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Article

Soil Microbial Communities and Their Relationship with Soil Nutrients in Different Density Pinus sylvestris var. mongolica Plantations in the Mu Us Sandy Land

by
Long Hai
1,2,
Mei Zhou
1,*,
Kai Zhao
3,*,
Guangyu Hong
2,
Zihao Li
2,
Lei Liu
2,
Xiaowei Gao
2,
Zhuofan Li
2 and
Fengzi Li
2
1
College of Grassland Science, Inner Mongolia Agricultural University, Hohhot 010011, China
2
Inner Mongolia Academy of Forestry Sciences, Hohhot 010011, China
3
College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010010, China
*
Authors to whom correspondence should be addressed.
Forests 2025, 16(3), 547; https://doi.org/10.3390/f16030547
Submission received: 27 February 2025 / Revised: 11 March 2025 / Accepted: 17 March 2025 / Published: 19 March 2025
(This article belongs to the Special Issue Soil Organic Matter Dynamics and Microbial Roles in Biogeochemical Cycles in Forestry)
Browse Figures
Versions Notes

Abstract

:
In the Mu Us Sandy Land, vegetation is closely related to soil microorganisms and nutrients. However, research on the relationship between soil microbial communities and nutrients in Pinus sylvestris var. mongolica plantations of different densities is still imperfect. This study selected Pinus sylvestris var. mongolica plantations with high, medium, and low densities, as well as bare sandy land, to analyze the relationship between vegetation density and soil nutrients, microbial community structure, and diversity indices. The results show that the following: (1) Medium-density plantations significantly increased soil organic matter, total nitrogen, and total potassium content, which were 4.3 times that of bare sandy land and 1.7 times that of high-density plantations; (2) In high-density plantations, the relative abundance of bacterial phyla Actinobacteriota and fungal phylum Ascomycota was higher; as plantation density decreased, the relative abundance of bacterial phyla Proteobacteria and Acidobacteriota and fungal phylum Basidiomycota increased, with different density plantations significantly affecting soil microbial community structure; (3) High-density plantations significantly increased the abundance of bacterial and fungal genera but also reduced bacterial diversity indices, while medium-density plantations were outstanding in enhancing fungal species richness and diversity, with the highest fungal Shannon index, indicating that medium density is conducive to fungal diversity enhancement; (4) Soil organic matter, total nitrogen, total phosphorus, total potassium, and pH value were the main environmental factors affecting soil microbial community structure. High-density plantations significantly affected soil microbial community structure by changing these soil nutrients and physicochemical properties, especially related to changes in total potassium and pH value. This study clarified the effects of Pinus sylvestris var. mongolica plantation density on soil nutrients and microbial community structure, revealing the intrinsic connection between soil nutrients and microbial communities, providing a theoretical basis for vegetation restoration in the Mu Us Sandy Land ecosystem, and helping to formulate scientific management strategies for Pinus sylvestris var. mongolica plantations to improve sandy land soil quality and promote the sustainable development of sandy land ecosystems.

1. Introduction

Soil microorganisms are the core drivers of material cycling and energy flow in terrestrial ecosystems. Their diversity directly affects the formation of soil fertility, the decomposition of organic matter, and the efficiency of nutrient transformation [1,2]. The community structure and functional diversity of soil microorganisms not only directly affect the formation of soil fertility and carbon sequestration functions but also form complex interaction networks with plants through mycorrhizal symbiosis and the secretion of metabolic products [3]. During the ecological restoration of sandy lands, the reconstruction of microbial communities is of special significance for maintaining the stability of artificial forest ecosystems [4]. On the one hand, it promotes carbon and nitrogen turnover through the decomposition of litter and root exudates, and on the other hand, it enhances the stability of soil aggregates through mycelial networks [5]. Previous studies have shown that differences in artificial forest density can significantly affect the survival strategies and functional expression of soil microorganisms by changing canopy structure, litter input, and root distribution depth [6]. For example, high-density coniferous plantations may selectively inhibit bacterial growth and promote fungal colonization by changing the C/N ratio and phenolic content of litter [7]. These findings highlight the scientific value of understanding the effects of artificial forest density from a microbial perspective. However, the current knowledge of the succession patterns of microbial communities and their environmental driving mechanisms under different density gradients in sandy land ecosystems is still limited.
Pinus sylvestris var. mongolica, as a pioneer tree species in the ecological restoration of northern China’s sandy lands, has played a key role in the Three-North Shelterbelt Project due to its drought resistance, strong soil tolerance, and windbreak characteristics [8,9]. Recent studies have found that P. sylvestris var. mongolica plantations can change soil enzyme activity spectra through litter input, with β-glucosidase and chitinase activities showing a significant positive correlation with microbial biomass carbon. Differences in plantation density may lead to the decoupling of this relationship [10,11]. Notably, density, as a core parameter in artificial forest management, directly affects the understory microenvironment and resource competition [12]. Existing research has mainly focused on the effects of single-density plantations on soil physicochemical properties or only on simplified indicators such as microbial biomass carbon and nitrogen [13,14], failing to reveal the systematic response of microbial community structure under different density gradients. The differences in the effects of P. sylvestris var. mongolica plantations of different densities on soil microbial communities and soil nutrients have not been fully studied. In-depth exploration of the changes in soil microbial communities and soil nutrients under different densities of P. sylvestris var. mongolica plantations is of great theoretical and practical value for revealing the functional mechanisms of P. sylvestris var. mongolica plantation ecosystems and optimizing sandy land ecological restoration strategies.
The Mu Us Sandy Land, located in the semi-arid ecological transition zone of China, is the interlacing area of the Loess Plateau and desert. Its problems of soil impoverishment and wind erosion have long restricted regional sustainable development [15]. P. sylvestris var. mongolica has become the core tree species for ecological barrier construction in this region through sand fixation, soil improvement, and reduction in surface wind speed [16]. However, the soil in P. sylvestris var. mongolica plantations in the Mu Us Sandy Land is generally alkaline, with strong nutrient accumulation on the surface and low organic matter content, limiting microbial activity due to carbon source supply [17]. Soil microbial community structures are sensitive to changes in P. sylvestris var. mongolica plantation density [18]. Therefore, exploring the coupling relationship between soil microbial communities and soil nutrients under different densities of P. sylvestris var. mongolica plantations can provide a theoretical basis for revealing the microbial driving mechanisms of sandy land ecosystem recovery and practical guidance for the optimization of artificial forest density and sustainable management. Given this, this study focused on P. sylvestris var. mongolica plantations of different densities in the Mu Us Sandy Land to address the following: (1) What is the relationship between sandy land P. sylvestris var. mongolica plantation density and soil nutrients and microbial diversity? (2) What are the main factors affecting the diversity of soil microorganisms in sandy land P. sylvestris var. mongolica plantations? Revealing the characteristics and driving factors of soil microbial diversity changes in P. sylvestris var. mongolica plantations of different densities in the Mu Us Sandy Land can provide a theoretical basis for the management of sandy land P. sylvestris var. mongolica plantations.

