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Article

Soil Acidification Alters Phosphorus Fractions and phoD-Harboring Microbial Communities in Tea Plantation Soils, Thus Affecting Tea Yield and Quality

by
Shunxian Lin
1,
Tingting Wang
2,
Junfeng Zheng
1,
Weiwei Lin
1,
Xiaoli Jia
3,
Qi Zhang
3,
Yulin Wang
2,
Jianghua Ye
3,* and
Haibin Wang
2,*
1
College of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou 363000, China
2
College of Life Science, Longyan University, Longyan 364012, China
3
College of Tea and Food Science, Wuyi University, Wuyishan 354300, China
*
Authors to whom correspondence should be addressed.
Horticulturae 2025, 11(10), 1191; https://doi.org/10.3390/horticulturae11101191
Submission received: 23 July 2025 / Revised: 12 September 2025 / Accepted: 18 September 2025 / Published: 3 October 2025
(This article belongs to the Special Issue Abiotic Stress Tolerance and Breeding Strategies in Tea Plants)
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Abstract

The effects of soil acidification on the phoD-harboring microbial community and the fractions of soil phosphorus in tea plantation soils are still unclear. In this study, tea plantations with different soil pH were used as the research object to analyze changes in soil phosphorus fractions, phoD gene abundance, phoD-harboring microbial community composition, and their relationship with tea yield and quality. The results showed that the content of tea polyphenols, caffeine, free amino acids, theanine, and tea yield decreased significantly after acidification. Moreover, the content of total phosphorus in the acidified soil also decreased significantly. Further analysis of soil phosphorus fractions showed that the acidification of the tea plantation soil resulted in a significant decrease in the content of different types of labile and moderately labile phosphorus, whereas the content of non-labile phosphorus exhibited the opposite trend. As the content of soil NaHCO3-Po, NaOH-Po, Resin-Pi, NaHCO3-Pi, NaOH-Pi, and HCl-Pi decreased significantly after acidification, its organic and inorganic phosphorus content also decreased significantly. Its phosphorus activation capacity decreased by 4.75% after soil acidification. Soil acidification significantly reduced the diversity of phoD-harboring microbial communities by 61.89%. Analysis of the phoD-harboring microbial community composition suggested that the microbial abundance of Acidobacteria and Proteobacteria showed a decreasing trend in acidified soils, while for Nitrospirae, Verrucomicrobia, Actinobacteria, and Planctomycetes, it showed an increasing trend. Correlation analysis showed that microorganisms with significantly decreasing abundance in tea plantation soils were significantly and positively correlated with soil pH, labile phosphorus, moderately labile phosphorus, phosphorus activation coefficients, and tea yield and quality after soil acidification. It is evident that soil acidification inhibited soil phosphorus availability by shifting phoD-harboring microbial community composition in tea plantation soils, thus affecting the yield and quality of above-ground tea leaves.

1. Introduction

Tea tree (Camellia sinensis) is an important cash crop grown in many tropical and subtropical countries that plays an important role in promoting agricultural development [1]. According to the statistics of the International Tea Committee (ITC), the world tea planting area reached 5.097 million hectares in 2023, which was 1.257 million hectares more than that in 2010, with a compound annual growth rate of 2.7% [1]. Moreover, with the rapid development of the tea industry, it is also facing the problem of increasingly serious soil acidification in tea plantations [2]. The above situation is mainly due to the fact that people, in order to increase tea production, have been applying nitrogen fertilizers for a long time and in large quantities, rarely applying organic fertilizers in fixed quantities, and not paying attention to the balanced ratio of other elements. Tea tree is an acidophilic crop, and its suitable soil pH is between 4.5 and 5.5 [1,2]. Yan et al. [3] conducted a study on the main tea-producing areas in China and found that 46.0% of the producing areas had soil pH < 4.5, and only 43.9% of the soils had a pH of 4.5 ~ 5.5, which is suitable for the normal growth of tea trees [3]. Over the past 20 to 30 years, the degree of soil acidification in tea gardens has far exceeded that of fruit, vegetable systems, and grains [3]. Increasing soil acidification has threatened the sustainability of tea plantations.
Soil acidification leads to deficiency of phosphorus, potassium, and magnesium in tea plantation soils [4]. Among them, phosphorus (P) is one of the important nutrients required by plants and an essential macronutrient for tea tree metabolism. Previous studies have shown that the lack of P seriously leads to metabolic disorders of tea tree leaves, which affect their yield and quality [5]. Soil P availability is limited in terrestrial ecosystems, probably because most P is usually present in the form unavailable to living organisms [6]. Soil P mainly consists of organic phosphorus (Po) and inorganic phosphorus (Pi) [6,7]. In general, organic P accounts for 30–65% of total soil P, occasionally up to 90%, and its mobility in soil is greater than inorganic P, which can be decomposed and converted into available P through the mineralization process of soil microorganisms and enzymes [8]. Soil P fractions also can be categorized into three groups: labile P, moderately labile P, and non-labile P. Among them, labile P is accessible to plants, especially Resin-P and NaHCO3-P, while moderately labile P is an important P source in soil. When soil labile P is deficient, moderately labile P can be converted into the P fraction that is directly utilized by plants [6,9,10].
Microorganisms also play a crucial role in regulating soil P dynamics [11]; especially P-associated soil microorganisms are involved in the biochemical evolution of each form of P [10]. Specifically, they play an important role in the distribution and transformation of soil P form content, and they increase soil-available P content by producing phosphatases to catalyze decomposition reactions or by altering soil pH through their own metabolism to increase water-soluble P [12], which is dependent on population structure and abundance of dephosphorylating microorganisms [13]. The phoD phosphate-dissolving bacteria carrying genes encoding phosphatases are important functional taxa involved in the P cycle, and studies have shown that phoD genes can be used as marker genes for soil organic P transformation [14,15]. Good soil texture and high effective nutrient content are conducive to the growth and reproduction of soil bacteria, thereby increasing the abundance and diversity of the phoD gene [16]. Previous studies indicate that the composition of phoD-harboring microbial communities is regulated through pH, total P, and organic P [6]. Applying chemical fertilizers alone can lead to soil acidification and a decrease in soil P content. However, the combined application of organic and inorganic fertilizers can enrich the phoD-harboring microorganisms, significantly increasing the soil-available P content [17]. Tian et al. found that biochar application under low P conditions promotes organic P mineralization of acid soils by altering the composition of the bacterial phoD gene community; Micromonosporaceae under C-rich and P-poor conditions may play a critical role in potential P mineralization [18].
Numerous scholars have conducted extensive studies on the effects of acidification on rhizosphere soil microorganisms [1,19]. Thus far, studies on the phoD gene have mainly focused on soybean, wheat, maize, etc. [18,20]. Whereas the effects of soil acidification on microorganisms encoded by the phoD gene in tea plantation soils and on the components of soil P are still unknown. Therefore, this study analyzed the changes in soil P fractions, phoD gene abundance, and the composition and structure of encoded microorganisms in tea plantations at different acidity to reveal the effects of soil acidification on soil P fractions and P-solubilizing microorganisms in tea plantations and their interrelations with tea yield and quality. The results of this study provide a theoretical basis for further improvement of soil P recycling in tea plantations, which is of great significance in promoting the sustainable development of tea plantations.

