once at the early stages of pest infestation. Butachlor, at a rate of 2.0 l ha^− 1, was applied pre-emergence to control weeds, while pyrazosulfuron, at 0.5 l ha^− 1, was used post-emergence. Tricyclazole, used at a rate of 0.6 kg ha^− 1, was applied as a foliar spray to manage fungal diseases, with a single application made at the early stage of disease symptoms. Manual hand weeding was also employed three times during the growth season. The physicochemical properties of the composite topsoil samples taken at varying soil depths ranging between 0 and 20 cm were assessed before sowing and after harvesting of the crop using samples collected through the five-point sampling method before partitioning.

Table 2 Source of GSR genotypes, names, specific codes, and gene bank accession numbers

Sampling and data recording

Total N content was measured using a colorimetric assay, which involves reacting the sample with specific reagents to produce a color change proportional to the N concentration [39]. Briefly, 0.2 g of soil and plant samples were digested separately in 3 ml of concentrated H₂SO₄ and 1.1 g digestion mixture (K₂SO₄, CuSO₄, and Se) on block digest for 4–5 h. The temperature was gradually increased, starting from 80 °C and ultimately reaching 350 °C, where it was maintained for one hour to achieve a light greenish texture. Later, the digested sample was shifted to a volumetric flask after cooling and the volume was gained up to 100 mL using distilled water, out of which, 20 mL of the digested sample was further distilled with 5 mL of separate 4% boric acid mixed indicator and NaOH solution, thereby titrated against standard 0.005 M HCl. Total N acquisition was determined as 1 ml of 0.005 M HCl equals 70 g. Meanwhile, a blank reading was also taken, and the formula used is given below.

$$\begin{array}{l}Total\:N\:Content\:\left(\%\right)\\=\frac{Sample-Blank\times\:0.005\times\:0.014\times\:100\times\:100}{Sample\:Weight\times\:20}\end{array}$$

Plant samples were taken between 9:00 AM and 12:00 PM during sunny days at five growth stages including tillering, booting, heading, grain-filling, and physiological maturity. Four hills were sampled each time, with two replicates per genotype and 2 replicates per treatment, where half of the hills were used to evaluate leaf and shoot morphological traits, and the remaining half were analyzed for physiological traits. For the assessment of N contents, two replicates per genotype were combined into one sample, and two replicates per treatment were used to determine dry mass. Root sampling involved removing a soil cube measuring 25 cm in length, 12 cm in width, and 25 cm in depth around each hill, capturing around 95% of the total root biomass [40]. Shoot and root samples taken for physiological analysis were initially fixed at 105 °C for half an hour, thereby dried at 80 °C to achieve a constant weight [41]. The N content in the dried samples was measured utilizing the semi-micro Kjeldahl method and an automatic Kjeldahl unit (FOSS-8400, Denmark) [42]. The overall leaf N content was also assessed using an elemental analyzer (Elementar Vario MACRO cube, Hanau, Germany). The tissue N concentration of aboveground parts and roots was assessed at the physiological maturity with an elemental analyzer to present the total N content (kg ha^− 1). To calculate the photosynthetic N-use efficiency, the plant photosynthetic rate (Pn) of full-grown rice leaf was determined between 8:00 AM to 12:00 PM by an infrared gas analyzer (IRGA) (IR400, Yokogawa Electric Corporation) and CIRAS-3 portable photosynthetic instrument (PP Systems, Amesbury, MA, USA).

$$\begin{array}{l}Photosynthetic\:N\:Use\:Efficiency\:\left(PNUE\right)\\=\frac{Photosynthetic\:Rate\:\left(Pn\right)}{Total\:Leaf\:N\:Content}\end{array}$$

To calculate the grain-filling parameters, randomly selected 200 panicles were labelled at 0 days in each plot. The sampling for grain-filling parameters was done at 1, 6, 12, 18, 24, 30, 36, and 42 after labelling. In brief, 20 panicles were taken each time, and superior and inferior grains at primary and secondary branches, respectively, were separated and counted. Thereby, after artificially stripping the hulls, the superior and inferior grains were oven-dried for dry weight calculation. The measured data was then fitted into Richard’s growth equation [43] and the growth duration method [44].

