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Article

Effects of Different Cultivation Substrates on the Growth of Podocarpus macrophyllus and the Rhizosphere Soil Microbial Community Structure

by
Xiaomin Liang
1,2,3,4,†,
Donghua Zhong
3,†,
Congyu Zhang
1,2,3,
Yongfang Pan
1,2,3,
Chenning Zhang
1,2,3,
Herong Guo
4,
Xiaoling Zhu
4,
Xiaocong Li
5,
Yuxuan He
1,2,3,
Shaopeng Huang
1,2,3,
Jincai Tu
1,2,3,
Ting Gao
3 and
Yuanjiao Feng
1,2,3,4,*
1
Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
2
Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China
3
College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
4
Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
5
Zhongshan Qian Song Yuan Flower Planting Co., Ltd., Zhongshan 528478, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2025, 15(5), 1055; https://doi.org/10.3390/agronomy15051055
Submission received: 20 March 2025 / Revised: 16 April 2025 / Accepted: 25 April 2025 / Published: 27 April 2025
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Abstract

:
Podocarpus macrophyllus is an evergreen tree with significant ornamental, economic, and medicinal value, widely used in landscape gardening and bonsai production. However, systematic research on the optimal substrate ratios required for its efficient cultivation remains relatively scarce. This study compared the effects of two cultivation substrates (SJ1: 80% native soil + 20% fine sand and SX2: 25% native soil + 25% coarse sand + 25% peat soil + 25% coconut coir) on the growth of P. macrophyllus. Soil physicochemical properties and plant physiological and biochemical indices were measured, and the rhizosphere microbial community structure was analyzed using Illumina MiSeq high-throughput sequencing. The results show that P. macrophyllus grown in the SX2 substrate exhibited significantly greater ground diameter, plant height, chlorophyll content, and soluble protein content than those in the SJ1 substrate. Microbial community analysis indicates that the two different substrates had little impact on alpha diversity. In the bacterial community, the dominant phylum in the SJ1 substrate was Acidobacteriota, whereas in the SX2 substrate, it was Pseudomonadota. In the fungal community, Ascomycota was the dominant phylum in both SJ1 and SX2. Redundancy analysis (RDA) reveals that water content and total porosity were the primary factors influencing the bacterial community structure. Based on physiological indicators and microbial community composition, the SX2 substrate was more conducive to the growth of P. macrophyllus in terms of plant height and ground diameter. Therefore, this study provides valuable insights for substrate selection and optimization in the cultivation of P. macrophyllus.

1. Introduction

P. macrophyllus is a valuable plant species with diverse applications, widely used in landscaping, timber processing, medicinal development, and environmental protection. Its wood is hard and fine-grained, making it an excellent material for high-end furniture, handicrafts, and decorative items, which contributes to its significant economic value [1,2,3]. In the medicinal field, the bark, leaves, and seeds of P. macrophyllus are rich in various bioactive compounds, including terpenoids, flavonoids, and steroids. These components exhibit significant anti-tumor, antioxidant, and anti-inflammatory properties, showing inhibitory effects on human colon cancer cells, lung cancer cells, and breast cancer cells. As such, the species holds great potential for development in the pharmaceutical and health supplement industries [4]. In addition, P. macrophyllus also possesses remarkable ecological functions, effectively absorbing harmful gases such as SO2 and CO2 from the air while regulating environmental humidity and improving air quality [5]. With the advancement of modern cultivation techniques, substrate selection has become a crucial factor affecting the growth and health of P. macrophyllus. As the fundamental medium for plant growth, the substrate not only regulates water and nutrient supply but also significantly influences the composition and functional activity of rhizosphere microorganisms, which are affected by environmental factors such as soil type, nutrient availability, and moisture conditions [6,7,8]. As a crucial bridge in plant–environment interactions, the rhizosphere microbial community plays an indispensable ecological role in plant growth promotion and disease resistance through various mechanisms, including enhancing nutrient absorption, secreting growth hormones, and inhibiting pathogenic microorganisms [9,10].
Different types of cultivation substrates exhibit significant differences in their physical properties (e.g., bulk density and water-holding capacity), chemical properties (e.g., pH and nutrient content), and biological properties (e.g., microbial composition and abundance) [11]. Common cultivation substrates include soil, peat, vermiculite, and perlite, each possessing unique physicochemical characteristics [12]. These properties directly or indirectly influence root water and nutrient absorption, thereby affecting the overall growth of plants [13]. A suitable cultivation substrate can provide strong support and a nutrient-rich environment for plants, promoting healthy growth [14]. Conversely, an inappropriate substrate may lead to poor plant growth or even plant death [15]. The rhizosphere microbial community consists of diverse microorganisms, including bacteria, fungi, and actinomycetes, which play a crucial role in plant nutrient absorption, pathogen suppression, and environmental adaptability [16]. On the one hand, rhizosphere microorganisms promote plant growth by secreting phytohormones and solubilizing insoluble nutrients [17]. On the other hand, certain rhizosphere microbes enhance plant resistance to pests and diseases while improving the plant’s growth microenvironment [18].
Existing studies have shown that the structure of the plant rhizosphere microbial community varies significantly under different substrate conditions. For example, substrate types such as soil and nutrient soil often lead to shifts in microbial community structure [19]. Certain substrates, such as peat soil, provide abundant nutrients that promote microbial proliferation, whereas well-aerated substrates, like coarse sand and ceramsite, improve soil aeration, facilitating microbial respiration [20,21]. Regarding P. macrophyllus, most research has focused on the direct relationship between substrate physicochemical properties and plant growth. However, the impact of substrate on the rhizosphere microbial community of P. macrophyllus has not been systematically studied, and in-depth analyses of microbial communities remain limited [22,23,24].
This study aims to investigate the effects of two different cultivation substrates on the growth characteristics of P. macrophyllus and the structure of its rhizosphere soil microbial communities in order to optimize cultivation and management strategies for the species. By comparing and analyzing the diversity, abundance, and ecological function of the rhizosphere microbial communities under two different substrates (SJ1: 80% native soil + 20% fine sand and SX2: 25% native soil + 25% coarse sand + 25% peat soil + 25% coconut coir), this study reveals the impact of cultivation substrates on the plant rhizosphere microbial community and further enhances the understanding of the potential effect of substrate selection on the growth and ecological function of P. macrophyllus. Previous studies have mostly focused on single factors, such as the effects of fertilization on plant growth and microorganisms or the impact of substrates on plant development, whereas this study integrates the physicochemical properties of substrates, the dynamics of microbial communities, and plant physiological responses, thereby filling a gap in the research on multidimensional interaction mechanisms and providing a theoretical basis for further optimization of P. macrophyllus cultivation and management [25,26].