2. Materials and Methods

2.1. Tea Plantation and Sample Collection

The experimental site for this study was located in Nanjing County, Fujian Province, China (24°37′ N, 117°02′ E) (Figure 1). This site has a subtropical monsoon climate, with an altitude of 585 m, an average annual temperature of 21.4 °C, and an average annual precipitation of 1821.1 mm. The site has a haplic arenosol soil with a clay loam texture. The tea tree varieties in the experimental tea plantations were Tieguanyin, and the age of the tea trees was thirteen years. Due to the lack of standardized management of tea plantations in the past few years, some plots that received excessive fertilizer application have experienced soil acidification. Other management measures (weeding, pest control, etc.) were treated the same in this experimental site. Hence, soil and leaves for the experiment were collected from two tea plantations with soil pH ranging from 3.5 to 4.0 (labeled AT) and 4.5–5.0 (labeled MT).
Among them, three plots were taken for each tea plantation; the area of each plot was no less than 40 m2 (4 m × 10 m). For each plot, five tea trees were randomly selected, then the dead leaves and branches on the soil surface were removed, and the main stem of the tea tree was used as the center point to collect soil with a radius of 10 cm and a depth of 15 cm away from the center point, and these soil samples from each plot were thoroughly mixed to form a composite sample, with a total weight of approximately 2000 g per plot, i.e., it was a replication. Three replications were set up from AT and MT. The collected fresh soil was sieved (<2 mm) and divided into two parts; one part was preserved at −80 °C for metagenomic analysis, and the remainder was air-dried for soil physicochemical index determination.

2.2. Soil Chemical Properties and P Fractions Determination

Soil physicochemical indexes were mainly determined as soil pH, total nitrogen, total P, total potassium, total organic carbon, and organic matter. Soil pH was determined by an electrode pH meter (PB-10; Sartorius, Shanghai, China) under a soil–water ratio of 1:2.5 [1]. Total nitrogen and total potassium were determined by Kjeldahl nitrogen fixation and NaOH hydrolysis methods, respectively. The soil was digested with HClO4-H2SO4 to convert organic P and inorganic P into orthophosphate, and then the total P in the soil was determined by the molybdenum–antimony colorimetric method [21]. Soil organic matter was determined by the potassium dichromate–ferrous sulfate titration method. The determination and solution preparation were referred to the method of Lu [22]. The soil physicochemical indexes of each sample were repeated three times.
The content of soil P components was determined by the sequential extraction method [9,10]. As follows, a 0.50 g air-dried soil sample was extracted with distilled water, 0.5 mol/L NaHCO3 (pH 8.5), 0.1 mol/L NaOH, and 1 mol/L HCl to obtain Resin-P, NaHCO3-P, NaOH-P, and HCl-extractable P in both Pi (NaHCO3-Pi, NaOH-Pi, Dil.HCl-Pi, and Conc.HCl-Pi, respectively) and Po (NaHCO3-Po, NaOH-Po, and Conc.HCl-Po, respectively) forms; then, the soil residues were digested with H2SO4 and H2O2 to obtain Residual-Pt (Figure 2). The Pi and Po contents in each fraction were measured as described by Cross et al. [7] and Cao et al. [10]. Based on P availability for crops and microorganisms, soil P was further classified into labile P (LP, including Resin-P, NaHCO3-Pi, and NaHCO3-Po), moderately labile P (MLP, including NaOH-Pi, NaOH-Po, and Dil.HCl-Pi), and non-labile P (NLP, including Conc.HCl-Pi, Conc.HCl-Po, and Residual-P) [10]. The P activation coefficient (PAC) was the ratio of the labile P content to the total P content.

