Phacelia and Buckwheat Cover Crops’ Effects on Soil Quality in Organic Vegetable Production in a High Tunnel System

Abstract

Cover crops (CCs) are regarded as beneficial to agricultural practice as an option for soil quality improvement in field production systems. The main goal of this study was to assess the impact of spring phacelia (Phacelia tanacetifolia Benth.) and buckwheat (Fagopyrum Mill.) in a crop rotation (CC–leek–parsley, 2020–2021) on the physicochemical and biological properties of the soil in an organic high tunnel system. Soil analyses involved measurements of bulk density, water capacity, soil aggregation, soil organic carbon (SOC), available soil nutrients, as well as microbial abundance and diversity. Phacelia generated more aboveground biomass (58.2 t fresh matter ha⁻¹) than buckwheat (33.0 t ha⁻¹), and their biomass contained 161 kg N ha⁻¹ and 67 kg N ha⁻¹, respectively. A large quantity of elements, such as N, Ca, P, S, B, and Cu, were found in phacelia biomass. More Mg and Na were found in buckwheat plants. The results showed that CC biomass significantly improved some of the soil physical and chemical properties, such as soil organic carbon stock and wet aggregate stability, and decreased soil bulk density. Cover crop treatments changed the dynamics of soil bacterial and fungus populations in a high tunnel system. Phacelia increased the quantity of ammonifiers and nitrifiers in the soil substantially. Further research with a long-term focus is needed to assess the impact of cover crops on soil properties, soil quality, and subsequent crop yields in high tunnel crop rotation and management systems.

1. Introduction

The design of an appropriate crop rotation is a vital strategy for farmers in all plant production systems. Cover cropping is a farming practice that has been known for years and is presently gaining attention worldwide [1]. Appropriate cover crop management, i.e., species choice, seeding rate and date selection, period and termination stage determination, and method selection, is key to avoiding the negative effects of cover crops (CCs) on the subsequent crop [2]. When correctly incorporated into a crop rotation, cover crops (CCs) can significantly contribute to enhancing soil health and quality, improving yields, and promoting environmental protection in sustainable crop production [3,4,5,6]. Their use should also be a constant practice in organic production under cover in the native soil of the production structure. High tunnels are a vital season extension for production in cold and temperate climates; however, maintaining soil health in these intensively managed spaces is challenging [7,8]. Cover cropping can advance the management of supplies for improving soil health and fertility and potentially decrease disease and the weed pressures that accumulate in intensively managed high tunnel systems [7,9,10]. High tunnel soil management is not an easy task for vegetable producers, especially in terms of simplified rotations, the breakdown of organic matter, the decrease in biological soil activity, salt accumulation, elevated alkalinity, etc. [10,11,12,13,14]. High tunnels are particularly appealing to organic producers of high-value fresh-market horticultural crops. Intensive vegetable production within high tunnels requires inputs of organic materials to sustain long-term soil productivity. Organic farmers aim to enhance soil fertility through the use of soil fertility management tools such as crop rotations, as well as agro-ecological service crops, including cover/green manure crops [5,15].

The effect of cover crops in the long term brings undoubted benefits in any cultivation system. Many studies suggest that diversified rotations with leguminous and non-leguminous cover crops improve desirable biogeochemical properties. Plant residue diversity increases the biological activity of the soil, contributing to improving the stability of the soil ecosystem and strengthening its resistance to pathogenic factors [16,17,18,19]. The microbiological activity of the soil, as well as plant root secretions, can improve the nutrient cycling and increase the nutrient use by crops from organic sources, as well as from soil reserves [12]. Nutrients from organic biomass introduced into the soil become available to plants only after they are released as a result of microbiological transformation [20,21]. Decay and nitrogen release usually happen quicker for biomass with lower C/N ratios and lignin and polyphenol contents [22]. The increase in soil biological activity also improves the soil structure and thus the air and water properties of the soil [14]. In addition to the process of mineralization of the organic matter supplied to the soil, there is also a process of humification, creating permanent humus compounds [23]. Though cover cropping is usually attributed to its ability to increase soil organic matter and microbial biomass pools, the definite amount of such changes depends on management and the environment, as well as the cover crop biomass buildup [19,24].

According to several studies, CC cultivation and integration significantly enhance soil microbial structure and populations. Microbiological activity is a key indicator of soil quality, determining, among other things, the carbon and nitrogen dynamic and the stable humus content in soil [25]. In a long-term study, the presence of diverse cover crop species (triticale, rye, vetch, pea, faba bean, radish, and phacelia) significantly enhanced soil organic carbon and stimulated microbial richness and diversity [21,26]. There is lack of research on the impact of CCs on the soil microbiome in crop production systems under plastic-covered structures where plants are grown directly in the native soil. Networks between the plants and soil microorganisms that control the transformation and mineralization of soil organic matter are the basis of the functioning of agricultural ecosystems [1,27]. The impact of different cover crop species and subsequent cash crops on nutrient cycling and the soil microbiome remains unknown in unheated tunnels. Existing cover crop research primarily concentrates on field crops [1,2,6]. However, there are few studies on the impact of using CCs in intensive rotations of vegetable crops under cover [5,7,8,12].