2. Materials and Methods

2.1. Sample Collection and Processing

The experiment was conducted in July 2022 at the Qiansongyuan Flower Planting Base in Zhongshan, Guangdong Province (22°51′27″ N, 113°22′13″ E). One-year-old, uniformly growing, and healthy P. macrophyllus seedlings were selected as experimental materials and cultivated in root-controlling containers. Two cultivation substrate treatments were set up, with three replicates per treatment. The substrate compositions were as follows: The SJ1 substrate, composed of 80% native soil and 20% fine sand, is cost-effective and easy to source but suffers from poor aeration and compaction, often failing to meet the needs for high-quality seedling cultivation. The SX2 substrate is a four-component composite ratio consisting of 25% native soil, 25% coarse sand, 25% peat soil, and 25% coconut coir, where the coarse sand improves the substrate’s aeration and drainage to prevent root hypoxia, the peat soil provides OM, water retention, and pH buffering, and the coconut coir adjusts the substrate structure, increases porosity, and promotes microbial diversity, while the 25% native soil maintains the foundation of the local soil microbial community. The peat soil and coconut coir used in the experiment were both purchased from Guangzhou Runjor Agricultural science and technology Co., Ltd., Guangzhou, China. During the experiment, all treatment groups followed the same cultivation management practices, including fertilization, irrigation, and pest and disease control, to minimize the influence of other environmental factors on the experimental results.
The sampling of soil and leaf samples was conducted in July 2024. For each plant, healthy and mature leaves were selected from the middle part of the canopy, rapidly frozen in liquid nitrogen, and stored in an ultra-low temperature freezer at −80 °C for subsequent physiological and biochemical analysis. When collecting rhizosphere soil, first remove surface weeds and fallen leaves, then use a sterile shovel to dig to a depth of 30–40 cm, remove the soil around the roots, and collect the soil tightly adhering to the root system [27]. The collected rhizosphere soil samples were divided into two portions: one was stored at −80 °C for microbial analysis, while the other was air-dried and passed through a 100-mesh sieve for physicochemical property determination (Figure 1).

2.2. Experimental Methods

A vernier caliper and a measuring tape were used to measure the ground diameter and plant height of P. macrophyllus, respectively. Chlorophyll content was determined using the 95% ethanol colorimetric method [28]. Soluble sugar (SS) and soluble protein (SP) contents were measured using the anthrone colorimetric method and the Coomassie Brilliant Blue G-250 staining method, respectively [29]. Water content (WC) was calculated by measuring the weight difference of soil samples before and after drying at high temperatures [30]. Soil bulk density (BD) was determined using the ring knife method [31]. Total soil porosity was measured following the method described by Zhu et al. [32].
The measurement methods for soil physicochemical properties and leaf nutrient content refer to Bao [33], and the specific determination methods of soil physical and chemical properties are as follows: The pH value (soil-to-water ratio of 1:2.5) was determined using the potentiometric method. Total nitrogen (TN) was measured via the sulfuric acid digestion Kjeldahl method. Total phosphorus (TP) was determined using the sodium bicarbonate extraction–molybdenum antimony anti-colorimetric method. Total potassium (TK) was measured using the ammonium acetate extraction–flame atomic absorption spectrophotometry method. Alkaline hydrolysis nitrogen (AN) content was quantified using the culture diffusion titration method. Organic matter (OM) content was determined using the potassium dichromate heating method. Soil available phosphorus (AP) content was measured using the sodium bicarbonate extraction–molybdenum antimony anti-colorimetric method. The soil’s available potassium (AK) content was determined using the ammonium acetate–flame photometry method. The specific methods for determining leaf nutrient content are as follows: organic carbon (C) content was measured using the potassium dichromate heating method. The nitrogen (N) content was determined using the Kjeldahl method. The phosphorus (P) content was measured using the sodium bicarbonate extraction–molybdenum-antimony anti-spectrophotometric method, while the potassium (K) content was determined using the ammonium acetate extraction–flame atomic absorption spectrophotometry method. The determination of the experimental samples was repeated three times to reduce the random error.