2. Materials and Methods

2.1. Plant Material and Study Area

The studied plant species is P. sylvestris var. mongolica. This study was conducted at the Wulan Taolegai Sand Control Station (38°61′ N, 108°82′ E) in Wushen county, Ordos City, Inner Mongolia, located in the heart of the Mu Us Sandy Land. It has a dry and semi-arid continental monsoon climate, with frequent strong winds in spring, concentrated precipitation in summer, mostly clear weather in autumn, and cold and dry winters with prevailing northwest winds. The average annual temperature is 6.0–8.0 °C; the average annual rainfall is about 360 mm; the annual evaporation is 2200–2800 mm, which is 4–10 times the rainfall; and the average annual wind speed is 4.8 m/s, with a maximum wind speed of about 28 m/s.

2.2. Research Methods

2.2.1. Plot Setup and Sample Collection

In the study area, three Pinus sylvestris var. mongolica plantations of different densities (high, medium, and low) and one bare sandy land (CK) were selected as four experimental sites. Soil samples were collected in August 2024. In each forest and bare land, three experimental plots (30 m × 30 m) were randomly set up. The selected plots had no livestock grazing or human destruction, and the distance between plots was more than 20 m. Nearby exposed sandy land was chosen as the control for the three types of forests. Soil samples were collected from 0–20 cm depth in 12 plots using a 5 cm diameter sterile soil drill. Plot information is shown in Table 1.
Soil samples were collected from the east, south, west, and north directions to ensure the uniformity of the soil samples. The soil samples from each sampling point were mixed to form a composite sample to ensure the representativeness of the samples. The samples were sieved through a 2 mm sieve to remove stones and plant tissues, and 1 kg of soil was taken and put into a sterile self-sealing bag, transported back to the laboratory in a 4 °C insulated box, air-dried indoors, and then dried at 105 °C for 6 h to measure pH, organic matter, and total nitrogen content. Another 50 g of soil was taken and put into a sterile centrifuge tube, transported back to the laboratory in liquid nitrogen, and stored in a −80 °C refrigerator for soil microbial high-throughput sequencing.

2.2.2. Soil Nutrient Analysis

Soil organic matter content was measured using the potassium dichromate oxidation with external heating method: air-dried soil samples were weighed into test tubes, an excess of potassium dichromate–sulfuric acid solution was added, and the mixture was heated in an oil bath at 170–180 °C for 5 min. After cooling, the mixture was transferred to a conical flask, titrated with a standard solution of ferrous sulfate using o-phenanthroline as an indicator, and the endpoint was reached when the color changed from orange-yellow to blue-green and then to brick-red. The organic carbon content was calculated and multiplied by 1.724 to obtain the organic matter content. Soil total nitrogen content was measured using the semi-micro Kjeldahl method: soil samples were weighed into Kjeldahl flasks, digested with concentrated sulfuric acid and mixed catalysts to ammonium nitrogen. After cooling, the mixture was transferred to a distillation apparatus, an excess of sodium hydroxide was added for distillation, and ammonia was absorbed with boric acid. The endpoint was reached using bromocresol green-methyl red as an indicator, and the total nitrogen content was calculated using a standard solution of hydrochloric acid. Soil total phosphorus content was measured using the alkali fusion-molybdenum blue colorimetric method: soil samples were weighed into platinum crucibles, melted with sodium carbonate at 920 °C, and then leached with hot water, dissolved with dilute sulfuric acid, and diluted to a fixed volume to obtain the test solution. The test solution was mixed with molybdenum–antimonate color-developing agent, allowed to stand at room temperature for 30 min, and the absorbance was measured at 700 nm using a spectrophotometer, with the total phosphorus content calculated using a standard curve. Soil total potassium content was measured using the alkali fusion-flame photometry method: soil samples were weighed into platinum crucibles, melted with sodium carbonate at 920 °C, and then leached with hot water, dissolved with dilute hydrochloric acid, and diluted to a fixed volume. The total potassium content was measured using a flame photometer and calculated using a standard curve. Soil pH value was measured using the potentiometric method: air-dried soil samples were weighed into beakers, and deionized water without carbon dioxide was added at a soil-to-water ratio of 1:2.5, stirred and allowed to stand for 30 min. The pH glass electrode and saturated calomel electrode were inserted, and the pH value was measured using a pH meter, with the meter calibrated using standard buffer solutions before measurement.

2.2.3. Soil Microbial Community Analysis

The total genomic DNA of the microbial community was extracted using the “genomic DNA isolation kit” from Tiangen Biotech (Beijing, China) according to the instructions. The quality of the extracted genomic DNA was detected using 1% agarose gel electrophoresis, and the concentration and purity of the DNA were measured using a NanoDrop2000 (Thermo Scientific, Waltham, MA, USA). The 16S rRNA gene and ITS gene were used as target genes for bacterial and fungal molecular ecological analysis, respectively, with amplification primers 338F/806R and ITS1F/ITS2R. High-throughput sequencing was performed by Shanghai Meiji Biomedical Technology Co., Ltd. (Shanghai, China) using the Illumina Nextseq2000 platform.