$$\:W=A(1+{Be}^{-kt}{)}^{\frac{-1}{N}}$$

Where W denotes grain weight, A shows the final grain weight, t represents the days after anthesis (d), and B, k, and N denote regression constants. To calculate the average grain-filling rate (GFR_avg), maximum grain-filling rate (GFR_max), days to reach maximum grain-filling (T_max), and the grain weight with the maximum grain-filling rate (W_max), a set of derived formulas from Richard equation was used as follows:

$$\:Grain\:Filling\:Rate\:\left(GFR\right)=\frac{{AKBer}^{-kt}}{(1+{Be}^{-kt}{)}^{\frac{(N+1)}{N}}}$$

$$\:Average\:Grain\:Filling\:Rate\:\left({GFR}_{Avg}\right)=\frac{AK}{2(N+2)}$$

$$\:Maximum\:Grain\:Filling\:Rate\:\left({GFR}_{Max}\right)=\frac{AK}{{(1+N)}^{\frac{(N+1)}{N}}}$$

$$\:Time\:to\:Maximum\:Grain\:Filling\:\left({T}_{Max}\right)=\frac{ln\:B-\text{ln}N}{K}$$

$$\:Maximum\:Grain\:Weight\:Accumulation\:\left({W}_{Max}\right)={A(N+1)}^{\frac{-1}{N}}$$

Where W is the total weight of the grain, A refers to the final grain weight; t denotes the the time after anthesis (d); and B, K, and N are the regression coefficients. The quality parameters were also measured using standard protocols for protein and amylose contents (%), brown and fine rice percentage (%), grain length (mm), grain width (mm), and chalkiness ratio. The agronomic N-use efficiency (NAE, kg kg^− 1), apparent N recovery efficiency (NRE, %), and N physiological efficiency (NPE, kg kg^− 1) were calculated by following formulas:

$$\:Agronomic\:N\:Use\:Efficiency\:\left(NAE\right)=\frac{{Y}_{N}-{Y}_{0}}{{T}_{N}}$$

$$\:Apparent\:N\:Recovery\:Efficiency\:\left(NRE\right)=\frac{{U}_{N}-{U}_{0}}{{T}_{N}}$$

$$\:Phsyiological\:N\:Use\:Efficiency\:\left(NPE\right)=\frac{{Y}_{N}-{Y}_{0}}{{U}_{N}-{U}_{0}}$$

Where Y₀ represents the grain yield (kg ha^− 1) while U₀ represents the total N content accumulated in the aboveground biomass at physiological maturity (kg ha^− 1) for the treatment without any application of N fertilizer. Y_N and U_N denote the grain yield (kg ha^− 1), and the total N accumulated in the aboveground biomass at physiological maturity (kg ha^− 1) for the treatment with respective N application (N) rates. T_N refers to the total N (kg ha^− 1) applied in each treatment.

From each surveyed field, ten plants were randomly selected for non-destructive measurement of leaf area index (LAI) using a plant canopy analyzer (Delta-T Devices Ltd., Burwell, UK). To further validate the results, the LI-3000 Portable Leaf Area Meter was used for non-destructive measurement of leaf area (https://www.licor.com/env/products/leaf-area/LI-3000 C/). Specific leaf area (SLA) was calculated by the manual destructive method where one-sided surface area of a fresh leaf was divided by its dry weight. Crop growth rate (CGR) was also measured by observing the dry biomass accumulation [45].

$$\:Crop\:Growth\:Rate\:\left(CGR\right)=\frac{W2-W1}{T2-T1}$$

Where W₁ and W₂ are dry weight accumulation on respective growth stages while T₁ and T₂ are the duration differences between growth stages under consideration.

To calculate the time of day of anthesis (TOA, hasr) as well as duration of anthesis (h), an area of 1m² was marked in each plot and titled as the subplot. Each subplot was critically observed every day during the entire anthesis phase every 30 min or less, from sunrise until the end of anthesis on the last spikelet about early afternoon. Usually, the onset of anthesis is explained as the time after sunrise when at least 5 panicles in the sub-population already started anthesis, with at least one opened spikelet visible on each of the 5 panicles. The maximum anthesis is when all panicles of the sub-plot have started anthesis where at least one spikelet opened on every panicle. Lastly, the end of anthesis is termed as when all the panicles in the sub-population have ended the anthesis (change of stamen color and its droopiness and spikelet closure). Grain yield and yield components were assessed except for border plants by marking the middle 1m² area in each plot and adjusting to the constant moisture content. Plant samples were collected from nine representative hills in each plot to evaluate yield and yield components and were then divided into straw, panicles, and grains.