2.3. High-Throughput Sequencing of Rhizosphere Soil Microorganisms

High-throughput sequencing, including complete genomic DNA extraction, PCR amplification, MiSeq library construction, and MiSeq sequencing, was performed by Guangdong MAGIGENE Biotechnology Co., Ltd.,Guangzhou, China. Soil microbial analysis was conducted by examining the V3–V4 variable region of the bacterial 16S rRNA gene and the ITS2 variable region of the fungal ITS rRNA gene to determine bacterial and fungal community structures. The primer sequences used are listed in Table 1. The raw sequencing data were processed through assembly and quality filtering to obtain valid sequences for further analysis.

2.4. Data Analysis

The raw data were preprocessed using Microsoft Excel 2019, and graphs were generated using Origin 18 software. An independent samples t-test was performed using SPSS 26.0 software to test the significance of the data (p < 0.05).
OTU clustering and species classification analysis were performed based on valid data using the MAGIGENE Cloud Platform (http://cloud.magigene.com/). The Alpha diversity indices for bacteria and fungi, including Chao1, ACE, Simpson, Shannon, and coverage, were calculated. Principal Coordinate Analysis (PCoA) was conducted based on the Bray–Curtis algorithm using three samples to examine the similarity of microbial community structures between samples. Additionally, ANOSIM (Analysis of Similarity) was used to assess whether there were significant differences in microbial community structures between sample groups. Redundancy analysis (RDA) was performed to examine the correlations between bacterial and fungal communities and various environmental factors across different samples.

3. Results

3.1. Analysis of Basic Physicochemical Properties of Different Cultivation Substrates

This study compared the physicochemical properties of rhizosphere soils under two different cultivation substrates (SJ1 and SX2). The results (Table 2) show significant differences between SJ1 and SX2 substrates in terms of water content (WC), PORT, TP, TK, AP, and AK. Specifically, the SMC in the SJ1 substrate was significantly higher than in SX2, while the PORT in SX2 was significantly higher than in SJ1, indicating that the SX2 substrate has better aeration properties. In addition, the TP and TK content in the SJ1 substrate were significantly higher than in SX2, while the AP and AK content in the SX2 substrate were significantly higher than in SJ1. Other physicochemical properties were relatively similar, with pH values falling within the neutral range. No significant differences were observed in the BD, OM, TN, and AN content.

3.2. Effects of Different Cultivation Substrates on the Growth Indicators of P. macrophyllus

As shown in Table 3, the two cultivation substrates had a significant effect on the ground diameter and plant height of P. macrophyllus. Under the SX2 substrate treatment, both the ground diameter and plant height were significantly higher than those under the SJ1 substrate treatment. Specifically, compared to SJ1, the ground diameter and plant height in the SX2 treatment increased by 32.15% and 68.40%, respectively.

3.3. Effects of Different Cultivation Substrates on the Physiological Indicators of P. macrophyllus

Under different cultivation substrates, the physiological indicators of P. macrophyllus exhibited certain variations. Specifically, the chlorophyll content of P. macrophyllus grown in the SX2 substrate was significantly higher than in the SJ1 substrate. Additionally, the SP content in the SX2 substrate was also notably higher than in the SJ1 substrate. However, there was no significant difference in SS content between the two substrates. There were no significant differences in other nutrient contents, such as the C, N, P, and K content, between the two substrates (Table 4).

3.4. Effects of Different Cultivation Substrates on Rhizosphere Bacteria of P. macrophyllus

3.4.1. Rarefaction Curve Analysis of Rhizosphere Bacteria of Podocarpus macrophyllus Under Different Cultivation Substrates

The richness rarefaction curves of bacterial samples gradually leveled off as the sequencing depth increased. The results (Figure 2) indicate that the sequencing data for each treatment were sufficiently large to accurately reflect the majority of the rhizosphere bacterial diversity characteristics in the samples.

3.4.2. Venn Analysis of Rhizosphere Bacteria of P. macrophyllus Under Different Cultivation Substrates

By analyzing the OTU distribution of rhizosphere bacteria in the two cultivation substrates, it was found that the SJ1 and SX2 substrates had 1057 and 1670 unique OTUs, respectively, while sharing 5200 OTUs (Figure 3). This indicates that although there are differences in the number of unique OTUs between the two substrates, they share a large proportion of OTUs in the rhizosphere soil bacterial community, suggesting that substrate variation has a certain impact on the composition of the bacterial community.

3.4.3. Alpha Diversity Index of Rhizosphere Bacteria of P. macrophyllus Under Different Cultivation Substrates

As shown in Table 5, the Alpha diversity indices of rhizosphere bacteria in P. macrophyllus exhibited some variations under the two cultivation substrates, but no significant differences were observed. In terms of species richness indices (Chao1 and ACE) and diversity indices (Simpson and Shannon), no significant differences were found between the SX2 and SJ1 substrates, indicating that the two cultivation substrates had little impact on the species richness and diversity of rhizosphere bacteria.
In terms of sequencing coverage (Goods_coverage), both substrates had a coverage rate of over 98%, indicating that the sequencing results adequately reflected the true composition of the rhizosphere bacterial community.

3.4.4. Beta Diversity of Rhizosphere Bacteria in P. macrophyllus Under Different Cultivation Substrates

PCoA analysis based on Bray–Curtis distance shows that two different substrates influenced the composition of rhizosphere soil bacterial communities. PC1 and PC2 explained 51.7% and 20.8% of the variance, respectively, with a cumulative explanation of 72.5%. As shown in the figure, samples from SJ1 and SX2 were distinctly separated along PC1 and PC2, with SJ1 samples primarily clustering on the left side of the plot, while SX2 samples tended to distribute on the right side (Figure 4).