Cover crops include many plant species grown for driving biomass production and are generally classified as leguminous, non-leguminous, or grasses [6]. The inclusion of non-legume broadleaf cover crops, such as popular buckwheat and phacelia, is crucial due to their rapidly decomposing residue, which surpasses that of most grass species. This characteristic aids in achieving a balance between minimizing nutrient loss and maintaining adequate fertility levels to support subsequent cash crops [1]. Buckwheat belongs to the eudicot family Polygonaceae, and phacelia from Boraginaceae are taxonomically different from other crops in a typical arable rotation and can thus prevent diseases, as well as possessing other advantages. The main methods used to reduce the spread of weeds in farming systems are increasing plant biodiversity via crop rotations and the application of soil cultivation technologies that induce the germination of weed seeds prior to the main tillage operations [15,28]. Rapidly growing and drought-tolerant phacelia are characterized by high root length density and area and are beneficial as a rotational cover crop or short-period catch crop [28]. Buckwheat, a highly productive species, has a deep-penetrating root structure that allows it to digest insoluble phosphorus (P) compounds deep within the soil profile and replenish the top horizons for future harvests [15,28,29]. These species accumulate significant N, similar to grasses, and help in reducing nitrate losses [1].

The aim of this study was to determine the impact of the use of phacelia and buckwheat cover crops grown in the spring season on the chemical, physical, and biological properties of the soil in a high tunnel system during cropping periods 2019–2021, with the following sequence of plants: spring cover crops/leek/parsley. We explored the deficiencies in our current understanding of cover crops in organic vegetable production under plastic covers. Our research highlights agrotechnical solutions integrating the selection of appropriate cover crops in a vegetable-intensive crop rotation in unheated high tunnels in an organic system.

2. Materials and Methods

2.1. Experiment Design

The experiment was set up in 2020. A high tunnel was situated at the experimental station of the University of Agriculture in Krakow, located in Mydlniki, Poland; the climate is classified as humid continental (Dfb) according to Köppen’s classification. This region of southern Poland (51°13′ N, 22°38′ E) experiences this specific climate type [30].

A tunnel 30 m long, 7 m wide, and 3.2 m high covered with LDPE (low-density polyethylene) film 0.165 mm thick was built in an east-to-west orientation at the aforementioned site in March 2014. According to PN-R-04032 (1998) [31], particle size analysis categorized the soil at the site as fine texture, matching the silty clay soil group with approximately 40% of clay particles. Four replications of cultivation plots were created inside the high tunnel. The control plot in this experiment was bare soil (1/3 of the tunnel area) covered with black plastic mulch (thickness 100 µm, transmission in the light range of 700–1100 nm: 0%, absorption: 95%, reflection: 5%) until the start of the leek planting.

2.2. Crop Rotation

The CC study plots were established in the tunnel in the spring of 2020 in four randomized replications. Each replicate plot measured 15 m². Prior to the start of the experiment, the soil was cultivated using a mechanical rotary cultivator. From 5 March 2020 to 3 June 2020, phacelia cultivar ‘Stala’ (Phacelia tanacetifolia Benth.) and buckwheat cultivar ‘Kora’ (Fagopyrum esculentum Mill.) were planted as cover crop treatments, with no application of fertilizers. The seeding rate in cover crops was 20 kg ha⁻¹.

Seeds were sown manually onto the plots and incorporated into the soil by shallow cultivation.

Table 1. High tunnel operations in the vegetable production with cover crops, 2020–2021.

Year	Date	Operation *
2020	23 April	Sowing of cover crop
	3 June	Cutting of cover crop
	16 June	Soil cultivation, planting of leek, Soil mulching
	5 October	Leek harvest
2021	16 March	planting of parsley
	15 June–14 September	Parsley harvesting

* Cultivation of all the species was conducted according to the principles of organic farming (certificates Pl-03-02786-16; PL-03-002786-17).

shows tunnel operations in 2020–2021, taking into account crop rotation (CC—leek—parsley). The CC biomass was cut down on June 3, weighed and evenly distributed, and the soil surface in the entire tunnel was covered with a black PP (poly propylene) 50 g m⁻² non-woven fabric. On June 16, seedlings of leeks (cv. ‘Lincoln’) were planted in the holes made in the plastic mulch with a spacing of 50 × 10 cm. The harvest was carried out on October 5. In 2021, following the same experimental setup and maintaining the PP non-woven mulch over winter, seedlings of leaf parsley (cv. Gigante d‘Italia) were planted on March 16 in new holes with a spacing of 50 × 20 cm. The harvesting was conducted from June 15 to September 14. In both 2020 and 2021, the plants were fertilized during the vegetation period with liquid organic fertilizers Rosahumus 2% (Humintech GMBH, humic acids—85%, K₂O—12%, Fe—0.6%) and Humistar 1% (Tradecorp, humic acids). Cultivation of all the species was conducted according to the principles of organic farming (certificates Pl-03-02786-16; PL-03-002786-17).

2.3. Soil Chemical Analysis

Following the termination of the phacelia and buckwheat cover crops on 3 June 2020, and after each cash crop harvest, soil samples were collected using a soil core sampler from a depth of 0–20 cm. Kopecký’s 250 cm³ cylinder was used to collect undisturbed samples in four replicates from soil (0–10 cm deep) to measure bulk density. Next, the soil cores were weighed, wetted (for capillary action), and dried at a temperature of 105 °C. From all the experimental plots, aggregates from undisturbed soil (0–20 cm deep) were gathered in six replicates. The procedure of sieving the bulk soil and extracting air-dried aggregates (<5 mm) was carried out. Five sieves with mesh sizes of 0.25, 0.5, 1.0, 1.5, and 2.5 mm were used for wet soil sieving. Forty grams of each soil sample were placed on the top of a stacked construction and soaked in distilled water for 5 min. Subsequently, through the process of raising and lowering the sieves with a motor-driven holder, the soil samples were wet-sieved in a water container. The stroke length was 5 cm, with a sieving frequency of 5 cycles per 20 min. After the wet-sieving process was completed, the soil from each sieve was oven-dried at a temperature of 105 °C and then weighed in each sieve, indicating water-stable aggregates in different size classes: 5.0–2.5, 2.5–1.5, 1.5–1.0, 1.0–0.50, and 0.50–0.25 mm.

