A two-year field study was conducted at the Agricultural Research Station, Agriculture University, Rajasthan, India (25°10’ N, 75°50′ E, and 267 m above msl) from 2018–19 to 2019–20 (Figure 1). The site experiences a subtropical climate with extremely warm and dry summers (April to June) and wet monsoons (July to September) during the soybean season and cold and harsh winters (November to January) during the wheat growing period. The mean maximum temperature ranges between 40 to 48.4°C during May–June, and the mean minimum temperature ranges between 2.0 to 8.5°C during December–January. The study area receives an annual rainfall of 660.6 mm, with the majority falling between the months of June–September. The experimental soil was moderately deep, well-drained, black Vertisols (United States Department of Agriculture classification), clay-loam in texture (sand 25.86%, silt 35.10%, and clay 38.94%), with neutral in soil reaction (7.41). The pre-crop topsoil (0–15 cm) contained organic C (5.1 g kg⁻¹), available N (104.5 mg kg⁻¹), P (9.4 mg kg⁻¹), K (196.0 mg kg⁻¹), S (7.5 mg kg⁻¹), and DTPA-extractable Zn (0.66 mg kg⁻¹), Fe (6.80 mg kg⁻¹), Cu (0.61 mg kg⁻¹), and Mn (7.21 mg kg⁻¹).

The study implemented various combinations of conservation tillage, organic, and chemical management practices, including nutrient and weed management, in a soybean-wheat cropping system. The treatments consisted of five scenarios, namely T1-conservation organic (CAO), T2-conservation chemical (CAC), T3-conventional chemical (CTC), T4-organic management + conventional tillage (OCT), and T5-package of practices (PoPs), which were randomly assigned in a randomized complete block design (RCBD) with four replications (Table 1). The plot size for each treatment was 389 m2 (48 m x 8.10 m). Before sowing the crops each year, well-decomposed farmyard manure (FYM) was incorporated into the soil based on the treatment requirements. The total N content in FYM was determined by Kjeldahl digestion following the distillation method (Jackson, 1973), and the FYM was also analyzed for total P, K, S, and Zn, Cu, Fe, and Mn contents through digestion with an HNO₃:HClO₄ (4:1) mixture and subsequent determination by vanadomolybdophosphoric acid, flame photometric method, and atomic absorption spectrophotometric method, respectively (Manna et al., 2012). The mean nutrient contents of FYM were analyzed as follows: N (0.50%), P (0.26%), K (0.50%), S (0.03%), Zn (24.80 ppm), Fe (173.90 ppm), Cu (5.15 ppm), and Mn (97.45 ppm). a slightly alkaline pH (7.41).

Table 1 presents the agricultural techniques employed for cultivating the test crops, soybean and wheat, during the 2018–19 and 2019–20 seasons. In the rainy (kharif) season, soybean (cv. RKS 45) was sown using a seed drill in mid-July at a spacing of 30 cm (intra-row) x 10 cm (intra-plant) with a seed rate of 80 kg ha⁻¹ and harvested in the last week of October. The experimental site was then irrigated for field preparation and sowing of the succeeding wheat crop in the winter (rabi) season. Wheat (cv. Raj 4,079) was sown at a spacing of 22.5 cm x 5 cm with a seed rate of 100 kg ha¹. Seeding was completed using a seed drill in the first week of December and harvested during the first week of April. Other crop management practices were carried out according to the assigned treatments (Table 1). During the 2018 kharif season, one life-saving irrigation was applied at the pod-filling stage [77 days after sowing (DAS)], while no irrigation was applied during the 2019 kharif season due to sufficient moisture availability at critical stages of soybean growth. However, during the rabi season, four irrigations were applied to the wheat crop at its critical growth stages during the experiment. For soybean, the total quantities of N, P, K, and S were applied as a basal dose, whereas for wheat, 100% of P, K, Zn, and 50% of N were applied at the time of sowing, and the remaining 50% of N was applied after the first irrigation (24 DAS) during the experiment.

