Fertility Status and Soil Quality Assessment of Chernozem and Stagnosol Soils Under Organic Farming Practices

Abstract

Modern agricultural practices increasingly threaten soil quality, prompting growing interest in organic farming as a sustainable alternative. This study evaluated the effects of organic management on soil fertility and quality in comparison to conventional and undisturbed systems, focusing on fertile Chernozem and less favorable Stagnosol soils. A minimum data set of indicators was used, including bulk density (BD), soil organic carbon (SOC) content and stock, hot water extractable organic carbon (HWOC), and enzymatic activities (dehydrogenase and urease). An integrative statistical framework (blocked ANOVA and PCA) was applied to examine interactions between soil properties and different management practices, while Pearson’s correlations were employed to explore relationships within the organic system. Organic management improved soil quality in two soils, with pronounced benefits in Stagnosol, even after 5–10 years. Conventional production systems exhibited lower biological activity, poorer chemical properties, and higher BD. Long-term organic management (>10 years) in Chernozem enhanced soil quality levels approaching those of undisturbed pasture, while medium-term organic systems showed transitional characteristics. Sensitive indicators such as BD, SOC and HWOC detected early changes in Chernozem, with enzyme activities providing additional insight in Stagnosol. However, SOC stock did not differ significantly between organic and conventional systems due to BD influence. Overall, these findings emphasize the importance of organic farming practices, especially for less fertile soils, and support the use of integrated indicators for soil quality assessment.

1. Introduction

The rising global population and growing demand for food pose significant challenges for both agricultural producers and agronomists. The world population is expected to reach around 10 billion by 2050, which will require an estimated 50% increase in food production, all while facing growing constraints on land, water, and other natural resources [1]. In addition to increasing production, agriculture today must ensure the availability of food that is nutritious, safe, and environmentally sustainable. However, the intensification of agricultural production and the pursuit of higher yields have often come at the expense of long-term soil health [2]. Heavy reliance on synthetic fertilizers, pesticides, and intensive tillage practices have contributed to soil degradation, including loss of organic matter, compaction, erosion, and reduced biological activity [3,4]. As a result, there is growing concern about the sustainability of modern agricultural systems, particularly with regard to their impact on soil quality and soil health. Moreover, climate change further exacerbates soil degradation processes, underscoring the need for resilient agricultural systems that enhance soil health and long-term productivity [5,6].

Soil quality is a complex and dynamic concept that reflects a soil’s capacity to function effectively within both natural and managed ecosystems. It encompasses the ability of soil to support plant growth, regulate water and nutrient cycles, sustain biological activity, and promote environmental resilience [7,8]. Soil health is closely related to soil quality, and according to Moebius-Clune et al. [9] it can be considered equivalent to dynamic soil quality as it is influenced by management decisions and land use patterns. It frames soil as a limited and dynamic living resource directly linked to plant health and the provision of ecosystem services. Unlike soil fertility, which primarily concerns the availability of nutrients for crop production, soil quality includes physical, chemical, and biological properties that contribute to both agricultural productivity and ecological sustainability [10]. In Serbia, as in many other countries with intensive agricultural activity, several soil degradation processes threaten long-term soil productivity and ecosystem stability. These processes include declining soil organic matter (SOM), erosion, compaction, acidification, and contamination with heavy metals or pesticide residues [11,12]. Research consistently shows that intensive agricultural production accelerates SOM depletion, although the extent of this loss depends on the production system, tillage practices, climatic conditions, and soil type [3,13,14]. According to Manojlović and Pivić [15], one of the most detrimental processes affecting agricultural soils, particularly in the region of Vojvodina, is the decline in SOM content in the surface soil layers. The loss of soil biological activity and nutrient imbalance are particularly concerning in areas with long-term monoculture and high inputs of synthetic fertilizers. Such conditions can lead to reduced crop resilience, lower soil fertility, and increased vulnerability to climate extremes. Addressing these challenges requires a shift toward management practices that promote soil regeneration and multifunctionality [16].

Organic farming has been increasingly recognized as a sustainable alternative to conventional agriculture, largely due to its potential to preserve soil quality and reduce environmental degradation. By avoiding synthetic inputs and prioritizing practices such as crop rotation, organic manure application, cover cropping, and minimal soil disturbance, organic systems promote the accumulation of SOM, enhance biological activity, and improve overall soil structure and function [17,18]. These benefits are particularly relevant in regions where long-term intensive cultivation has led to soil degradation.

In this region, conventional agriculture is characterized by the use of synthetic fertilizers and pesticides, intensive tillage, and standard crop rotation practices, representing the predominant farming system in Serbian arable lands. In addition, the decline in livestock production has led to lower application of organic manure, potentially impacting soil fertility in these systems.

Although the positive effects of organic farming on soil quality have been widely reported worldwide, many existing studies in our region are limited by small test area, short-term experiments, or controlled experimental conditions that do not fully reflect real field environments. In Serbia, the first investigation of soil fertility under organic agriculture, conducted across seven locations and 55 plots, found no significant differences between organic and conventional farming systems in the first years of transition due to the short transition period and generally high soil fertility [19,20]. However, these findings were constrained by the short-term scope of the study and by the lack of differentiation between soil types, preventing a deeper understanding of long-term impacts. Scientific evidence on the long-term impact of organic management on soil fertility and quality in this region therefore remains scarce and fragmented, particularly when comparing different soil types and management histories. There is a clear need for more comprehensive, indicator-based evaluations under real field conditions, which can provide practical insights for land managers and policymakers aiming to promote sustainable agriculture.

Soil quality assessment requires selecting a minimum data set (MDS) of indicators that capture key physical, chemical, and biological soil functions. Indicators most sensitive to land management practices are preferred, as they best reflect changes in soil quality and fertility resulting from different agricultural systems [8]. Selecting appropriate indicators within the MDS is critical for accurately reflecting soil functionality and guiding sustainable agricultural decision-making.

The study focuses on two contrasting soil types commonly present in Serbian agricultural landscapes: the fertile Chernozem, known for its high SOM content and favorable structure, and the less favorable Stagnosol, characterized by its acidity and poor permeability.

Therefore, the aim of this study was to evaluate selected physical, chemical, and biological indicators of soil quality under different land-use systems (long-term organic, medium-term organic, and conventional agriculture, as well as natural pasture as a control), on these two soil types. By applying an MDS of indicators, this research aims to assess how organic management practices influence soil fertility and overall quality in comparison to conventional and undisturbed systems on selected soil types.

Specifically, this study addressed the following research questions:

RQ1: Does organic farming improve soil quality under the agroecological conditions of the study area, and is a period of at least five years sufficient to demonstrate differences between organic and conventional production systems?