Statistical analysis

For statistical analysis of experimental variables, one-way analysis of variance (ANOVA) was applied to evaluate differences among treatments using SPSS V22.0 software (Softonic International, Spain) and validated by the Statistix V8.1 (Analytical Software, Tallahassee, Florida, United States). The F-test, performed through ANOVA, determines whether there are any statistically significant differences among the means of the treatments. However, it does not specify which specific treatments differ from each other. Significant differences between treatments are presented by different letters according to Tukey’s HSD test at 0.05 probability (p < 0.05). Duncan’s multiple range test (DMRT) was employed to assess the specific differences between pairs of treatment means. The use of Tukey’s HSD test and DMRT in our study was based on the need to perform multiple comparisons among treatment means after detecting significant differences through an F-test. These tests control for Type I errors and provide a clear understanding of how each treatment compares to others. Graphical presentation of the data was done through Origin-2018 software (OriginLab, Northampton, USA) and SigmaPlot 14.0 (http://www.systat.de/spw_installation_EN.html).

Results

Total N content after harvesting

Co-application of organic sources with synthetic fertilizers substantially affected the total soil N content (Table 3). The overall organic matter (OM) content increased in compost treatment from 28.14 g kg^− 1 to 29.03 g kg^− 1 followed by the FYM treatment. The two-year mean data showed poultry compost mixed application with synthetic urea produced the maximum total N contents (TNC) (1.36 g kg^− 1), followed by FYM mixed with synthetic urea (1.34 g kg^− 1). The same trend was seen with other physicochemical properties where the highest values of TPC (18.58 g kg^− 1) and TKC (16.42 g kg^− 1) in compost applied treatment.

The highest RAN, RAP, and RAK were noticed in the poultry compost treatment with values of 78.89 mg kg^− 1, 36.43 mg kg^− 1, and 117.21 mg kg^− 1, respectively, followed by FYM treatment. The ratios of the treatments and the years’ average had a significant effect while the two-year ratio interaction presented no significant effect on the TNC of rice. The TNC increased by 8.3% in the rest of the plots and decreased by 11.3% in the control treatment plots using the two-year average.

Table 3 Mean values of the physicochemical properties of composite top-soil samples taken before sowing and after crop harvesting at varying soil depths ranging between 0–20 cm

Plant photosynthesis and physiology

The leaf N content and photosynthetic N use efficiency (PNUE) showed an increasing trend towards the co-application of organic and inorganic fertilizers (Fig. 1). The two-year mean data for photosynthetic rate (Pn) (data not presented here) showed that all genotypes increased leaf N content with mixed application and decreased towards synthetic urea application or no application. The highest leaf N content was noticed in compost mixed treatment with the values of 3.06 mg cm^− 2 in genotype NUYT-4 followed by 2.75 mg cm^− 2 in FYM mixed plots. The shoot dry weight (SDW) of all genotypes was substantially higher for all genotypes in organic fertilizer treatments (Fig. 1). Maximum SDW was observed in compost-applied treatment with the value of 77.62 g hill^− 1 in NUYT-1 followed by NUYT-5 (76.08 g hill^− 1). In the same way, FYM applied treatment furnished comparatively reduced SDW with the value of 68.58 g hill^− 1 in NUYT-5 followed by NUYT-2 (65.52 g hill^− 1). The data indicates that organically modified plots may promote root-shoot growth by optimizing and regulating root-shoot interactions during all growth stages which paved the way for efficient adsorption of available N.

Fig. 1

Effect of partial replacement of synthetic urea with organic fertilizers on shoot dry weight (SDW, g hill^− 1) and leaf N content (%) at maturity on different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

The root dry weight (RDW) first increased and thereby started to decrease from the tillering towards the maturity stage. The largest values of RDW were seen in compost-applied plots with the highest value in NUYT-5 (8.36 g hill^− 1) followed by NUYT-6 and NUYT-1 with values of 8.20 g hill^− 1 and 8.07 g hill^− 1, respectively (Fig. 2). The two-year mean for RDW furnished decreased values in synthetic urea-applied and control treatments with maximum values in NUYT-6 (6.31 g hill^− 1 and 5.40 g hill^− 1, respectively). The overall root N contents increased under partially modified treatments in all genotypes (Fig. 2). The highest values of root N contents at maturity were seen in compost-applied plots with values of 3.35% in NUYT-3 followed by 3.16% in the same genotype (Fig. 2).

