Effects of Actinomycete Act12 on Soil Microbial Community Structure and Plant Traits of Ziziphus jujuba Mill.

Abstract

Biocontrol agents play a crucial role in agricultural production by reducing the use of pesticides and chemical fertilizers, controlling pests and diseases, and enhancing crop yield and quality. While extensive research has focused on the growth-promoting and yield-increasing effects of biocontrol agents on herbaceous plants, their impact on woody crops such as trees and shrubs has not been reported. This study investigates the effects of the actinomycete strain Act12, applied via root drenching and foliar spraying, on the flowering and fruit set rates, leaf physiology and enzyme activity, and fruit characteristics and yield of the jujube tree (Ziziphus jujuba Mill.). Additionally, this study analyzes the physicochemical properties of the soil and the diversity and community structure of its microorganisms. The results indicate that treatment with Act12 significantly altered the α and β diversity of soil microorganisms and enhanced the interaction networks among them. This led to increased levels of available nitrogen, phosphorus, and potassium in the soil, significantly improving nutrient availability. Consequently, there was an improvement in the number of flower buds and fruits, as well as an increase in the longitudinal diameter and individual fruit weight of the jujube. These effects significantly enhanced the yield and total sugar content of the winter jujube. Given these findings, Act12 can be considered an effective microbial agent for enhancing the yield and quality of winter jujube when applied to the soil.

1. Introduction

Winter jujube (Ziziphus jujuba Mill.), a woody plant from the Rhamnaceous family, is noted for its high vitamin content and its beneficial effects in nourishing yin and supplementing yang, making it of significant economic value [1]. China is the world’s largest producer of winter jujube, accounting for over 98% of global production, with winter jujube (Ziziphus jujuba cv. Dongzao) being the predominant variety for fresh consumption [1]. Currently, greenhouse cultivation is the main production mode for the winter jujube industry. This method, characterized by the long-term cultivation of the same crop in the same location combined with excessive use of chemical fertilizers and pesticides, is highly susceptible to root diseases in winter jujube. These diseases can lead to significant decreases in fruit yield and quality, resulting in substantial economic losses [2,3].

Extensive research indicates that dysbiosis and deterioration of soil microbiota in the root zone are primary causes of plant root diseases, and subsequent declines in yield and quality [4]. For instance, long-term cultivation of a single crop can selectively influence soil microbiota through the secretion of root exudates or the decomposition of residual plant materials. This selectivity leads to reduced diversity and stability in the soil microbial community structure, shifting towards conditions less favorable for healthy crop growth. Such changes, including a decrease in beneficial microbes and an increase in harmful ones, alter the plant’s physiological traits and metabolic processes, ultimately resulting in decreased yield and quality [5,6].

Compared to bulk soil, which is unaffected by root activities, the root–soil interface, or rhizosphere, presents a complex physicochemical environment that offers a unique ecological niche. This niche is shaped by the combined selection pressures of physical, chemical, and biological factors, leading to the formation of a rhizosphere-specific microbiome [7]. The interactions between these microbial communities and the host plant extend the functional repertoire of the host, effectively acting as a second genome. These interactions can influence plant trait expression and genetics, thereby affecting plant productivity and soil health among other ecosystem functions [8]. Regulating the microbial ecology of the plant rhizosphere is considered a crucial approach to addressing the challenges of continuous cropping.

Actinomycetes are a group of microorganisms widely found in the plant rhizosphere, known for their robust bioactivity. They can enhance plant growth, induce systemic resistance, and control bacterial and fungal diseases in plants [7,8]. Research has demonstrated that inoculating plants with actinomycetes not only increases the biomass of cucumbers and melons, promoting their growth and inducing resistance, but also helps prevent fungal diseases in tomatoes and aconites [9,10,11], and enhances the content of active compounds in Salvia miltiorrhiza [12].