RQ2: Are organic carbon content, enzymatic activities, and bulk density sensitive and early indicators of changes caused by different land management systems?

RQ3: Does the duration of organic management (medium-term vs. long-term) influence the extent of improvements in soil quality indicators?

RQ4: Do Chernozem and Stagnosol soils respond differently to organic management?

2. Materials and Methods

2.1. Study Area and Climate

To assess soil quality under organic production, this study was conducted in the Autonomous Province of Vojvodina, northern Serbia, and the Kolubara District in western Serbia. Both regions are characterized by a moderately continental climate, with locally pronounced variations. Summers are typically hot and dry, while winters are cold. The average annual temperature is approximately 11 °C, while the amount of precipitation varies between 600 and 750 mm and increases with altitude [21]. Although the Kolubara District exhibits diverse topography that can influence local microclimates, the investigated plots were located at lower altitudes, where the climate conditions are comparable to those in Vojvodina.

Soil sampling was carried out on 15 private farms (Figure 1) on two soil types, Chernozem and Stagnosol, with contrasting soil conditions, especially differing in pH values. Chernozem samples were collected in 2019, while Stagnosol samples were collected in 2023, at different locations. Sampling was conducted in autumn from the topsoil, ensuring consistency across sites and years. Although sampling was conducted in different years, climatic conditions during those periods did not deviate significantly from the multi-year averages. Both 2019 and 2023 were among the warmer years, characterized by moderate precipitation, average annual temperatures of around 14.8 °C, and total annual precipitation ranging from 730 to 790 mm [22,23].

2.2. Soil Sampling and Site Selection

Sampling sites were selected based on soil type and the time since organic farming was established, with all organically managed plots under such practices for at least five years. Samples were collected from plots within active agricultural holdings, under actual farming conditions, and without any prior experimental treatment (Table S2). Site selection was aligned with current land use, which included organic and conventional farming systems, as well as pastureland serving as a control.

Soil samples were collected post-harvest from fields cultivated with cereals and vegetables. At each site, samples were taken from two organically managed plots. To evaluate the effect of the farming system on selected soil quality indicators, additional samples were collected from a nearby conventionally managed plot and an adjacent pasture. All samples were taken from the topsoil layer (0–25 cm).

Chernozem soils were sampled at ten locations: five under organic management for 5 to 10 years, and five under long-term organic management (10 to 20 years). Stagnosol soils were sampled at five locations, all managed organically for 5 to 10 years. In total, 60 soil samples were collected. Prior to laboratory analysis, the samples were air-dried, homogenized, and sieved through a 2 mm mesh for basic physical and chemical analyses.

2.3. Soil Laboratory Analyses and Calculations

The basic physical and chemical properties of the investigated soils were measured The selected parameters represent key indicators of soil fertility and biological activity, particularly in the context of organic and conventional farming systems.

The mechanical composition was determined using the pipette method, based on the sedimentation of particles in still water, and the textural class was classified according to the Tommerup classification [24]. Soil reaction (pH) was measured potentiometrically in a water suspension (soil to water ratio 1:2.5), as well as in a 1 M KCl solution, using the same ratio [25]. Calcium carbonate (CaCO₃) content was determined volumetrically using a Scheibler calcimeter. Available phosphorus (AL-P₂O₅) and potassium (AL-K₂O) contents were determined using the AL method, according to Egner et al. [26].

Bulk density (BD) was determined using Kopecky cylinders. Soil organic carbon (SOC) content (%) was determined by the Tyurin method [27]. SOC stocks (t ha⁻¹) were calculated according to the IPCC [28] methodology, based on SOC content (g kg⁻¹), BD (g cm⁻³), and sampling depth (cm), using the following formula:

SOC (t ha⁻¹) = SOC (g kg⁻¹)/1,000,000 × depth (cm) × BD (g cm⁻³) × 10,000 × 1000.

Hot water-extractable organic carbon (HWOC) was measured according to a modified procedure by Ghani et al. [29], in the third soil fraction (250–253 µm) obtained after wet sieving. Dehydrogenase activity (DHA) was determined spectrophotometrically following the method of Thalmann [30], while urease activity (UA) was assessed using the distillation-titration method [31].

2.4. Statistical Analysis

All statistical analyses were performed using STATISTICA software (version 14.1, TIBCO Software Inc., San Ramon, CA, USA). To assess the effect of the production system (organic, conventional) and pasture on selected soil quality parameters (BD, SOC content and stock, HWOC, DHA, and UA), a one-way analysis of variance (ANOVA) with a blocking factor (randomized complete block design, RCBD) was applied. Statistical analyses were conducted separately for each soil type (Chernozem and Stagnosol), with sampling location considered as a blocking factor to reduce the impact of uncontrolled environmental variability. Where significant differences were observed (p < 0.05), Tukey’s HSD test was used for post hoc comparison of means.

Pearson’s correlation coefficients were calculated to examine relationships among soil properties and enzymatic activities within the organic production system only. Correlation matrices were generated separately for each soil type, and statistical significance was set at p ≤ 0.05. To facilitate interpretation, the results were visualized using heatmaps, with color gradients representing the strength and direction of the correlation coefficients.

To explore multivariate relationships among the analyzed soil parameters (BD, SOC content, HWOC, DHA, and UA) and to assess sample groupings based on the production system, principal component analysis (PCA) was performed using standardized (Z-score transformed) data. PCA was conducted separately for Chernozem and Stagnosol soils to account for differences in origin (i.e., soil type and formation) and soil properties.

3. Results

3.1. Basic Physical and Chemical Properties of Investigated Soils

The mechanical composition of Chernozem soils showed minor variation among land-use systems (

Table 1. Texture and particle-size distribution of Chernozem under different land-use systems.