Fig. 2

Effect of partial replacement of synthetic urea with organic fertilizers on root dry weight (RDW, g hill^− 1) and root N content (%) at maturity on different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Nitrogen adsorption, uptake, and utilization efficiency

Apparent N recovery efficiency (NRE), physiological N use efficiency (NPE), and agronomic N use efficiency (NAE) decreased with sole reliance on synthetic N fertilizer while it increased in organically modified treatments (Fig. 3). The highest values were in compost treatment in NUYT-3 followed by NUYT-6 (66.74% and 64.15%, respectively). The FYM treatment produced the higher values in NUYT-3 followed by NUYT-4 (62.12% and 60.82%, respectively). Based on two-year mean data of NRE, NUYT-3 and NUYT-5 were marked as the category with the highest N-adsorption efficiency, NYUT-2 and NUYT-4 were categorized as medium and NUYT-1 and NUYT-6 were categorized as poor N adsorption efficiency. The same trend was seen regarding NPE and NAE with the highest values in compost treatment at 49.63 kg kg^− 1 and 30.83 kg kg^− 1, respectively (Fig. 3).

Fig. 3

Effect of partial replacement of synthetic urea with organic fertilizers on apparent N recovery efficiency (NRE, %), physiological N use efficiency (NPE, kg kg^− 1), and agronomic N use efficiency (NAE, kg kg^− 1) at maturity on different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Grain-filling rate and grain weight accumulation

Richard’s equation was employed during the grain-filling phase to assess the grain-filling rate and grain weight accumulation. NUYT-3 produced the highest grain weight of superior and inferior grains in compost treatment with values of 27.31 mg grain^− 1 and 13.12 mg grain^− 1, respectively (Fig. 4). Evaluation of variation in dry weight accumulation between study years amongst all genotypes showed an unpretentious decrease in the weight of superior and inferior grains in urea-applied treatment. In FYM treatment, the highest grain weight accumulation of superior grains was seen in NUYT-1 with a value of 26.23 mg grain^− 1, whereas inferior grains of NUYT-3 produced higher grain weight (12.57 mg grain^− 1) (Fig. 4). N plays a critical role in the growth and development of rice plants where the concrete foundation of efficient N adsorption in compost and FYM treatment presented a significant increase in grain weight by expanding the source-sink capacity of the plant (Fig. 4).

Fig. 4

Effect of partial replacement of synthetic urea with organic fertilizers on dry weight accumulation (mg grain^− 1) of superior and inferior grains of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

The maximum grain-filling rate of superior and inferior grains during the initial phase of grain-filling was seen in NUYT-3 under compost treatment with 10.03 mg grain^− 1 day^− 1 and 5.15 mg grain^− 1 day^− 1 followed by FYM treatment in the same genotype with 9.33 mg grain^− 1 day^− 1 and 3.36 mg grain^− 1 day^− 1, respectively (Fig. 5). The overall grain-filling stage comprised 42–45 days depending on the genotypes’ environmental conditions and genetic make-up. Superior and inferior grains in NUYT-6 showed the minimum rate of maximum grain-filling during early stages with the potential of 1.78 mg grain^− 1 day^− 1 and 1.06 mg grain^− 1 day^− 1, respectively. The dry weights of superior grains among all genotypes showed the same increased weights trend (typical S-curve) in compost followed by FYM treatment due to better utilization of slowly available N content. In contrast, the dry weight in inferior grains presented a low filling rate (Fig. 5).

Inferior grains furnished a boosted curve for grain-filling rates with increasing values during the last phase of grain-filling. During the middle phase, inferior grains in NUYT-1 and NUYT-6 presented an irregular curve with relatively poor grain weight accumulation that might be ascribed to the prevalence of environmental conditions. The time acquired to achieve maximum grain-filling changed significantly among treatments indicating the difference in utilization of available N content which proposed varying impacts on genotypes. Considering the superior grains, the two-year mean time difference between compost and FYM to reach maximum grain-filling was minor with a value of 5 days and 3 days, and for superior grains 7 days and 5 days, respectively. However, the mean time difference to reach maximum grain-filling between the organic and inorganic sets of treatments was significantly higher as synthetic urea treatment took 4 days more than organic ones. Higher grain-filling rates in compost and FYM treatments resulted in higher and faster assimilate accumulation which led to constant and enhanced grain-filling.

