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Article

Short-Term Phosphorus Fertilization Alters Soil Fungal Community in Long-Term Phosphorus-Deprived Yellow Soil Paddy Fields

by
Huan Yang
1,2,
Yehua Yang
1,2,
Huaqing Zhu
1,2,
Han Xiong
1,2,
Yarong Zhang
1,2,
Yanling Liu
1,2,
Xingcheng Huang
1,2,*,
Yu Li
1,2,* and
Taiming Jiang
1,2
1
Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
2
Scientific Observing and Experimental Station of Arable Land Conservation and Agricultural Environment, Ministry of Agriculture, Guiyang 550006, China
*
Authors to whom correspondence should be addressed.
Agriculture 2025, 15(3), 280; https://doi.org/10.3390/agriculture15030280
Submission received: 23 December 2024 / Revised: 21 January 2025 / Accepted: 27 January 2025 / Published: 28 January 2025
(This article belongs to the Section Agricultural Soils)
Browse Figures
Versions Notes

Abstract

:
Phosphorus (P) in soil is important in the process by which soil microbial communities regulate soil enzyme activity. We aim to explore how short-term P fertilization affects the composition and functionality of the soil fungal community, offering insights into the complex responses of soil fungi to fertilization. Soil samples from a long-term experiment with no P fertilization were collected for pot experiments. The pot experiment included four treatments: non-P fertilizer (NK), chemical P fertilizer (NPK), 1/2 organic fertilizer + 1/2 chemical fertilizer (MNP), and organic fertilizer (M). High-throughput sequencing was employed to analyze the composition, diversity, and functionality of soil fungal communities. Results showed that short-term P addition significantly increased the soil fungal Shannon and Pielou e indices, with increases of 34.48%~59.00% and 29.79%~53.19%, respectively. Ascomycota and Basidiomycota were the most abundant fungal phyla, whereas Cladosporium and Emericellopsis were the most abundant genera. The main factors affecting soil fungal community composition were total nitrogen (TN) and organic matter (OM). A linear discriminant analysis effect size (LEfSe) analysis indicated that Mortierellomycota were significantly enriched under the NPK treatment. A FUNGuild analysis revealed that, compared to the NK treatment, the relative abundance of Animal Pathogen–Endophyte–Lichen Parasite–Plant Pathogen–Wood Saprotroph was reduced by 67.54%, 46.93%, and 44.10% under NPK, MNP, and M treatments, respectively. The relative abundance of Plant Pathogen was less than 1% in the NPK and the MNP treatments. These results indicate that short-term P addition increased soil nutrient levels and soil fungal community diversity. Chemical P fertilizer significantly improved the fungal community structure in yellow paddy soils, enhancing beneficial fungi and suppressing pathogens.