Location	Land Use	Sand (%)	Silt (%)	Clay (%)	Soil Texture	Location	Land Use	Sand (%)	Silt (%)	Clay (%)	Soil Texture
1	Organic plot I *	62.72	26.56	10.72	Loam	6	Organic plot I **	40.60	41.84	17.56	Clay loam
	Organic plot II *	76.16	14.76	9.08	Fine sandy loam		Organic plot II **	40.08	40.04	19.88	Clay loam
	Conventional plot	59.08	29.00	11.92	Loam		Conventional plot	43.20	37.36	19.44	Clay loam
	Pasture	79.84	11.52	8.64	Fine sandy loam		Pasture	44.28	38.36	17.36	Clay loam
2	Organic plot I *	60.16	28.28	11.56	Loam	7	Organic plot I **	52.12	35.28	12.60	Loam
	Organic plot II *	65.52	23.44	11.04	Fine sandy loam		Organic plot II **	51.76	33.12	15.12	Clay loam
	Conventional plot	60.68	28.08	11.24	Loam		Conventional plot	52.08	36.80	11.12	Loam
	Pasture	73.60	17.76	8.64	Fine sandy loam		Pasture	55.52	31.64	12.84	Loam
3	Organic plot I *	53.36	33.20	13.44	Loam	8	Organic plot I **	38.24	39.20	22.56	Clay loam
	Organic plot II *	51.96	32.28	15.76	Clay loam		Organic plot II **	35.44	42.20	22.36	Clay loam
	Conventional plot	46.44	38.88	14.68	Loam		Conventional plot	35.36	36.96	27.68	Loamy clay
	Pasture	60.56	30.20	9.24	Loam		Pasture	40.64	37.68	21.68	Clay loam
4	Organic plot I *	60.16	27.64	12.20	Loam	9	Organic plot I **	42.04	36.88	21.08	Clay loam
	Organic plot II *	57.60	28.76	13.64	Loam		Organic plot II **	43.32	37.40	19.28	Clay loam
	Conventional plot	57.60	30.36	12.04	Loam		Conventional plot	49.12	34.40	16.48	Clay loam
	Pasture	67.68	19.68	12.64	Fine sandy loam		Pasture	47.12	36.44	16.44	Clay loam
5	Organic plot I *	38.68	37.28	24.0	Clay loam	10	Organic plot I **	49.12	36.16	14.72	Loam
	Organic plot II *	37.28	40.64	22.10	Clay loam		Organic plot II **	45.60	38.88	15.52	Clay loam
	Conventional plot	35.16	38.44	26.4	Loamy clay		Conventional plot	48.16	35.36	16.48	Clay loam
	Pasture	42.86	37.24	19.9	Clay loam		Pasture	49.76	36.56	13.68	Loam

* Organic plot over 10 years; ** Organic plot 5–10 years.

). Most soils were classified as loam or clay loam, with sand content ranging from 35% to 76%, silt from 11% to 42%, and clay from 8% to 27%. Conventionally managed plots exhibited the highest clay content, occasionally resulting in a loamy clay texture in some cases. In contrast, pasture and long-term organic management plots most often had loam or fine sandy loam textures, corresponding to lower clay fractions.

The texture of Stagnosol soils varied from clay loam to silty clay loam and loamy clay across all land-use systems (

Table 2. Texture and particle-size distribution of Stagnosol under different land-use systems.

Location	Land Use	Sand (%)	Silt (%)	Clay (%)	Soil Texture
11	Organic plot I **	35.72	47.76	16.52	Silty clay loam
	Organic plot II **	35.52	44.88	19.60	Clay loam
	Conventional plot	36.84	40.64	22.52	Clay loam
	Pasture	40.04	45.12	14.84	Silty loam
12	Organic plot I **	40.28	38.52	21.20	Clay loam
	Organic plot II **	41.44	41.56	17.00	Clay loam
	Conventional plot	33.20	41.12	25.68	Loamy clay
	Pasture	43.32	41.16	15.52	Clay loam
13	Organic plot I **	34.36	36.00	29.64	Loamy clay
	Organic plot II **	36.80	38.00	25.20	Loamy clay
	Conventional plot	42.28	30.32	27.40	Loamy clay
	Pasture	44.48	30.60	24.92	Clay loam
14	Organic plot I **	33.12	45.08	21.80	Silty clay loam
	Organic plot II **	34.32	40.20	25.48	Loamy clay
	Conventional plot	32.16	40.96	26.88	Loamy clay
	Pasture	34.04	37.20	28.76	Loamy clay
15	Organic plot I **	29.40	47.96	22.64	Silty clay loam
	Organic plot II **	34.72	46.12	19.16	Silty clay loam
	Conventional plot	35.70	39.18	25.12	Loamy clay
	Pasture	34.76	45.04	20.20	Silty clay loam

** Organic plot 5–10 years.

). Clay content was generally higher than in Chernozem, ranging from 14.84% to 29.64%, with the highest values observed in conventionally managed plots. Pasture and organically managed plots typically exhibited intermediate clay levels and finer textures, such as silty clay loam. Silt content was also relatively high, indicating a predominantly fine-textured soil environment.

The chemical properties of Chernozem exhibited moderate variability across land-use systems. Slightly alkaline pH values were consistent among all plots, with only minor differences between management systems. CaCO₃ content varied across systems, with slightly higher mean values observed in conventional plots. The levels of AL-P₂O₅ and K₂O differed among systems. The highest mean AL-P₂O₅ content was recorded in conventional plots, while organic systems showed slightly lower but more consistent values. In contrast, AL-K₂O levels were higher in organically managed soils compared to conventional ones, with the highest mean observed under pasture. Detailed data are presented in

Table 3. Basic chemical properties of the investigated soils under different land-use systems.

Land Use	pH H2O		pH KCl		CaCO3 (%)		AL-P2O5 mg 100 g−1		AL-K2O mg 100 g−1
Chernozem
Organic plot * (mean I + II)	7.93 ± 0.28		7.20 ± 0.40		8.83 ± 4.74		21.69 ± 6.15		25.97 ± 6.71
	Min 7.53	Max 8.34	Min 6.45	Max 7.63	Min 2.76	Max 17.75	Min 12.94	Max 31.06	Min 15.03	Max 35.32
Organic plot ** (mean I + II)	8.00 ± 0.18		7.15 ± 0.30		8.83 ± 6.28		21.39 ± 7.80		25.65 ± 4.49
	Min 7.65	Max 8.22	Min 6.57	Max 7.43	Min 2.97	Max 20.43	Min 12.50	Max 39.22	Min 20.02	Max 36.45
Conventional plot	7.90 ± 0.43		7.11 ± 0.51		9.80 ± 5.29		22.91 ± 11.75		22.99 ± 4.43
	Min 8.00	Max 8.16	Min 5.70	Max 7.48	Min 2.75	Max 20.19	Min 7.85	Max 49.64	Min 13.93	Max 27.81
Pasture	7.96 ± 0.14		7.25 ± 0.19		8.67 ± 5.51		17.10 ± 7.96		28.21 ± 8.72
	Min 7.77	Max 8.15	Min 6.94	Max 7.53	Min 3.81	Max 21.68	Min 5.56	Max 29.93	Min 17.63	Max 39.78
Stagnosol
Organic plot ** (mean I + II)	6.65 ± 0.49		5.74 ± 0.54		2.52 ± 0.47		31.27 ± 19.34		37.74 ± 8.98
	Min 5.63	Max 7.18	Min 4.65	Max 6.24	Min 1.64	Max 3.28	Min 3.53	Max 49.57	Min 22.51	Max 48.31
Conventional plot	6.04 ± 0.78		5.05 ± 0.85		2.52 ± 0.30		14.96 ± 23.32		26.28 ± 5.47
	Min 5.14	Max 7.29	Min 4.08	Max 6.43	Min 2.05	Max 2.77	Min 0.88	Max 56.39	Min 21.15	Max 34.54
Pasture	6.22 ± 0.37		5.29 ± 0.46		2.79 ± 0.46		12.26 ± 14.25		23.11 ± 11.07
	Min 5.59	Max 6.49	Min 4.53	Max 5.72	Min 2.05	Max 3.18	Min 0.37	Max 34.32	Min 11.66	Max 38.73