Currently, most studies focus on the role and mechanisms of actinomycetes in disease prevention and growth promotion in herbaceous plants. However, there is limited knowledge about their application value in woody and shrub economic crops, overlooking their potential to address the challenges of decreased yield and quality in greenhouse-cultivated winter jujube.

In light of previous research on the disease prevention and growth promotion effects of Streptomyces pactum Act12 on plants—for example, it has the functions of nitrogen fixation, potassium solubilization, phosphorus solubilization, promoting wheat root growth, and stabilizing the rhizosphere microbial community of tomatoes and aconite [13,14,15]—this study aims to apply Act12 to mature winter jujube orchards primarily through root irrigation supplemented by foliar spraying. The research will analyze the impact of this microbial application on the physiological morphology of winter jujube trees and the yield and quality of winter jujube. It will also explore the mechanisms of action from the perspectives of the structure, composition, and interactions of the soil microbial community in the root zone. The goal is to provide a scientific basis for the rational application of microbial agents to enhance the quality of winter jujube and achieve stable and high yields.

2. Materials and Methods

2.1. Overview of the Study Area

This study was conducted in the greenhouse facilities of the Jin’an Wu Dong Jujube Nursery Industry Park in Jingyang County, Shaanxi, China (108°83′ E, 34°53′ N), which is characterized by a warm temperate continental monsoon climate. This climate features distinct seasonal variations in temperature and humidity, with an annual average temperature of 13 °C. The winter season can see temperatures drop to as low as −20.8 °C, while summer temperatures can peak at 41.4 °C. The average annual precipitation is 548.7 mm, with about 70% of the yearly rainfall occurring between June and September. According to soil survey data from Jingyang County, the soil type within the greenhouse is loess [16].

2.2. Experimental Design

This study designed two treatments, designated as the control group (CK) and the Act12 microbial agent treatment group. The test crop was the winter jujube tree, aged three years, with a planting density of 1 m × 0.5 m. The specific treatment methods were as follows: for the control group (CK), 4 kg of organic fertilizer was uniformly applied around each winter jujube tree; for the Act12 microbial agent treatment group, a mixture of 4 kg of organic fertilizer and 20 g of microbial agent was uniformly applied to each winter jujube tree. This was followed by the application of 5 kg of a 200-fold diluted actinomycete agent and 150 mL via root drenching and foliar spray, respectively. The organic fertilizer used in the experiment was purchased from China Sinochem Group. The fertilizer contained 28.3% organic matter (SOC), 3.8% total nitrogen (TN), 2.6% total phosphorus (TP), and 3.1% total potassium (TK). The microbial agent used was S. pactum Act12, isolated and screened by the research team, with detailed information available in the studies by Li et al. [13] and Ma et al. [14]. All treatments were implemented on 1 May 2019.

2.3. Collection and Determination of Soil Samples

Soil samples were collected concurrently with fruit harvesting in November 2019. Eighteen jujube trees with similar and healthy growth were selected for each of the two treatments. Soil samples were collected from the surface layer (0–20 cm) within the root zone of each tree, using a five-point sampling method within a 30 cm radius around the trunk. We first removed the surface soil layer using a spade to obtain rhizosphere soil samples. Subsequently, we employed small brushes and trowels to carefully collect the soil directly adhering to and surrounding the roots, constituting the rhizosphere soil. The soil samples from every three trees were combined to create one composite sample, resulting in 6 samples per treatment. Each sample was then divided into two portions for further analysis. One portion was placed in an ice box and transported to the laboratory, where it was stored in a −80 °C freezer for microbial analysis. The other portion was air-dried naturally in the laboratory, ground, and sieved for the determination of soil physicochemical properties.

Soil pH was determined using potentiometry; available phosphorus (AP) in the soil was measured using a sodium bicarbonate extract solution with the molybdenum antimony colorimetric method; soil nitrate nitrogen (NO₃⁻) and ammonium nitrogen (NH₄⁺) were determined using a NaHCO₃ solution extraction followed by analysis with a flow analyzer; available potassium (AK) was measured using an ammonium acetate extraction followed by flame photometry; total carbon (TC) and organic carbon (OC) were both determined using an automatic carbon–nitrogen analyzer.