1. Introduction

Phosphorus (P) is an essential element for plant growth and plays a crucial role in seed germination, in root development, and in improving crop quality [1,2,3]. The available P in soils is often insufficient to meet the needs of crops for growth [4]. Phosphorus fertilizer can provide the P necessary for crop growth in farmlands, thereby improving crop yield and quality [5,6]. However, during agricultural production in China, the indiscriminate application of P fertilizer often occurs, which has led to an increasingly significant observation of low fertilizer use efficiency at high levels of fertilizer application, which has had a negative impact on the overall health of agricultural ecosystems [7,8]. Therefore, adjusting fertilization strategies and supplementing P to P-deficient soils through different fertilizers is important for elucidating appropriate fertilization methods for soils experiencing long-term P deficiency and guiding agricultural fertilization management practices. Soil fungi, an important group of soil microorganisms, serve as one of the main indicators of soil health and play significant roles in maintaining soil fertility, increasing crop productivity, and driving nutrient cycling [9,10,11]. Fungi decompose some organic matter in soil that is difficult for bacteria to break down, release carbon and nutrients into the soil solution, promote soil organic carbon sequestration, and are important regulators of the soil carbon balance [12]. Therefore, exploring the recovery and improvement of fungal communities and functional groups in soils experiencing long-term P deficiency after a short duration of P fertilizer addition can increase the understanding of the response mechanism of soil fungal communities to fertilization and provide a theoretical basis for fertilization, safe rice production, and the promotion of sustainable soil development in Guizhou yellow paddy soils.
Research has shown that, compared with no fertilization or unbalanced fertilization, balanced fertilization (NPK) can improve microbial community structure and increase microbial diversity [13,14]. Manure significantly increased fungal relative abundance and reduced fungal diversity and species richness. Chemical fertilization has a minimal effect on fungal diversity but significantly increases the relative abundance of pathogenic fungi (Fusarium and Colletotrichum) [15]. Additionally, a 38-year long-term fertilization experiment revealed that organic fertilizer had a more significant effect on bacterial communities than chemical fertilizers did, whereas fungal communities were more sensitive to chemical fertilizer application [16]. Wang [5] reported that P deficiency increased the relative abundance of Ascomycota, whereas P addition increased the relative abundances of Basidiomycota and Mortierellomycota. Compared with chemical fertilizer, a combination of P and organic fertilizers was more effective at increasing the number and diversity of soil fungi. Other studies have shown that chemical fertilizers promote the growth of soil pathogenic fungi, whereas organic fertilizers promote the growth of saprotrophic and mycorrhizal fungi and inhibit soil-borne pathogens [17,18]. These studies indicate that organic fertilizer application and balanced fertilization have positive effects on increasing or maintaining soil microbial community diversity and relative abundance. No fertilization or unbalanced fertilization over the long-term leads to microbial community imbalances, which negatively affect soil health.
Most studies on microbial community responses to fertilization have been focused on bacteria [19,20,21], with less attention given to fungi [22]. Soil fungal communities are typically influenced by soil nutrient status and environmental conditions [23]. Fertilization introduces nutrients that reduce the dependence of the microbial community on plant-derived carbon and activate numerous dormant fungal species. However, chemical fertilizer application may lead to soil acidification and nutrient loss, weakening the plant-microbial network in the soil [24,25]. Some studies suggest that P fertilizers alter soil physicochemical properties (AP, OM, and pH), thereby restructuring rhizosphere fungal communities [5]. Other studies have shown that changes in fungal community structure in alpine meadows and plateau grasslands are more strongly related to soil organic carbon (SOC), nitrogen, and P contents than to soil pH [26,27].
Long-term unbalanced fertilization results in a decrease in soil fertility, reduced crop yield, and diminished microbial diversity. Therefore, improving the fungal community structure in soils under long-term unbalanced fertilization is one of the main issues in soil health research, yet studies on this topic are scarce. Given the important role of fungi in soil functions and ecosystems, as well as the growing concern over the ongoing loss of biodiversity, it is increasingly important to study the impact of short-term P fertilization on soil fungal communities. On the basis of long-term experiments at the Scientific Observation and Experimental Station of the Arable Land Conservation and Agricultural Environment, we focused on paddy soils to investigate the effects of short-term P fertilization on fungal community structure and functional groups in soils with long-term P deficiency. Furthermore, the relationship between fungal community composition and soil properties was analyzed, offering a theoretical foundation for sustainable yellow soil management in Guizhou.

2. Materials and Methods

2.1. Study Site

The study site is located at the Guizhou Agricultural Academy of Scientific Observing and Experimental Station of the Arable Land Conservation and Agricultural Environment (E: 106°39′52″, N: 26°29′49″) in Huaxi District, Guiyang city, Guizhou Province. The experimental area is situated in the yellow soil hilly area of central Guizhou Province, belonging to a subtropical monsoon climate with an average altitude of 1071 m. The average annual temperature in 2021 was 16.2 °C, and the annual rainfall was 1335.6 mm. The soil originates from Triassic limestone and sandstone shale residues, with a soil type classified as Anthrosols formed on yellow soil parent material. The experiment was officially started in 1995. Prior to the experiment, the soil physicochemical properties were measured, revealing a pH of 6.75, with organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkaline nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of 44.50 g·kg−1, 1.96 g·kg−1, 2.30 g·kg−1, 13.8 g·kg−1, 134 mg·kg−1, 13.4 mg·kg−1, and 294 mg·kg−1, respectively.

