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Article

Effects of Auricularia auricula Residue on Soil Physicochemical Properties, Microbial Community Composition, Diversity, and Rice Yield

by
Weidong Yuan
1,†,
Tingxuan Zong
2,†,
Bin Yu
3,†,
Ya Xin
1,
Jia Lu
1,
Qin Qiu
4,
Lin Ma
4,* and
Jiling Song
1,*
1
Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
2
Zhejiang Agricultural Technical Extension Center, Hangzhou 310020, China
3
Hangzhou Agricultural Technical Extension Center, Hangzhou 310020, China
4
Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2025, 15(10), 2313; https://doi.org/10.3390/agronomy15102313
Submission received: 3 September 2025 / Revised: 24 September 2025 / Accepted: 27 September 2025 / Published: 30 September 2025
(This article belongs to the Section Soil and Plant Nutrition)
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Abstract

The return of mushroom residue to the field is an effective measure to improve soil fertility and maintain agroecosystem productivity. We investigated the effects of returning Auricularia auricula residue to the field on the soil nutrients, enzyme activities, and microbial communities in rice–A. auricula rotation farmland. The return of 67.5 ton/ha A. auricula residue to the field significantly increased the contents of ammonium nitrogen, total nitrogen, total potassium, total phosphorus, available potassium (QK), available phosphorus, and organic matter by 180.49%, 70.41%, 16.3%, 54.35%, 137.33%, 38.84%, and 59.29%, respectively. The activities of urease, sucrase, β-glucosidase (β-GC), and acetyl-β-d-glucosidase significantly increased by 32.98%, 407.78%, 206.85%, and 186.26%, respectively; catalase and leucine aminopeptidase activities increased by 244.42% and 130.90% with the return of 54 ton/ha residue. Mushroom residue return increased the Chao1 and Shannon indices of the bacterial community but decreased the diversity of the fungal community. Redundancy analysis showed that QK, β-GC, and urease were closely associated with shifts in microbial community structure. Therefore, returning 67.5 ton/ha (149,925 bags) A. auricula residue to the field can enhance soil ecological functions by improving soil nutrients, enzyme activities, and microbial community structure.

1. Introduction

China has high fungal species diversity and abundant fungal resources, making it one of the world’s largest producers of edible mushrooms. Specifically, China’s annual production of edible mushrooms accounts for more than 70% of the total global production [1]. However, with rapid development of the edible mushroom industry, the production of mushroom residue by-products has also shown a sharp increase. The annual output of mushroom residue in China has exceeded 8.0 × 107 tons, among which 2.4 × 107 tons are Auricularia auricula residue [2]. As an accompanying by-product of the production process of edible fungi, mushroom residue is rich in organic matter (45.3–67.8%), total nitrogen (TN; 1.2–2.5%), total phosphorus (TK; 0.4–0.8%), polysaccharides, amino acids, and other nutrients [3]. From the perspective of resource recycling and reuse, mushroom residue has significant potential value. The return of mushroom residue to the field has been widely used in global agricultural production practices as an effective measure to improve the soil environment and enhance fertility [4]. It is now well-established that the return of mushroom residue to the field not only provides the necessary nutrients for crop growth [5] but also has the effect of regulating the physical structure [6] and optimizing the biological function [7] of the soil. Tang et al. [8] showed that the return of mushroom residue to the field can significantly increase the TN, TK, and humus contents in the soil of single-season planted crops, thereby effectively improving soil fertility. Zhang et al. [9] found that the nitrogen and organic matter contents of soil were significantly increased after the implementation of shiitake and Agaricus bisporus mushroom residue in a rice–wheat rotation farmland.
Soil enzymes and microorganisms are essential indicators of soil biological properties, significantly influencing processes such as soil nutrient cycling and organic matter decomposition [10]. The decomposition and transformation processes of mushroom residue returned to the field are largely driven by soil microorganisms. The incorporation of mushroom residue into the soil provides a rich and diverse carbon source, promoting the proliferation and growth of soil microbial communities [11]. Wang et al. [12] demonstrated that returning mushroom residue to the field alters the community structure of Proteobacteria and increases the abundance of bacteria associated with complex organic matter degradation. Peng et al. [13] revealed that combining mushroom residue with a chemical fertilizer significantly enhanced soil fertility, improved soil enzyme activity and bacterial abundance, and reshaped the bacterial community structure compared to the impacts of the chemical fertilizer alone. Therefore, studying soil microorganisms is highly beneficial for maintaining and optimizing soil ecosystem functions.
A. auricula is one of the most widely produced edible fungi species in Zhejiang Province. Rice–A. auricula rotation is a new eco-efficient cultivation mode that can fully utilize the land, light, and temperature resources in the autumn and winter after rice production. This rotation system can also reduce the occurrence of diseases and pests in the cultivation process of A. auricula while increasing the yield of rice, thereby achieving significant ecological and economic benefits [14]. Given this background, the aim of this study was to investigate the effects of A. auricula residue returned to the field on soil nutrients, enzyme activities, bacterial and fungal diversity, and microbial community structure under a rice–A. auricula rotation system, and to promote the resource utilization of more mushroom residues. To this end, we analyzed the patterns of soil nutrient and microbial community changes and their intrinsic relationships with soil enzyme activity. This research seeks to provide a scientific foundation for the rational utilization of A. auricula residue and establishment of a practice for the precise regulation of soil nutrients to ultimately realize enhanced crop yield and improved soil biological functions.