2.3. Determination of Tea Yield and Quality

At the same time as collecting the tea tree soils, the leaves of each tea tree were collected. The bud number in a 0.3 m × 0.3 m iron frame was randomly counted in each tea tree; one bud and two leaves of the tea tree were collected from each tea tree, and one replicate was set up after sufficient mixing, and three replicates were set up for each area. Tea yield per hectare was estimated by the number of buds × the weight of a single bud per unit area. The fresh leaves were then inactivated in an oven at 105 °C for 60 min, then dried at 80 °C to a constant weight, and milled before the experiment.
The tea powder after grinding and sieving was used to determine the quality indicators. The determination of tea polyphenols, caffeine, total free amino acids, and theanine referred to “Technical specification for tea production, processing and safety testing” [23]. Among them, tea polyphenol content was determined by the the Folin-Ciocalteu colorimetric method, caffeine content was determined by ultraviolet spectrophotometry, total free amino acid content was determined by ninhydrin colorimetry and then by visible spectrophotometry, and theanine content was determined by high-performance liquid chromatography. The content of various types of catechins was determined using the high-performance liquid chromatograph (Agilent1280, Agilent Technologies, Inc., Santa Clara, CA, USA) in accordance with “Test Method for the Contents of Tea Polyphenols and Catechins in Tea” (GBT 8313-2008) [23]. Catechins are classified into non-ester catechins and ester catechins. Moreover, non-ester catechins include catechin, epicatechin, gallocatechin, and epigallocatechin; ester catechins include catechin gallate, epicatechin gallate, gallocatechin gallate, and epigallocatechin gallate. Astringency index = ester catechins/total catechins.

2.4. DNA Extraction and Metagenomics Sequencing

The soil DNA was extracted using the Bio-Fast Soil DNA Extraction Kit (BioFlux, Hangzhou, China) following the manufacturer’s instructions with 0.5 g. The DNA quality was then assessed by NanoDrop 200C (Thermo Fisher Scientific, Waltham, MA, USA), and the DNA integrity was detected by 1% agarose gel. Qualified DNA samples were then processed to complete the whole library preparation. After a qualified library inspection, each library was sequenced using the Illumina HiSeq X-ten platform (Illumina, San Diego, CA, USA) with the PE150 strategy.
In order to ensure the accuracy and reliability of the results of the subsequent analysis, the raw data obtained by sequencing on the Illumina sequencing platform were first preprocessed to obtain valid data (clean data). After pre-processing, clean data were obtained and assembled using MEGAHIT assembly software (Version 1.0.4) to select Scaftigs ≥ 300 bp, and then MetaGeneMark was used for ORF prediction to select genes with nucleic acid lengths ≥ 100 bp and translate them into amino acid sequences, and then all predicted gene sequences of the samples were clustered using CD-HIT (V4.5.8). The gene sets were compared with the NR database using BLASP (BLAST Version 2.2.28+5) and the NR database’s corresponding taxonomic information database [24] to obtain annotations of microbial species involved in P cycling-related microorganisms, and then the relative abundance of the species was calculated using the sum of the species’ corresponding gene abundances [25].

2.5. Statistical Analysis

All experimental data were expressed as mean ± standard error (SE). Data differences between samples were analyzed by the t-test using SPSS 21.0 statistical software. The bar chart was produced using Origin Pro 9.0 software. Co-occurrence networks were generated using the igraph package and visualized with the Gephi interactive platform (version 0.9.2). The distribution of phoD-harboring microbial communities in tea tree soils with different acidity at the class level was visualized using Circos software (version 0.69). Rstudio software (version 4.2.3) was used to perform orthogonal partial least squares discriminant analysis (OPLS-DA, ropls, and mixOmics packages), correlation analysis (corrplot program package), principal component plots (PCA), and redundancy analysis (RDA, vegan 2.6.4 program package).

3. Results

3.1. Effect of Soil Acidification on Tea Quality

The effect of soil acidification on tea yield and quality showed (Figure 3) that soil acidification resulted in a significant (p < 0.05) decrease in tea yield and the content of various quality indexes, as evidenced by a 15.24% decrease in tea yield in AT (pH 3.5–4.0) compared to MT tea plantation (pH 4.5–5.0) and a 14.42%, 17.46%, 25.82%, and 3.41% decrease in tea quality indexes such as tea polyphenols, caffeine, free amino acids, and theanine, respectively. Further analysis showed that the astringency index of AT was significantly higher (p < 0.05) than that of ST by 3.46%. It is evident that soil acidification reduced tea yield and quality.

3.2. Effect of Soil Acidification on Soil Chemical Properties

The physicochemical indexes of tea plantation soils with different acidity were shown in Table 1. The soil pH of the tea plantations taken was 3.75 (AT) and 4.74 (MT). Total nitrogen and total phosphorus content of tea plantation soils both showed a significant upward trend with increasing soil pH, while there was no significant difference in total potassium content. Notably, total phosphorus content in MT soil was significantly increased by 21.77% (p < 0.05) compared to acidified tea plantation soil.

3.3. Effect of Soil Acidification on Soil P Fractions

There were differences in the content of P fractions in tea plantation soils with different acidity (Table 2). The labile P content of tea plantation soils with different acidity accounted for 32–37%, moderately labile P accounted for 37–40% of the total, and non-labile P accounted for 23–30% of the total, respectively (Figure 4B). In the specific analysis, the labile P content of acidified tea plantation soil decreased significantly, which was mainly due to its Resin-Pi, NaHCO3-Pi, and NaHCO3-Po content decreasing by 57.79, 26.16, and 25.54%, respectively. The three moderately labile P contents of NaOH-Pi, NaOH-Po, and Dil.HCl-Pi in the acidified tea plantation soil also showed significant (p < 0.05) decreases of 21.52, 21.42, and 27.74%, respectively. For non-labile P, the contents of Conc.HCl-Pi, Conc.HCl-Po, and Residual-P in AT were significantly higher (p < 0.05) than that in MT, making the content of non-labile P in the soil of the acidified tea plantation 301.35 mg/kg (AT), significantly higher than MT (284.28 mg/kg) (Figure 4A). Residual-P content in the acidified tea plantation soil was significantly higher by 8.46%.
Since NaHCO3-Po and NaOH-Po, Resin-Pi, NaHCO3-Pi, NaOH-Pi, and Dil.HCl-Pi in the acidified soil decreased significantly, resulting in a significant decreasing trend in their organic and inorganic P contents (Table 2 and Figure 4) (p < 0.05). The total content of soil organic P in AT decreased by 20.90%, while the organic P content showed a further reduction of 27.59% (Figure 4C). The P activation coefficients of tea plantation soils with different acidity were 32.17% (AT) and 36.92% (MT), respectively, and the P activation capacity of tea plantation soils decreased significantly by 4.75% after acidification (Figure 4D).