The pH of the soil was determined at a soil-to-water ratio of 1:2. The soil organic carbon (SOC) content was measured using the dichromate oxidation method [32]. Additionally, by using the universal method, the available form of macronutrients and sodium was analyzed in 0.03 mol dm³ CH₃COOH (Acetic acid P.P.H Standrad Sp. z o.o., Lublin, Poland). Micronutrients (the extractable form) were determined in 1 mol dm³ HCl (Hydrochloric acid P.P.H Standrad Sp. z o.o., Lublin, Poland) [32]. The available forms of nutrients were determined using the inductively coupled argon plasma atomic emission spectroscopy (ICP-OES) technique.

2.4. Cover Crop Analysis

Before the termination of the spring cover crops, samples of the aboveground biomass were collected from 4 × 1 m² sections within each replicate plot. The plants were weighed to determine the total fresh biomass. The collected leaf tissue samples underwent the following procedure. They were washed with distilled water, dried at 65 °C for 48 h, and then ground for elemental analysis. Macronutrients and micronutrients were determined using the ICP-OES technique following microwave digestion in HNO₃ (Nitric acid Merck). Elemental analyses were performed using a Prodigy High Dispersion ICP-OES Spectrometer (Teledyne Leeman Labs, Hudson, NH, USA). The total nitrogen content of the plant material was determined using the Kjeldahl method [32,33].

2.5. Microbiological Analysis

An aliquot of 10 g (fresh weight) of the mixed material from each soil sample was suspended in 90 mL sterile 0.85% sodium chloride solution (Chempur, Mumbai, India). The soil suspensions were shaken for 30 min in a rotary shaker (150 rpm) at room temperature for desorption of bacterial cells. The soil suspension was allowed to settle for 1 min, and 10⁻¹ dilutions (highest dilution step: 10⁻¹⁰) were prepared. These processes were carried out in sterile conditions to avoid contamination. Microbiological tests were performed on the soil for:

The quantity of common soil microorganisms, including bacteria, and fungi were determined by the plate counting method:

-

Total number of bacteria (CFU—colony-forming unit): enriched agar (BIOMAXIMA), incubation 24 h at 37 °C [34].

-

Total number of fungi (CFU): Sabouraud Dextrose Agar with Chloramphenicol (BIOMAXIMA) incubation at 25 °C for 5 days [34].

-

The most probable number (MPN) of ammonifying bacteria (MPN per 100 cm⁻³) on broth medium with 3% peptone addition (pH 7.2) after 7 days of incubation at 26 °C. The presence or absence of ammonium was determined using Nessler’s reagent (Chempur, Mumbai, India) [35,36].

-

The most probable number (MPN) of nitrifying bacteria oxidizing NO₂ -N on the mineral culture medium with NaNO₂ acc. to Winogradsky. Incubation was conducted for twenty-eight days at 28 °C. The presence or absence of NO₂ was determined using Griess reagent (Chempur, Mumbai, India) [37],

-

The most probable number (MPN) of denitrifying bacteria (MPN per 100 cm³) on Giltay medium (Chempur, Mumbai, India) with Durham test tubes at pH 7.0 after 14 days of incubation at 25 °C. The presence or absence of denitrification was determined using alpha-naphthylamine [35,36].

2.6. Statistical Analysis

Statistical analyses for soil physico-chemical parameters compared the main effects of soil treatments, specifically cover crops. All data were analyzed using one-way ANOVA, and the means for each treatment were separated using the Fisher LSD test.

Each microbiological analysis was performed in duplicate, using three independent series of dilutions and culture incubations. The obtained results of microorganism frequencies were statistically analyzed using the one-way (treatments) or two-way (two factors: treatment and date of soil analysis) analysis of variance (ANOVA). The assumptions of variance analysis were verified, using the normality test (Kolmogorov–Smirnov) and the equality of variance test (Levene). The resultant mean values were compared using the Fisher’s Least Significant Difference (Fisher’s LSD) test with a significance level of p = 0.05. All data were analyzed using Statistica 13.3 software (Statsoft Inc., Kraków, Poland).

3. Results

3.1. Cover Crop Analysis

During the 41 days of spring vegetation (end of April to the beginning of June), phacelia produced a higher amount of aboveground fresh biomass (58.2 t ha⁻¹) compared to buckwheat (33.0 t ha⁻¹). The nitrogen content in their biomass was 161 kg N ha⁻¹ and 67 kg N ha⁻¹, respectively (

Table 2. Total fresh aboveground biomass (t FM ha⁻¹), dry biomass (t DM ha⁻¹), dry matter (%), and total N contribution (kg N ha⁻¹) of cover crops grown in a high tunnel.