2.2. Experimental Design

In this study, yellow soil from paddy fields, without long-term P fertilizer treatment, was collected in 2020 for the pot experiments. A pot experiment was conducted with four treatments: (1) non-P fertilizer (NK), (2) chemical P fertilizer (NPK), (3) 1/2 organic fertilizer + 1/2 chemical fertilizer (MNP), and (4) organic fertilizer (M). The experiment was conducted in a randomized complete block design with four replications per treatment and two rice plants planted in 25 kg of soil per pot. Before rice transplanting, phosphorus and potassium fertilizers or organic fertilizers were applied as base fertilizers according to the treatments (Table 1). For the chemical fertilizer treatments, urea was applied twice during the rice growing season. The organic fertilizer used was cow manure (with an average content of C of 10.4%; N, 2.7 g·kg−1; P2O5, 1.3 g·kg−1; and K2O, 6.0 g·kg−1), and the chemical fertilizers used were urea (N, 46%), superphosphate (P2O5, 16%), and potassium chloride (K2O, 60%). In addition to fertilization, other management measures in the pot experiments were consistent.

2.3. Soil Sampling and Measurements

2.3.1. Soil Sample Collection

Soil sampling was conducted after the rice harvest in November 2022. One soil sample was randomly collected from each potted plant, and after visible organic matter, stones, and rice roots were removed, the sample was divided into two parts. A portion of each fresh soil sample was sieved through a 2 mm sieve and then air-dried at room temperature to determine the soil physicochemical properties, while another portion was stored at −80 °C for the subsequent DNA extraction and analysis of fungal community structure.

2.3.2. Determination of Soil Physical and Chemical Properties

The soil pH was measured at a soil/water ratio of 1:2.5, the soil organic matter (OM) content was determined using the potassium dichromate volumetric method, soil total nitrogen (TN) was determined by Kjeldahl nitrogen fixation, available phosphorus (AP) was determined using the Olsen method with a UV–visible spectrophotometer, and available potassium (AK) content was determined using flame photometry [28].

2.3.3. DNA Extraction and Illumina Sequencing

Soil DNA was extracted and tested for concentration and quality following the manufacturer’s instructions (Omega Bio-tek, Norcross, GA, USA). After DNA extraction, the concentration and quality of the DNA were measured using a NanoDrop NC2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and agarose gel electrophoresis. The ITS region of fungal rRNA was amplified using specific primers, ITS1F (5′-CTTGGTCATTTAGGAGATAA3′) and ITS2R (5′-GCTGGTTCTTCATCGATGC-3′). The PCR reaction mixture was prepared, followed by an initial denaturation at 95 °C for 3 min, followed by 27 cycles of amplification. Each cycle began with denaturation at 95 °C for 30 s, followed by annealing at 55 °C for 30 s, and extension at 72 °C for 45 s, to synthesize DNA. The amplified product was analyzed using 2% agarose gel electrophoresis, and the target fragment was excised, and purified with the PCR Clean-Up Kit (YuHua, Shanghai, China) as per the manufacturer’s instructions. DNA concentration was measured with a Qubit 4.0 (Thermo Fisher Scientific, USA). Majorbio Bio-Pharm Technology Co. Ltd.’s (Shanghai, China) Illumina MiSeq high-throughput sequencing platform was used to sequence the amplified products and complete library construction.

2.4. Statistical Analysis

A soil bioinformatics analysis was performed using the Majorbio Cloud platform (https://cloud.majorbio.com, accessed 20 September 2024). The statistical analysis was conducted using SPSS software (SPSS Inc., Chicago, IL, USA), and one-way ANOVA was used to calculate significant differences in soil physicochemical properties and alpha diversity indices under the different fertilization conditions (LSD test, p < 0.05 for significant differences, p < 0.01 for highly significant differences). A principal component analysis (PCA) and redundancy analysis (RDA) were conducted using Canoco 5.0. PCA was used to determine the beta diversity of fungal communities, whereas RDA was used to determine the relationships between soil properties and fungal community structure. The identification of significantly enriched soil fungal communities under different fertilization treatments used the linear discriminant analysis effect size (LEfSe) method [29]. FunGuild prediction [30] was used to analyze the functional classification and abundance of fungi under different fertilization treatments.

3. Results

3.1. Changes in Soil Physicochemical Properties After Phosphorus Fertilization

Compared with the NK treatment, the M and MNP treatments significantly increased the soil pH by 1.83% and 1.98%, respectively (Table 2). The highest OM content was observed under the M treatment at 46.63 g·kg−1, which was significantly greater than that under the NK treatment at 27.06%, the NPK treatment at 25.59%, and the MNP treatment at 19.87%. The TN content in the soil under the M treatment was 2.01 g·kg−1, which was significantly greater than that under the NK treatment by 5.24%. The AP content in each treatment was as follows: MNP > M > NPK > NK. There was no significant difference between the M and NPK treatments. Compared with that under the NK treatment, the AK content under the MNP and M treatments was significantly lower (by 21.75% and 34.21%, respectively).