±Standard deviation; N—number of samples. Chernozem: Organic plot * (over 10 years): N = 10; Organic plot ** (5–10 years): N = 10; Conventional plot: N = 10; Pasture: N = 10; Stagnosol: Organic plot ** (5–10 years): N = 10; Conventional plot: N = 5; Pasture: N = 5.

.

Table 3 presents the basic chemical properties of Stagnosol under different land- use systems. The pH values indicate an acidic soil reaction, with slightly higher values observed in organically managed plots. The lowest pH values were recorded in conventionally managed plots, potentially reflecting acidification resulting from intensive mineral fertilization. The concentrations of AL-P₂O₅ and K₂O varied considerably across land-use types, with the highest levels found in organically managed soils, and the lowest observed under pasture. Minor variations in CaCO₃ content were also observed among the plots.

3.2. Bulk Density

Bulk density values varied depending on soil type and production system, as shown in Figure 2. In Chernozem, the highest value was recorded under conventional management (1.35 g/cm³), while lower values were observed in organically managed plots, particularly those under long-term organic management (>10 years; 1.24 g/cm³). A significantly higher BD value was recorded in plots under 5–10 years of organic production (1.30 g/cm³) compared to those managed organically for over 10 years.

In Stagnosol, BD was also highest under conventional management (1.31 g/cm³), while the lowest values were found in organic (1.19 g/cm³) and pasture (1.18 g/cm³) systems. In both soil types, organic and pasture systems exhibited reduced BD compared to conventional management, indicating potential improvements in soil structure related to reduced or no tillage and greater SOM inputs.

3.3. Soil Organic Carbon

Soil organic carbon content varied significantly across different land-use systems and soil types (Figure 3a). In Chernozem, the highest SOC content was recorded in pasture soils (2.54%), which was significantly higher than in all managed systems. This was followed by long-term organic management (2.03%) and conventional management (1.83%), while the lowest value was observed under medium-term organic management (1.72%). Additionally, SOC content in the long-term organic system was significantly higher than in the medium-term organic system, indicating the positive effect of prolonged organic practices on SOC accumulation.

In Stagnosol, the highest SOC content was observed under pasture (1.99%) and organic management (1.81%). In contrast, the lowest value was recorded under conventional management (1.40%), which was significantly lower than in both PG_ORG and PG_PAST. These results indicate that land use and management practices have a considerable effect on SOC content. Natural pasture consistently maintained higher SOC levels in both soil types, highlighting its importance in soil carbon preservation.

Soil organic carbon reserves in the 0–25 cm soil layer differed significantly with respect to both soil type and production system (Figure 3b). In Chernozem, the highest SOC stock was found in pasture soils (79.02 t ha⁻¹), which was significantly higher than in all other production systems. Soils under conventional (61.42 t ha⁻¹) and long-term organic management (60.45 t ha⁻¹) exhibited moderate SOC stocks, while the lowest value was found in plots managed organically for 5–10 years (56.05 t ha⁻¹).

In Stagnosol, pasture soils again exhibited the highest SOC reserves (59.40 t ha⁻¹), followed by organically managed soils (52.61 t ha⁻¹), while the lowest values were found in conventionally managed plots (45.17 t ha⁻¹). The difference between pasture and conventional systems was significant, whereas organically managed soils did not differ significantly from either system.

Table 4. Relative changes (%) in SOC content and stock in organic and conventional systems compared to pasture and conventional management.

System	SOC Content Change vs. Pasture (%)	SOC Content Change Organic vs. Conventional (%)	SOC Stock Change vs. Pasture (%)	SOC Stock Change Organic vs. Conventional (%)
		Chernozem
Organic plot * (mean I + II)	−20.08	10.93	−23.50	−1.58
Organic plot ** (mean I + II)	−32.28	−6.01	−29.07	−8.74
Conventional plot	−27.95		−22.27
		Stagnosol
Organic plot ** (mean I + II)	−9.55	28.57	−11.43	16.47
Conventional plot	−29.65		−23.96

* Organic plot over 10 years; ** Organic plot 5–10 years.

presents the relative changes in SOC content and SOC stock under organic and conventional systems compared to pasture (representing natural conditions) and to conventional management, in order to evaluate the effects of organic farming. In both soil types, all values were lower compared to pasture, indicating that SOC losses occurred across all systems relative to the natural state. However, the results show that long-term organic management in Chernozem reduces SOC losses in comparison to conventional systems. Under medium-term organic management, both SOC content and stock were lower compared to both pasture and conventional production, suggesting that 5–10 years is still insufficient to overcome the negative effect of previous conventional practices.

In contrast, in Stagnosol organic production (5–10 years) resulted in notably smaller SOC losses compared to conventional production, with positive differences of +28.57% in SOC content and +16.47% in SOC stock. This indicates that even short-term organic practices can enhance SOC status in less fertile soils such as Stagnosol.

Hot-Water Extractable Organic Carbon

Figure 4 illustrates the concentrations of HWOC across different production systems and soil types. In Chernozem, the lowest HWOC concentration was recorded in the 5–10-year organic system (369.59 µg g⁻¹), which was significantly lower than in the other systems. No statistically significant differences were observed among the >10-year organic (558.75 µg g⁻¹), conventional (555.99 µg g⁻¹), and pasture (558.18 µg g⁻¹) systems, all of which exhibited comparably higher HWOC levels.

In Stagnosol, the highest HWOC concentration was observed in the organic system (545.81 µg g⁻¹), while the lowest was recorded under conventional management (351.22 µg g⁻¹). Pasture soils (497.78 µg g⁻¹) exhibited intermediate values that did not differ significantly from either organic or conventional systems. Overall, organic systems tended to promote higher HWOC concentrations in both soil types, with the effect being more pronounced in Stagnosol. These patterns suggest that organic management may enhance labile carbon pools, especially in less fertile or more sensitive soils.