Treatment	Biomass (kg m−2)	Freh Biomass t FM ha−1	Dry Matter DM (%)	Biomass t DM ha−1	kg N ha−1
Phacelia	5.85 b	58.2 b	11.8 b	6.10 b	161.7 b
Buckwheat	3.30 a	33.0 a	10.2 a	3.37 a	67.4 a

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). Significantly higher contents of nutrients, such as N, Ca, P, S, B, and Cu, were determined in the phacelia biomass. Buckwheat plants had higher levels of Mg, Na, and trace elements such as Fe, Mn, Zn, and Ti (

Table 3. Concentrations of macronutrients (% in DM), micronutrients, and Ti (mg kg⁻¹ DM) in the biomass of cover crops grown in a high tunnel.

Treatment	N	Ca	K	Mg	P	S	Na
Phacelia	2.65 b	3.18 b	3.80 a	0.24 a	0.35 b	0.23 b	0.31 a
Buckwheat	2.00 a	1.52 a	4.12 a	0.42 b	0.28 a	0.18 a	0.52 b
	B	Cu	Fe	Mn	Zn	Ti
Phacelia	26.8 b	7.57 b	158 a	27.9 a	24.1 a	3.44 a
Buckwheat	15.1 a	5.70 a	314 b	45.5 b	38.8 b	8.10 b

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

).

The yield of vegetable crops (leek and parsley) varied noticeably. In the plot following phacelia, whole-plant leek yield was the highest, being 17–18% greater than that of the other plots (data not presented). In contrast, leeks grown after buckwheat contained higher levels of sugars and phenolic compounds. Phacelia cover cropping increased the antioxidant activity in leek plants. The total yield of parsley leaves was significantly higher in the plots after phacelia and buckwheat compared to the control, by 55% and 41%, respectively. The highest vitamin C content in parsley leaves was obtained after phacelia cropping. The results may suggest that phacelia is the optimum species for use as a cover crop for leeks in vegetable rotation in high tunnel organic production.

3.2. Soil Physical and Chemical Analysis

Our research showed that after cover crop plant termination in 2020, soil parameters such as bulk density (BD), water capacity (WC), and soil organic carbon (SOC) were comparable to those determined in the control soil covered with black plastic mulch during the cover crop growth period (

Table 4. Bulk density (g cm³), water capacity (WC %ww and %wv), and soil organic carbon (SOC%) in soils within a high tunnel in 2019–2021.

Treatment	Bulk Density g cm−3	WC %ww	WC %wv	SOC %
2019	1.27	36.3	45.0	1.27
After cover plant termination
Control	1.29 a	34.2 a	44.2 b	1.49 a
Phacelia	1.23 a	33.1 a	41.9 a	1.47 a
Buckwheat	1.28 a	32.5 a	43.2 ab	1.49 a
After leek cropping
Control *	1.42 c	34.7 a	47.4 a	1.56 a
Phacelia	1.31 a	36.1 a	47.3 a	1.51 a
Buckwheat	1.37 b	33.8 a	47.4 a	2.30 b
After parsley cropping
Control	1.42 a	35.6 a	50.1 a	1.76 a
Phacelia	1.40 a	35.2 a	48.7 a	1.91 b
Buckwheat	1.38 a	36.0 a	50.0 a	2.01 c

Notes: * the control plot in this experiment was bare soil covered with black plastic mulch until the start of an experiment; means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). In contrast, in the 2021 sequence, we observed significant changes in these parameters after growing leek cash crop. The bulk density of the soil with CC treatments was significantly lower than in the control soil. Soil analyses also showed a significant increase in the organic carbon content in the soil with buckwheat treatment. Considering the crop rotation used in 2020–2021 (cover crop–leek–parsley), cover crops generally increased the amount of SOC in the soil (Table 4).

In both years of the experiment, the highest water-stable aggregate index (WSI), represented by the sum of the 0.25–5.0 mm water-stable aggregate fractions, was observed in soils with cover crops (

Table 5. Percentages of five classes of soil water-stable aggregates (mm) in soils in the year after leek and parsley production in the high tunnel (2019, after cash crop harvest; 2021).

Treatment	5.0–2.5	2.5–1.5	1.5–1.0	1.0–0.5	0.5–0.25	∑ 0.25–5.0 WSI%
2019	25.3	21.1	16.9	16.0	9.3	88.5
After leek cropping
Control	29.2 a	14.7 a	13.6 a	15.9 a	12.3 b	85.6 a
Phacelia	36.3 a	17.2 b	13.4 a	13.6 a	7.7 a	88.1 ab
Buckwheat	34.9 a	18.3 b	15.3 a	14.0 a	7.5 a	89.9 b
After parsley cropping
Control	14.3 a	10.6 a	11.7 a	25.3 ab	21.3 c	83.2 a
Phacelia	21.8 b	15.3 b	16.8 b	21.5 a	12.8 a	88.3 b
Buckwheat	15.6 a	13.4 ab	16.1 b	26.3 b	16.6 b	88.0 b

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). In 2021, after the leek harvest, aggregates with diameters of 2.5–1.5 mm constituted 14.7–18.3%. The formation of water-stable aggregates differed significantly among the treatments. The mean values showed a significantly higher percentage of macro-aggregates in the soil treatments with cover crops compared to the untreated control. In 2021, for parsley cropping, the highest percentage of water-stable macro-aggregates, 5.0–2.5 mm and 2.5–1.5 mm, was found in the soil with the phacelia treatment (21.8% and 15.3%, respectively). Cover crop treatment also significantly increased the percentage of water-stable aggregates 1.5–1.0 mm in diameter in relation to the control soil. However, the highest percentages of micro-aggregates 0.5–0.25 mm in diameter were found in the control soils.