2. Materials and Methods

2.1. Experimental Site

The experiment was carried out at the Hecheng Edible Fungi Cooperative, located in Tonglu County, Hangzhou, Zhejiang Province, China (29.92° N, 119.18° E, altitude 160 m). This area has a mid-subtropical monsoon climate, with an average maximum temperature of 15.4 °C in summer and an annual precipitation ranging from 1500 to 1600 mm. In mid-October 2022, after the rice harvest, A. auricula cultivation was initiated using sawdust and bran as the primary substrates, with each bag weighing approximately 1.6–1.7 kg. Approximately 119,940 (F1 treatment) or 149,925 (F2 treatment) bags were deployed per hectare. Harvesting was completed by mid-April 2023, yielding an average dry mushroom residue of 450 g per bag. The mushroom residue was then directly returned to the field after bag removal. Rice (variety Yongyou 1540) was transplanted in early June 2023, with a fertilization rate of 450 kg/ha compound fertilizer and 150 kg/ha urea. This amount of fertilizer is one-third less than the normal recommended amount. Field management followed standard cultivation practices [15].

2.2. Experimental Sampling and Design

The experiment included three treatments: treatment 1 (K0) involved no application of mushroom residue, treatment 2 (F1) involved the application of mushroom residue at 54 ton/ha (119,940 bags), and treatment 3 (F2) involved the application of mushroom residue at 67.5 ton/ha (149,925 bags). Each treatment was set up with three replicates by randomization, and each replicate covered 0.0667 ha. Rice yields were measured in all paddies for each replicate. The rice was threshed and sun-dried (adjusted to a 14% moisture content) to obtain the yield. After the rice harvest, all of soil samples were collected from the plough layer (0–20 cm) using an “S”-shaped five-point sampling method. Five random soil samples were mixed, sieved through a 1 mm mesh, and divided into two portions: one portion was air-dried for soil fertility assessment, and the other was stored at −20 °C for soil enzyme activity analysis and microbial sequencing.

2.3. Soil Fertility Analysis

Nitrate nitrogen (NN) was determined by the phenol disulfonic acid colorimetric method [16], and available nitrogen (AN) was determined by the potassium chloride leaching–indophenol blue colorimetric method [17]. Available potassium (QK) and available phosphorus (QP) were measured using the flame photometry and Olsen-P method, respectively [18]. The total nitrogen (TN) content was determined by the Kjeldahl method [19], total phosphorus (TK) was determined by flame photometry [20], total phosphorus (TP) was determined by the molybdenum–antimony anti-colorimetric method [19], and organic matter (OMT) was analyzed using the potassium dichromate oxidation method [21]. Soil water content (WAT) was determined by the drying method [22]. Soil pH and electrical conductivity (EC) were measured using a pH meter (Sartorius PB-10, Goettingen, Germany) and a conductivity meter (DDSJ-308F, Leici, China), respectively, after extraction with deionized water (soil–water = 1:5, W/V) [4,22].

2.4. Soil Enzyme Activity Analysis

Leucine aminopeptidase (LAP) activity was determined by spectrophotometry (405 nm) [23], and sucrase (SC) activity was assessed using the 3,5-dinitrosalicylic acid colorimetric method (540 nm) [24]. Nitrate reductase (NR) activity was determined by the sulfanilamide colorimetric method (520 nm) [25]. Catalase (CAT) activity was measured by potassium permanganate titration (240 nm) [26]. Soil urease (UE) activity was determined using the sodium phenolate–sodium hypochlorite colorimetric method (630 nm) [24]. β-Glucosidase (β-GC) and acetyl-β-D-glucosaminidase (NAG) activities were analyzed via the nitrophenol colorimetric method (400 nm) [27]. Soil with a dry weight of 0.5 g was incubated separately with the substrate and the modified universal buffer (pH 7.0) at 37 °C for 4 h (UE, β-GC, NAG, LAP), 24 h (SC, NR) or 5 min (CAT).