2.4. Extraction and Determination of Soil DNA

Total soil DNA was extracted from 0.25 g of freeze-dried soil using the PowerLyzer™ PowerSoil^® DNA Isolation Kit (MOBIO Laboratories, Inc., Carlsbad, CA, USA) following the manufacturer’s directions. The extracted DNA concentration and purity was quantified using a Nanodrop ND-2000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

The barcoded primers 341F/805R (5′-CCTACGGGNGGCWGCA-3′/5′-GACTACHVGGGTATCT AATCC-3′) and ITS3/ITS4R (5′-GCATCGATGAAGAACGCAGC-3′/5′-TCCTCCGCTTATTG ATATGC-3′) were used to amplify the V3–V4 region of the 16S rRNA gene and the fungal ITS2 region, respectively [17]. Sample-specific 7 bp barcodes were incorporated into the primers for multiplex sequencing. The PCR amplification was carried out in a total volume of 25 μL containing 5 μL 5 × reaction buffer, 5 μL 5 × GC buffer, 2 μL dNTPs (2.5 mM), 1 μL forward primer (10 μM), 1 μL reverse primer (10 μM), 2 μL DNA template, 8.75 μL ddH₂O, and 0.25 μL Q5 High-Fidelity DNA Polymerase (NEB, Ipswich, MA, USA). The PCR protocol consisted of an initial denaturation step at 98 °C for 2 min, 25–30 cycles of denaturation at 98 °C for 15 s, annealing at 55 °C for 30 s, and extension at 72 °C for 30 s; a final extension at 72 °C for 5 min; and a hold at 10 °C [17]. After removing the adaptors and primer sequences, the raw sequences were assembled for each sample according to the unique barcode using the QIIME pipeline (Quantitative Insights Into Microbial Ecology, v 1.8.0, https://qiime2.org) [18]. The short (<300 bp) and low-quality (mismatched with two bases and the total base error rate > 1) reads were filtered. Both bacterial and fungal sequences were clustered based on 97% similarity. Singletons, one sequence present in only one sample, were removed and all samples were rarefied to the same number of reads as the sample with the lowest reads (31,000 16S rRNA and 37,000 ITS reads per sample). Each representative sequence was assigned with an RDP classifier for taxonomical identification with a threshold of 0.8 for bacteria and 0.7 for fungi. All sequences were deposited in the NCBI Sequence Read Archive (SRA) database (Accession number: PRJNA1098866).

2.5. Plant Sample Collection and Indicator Measurement

Main properties of winter jujube leaves

The main properties of leaves and fruits were assessed in both the first and second years following the application of the microbial agent. The properties measured in the leaves included intercellular CO₂ concentration, stomatal conductance, water vapor deficit, net photosynthesis, transpiration, and chlorophyll content. All leaf traits, except for chlorophyll content, were measured using the Li-6400 Portable Photosynthesis System (Li-Cor Inc., Lincoln, NE, USA). Specifically, during the peak growth period of the leaves in July, 3–5 sunny days were selected to measure these indices on seven sun-exposed healthy leaves from each treatment between 10:00 AM and 12:00 PM. After the photosynthetic traits were measured, the leaves were taken back to the laboratory where chlorophyll content was determined using a chlorophyll meter (SPAD-502PLUS, KONICA MINOLTA, Tokyo, Japan).

Yield and quality of winter jujube

During the various growth stages of winter jujube, it is essential to timely measure the fruit growth characteristics, including fruit set rate, number of fruits per winter jujube tree, individual fruit weight, fruit yield per plant, and total yield. Additionally, the total sugar (TS), vitamin C (VC), and total acid content (TA) of the winter jujube fruits are determined using national standard methods [1].