3.4. Enzymatic Activities

Dehydrogenase activity showed considerable variation depending on soil type and production system (Figure 5a). The highest DHA was recorded in pasture soils in both Chernozem and Stagnosol, confirming the positive impact of undisturbed conditions on microbial functioning.

In Chernozem, DHA in pasture soils (365.68 µg TPF g⁻¹ soil h⁻¹) was significantly higher than in all managed systems, with no significant differences among organically (169.73 µg TPF g⁻¹ soil h⁻¹ for 5–10 years and 165.67 µg TPF g⁻¹ soil h⁻¹ for >10 years) and conventionally managed ones (137.42 µg TPF g⁻¹ soil h⁻¹). In contrast, Stagnosol exhibited more pronounced differences among systems: DHA was highest under pasture (167.94 µg TPF g⁻¹ soil h⁻¹), followed by organic (136.42 µg TPF g⁻¹ soil h⁻¹) and conventional systems (79.00 µg TPF g⁻¹ soil h⁻¹), with all differences being statistically significant.

Urease activity varied notably between soil types and production systems (Figure 5b). The highest UA was consistently observed in pasture soils, both in Chernozem (248.07 µg NH₄⁺–N g⁻¹ soil h⁻²) and Stagnosol (162.12 µg NH₄⁺–N g⁻¹ h⁻²), confirming the positive influence of undisturbed conditions on microbial processes. Among managed systems, UA in Chernozem showed limited variation, with similar values under conventional (132.80 µg NH₄⁺–N g⁻¹ soil h⁻²), medium-term organic (128.47 µg NH₄⁺–N g⁻¹ soil h⁻²), and long-term organic management (124.24 µg NH₄⁺–N g⁻¹ h⁻²), with no significant differences. However, Stagnosol exhibited clearer separation among systems: organic management (149.86 µg NH₄⁺–N g⁻¹ h⁻²) supported significantly higher activity than conventional management (102.78 µg NH₄⁺–N g⁻¹ h⁻²). These findings indicate that pasture promotes the highest UA regardless of soil type, while organic management enhances UA particularly in more sensitive soils, such as Stagnosol.

In summary, pasture soils exhibited the highest enzymatic activity in both Chernozem and Stagnosol soils, reflecting the benefits of minimal disturbance and continuous organic matter inputs. Organic management also contributed to enhanced microbial function, particularly in Stagnosol, where enzymatic responses were more pronounced. These patterns highlight the sensitivity of microbial activity to land-use practices and emphasize the importance of sustainable management for maintaining soil biological activity.

3.5. Soil Parameter Relationships in the Organic System

To better understand the relationships among the investigated parameters within the organic management system, Pearson’s correlation analysis was conducted separately for Chernozem and Stagnosol soil types.

In Chernozem under organic management for more than 10 years (Figure 6a), a significant positive correlation was observed between SOC content and UA (r = 0.69*). Other positive correlations, which were not significant, were found between HWOC and UA (r = 0.38), SOC stock and DHA (r = 0.43), and SOC content with both SOC stock (r = 0.46) and HWOC (r = 0.45). Negative correlations were noted between BD and UA (r = −0.37), BD and HWOC (r = −0.27), and SOC content and DHA (r = −0.36). However, these correlations were not significant.

Under 5–10 years of organic production, correlation analysis revealed several significant relationships among the examined soil parameters (Figure 6b). A significant negative correlation was observed between BD and HWOC (r = −0.84*), indicating that more compact soils tend to have lower levels of easily available SOC. Bulk density also showed a negative correlation with UA (r = −0.55), which was not significant.

SOC content showed a significant positive correlation with SOC stock (r = 0.99*), and both were positively correlated with DHA (r = 0.89*), suggesting that higher SOC supports greater microbial activity. A positive correlation was also found between UA and HWOC (r = 0.81*), highlighting the link between easily available carbon and soil enzyme activity. These results emphasize the close relationships between soil physical properties, SOC content and fractions, and enzymatic activities, which together are key indicators of soil fertility and quality.

In Stagnosol, several notable correlations were observed among the examined parameters (Figure 6c). A significant negative correlation was found between BD and SOC content (r = −0.71*). Significant positive correlations were found between SOC content and SOC stock (r = 0.87*), and between SOC stock and HWOC (r = 0.75*), indicating that higher levels of total SOC are associated with greater availability of labile carbon fractions. Additionally, UA was significantly correlated with DHA (r = 0.67*), suggesting coordinated microbial processes involved in carbon and nitrogen cycling. Positive correlations were also observed between DHA and HWOC (r = 0.41), DHA and BD (r = 0.51), and SOC content and HWOC (r = 0.52), although these were not significant. A negative correlation, not significant, was found between SOC stock and BD (r = −0.37).

3.6. PCA of Soil Properties Under Different Management Systems

To explore the multivariate relationships among soil properties and to distinguish the effects of different management systems on soil quality, PCA was performed based on five soil parameters (BD, SOC content, HWOC, UA and DHA), separately for each soil type. In the Chernozem soils, the first two principal components (PC1 and PC2) together explained 75.85% of the total variance, with PC1 accounting for 55.64% and PC2 for 20.21%.

PC1 was primarily influenced by strong negative loadings of SOC content (−0.88), DHA (−0.88) and UA (−0.87), indicating that these biological and chemical indicators of soil fertility co-varied along the negative axis of PC1. In contrast, BD was the only parameter with a positive loading on PC1 (0.61), reflecting its inverse relationship with SOC and enzymatic activity. This parameter was clearly separated from the other variables along this axis (Figure 7a), indicating two main gradients: one from biologically enriched soils (high SOC and enzyme activity) located on the negative side of PC1, toward more compact and biologically limited soils (higher BD, lower SOC and enzyme activity) on the positive side. PC2 was mainly associated with a high positive loading for HWOC (0.93), indicating that PC2 captured variability related to the labile fraction of SOC, independently from other parameters.

The projection of cases (Figure 7b) showed that pasture soils formed a distinct cluster, located on the negative side of PC1, indicating higher levels of SOC and enzymatic activities. Soils under organic management for more than 10 years were also generally located in the same region with a few exceptions, suggesting similar improvements in soil quality. In contrast, soils under conventional management were mostly grouped on the positive side of PC1, corresponding to lower biological activity and SOM content, and higher BD. Samples under organic management for 5–10 years were more dispersed and grouped closer to the origin or slightly toward the positive PC1 axis, tended to occupy intermediate positions between the long-term organic, pasture and conventional systems.