Composite soil sampling, involving four depth intervals (0–15, 15–30, 30–45, and 45–60 cm), was done form each plot using a soil auger with 6.0 cm internal diameter after harvest of each crop. The samples were dried in shade and then ground and passed through a 2.0 mm sieve for further laboratory analysis. The soil was analyzed for pH and electrical conductivity (EC; 1,2.5 w/v; Jackson, 1973), organic C (SOC; Walkley and Black, 1934), cation exchange capacity (CEC; Jackson, 1973), and exchangeable Ca and Mg (Jackson, 1973). The soil was also analyzed for also available nutrients like N (Subbiah and Asija, 1956), P (Olsen et al., 1954), K (Schollenberger and Simon, 1945), S (Chesnin and Yien, 1950), Zn, Fe, Cu, and Mn (Lindsay and Norvell, 1978). Bulk density (BD) of experimental site was measured using a core sampler (Blake and Hartge, 1986), and the soil porosity was calculated by the following equation:

At maturity, soybean and wheat crops were harvested manually for economic yield, and the equivalent yield and system productivity were calculated using the following equations:

System productivity was calculated by adding the soybean yield and soybean equivalent yield of the wheat for the respective years.

The minimum support price (MSP) was for soybean (₹ 34,000 t⁻¹ and ₹ 37,000 t⁻¹) and wheat (₹ 18,400 t⁻¹ and ₹ 19,250 t⁻¹) during the year 2018–19 and 2019–20, respectively. 1 USD ($) = 82 INR (₹).

The data presented in this study were pooled from both years and analyzed using two-way analysis of variance (ANOVA) in Statistical Analysis Software v9.4 (SAS Institute, 2016; Supplementary Table S1) and R statistical software (R Core Team, 2016). The relationship between various treatment scenarios and variables was calculated, and the variables were classified based on stability and mean (Yan and Kang, 2002). The effect of different treatments on soil chemical properties was analyzed using a biplot analysis through principal component (PC) with the support of R Studio (RStudio Team, 2014). A Pearson’s correlation matrix (correlogram) was constructed to determine the degree of correlation between the tested soil variables.

It was observed that the effects of different management practices on soil bulk density (BD), particle density (PD), and porosity under the soybean-wheat cropping system were non-significant (p > 0.05; Table 2). However, the conservation organic crop management practice resulted in a reduction of BD (1.2 Mg m−3) and subsequently increased soil porosity (51.8%) at the topsoil (0–15 cm). Previous studies have shown that minimum tillage and the application of organic manures for many consecutive years can reduce soil bulk density and increase porosity (Govaerts et al., 2009; Gathala et al., 2011). Soil bulk density is an important indicator of changes in soil physical condition and water holding capacity due to different tillage practices (Jin et al., 2007). Alam et al. (2014) observed a significant reduction in soil bulk density under zero tillage, minimum tillage, conventional tillage, and deep tillage when compared to initial values, which supports the results of our study.

Unlike soil physical properties, tillage and crop management practices had significant influence (p < 0.05) on soil physico-chemical properties involving pH, EC, and SOC (Figures 2A–C). Conservation organic (CAO) and OCT resulted in lowering pH towards neutrality. Similarly organic management (CAO and OCT) significantly reduced EC as compared to CTC and PoPs. There was an increasing trend in pH and along the soil depths, irrespective of the treatments. Averaged across the depths, although CAO and OCT recorded higher CEC but remained at par with other treatments (Figure 2D). SOC showed a depleting trend along with increasing soil depth across the treatments (Figure 2). At 0–15 cm, the highest SOC was recorded under conservation organic (6.8 g kg⁻¹) followed by organic management + conventional tillage (6.6 g kg⁻¹), and the least was observed in the package of practices (5.6 g kg⁻¹). A similar trend was also noticed for other soil depths. Averaged over the soil depths, conservation organic (CAO) recorded 16.3% higher SOC as compared to PoPs over 2 years of experimentation.