2.5. DNA Extraction, Polymerase Chain Reaction (PCR) Amplification, and Sequencing of Soil Samples

For each treatment, a 0.5 g soil sample was accurately weighed, and genomic DNA was extracted using the TGuide Magnetic Bead Soil DNA Kit (Tiangen Biotech, DP812, Beijing, China). Using the extracted DNA as a template, bacterial 16S rRNA genes were amplified at the V3V4 region with primers 338F (5′-ACTCCTACGGGAGGCAGCA-3′) and 806R2 (5′-GGACTACNVGGGTWTCTTAAT-3′), while fungal ITS genes were amplified in the ITS1 region with primers ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2 (5′-GCTGCGTTCTTCATCGATGC-3′). Equal amounts of sterile ddH2O were used as negative controls throughout the DNA extraction and PCR processes.
The PCR system consisted of 50 ng DNA, 0.3 μL each forward and reverse primer (10 μM), 5 μL KOD FX Neo Buffer, 2 μL dNTPs (2 mM each), 0.2 μL KOD FX Neo, and ddH2O to a final volume of 10 μL. PCR conditions were as follows: initial denaturation at 95 °C for 3 min; 25 cycles of 95 °C for 30 s, 50 °C for 30 s, and 72 °C for 40 s; final extension at 72 °C for 5 min; and hold at 4 °C. PCR products were purified using VAHTSTM DNA Clean Beads and recovered by 1.8% agarose gel electrophoresis. High-throughput sequencing was performed on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

2.6. Data Processing and Statistical Analyses

Statistical analyses were conducted using SPSS 27.0. Differences among treatments in soil fertility indicators and enzyme activities were compared with one-way analysis of variance and Duncan’s test (significance level p < 0.05). Primer sequences were identified and trimmed using cutadapt v2.7.8, low-quality sequences were filtered using Trimmomatic v0.33, and paired-end reads were assembled using FLASH v1.2.11. The spliced data were denoised, and chimeric sequences were removed using QIIME2 v2020.6 to obtain final valid data (non-chimeric reads). The ASVs were obtained by using DADA2 (version 2020.06) to denoise the sequences. Alpha diversity indices, including the Chao1, Simpson, Shannon, and ACE indices, were determined by QIIME2 v2020.6. Taxonomic classification of bacterial and fungal communities was achieved by aligning feature sequences to the respective Silva 138 (confidence 0.7) and UNITE.8.0 (confidence 0.7) reference databases, with dominant taxa identified at the genus and phylum levels based on relative abundance. Redundancy analysis (RDA), using origin 21.0, and heatmap correlation analysis based on the Spearman (R v3.6.3) rank correlation coefficient algorithm was employed to elucidate the interactions between environmental factors and microbial community structures.

3. Results

3.1. Effects of Mushroom Residue Application on Soil Nutrients, Physicochemical Properties, Extracellular Enzyme Activities, and Rice Yield

The application of mushroom residue significantly influenced the soil nutrient content. As shown in Figure 1a,b, with increasing amounts of mushroom residue, the levels of AN, TN, TK, TP, QK, QP, and organic matter exhibited a gradual increase, reaching their highest values in the F2 treatment (application of mushroom residue at 67.5 ton/ha, corresponding to 149,925 bags). In contrast, NN content was the highest in the K0 treatment (no mushroom residue applied) at 1.90 mg/kg. Therefore, mushroom residue application effectively promoted the accumulation of organic matter and nutrients in the soil. Additionally, the pH, water content, and electrical conductivity showed gradual increases with higher mushroom residue application levels (Figure 1c). These results demonstrate that using A. auricula residue enhances soil nutrient levels and influences soil physico-chemical properties of the soil.
Soil enzymes play a crucial role in nearly all chemical reactions within the soil and are highly sensitive to environmental changes. As shown in Figure 1d,e, the activities of urease, sucrase, β-GC, and NAG exhibited gradual increases with higher mushroom residue application levels, reaching their peak values in the F2 treatment. In contrast, the activities of catalase and LAP showed an initial increase followed by a decrease, peaking in the F1 treatment (54 ton/ha residue, corresponding to 119,940 bags). This suggests that an appropriate amount of mushroom residue is more conducive to the expression of oxidative stress-related enzymes. Conversely, NR activity displayed an opposite trend, initially decreasing and then increasing with a higher level of mushroom residue application, reaching its highest value in the K0 treatment at 5.06 U/g. These results indicate that the addition of A. auricula residue significantly influences the activities of various extracellular enzymes in the soil. However, different enzymes exhibited distinct response patterns to mushroom residue application, which is attributed to their unique characteristics and functional roles in soil ecological processes.
The application of A. auricula residue also significantly influenced rice yield. As shown in Figure 1f, rice yield exhibited a gradual increase with higher mushroom residue application levels, reaching its peak value in the F2 treatment at 9.7 ton/ha, representing a significant increase of 21.57% compared to that of the K0 treatment. The F1 treatment followed, with a yield of 9.3 ton/ha, which was 17.14% higher than that of the K0 treatment. These results demonstrate that the rice–A. auricula rotation system significantly enhances rice yield.