These results indicate that long-term organic management positively affects the key soil indicators examined in this study, aligning more closely with the conditions observed in undisturbed pasture, while medium-term organic management (5–10 years) may show transitional characteristics, with improvements emerging but not yet consistent across all samples. Conventional systems show less favorable characteristics and samples showed greater dispersion, indicating higher variability within this group. Additionally, the separation along PC2 highlights the distinct contribution of HWOC as an independent indicator of labile organic matter dynamics within Chernozem soils.

In Stagnosol soils, the first two principal components (PC1 and PC2) explained 72.94% of the total variance, with PC1 accounting for 46.22% and PC2 for 26.72%. Therefore, further analyses and biplot visualization focused on these two components. PC1 was primarily determined by the highest negative loadings of SOC content (−0.79), UA (−0.77), DHA (−0.65), and HWOC (−0.69), indicating a common gradient reflecting biologically and chemically active soil conditions (Figure 8a). In contrast, BD was mainly associated with PC2, contributing positively (0.85), representing an independent axis of variation orthogonal to the other indicators and revealing a clear separation between soils with higher SOC and HWOC content and biological activity, and those with a more compact structure and lower fertility.

The case projection (Figure 8b) illustrated notable differences among management systems. Pasture soils were mainly positioned on the negative side of PC1 and clustered distinctly, reflecting higher SOC content, HWOC, and enzymatic activities. Organically managed soils (5–10 years) occupied an intermediate position between pasture and conventionally managed soils along the PC1 axis but were generally more closely aligned with pasture soils. In contrast, conventionally managed soils were grouped on the positive side of PC1 and upper side of PC2, suggesting lower biological activity and SOC content, along with higher BD.

These results indicate that even within the limitations of Stagnosol soils and after only 5–10 years of application, organic management practices led to measurable improvements in soil biological and chemical quality, approaching the levels observed under undisturbed pasture conditions.

4. Discussion

The basic physicochemical properties of the investigated soils, especially pH and texture, are presented to provide an overview of the soil environment, providing the necessary context for interpreting variations in selected soil quality indicators, including BD, SOC, HWOC, and enzymatic activities. These properties generally reflected the expected characteristics of Chernozem and Stagnosol soils in the study region and helped explain observed differences in the response of soil quality indicators to different management systems; therefore, they were not the main focus of this study.

4.1. Effects of Organic Farming on Bulk Density

Bulk density values observed in this study showed significant differences between management systems on both soil types, with organically managed soils generally exhibiting lower BD compared to conventionally managed ones. This trend is consistent with previous studies reporting that organic amendments and reduced tillage practices improve soil structure and porosity, thereby decreasing soil compaction [32,33,34,35]. According to Bronick & Lal [36], BD is a sensitive indicator of soil structural quality, strongly influenced by both soil type and management practices that affect pore space and compaction. In the present study, BD values were also generally lower in pasture plots compared to conventionally managed soils, which is consistent with earlier findings [37].

The lower BD in organically managed and pasture plots likely reflects increased SOM content and enhanced soil aggregation, which promote better aeration and root penetration. Conversely, higher BD observed in conventionally managed soils may be attributed to intensive machinery use and reduced organic matter inputs, leading to soil compaction and decreased porosity. These differences are important, as BD directly influences water infiltration, nutrient availability, and microbial activity, factors that ultimately affect soil fertility and crop productivity [36].

The observed significant differences in BD in Chernozem soils between organically managed plots of 5–10 years and those under organic management for over 10 years highlight the progressive improvement of soil physical properties over time. These findings suggest that the duration of organic management (i.e., medium-term 5–10 years vs. long-term over 10 years) plays a critical role in enhancing soil porosity and reducing compaction. This emphasizes the broader importance of adopting organic practices in sustainable agriculture. In line with these results, Bilibio et al. [38] reported a 7% reduction in BD in the 0–24 cm surface layer after 10 years of organic conservation tillage. Similarly, in the long-term studies Williams et al. [39] found significantly lower BD and improved aggregate stability after 40 years under organic management.

According to Blanco-Canqui et al. [40], BD is the most frequently measured physical soil property in organic farming systems. In their review of 33 studies, 17 studies (52%) reported that organic practice didn’t have effect on BD, 15 out of 33 studies (45%) reported a reduction in BD under organic practices (ranging from 2% to 21% in the topsoil 30 cm), and only one study (3%) showed an increase compared to conventional systems. These findings reflect the variability of BD responses to organic management, which can depend on soil type, climate, duration of application, and specific practices used. In our study, the consistently lower BD observed in organically managed soils supports the group of studies reporting a beneficial effect of organic practices on reducing soil compaction, primarily due to the application of organic fertilizers and reduced tillage (Table S2).

4.2. Effects of Organic Farming on Soil Organic Carbon

Soil organic carbon is a key indicator of soil fertility and quality, acting as a long-term reservoir of nutrients and playing a vital role in maintaining soil structure, water retention, and supporting microbial activity [41]. Importantly, changes in SOC pools often occur slowly, and measurable effects of management practices such as organic farming may require extended periods of consistent application to become evident [19]. In contrast, HWOC represents a labile and readily available fraction of SOC, more directly linked to microbial biomass and short-term nutrient cycling processes [42].

Both SOC content and SOC stock are essential indicators of soil carbon status, providing complementary information about carbon concentration and total carbon storage in soils [43]. In the present study, both SOC content and stock (0–25 cm depth) were significantly higher in pasture plots compared to all managed systems in Chernozem. In Stagnosol, SOC content was significantly higher under pasture and organic management compared to conventional management. SOC stock was also highest in pasture plots, but the difference was significant only when compared to conventionally managed plots. This is consistent with existing literature indicating that minimally disturbed ecosystems, such as permanent pasture, tend to accumulate higher levels of SOC due to continuous plant residue input and lack of tillage [32,44,45].

Among the cultivated systems in Chernozem, SOC content was significantly higher in the long-term organic system (>10 years) compared to the medium-term organic system, confirming that extended organic practices positively impact SOC levels. This pattern aligns with the general trend reported in the literature, indicating that longer durations of organic management are associated with greater SOC accumulation. Studies show that longer-term application of organic practices (10+ years), especially in combination with reduced or minimum tillage and organic fertilizers, leads to a gradual and stable increase in SOC content, while the effects in short- and medium-term systems are often more modest or depend on other factors (climate, soil type, tillage, etc.). In the study by Velmourougane [46], a significant increase in SOC content (15.6%) was observed after 12 years of organic management. Similarly, Krauss et al. [47] reported a 25% higher SOC content in the topsoil layer (0–10 cm) under reduced tillage in organic farming after 15 years, compared to conventional ploughing. Mihelič et al. [48] found that after 12 years of organic farming with minimum tillage, the uppermost soil layer (0–10 cm) had 10% higher SOC content (1.60%) compared to conventional farming (1.45%). After 21 years in the same study, SOC content under organic management had increased to 1.94%, which was 43% higher than under conventional tillage.