3.2. Effect of Phosphorus Fertilizer on Soil Fungal α-Diversity Indices

On the basis of the sequencing results, we analyzed the Chao1 index, Shannon index, Simpson index, and Pielou e index of soil fungi. Compared with those in the NK treatment, the Shannon index and Pielou e index of soil fungi significantly increased after the short-term addition of P fertilizer, increasing by 34.48%~59.00% and 29.79%~53.19%, respectively. The Chao1 index significantly increased by 18.82% and 19.19% in the MNP and M treatments, respectively, compared to the NK treatment. The soil fungal Simpson index was the lowest under the NPK treatment, significantly lower than that under the NK treatment at 78.95%, and there was no significant difference compared with those under the MNP and M treatments (Table 3).

3.3. Effect of Phosphorus Fertilizer on Soil Fungal Community Composition

We compared the soil fungal community composition at the phylum and genus levels after adding different P fertilizers. In this study, there were 4 fungal phyla and 16 fungal genera with relative abundances > 1%. Ascomycota was the most abundant fungal phylum, accounting for 61.43%~84.26% of the whole fungal community (Figure 1a). Compared with those in the NK treatment, the relative abundance of Ascomycota decreased by 13.16%, 27.09%, and 18.53% in the NPK, MNP, and M treatments, respectively. The relative abundances of Basidiomycota, Chytridiomycota, and Rozellomycota were 12.29%~29.01%, 0.39%~1.63%, and 0.20%~1.33%, respectively. Compared with those in the NK treatment, the relative abundances of three soil fungal phyla increased in the MNP and M treatments. Among the top 16 genera with relatively high abundances, Cladosporium and Emericellopsis had the highest relative abundances, ranging from 17.34% to 53.42% and 5.94% to 13.62%, respectively (Figure 1b). The relative abundance of Vishniacozyma was highest at 13.86% in the MNP treatment and lowest at 1.48% in the NPK treatment. The relative abundance of Arrhenia under the NK treatment was 1.98%, whereas the relative abundance of Ceratorhiza under the M treatment was 5.62%. Compared with that under the NK treatment, the relative abundance of Fusarium under the organic fertilizer treatments (MNP and M) decreased by 34.54% and 41.36%, respectively.
PCA revealed that the first two principal component axes explained 37.57% and 23.88% of the variation in fungal communities at the phylum level (Figure 2a) and 25.77% and 9.07% of the variation at the genus level (Figure 2b), respectively. The fungal communities were significantly different at the phylum level between the NK and NPK treatments. The fungal communities were significantly different at the genus level among the NPK, NK, and MNP treatments.

3.4. Response of Specific Fungal Groups to Different Phosphorus Fertilizers

The soil fungal communities were analyzed by LEfSe from the phylum to the genus level to determine the fungal taxa significantly enriched in the soil after the addition of different P fertilizers. The results revealed that there were 51 significantly enriched fungal groups in the different fertilization treatments, with the highest number of significantly enriched fungal groups (36) in the NPK treatment and the lowest number of significantly enriched fungal groups (4) in the NK and MNP treatments (Figure 3). Only soil fungi under the NPK treatment, namely, Mortierellomycota, were significantly enriched at the phylum level. Glomerellales were significantly enriched at the order level, Plectosphaerelaceae were significantly enriched at the family level, and Chordomyces and Gibellulosis were significantly enriched at the genus level in the NK treatment. Chaetomiaceae were significantly enriched at the family level in the MNP treatment, whereas Hannella, Stachybotrys, and Coprinellus were significantly enriched at the genus level. In the M treatment, Orbiliomycetes, Orbiliales, Orbiliaceae, Microasciale, Microascaceae, Seudomonas, and Duddingtonia were significantly enriched.