2.2.4. Data Processing and Analysis

The fastp [19] software (https://github.com/OpenGene/fastp (accessed on 5 September 2024), version 0.19.6) was used to quality control the original paired-end sequencing sequences, and the FLASH [20] software (http://www.cbcb.umd.edu/software/flash (accessed on 5 September 2024), version 1.2.11) was used to splice the sequences. Non-redundant sequences were extracted from the optimized sequences, and single sequences without duplicates were removed. Operational taxonomic units (OTUs) were clustered at 97% similarity, and chimeras were removed during the clustering process to obtain the representative sequences of OTUs. All optimized sequences were mapped to the representative sequences of OTUs, and sequences with a similarity of more than 97% to the representative sequences were selected to generate the OTU table. R language (version 3.3.1) was used to draw community bar charts, the pheatmap package (1.0.8) in R language was used to draw community heatmap charts, and the vegan package (version 2.4.3) in R language was used for RDA and CCA analysis and plotting. The mothur software (version v.1.30.2, https://mothur.org/wiki/calculators/ (accessed on 5 February 2025)) was used to calculate the α-diversity indices and coverage of the samples, including Shannon index, Simpson index, Coverage index, and Chao index. All data analysis was carried out on the Meiji Bio Cloud Platform (https://cloud.majorbio.com (accessed on 5 February 2025)). Additionally, Origin2022 software was used to draw graphs of soil nutrients and α-diversity indices with density changes.

3. Results

3.1. Soil Nutrients in Different Density P. sylvestris var. mongolica Plantations

Figure 1 shows that there were significant differences in soil organic matter content among P. sylvestris var. mongolica plantations of different densities. The SOM content in MD plantations was the highest (2.49 g/kg), significantly higher than that in HD (1.03 g/kg) and LD (1.38 g/kg) plantations, and significantly higher than that in CK (0.58 g/kg). The SOM content in MD plantations was about 4.3 times that of CK, indicating that plantation density has an important regulatory effect on SOM accumulation, with MD significantly enhancing SOM accumulation, while HD and LD had weaker effects. The trend of TN content was consistent with that of SOM, with MD having the highest content (0.19 g/kg), followed by LD (0.15 g/kg), HD (0.11 g/kg), and CK (0.10 g/kg). The TN content in MD was 1.7 times that of HD, indicating that MD is more conducive to the biological retention of nitrogen and the mineralization of organic matter. The TP content showed little difference among different density plantations, with LD (0.17 g/kg) slightly higher than MD (0.15 g/kg) and HD (0.14 g/kg), but significantly higher than CK (0.13 g/kg). The TK content was highest in MD (23.36 g/kg), followed by LD (23.25 g/kg), HD (22.55 g/kg), and CK (22.31 g/kg), with MD promoting potassium accumulation. The soil pH value was lowest in MD (6.89), followed by HD (6.97) and LD (7.01), and highest in CK (7.05). The decrease in pH value in MD may be related to the accumulation of acidic substances produced by organic matter decomposition and root exudates. Overall, MD was more effective in improving SOM, TN, and TP content, while the effects of different density plantations on TK content and pH value were relatively smaller.

3.2. Composition and Diversity of Soil Microbial Communities in Different Density P. sylvestris var. mongolica Plantations

3.2.1. Species Composition at the Phylum Level

Figure 2A shows that? in terms of bacterial phylum diversity, Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant phyla with relatively high abundance. Actinobacteriota had a relatively high abundance in all groups, about 0.25–0.3, indicating its important position in the soil bacterial community of the Mu Us Sandy Land. With increasing density, the relative abundance of Actinobacteriota gradually decreased, while that of Proteobacteria and Acidobacteriota increased. This suggests that HD has an inhibitory effect on the growth environment of certain bacterial phyla, while promoting the growth of other phyla. As density decreased from high to low, the relative abundance of the major bacterial phyla changed relatively gently, and there was no obvious pattern of increase or decrease compared with CK. The relative abundance of other phyla such as Chloroflexi and Gemmatimonadota was relatively low, and the changes among different treatment groups were also small.
Figure 2B shows that the effect of density on fungal community composition was more significant. In terms of fungal phylum diversity, Ascomycota and Basidiomycota were the dominant phyla. The relative abundance of Ascomycota was the highest in CK, close to 0.8, significantly higher than that in other groups. With increasing density, the relative abundance of Ascomycota gradually decreased, while that of Basidiomycota gradually increased. This may mean that high-density forest environments are more conducive to the growth of Basidiomycota, while having an inhibitory effect on the growth of Ascomycota. This change indicates that vegetation affects soil fungal community structure, and the degree of impact varies with different densities. Overall, there were differences in the composition of soil microbial communities at the phylum level among P. sylvestris var. mongolica plantations of different densities. In terms of bacteria, the relative abundance of Actinobacteriota was the highest in HD, and the relative abundance of Proteobacteria and Acidobacteriota increased with decreasing density. In terms of fungi, the relative abundance of Ascomycota was the highest in HD, and the relative abundance of Basidiomycota increased with decreasing density. The composition of bacterial communities was less affected by density, while fungal communities were more sensitive to density.