Manojlović et al. [49] reported that in a long-term study on Chernozem soil, different tillage systems, including plowing, chisel tillage, disc tillage and no-till, had the most pronounced effect on SOC concentration and SOC stock in the 0–10 cm layer, where the impact of no-till was particularly evident. In our study, SOC stock did not differ significantly among all cultivated systems, even under long-term organic management, indicating comparable carbon storage levels across them. A comparable trend was reported by Hu et al. [50], who found no consistent differences in SOC stock at 0–25 cm depth, despite higher estimated carbon inputs under organic compared to conventional management. Similarly, Raimondi et al. [51] reported that after 15 years of organic management did not result in significantly higher SOC compared to conventional farming. A meta-analysis by Hijbeek et al. [52] showed that additional organic inputs did not consistently improve crop yields in European arable systems. Their findings suggest that the effects of organic management on SOC accumulation may also be limited when nutrient availability is not a limiting factor, when soils already have high baseline SOC levels, or if changes in management intensity are minor or not sustained over time.

In Stagnosol soils, SOC content was significantly higher under organic management (5–10 years) compared to conventional management. However, although SOC stock was higher in organically managed plots than in conventionally managed plots, the difference was not significant. These results are consistent with the observations of Gattinger et al. [53], who reported that differences in SOC concentrations between farming systems tend to become more evident with longer trial durations, but can already be detectable and most pronounced in the early years of conversion. Our findings partially align with those of Mihelič et al. [48], who reported significantly higher SOC concentrations and stocks in the topsoil (0–20 cm) after only five years of conversion to organic farming, with an average increase of 12%.

Under the conditions of this study, the effect of organic management on SOC stock appears to be influenced by multiple interacting factors. Bulk density, which directly affects the calculation of SOC stock, is one of the key variables in this context [54]. One possible explanation for the lack of significant differences between organic and conventional systems is the relatively short duration of organic management (5–10 years and >10 years), which may still be insufficient to produce measurable changes in stable SOC pools, particularly in soils with historically high SOC content, such as Chernozem. Moreover, the physical and chemical characteristics of Stagnosol, such as poor drainage, low permeability, and periodic waterlogging, can limit microbial activity and slow the stabilization of organic inputs. Clay content, which was generally higher in Stagnosol in our study, plays a key role in SOC stabilization, and strongly influences SOC stocks through physical protection within microaggregates [55,56].

Additionally, if differences in agronomic practices, such as tillage and the application of organic inputs (e.g., manure), between conventional and organic systems were minimal, the expected benefits of organic management on SOC accumulation may have been limited [52,57]. These findings are consistent with previous studies showing that SOC responses to organic farming are highly context-dependent and often require longer time frames to become significant [13,58,59]. A similar conclusion was reached by Manojlovic et al. [19] and Manojlović and Čabilovski [20], who indicated that a short transition period to organic farming was not sufficient for the positive impacts to be reflected in soil fertility. They also emphasized that better integration of crop production with animal husbandry could further enhance soil quality. Moreover, the authors pointed out that favorable natural conditions are essential for the successful implementation of organic farming.

Effects of Organic Farming on Hot-Water Extractable Organic Carbon

As an available and biologically active fraction of SOC, HWOC exhibited markedly different distribution patterns between the soil types, reflecting variations in SOM dynamics. In Chernozem, similar HWOC levels (in the 250–53 µm fraction) were recorded across pasture, conventional, and long-term organic plots, all of which had significantly higher values compared to organic fields managed for 5–10 years. According to Ćirić et al. [60], labile soil carbon fractions such as HWOC are important indicators of management-induced changes in soil. The actual accumulation of HWOC may depend on the amount and frequency of organic inputs [61]. In our study, farmers applied an average of 15–40 t/ha of farmyard manure per year, depending on crop type, with occasional lower input rates. While these rates broadly align with organic farming recommendations [62], variability in application intensity and organic matter composition suggests that the accumulation of HWOC may require longer periods of organic inputs and/or the establishment and adaptation of stable microbial communities, which may not yet be fully developed in younger organic systems. This confirms the strong positive correlation observed between UA and HWOC, highlighting the close relationship of soil enzymatic processes and labile carbon pools in organic farming systems.

In contrast, in Stagnosol, the highest HWOC content was found in organically managed plots (5–10 years), significantly exceeding levels observed under conventional management. This could indicate more efficient microbial processing and transformation of organic inputs under organic practices in hydromorphic soil conditions [61]. The hydromorphic nature of Stagnosol, characterized by elevated moisture and periodic water saturation, creates distinct microbial habitats that may respond more rapidly to organic inputs. These conditions, combined with consistent farmyard manure application rates (20–40 t/ha annually, with no exceptions observed), can promote faster turnover and transformation of SOM, resulting in a quicker increase in labile carbon fractions like HWOC, even within a relatively short timeframe. Similarly, Bongiorno et al. [63] reported that labile SOC fractions, including HWOC, respond more rapidly to organic amendments in hydromorphic or moisture variable soils.

The contrasting HWOC trends in Chernozem and Stagnosol soils under 5–10 years of organic management likely reflect inherent differences in soil properties and microbial dynamics. In fertile and well-structured Chernozem, lower HWOC levels in medium-term organic plots could indicate that labile carbon pools take longer to accumulate during the early stages of organic management. Additionally, residual effects from previous conventional management may still influence SOC fractions in these systems. This is consistent with previous studies. Tobiašová et al. [64,65] showed that carbon stabilization in soil aggregates, particularly in Chernozem-type soils, strongly depends on long-term organic inputs and aggregate formation. Macroaggregates (>3 mm) play a key role in preserving labile carbon over time. Similarly, Dubovik & Dubovik [66] found that in Chernozem the labile humic substance content is tightly bound to aggregate structure and slope position, suggesting that soil physical context modulates how SOC fractions accumulate. Additionally, the higher clay content in Stagnosol soils likely contributed to the retention and partial stabilization of HWOC through physical protection mechanisms. The combined effect of organic inputs and fine-textured soil may explain the greater accumulation of HWOC in organically managed stagnosol soils.