Organic carbon in soil ecosystem is mostly controlled through a complex interaction between soil edaphic factors and land husbandry (Yadav et al., 2020). Residues and dead-decaying debris of crops are the main contributor to the organic carbon accumulation in the soil (Lal, 2004). Previous reports indicated that SOC can be increased by reduced tillage (Neugschwandtner et al., 2014) and by crop residues retention (Hati et al., 2015). Onward 60 cm depth, significant increase in SOC under CAO might be due to relatively high quantity of organic inputs through FYM and minimal soil disturbance resulting better permanency of soil organic matter (Hati et al., 2015; Mohanty et al., 2020; Yadav et al., 2020). A likewise increment in SOC under OCT again suggests that SOC accrual was chiefly governed by FYM addition rather than by tillage practices. Earlier, Meena et al. (2019) also demonstrated that FYM addition can significantly increase SOC content in the soil. Apart from increasing SOC, continuous addition of high quantity of FYM can also decrease soil pH (Hao and Chang, 2002; Rayne and Aula, 2020) by lowering the conductance, which corroborates our observation. On the other side, increase in CEC under CAO and OCT may be attributed to the presence of organic matter in manure that decomposes to increase the negatively charged sites on carboxyl and phenolic hydroxyl groups (Hao and Chang, 2002; Miller et al., 2016).

Tillage and crop management had a significant (p < 0.05) impact on the availability of primary nutrients (N, P, and K) as shown in (Figures 2E–G). The CAO crop management treatment had the highest availability of primary nutrients across all soil depths and was significantly (p < 0.05) higher than the PoPs treatment. Compared to PoPs, the CAO and CAC treatments showed about a 10.0% increase in N availability. Nitrogen availability decreased across all treatments from 126.2 (0–15 cm) to 89.9 mg kg−1 (45–60 cm). Similarly, compared to CTC and PoPs, conservation tillage with organic and chemical management greatly increased the availability of P (7.9 to 14.7%) and K (5.5 to 7.4%). This is further illustrated in the biplot analysis (Figure 3). Additionally, the availability of P and K decreased with increasing soil depth across all treatments. On the other hand, a strong positive correlation between SOC and the availability of primary nutrients was observed (Figure 4).

The higher availability of N , P , and K in conservation tillage with organic and inorganic nutrient and weed management may be attributed to the increased supply of organic matter and improved soil ecosystem for nutrient cycling. Organic manures, in general, act as slow-release fertilizers, and their decomposition leads to an enhanced availability of nutrients (Mandal et al., 2000; Meena et al., 2019). Previous studies have shown that combining N fertilizer with quality crop residues can have a positive interactive effect on mineral N (Gentile et al., 2008). In contrast, straw incorporation in soil has been found to increase microbial biomass and N mineralization, leading to a higher nutrient supply in soil (Eagle et al., 2000; Choudhary et al., 2018; Dhaliwal et al., 2023b). These observations suggest that both organic and inorganic nutrient management can increase nutrient availability in soils, supporting our findings. Additionally, changes in SOC due to tillage practices can influence N content, with conventional tillage resulting in greater losses due to frequent tillage, higher leaching, and mineralization losses (Lal, 1997; Cui et al., 2023). This may explain the lower N availability observed under CTC.

Again, higher availability of N and P was observed in surface soil under zero tillage and minimum tillage. The build-up of available P in soil is attributed to its constrained downward movement, as reported in previous studies (NzeMemiaghe et al., 2022). The higher availability of K and P under conservation and organic management practices might be attributed to reduced fixation or solubilization of fixed forms due to the higher prevalence of organic acids as well as mineralization of added organic manure, as reported in previous investigations (Yadav and Kumar, 2002; Berner et al., 2008; Mahanta and Rai, 2008; Elayarajan et al., 2015; Meena et al., 2019). Moreover, mobilization of non-exchangeable K into the soil solution might have increased its availability in the soil under conservation and organic management practices (Venkatesh et al., 2017). Simultaneous increase in soil organic carbon and availability of nutrients with crop residue amendments has also been reported in soybean (Singh and Rai, 2004) and is in line with our observation on positive correlation between SOC and primary nutrients.

The availability of Ca, Mg, S, (Figures 5A–C) and micronutrients (Figures 5D–G - available Zn, Fe, Cu, and Mn) at different soil depths was significantly (p < 0.05) affected by tillage and crop management practices (Figure 5). The CAC treatment showed the highest availability of exchangeable Ca and Mg, which was significantly (p < 0.05) higher than the CAO and OCT treatments. Conversely, S availability was comparable between CAC and PoPs but remained significantly (p < 0.05) higher than the other treatments. Notably, the least availability of secondary nutrients was observed in OCT. Zinc availability was significantly (p < 0.05) higher with PoPs, followed by CAO (Figure 5). Furthermore, Fe and Mn availability increased by 6.5 and 17.3%, respectively, with CAO compared to PoPs management. However, Cu availability was significantly (p < 0.05) higher with CAC than the other treatments. Similar to primary nutrients, the availability of secondary and micronutrients also decreased with increasing soil depth across all treatments. Apart from the availabilities, a close view of the biplot graphs revealed distinct position of S and Zn across the soil depths (Figure 3).