3.2.2. Species Composition at the Class Level

Figure 3A shows that, in terms of bacterial class diversity, Actinobacteria, Alphaproteobacteria, Vicinamibacteria, Blastocatellia, and Gammaproteobacteria were the dominant classes with relatively high abundance. Actinobacteria accounted for a certain proportion in all groups, about 0.1–0.15, and was an important component of the bacterial community. P. sylvestris var. mongolica plantations of different densities had a certain impact on the species composition of soil bacteria at the class level. For example, the relative abundance of Alphaproteobacteria was higher in HD and lower in CK; the relative abundance of Gammaproteobacteria was higher in CK and lower in plantations. This indicates that the planting density of P. sylvestris var. mongolica changed the relative abundance of some bacterial classes, which may be related to plant root activities and litter input. The relative abundance of other bacterial classes such as Chloroflexia, Thermolephilia, and Gemmatimonadetes was relatively low, and the changes among different groups were relatively small.
Figure 3B shows that, in terms of fungal class diversity, Agaricomycetes, Pezizomycetes, Eurotiomycetes, and Dothideomycetes were the dominant classes. The relative abundance of Pezizomycetes was higher in CK, while the relative abundance of Agaricomycetes and Eurotiomycetes increased in different densities. Density had a significant impact on the species composition of fungi at the class level. With decreasing density, the relative abundance of Agaricomycetes first decreased and then increased, while the relative abundance of Pezizomycetes showed the opposite trend. This change indicates that planting vegetation significantly altered the structure of soil fungal communities, and the succession direction of fungal communities was different under different densities. The relative abundance of other fungal classes such as Leotiomycetes, Mortierellomycetes, and Tremellomycetes was relatively low, with some fluctuations among different groups, but the changes were relatively small. Overall, density significantly affected the diversity and composition of soil microorganisms. High-density plantations were more conducive to the growth of certain bacterial and fungal groups, while low-density plantations promoted the increase in abundance of other groups.

3.2.3. Species Composition at the Genus Level

Figure 4A shows that there were significant differences in the abundance of bacterial genera at different densities. The color changes among HD, MD, LD, and CK were large, indicating that density had a significant impact on bacterial communities. Specifically, RB41 had a higher abundance in HD, lower in MD and LD, and the lowest in CK. norank_o_Vicinamibacterales had a higher abundance in HD, decreased in MD and LD, and the lowest in CK. Pseudonocardia had a higher abundance in HD and lower in other treatments. Nordella had a higher abundance in HD, decreased in MD and LD, and the lowest in CK. MND1 had a higher abundance in HD and lower in other treatments. Mycobacterium had a higher abundance in HD and lower in other treatments. Streptomyces had a higher abundance in HD and lower in other treatments. Sphingomonas had a higher abundance in HD and lower in other treatments. In summary, many bacterial genera had higher abundance in HD, indicating that HD promoted the growth of these bacteria. The abundance of some bacterial genera decreased in MD and LD, but some genera still maintained higher abundance. The abundance of most bacterial genera was lower in CK, indicating that vegetation cover had a significant impact on the richness of bacterial communities.
Figure 4B shows that there were significant differences in the abundance of fungal genera at different densities. Malloccybe had a higher abundance in HD, decreased in MD and LD, and the lowest in CK. Geopora had a higher abundance in HD and lower in other treatments. Inocybe had a higher abundance in HD and lower in other treatments. Trichoderma had a higher abundance in HD and lower in other treatments. Fusarium had a higher abundance in HD and lower in other treatments. Aspergillus had a higher abundance in HD and lower in other treatments. Penicillium had a higher abundance in HD and lower in other treatments. In summary, many fungal genera had higher abundance in HD, indicating that HD promoted the growth of these fungi. The abundance of some fungal genera decreased in MD and LD, but some genera still maintained higher abundance. The abundance of most fungal genera was lower in CK, indicating that vegetation cover had a significant impact on the richness of fungal communities. In conclusion, HD significantly increased the abundance of bacterial and fungal genera, and although some genera decreased in MD and LD, the overall abundance was still higher than that in CK, indicating that vegetation cover had a positive impact on soil microbial communities. The lowest abundance of microorganisms in CK indicated that the absence of vegetation cover had a negative impact on soil microbial diversity. Therefore, reasonably increasing the density of larch plantations is helpful for enhancing soil microbial diversity.

3.2.4. Species Composition at the OTU Level

OUT (Operational Taxonomic Unit) is a classification unit used in microbial ecology to categorize organisms based on genetic similarity. Figure 5A shows that in terms of bacterial OTU diversity, the number of shared bacterial OTUs among the four groups (HD, MD, LD, CK) was 2780, accounting for 11.23% of the total OTU number, indicating that there were certain common bacterial groups in different conditions. At the same time, each group also had its unique OTUs. For example, CK had 1416 unique OTUs, accounting for 22.25%; HD had 733 unique OTUs, accounting for 12.77%. This indicates that bare sandy land and P. sylvestris var. mongolica plantations each had unique bacterial community compositions. As the planting density of P. sylvestris var. mongolica changed from HD to MD and LD, the number and proportion of unique OTUs were different. MD had 984 unique OTUs, accounting for 15.89%; LD had 1042 unique OTUs, accounting for 16.16%. Density affected the composition of soil bacterial OTUs, and different densities formed bacterial community structures with differences. In summary, at the OTU level, the number of unique OTUs in bare sandy land was the highest, indicating that the absence of vegetation cover led to higher bacterial diversity. As the density of P. sylvestris var. mongolica increased, the number of unique OTUs gradually decreased, especially in high-density plantations, where the number of unique OTUs was relatively low. This may indicate that high-density P. sylvestris var. mongolica plantations had a certain inhibitory effect on bacterial community diversity at the OTU level.
Figure 5B shows that, in terms of fungal OTU diversity, HD had 211 unique OTUs, accounting for 27.91%. MD had 287 unique OTUs, accounting for 31.75%. LD had 299 unique OTUs, accounting for 32.08%. CK had 308 unique OTUs, accounting for 37.98%. HD and MD shared 56 OTUs, accounting for 3.37%. HD and LD shared 95 OTUs, accounting for 3.67%. HD and CK shared 68 OTUs, accounting for 4.34%. MD and LD shared 128 OTUs, accounting for 6.97%. MD and CK shared 53 OTUs, accounting for 3.04%. LD and CK shared 60 OTUs, accounting for 2.27%. There were 201 shared OTUs, accounting for 5.91%. The number of unique OTUs in CK was still the highest, indicating that the absence of vegetation cover led to higher fungal diversity. As the density of P. sylvestris var. mongolica increased, the number of unique OTUs gradually decreased, but the trend was not as obvious as in bacteria. This means that the response of fungi to vegetation cover was different from that of bacteria, or that fungal communities were less sensitive to environmental changes. In summary, the diversity of microorganisms in bare sandy land was higher at the OTU level, possibly because the lack of vegetation cover led to a wider range of ecological niches in the soil, promoting an increase in diversity.