In our study, a strong positive correlation was observed between SOC and HWOC in Stagnosol soils, indicating that increases in total SOC are closely accompanied by increases in its labile fraction. This relationship emphasizes the integrated role of both stable and dynamic carbon pools in supporting soil biological activity and nutrient availability. Similar correlations have been reported in other studies, suggesting that HWOC can serve as a sensitive early indicator of SOC changes under different land use and management regimes [9,29,60,67]. These findings collectively underscore the importance of both the quantity (SOC) and quality (HWOC) of organic carbon in soil health assessments. Although long-term organic management may not always lead to significant increases in total SOC levels, its effects on labile fractions such as HWOC are often more variable, depending on soil type, composition of organic inputs, management intensity and history, and the duration of organic practices.

4.3. Effects of Organic Farming on Soil Enzymatic Activities

Soil enzymes such as UA and DHA are widely recognized as sensitive bioindicators reflecting microbial metabolism, nutrient cycling, and SOM turnover [68,69]. Their activities respond rapidly to management practices, organic inputs and environmental conditions, thus providing early signals of changes in soil quality and valuable insights into biological functioning under different land-use systems [70,71].

In this study, UA and DHA activities showed significant and parallel variations across different soil types and management systems, suggesting a coordinated microbial response to changes in soil conditions and organic inputs. Similar synchronous increases in the two enzymes were reported by Krzywy-Gawrońska [72], Zaborowska et al. [73], and Kwiatkowski et al. [74] under different soil and management conditions. Taken together, these findings emphasize the coordinated nature and joint sensitivity of UA and DHA responses to substrate availability and edaphic factors.

In Chernozem soils, UA was significantly higher in pasture than in all other management systems, while no significant differences were found among the managed systems themselves. Dehydrogenase activity also showed the same trend, with the highest values in pasture plots. In Stagnosol soils, enzyme activities showed a similar pattern, with the highest UA and DHA in the pasture plots. In this soil type, UA was significantly higher in the pasture and organically managed plots compared to conventional ones, while DHA was highest in pasture soils and greater under organic than conventional management. Overall, a consistent pattern was observed in both soil types, with the highest enzymatic activities in pasture soils and lower values in conventionally managed plots, suggesting that reduced soil disturbance, permanent vegetation cover, and continuous organic inputs promote a more active microbial community. Similarly, Błońska et al. [75] reported that enzyme activity is strongly influenced by SOM content. The elevated UA and DHA in pastures compared to tilled soils likely reflect the combined effects of vegetation type and lack of plowing. Moreover, studies comparing pasture and arable land use have shown that converting cropland to pasture enhances soil enzyme activities. For example, Yu et al. [76] observed an increase in specific enzymes, such as UA, after conversion to various types of pasture.

In Stagnosol soils, a significantly higher activity of UA and DHA was observed in organically managed plots (5–10 years) compared to conventional ones, highlighting the sensitivity of biological indicators to management practices. These results emphasize the potential of enzymatic assays as early and responsive indicators of changes in soil biological functioning, particularly in soils with inherently lower fertility and in systems transitioning toward sustainable land use. Our results are consistent with global meta-analyses and field studies reporting 25–80 % higher UA and DHA under organic management [62,74,77]. For example, Kwiatkowski et al. [74] observed higher activity of all tested enzymes, including UA and DHA, in organic systems, while Futa et al. [77] reported, on average, 25% higher DHA and 28% higher UA compared to conventional management.

The study by Wen et al. [78] clearly indicates that conservation tillage is an effective strategy to enhance soil enzyme activity on global croplands. Practices such as reduced tillage or no-till in combination with straw return, similar to those applied in our investigated plots, have strong potential to improve soil biological activity. This is consistent with our findings, where higher UA under organic management may be attributed to the regular application of organic amendments, which provide a continuous nitrogen source and stimulate microbial communities capable of urea hydrolysis. Likewise, the increased DHA observed in organic systems reflects enhanced microbial oxidative metabolism, often associated with improved SOM quality and availability. Similar trends were reported by Krzywy-Gawrońska [72] and Zaborowska et al. [73], who documented increased enzyme activities in soils fertilized with compost as a result of enhanced microbial activity and improved SOM quality. In contrast, lower enzyme activities recorded in conventionally managed plots may result from more intensive tillage, reduced organic inputs, and potential adverse effects of synthetic agrochemicals on soil microbial communities [71].

Rieznik et al. [79] reported that in Chernozem soils the most pronounced enzymatic changes occurred in the topsoil layer (0–10 cm). They also noted that organic farming enhanced enzyme activity, including DHA, to levels comparable with those in uncultivated soils. In our study, however, the increase in DHA under organic management in Chernozem soils was not significant, suggesting that insufficient time may have passed for measurable differentiation to emerge between organic and conventional systems. Moreover, we observed strong positive correlations between SOC and DHA, as well as between HWOC and UA in the organic system (5–10 years), and between SOC and UA in the organic system (>10 years) on Chernozem soils. These findings emphasize the importance of the temporal dimension in organic farming, as the accumulation of SOC and the establishment of functionally stable microbial communities typically require several years of consistent organic management. Therefore, the long-term application of organic inputs is essential to achieve sustained and significant increases in enzymatic activity, as confirmed by long-term field studies and meta-analyses, such as those by Fließbach et al. [58] and Lori et al. [62].

5. Conclusions

This study provides new evidence that organic farming practices lead to measurable improvements in soil quality under the given agro-ecological conditions, particularly in less fertile soils such as Stagnosol.

By applying a minimum data set (MDS) in combination with an integrative statistical framework, clear differences in soil quality were observed across land-use systems and different durations of organic management. Conventionally managed soils were characterized by higher BD, less favorable chemical properties, and lower biological activity in both selected soil types. In contrast, organically managed soils on Stagnosol showed measurable improvements in physical, chemical, and microbiological properties, while long-term organic practices on Chernozem further enhanced BD, SOC and HWOC content compared to medium-term management.

These findings provide early evidence of soil regeneration processes under organic management and underscore the value of integrated, indicator-based approaches for assessing soil quality and monitoring progress toward climate-adaptive and regenerative farming systems.

The practical implications of this research are relevant for land managers and producers seeking to improve long-term soil fertility and mitigate the negative impacts of conventional agricultural practices, thereby strengthening the potential for organic production in the region. Future studies should further explore long-term trends in stable carbon pools, microbial functions, and management practices, extending the research to other low-fertility soils and larger sample sizes with more comprehensive management data. Such work will build on the present findings and guide the development of resilient, climate-adaptive agricultural systems in the face of increasing soil degradation and climate change pressures.