2.6. Statistical Analysis

One-way ANOVA was used to compare the differences in plant physiological properties and microbial alpha diversities (Chao1, Simpson’s diversity and Shannon–Wiener indices) between control and treatment by Student’s t test in SPSS 22.0. Statistically significant difference was defined at the level of p < 0.05. The correlation among predominant phyla diversity and plant physiological properties were assessed by Pearson correlation analysis in R 4.0.3. Non-metric multidimensional scaling (NMDS) based on the Bray–Curtis dissimilarity algorithm was used to assess the difference in community structures between control and treatment.

Fifty top-ranked genera of bacteria and likewise fungi ranked by total abundance in all soil samples were merged into two groups according to treatment and control. A Spearman correlation matrix between the abundance of different genera was constructed for each group. Both the correlation matrix (R matrix) and the significance matrix (P matrix) were built using the Hmisc package in R. Then, those data with significant correlations (p < 0.05) and |r_s| > 0.8 were loaded into Gephi software 9 [19] to construct co-occurrence networks and to calculate several topological feature.

3. Results

3.1. Effect of Act12 Addition on Physiological and Production Indicators of Winter Jujube Trees

The physiological characteristics of the leaves, flowering status, fruit quantity was all influenced by the application of the S. pactum Act12 treatment (

Table 1. Photosynthesis of winter jujube.

Treatment		Net Photosynthetic Rate (NPR) (μmol·m−2s−1)	Stomatal Conductance (10−2 μmol H2O·m−2s−1)	Intercellular CO2 Concentration (Ci) (μmolCO2·mol−1)	Rate of Transpiration (g·m−2h−1)	Single-Leaf Water Utilization (μmol·mmol−1)
CK	Measured value	13.1 ± 2.1 a	0.5 ± 0.1 a	301.9 ± 16.2 b	10.7 ± 0.5 a	2.3 ± 0.2 a
Act12	Measured value	12.9 ± 1.7 a	0.5 ± 0.2 a	313.3 ± 8.0 a	9.2 ± 2.3 b	2.3 ± 0.4 a
	ΔCK%	−1.5	0.0	3.8	−14.0	0.0

Different letters indicate significant differences at p < 0.05.

, Figure 1). Compared to the control (CK), the net photosynthetic rate, stomatal conductance, and single-leaf water use efficiency in the Act12 treatment showed no significant differences, but the transpiration rate significantly decreased (p < 0.05), whereas the intercellular CO₂ concentration increased. The Act12 treatment also resulted in differences in leaf enzyme activity, with significantly higher PAL enzyme activity compared to the control (CK), while POD enzyme activity was lower. Act12 significantly increased the number of flower buds and fruits (p < 0.05), with increases of 41.7% and 14.5% compared to CK, respectively, and improved the fruit set rate by 4.0%.

Ultimately, Act12 significantly enhanced the yield and quality of the winter jujube fruits. Under Act12 treatment, the longitudinal diameter and weight of the fruits were significantly higher than those of the CK, measuring 34.9 ± 3.6 mm and 20.8 ± 6.5 g, respectively, representing increases of 5.4% and 18.2% over CK. Compared to CK, the yield also increased by 29.6% under the influence of Act12. Additionally, the total sugar content of the fruits under Act12 treatment reached 237.07 ± 32.50 mg g⁻¹, significantly higher than CK.

3.2. Changes in Soil Nutrient Content

The addition of Act12 significantly increased the soil’s available phosphorus (AP), ammonium nitrogen (NH₄⁺), total carbon (TC), and available potassium content (AK), while the effects on soil pH and organic carbon (OC) were inversely significant (p < 0.05), indicating that the microbial agent accelerated the decomposition and transformation of soil organic matter. There were no significant differences in soil nitrate nitrogen between Act12 treatment and CK (p > 0.05, Figure 2).