In 2020, following the termination of cover crops, the phacelia and buckwheat treatments significantly increased soil pH values (pH 7.28 and 7.31, respectively) compared to control soil (pH 7.05). Conversely, higher levels of NO₃-N and NH₄-N were observed in the control soil (

Table 6. Soil reaction (pH in H₂O), salinity (EC, electrical conductivity µS cm⁻¹), macronutrients, and sodium (mg dm⁻³ of fresh soil) in soils within the high tunnel from 2020 to 2021.

Treatment	pH	EC	NH4-N	NO3-N	Ca	K	Mg	P	S	Na
After cover plant termination
Control	7.05 a	421 a	0.52 a	71.4 b	1216 a	110 a	99 a	29 a	113 a	43 a
Phacelia	7.28 b	437 a	0.55 a	33.5 a	1267 a	102 a	116 a	31 a	106 a	46 a
Buckwheat	7.31 b	490 a	0.39 a	31.4 a	1258 a	105 a	119 a	30 a	132 a	52 a
After parsley harvest
Control	8.01 a	485 b	0.02 a	33.8 b	1934 a	99 a	200 a	41 a	91 ab	74 a
Phacelia	7.96 a	373 ab	3.88 b	16.4 a	2205 a	123 ab	229 a	46 a	67 a	83 a
Buckwheat	7.81 a	293 a	trace	27.7 b	1924 a	216 b	217 a	58 a	127 b	80 a

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). In 2020, the control soil covered with black plastic mulch exhibited elevated levels of soluble nitrate nitrogen, likely influenced by moderate soil moisture and temperature conditions in the high tunnel.

In 2021, following the harvest of the cash crop, the cover crop treatments, particularly buckwheat, substantially reduced soil electrical conductivity (EC) or salinity, compared to the control (Table 6). High tunnel soils typically exhibit higher EC levels compared to open-field conditions, particularly in intensive vegetable production where substantial amounts of animal manure or mineral fertilizers are applied. Conversely, tunnel soils do not undergo regular leaching from rainwater, leading to the accumulation of soluble salts from the use of hard water for irrigation purposes.

Higher concentrations of ammonium nitrogen in the soil treated with phacelia cover crop were observed at the end of experiment in 2021, along with the lowest values of NO₃-N compared to other treatments. On the contrary, after the incorporation of buckwheat residues, soil analysis indicated the ability to enrich soil with major nutrients, in particular, potassium and sulfur (Table 6).

In 2020–2021, with the exception of boron (B), which had a low concentration of <1 mg B kg⁻¹ DM of soil, micronutrient concentrations in soil were optimal for plant nutrition (

Table 7. Microelement concentration (mg kg⁻¹ of dry soil) in soils within the high tunnel (2020, after cover crop termination; 2021, after cash crop harvest).

Treatment	B	Cu	Fe	Mn	Zn	Ti
After cover plant termination
Control	0.63 a	5.96 a	2492 a	382 a	55.7 a	11.3 a
Phacelia	0.80 a	5.71 a	2446 a	385 a	56.5 a	11.0 a
Buckwheat	0.74 a	5.72 a	2437 a	370 a	56.9 a	10.9 a
After growing parsley
Control	0.96 a	5.87 a	1836 a	237 a	55.8 a	7.98 a
Phacelia	0.95 a	5.87 a	1825 a	242 a	55.8 a	7.80 a
Buckwheat	0.83 a	5.81 a	1836 a	248 a	55.2 a	7.71 a

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). After termination of cover crops, an elevated, but not statistically significant, concentration of B was found in the CC crop soils compared to the control soils.

3.3. Soil Microbiological Analysis

Cover crop treatments changed the dynamics of soil bacterial and fungal populations in the high tunnel. Compared to fallow soil, cover crops enhanced the size of the overall microbial and fungal communities. This observation was particularly evident following the harvest of the cash crop in 2021. Upon termination of the cover crops (CCs), the soil harbored the highest count of mesophilic bacteria in plots where phacelia was utilized as a cover crop (

Table 8. Total number of bacteria (CFU) and fungi in the soil after cover crop treatment (2020–2021).

Treatment	Date of Analysis	Bacteria CFU g−1 DM of Soil	Fungi CFU g−1 DM of Soil
Control	after CC termination 3 June 2020	7.5 × 106 c	4.2 × 103 c
Phacelia		3.8 × 107 e	1.9 × 104 g
Buckwheat		7.8 × 106 d	8.4 × 103 f
Control	after leek harvest 29 March 2021	4.7 × 105 b	3.4 × 103 b
Phacelia		7.8 × 107 f	5.3 × 103 d
Buckwheat		9.2 × 106 d	8.0 × 103 e
Control	after parsley harvest 10 December 2021	1.7 × 105 a	2.2 × 103 a
Phacelia		9.7 × 106 g	5.8 × 103 d
Buckwheat		7.0 × 106 c	4.0 × 103 c
Mean for treatments
Control		2.7 × 106 a	3.2 × 103 a
Phacelia		4.2 × 107 c	1.0 × 104 c
Buckwheat		8.0 × 106 b	6.8 × 103 b
Mean for date of analysis
3 June 2020		1.8 × 107 b	1.1 × 104 c
29 March 2021		2.9 × 107 c	5.6 × 103 b
10 December 2021		5.6 × 106 a	3.9 × 103 a

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). It is noteworthy that the biomass of phacelia introduced into the soil was significantly greater than that of buckwheat (Table 2). Soil analyses performed at that time also showed that the highest number of fungi was found on the plot with cover crop treatments in relation to the control (Figure 1). The mean number of fungi was significantly higher after phacelia cover crop termination (1.0 × 10⁻⁴ CFU DM of soil) than after buckwheat (6.8 × 10⁻³ CFU DM of soil) (Table 8).