3.2.5. Changes in Soil Microbial Diversity Indices

α-diversity analysis mainly assessed the richness and diversity of microbial communities in environmental samples through multiple diversity indices and explored the differences in α-diversity indices between control and treatment groups. The Chao index was used to estimate species richness, with higher values indicating higher species richness. The Coverage index reflected the coverage of samples for the community, with values closer to 1 indicating better representation of the community by the samples. The Shannon index measured species diversity, with higher values indicating higher species diversity. The Simpson index mainly reflected the impact of dominant species on the community, with lower values indicating higher species diversity. Figure 6A shows that, among the bacterial diversity indices, CK had the highest Chao index (4265), followed by LD (4179), MD (4046), and HD (3808). As density increased, bacterial species richness showed a decreasing trend, possibly due to HD changing the soil microenvironment and affecting the survival of some bacteria. The Coverage index of HD was the highest (0.979), and the Coverage indices of all groups were close to 0.975–0.977. This indicates that the samples well represented the bacterial community, and the experimental results were reliable. CK had the highest Shannon index (6.62), indicating that the bacterial diversity in bare sandy land was the highest, while HD, MD, and LD had relatively lower Shannon indices with little difference. HD had the smallest Simpson index (0.003), indicating that the impact of dominant species on the bacterial community was the greatest.
Figure 6B shows that, among the fungal diversity indices, HD had the lowest Chao index (341), while MD (411) and LD (447) had higher indices, and CK was in the middle (361). This indicates that the planting of P. sylvestris var. mongolica increased the species richness of soil fungi, and medium and low-density plantations were more conducive to fungal species richness than CK. The Coverage indices of all groups were very high, close to 0.998, and the Coverage index of HD was relatively high (0.999). This indicates that the samples well represented the fungal community, and the experimental data could accurately reflect the composition of the fungal community. MD had the highest Shannon index (3.39), followed by LD (3.13), CK (2.98), and HD (2.84). This indicates that the fungal species diversity in MD was the highest, and the effect was best under medium-density conditions. MD had the lowest Simpson index (0.08), indicating that the impact of dominant species on the fungal community in medium-density P. sylvestris var. mongolica plantations was relatively small, and species diversity was higher. Overall, density had different impacts on the diversity of soil bacteria and fungi. Bacterial diversity showed little difference among different densities, while fungal diversity was more affected by density, with MD being relatively prominent in enhancing fungal species richness and diversity.

3.3. Main Environmental Factors Affecting Soil Microbial Community Structure

RDA/CCA is a sorting method developed based on correspondence analysis, combining correspondence analysis with multiple regression analysis. Each step of the calculation is regressed with environmental factors, also known as multiple direct gradient analysis. Before ordination analysis, we used Detrended Correspondence Analysis (DCA) to decide whether to use Redundancy Analysis (RDA) or Canonical Correspondence Analysis (CCA). We chose CCA when the gradient length of the first DCA axis was ≥3.5 and RDA when it was <3.5. This helps determine the most suitable analysis method for the data, accurately revealing the relationships between environmental factors and species communities. This analysis is mainly used to reflect the relationship between microbial communities and environmental factors. RDA is based on a linear model, while CCA is based on a unimodal model. The analysis can detect the relationships among environmental factors, samples, and microbial communities or the relationships between any two of them. In Figure 7A, the RDA analysis of bacterial diversity and soil nutrients showed that RDA1 and RDA2 explained 13.32% and 7.20% of the variation, respectively. The arrows of TP, TN, SOM, and TK were close to the distribution of HD, MD, and LD, indicating that these soil nutrient factors had a close relationship with bacterial community structure. The arrows of TP and TN were long and in the same direction, suggesting that they had a greater impact on bacterial community structure. The arrow of pH had a larger angle with the arrows of other soil nutrient factors, indicating that the impact of pH on bacterial community structure was different from that of nutrient factors. The sample points of HD were relatively concentrated in the upper part of the graph, while those of MD and LD were more dispersed, and those of CK were in the lower right part. This indicates that there were differences in bacterial community structure among P. sylvestris var. mongolica plantations of different densities, and they were clearly different from CK, possibly due to the changes in soil nutrients and physicochemical properties caused by P. sylvestris var. mongolica plantations, which in turn affected bacterial communities.
In the CCA analysis of fungal diversity and soil nutrients in Figure 7B, CCA1 and CCA2 explained 10.93% and 7.77% of the variation, respectively. The arrow of pH pointed to the upper left, while those of TN and SOM pointed to the lower left, indicating that pH had a significant impact on fungal diversity, while TP and SOM were related to other fungal groups. The distribution of sample points under different density treatments showed that the sample points of HD were mainly in the upper part, those of MD and LD were in the middle and lower parts, and those of CK were more dispersed. This indicates that the diversity of bacteria and fungi in high-density plantations was related to higher TP and pH values, while medium and low-density treatments were related to higher SOM and TN. In summary, SOM, TN, TP, TK, and pH were the main environmental factors affecting soil microbial community structure. HD had a significant impact on bacterial and fungal diversity, which was closely related to changes in TK and pH values.