3.3. Changes in the Inter-Root Microbiome

3.3.1. Impact on Microbial Diversity

The clustering results (Figure 3) of the operational taxonomic units (OTUs) at 97% similarity level from the winter jujube root zone microbial sequencing showed that the differences in the α-diversity indices (Chao1) and diversity indices (Shannon and Simpson) for bacteria and fungi were not significant between the control and treatment groups (p > 0.05). Non-metric multidimensional scaling analysis based on Bray–Curtis distance indicated distinct differences in β-diversity of bacteria and fungi between the control and treatment, with separation occurring along the first and second principal axes (stress values of 0.0247 and 0.0027, respectively).

3.3.2. Inter-Root Microbial Community Structure

At the order level, the composition of bacterial and fungal communities in the rhizosphere soil exhibited some differences between the two treatments (Act12 and CK). For the bacterial community (Figure 4A), the commonly shared orders were Pseudomonadales, Rhizobiales, Sphingomonadales, and Enterobacteriales, with relative abundances ranging 26.5–31.93%, 17.45–22.96%, 10.35–14.34%, and 9.21–20.65%, respectively. The abundances of Aeromonadales and Actinomarinales were significantly higher (p < 0.05) in the Actinomycetes treatment compared to the control (Figure 4C).

Regarding the fungal community (Figure 4B), the commonly shared and abundant orders across all samples were Microascales and Hypocreales, with relative abundances ranging from 33.9–40.5% and 23.8–34.5%, respectively. The abundance of Mucorales was significantly higher (p < 0.05) in the Actinomycetes treatment, while the abundances of Capnodiales, Tritirachiales, and Sporidiobolales were significantly lower (p < 0.05) compared to the control (CK) (Figure 4D).

3.3.3. Soil Microbial Co-Occurrence Network Structure

To identify potential interactions among microbes, a co-occurrence network analysis was conducted on the 50 most abundant genera of bacteria and fungi (Figure 4E,F and

Table 2. General Characteristics of Co-occurrence Networks.

Samples	Nods	Edge	Average Degree	Average Weighted Degree	Network Diameter	Modularity	Average Clustering Coefficient	Average Path Length
Control	98	377	7694	0.84	7	3.33	0.576	3.483
Act12	98	525	10714	2.243	9	1.491	0.582	3.158
Proportion of negative and positive correlation between two genera
	P-P	N-N	P-B-F	P-B-B	P-F-F	N-B-F	N-B-B	N-F-F
Control	56%	44%	21%	23%	12%	27%	10%	7%
Act12	62%	38%	20%	15%	27%	20%	11%	7%

Notes: P-P and N-N represent positive or negative correlations between two genera, respectively; P-B-B, P-B-F, and P-F-F represent positive correlations between two genera of bacteria, bacteria and bacteria, and fungus, respectively; N-B-B, N-B-F, and N-F-F represent negative correlations between two genera of bacteria, bacteria and bacteria, and fungus, respectively.

). The results showed that the microbial genera involved in the network construction under both the Act12 treatment and the control could be classified into these phyla: Ascomycota, Proteobacteria, Basidiomycota, Bacteroidetes, Firmicutes, Actinobacteria, and Mucoromycota.

In terms of network structural parameters, the S. pactum Act12 treatment increased the number of edges, average degree, network diameter, and average clustering coefficient of the soil microbial co-occurrence network, while reducing the number of modules and the average path length. Additionally, the Act12 treatment influenced the positive and negative correlations among bacteria–bacteria, bacteria–fungi, and fungi–fungi interactions. Under the Act12 treatment, the positive correlations among genera were slightly higher than in the control, with the differences in positive correlations primarily arising among fungi–fungi interactions. Conversely, negative correlations were reduced, mainly between bacteria and fungi. Thus, the Act12 treatment enhanced overall positive correlations by increasing positive interactions among fungi and reduced overall negative correlations by decreasing negative interactions between bacteria and fungi.

