The study location is situated in India’s 7.2 agro-ecological subregion, and the growing season lasts between 120 and 150 days. The region has a semi-arid (dry) climate with three distinct seasons: the summer (March to May), the rainy season (kharif), which lasts from June to September, and the winter (rabi) (October to February). At the Gungal Research farm of the ICAR-Central Research Institute for Dryland Agriculture (17°40′ 40.4″ N latitude and 78°39′, 55.7″ E longitude and at a mean sea level of 626 m), Hyderabad, Telangana, India, the field experiment was carried out for 10 years between 2012 and 2021.The farm represents a semi-arid tropical region with a mean annual temperature of 25.7°C and rainfall of 746 mm. The monthly rainfall during the crop season (July–December) during the study period (2012–2021) and the monthly maximum and minimum temperature prevailed during the period are given in Figures 1, 2. Soil of the experimental site is sandy loam; slightly acidic in reaction (pH 6.51), EC was in normal range (0.05–0.07 dS m⁻¹), low in organic carbon (0.43%), available N (229.1 kg ha⁻¹), high in available P (24.7 kg ha⁻¹), and medium in available K (218.1 kg ha⁻¹) (3).

Three production systems viz. organic, integrated and control (chemical inputs), and three field crops viz. sunflower (Helianthus annuus L.), pigeonpea [Cajanus cajan (L.) Millsp.], and greengram [Vigna radiata (L) Wilczek] were studied in this experiment every year. The experiment was laid out in strip plot design. All the treatments were replicated thrice in a plot size of 12 m × 4 m. The package of practices in each crop are presented in Table 1. The FYM was sourced from the same place every year and the average composition of 0.5% N, 0.25% P, 0.4% K, 27.9 ppm Cu, 228.7 ppm Mn, 452 ppm Fe, and 143.1 ppm Zn (3).

The FYM was treated with Trichoderma viridae at 2.5 kg ha⁻¹, as a prophylactic measure against soil borne diseases as explained by Gopinath et al. (26). The details of application of nutrients in different treatments are given in Tables 2, 3. Under integrated method, one fourth of the N was applied through FYM. The remaining N and total P and K was applied through mineral fertilizers. In sunflower crop, N was applied in basal and two other splits (30 and 60 DAS). However, in pigeonpea and greengram the nutrients were applied basal.

Every year, the crops were sown after the receipt of monsoon rainfall in the month of June. The organic plots were maintained chemical free throughout the years. Manual weeding and manually operated wheel-hoe were used to keep the plots wee free. The prophylactic measure used are described by the authors in their earlier paper (3). Crops were harvested and the yields were converted to pigeonpea equivalent yield (PEY) as per De Wit (27):

P E Y ( k g h a − 1 ) = [Yield of sunflower or greengram (kg ha⁻¹) × price of sunflower or greengram seed (Rs kg⁻¹)/price of pigeonpea (Rs kg⁻¹)].

A core sampler was used to collect the soil samples before the application of various nutrients and after the crop harvest in 2021 from various soil depts (0–20, 20–40, and 40–60 cm). The soil samples for various microbial activity were kept at 4°C and analyzed within 2 weeks. Bulk density of the soil was determined using metallic cores of known volume. The detailed procedures are explained by the author in their earlier paper (3).

Keen Rackzowski box method was used to determine the WHC and total porosity (28). Potentiometric method as described by Jackson (29) was used for determining soil pH. Available N, P, and K were determined using Kjeldahl method, Olsen’s method and flame photometer method (29–31). Micronutrients were determined using the atomic absorption spectrometry (32). Soil organic carbon was multiplied with BD to arrive at soil carbon stock (33).

Various microbial activities like dehydrogenase (DHA), soil microbial biomass carbon (MBC), urease and acid phosphatase was analyzed/measured using methods of Casida et al. (34), Vance et al. (35), Tabatabai and Bremner (36), and Tabatabai and Bremner (37).

The dried seeds were stored at room temperature prior to analysis for various parameters. The samples of greengram and pigeonpea were analyzed for chemical parameters after tri-acid digestion. Nitrogen content was determined by Kjeldahl method (38). Protein content was determined by using the formula: N × 5.4 (39). Phosphorus content was analyzed photometrically (40). Potassium content was determined by using flame photometer and micronutrients (Fe, Cu, Mn, and Zn) by using atomic absorption spectroscopy. Sunflower oil was extracted using hexane on Soxhlet apparatus using the methodology of Anjani and Yadav (41).