At each soil analysis date, most bacteria were determined in combination with phacelia (Figure 1). In 2021, a higher number of fungi was established in soil with cover crop treatments compared to the control (Table 8).

The most probable number (MPN) method is a culture-based technique commonly used in environmental microbiology to examine microbial populations in liquid substrates [34]. The experiment assessed the differences between three groups of microorganisms. The phacelia site was characterized by a significantly higher number of ammonifiers in 2020 (9.5 × 10⁻⁶ CFU DM of soil) and in 2021 (9.2 × 10⁻⁶ CFU DM of soil) compared to other treatments (

Table 9. Most probable number (MPN) of ammonifiers, Nitrifiers, and denitrifiers in 1 g⁻¹ DM of soil (p < 0.05) in soil after cover crop treatment, 2019.

Treatment	Date of Analysis	Ammonifers	Nitrifiers	Denitrifiers
Control	after CC termination	1.5 × 106 a	2.5 × 105 a	8.2 × 104 e
Phacelia		9.5 × 106 e	5.6 × 105 d	1.8 × 104 a
Buckwheat		5.2 × 106 c	6.3 × 105 e	4.0 × 104 c
Control	after leek harvest	1.4 × 106 a	2.2 × 105 a	8.4 × 104 f
Phacelia		9.2 × 106 e	5.5 × 105 d	1.9 × 104 b
Buckwheat		8.6 × 106 d	3.8 × 105 c	2.0 × 104 b
Control	after parsley harvest	3.4 × 106 b	2.6 × 105 a	8.1 × 104 e
Phacelia		5.5 × 106 c	3.0 × 105 b	1.5 × 104 a
Buckwheat		7.5 × 106 d	2.4 × 105 a	5.4 × 104 d
Mean for treatments
Control		2.3 × 106 a	2.5 × 105 a	8.3 × 104 c
Phacelia		8.1 × 106 c	4.7 × 105 c	1.8 × 104 a
Buckwheat		6.7 × 106 b	4.4 × 105 b	3.8 × 104 b
Mean for date of analysis
03.06.2020		5.5 × 106 a	5.0 × 105 c	4.7 × 104 b
29.03.2020		6.0 × 106 a	3.9 × 105 a	4.1 × 104 a
10.12.2021		5.5 × 106 a	2.7 × 105 a	5.0 × 104 c

Means followed by a common letter are not significantly different by the Fisher’s LSD test at the p < 0.05 level of significance.

). The same was true for nitrifying group. The MPN of ammonifiers determined at the end of the experiment (10 December 2021) was the highest in soil treated with buckwheat cover crop (7.5 × 10⁻⁶ CFU DM of soil). In every term of soil analysis, the lowest amount of nitrifying bacteria was detected in the control soil. An inverse relationship was demonstrated for the group of denitrifiers (Table 9).

4. Discussion

In the presented experiment, we verified how spring cover crops affect the soil’s physical, chemical, and biological properties in organic vegetable production in unheated high tunnels. The microclimate conditions in this structure allowed a large biomass of phacelia and buckwheat crops to be obtained from the end of April to the beginning of the June period. Inside this closed tunnel on a typical day in this season, the mean temperature in the morning was 4.2 °C higher than outside. In the afternoon, this difference increased, reaching 5.8 °C. The CO₂ concentration was more than twice as high in the tunnel as outside [10]. The spring cover crop fresh biomass was greater for phacelia than for buckwheat, and it resulted in better weed suppression in the tunnel trial (data not presented). McKenzie-Gopsill et al. (2022) [29] and Koudahe et al. (2022) [1] reported highly productive forbs, including buckwheat, and phacelia provided the greatest weed suppression in monoculture.

In our study, cover crop enhanced some vital soil properties, including bulk density, organic matter content, and water-stable aggregate index compared to the untreated soil. Scavo et al. (2022) [6] found that cover crops have beneficial effects on bulk density, porosity, water infiltration, and water holding capacity. Compaction in organic crop fields in no-till systems alters soil nutrient and water dynamics and can reduce crop growth and yield. Haruna et al. (2020) [27] indicated that CCs decrease soil bulk density by around 4%, increase macrospores by 33%, and increase water infiltration by 629%, with respect to control soil without CC treatments. Nascente et al. (2016) [18], Nascente and Stone (2018) [38], and Adeli et al. (2020) [39] also reported that CC usage reduced soil bulk density. Bodner et al. (2014) [28] found that different root architectures of cover crops impacted soil porosity as well as pore size distributions and soil water infiltration.