3.4. Effect of Soil Acidification on Soil phoD Gene and phoD-Harboring Microbial Community

The response of the phoD gene-encoded microbial community to soil acidification was further investigated. It was found that the abundance of phoD-encoded microorganisms decreased significantly by 61.89% (p < 0.01) after soil acidification (Figure 5A). A total of 256 phoD-harboring microorganisms were detected in all samples, of which 160 were detected in AT and 193 in MT. There were 97 microorganisms shared by AT and MT, accounting for 37.89% of the total microorganisms (Figure 5B). In order to compare the association of microbial communities encoded by phoD in tea plantation soils with different acidity, co-occurrence network analysis was performed. It was found that the AT network consists of 50 nodes and 461 edges, and the MT network consists of 50 nodes and 478 edges (Figure 5C). It can be seen that the relationship of phoD-harboring microorganisms suitable for normal growth of tea trees was more complex than that of acidified soil. Further analysis revealed that all phoD-harboring microorganisms belonged to the bacteria and could be classified into seven phyla, mainly Acidobacteria, Proteobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, etc., and varied among different samples (Figure 5D). Further microbial diversity analysis using NMDS to explore the extent of variation in the complexity of phoD-harboring microbial communities in tea plantation soil indicated that AT and MT were significantly different (NMDS: Stress = 0.00, PERMANOVA, p < 0.01) (Figure 5E). PCA principal component analysis indicated that PC1 and PC2 explained 85.88% of the total variance in microbial community structure, and AT and MT were clearly distinguished as significantly different (Figure 5F). It can be seen that soil acidification had a significant effect on the composition and structure of phoD-harboring microbial communities in tea plantation soils.
The OPLS-DA model was further used to screen for key phoD-harboring microorganisms that could characterize the differences in the samples. The results showed that the model fitted the AT and MT with an R2Y value of 0.913 (p < 0.05) and a predictability Q2 value of 0.999 (p < 0.05) (Figure 6A). It can be seen that the fit of the OPLS-DA model was good and credible for further analysis. The OPLS-DA score plot showed (Figure 6B) that OPLS-DA could effectively distinguish soil samples from tea plantations with different acidity, with 5.45% intra-group and 85.9% inter-group differences. Accordingly, there were significant differences in phoD-harboring microbial communities in rhizosphere soils of tea trees with different acidity and high reproducibility between replicates. Then, S-plot analysis showed that 195 key differential phoD-harboring microorganisms (VIP > 1) were obtained (Figure 6C, Table S1).
The phoD-harboring microorganisms with key differences were categorized and analyzed, removing those that could not be matched (others), and at the phylum level, were classified as Acidobacteria, Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, and Planctomycetes (Figure 6D). Among them, the abundance of Acidobacteria and Proteobacteria showed a decreasing trend in acidified soil, while for Nitrospirae, Verrucomicrobia, Actinobacteria, and Planctomycetes, the abundance showed an increasing trend (p < 0.05). For classification at the class level (Figure 6E), eleven key microorganisms were obtained in which the abundance of Acidobacteriia, α-proteobacteria, and Solibacteres decreased significantly in the acidified tea plantation soil, whereas other microorganisms showed a significant (p < 0.05) increase, such as Nitrospira and γ-proteobacteria. Further classification at the genus level revealed that 28 key genera of microorganisms were obtained (Table S1). The analysis of the top 10 most abundant microbial species at the genus level revealed that the abundance of Candidatus Solibacter, Candidatus Koribacter, Caulobacter, and Acidobacterium showed a significant decreasing trend in the soil of acidified tea plantations, while the abundance of Nitrospira, Terracidiphilus, Silvibacterium, and Sphingomonas showed a significant increasing trend (p < 0.05) (Figure 6F). It is evident that the diversity and structure of phoD-harboring microbial communities in acidified soils changed significantly, which in turn may have affected tea tree growth.