4. Discussion

4.1. Impact of Density on Soil Nutrients

In the P. sylvestris var. mongolica plantation ecosystem of the Mu Us Sandy Land, plantation density had a significant impact on soil nutrients. This study found that the soil organic matter content in medium-density plantations was significantly higher than that in high-density and low-density plantations. This difference mainly originated from the balanced state of canopy structure and litter input in medium-density plantations [21]. The internal distribution of trees in medium-density plantations was reasonable, with moderate competition intensity, providing favorable conditions for tree growth. The root systems of trees could fully extend in the soil, and their physiological activities were active, secreting organic compounds that stimulated the metabolic activity of soil microorganisms, accelerating the decomposition and transformation of soil organic matter [22,23]. At the same time, the turnover process of root systems supplemented organic matter to the soil, becoming an important source of organic matter accumulation [24]. In addition, medium-density plantations produced a larger amount of litter, and the decomposition rate was suitable, further increasing the content of soil organic matter and total nitrogen [25]. In contrast, high-density plantations had intense tree competition, reduced litter production, and poor light conditions, which were not conducive to litter decomposition, limiting the accumulation of organic matter and total nitrogen. Low-density plantations had limited tree numbers, and the total amount of litter was insufficient, resulting in less accumulation of soil organic matter and total nitrogen. The higher soil organic matter content in medium-density plantations provided a material basis for the fixation and storage of nitrogen, and the nitrogen released from litter decomposition, combined with microbial nitrogen fixation, promoted nitrogen accumulation. However, in high-density plantations, root exudates may inhibit the activity of nitrifying bacteria, reducing the availability of nitrogen [26]. This study also found that the total phosphorus content in low-density P. sylvestris var. mongolica plantations was the highest, which may be related to the changes in soil microbial community structure and function under low-density conditions [27]. Low-density environments provided suitable growth conditions for phosphate-solubilizing microorganisms, which could convert insoluble phosphorus into available phosphorus forms, increasing soil total phosphorus content. In addition, the sparse distribution of root systems in low-density plantations was conducive to phosphorus absorption and activation. Organic acids, protons, and phosphatases secreted by root systems could change the rhizosphere microenvironment and enhance the activation ability of phosphorus [28]. The total potassium content in the soil showed little difference among different density plantations, mainly because potassium is relatively stable in the soil and has strong migratory properties, which can compensate for the differences caused by plant absorption, and the absorption efficiency of potassium by plants was similar among different density plantations [29].
The dynamic changes in soil pH value were closely related to the growth metabolism of P. sylvestris var. mongolica and soil microbial activity. The soil pH value in medium-density P. sylvestris var. mongolica plantations was lower, mainly due to the accumulation of organic compounds secreted by tree roots, acidic substances produced by litter decomposition, and organic acids produced by soil microbial metabolism [30]. In contrast, the soil pH value in bare sandy land and low-density P. sylvestris var. mongolica plantations was higher. The alkaline characteristics of bare sandy land soil originated from its pedogenesis and material composition, and the low vegetation cover in low-density plantations had limited impact on the soil, failing to effectively change the alkaline characteristics of the soil. The significantly lower soil pH value in medium-density plantations than in bare sandy land indicated that P. sylvestris var. mongolica plantations significantly changed the soil microenvironment, especially the acidity and alkalinity, through biological activities. Organic acid and other acidic substances produced by organic matter decomposition and plant root exudates were the main chemical sources of soil pH value reduction [31]. In high-density P. sylvestris var. mongolica plantations, intense competition for water among trees led to reduced soil water content, increased evaporation, and the accumulation of salts in the surface layer, forming salt accumulation. Salt accumulation to some extent neutralized or diluted the concentration of acidic substances in the soil, weakening the accumulation of acidic substances, resulting in a smaller decrease in soil pH value in high-density plantations.

4.2. Impact of Density on Soil Microbial Community Structure

In the Mu Us Sandy Land ecosystem, P. sylvestris var. mongolica, as an important vegetation type, had a complex and key impact on the structure of soil microbial communities. In terms of bacteria, the analysis of species composition from the phylum level to the genus level showed that there were differences in the soil bacterial community structure among P. sylvestris var. mongolica plantations of different densities. For example, at the phylum level, Actinobacteriota, Proteobacteria, and Acidobacteriota were dominant phyla, but their relative abundances varied among different densities. At the genus level, the dominant genera and their relative abundances were different among groups, and the number of unique OTUs also varied, reflecting that P. sylvestris var. mongolica plantations of different densities shaped unique bacterial communities. In terms of diversity indices, the Chao index showed that the bacterial species richness in bare sandy land was the highest and decreased with increasing P. sylvestris var. mongolica planting density; while the Shannon index and Simpson index indicated that bacterial species diversity was similar among different densities. RDA analysis further showed that soil nutrients (SOM, TN, TP, TK) and pH value had a significant impact on bacterial community structure, and the different distribution of sample points of P. sylvestris var. mongolica plantations of different densities in the sorting graph indicated that density indirectly affected bacterial communities by changing soil nutrients. In terms of fungi, Ascomycota and Basidiomycota were dominant phyla at the phylum level, and their relative abundances changed with P. sylvestris var. mongolica planting density. At the genus level, the composition and relative abundance of fungal genera were different among treatment groups, and the number of unique OTUs also varied. Among the diversity indices, the Chao index and Shannon index indicated that the fungal species richness and diversity in medium-density P. sylvestris var. mongolica plantations were the highest, while those in bare sandy land were the lowest. CCA analysis pointed out that soil TK had a significant impact on fungal community structure, and the sample points of P. sylvestris var. mongolica plantations of different densities and bare sandy land were clearly separated in the sorting graph, reflecting the significant impact of density on fungal community structure.
There are differences in root distribution and litter quantity and quality of P. sylvestris var. mongolica plantations with different densities [32]. Due to the fierce competition of trees, the decomposition rate and nutrient release of litter in high-density P. sylvestris var. mongolica plantations are different from those in medium and low-density stands, which affects the living environment and food resources of soil microorganisms, and then changes the microbial community structure [33,34]. For example, high-density stands may affect the metabolic activity and community composition of microorganisms due to strong shading effects and changes in light and temperature conditions in the soil surface [35]. Some studies have shown that vegetation type and density can significantly affect the structure of soil microbial communities. Xiao [36] found that, in artificial forests in arid regions, an increase in tree density led to changes in soil microbial biomass and diversity, which is consistent with the results of this study that P. sylvestris var. mongolica plantations of different densities affected soil microbial community structure. However, there were some differences in the results of some studies [37]. These differences may be due to different climatic conditions, initial soil conditions, and tree species characteristics in the study areas [38]. In addition, the understorey vegetation is also considered a major driver influencing microbial communities. Different stand densities affect the growth of understorey vegetation. As stand density increases, its species richness, diversity, and biomass may change, typically increasing at optimal densities. However, in some degraded ecosystems, understorey vegetation growth is restricted due to competition for light, water, and nutrients with trees. The understorey vegetation indirectly affects soil microbial community composition and function by influencing soil nutrient cycling, structure, and microclimate. In summary, this study revealed the significant impact of P. sylvestris var. mongolica plantations of different densities on the soil microbial community structure in the Mu Us Sandy Land and the close relationship with soil nutrients. Although there were some differences from the results of some studies, these findings provided an important basis for further understanding the interactions among vegetation, soil, and microorganisms in sandy land ecosystems and for the rational management of P. sylvestris var. mongolica plantations.