Soil aggregation and soil structure are vital for soil productivity. Soil aggregate dynamics are impacted by many factors, including soil, plant root activity, soil chemical properties, and environmental and agronomic conditions [40]. Plant roots and microorganisms can modify and stabilize the soil aggregates through processes such as bonding and glueing soil particles via the secretion of mucilage and other extracellular natural polymers of high molecular weight (polysaccharides) [1,27]. Crawford et al. (2011) [41] provided evidence that the soil–microbe system is self-organizing as a result of feedback between microbial activity and soil aggregation. Plants can rearrange soil structure, but this effect is strongly dependent on soil texture. Bacq-Labreuil et al. (2019) [42] indicated that for clay soil, phacelia plants significantly increase the number of aggregates <1000 μm and surface density. In the presented study, a considerably higher percentage of macro-aggregates in the cover crop soil treatments compared to the untreated control was observed in silty clay soil. This finding is supported by earlier research by Domagała-Świątkiewicz et al. (2019) and (2022) [12,13], which studied hairy vetch, vetch–rye biculture, and pea, pea–oat biculture, respectively.

Sharma et al. (2018) and Blanco-Canqui et al. (2018) [3,4] demonstrated that cover cropping favored an increase in soil organic carbon (SOC) in silt–loam soils more than in sandy soils, particularly in no-till systems over a long period. In this study, after the cover crop termination of cover crops in 2020, the soil organic carbon content in tunnel soils was not significantly different. In the subsequent cropping season (after leek and parsley cropping in 2021), the highest SOC values were noted for the soils treated with buckwheat. However, taking into account the whole crop rotation in 2020–2021, CCs generally increased the amount of SOC in the soil compared to the control treatment (Table 4). Koudahe et al. (2022) [1] reported that the annual contributions of fresh organic matter as cover crop residues might be relatively small compared to established soil organic matter pools, especially after residue losses following decomposition. These findings indicate that the investigated CCs can increase SOC accumulation, though not uniformly. The additional biomass (and organic carbon) input from cover crop cultivation can potentially increase soil organic carbon (SOC) concentration by augmenting crop residues [23]. Phacelia residues have a higher N biomass concentration in comparison to buckwheat (2.65% vs. 2.0% N in DM), which accelerates net mineralization and nitrification after their incorporation into the soil. However, Mooshammer et al. (2014), Brennan and Acosta-Martinez (2017), and Koudahe et al. (2022) [1,11,43] demonstrated that C from lignified roots of broadleaf cover crops may persevere longer in the soil, increasing the long-term root contributions to SOM and possibly also soil organic nitrogen. Soil analysis performed at the end of the presented experiment demonstrated higher SOC at the site with phacelia treatment than that determined immediately after the CC termination. Soil organic matter protects and stabilizes aggregates from water destruction [40]. In the conducted research, a higher water-stable aggregate index (WSI) correlated with higher organic matter content in the soil determined at the end of the experiment.

A more sustainable agriculture requires integrated nutrient management in combination with renewable nutrient sources. The goal of integrated nutrient management is to increase crop nutrient use while reducing losses [20]. Domagała-Świątkiewicz et al. (2024) showed that nutrient recycling from non-legume CC organic residues can increase the amounts of soluble nutrients in the soil, making them available for the subsequent crop [44]. High concentrations of K, SO₄-S, and P (differences for P were not statistically significant) were found in the soil under the deep rooting buckwheat treatment. Root architecture under genetic control regulates soil exploration and therefore nutrient acquisition. A high specific root length has been linked to high root N concentration and supports high nutrient absorption capability [28,45,46]. Domagała-Świątkiewicz et al. (2019) [12] reported higher potassium content in vetch-treated soil and higher Ca, Mg, K, and P under the pea–oat treatment than in bare soil in high tunnel production. Gao et al. (2017) [21] showed wheat cover crop increased cucumber seedling growth and plant N, P, and K concentrations, but decreased soil available N, P, K, Mn, and B contents. Compared to bare fallow systems, a cover crop system may reduce N leaching by 40% (legume plants) to 70% (non-legume) of N [47]. However, authors concluded that these reductions in leaching losses were mainly due to avoidance of bare fallow periods. The majority of the nutrients absorbed by cover crops are then released for use by the main crop via breakdown of the biomass and mineralization of leftovers. Leaf and root features have been linked to plant abilities to acquire, use, and preserve resources and have been used to qualify plant acquisition strategies [1,6,22]. Phacelia showed high root length density and root area [28]. This is especially significant for nutrients accessible by diffusion, such as P and K, due to their limited mobility [46]. In our study, these features were linked to high N, P, S, Ca, B, and Cu biomass concentrations in relation to buckwheat in our research. Root length density increases nutrient uptake by increasing root area. Buckwheat is distinguished by its large root diameter. The key distinction from phacelia is the lower density of root length and surface area of buckwheat. High root diameter is associated with a lengthy root life span, a better resistance to water stress, and higher rates of water transport within the root [48]. Buckwheat has been recognized as such a highly efficient P cover crop that significantly increases P availability for the next plant in the crop rotation after biomass incorporation into the soil. In the presented study, biomass of buckwheat was richer in K, Mg, Na, and trace elements, such as Fe, Mn, and Zn, than phacelia plants. However, soil analysis showed the ability of buckwheat residues to enrich soil with major nutrients, in particular, potassium, sulfur, and phosphorus (differences not statistically significant).