3.4.5. Analysis of Rhizosphere Bacterial Community Composition of P. macrophyllus Under Different Cultivation Substrates

At the phylum level, the rhizosphere bacterial communities of P. macrophyllus in both substrates were mainly composed of dominant phyla, including Pseudomonadota, Acidobacteriota, Chloroflexota, Bacteroidota, and Actinobacteriota (Figure 5). The relative abundance of bacterial phyla varied between the SJ1 and SX2 substrates. Specifically, the relative abundance of Pseudomonadota in the SJ1 and SX2 substrates was 24.29% and 33.80%, respectively, indicating a higher abundance of this phylum in the SX2 substrate. The relative abundance of Acidobacteriota in the SJ1 and SX2 substrates was 27.76% and 22.93%, respectively, indicating a higher abundance in the SJ1 substrate. The relative abundance of Chloroflexota was 13.66% in SJ1 and 12.14% in SX2, showing minimal variation between the two substrates. The relative abundances of Bacteroidota and Actinobacteriota in the SJ1 substrate were 6.86% and 6.73%, respectively, while in the SX2 substrate, they were 6.95% and 3.63%, respectively. This suggests that the abundance of Actinobacteriota was lower in the SX2 substrate. The relative abundance of other bacterial phyla also varied between the two substrates, but the overall changes were minor, and their relative abundances remained low. Overall, the dominant bacterial phyla in both SJ1 and SX2 substrates were similar, but their abundances differed to some extent, indicating that the two different substrates influenced the bacterial community structure.

3.4.6. Effects of Environmental Factors on the Structure of Rhizosphere Bacterial Communities Under Different Cultivation Substrates

Redundancy analysis (RDA) was conducted to examine the relationship between soil bacterial community structure and environmental factors (Figure 6). The results indicate that environmental factors accounted for 75% of the total variation in bacterial community differences. Among them, RDA1 and RDA2 explained 53.2% and 21.8% of the total variance, respectively. The analysis reveals that the bacterial community structure in the SJ1 substrate was significantly correlated with water content (WC), while the bacterial community structure in the SX2 substrate was primarily influenced by pH and PORT.

3.5. Effects of Different Cultivation Substrates on Rhizosphere Fungi of P. macrophyllus

3.5.1. Rarefaction Curve Analysis of Rhizosphere Fungi of Podocarpus macrophyllus Under Different Cultivation Substrates

The richness rarefaction curves of fungal samples gradually leveled off as the sequencing depth increased. The results (Figure 7) indicate that the sequencing data for each treatment were sufficiently large to accurately reflect the rhizosphere’s fungal diversity in the samples.

3.5.2. Venn Analysis of Rhizosphere Fungi of P. macrophyllus Under Different Cultivation Substrates

By analyzing the distribution of rhizosphere fungal OTUs in two cultivation substrates, it was found that the SJ1 substrate and SX2 substrate have 256 and 132 unique OTUs, respectively, and they share 638 OTUs in common (Figure 8). This suggests that although there are differences in the number of unique OTUs between the two substrates, they share a relatively large proportion of OTUs in the rhizosphere soil fungal community, indicating that changes in the substrate have a certain impact on the composition of the fungal community.

3.5.3. Alpha Diversity Index of Rhizosphere Fungi of P. macrophyllus Under Different Cultivation Substrates

As shown in Table 6, the two cultivation substrates exhibited some changes in the Alpha diversity index of the rhizosphere fungi of P. macrophyllus, but no significant differences were observed. In terms of the species richness indices (Chao1 and ACE) and diversity indices (Simpson and Shannon), the differences between the SX2 and SJ1 substrates were not significant, indicating that the two substrates had little impact on the species richness and diversity of the rhizosphere fungi of P. macrophyllus.
In terms of sequencing coverage (Goods_coverage), both substrates showed a coverage of over 99%, indicating that the sequencing results accurately reflect the true composition of the rhizosphere fungal community.

3.5.4. Beta Diversity of Rhizosphere Fungi in P. macrophyllus Under Different Cultivation Substrates

Based on the Bray–Curtis distance PCoA analysis, it was shown that two different substrates have an impact on the composition of the rhizosphere soil fungal community. PC1 and PC2 explained 48.7% and 18.4% of the variance, respectively, with a cumulative explanation of 67.1%. From the figure, it can be seen that the SJ1 and SX2 samples are clearly separated along PC1 and PC2. The SJ1 samples are primarily concentrated on the left side of the plot, while the SX2 samples tend to be distributed on the right side (Figure 9).

3.5.5. Analysis of the Rhizosphere Fungal Community Composition of Podocarpus macrophyllus Under Different Cultivation Substrates

At the phylum level, the rhizosphere fungal communities of Podocarpus macrophyllus under the two substrates were mainly composed of dominant phyla such as Ascomycota, unclassified_k_Fungi, Mortierellomycota, Basidiomycota, Glomeromycota, and Chytridiomycota, among others (Figure 10). In the SJ1 substrate, Ascomycota dominated the fungal community, accounting for 80.52%, followed by unclassified_k_Fungi at 7.11%. Mortierellomycota, Basidiomycota, and Glomeromycota accounted for 4.65%, 3.61%, and 2.63%, respectively. In the SX2 substrate, Ascomycota was also the major component, making up 68.39%, while the proportion of unclassified_k_Fungi significantly increased to 20.23%. In addition, Mortierellomycota and Basidiomycota had relatively small proportions in the SX2 substrate, accounting for 3.11% and 3.54%, respectively. Glomeromycota and Chytridiomycota had low proportions in both substrates, at 0.53% and 1.13%, respectively. These results suggest that there are certain differences in the composition of fungal communities between the different cultivation substrates, particularly in the proportions of Ascomycota and unclassified_k_Fungi.