3.5. Relationships of phoD-Harboring Microorganisms with Soil Properties and Quality of Tea

By establishing the correlation between soil pH, P fraction content, tea yield, and tea quality, the results showed (Figure 7) that soil pH was significantly and positively correlated with soil total P, organic P, inorganic P, labile P, moderately labile P, P activation coefficient, phoD gene abundance, and tea yield and quality (p < 0.05), and significantly and negatively correlated with non-labile P and tea astringency index (p < 0.05). It can be seen that soil acidification reduced soil P activation efficiency.
In order to explore the relationship between phoD-harboring key microorganisms and environmental parameters, we conducted a redundancy analysis on phoD-harboring key microorganisms in rhizosphere soil with soil P components, tea growth, and quality indexes. The results showed (Figure 8A) that the phoD-encoded key microbial class and soil physicochemical indexes, tea yield, and quality indexes showed that soil pH, P fractions (total P, organic P, inorganic P, labile P, moderately labile P, P activation coefficients), and phoD gene abundance were significantly (p < 0.05) positively correlated with the abundance of Actinobacteria, α-proteobacteria, and Solibacteres and significantly (p < 0.05) negatively correlated with the abundance of Nitrospira, γ-proteobacteria, Actinobacteria, and Planctomycetia. Redundancy analysis (Figure 8B) of key microbial genera encoded by phoD in tea rhizosphere soils and soil physicochemical indexes, tea yield, and quality indexes showed that soil pH, P fractions (total P, organic P, inorganic P, labile P, moderately labile P, and P activation coefficient), and phoD gene abundance were significantly positively correlated with the abundance of Candidatus Solibacter, Candidatus Koribacter, Caulobacter, Acidobacterium, Rudaea, and Pseudolabrys (p < 0.05) and were significantly negatively correlated with the abundance of Nitrospira, Terracidiphilus, Silvibacterium, and Sphingomonas (p < 0.05). Meanwhile, all microorganisms significantly increased in acidified tea plantation soil were significantly negatively correlated with tea yield and quality (tea polyphenols, caffeine, free amino acids, and theanine). It can be seen that soil acidification caused changes in the structure of phoD-harboring microbial communities, reduced the efficiency of soil P activation, and decreased the content of absorbable and available P, which was detrimental to the growth of tea trees.

4. Discussion

4.1. Effect of Soil pH on Yield and Quality of Tea

Soil pH is a key factor in measuring soil condition, which directly affects plant growth [26]. Our research found that tea yield decreased significantly after acidification (Figure 3). Sun et al. [27], based on hydroponic experiments, found that the number and area of new roots of tea seedlings decreased significantly, and the plant height and biomass of tea trees decreased significantly when pH < 4.5. Soil acidification will cause a significant decrease in the leaf area, plant height, and photosynthesis physiological rate of tea plants [28], which in turn leads to a decline in tea production (Figure 3). Tea polyphenols, caffeine, and free amino acids are important indexes for assessing tea quality. Theanine is a unique amino acid in tea, and the higher its content, the better the quality of tea [29]. In this study, it was found that the content of tea polyphenols, caffeine, free amino acids, and theanine also decreased significantly after acidification (Figure 3), which was consistent with the results of the previous study [1] and further illustrated that tea tree growth was impeded, and tea yield and quality decreased when soil pH was below 4.5.

4.2. Effect of Soil pH on Soil Physicochemical Properties and P Fractions

Plants need to absorb nutrients from the soil for their growth, and soil acidification can lead to the deficiency of nutrients such as P and potassium in tea plantation soil [4]. This study also found that total nitrogen and P content in tea plantation soil decreased significantly after acidification (Table 1). The biological availability of phosphorus is not only determined by its total content but also closely related to its morphological distribution, and Hedley classification accurately distinguishes the forms of P that are directly utilized by plants [30]. Therefore, we conducted a further analysis of the different phosphorus fractions. Resin-P is one of the soluble inorganic P with the highest plant uptake efficiency [31]. In this study, Resin-P in ST soil was found to be 2.4 times higher than in AT (Table 2), which showed that P, which is most readily available for direct uptake and utilization by tea trees, declined in acidified tea plantation soil. NaHCO3-Pi, which is P on the surface of iron and aluminum oxide crystals, is also one of the sources of available P and is stable for a longer period of time [31,32]. NaHCO3-Po, although organic P, is readily soluble and mineralized and can also be converted into available P for timely plant uptake [7]. The contents of the above three types of labile P in the acidified tea plantation soil were significantly reduced (Table 2, Figure 4A), which indicates that soil acidification not only leads to a decrease in the total P content but also directly results in a significant decrease in the amount of effective P available for uptake and utilization by tea trees. Moderate labile P content accounted for 37% to 40% of total P (Figure 4A) and was also the main component of soil P in each tea plantation. Among them, NaOH-P mainly consists of phosphate combined with metal oxides such as Fe, Al, and humic acid, which can only be directly absorbed and utilized by plants after a long period of mineralization [9] and is a potential source of P available for plant uptake and utilization by the soil. However, the moderately labile P content of acidified tea plantation soil decreased significantly (Table 2, Figure 4A), showing a low potential for soil P supply. The contents of the three different types of non-labile P in the acidified soil all significantly increased (Table 2, Figure 4A), but non-labile P is difficult to convert into effective P forms for plant uptake and utilization [33], which is not conducive to the nutrient cycling of the tea plantation soil.
Inorganic P is the form of P that can be directly absorbed and utilized by plants, whereas organic P has a greater mobility in the soil and can be converted into available P through decomposition [8,34]. It was found that soil acidification resulted in a significant decrease in inorganic and organic P content in tea plantation soils (Figure 4B), which indicated that P sources available directly to tea trees were reduced by acidification, while long-term slow-release P sources available to the crop and soil microorganisms were also significantly reduced. The P activation coefficient is an important index reflecting the effectiveness of soil P, and the greater its value, the higher the crop yield and P uptake. P can promote photosynthesis and increase the accumulation of sugar, which can be further converted into secondary metabolites such as polyphenols, which have a significant effect on tea yield and quality [5]. The results of this study showed that soil pH, labile P, moderately labile P, total organic P, inorganic P, and P activation coefficients were all significantly and positively correlated with aboveground yield and quality indicators of tea (Figure 7). It can be seen that soil acidification reduces the P content in tea plantation soil that can be absorbed and used by tea trees and weakens the activation capacity of P, thus inhibiting the normal growth of tea trees, affecting the yield and quality of tea.