3.5. Functional Prediction of Soil Fungal Community

We used the fungal classification tool FunGuild to assign fungal OTUs to specific nutritional groups under different treatments and then further subdivided them into specific functional groups. The analysis revealed 11 fungal functional groups with a relative abundance > 1%, among which the functional group with the highest relative abundance was the Animal Pathogen–Endophyte–Lichen Parasite–Plant Pathogen–Wood Saprotroph. Compared with those under the NK treatment, the relative abundances of Animal Pathogen–Endophyte–Lichen Parasite–Plant Pathogen–Wood Saprotroph decreased by 67.54%, 46.93%, and 44.10%, respectively, under the NPK, MNP, and M treatments (Figure 4). The relative abundances of Undefined Saprotroph under the NK, NPK, MNP, and M treatments were 16.92%, 36.18%, 20.82%, and 25.35%, respectively. The relative abundance of Fungal Parasite–Undefined Saprotroph was highest at 23.35% in the MNP treatment and lowest at 3.22% in the NPK treatment. The relative abundance of Plant Pathogen was 5.84% in the M treatment, 1.65% in the NK treatment, and <1% in the NPK and MNP treatments. Compared with that under the NK treatment, the relative abundance of Dung Saprotroph–Ectomycorrhizal–Soil Saprotroph–Wood Saprotroph increased by 194.67%, 188.00%, and 284.00% under the NPK, MNP, and M treatments, respectively.

3.6. Relationships Between Soil Fungal Community Composition and Soil Physicochemical Properties

The redundancy analysis (RDA) was used to investigate the relationships between soil fungal communities and soil physicochemical properties at the phylum level. The results revealed that the explanatory power of the first and second axes in the redundancy analysis at the phylum level was 30.78% and 3.47%, respectively, indicating that soil physicochemical properties contributed to the differences in soil fungal communities. Soil organic matter (OM, R2 = 0.4346, p = 0.02) and total nitrogen (TN, R2 = 0.4357, p = 0.031) were the main factors influencing fungal community composition (Figure 5a). The relative abundances of Ascomycota and Basidiomycota were closely related to the angle between OM and TN, indicating a significant negative correlation (Figure 5b).

4. Discussion

4.1. The Addition of Phosphorus Fertilizer Can Increase Soil Fungal Diversity

Microbial diversity is often regarded as one of the factors required for the sustainable operation of soil systems and is closely related to soil ecosystem function, stability, and resilience [31,32]. Our results revealed that, compared with those in the NK treatment, the Shannon index and Pielou e index of soil fungi significantly increased after the short-term addition of P fertilizer. The Chao1 index significantly increased in response to the addition of organic fertilizer (MNP and M) (Table 3). These findings indicate that short-term P fertilization not only alleviates phosphorus limitation but may also enhance fungal community diversity and richness by improving the soil environment. Soil fungal richness responds more strongly to organic fertilizers than to chemical fertilizers. In P-deficient soils, adding organic fertilizers can effectively increase fungal richness, as they provide additional carbon and nutrients, improving the soil microenvironment [33,34]. Studies show that soil fungal activity is closely linked to carbon availability. In long-term P-deficient soils, organic fertilization activates more microbial populations that utilize the carbon and nutrients in the organic fertilizers, significantly increasing fungal community richness [35,36,37].