3.5.6. Effects of Environmental Factors on the Structure of Rhizosphere Fungal Communities Under Different Cultivation Substrates

The relationship between the soil fungal community structure and environmental factors was analyzed using RDA (Figure 11). The results indicate that environmental factors explained a total of 97.1% of the variation in the fungal community. Specifically, RDA1 and RDA2 explained 82.0% and 15.1% of the total variation, respectively. The analysis shows that the fungal community structure in the SJ1 substrate was primarily significantly correlated with WC, while the fungal community structure in the SX2 substrate was mainly influenced by pH and PORT.

4. Discussion

4.1. Physicochemical Properties of Different Cultivation Substrates

The selection of an appropriate cultivation substrate is crucial for plant growth and development. High-quality cultivation substrates provide seedlings with an optimal rhizosphere environment, including adequate nutrient supply, aeration, and water retention. The chemical and physical properties of different substrates vary significantly depending on their composition and proportion. These physicochemical characteristics play a decisive role in seedling quality [34,35]. The water content of the SJ1 substrate was significantly higher than that of the SX2 substrate, which is closely related to its high proportion of native soil. Native soil contains a higher clay content, giving it a strong water retention capacity. However, its dense structure may result in lower PORT, potentially restricting oxygen diffusion in the rhizosphere, which could affect the activity of aerobic microorganisms and root respiration. In contrast, the SX2 substrate exhibited significantly higher PORT, indicating better aeration. The addition of coarse sand increased the proportion of macropores, improving drainage, while the fibrous structure of peat and coir further optimized the water–air balance. These improvements in physical properties may create a more favorable environment for root extension and microbial activity [36]. The OM content and TN in the two substrates showed no significant differences. However, the introduction of peat and coir in the SX2 substrate may enhance the release of available nutrients due to their high humic acid content [37]. The AP and AK contents in the SX2 substrate were significantly higher than those in the SJ1 substrate. This may be attributed to the addition of peat and coir, which improved soil structure and nutrient release, thereby promoting plant growth [38]. The high porosity and readily available nutrient characteristics of the SX2 substrate make it more suitable for container seedling cultivation or controlled-environment agriculture. Its excellent drainage capacity helps reduce the risk of waterlogging during the rainy season, while the fibrous structure of peat soil and coconut coir contributes to long-term substrate stability, lowering the cost associated with frequent substrate replacement during cultivation. However, attention should be paid to the non-renewable nature of peat resources, and future studies may explore optimized ratios using sustainable alternatives such as coconut coir to replace peat.

4.2. Effects of Different Cultivation Substrates on the Physicochemical Properties of P. macrophyllus

In agricultural production and horticultural practices, different cultivation substrates provide varying growth environments for plants [39]. The two cultivation substrates (SJ1 and SX2) exhibited significant differences in the growth indices of P. macrophyllus. P. macrophyllus showed significantly greater ground diameter and plant height in the SX2 substrate compared to the SJ1 substrate. This result may be closely related to the synergistic effect of peat and coir in the SX2 substrate. The fibrous structure of peat and coir significantly improved the substrate’s aeration and water retention, thereby promoting root development and nutrient absorption. This, in turn, indirectly supported the plant’s vertical growth (height) and radial expansion (ground diameter) [40]. AP and AK are essential nutrients that plants can absorb and utilize, playing a crucial role in supporting plant growth and development. The increase in the content of these nutrients contributes to the growth of plant height and ground diameter [41,42].
In terms of physiological indicators, the two substrates showed significant differences in their effects on the chlorophyll and SP content of P. macrophyllus. The chlorophyll content in the SX2 substrate was significantly higher than in the SJ1 substrate, suggesting that the SX2 substrate may be more conducive to photosynthesis, thereby enhancing the photosynthetic capacity of P. macrophyllus leaves. Similarly, the SP content under the SX2 substrate treatment was significantly higher than the SJ1 substrate. The higher chlorophyll content in the SX2 substrate may be attributed to the absorption-promoting effect of humic acid in peat soil. Humic acid can enhance chlorophyll stability by chelating metal ions [43,44]. The higher SS content in the SJ1 substrate may be related to its higher P content, as a key element in energy metabolism (ATP synthesis), and K content, which regulates osmotic pressure to promote the accumulation of photosynthetic products [45,46].
There were no significant differences in the contents of other physiological indicators, such as the C, N, P, and K content, between the different substrates. This may indicate that the two substrates have a relatively similar impact on the growth and physiological activities of P. macrophyllus in terms of these basic nutrient elements or that P. macrophyllus itself has certain regulatory mechanisms, allowing it to adapt to nutrient differences in the substrates to some extent and maintain its normal physiological functions. The SX2 substrate significantly improved the growth parameters and photosynthetic efficiency of P. macrophyllus by enhancing the rhizosphere microenvironment, which holds substantial economic value in shortening the seedling cultivation cycle. In the commercial production of P. macrophyllus, SX2 is recommended as the preferred substrate. Reasonable selection and optimization of substrates can not only improve seedling quality and shorten the cultivation cycle but also reduce the inputs for fertilization and pest control, thereby achieving efficient and sustainable horticultural production.