3.3.4. Soil Microorganisms Effect the Fruit Yield, Quality, and Soil Nutrients

Jujube fruit yield was positively influenced by higher ammonium nitrogen content, lower pH, and lower organic carbon (|R²| > 0.8). In contrast, titratable acidity (TA) and total soluble solids (TS) were enhanced by available potassium, while vitamin C (VC) content exhibited the opposite trend, being promoted by pH and organic carbon.

Soil microorganisms were closely associated with soil nutrient conditions, as well as jujube yield and quality (Figure 4G). As key microbes, Ascomycota showed a significant positive correlation with fruit yield, while Proteobacteria and Bacteroidetes significantly increased the VC content in fruits. Firmicutes, on the other hand, significantly raised soil pH, indirectly promoting VC accumulation.

4. Discussion

In agricultural and natural ecosystems, soil microbes play a crucial role in the healthy growth of plants. To prevent and reduce pest and disease damage and promote plant growth, researchers have screened microbes from nature that inhibit plant pests and diseases. These microbes are then applied to the soil in the form of biofertilizers to control soil-borne diseases [7,8]. Additionally, soil microbes serve as an important indicator of soil health and vitality during plant growth, playing a significant role in predicting and supporting plant development [7]. This study focuses on perennial winter jujube trees, employing the disease-preventing and growth-promoting S. pactum Act12. By applying Act12, the research investigates the soil microbial community and the physiological characteristics of the winter jujube, providing crucial insights for the health of winter jujube trees and the prevention of pests and diseases.

The application of S. pactum Act12 did not significantly affect the α-diversity of bacteria and fungi in the soil of winter jujube root, which is inconsistent with the findings of Li et al. [15] on tomatoes. Li et al. [15,20] suggested that the application of S. pactum Act12 directly enhances plant photosynthesis, providing more carbon and nitrogen sources for microbes. The different preferences of bacteria and fungi for these nutrients led to a significant increase in bacterial diversity and abundance, while the fungal community showed no significant change [21]. In this study, although the application of S. pactum Act12 helped improve leaf photosynthesis, it had little impact on the diversity of bacteria and fungi. The different responses of the two plants to S. pactum Act12 may be related to plant transport mechanisms; in shrubs (winter jujube trees), the products of leaf photosynthesis are not easily transported to the roots in the short term, whereas in short-cycle herbaceous plants like tomatoes, the transfer of photosynthetic materials between roots and leaves can occur more rapidly.

Non-metric multidimensional scaling (NMDS) analysis revealed distinct community structures of soil bacteria and fungi. This indicates that the application of S. pactum Act12 altered the soil microbial community structure. Changes in soil microbial community structures induced by biocontrol agents have been reported across different strains and plant types [9,10,11]. These findings collectively demonstrate the capacity of biocontrol agents to reshape soil microbial communities, thereby creating new soil microecological environments. The composition and abundance of microbial communities determine metabolic and biodegradation capabilities of plant and are closely related to the species. In this study, the relative abundance of the phylum Bacteroidetes was higher than that of Firmicutes among bacteria, while the fungi Mucoromycota, Rozellomycota, and Mortierellomycota were dominant.

This contrasts with the findings of Li et al. in tomato and aconite soil microbial communities [13,15], and similar patterns at the genus level have also been observed [22], indicating that plants play a decisive role in shaping the composition and abundance of soil microbial communities. The impact of S. pactum Act12 may primarily manifest in the relative abundance of species. Li et al. [15] found that the application of S. pactum Act12 in tomatoes led to a decrease in the abundance of Bacteroidetes and an increase in Proteobacteria, which is the opposite of the results in our study. This discrepancy may be due to different plants affecting soil microbes differently and the specific microbial assembly mechanisms among different plants [23]. Tan et al. [24] and Xiong et al. [25] found the highest abundance of Ascomycota and Basidiomycota in soils of Panax notoginseng under continuous cropping and in vanilla soils susceptible to Fusarium wilt, consistent with the findings of our study. S. pactum Act12 modulates microbial community composition and enhances fruit quality and yield. Additionally, the treatment with S. pactum Act12 led to an increase in the abundance of Mucoromycota, which thrives on soil, animal feces, and plant and animal residues. Given the propensity of Mucoromycota to cause rot in fruits and vegetables, more attention should be given to the preservation of harvested fruits under S. pactum Act12 treatment.