Fig. 5

Effect of partial replacement of synthetic urea with organic fertilizers on grain-filling rate (mg grain^− 1 day^− 1) of superior and inferior grains of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Crop growth rate, leaf area index, and specific leaf area

The leaf area index (LAI) evaluates the growth ratio of the plant under specific conditions and proposes the final grain yield, whereas the specific leaf area (SLA) evaluates the plant growth in terms of the canopy’s total leaf area for one plant. Additionally, SLA also determines sunlight interception as well as the light use efficiency which is one of the critical variables in plant growth because it estimates the per unit biomass production. LAI and SLA were observed and measured on five growth stages including tillering, booting, heading, grain-filling, and physiological maturity which showed a progressive and increasing trend till heading and thereby started to decrease (Fig. 6). The highest values of SLA were observed at booting in NUYT-5 in compost treatment with a two-year mean value of 42.86 kg m^− 2 followed by FYM treatment (41.26 kg m^− 2). At physiological maturity, the highest values for SLA were in NUYT-3 in compost treatment (34.85 kg m^− 2) followed by FYM treatment (34.39 kg m^− 2). Maximum LAI at the heading stage was measured in NUYT-5 (7.95) in compost treatment followed by NUYT-2 (7.89) (Fig. 7). The FYM treatment plots also had higher values for LAI, however, the synthetic urea treatment had decreased LAI values due to limited and inefficient N adsorption.

Fig. 6

Effect of partial replacement of synthetic urea with organic fertilizers on specific leaf area (SLA, kg m^− 2) of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Crop growth rate (CGR) is defined as the dry matter accumulation per unit area of the plant. Specifically, CGR can be termed as the measure of the increase of plant dry biomass over a unit area for a duration between two growth stages. Total dry matter accumulation (TDM) was highest in compost followed by FYM treatments due to efficient slow adsorption and uptake of available N (Fig. 8). TDM was calculated on tillering, booting, heading, grain-filling, and physiological maturity which furnished the 4 times CGR measurements including CGR-1 (tillering-booting), CGR-2 (booting-heading), CGR-3 (heading-grain-filling), and CGR-4 (grain-filling-physiological maturity). Provision of sustained and optimum N is one of the critical factors ensuring optimum plant growth, where this study showed relevance as N availability, adsorption, uptake, and use efficiency were higher in partial organic treatments. The highest CGR between booting-heading was noticed in NUYT-5 with values of 24.85 g m^− 2 day^− 1 in compost-applied treatment while FYM treatment showed the higher values relative to urea plots in NUYT-4 (23.91 g m^− 2 day^− 1) (Fig. 8).

Fig. 7

Effect of partial replacement of synthetic urea with organic fertilizers on leaf area index (LAI) of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Fig. 8

Effect of partial replacement of synthetic urea with organic fertilizers on crop growth rate (CGR, g m^− 2 day^− 1) of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Difference in time of day of anthesis and duration of anthesis

Variation in duration of anthesis (h) and time of day of anthesis (TOA, hasr) was observed critically during the anthesis phase for 10 days because day length, solar radiation, and agronomic fertilizer management impacted the anthesis during both study years (Table 4). The two-year mean showed that agronomic management impacted the anthesis as the onset of anthesis was earliest in all genotypes under compost-applied (4.9 hasr, NUYT-3) treatment. The time taken to reach maximum anthesis was minimum in compost-applied plots with the value of 5.9 hasr in NUYT-3. The difference in TOA between treatments was marginally significant and there was a small standard error mean due to an increased number of daily observations throughout the anthesis period. TOA values differed non-significantly between study years due to marginal differences in prevailed environmental conditions. Nonetheless, across the two-year mean, various factors were considered to correlate with the observed components of TOA. Increased adsorption of N content during early growth stages paved the way for better adaptation under stressful and changed environmental conditions.