4.2. The Addition of Chemical Phosphorus Fertilizer Significantly Improved the Fungal Community Structure

The dominant phyla of soil fungi in the different treatments included mainly Ascomycota and Basidiomycota (Figure 1a). The relative abundance of Ascomycota was lower after the application of P fertilizer than in the treatment without P fertilizer, indicating that Ascomycota is more sensitive to a soil P deficiency response. This finding is consistent with a long-term study by Wang [3]. In contrast to the decrease in Ascomycota abundance, Basidiomycota presented an increase in relative abundance following P fertilization. Previous studies have indicated that nutrient limitation creates a competitive relationship between Ascomycota and Basidiomycota, leading to a negative correlation in their relative abundances [38].
The principal component analysis (PCA) revealed the significant separation of fungal communities at the phylum and genus levels between the NK and NPK treatments (Figure 2), indicating that the application of chemical P fertilizer plays a significant role in altering the fungal community structure in yellow paddy soil. This may be due to the simple and unstable structure of fungal communities in long-term P-deficient soils. Chemical P fertilizer addition disrupts the original ecological balance, introducing new material and energy inputs [39]. Different fungal taxa respond differently to phosphorus; some phosphorus-sensitive taxa that efficiently utilize phosphorus proliferate rapidly, while others are suppressed, leading to significant changes in fungal communities at the phylum and genus levels [40].
The LEfSe analysis further revealed that the fungi enriched in the NPK treatment were mostly beneficial species (Figure 3), such as Trichoderma, an important biocontrol fungus that suppresses soil pathogens by secreting antibiotics or competitively excluding them [41]. Additionally, Mortierella, a phosphate-solubilizing fungus, can convert insoluble phosphorus compounds into plant-available soluble phosphorus, improving the phosphorus supply to the soil, and may also have potential for the biocontrol of Plant Pathogens [42]. Orbiliomycetes, which were enriched under the M treatment, play a significant role in soil health, as studies suggest that Orbiliomycetes contribute to the decomposition of organic matter and affect soil health and plant growth [43]. However, fungi such as Stachybotrys in the MNP treatment group and Pseudallescheria in the M treatment group may be associated with plant diseases. Stachybotrys can inhibit root development by producing mycotoxins, increasing the susceptibility of plants to other pathogens by affecting their stress resistance [44]. Pseudallescheria can damage plant cell structures by secreting specific enzymes and toxins, and it can spread rapidly in waterlogged paddy soils [45,46].
Saprophytic fungi are the main decomposers in soil, vital for breaking down organic matter [47]. Pathogenic fungi obtain nutrients by destroying host cells, which has a negative effect on plant growth [48,49]. In this study, the short-term addition of P fertilizer reduced the relative abundance of Animal Pathogen–Endophyte–Lichen Parasite–Plant Pathogen–Wood Saprotroph, while increasing the relative abundance of Dung Saprotroph–Ectomycorrhizal–Soil Saprotroph–Wood Saprotroph (Figure 4). These findings indicate that alleviating P limitation in paddy soil can inhibit the growth of pathogenic fungi in the soil, promote the growth of saprophytic fungi, and improve fungal community structure. These findings are consistent with those of a 9-year P addition experiment by Li [50]. A further comparison among the different P fertilizer treatments revealed that the relative abundance of pathogenic fungi was the lowest under the NPK treatment, while the relative abundance of Fungal Parasite–Undefined Saprotroph was the highest under the MNP treatment, and the relative abundance of Plant Pathogen was the highest under the M treatment. This may be due to the significant enrichment of the pathogenic antagonistic fungus Mortierella under the NPK treatment, which can provide P sources for beneficial microorganisms while inhibiting the growth of pathogenic fungi [51,52]. On the other hand, both mycorrhizal fungi and pathogenic fungi require nutrients for growth. The increase in nutrient input from organic fertilizers may be conducive to promoting the growth of pathogenic fungi, and the increase in pathogenic fungi may also be due to the introduction of exogenous organic fertilizers [22,53].

4.3. Soil Total Nitrogen and Organic Matter Contents Are Key Factors Affecting the Composition of Fungal Communities

The redundancy analysis (RDA) based on soil fungal community composition and physicochemical properties showed that P fertilization significantly altered TN and OM contents, indirectly reshaping the fungal community structure. Liu [34] also reached similar conclusions, further highlighting the complex interactions between nutrient availability and fungal community dynamics. An in-depth analysis revealed that Ascomycota and Basidiomycota were significantly negatively correlated with TN and OM contents (p < 0.05), a phenomenon likely driven by multiple mechanisms. On one hand, a nitrogen surplus may alter the competitive dynamics of soil microbial communities [54]. Under nitrogen-rich conditions, Ascomycota and Basidiomycota may be at a competitive disadvantage, leading to their decreased abundance. On the other hand, high nitrogen levels could favor fungal groups that can effectively utilize nitrogen sources, suppressing the growth of Ascomycota and Basidiomycota that rely on other nutrients, thus changing the overall fungal community structure [55]. OM content, as an important factor affecting fungal communities, also exerts a complex influence. Higher OM content provides abundant carbon sources for soil microbes, which generally supports a more diverse fungal community [56]. However, excessive OM might disrupt nutrient cycling, affecting the composition of fungal communities such as Ascomycota and Basidiomycota [57].
Ye [38] reported that fertilization altered fungal community structure by modifying soil pH. However, our study revealed only minor pH variations (0.01–0.13) across different treatments, and fungal community composition was weakly influenced by pH, possibly due to the broader optimal pH range for fungal growth [58]. Short-term P fertilization alleviated P limitation, but the correlation between the AP content and fungal community composition was not significant. This may occur because the growth of certain fungal communities is more dependent on the contents of other nutrients, such as nitrogen and carbon [10]. Additionally, fungal communities may utilize difficult-to-absorb P sources in soil through different mechanisms (such as the secretion of extracellular enzymes), which are not directly related to the soil AP content [59]. Therefore, the impact of P fertilization on fungal communities not only involves direct changes in nutrient content but may also alter the soil microbial community structure and function through complex ecological mechanisms.
Short-term P fertilization not only improved soil fungal community structure but also promoted soil health by activating beneficial microbes and suppressing pathogens. This finding provides valuable insights for soil management strategies, especially in P-deficient soils, where proper P application can enhance soil fertility and support ecosystem stability and restoration. Future research should explore the long-term impacts of different fertilization strategies on microbial communities and how to optimize the role of beneficial microbes to develop more sustainable soil management practices.