4.3. Effect of Soil pH on Soil phoD-Harboring Microbial Community Structure

In the process of soil P cycling, P-solubilizing microorganisms encoded by the phoD gene play a key role in P morphology transformation by converting insoluble P in the soil into available P that can be directly absorbed by plants through enzymatic and acidolytic actions [35]. Studies have shown that phoD-harboring microorganisms are widely distributed among archaea, bacteria, and fungi in forest, grassland, and farmland soils [25], but this study found that phoD-harboring microorganisms in tea plantation soil are bacteria (Figure 5D). Hu et al. [15] found that the phoD gene copy number increased significantly with increasing soil pH in karst soil. Soil acidification resulted in a significant decrease in the diversity and abundance of phoD-harboring microbial communities in tea plantation soils (Figure 5A,B). In general, healthy soils have higher microbial diversity and activity [36]. Hu et al. [15] also found that in karst soil, the phoD gene copy number increased significantly with increasing soil pH. In addition, phoD-harboring microorganisms in tea plantation soils with different acidity were dominated by Acidobacteria, Proteobacteria, Nitrospirae, Planctomycetes, and Verrucomicrobia (Figure 5D), which is consistent with the results of previous studies in other soil types [37,38]; their ubiquitous presence in the phoD-harboring microbial community highlights their key roles in soil P transformation.
The phoD-encoded P solubilizing microbial communities in tea plantation soils with different acidity levels showed significant differences in composition and structure (Figure 5E,F), suggesting that soil pH is a key factor influencing phoD-harboring microbial communities. Acidobacteria are generally considered to prefer oligotrophic environments with limited resources [39]. Proteobacteria participate in the soil P cycle by promoting the release of insoluble P from the soil through their metabolic activities [40]. The microbial abundance of Acidobacteria and Proteobacteria in tea plantation soils decreased significantly after acidification (Figure 6D). In addition, Nitrospirae plays a nitrification or denitrification role in the soil nitrogen cycle [41], and the abundance of genes involved in nitrification and denitrification significantly increased in the soil of tea plantations after acidification. Zhao et al. [42] demonstrated that a few parasitic Actinobacteria can cause diseases in some plants and animals. Actinobacteria may be outcompeted by Proteobacteria, resulting in a reduced contribution to the microbial community in nutrient-rich environments. Actinobacteria increased significantly in the soil of tea plantations after acidification (Figure 6D), which is not conducive to maintaining a healthy soil environment.
After soil acidification, the abundance of Acidobacteriia, α-proteobacteria, Solibactere, Candidatus Solibacter, Candidatus Koribacter, Caulobacter, and Acidobacterium in tea plantation soil decreased significantly (Figure 6E,F), but these microorganisms were significantly and positively correlated with soil pH and available P fractions, while in contrast, the abundance of Nitrospira, γ-proteobacteria, Terracidiphilus, Silvibacterium, and Sphingomonas was significantly increased and negatively correlated with the above soil indexes (Figure 6). Among them, Candidatus Solibacter has been shown to be involved in nutrient cycling in soil, and increasing its abundance can help accelerate nutrient transformation, enhance the content of available nutrients in soil, and promote nutrient uptake by plants [43]. However, Sphingomonas, a genus of Gram-negative bacteria, is widely distributed in various environments and is involved in plant growth promotion and soil health maintenance [44], and its increased abundance in acidified soils may be to alleviate the unhealthy problems caused by soil acidification (Figure 6F). These results highlight the interconnections between soil nutrient cycles. Together, they form the microbial foundation for soil P cycling and play a key role in P transformation in acidified tea plantation ecosystems. Meanwhile, soil acidification led to significant changes in the diversity and structure of phoD-harboring microbial communities in tea plantation soils, which in turn affected structural changes in soil P fractions and ultimately affected the yield and quality of tea leaves (Figure 8). Khan et al. [8] found that an adequate amount of mineral fertilizer alone or combined with organic fertilizer plus downslope cultivation is more effective in promoting soil P availability by enhancing the activity of ALP and phoD genes. We can regulate P management by maintaining soil microorganisms.

5. Conclusions

This study systematically investigated the effects of soil acidification on soil P fractions, the structure of phoD-harboring microbial communities, and their interrelations with tea yield and quality in tea plantations. The results demonstrate that soil acidification is an important limiting factor for the phoD-harboring microbial communities in tea plantation soils, significantly reducing the abundance of phoD genes involved in organophosphorus transformation and affecting the composition of phoD-harboring microbial communities. Specifically, the abundance of microorganisms such as Nitrospira, γ-proteobacteria, Terracidiphilus, and Sphingomonas significantly increased after soil acidification, while the abundance of Acidobacteria, α-proteobacteria, Solibacter, Candidatus Solibacter, etc., key microorganisms involved in soil nutrient cycling, decreased significantly. This change in the phoD-harboring microbial community structure led to a decrease in the content of soil-available P content, such as labile P and moderately labile P, and a weakening of soil P activation capacity, as well as promoting the accumulation of hazardous substances, which ultimately negatively affected the yield and quality of tea leaves. This study provides an important theoretical basis for the restoration of acidified tea plantation soil and the promotion of efficient soil P.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/horticulturae11101191/s1. Table S1. A table representing 195 key differential phoD-harboring microorganisms in tea plantation soils with different acidity (VIP > 1).

Author Contributions

Conceptualization, S.L., T.W., J.Y. and H.W.; methodology, S.L., T.W., J.Z., W.L., X.J., Q.Z., Y.W., J.Y. and H.W.; investigation, X.J., Q.Z. and Y.W.; formal analysis, S.L., T.W., J.Z. and W.L.; visualization, S.L. and T.W.; writing—original draft, S.L., T.W., J.Z. and W.L.; writing—review and editing, X.J., Q.Z., Y.W., J.Y. and H.W.; supervision and project administration, J.Y. and H.W.; funding acquisition, S.L., J.Y. and H.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Scientific Research of Young and Middle-aged Teachers Foundation of Fujian Province (JAT231254), the Natural Science Foundation of Fujian Province (2020J01369, 2020J01408), the Natural Science Foundation of Zhangzhou (ZZ2024J43), and the Doctoral Research Startup Fund Project of Zhangzhou Institute of Technology (ZZYB2402).