Microbial characteristics are generally considered complex indicators of soil health due to clear relationships between microbiome, soil characteristics, plant quality, and environment sustainability [49]. As a result, microbes may serve as an effective indicator of soil health change, offering an early signal of soil quality improvement or an early warning of soil degradation [50]. All soil organic matter needs to pass through the soil microbial biomass. Current work suggests that the most stable soil organic matter originates from microbial conversion or represents dead microbial biomass [51]. Cover cropping in a crop rotation increased total microbial community size, fungal abundance, and enzyme activities associated with carbon (C) and nutrient cycling. Changes in soil microbial abundance may contribute to the increases in SOC under cover crops [19]. Microorganisms in the soil impact aggregate formation and water transport in soil profile [40]. Bacteria are the most prevalent microorganisms in soil, followed in decreasing numerical order by fungus, soil algae, and soil protozoa. Soil microbes are both producers and components of soil organic carbon, a material that sequesters carbon into the soil for extended periods. Figure 1 shows that the tunnel agroecosystem had a higher number of colonies generated in both fungus and bacteria. Microorganisms have the ability to fit environmental conditions by regulating their activity, biomass, and community structure [52]. Brennan and Acosta-Martinez (2017) [11] showed that ratio of fungal to bacterial indicators decreased over time, and Gram-positive bacteria increased after six years of commercial-scale production in five organic vegetable systems. Fungal decomposers may redistribute N from leaves to more recalcitrant tissues (steams, roots) during decomposition [24]. In our research, phacelia enhanced the occurrence of saprophytic fungi in comparison to buckwheat (Table 8). Gram-negative bacteria and fungi have been characterized as being engaged in the quick absorption of C stored in rhizome deposits [53]. Another study found that fungi, particularly non-mycorrhizal types, were a major influence in distinguishing the microbial community composition of various cover crops about two months after seeding [54]. Microbiological distinction was evident between treatments after buckwheat and phacelia cover plant cultivation, indicating that both plant species altered the structure of microbial communities, but not to the same extent, which may be due to the nature of the root features of this species [43]. Furthermore, changes in microbial community organization can have a major influence on the bio-physical structure of the soil. The feedback between soil structure and microbial activity is connected with porosity. In our study of the soil with CC treatments, a significant higher total number of bacteria and fungi as well as lower bulk density than in the control soil was established. Fungal-dominated communities, for example, improve porosity at sizes critical for water storage, flow, and gas exchange [41].

Nitrogen absorption by plants is accomplished through the biological oxidation of ammonium to nitrate via nitrite, a process known as nitrification [55]. Bacteria performs the majority of ammonia oxidation in soil, which is the fundamental stage in the oxidation process converting ammonia to nitrate and is considered the rate-limiting phase of nitrification in most soil systems [56]. In our investigation, higher concentrations of ammonium nitrogen in the soil treated with phacelia cover crop were observed at the end of experiment in 2021, as well as the lowest NO₃-N in relation to other combinations (Table 9). This phenomenon might be attributed to an increase in nitrification activity. The phacelia site was characterized by a significantly higher number of ammonifiers in 2020 and in 2021 in comparison to other treatments. This may indicate different rates of decomposition of CC residues in the rotation cycle, due to their altered chemical composition. Bacterial genera’s susceptibility to changes in the soil environment varies, and hence, their reactions to soil environmental factors may differ [57,58,59]. Romdhane et al. (2019) [60] found that changes in soil properties due to cover crop management were linked to fluctuations in the number of ammonia oxidizers and denitrifiers, but the overall bacterial richness was not dependent. Our finding is consistent with research indicating that plant type can indirectly impact bacterial populations by modifying soil N status [13,21,60].

Within the N cycle, denitrifiers are responsible for N losses to the atmosphere, therefore reducing available N for crop. Soils with two non-legume cover species (cereal rye and phacelia), which also produced the highest cover crop biomass, exhibited a higher bacterial species richness than the soils with eight legume cover species [59]. In our research on every term of soil analysis, the highest amount of denitrifiers was detected at control sites. The most probable number (MPN) of denitrifiers was correlated with high nitrate content in soils at control sites, especially after cover plant termination (3 June 2020).

5. Conclusions

Our research focused on the potential benefits of phacelia and buckwheat cover crops (CCs) for soil quality in high tunnel cropping systems within temperate climates. We investigated the ability of cover crops to produce large biomass during spring in cold tunnels managed organically. We studied non-leguminous Phacelia tanacetifolia and Fagopyrum esculentum used as cover crop in crop rotation species during 41 days of spring vegetation (from the end of April to the beginning of June) in the moderately warmer and sheltered tunnel environment. The crops yielded between 58 and 33 tonnes per hectare of fresh matter and from 162 to 67 kg per hectare of nitrogen, respectively. The crops yielded between 58 and 33 tonnes per hectare of fresh matter and from 162 to 67 kg per hectare of nitrogen, respectively. These cover crops elevated soil carbon levels and enhanced the stability of wet aggregates. Our study affirmed the substantial influence of cover crop residues on soil biological properties. Particularly, we observed a positive correlation between increased soil organic carbon levels and a higher abundance of bacterial and fungal colonies. CC plant residue can modify microbial activity and therefore impact soil bacterial and fungus populations. The use of phacelia and buckwheat cover plants intensified activity of various microbiological processes, including ammonification, nitrification, and denitrification. We noted that the stimulating effect on bacterial activity persisted for a longer duration in soils with buckwheat cover crops compared to those with phacelia. As highlighted in our earlier research [13], these results underscore the significant role of cover cropping practices in high tunnels as key drivers of both the composition of the total bacterial and fungal community and the abundance of N-cycling microbial associations. Additional research is necessary to standardize the utilization of cover crops across diverse cropping systems and varying climatic conditions. Long-term investigations are particularly essential to evaluate the impacts of cover crops on soil properties, quality, and subsequent crop yields within high tunnel crop rotation and management systems.