Table 4 Effect of partial replacement of synthetic urea with organic fertilizers on time of day of anthesis (TOA, hasr) and duration of anthesis (h) of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Variation in grain yield and yield components

The overall values for yield-contributing traits increased with the increased N adsorption and availability amongst all genotypes where the grain yield (GY) and biological yield (BY) were significantly higher in organically amended treatments relative to sole urea application (Table 5). Plant height and effective tillers per hill increased in the organic treatments with the highest values of 110 cm and 25 in compost treatment followed by 100 cm and 19 in FYM treatment, respectively. Compared with compost and FYM treatments, the grains per panicle and panicle weight significantly decreased in solely urea-applied plots amongst all genotypes (Table 5). NUYT-6 furnished the highest BY and GY in compost-applied treatment with values of 3.45 kg m^− 2 and 1.04 kg m^− 2, respectively. Panicle length (PL) and seed setting rate were highest in compost-applied plots which employs increased plant productivity under efficient N utilization conditions implying that increased GY for compost and FYM plots was majorly attributed to increased seed setting rate (sufficient and intermediate N availability and adsorption conditions, respectively).

Table 5 Effect of partial replacement of synthetic urea with organic fertilizers on yield and yield-contributing traits of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Variation in quality parameters

The correlative analyses for two-mean data showed a strong correlation between N source and quality contributing components. The protein and amylose contents were maximum in the compost-applied treatment (9.4% and 18.9%, respectively) followed by the FYM-applied treatment (9.2% and 18.3%, respectively) (Table 6). There was a significant positive correlation between grain quality components and organic sources of N mentioning that better N adsorption and uptake along with environmental variables had been the main controlling factors for grain quality. NUYT-2 under compost-applied plots furnished maximum fine rice rate (69.1%) followed by FYM treatment (69.0%).

Similarly, grain length (GL) and grain width (GW) showed increasing values in compost and FYM treatments amongst all genotypes. The balanced N release from organic sources supports uniform grain development, leading to longer and wider grains. Maximum GL and GW were noticed in compost treatment with the highest values of 5.73 mm and 2.67 mm, respectively (Table 6). The two-year mean results proposed that organic fertilizers were effective in enhancing grain nutrient levels, causing a significant increase in extractable and soluble essential nutrients. Improved soil health from organic fertilizers reduces stress on plants and improves grain-filling resulting in more uniformly filled grains with fewer chalky areas with improved overall appearance and quality of the grain.

Table 6 Effect of partial replacement of synthetic urea with organic fertilizers on quality-contributing traits of different green super rice (GSR) elite lines (two-year mean 2022 and 2023)

Discussion

Relationship between plant N adsorption and growth and yield

The nitrogen (N) use efficiency (NUE) in rice is a multifaceted indicator encompassing several processes, including N adsorption, transportation, distribution, and assimilation. These processes are crucial in defining various forms of NUE, such as physiological NUE, apparent N recovery efficiency, N utilization efficiency, agronomic NUE, N uptake efficiency, remobilization efficiency, and N transport efficiency [46, 47]. Generally, plants uptake the N from available soil N contents for biomass production, which establishes the NUE of the rice plant [48, 49]. In the current study, the measurement of N accumulation at physiological maturity was used as screening criteria to evaluate the best proposed partial replacement techniques, to assess the effectiveness of N adsorption and N uptake on grain yield. In this study, grain yield (GY) and total N content (TNC) increased under partial replacement of synthetic fertilizer and were substantially higher than sole urea application. Biological yield (BY) specifically aboveground dry matter accumulation presents the foundation material for the grain yield formation. Generally, dry matter accumulation for rice between heading to maturity mainly accounts for about 90% of grain weight gain which deduces the higher dry weight accumulation between heading to physiological maturity, the more the grain yield [50, 51]. Increased grain N contents and dry weight accumulation during later stages of spikelet differentiation may promote the production of large panicles. These findings reinforce the notion that organic fertilizers, when used in conjunction with inorganic sources, can improve the overall N dynamics within the plant, leading to better crop performance [52, 53].

The residual impact of inorganic and organic N sources on available N status presented that decreased soil N concentration was noticed where the N source was the sole mineral fertilizer as compared to remaining co-application treatments [54, 55]. Higher N concentrations were observed in compost-applied plots followed by FYM, corroborating previous research that has shown the benefits of organic amendments in enhancing soil fertility and organic matter content [56, 57]. These findings suggest that the complementary use of organic and inorganic fertilizers is a sustainable and eco-efficient strategy for improving NUE and maintaining soil health. The increased soil organic carbon (SOC) and available NPK levels observed in organic-inorganic co-application treatments further support this conclusion [58, 59]. Over the long period, about an 80% increase in soil organic matter was seen over a 2-decade long-term application of FYM as compared to about a 10% increase with synthetic NPK fertilizer application [60, 61]. Therefore, our study advocates for the integrated use of organic and inorganic fertilizers to enhance crop productivity while preserving soil health.