5. Conclusions

The short-term application of P fertilizer significantly increases the Shannon index and Pielou e index of soil fungal communities, with organic fertilizer further increasing the fungal Chao1 index. Ascomycota and Basidiomycota were the dominant fungal phyla in yellow paddy soil. Under chemical P fertilizer application, Mortierellomycota were significantly enriched, whereas the relative abundance of pathogenic fungi decreased significantly. In addition, the RDA results revealed that soil TN and OM are important factors for predicting changes in soil fungal community composition. These findings suggest that short-term chemical P fertilization in P-deficient soil is more effective than organic fertilizer application in regulating both beneficial and pathogenic fungi, offering new insights into soil management for sustainable crop production.

Author Contributions

Conceptualization: H.Y., Y.Y., X.H., Y.L. (Yu Li) and T.J.; methodology: H.Y. and X.H.; software: H.Y., Y.L. (Yanling Liu) and Y.Y.; validation: X.H., H.Z., Y.L. (Yanling Liu), Y.Z. and Y.L. (Yu Li); formal analysis: H.Y., Y.L. (Yanling Liu) and Y.Y., writing—original draft preparation: H.Y.; writing—review and editing: Y.Y., H.Z., H.X., Y.L. (Yanling Liu), Y.Z. and Y.L. (Yu Li); supervision: X.H., Y.Y. and Y.L. (Yu Li); project administration: H.Y.; funding acquisition: X.H., Y.Y., Y.L. (Yanling Liu) and Y.L. (Yu Li); data collection: H.Z., H.X. and Y.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Key R&D Program (2024YFD1900105-04); the Science and Technology Innovation Special Project of the Guizhou Academy of Agricultural Sciences ([2022]09); the Germplasm Resource Special Project of the Guizhou Academy of Agricultural Sciences ([2023]12); the Science and Technology Innovation Special Project of the Guizhou Academy of Agricultural Sciences ([2023]13); the Youth Science and Technology Fund of the Guizhou Academy of Agricultural Sciences ([2022]20); and the Research and Development Fund Project of the Guizhou Institute of Soil and Fertilizer ([2022]12).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The data used in this study can be obtained from the corresponding author upon reasonable request.

Conflicts of Interest

The authors declare that there is no conflict of interest.