Overall, the availability of secondary and micronutrients in the soil was greatly improved by the addition of nutrients from organic and inorganic sources, as well as by tillage practices that affected both the quantity and mineralization of nutrients in the soil. Our results support the findings of Gadana et al. (2020), who also reported a positive impact of soil management practices on exchangeable cations and soil micronutrients. Crop residue retention and the addition of organic manure and mineral fertilizers provided an added advantage for better microbial growth, which accelerated nutrient mineralization and led to enhanced nutrient availability (Kiboi et al., 2021). It is worthy to note that the availability of secondary nutrients remained high for the treatments receiving chemical fertilizers in conjunction with manure. In this study, we used single superphosphate as the P source, which contains a fairly high quantity of Ca and S (Barker, 2019). Therefore, the increased availability of these nutrients in chemically fertilized plots is not surprising.

Regardless of the management practices, the soil in this study showed high availability of micronutrients in comparison to the critical limits identified for Indian soils (Katyal and Sharma, 1991; Debnath et al., 2022), which contrasts with the marginal to medium status of available Fe and Zn and the medium to high status of available Mn and Cu concentration in farmed Vertisol parcels in India (Somasundaram et al., 2009). Therefore, conservation tillage coupled with organic nutrient management may be a sustainable practice to maintain the availability of micronutrients in the soils of this region. However, their removal from crop biomass with continuous cropping may decrease their phytoavailability in soils in the future. Periodical soil testing may thus help to decipher their depletion in soil so as to undertake appropriate remedial measures. Distinct position of S and Zn in biplots suggests their role as key indicators of sustaining soil health in the soybean–wheat systeam in arid ecology. Therefore, periodic monitoring of their availability remains indispensable to avoid yield trade-offs due to their short supply.

Compared to the 30–45 cm depth, a slightly higher availability of micronutrients was observed at the 45–60 cm depth, possibly due to leaching from the upper layer and accumulation at a later soil depth. However, this effect was absent for secondary nutrients, suggesting their leaching into deeper soil layers. This indicates that the leaching of micronutrients into deeper soil layers was possibly prevented by the formation of organo-mineral complexes or chelation due to organic inputs and increased soil organic matter (SOM). The higher availability of Zn with PoPs and CAO may be due to Zn application and organic matter addition, respectively. Our results also suggest that conservation tillage had a significant effect on Fe availability. Similarly, Jayaraman et al. (2021b) reported that available Fe concentration was relatively higher under no-till than conventional tillage in vertisols of Central India. The hierarchical clustering analysis of different soil properties suggests that organic matter addition has significantly improved the availability of Cu and Mn (Figure 6).

The soybean-wheat cropping system registered the maximum system productivity (SEY) in CAC with a yield of 4.62 t ha⁻¹, which was significantly higher by 13.96 and 18.17% compared to CAO and OCT, respectively (Table 3). However, SEY of CAC and PoPs was statistically similar. Although nutrient availability increased with organic nutrient management combined with conservation or conventional tillage practices, it did not enhance SEY. This suggests that other factors may have influenced the yields of different treatments. Kravchenko Alexandra et al. (2017) also reported yield penalties of 10–30% under organic management during the initial years. Effective weed management and timely availability of nutrients to the crop under CAC could be the prominent reasons for comparatively higher yields. Tillage operation, nutrient management, and leguminous crops can significantly influence crop yields in a cropping system (Alam et al., 2020). Meena et al. (2022a, 2022b) also reported that CAC evolved as a better crop management practice under the soybean-wheat cropping system, producing the maximum economic yield of soybean over a regime of practice involving the recommended package of practices: conventional tillage + chemical, conservation tillage + organic, and conventional tillage + organic nutrient management.