Microbial network structures are frequently utilized to analyze key soil microbes, their interactions, and the stability of microbial community structures [26]. In this study, no significant differences were observed in the microbial species involved in network module construction at the phylum level between the two treatments, suggesting that the key microbial species maintaining community structure stability are similar. The microbial network structure treated with S. pactum Act12 displayed higher connectivity and average degree than the control, indicating that Act12 treatment increased the closeness among the microbial nodes. Conversely, the number of modules and average path length were lower than in the control, suggesting that the Act12 treatment narrowed the microbial ecological niches, making their response to environmental changes more sensitive. Positive and negative correlations within the network structure typically represent complex interactions among organisms in the ecosystem. Compared to the control, the Act12 treatment increased the proportion of positive correlations and decreased the proportion of negative correlations, with the largest changes in positive and negative correlations arising from interactions among fungi and bacteria, respectively. Therefore, consistent with most studies, the addition of exogenous substances or human activities alters the co-occurrence network structure of soil microbes [27,28], but differences in interactions within soil fungi and bacteria between treatments require further investigation. Key Microbial Players in the Symbiotic Network: Proteobacteria and Firmicutes Positively Correlate with Fruit Yield and Quality.

During the application of microbial fertilizers, we focused not only on the changes in soil microbial communities but also analyzed their effects on winter jujube traits, yield, and quality. In this study, the treatment with S. pactum Act12 increased leaf stomatal conductance and net photosynthetic rate, while reducing the vapor pressure deficit, indicating that the microbial agent helps to enhance the plant’s photosynthetic capacity, thereby accumulating more organic matter. Additionally, the effects of the microbial agent on intercellular CO₂ concentration and transpiration were related to the growing season. In the drier year of 2019, with higher temperatures, the water consumption due to transpiration was significantly higher, and the microbial agent promoted plant growth, resulting in higher biomass and thus greater water consumption through transpiration. The impact of the microbial agent on fruit setting was also multifaceted; the fruit setting rate, the weight of jujube fruit per fruiting branch, and the weight of individual fruits were significantly increased under microbial treatment in both growing seasons, with the yield per plant in 2020 almost doubling. S. pactum Act12 may induce changes in substance synthesis and the plant’s pest defense system, but since no significant disease was observed in the winter jujube trees in the study area, it is not yet possible to determine whether the microbial agent promotes the growth of winter jujube leaves and fruits by preventing disease in the short term. From the above indicators, it is evident that the microbial agent has a multifaceted impact on winter jujube trees, affecting everything from the root system to the leaves and fruits. Based on this, we believe that a long-term observation mechanism should be established to study the incidence of pests and diseases in winter jujube trees, the stability of fruit yield, fruit quality, and the difficulty of preservation. Furthermore, the correlation between the dominant soil microbes and the characteristics of leaves and fruits suggests that the dominant soil microbes may have a targeted effect on certain properties of winter jujube trees.

5. Conclusions

In this article, the winter jujube tree (Ziziphus jujuba Mill.) serves as the subject of study, with S. pactum Act12 applied through root drenching and foliar spraying to analyze its effects on the biological traits of the winter jujube tree and on soil microbiota. The results indicate that the application of the microbial agent significantly altered the structure of the soil microbial community and the abundance of some dominant microbes, and it also tightened the co-occurrence network structure of the microbes. Dominant microbes may play different roles in specific properties of leaves and fruits. This ultimately led to a significant increase in the yield and total sugar content of the winter jujube trees treated with S. pactum Act12. These findings provide a reference for the use of S. pactum Act12 in winter jujube production; however, this study did not cover aspects such as the stability of fruit yield, fruit quality, and preservation difficulties, which should be given attention in future research.