Data Availability Statement

The datasets presented in this study are included in this article. Further inquiries can be directed to the corresponding authors.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Location of the experimental site. This map created by us using QGIS 2.0.
Figure 1. Location of the experimental site. This map created by us using QGIS 2.0.
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Figure 2. Soil P fraction sequential extraction method.
Figure 2. Soil P fraction sequential extraction method.
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Figure 3. Effect of soil acidification on yield and quality of tea. Note: AT, tea soil with a pH of 3.75; MT, tea soil with a pH of 4.74; * represents a significant difference at the p < 0.05 level.
Figure 3. Effect of soil acidification on yield and quality of tea. Note: AT, tea soil with a pH of 3.75; MT, tea soil with a pH of 4.74; * represents a significant difference at the p < 0.05 level.
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Figure 4. Content and proportion of P fractions in tea plantation soils with different acidity. Note: AT, tea plantation soil with a pH of 3.75; MT, tea plantation soil with a pH of 4.74. (A) Content of different phosphorus fractions in tea soils with different acidity. (B) Proportion of three different P fractions in tea soils with different acidity. (C) Content of soil inorganic P (Pi) and organic P (Po) in tea soils with different acidity. (D) Phosphorus activation coefficient of tea soils with different acidity. *, significant difference at the 0.05 level.
Figure 4. Content and proportion of P fractions in tea plantation soils with different acidity. Note: AT, tea plantation soil with a pH of 3.75; MT, tea plantation soil with a pH of 4.74. (A) Content of different phosphorus fractions in tea soils with different acidity. (B) Proportion of three different P fractions in tea soils with different acidity. (C) Content of soil inorganic P (Pi) and organic P (Po) in tea soils with different acidity. (D) Phosphorus activation coefficient of tea soils with different acidity. *, significant difference at the 0.05 level.
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Figure 5. Analysis of the number and similarity of phoD-harboring microorganisms detected in tea plantation soils with different acidity. Note: AT, tea plantation soil with a pH of 3.75; MT, tea plantation soil with a pH of 4.74. (A) Abundance of phoD functional genes in tea plantation soils with different acidity. (B) Venn diagram analysis of phoD-harboring microorganisms in tea plantation soils. (C) Co-occurrence networks of phoD-harboring microbial communities in tea plantation soils with different acidity. (D) Distribution of phoD-harboring microbial communities at the phyla and class level in tea plantation soil with different acidity. (E) NMDS analysis of soil phoD-harboring microbial diversity in tea plantation soils with different acidity. (F) PCA analysis of soil phoD-harboring microbial diversity in tea plantation soils with different acidity.
Figure 5. Analysis of the number and similarity of phoD-harboring microorganisms detected in tea plantation soils with different acidity. Note: AT, tea plantation soil with a pH of 3.75; MT, tea plantation soil with a pH of 4.74. (A) Abundance of phoD functional genes in tea plantation soils with different acidity. (B) Venn diagram analysis of phoD-harboring microorganisms in tea plantation soils. (C) Co-occurrence networks of phoD-harboring microbial communities in tea plantation soils with different acidity. (D) Distribution of phoD-harboring microbial communities at the phyla and class level in tea plantation soil with different acidity. (E) NMDS analysis of soil phoD-harboring microbial diversity in tea plantation soils with different acidity. (F) PCA analysis of soil phoD-harboring microbial diversity in tea plantation soils with different acidity.
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Figure 6. Screening of key differential phoD-harboring microorganisms in tea plantation soils with different acidity. (A) Test plot of OPLS-DA model tea plantation soils with different acidity. (B) Scores OPLS-DA plot for analysis of within- and between-group differences in tea plantation soils with different acidity. (C) OPLS-DA S-Plot for screening of key differential phoD-harboring microorganisms in tea plantation soils with different acidity. Red indicates that the VIP absolute value is greater than 1, and green indicates that the VIP absolute value is less than 1. (D) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the phylum level. (E) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the class level. (F) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the genus level.
Figure 6. Screening of key differential phoD-harboring microorganisms in tea plantation soils with different acidity. (A) Test plot of OPLS-DA model tea plantation soils with different acidity. (B) Scores OPLS-DA plot for analysis of within- and between-group differences in tea plantation soils with different acidity. (C) OPLS-DA S-Plot for screening of key differential phoD-harboring microorganisms in tea plantation soils with different acidity. Red indicates that the VIP absolute value is greater than 1, and green indicates that the VIP absolute value is less than 1. (D) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the phylum level. (E) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the class level. (F) Relative abundance analysis of key differential phoD-harboring microorganisms in tea plantation soils with different acidity at the genus level.
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Figure 7. Correlation analysis between soil P fractions, tea yield, and quality. Note: TP, total P; Pi, inorganic P; Po, organic P; LP, labile P; MLP, moderately labile P; NLP, non-labile P; phoD, phoD gene abundance; PAC, P activation coefficient; TY, tea yield; TPP, tea polyphenols; TC, tea caffeine; TFA, tea free amino acids; TT, theanine; AI, astringency index of tea.
Figure 7. Correlation analysis between soil P fractions, tea yield, and quality. Note: TP, total P; Pi, inorganic P; Po, organic P; LP, labile P; MLP, moderately labile P; NLP, non-labile P; phoD, phoD gene abundance; PAC, P activation coefficient; TY, tea yield; TPP, tea polyphenols; TC, tea caffeine; TFA, tea free amino acids; TT, theanine; AI, astringency index of tea.
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Figure 8. Interaction analysis of key genera of microorganisms, soil physicochemical indexes, tea yield, and quality with different acidity. (A) redundancy analysis of key phoD-harboring class of microorganisms with soil P fractions, tea yield, and quality. (B) redundancy analysis of key phoD-harboring genera of microorganisms with soil P fractions, tea yield, and quality. Note: TP, total P; Pi, inorganic P; Po, organic P; LP, labile P; MLP, moderately labile P; NLP, non-labile P; PAC, P activation coefficient; phoD, phoD gene abundance; TY, tea yield; TPP, tea polyphenols; TC, tea caffeine; TFA, tea free amino acids; TT, theanine; AI, astringency index of tea.
Figure 8. Interaction analysis of key genera of microorganisms, soil physicochemical indexes, tea yield, and quality with different acidity. (A) redundancy analysis of key phoD-harboring class of microorganisms with soil P fractions, tea yield, and quality. (B) redundancy analysis of key phoD-harboring genera of microorganisms with soil P fractions, tea yield, and quality. Note: TP, total P; Pi, inorganic P; Po, organic P; LP, labile P; MLP, moderately labile P; NLP, non-labile P; PAC, P activation coefficient; phoD, phoD gene abundance; TY, tea yield; TPP, tea polyphenols; TC, tea caffeine; TFA, tea free amino acids; TT, theanine; AI, astringency index of tea.
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Table 1. Basic physicochemical indexes of rhizosphere soil of tea tree.
Table 1. Basic physicochemical indexes of rhizosphere soil of tea tree.
Physicochemical PropertypH
Value		TNTPTKOM
(g/kg)(g/kg)(g/kg)(mg/kg)
AT3.75 ± 0.02 b1.38 ± 0.01 b0.99 ± 0.01 b1.73 ± 0.09 a36.28 ± 0.18 a
MT4.74 ± 0.03 a1.74 ± 0.11 a1.21 ± 0.01 a1.77 ± 0.12 a31.34 ± 0.59 b
Note: pH, soil pH value; TN, total nitrogen content; TP, total phosphorus content; TK, total potassium content; OM, organic matter content. Different lowercase letters indicate the significant difference at p < 0.05 levels between different samples.
Table 2. The content of soil P fractions (mg/kg) in tea plantation soils with different acidity.
Table 2. The content of soil P fractions (mg/kg) in tea plantation soils with different acidity.
Phosphorus FractionsATMT
Resin-Pi15.25 ± 0.29 b36.13 ± 0.01 a
NaHCO3-Pi148.25 ± 0.07 b200.77 ± 0.14 a
NaHCO3-Po156.17 ± 0.66 c209.75 ± 0.56 a
NaOH-Pi156.58 ± 0.8 b199.51 ± 0.43 a
NaOH-Po174.04 ± 2.29 b221.47 ± 0.56 a
Dil.HCl-Pi41.94 ± 0.57 b58.04 ± 0.31 a
Conc.HCl-Pi100.94 ± 0.2 a96.24 ± 0.03 b
Conc.HCl-Po107.54 ± 0.05 a102.41 ± 1.2 b
Residual-P92.87 ± 1.91 a85.63 ± 0.77 b
Note: AT, tea plantation soil with a pH of 3.75; MT, tea plantation soil with a pH of 4.74; Pi, inorganic P; Po, organic P; NaHCO3-Pi/Po, 0.5 mol/L NaHCO3 extracted inorganic/organic P; NaOH-Pi/Po, 0.1 mol/L NaOH extracted inorganic/organic P; Dil.HCl-P, diluted HCl extracted inorganic P; Conc.HCl-Pi/Po, concentrated HCl extracted inorganic/organic P. Different lowercase letters in a single column represent significant differences among the treatments at p < 0.05 (n = 3).
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MDPI and ACS Style