4.3. Effects of Different Cultivation Substrates on the Rhizosphere Microbial Community Structure of P. macrophyllus

The SJ1 and SX2 substrates had little effect on the composition of the rhizosphere bacterial community. There were no significant differences in the Alpha diversity indices of the bacterial communities between the SJ1 and SX2 substrates, indicating that the two substrates did not cause significant changes in the evenness and diversity of the bacterial communities. In the β-diversity analysis, the PCoA plot shows a clear separation between the SJ1 and SX2 substrates, but the Anosim test results did not reach a significant level. RDA analysis further confirms that environmental factors such as water content and PORT played a key role in the variations of the bacterial community structure. Under the two different substrates, the SJ1 substrate was associated with higher water content, while the SX2 substrate was linked to greater aeration and porosity, which may have contributed to the differences in bacterial communities between the two substrates. This result may be closely related to the addition of peat and coir in the SX2 substrate. Peat is rich in OM, providing a plentiful carbon source for heterotrophic bacteria (such as Pseudomonadota and Bacteroidota) [47], while the fibrous structure of coir improves substrate aeration, promoting the growth of aerobic bacteria (such as nitrifying bacteria and phosphate-solubilizing bacteria) [48]. Also, the addition of coarse sand further enhanced the drainage capacity of the substrate, reducing the formation of anaerobic conditions and thereby supporting a more diverse bacterial community [49,50]. In contrast, the higher clay content in the SJ1 substrate may have led to greater soil bulk density, restricting oxygen supply to the roots and consequently inhibiting bacterial diversity [51]. The rhizosphere bacterial communities in both substrates were primarily dominated by Pseudomonadota, Acidobacteriota, and Chloroflexota, but their relative abundances varied between the two substrates. The relative abundance of Pseudomonadota was significantly higher in the SX2 substrate than in the SJ1 substrate. Pseudomonadota include various functional bacteria (such as nitrogen-fixing bacteria and plant growth-promoting bacteria). This phylum consists mainly of aerobic heterotrophic bacteria, whose proliferation may benefit from improved substrate aeration, which enhances the diffusion of root exudates [52,53]. RDA analysis indicates that WC and PORT were the primary environmental variables influencing the bacterial community structure. OM content and pH also had some impact, possibly by providing abundant carbon sources and energy, thereby supporting the enhancement of bacterial diversity [54].
The SJ1 and SX2 substrates had little impact on the composition of the rhizosphere fungal community. There were no significant differences in the Alpha diversity index of fungi between the two substrates, but their community composition exhibited distinct variations. Ascomycota, commonly known as sac fungi, are widespread saprophytic and plant pathogenic fungi in soils. Their communities rely on high-humidity environments to decompose organic matter. The higher moisture content in the SJ1 substrate provides suitable ecological conditions for their growth, whereas the significantly lower moisture content in the SX2 substrate may inhibit the physiological activity of these moisture-dependent fungi, leading to a decrease in their abundance [55]. Additionally, the total porosity of the SX2 substrate is significantly higher than that of the SJ1 substrate, indicating better aeration. While good aeration benefits the growth of certain aerobic fungi and enhances the decomposition efficiency of complex organic matter such as lignin, it may also intensify resource competition with Ascomycota. Consequently, some Ascomycota taxa may lose their ecological niche in this process, leading to a corresponding decrease in their abundance. Glomeromycota, commonly known as arbuscular mycorrhizal fungi (AMF), are typical endophytic fungi that form symbiotic relationships with plant roots, assisting host plants by absorbing hard-to-utilize nutrients from the soil [56]. Although the high porosity of the SX2 substrate enhances aeration, it also reduces the substrate’s water retention capacity, thereby weakening the support of moisture for the microbial habitat, particularly for AMF fungi that rely on hyphal networks and rhizosphere associations as their main survival strategy, as this structurally unstable physical environment severely limits the establishment of their communities. The significantly higher levels of AP and AK in the SX2 substrate compared to SJ1 may reduce the plant’s dependence on arbuscular mycorrhizal fungi (AMF), as in the short term, plants can directly absorb readily available nutrients from the soil without relying on symbiotic systems, thereby diminishing the driving force for forming mutualistic relationships with Glomeromycota. This ecological feedback mechanism, triggered by changes in host behavior, may also be an important intrinsic reason for the decreased abundance of Glomeromycota in the SX2 substrate [57]. The abundance of unclassified fungi significantly increased, which may reflect the presence of unknown functional groups introduced by peat soil and coir, and their ecological functions require further investigation. β-diversity analysis reveals a distinct separation of fungal communities between the two substrates, with this variation closely related to water content and OM content. RDA analysis indicates that water content was the primary factor influencing fungal community structure, while pH, BD, and PORT also contributed to fungal distribution to some extent.

5. Conclusions

In summary, this study investigates the microbial community structure and species diversity in two different substrates, revealing the changes in microbial community structure and species diversity in the different substrates, as well as the relationship between the rhizosphere of P. macrophyllus and microorganisms in these substrates. The results show that the SX2 substrate (25% native soil + 25% coarse sand + 25% peat + 25% coconut coir) was the most beneficial for the growth of P. macrophyllus, as it improved soil physicochemical properties and promoted plant development. Therefore, the SX2 substrate can be regarded as an optimized formulation suitable for practical cultivation, with the potential to be further refined into a more economical and environmentally friendly solution to enhance cultivation efficiency.
Based on the SX2 substrate formulation, future research can further explore substrate combinations with greater cost-effectiveness and environmental benefits, promoting their broader application in the cultivation of P. macrophyllus. Meanwhile, considering the pivotal role of microorganisms in plant health, it is recommended to integrate advanced technologies such as metagenomics to investigate the specific mechanisms of key functional microbes involved in nutrient uptake and disease resistance.
The findings of this study not only provide theoretical support for the efficient cultivation of P. macrophyllus but also offer insights and references for substrate optimization in other woody ornamental plants or crops requiring improved rhizosphere ecology, demonstrating promising potential for broader application and promotion.