Relationship between plant N uptake and morphophysiological traits

The co-application of organic and inorganic fertilizers demonstrated a significant advantage in enhancing shoot dry weight (SDW), root dry weight (RDW), leaf N content, and root N content at physiological maturity compared to the sole application of synthetic fertilizers. This improvement indicates enhanced N adsorption and uptake, which, in turn, promoted better morphophysiological development in the rice genotypes studied [62]. The increase in root-shoot ratios observed at the tillering stage under organic fertilizer treatments suggests that plants were effectively mobilizing carbohydrates to support root growth. This early-stage root development is critical, as it establishes a strong foundation for beneficial root morphophysiological traits that support the plant during later growth stages.

Research has shown that rice plants develop larger root biomass with elongated roots under conditions that favor better N adsorption [63, 64]. The competition between shoot and root growth for carbohydrate resources means that roots with improved morphophysiological traits will absorb more carbohydrates and energy, which can limit shoot growth but ultimately result in a more robust root system [65, 66]. The residual effect of combined and sole application of inorganic and organic fertilizers demonstrated a decrease in N contents when applied solely in mineral form compared to the co-use of organic and inorganic fertilizers [66,67,68]. Enhancing soil fertility in organic cropping systems improves soil biological properties which ultimately affects the N availability to the plants. Co-application of organic manures and synthetic fertilizers improves N mobilization and soil microbial activities [69].

Root and shoot traits showed great variability in the self-adaptability of the genotypes under varying N application regimes. In this study, all genotypes exhibited higher leaf and root N contents, increased SDW and RDW, higher root-shoot ratio, and increased root length at all growth stages under the co-application of organic and inorganic fertilizers. This featured that all genotypes showed early plant morphophysiological adaptation to slow but consistent N supply under organic treatments presenting a strong correlation between morphophysiological traits and yield. Notably, the seed-setting rate showed a positive correlation with root and shoot morphophysiological characteristics during the grain-filling stage. It is widely accepted that rice plants develop larger roots with enhanced physiological activity under conditions of efficient N adsorption, such as those provided by the co-application of organic and inorganic inputs, compared to conditions of limited N adsorption [70,71,72]. Conversely, the faster, imbalanced, and increased N supply from sole synthetic N applications weakened the relationship between N uptake, plant morphological traits, and grain yield over time. This finding suggests that the physiological characteristics of roots are critical factors limiting yield during the later growth stages [73].

Relation between N uptake and grain-filling

Excessive and irregular use of nitrogen (N) fertilizers has long been associated with reduced nitrogen use efficiency (NUE), leading to significant environmental challenges such as leaching, volatilization, eutrophication, and ultimately soil degradation [74,75,76]. These issues not only threaten rice productivity but also raise concerns about the sustainability of intensive rice farming systems. To address these challenges, many N management practices have been undertaken including site-specific nutrient management, slow-release fertilizers, deep placement, and integrative crop management [77, 78]. While these practices have shown positive results, their widespread adoption has been hindered by economic constraints, labor requirements, and limitations in existing technologies. In contrast, mixing organic and inorganic fertilizers presents more sustainable and practical for the paddy rice system which improves soil fertility and structural stability while minimizing environmental concerns [79, 80]. This is particularly relevant as rice grain yield depends on the effective assimilation of nutrients by photosynthetic tissues and the subsequent translocation of these assimilates to the grain, processes commonly referred to as the “source” and “sink,” respectively [81, 82]. In the current study, increasing grain-filling rate and improved grain-weight accumulation were observed in the co-application of organic and mineral fertilizer treatments. These findings are consistent with previous research, which has demonstrated that organic fertilizers enhance the efficiency of photosynthetic tissues, leaf photosynthesis, specific leaf area, and chlorophyll content, thus improving dry matter accumulation thereby causing an increase in total source translocation [83, 84]. Additionally, the application of organic fertilizers was found to improve the number of fertile panicles and the overall number of spikelets on a panicle [85]. The relationship between organic fertilization and source-sink dynamics has been extensively studied, with numerous investigations highlighting the strong correlation between organic inputs and improved dry-weight accumulation. These studies have quantified the source-sink association to determine whether rice is source- or sink-limited under varying conditions [86,87,88]. For instance, a study has shown the improved dynamics of source activities and sink demand during grain-filling through an extended quantified modelling approach [89]. In line with these findings, the present study assessed variations in grain-filling and source-sink translocation under different N regimes. The results revealed that the co-use of inorganic and organic fertilizers positively influenced the source-sink relationship, as evidenced by increased grain-filling rates and dry weight accumulation. These observations underscore the importance of understanding and managing source-sink dynamics in rice production, particularly when adopting sustainable fertilization strategies.