4.3. Impact of Soil Nutrients on Soil Microorganisms

Soil nutrients were closely associated with bacterial communities. In the RDA analysis, the arrows of these nutrient factors were close to some sample points, with the arrows of TP and TN being long and in the same direction, indicating that they had a greater impact on bacterial community structure and a synergistic effect. High nutrient content provided sufficient nutrients for bacteria, and bacteria involved in nitrogen and phosphorus cycling grew well in environments rich in nitrogen and phosphorus, affecting bacterial community structure. In a study of agricultural ecosystems, it was found that the application of nitrogen and phosphorus fertilizers changed the composition of soil bacterial communities and increased the abundance of bacteria related to nitrogen and phosphorus transformation [39]. The arrow of pH value had a different impact on bacterial community structure, with its arrow direction having a larger angle with other nutrient factor arrows. pH value affected the soil chemical environment and indirectly acted on bacterial communities by affecting the solubility and availability of soil nutrients. Different bacteria have distinct pH adaptation ranges, and extreme pH values can inhibit the growth of some bacteria [40]. In this study, the soil pH values in CK and LD differ, affecting the composition of soil microbial communities. For instance, in CK, alkaliphilic bacteria like Bacillus and Pseudomonas, which can survive in high-pH environments and perform ecological functions, may thrive. In LD, the soil pH is closer to neutral or slightly acidic, favoring the survival of acidophilic bacteria such as Streptomyces and Azotobacter. The survival and reproduction of these acidophilic and alkaliphilic bacteria alter the overall composition of the soil microbial community, impacting the function and stability of the soil ecosystem. Some studies have shown that, in acidic soils, the relative abundance of acidophilic bacteria such as Acidobacteriota is higher. In the CCA analysis of fungal communities and soil nutrients, soil TK had a significant impact on fungal community structure. Potassium elements in the soil are involved in various physiological processes of fungi, affecting their growth, reproduction, and metabolism. For example, an appropriate amount of potassium can enhance the stability of fungal cell walls and improve their resistance to environmental stress, thereby affecting the composition and distribution of fungal communities [41]. Soil TP, TN, and SOM also had an impact on fungal communities. These nutrients are the material basis for fungal growth and metabolism, and changes in their content affect fungal nutrient acquisition and niche competition, thereby changing fungal community structure [42]. For example, high organic matter content in the soil provides a rich carbon source for saprophytic fungi, promoting their growth and reproduction.
The impact of soil nutrients on soil microorganisms mainly stems from the high dependence of microorganisms on their living environment [43]. Soil nutrients are essential for microbial growth and metabolism. Different microbial groups have varying nutrient requirements and utilization capabilities. Changes in nutrient content and ratios can alter microbial community structures. In different density forests, soil nutrient differences affect soil microbial community composition [44]. In HD forests, fierce soil nutrient competition may lead to nutrient depletion and imbalance. This favors microbes that efficiently use limited nutrients or fix nitrogen. In MD forests, relatively balanced soil nutrients support diverse microbial communities. LD forests have less competition, better soil conditions, and more organic matter decomposition, allowing for a wider range of microbes to thrive. In contrast, CK has poor soil nutrients, with only a few stress-tolerant microbes able to survive. Soil physicochemical properties such as pH value affect the survival environment of microorganisms, such as enzyme activity and cell membrane permeability, thereby affecting microbial growth and reproduction. Most studies have shown that soil physicochemical properties have a significant impact on soil microbial community structure, but there are differences in the degree and manner of impact [45]. For example, some studies have found that soil organic matter and nitrogen content are the main factors affecting bacterial and fungal community structures in forest ecosystems, which is similar to the results of this study [46,47]. However, other studies have pointed out that, in some grassland ecosystems, soil water content has a more significant impact on microbial community structure than nutrients and pH value, which is different from the results of this study. This may be due to differences in ecosystem types, climatic conditions, and soil textures in the study areas [48]. In summary, soil nutrients had a significant impact on the soil microbial community structure of P. sylvestris var. mongolica plantations of different densities in the Mu Us Sandy Land. High-density and medium-density plantations significantly increased the diversity of bacteria and fungi by increasing soil nutrient content.

5. Conclusions

This study thoroughly explored the relationship between soil microbial communities and soil nutrients in P. sylvestris var. mongolica plantations of different densities in the Mu Us Sandy Land, and the following main conclusions were drawn: 1. The planting density of P. sylvestris var. mongolica significantly affected soil nutrients. Medium-density plantations were the most effective in increasing soil organic matter, total nitrogen, and total phosphorus content, with little difference in total potassium content and pH value among different densities. Rational planting density is conducive to improving soil fertility. 2. High-density and medium-density P. sylvestris var. mongolica plantations significantly increased the diversity of soil bacteria and fungi by increasing soil nutrient content, while low-density plantations and bare sandy land controls had lower soil microbial diversity. 3. Soil organic matter, total nitrogen, total phosphorus, and pH value were the main factors affecting soil microbial community structure. High-density and medium-density P. sylvestris var. mongolica plantations promoted the growth and diversity of soil microorganisms by improving these soil nutrients. This study revealed the complex relationship between P. sylvestris var. mongolica plantation density, soil nutrients, and microbial communities in the Mu Us Sandy Land (Figure 8), providing a scientific basis for vegetation restoration and sustainable management of sandy land ecosystems.