Author Contributions

Conceptualization, Y.F., T.G., H.G. and X.Z.; methodology, Y.F. and H.G.; software, D.Z. and X.L. (Xiaomin Liang); formal analysis, X.L. (Xiaomin Liang), Y.F. and C.Z. (Chenning Zhang); investigation, X.L. (Xiaomin Liang), D.Z., C.Z. (Congyu Zhang), Y.P., C.Z. (Chenning Zhang), Y.H., S.H. and J.T.; validation, Y.H., S.H. and J.T.; data curation, X.L. (Xiaomin Liang), D.Z., Y.F. and C.Z. (Chenning Zhang); writing—original draft preparation, X.L. (Xiaomin Liang), D.Z. and C.Z. (Congyu Zhang); writing—review and editing, Y.F. and T.G. and T.G.; supervision, Y.F., H.G. and X.Z.; project administration, Y.F. and X.L. (Xiaocong Li); resources, X.L. (Xiaocong Li) and T.G. All authors have read and agreed to the published version of the manuscript.

Funding

This research was financially supported by the National Natural Science Foundation of China (31971550), the Rural Science and Technology Specialist Project of Guangdong Province, China (KTP20210260, KTP20240456), and the Zhongshan City Horizontal Project (2023ZSCXZX01).

Data Availability Statement

The data presented in this study are available upon request from the corresponding author.

Conflicts of Interest

Author Xiaocong Li was employed by the company Zhongshan Qian Song Yuan Flower Planting Co., Ltd., The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Figure 1. The geographical location of the experimental field.
Figure 1. The geographical location of the experimental field.
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Figure 2. Rarefaction curves of rhizosphere soil bacteria under different cultivation substrates.
Figure 2. Rarefaction curves of rhizosphere soil bacteria under different cultivation substrates.
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Figure 3. The number of shared and unique OTUs of rhizosphere soil bacteria in different cultivation substrates.
Figure 3. The number of shared and unique OTUs of rhizosphere soil bacteria in different cultivation substrates.
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Figure 4. PCoA analysis of bacteria in rhizosphere soil of different cultivation substrates.
Figure 4. PCoA analysis of bacteria in rhizosphere soil of different cultivation substrates.
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Figure 5. Relative distribution of dominant bacterial phylum classification level in rhizosphere soil of different cultivation substrates.
Figure 5. Relative distribution of dominant bacterial phylum classification level in rhizosphere soil of different cultivation substrates.
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Figure 6. RDA analysis of rhizosphere soil bacteria in different cultivation substrates. WC represents water content; BD represents soil bulk density; OM represents organic matter; and PORT represents total porosity.
Figure 6. RDA analysis of rhizosphere soil bacteria in different cultivation substrates. WC represents water content; BD represents soil bulk density; OM represents organic matter; and PORT represents total porosity.
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Figure 7. Rarefaction curves of rhizosphere soil fungi under different cultivation substrates.
Figure 7. Rarefaction curves of rhizosphere soil fungi under different cultivation substrates.
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Figure 8. The number of shared and unique OTUs of rhizosphere soil fungi in different cultivation substrates.
Figure 8. The number of shared and unique OTUs of rhizosphere soil fungi in different cultivation substrates.
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Figure 9. PCoA analysis of rhizosphere soil fungi in different cultivation substrates.
Figure 9. PCoA analysis of rhizosphere soil fungi in different cultivation substrates.
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Figure 10. Relative distribution of dominant fungal phyla at the classification level in the rhizosphere soil of different cultivation substrates.
Figure 10. Relative distribution of dominant fungal phyla at the classification level in the rhizosphere soil of different cultivation substrates.
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Figure 11. RDA analysis of the rhizosphere soil fungal community in different cultivation substrates. WC represents water content; BD represents soil bulk density; OM represents organic matter; and PORT represents total porosity.
Figure 11. RDA analysis of the rhizosphere soil fungal community in different cultivation substrates. WC represents water content; BD represents soil bulk density; OM represents organic matter; and PORT represents total porosity.
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Table 1. Sequencing and primer sequence name.
Table 1. Sequencing and primer sequence name.
Sequencing TypePrimer NamePrimer SequencesSequencing Target Role
16S338F5′-ACTCCTACGGGAGGCAGCA-3′Combined with the conserved region of the 16S gene, amplification of the V3 region was initiated.
806R5′-GGACTACHVGGGTWTCTAAT-3′Combined with the conserved sequence of the V4 region, reverse amplification was performed.
ITSITS3-F5′-GCATCGATGAAGAACGCAGC-3′Combined with the starting end of the ITS2 region, amplification was initiated.
ITS4-R5′-TCCTCCGCTTATTGATATGC-3′Reverse amplification of the end of the ITS2 region, paired with ITS3, to ensure highly specific amplification.
Table 2. Physicochemical properties of rhizosphere soil in different cultivation.
Table 2. Physicochemical properties of rhizosphere soil in different cultivation.
SubstratespHWC (%)BD (g/cm3)PORT (%)OM (g/kg)TN (g/kg)TP (g/kg)TK (g/kg)AN (g/kg)AP (g/kg)AK (g/kg)
SJ17.07
±0.09		22.04
±2.18		1.10
±0.08		36.77
±3.25		29.56
±0.35		1.57
±0.10		1.08
±0.06		18.88
±0.32		93.33
±1.17		74.48
±1.07		70.55
±3.26
SX27.17
±0.3		7.28
±1.04		1.16
±0.06		55.74
±2.34		31.90
±8.43		1.07
±0.20		0.73
±0.09		16.12
±0.37		82.83
±4.21		90.67
±2.65		143.45
±20.41
p0.3490.0040.5960.0090.8080.0910.0320.0050.0740.0050.024
Significancens**ns**nsns***ns***
WC represents water content; BD represents soil bulk density; PORT represents total porosity; OM represents organic matter; TN represents total nitrogen; TP represents total phosphorus; TK represents total potassium; AN represents alkaline hydrolysis nitrogen; AP represents soil available phosphorus; and AK represents soil available potassium. Data are presented as mean ± standard error (n = 3). “ns” indicates no significance; “*” represents p < 0.05; and “**” represents p < 0.01.
Table 3. Effects of different cultivation substrates on ground diameter and plant height of P. macrophyllus.
Table 3. Effects of different cultivation substrates on ground diameter and plant height of P. macrophyllus.
TreatmentGround Diameter (mm)Plant Height (cm)
SJ122.52 ± 1.20104.33 ± 4.84
SX229.67 ± 0.74175.69 ± 3.41
p0.007<0.001
Significance*****
Data are presented as mean ± standard error (n = 3). “**” represents p < 0.01; and “***” represents p < 0.001.
Table 4. Effects of different cultivation substrates on physiological and nutrient indicators of P. macrophyllus.
Table 4. Effects of different cultivation substrates on physiological and nutrient indicators of P. macrophyllus.
SubstratesChl (mg/g)SS (mg/g)SP (mg/g)C (g/kg)N (g/kg)P (g/kg)K (g/kg)
SJ110.93 ± 2.063.31 ± 0.351.10 ± 0.04849.26 ± 9.6217.37 ± 1.412.08 ± 0.1510.87 ± 0.75
SX218.04 ± 1.352.79 ± 0.081.33 ± 0.06867.99 ± 10.9218.36 ± 1.561.97 ± 0.157.55 ± 1.13
p0.0410.2250.0450.2670.6640.6210.071
Significance*ns*nsnsnsns
Chl represents chlorophyll content; SS represents soluble sugar; SP represents soluble protein; C represents organic carbon; N represents nitrogen content; P represents phosphorus content; K represents potassium content. Data are presented as mean ± standard error (n = 3). “ns” indicates no significance; “*” represents p < 0.05.
Table 5. Alpha diversity index of bacteria in rhizosphere soil of different cultivation substrates.
Table 5. Alpha diversity index of bacteria in rhizosphere soil of different cultivation substrates.
TreatmentChao1ACESimpsonShannon_2Goods_Coverage
SJ14320.53 ± 82.095054.37 ± 86.470.0034 ± 0.00029.79 ± 0.030.9882 ± 0.0070
SX24842.00 ± 186.815526.88 ± 160.600.0036 ± 0.00069.85 ± 0.140.9901 ± 0.0073
P0.0630.7030.0610.6980.128
Significancensnsnsnsns
Data are presented as mean ± standard error (n = 3). “ns” indicates no significance.
Table 6. Alpha diversity index of rhizosphere soil fungi in different growth substrates.
Table 6. Alpha diversity index of rhizosphere soil fungi in different growth substrates.
TreatmentChao1ACESimpsonShannon_2Goods_Coverage
SJ1571.40 ± 57.99632.27 ± 49.100.0297 ± 0.00316.43 ± 0.030.9983 ± 0.0002
SX2496.70 ± 11.03572.17 ± 8.460.0557 ± 0.02395.84 ± 0.390.9984 ± 0.0001
p0.2690.8540.2940.2720.854
Significancensnsnsnsns
Data are presented as mean ± standard error (n = 3). “ns” indicates no significance.
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MDPI and ACS Style