Relationship between N uptake and grain quality

Organic fertilizers increase soil OM, which enhances the availability of N crucial for protein synthesis. The balanced N supply from compost and FYM supports the metabolic processes involved in starch synthesis which helps in achieving optimal amylose content important for the texture and cooking quality of rice. The physicochemical traits of rice grain are intricately linked to various factors including management practices, cultural techniques, processing methods, and genetic makeup [90, 91]. Mixed application of inorganic and organic fertilizers improved the quality traits such as protein, amylose, and fats alongside physical properties such as grain length and grain width relative to the sole application [92, 93]. The variation in amylose, protein, and fat contents is complex because they depend not only on genetic makeup but also on cultural management and milling practices [94, 95]. Generally, the amylose, fat, and protein contents are essential to assess the grain quality in rice. Low amylose contents lead to sticky rice grains while higher amylose contents can result in harder grains that are more prone to breakage. Moreover, higher amounts of fats and protein content increase the nutritional value of rice grains. In the current study, rice grains under organic treatments had the highest and optimally required protein, amylose, and other positive quality traits. This suggests that the co-application of organic and inorganic fertilizers can optimize the production of amyloplasts and starch contents, leading to more compact and well-developed endosperm components. Specifically, the formation and development of the endosperm, including its components such as amyloplasts and starch granules, were found to be optimal under organic treatments. In the rice endosperm, the protein percentage falls typically around 8% of air space between starch granules and amyloplasts where protein particle is spherically shaped size differs between 0.5 μm and 4.0 μm which occupies maximum grain content [96,97,98]. The study found that rice grains grown solely under inorganic fertilizers had unclear cell walls, numerous air spaces, and round starch granules while in contrast, the rice grains grown under organic inputs have limited air spaces, distinct cell walls, and polygonal starch contents [99, 100]. Crop plants essentially take up nutrients in ionic forms, regardless of whether the source is organic or inorganic, however, the composition of the soil environment, influenced by different nutrient sources, can affect nutrient availability, plant metabolism, and ultimately the expression of certain phenotypic traits [101]. Organic nutrient sources, for instance, may improve soil structure, enhance microbial activity, and release nutrients more gradually, which can interact with the genetic potential of plants in ways that might not be immediately apparent [102]. These interactions can lead to variations in nutrient uptake timing, efficiency, and utilization, potentially influencing grain quality. Furthermore, while the genetic potential of a plant is largely determined by its genotype, environmental factors, including nutrient management, can modulate the expression of certain traits. For instance, the synthesis of proteins, starches, and other compounds in the grain may be influenced by the availability and form of nitrogen during key stages of grain filling [103].

Conclusion

By evaluating the effects of different combinations of mineral N fertilizer with organic inputs on elite GSR genotypes, this research aimed to improve soil and plant N content, as well as overall crop productivity. The current study compared the morphological and physiological plant responses under varying N regimes across different GSR genotypes. The results demonstrated that all genotypes showed stronger responses to slow and continuous N supply from organic sources leading to higher yield potential. Specifically, the co-application of organic and inorganic fertilizers, resulted in higher TNC (1.36 g kg^− 1), SDW (77.62 g hill^− 1), RDW (8.36 g hill^− 1), leaf N content (3.06 mg cm^− 2), and root N content (3.35%) specifically in compost-applied treatment relative to the sole application of mineral fertilizer. The improved root and shoot morphophysiological traits under organic inputs contributed to higher N uptake and grain yield, likely due to the enhanced content and activities of growth hormones during the later growth stages, which increased the seed setting ratio and ultimately boosted yield. Morphophysiological traits played a significant role in determining the N adsorption ability with a larger root system and improved physiological activity enhancing N uptake. However, future research is recommended to better understand the pathways involved in the co-application rate, source, ratio, and period in regulating the plant morphophysiological characteristics and N adsorption to optimize plant N uptake and crop productivity of rice-based systems.