Author Contributions

Conceptualization, L.H. and M.Z.; methodology, L.H. and L.L.; software, K.Z. and F.L.; validation, L.H. and K.Z.; formal analysis, G.H. and Z.L. (Zihao Li); investigation, K.Z., L.L., and F.L.; resources, L.H., M.Z., and G.H.; data curation, K.Z. and L.H.; writing—original draft preparation, K.Z. and L.H.; review and editing, K.Z. and L.H.; visualization, K.Z.; supervision, M.Z. and K.Z.; project administration, L.H., Z.L. (Zhuofan Li) and X.G.; funding acquisition, L.H. and M.Z. All authors have read and agreed to the published version of the manuscript.

Funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was funded by The National Key R & D Program (2022YFF1302503-3) and The National Natural Science Foundation of China Regional Science Foundation Project ‘Study on the Response of Soil Carbon Accumulation and Vegetation Process in Sandy Land during Desertification Reversion’ (41867043).

Data Availability Statement

The data presented in this study are available upon request from the corresponding author or first author. The data are not publicly available due to the fact that the data are obtained from paid experiments.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Changes in soil nutrients in P. sylvestris var. mongolica plantation with different densities. Note: SOM represents soil organic matter, TN represents soil total nitrogen, TP represents soil total phosphorus, and TK represents soil total potassium. HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 1. Changes in soil nutrients in P. sylvestris var. mongolica plantation with different densities. Note: SOM represents soil organic matter, TN represents soil total nitrogen, TP represents soil total phosphorus, and TK represents soil total potassium. HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 2. The relative abundance of soil bacterial (A) and fungal (B) communities at the main phylum level in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 2. The relative abundance of soil bacterial (A) and fungal (B) communities at the main phylum level in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 3. The relative abundance of soil bacterial (A) and fungal (B) communities in different densities of P. sylvestris var. mongolica plantation. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 3. The relative abundance of soil bacterial (A) and fungal (B) communities in different densities of P. sylvestris var. mongolica plantation. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 4. Relative abundance of main genera of soil bacteria (A) and fungi (B) communities in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 4. Relative abundance of main genera of soil bacteria (A) and fungi (B) communities in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 5. Venn diagram of the main OTU levels of soil bacterial (A) and fungal (B) communities in different densities of P. sylvestris var. mongolica plantation. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 5. Venn diagram of the main OTU levels of soil bacterial (A) and fungal (B) communities in different densities of P. sylvestris var. mongolica plantation. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 6. α-diversity index of bacteria (A) and fungi (B) in P. sylvestris var. mongolica plantation with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 6. α-diversity index of bacteria (A) and fungi (B) in P. sylvestris var. mongolica plantation with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
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Figure 7. RDA/CCA analysis of soil bacterial (A) and fungal (B) communities and soil nutrients in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Figure 7. RDA/CCA analysis of soil bacterial (A) and fungal (B) communities and soil nutrients in P. sylvestris var. mongolica plantations with different densities. Note: HD represents high density, MD represents medium density, LD represents low density, and CK represents bare sandy land.
Forests 16 00547 g007
Forests 16 00547 g008
Figure 8. Relationship model between soil microbial community and soil nutrients in different density Pinus sylvestris var. mongolica plantations in Mu Us Sandy Land. With the increase in vegetation density, the content of soil nutrients and the activity of microorganisms also increased correspondingly, indicating that there was a positive correlation between vegetation density and soil nutrients and microorganisms. Note: ‘**’ indicates a significant increase or decrease.
Figure 8. Relationship model between soil microbial community and soil nutrients in different density Pinus sylvestris var. mongolica plantations in Mu Us Sandy Land. With the increase in vegetation density, the content of soil nutrients and the activity of microorganisms also increased correspondingly, indicating that there was a positive correlation between vegetation density and soil nutrients and microorganisms. Note: ‘**’ indicates a significant increase or decrease.
Forests 16 00547 g008
Table 1. Plot information.
Table 1. Plot information.
TypeLongitudeLatitudeElevation/mAge/aDensity/hm2Average Tree Height/m
High Density (HD)109.23906338.8723211269.56936005.8
Medium Density (MD)109.23853538.8718851270.56924005.6
Low Density (LD)109.23810338.8714971268.56918005.3
Bare Sandy (CK)109.29397438.8078761267.04///
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Hai, L.; Zhou, M.; Zhao, K.; Hong, G.; Li, Z.; Liu, L.; Gao, X.; Li, Z.; Li, F. Soil Microbial Communities and Their Relationship with Soil Nutrients in Different Density Pinus sylvestris var. mongolica Plantations in the Mu Us Sandy Land. Forests 2025, 16, 547. https://doi.org/10.3390/f16030547

AMA Style

Hai L, Zhou M, Zhao K, Hong G, Li Z, Liu L, Gao X, Li Z, Li F. Soil Microbial Communities and Their Relationship with Soil Nutrients in Different Density Pinus sylvestris var. mongolica Plantations in the Mu Us Sandy Land. Forests. 2025; 16(3):547. https://doi.org/10.3390/f16030547

Chicago/Turabian Style

Hai, Long, Mei Zhou, Kai Zhao, Guangyu Hong, Zihao Li, Lei Liu, Xiaowei Gao, Zhuofan Li, and Fengzi Li. 2025. "Soil Microbial Communities and Their Relationship with Soil Nutrients in Different Density Pinus sylvestris var. mongolica Plantations in the Mu Us Sandy Land" Forests 16, no. 3: 547. https://doi.org/10.3390/f16030547

APA Style

Hai, L., Zhou, M., Zhao, K., Hong, G., Li, Z., Liu, L., Gao, X., Li, Z., & Li, F. (2025). Soil Microbial Communities and Their Relationship with Soil Nutrients in Different Density Pinus sylvestris var. mongolica Plantations in the Mu Us Sandy Land. Forests, 16(3), 547. https://doi.org/10.3390/f16030547

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