Liang, X.; Zhong, D.; Zhang, C.; Pan, Y.; Zhang, C.; Guo, H.; Zhu, X.; Li, X.; He, Y.; Huang, S.; et al. Effects of Different Cultivation Substrates on the Growth of Podocarpus macrophyllus and the Rhizosphere Soil Microbial Community Structure. Agronomy 2025, 15, 1055. https://doi.org/10.3390/agronomy15051055

AMA Style

Liang X, Zhong D, Zhang C, Pan Y, Zhang C, Guo H, Zhu X, Li X, He Y, Huang S, et al. Effects of Different Cultivation Substrates on the Growth of Podocarpus macrophyllus and the Rhizosphere Soil Microbial Community Structure. Agronomy. 2025; 15(5):1055. https://doi.org/10.3390/agronomy15051055

Chicago/Turabian Style

Liang, Xiaomin, Donghua Zhong, Congyu Zhang, Yongfang Pan, Chenning Zhang, Herong Guo, Xiaoling Zhu, Xiaocong Li, Yuxuan He, Shaopeng Huang, and et al. 2025. "Effects of Different Cultivation Substrates on the Growth of Podocarpus macrophyllus and the Rhizosphere Soil Microbial Community Structure" Agronomy 15, no. 5: 1055. https://doi.org/10.3390/agronomy15051055

APA Style

Liang, X., Zhong, D., Zhang, C., Pan, Y., Zhang, C., Guo, H., Zhu, X., Li, X., He, Y., Huang, S., Tu, J., Gao, T., & Feng, Y. (2025). Effects of Different Cultivation Substrates on the Growth of Podocarpus macrophyllus and the Rhizosphere Soil Microbial Community Structure. Agronomy, 15(5), 1055. https://doi.org/10.3390/agronomy15051055

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