Lin, S.; Wang, T.; Zheng, J.; Lin, W.; Jia, X.; Zhang, Q.; Wang, Y.; Ye, J.; Wang, H. Soil Acidification Alters Phosphorus Fractions and phoD-Harboring Microbial Communities in Tea Plantation Soils, Thus Affecting Tea Yield and Quality. Horticulturae 2025, 11, 1191. https://doi.org/10.3390/horticulturae11101191

AMA Style

Lin S, Wang T, Zheng J, Lin W, Jia X, Zhang Q, Wang Y, Ye J, Wang H. Soil Acidification Alters Phosphorus Fractions and phoD-Harboring Microbial Communities in Tea Plantation Soils, Thus Affecting Tea Yield and Quality. Horticulturae. 2025; 11(10):1191. https://doi.org/10.3390/horticulturae11101191

Chicago/Turabian Style

Lin, Shunxian, Tingting Wang, Junfeng Zheng, Weiwei Lin, Xiaoli Jia, Qi Zhang, Yulin Wang, Jianghua Ye, and Haibin Wang. 2025. "Soil Acidification Alters Phosphorus Fractions and phoD-Harboring Microbial Communities in Tea Plantation Soils, Thus Affecting Tea Yield and Quality" Horticulturae 11, no. 10: 1191. https://doi.org/10.3390/horticulturae11101191

APA Style

Lin, S., Wang, T., Zheng, J., Lin, W., Jia, X., Zhang, Q., Wang, Y., Ye, J., & Wang, H. (2025). Soil Acidification Alters Phosphorus Fractions and phoD-Harboring Microbial Communities in Tea Plantation Soils, Thus Affecting Tea Yield and Quality. Horticulturae, 11(10), 1191. https://doi.org/10.3390/horticulturae11101191

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