Using the International Rice Research Institute (IRRI) Star and ANOVA, data were statistically evaluated. Tukey’s HSD post hoc comparisons were used to clarify significant differences in means (p < 0.05).

Different production systems significantly influenced the protein content of pigeonpea seed (Table 4). Pigeonpea grown under integrated production system being on par with organic system recorded significantly higher protein content (20.0%) than that of Control (chemical inputs). However, different production systems had no significant influence on protein content of greengram seed. Organic production system being on par with integrated production system recorded significantly greater P content in both pigeonpea and greengram seeds compared to Control (chemical inputs). Significantly greater K content of both pigeonpea and greengram was recorded with organic production system than other treatments. The micronutrient (Fe, Zn, Cu, and Mn) contents of both pigeonpea and greengram seeds varied significantly with different production systems (Table 4). Organic production system being on par with integrated production system registered significantly higher Fe and Zn contents in seeds of both crops compared to Control (chemical inputs). The Zn and Cu contents of organically grown pigeonpea and greengram seed was greater than that of other production systems.

Different production systems had significant effect on sunflower oil content (Figure 3). Integrated production system being on par with Control (chemical inputs) had greater oil content than that of organic production system. Regarding fatty acid composition of oil, organically produced sunflower oil being on par with that of integrated production system had a higher content of oleic acid than Control (chemical inputs). However, no statistical differences were evident among different production systems in terms of palmitic acid, stearic acid and linoleic acid contents.

Yield of all the different crops and cropping system was significantly different in terms of pigeonpea equivalent yield (PEY) in all the years (Figure 4). Rainfall distribution and amount has a greater impact on the yield. Sufficient and well distributed rainfall during 2012 and 2013 resulted in higher yield due to less crop stress. Intermittent dry spells and less rainfall during the others years resulted in PEY less than 1,000 kg ha⁻¹ (Figure 1).

In the first year, the integrated production system greatly outperformed the organic and control (chemical inputs) treatments in terms of PEY production (2012). In the second year, both integrated and organic production systems were comparable (Figure 5) implying the narrowing of gap. However, no significant changes in PEY was observed during the 2014–2017, presumably as a result of extremely low yields in all treatment groups. When compared to the control (chemical inputs), integrated production system produced more PEY in 2017 and 2018 than an organic production system did (Figure 5). During 2019–2021, both organic and integrated production systems recorded similar but significantly higher PEY than Control (chemical inputs).

In our study, the performance of crops varied under different production systems. When the yield data was adjusted for year effect, pigeonpea performed better under organic production system than under other treatments across all the years except 2018 (Figure 8). Averaged across the years, pigeonpea seed yield (721–737 kg ha⁻¹) was similar under both organic and integrated production systems compared to Control (chemical inputs) (672 kg ha⁻¹). In greengram, the seed yields were higher under integrated production system during initial 5 years, whereas organic system recorded marginally higher yields during the latter 5 years compared to other treatments (Figure 9). On average, greengram seed yield (699–706 kg ha⁻¹) was similar under both organic and integrated production systems. Results here are compared with past studies (3, 42–45), where organic crop yields were lower than conventional crop yields during initial years. As the nutrient cycling processes in organic systems change from inorganic N fertilization to organic amendments, lower crop yields in the plots under organic production systems may have been related to the less readily available nutrients in the early years of transition (46–49).

However, integrated production system recorded higher seed yield of sunflower in all the years except during last 2 years where seed yield was marginally higher under organic production system than other treatments (Figure 10). A gradual improvement in seed yield of sunflower was observed under organic production system whereas, the seed yield showed a declining trend in the plots under Control (chemical inputs), over the years. The yield gap between organic and integrated production systems narrowed down after 8 years of study. Integrated production system, averaged across the years, recorded 9.2–10.0% higher seed yield than that of organic and Control (chemical inputs) treatments. Many comparisons between organic and conventional production systems are mostly from relatively short-term experiments (50, 51). However, there are few well documented long-term (more than 10 years) comparisons between organic and conventional production systems. Similarly to our study, Schrama et al. (45) reported that the yield gap between organic and conventional production systems declined during a 13-year experimental period, suggesting that the yield gap between organic and conventional production systems may decline over time.