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Agriculture 15 00280 g001
Figure 1. Relative abundances of soil fungi at the phylum (a) and genus (b) levels. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Figure 1. Relative abundances of soil fungi at the phylum (a) and genus (b) levels. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Agriculture 15 00280 g002
Figure 2. The principal component analysis (PCA) of soil fungi at the phylum (a) and genus (b) levels. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Figure 2. The principal component analysis (PCA) of soil fungi at the phylum (a) and genus (b) levels. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Agriculture 15 00280 g003
Figure 3. The LEfSe analysis of the soil fungal communities. Only taxa meeting an LDA significance threshold of 2 for fungal communities are shown. The five rings of the cladogram represent phyla (innermost), classes, orders, families, and genera (outermost). NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Figure 3. The LEfSe analysis of the soil fungal communities. Only taxa meeting an LDA significance threshold of 2 for fungal communities are shown. The five rings of the cladogram represent phyla (innermost), classes, orders, families, and genera (outermost). NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Figure 4. FUNGuild function prediction of soil fungal communities. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Figure 4. FUNGuild function prediction of soil fungal communities. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Agriculture 15 00280 g005
Figure 5. The redundancy analysis of soil physicochemical properties in relation to different sample groups (a) and fungal phyla (b). OM, organic matter; TN, total N; AP, available P; AK, available K. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Figure 5. The redundancy analysis of soil physicochemical properties in relation to different sample groups (a) and fungal phyla (b). OM, organic matter; TN, total N; AP, available P; AK, available K. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Table 1. Different experimental treatments and annual fertilizer amounts.
Table 1. Different experimental treatments and annual fertilizer amounts.
TreatmentManure (g·pot−1)Total Nutrient Content (g·pot−1)
NP2O5K2O
NK0.001.600.000.80
NPK0.001.600.800.80
MNP296.301.600.791.78
M592.591.600.773.56
Note: NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Table 2. Soil physicochemical properties.
Table 2. Soil physicochemical properties.
TreatmentpHOM (g·kg−1)TN (g·kg−1)AP (mg·kg−1)AK (mg·kg−1)
NK6.56 ± 0.02 b36.70 ± 1.38 b1.91 ± 0.02 b8.13 ± 0.31 c361.00 ± 8.58 a
NPK6.57 ± 0.01 b37.13 ± 2.57 b1.96 ± 0.05 ab9.15 ± 0.37 b351.50 ± 12.46 a
MNP6.69± 0.01 a38.90 ± 1.74 b2.00 ± 0.01 ab10.47 ± 0.32 a282.50 ± 12.08 b
M6.68 ± 0.02 a46.63 ± 1.15 a2.01 ± 0.04 a9.34 ± 0.16 b237.50 ± 11.59 c
Note: Different lowercase letters in the same column represent significant differences between treatments (p < 0.05) based on the one-way ANOVA. OM, organic matter; TN, total N; AP, available P; AK, available K. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
Table 3. Soil fungi α-diversity index.
Table 3. Soil fungi α-diversity index.
TreatmentChao1 IndexShannon IndexSimpson IndexPielou e Index
NK300.36 ± 15.46 b2.61 ± 0.41 b0.19 ± 0.06 a0.47 ± 0.07 b
NPK318.42 ± 8.92 ab4.15 ± 0.02 a0.04 ± 0.00 b0.72 ± 0.01 a
MNP356.88 ± 7.56 a3.60 ± 0.22 a0.09 ± 0.02 ab0.62 ± 0.04 a
M357.99 ± 20.50 a3.51 ± 0.21 a0.09 ± 0.02 ab0.61 ± 0.04 a
Note: Different lowercase letters in the same column represent significant differences between treatments (p < 0.05) based on the one-way ANOVA. NK, non-P fertilizer; NPK, chemical P fertilizer; MNP, 1/2 organic fertilizer + 1/2 chemical fertilizer; M, organic fertilizer.
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Yang, H.; Yang, Y.; Zhu, H.; Xiong, H.; Zhang, Y.; Liu, Y.; Huang, X.; Li, Y.; Jiang, T. Short-Term Phosphorus Fertilization Alters Soil Fungal Community in Long-Term Phosphorus-Deprived Yellow Soil Paddy Fields. Agriculture 2025, 15, 280. https://doi.org/10.3390/agriculture15030280

AMA Style

Yang H, Yang Y, Zhu H, Xiong H, Zhang Y, Liu Y, Huang X, Li Y, Jiang T. Short-Term Phosphorus Fertilization Alters Soil Fungal Community in Long-Term Phosphorus-Deprived Yellow Soil Paddy Fields. Agriculture. 2025; 15(3):280. https://doi.org/10.3390/agriculture15030280

Chicago/Turabian Style

Yang, Huan, Yehua Yang, Huaqing Zhu, Han Xiong, Yarong Zhang, Yanling Liu, Xingcheng Huang, Yu Li, and Taiming Jiang. 2025. "Short-Term Phosphorus Fertilization Alters Soil Fungal Community in Long-Term Phosphorus-Deprived Yellow Soil Paddy Fields" Agriculture 15, no. 3: 280. https://doi.org/10.3390/agriculture15030280

APA Style

Yang, H., Yang, Y., Zhu, H., Xiong, H., Zhang, Y., Liu, Y., Huang, X., Li, Y., & Jiang, T. (2025). Short-Term Phosphorus Fertilization Alters Soil Fungal Community in Long-Term Phosphorus-Deprived Yellow Soil Paddy Fields. Agriculture, 15(3), 280. https://doi.org/10.3390/agriculture15030280

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