A large number of studies have been reported that attempt to investigate if there is a difference in the nutritional value of organically and conventionally grown food (52, 53). In general, our results showed marginally lower protein, and higher K and micronutrient (Fe, Zn, Cu, and Mn) contents of both pigeonpea and greengram seeds under organic management than other treatments. Gopinath et al. (54) and Saha et al. (55) also reported similar results. According to Worthington (56), organic produce from various crops had 21% more iron, 29% more magnesium, and 13.6% more phosphorus. According to a study by Lairon (53), organic food has 21 and 29% more iron and magnesium than non-organic food. In sunflower, integrated production system being on par with Control (chemical inputs) had greater oil content than that of organic production system. However, different production systems had no significant effect on fatty acid composition except that organic sunflower oil had higher content of oleic acid.

Numerous desirable soil characteristics, such as a reduction in bulk density, increased porosity, and increased water-holding capacity, have been linked to the use of organic amendments (14, 16, 26, 45, 57, 58). According to earlier studies (16, 18, 19, 59), organic production systems had higher pH levels in mildly acidic soils than their conventional counterparts. Our findings on the impact of organic systems on various chemical properties of soil are similar to those of those earlier studies.

One of the important environmental benefits due to a shift from conventional to organic production systems is an improvement in soil carbon content (11, 60). The SOC was significantly higher in the plots under organic management compared with mineral fertilizer and integrated production treatments. This increment in SOC might be attributed to the direct addition of organic source of plant nutrients which in turn led to lesser mineralization owing to its wider C: N ratio (61, 62). Previously, some long-term experiments reported notable improvements in SOC content through incorporation of organic manures (63). In a similar line, Aoyama et al. (64) observed increased level of organic matter in soil after 18 years of experimentation with the addition of organic manure. Hati et al. (65), Ramesh et al. (66), and Gopinath et al. (3) also reported higher SOC with organic nutrients application on long term basis.

Higher soil P was found in integrated system as reported by Chen et al. (67). Slower release of organic materials, particularly during initial years under organic production results in lower availability of plant nutrients in organic plots (47, 48). Patel et al. (68) also reported an increase in available P with integrated application of NPK and FYM in a long-term experiment with soybean-wheat cropping system. On the other hand, available K was found higher in organic system. Greater available K with organic nutrition has been documented by Bulluck et al. (57) and Panwar et al. (69). This beneficial effect with organic manure application might be attributed to organic source induced release of organic colloids with more cation exchange sites which adds up more amount of available K by attracting them from the non-exchangeable pool (70). The improved agricultural practices such as soil organic amendments play vital role in soil micronutrient availability (22). Higher DTPA-extractable micronutrient (Cu, Mn, Fe, and Zn) contents under organic production system may be attributed to FYM addition and enhanced soil microbial properties might have improved the micronutrient status of the soil.

Soil organic carbon (SOC) is consisted of a vital fraction termed as microbial biomass carbon (MBC) of soil (71). Microbial biomass carbon (MBC) and dehydrogenase activity (DHA) are crucial indicators for soil quality (72). These indicators also provide clear reflection of soil microbial activity, specifically representing the metabolically active fraction of soil microbial population (73, 74). Improved MBC might be attributed to the property of organic manure to be a more soluble source of substrate for better microbial proliferation in soil (75). Accordingly, implementation of organic management might have accelerated the availability of substrates and stimulated the metabolic activity of soil microbes, which leads to enhanced dehydrogenase activity as confirmed by the outcomes of Basak et al. (76). The reason behind this stimulation of soil dehydrogenase may be due to addition of substrates containing several intra- and extra-cellular enzymes through the incorporation of organic manures. Similar result was also reported by Saviozzi et al. (77) and Smitha et al. (78). Similarly, phosphatase activity in soil is likely to get amplified in response to organic nutrient management compared to chemical inputs (25, 79). In our study, higher activity of acid phosphatase with organic production system might be attributed to the accelerated microbial activity due to improved organic carbon content of the soil. However, increased level of urease enzyme under organic management may be because of persistent availability of substrates with C-N bonds for the enzyme to work. Few other researchers have also reported similar type of improvement in urease activity with the application of organic manures (80–82).