3.2. Effects of Mushroom Residue Application on Soil Microbial Diversity

Significant differences in bacterial and fungal diversity were observed among the treatments (Figure 2). Alpha-diversity analysis of the bacterial communities (Figure 2a) revealed that the ACE, Chao1, Shannon, and Simpson indices were the highest in the F2 treatment, with no significant differences between the F2 and F1 treatments; compared to those of the K0 group, these indices increased by 9.26%, 9.2%, 1.65%, and 0.03%, respectively. In contrast, fungal communities (Figure 2b) exhibited the lowest ACE, Chao1, and Shannon indices in the F2 treatment, which decreased by 52.68%, 22.61%, and 51.81%, respectively, relative to those of K0. The Simpson index was the lowest in the F1 treatment (no significant difference from F2), showing a 3.05% reduction compared to that of K0. These results indicate that mushroom residue application effectively enhances bacterial richness (Chao1), evenness (ACE), and diversity (Shannon and Simpson), but reduces fungal richness, evenness, and diversity to some extent.

3.3. Distribution of Soil Microbial Species

The composition of the soil bacteria communities at the phylum and genus levels differed significantly among treatments after the return of the mushroom residue to the field. At the phylum level (Figure 3a), dominant taxa (mean relative abundance ≥ 2.4%) included Acidobacteriota (29.13–38.13%), Proteobacteria (26.41–30.7%), Chloroflexi (5.99–6.47%), Myxococcota (4.13–9.09%), Gemmatimonadota (3.28–5.13%), Methylomirabilota (1.13–4.25%), Desulfobacterota (1.61–3.96%), Nitrospirota (2.07–3.96%), and Bacteroidota (1.85–2.68%). The relative abundances of Myxococcota and Desulfobacterota increased with higher mushroom residue application levels, while the relative abundances of Gemmatimonadota, Methylomirabilota, Nitrospirota, and Bacteroidota peaked in the F1 treatment (with moderate residue application).
To analyze the relevant data more accurately, unclassified data were removed at the genus level (Figure 3b). The top 10 genera were Candidatus_Solibacter (2.64–4.23%), Anaeromyxobacter (1.7–4.25%), Bryobacter (1.61–2.92%), Candidatus_Koribacter (1.04–2.38%), Rhodanobacter (0.62–3.15%), Haliangium (0.62–2.25%), and Acidibacter (0.62–1.58%). The relative abundances of Anaeromyxobacter and Haliangium significantly increased with higher levels of residue application, whereas those of Candidatus_Koribacter and Rhodanobacter decreased.
Significant differences in fungal community composition at the phylum and genus levels were also observed among the treatments. At the phylum level (Figure 3c), the dominant taxa (mean relative abundance ≥ 1%) included Ascomycota (51.47–63.73%), Basidiomycota (4.26–31.69%), Mortierellomycota (1.69–11.63%), Rozellomycota (2.03–5.35%), Chytridiomycota (0.62–4.61%), and Olpidiomycota (0.08–5.13%). Compared to those of the K0 treatment, the relative abundances of Ascomycota and Basidiomycota significantly increased with mushroom residue application.
For a more precise analysis, unclassified taxa were excluded at the genus level (Figure 3d). The top 10 fungal genera were Agrocybe (0.04–26.0%), Mortierella (1.66–11.27%), Schizothecium (1.49–7.19%), Pyrenochaetopsis (1.14–5.69%), Fusarium (0.13–7.53%), Trichoderma (0.15–6.7%), Podospora (0.2–5.93%), Echria (0.47–1.57%), Sarocladium (0.09–2.53%), and Fusicolla (0.11–1.96%). Compared to those of the K0 treatment, the relative abundances of Agrocybe, Schizothecium, Pyrenochaetopsis, Fusarium, Podospora, Echria, and Sarocladium significantly increased. Notably, the relative abundance of Sarocladium increased with higher levels of mushroom residue returned to the field, while Trichoderma, Mortierella, and Fusicolla had their highest relative abundances in the treatment without the application of mushroom residue.

3.4. Redundancy Analysis (RDA) of Soil Nutrients, Enzyme Activities, and Microbial Diversity

RDA revealed significant correlations between soil nutrients, enzyme activities, and bacterial and fungal communities following the return of A. auricula residue to the field. As shown in Figure 4a, RDA1 explained 98.94% of the total variance among soil nutrients, enzyme activities, and bacterial communities. Among them, QK, β-GC, and urease were found to have relatively high correlations with the bacterial community. Similarly, Figure 4b demonstrates that RDA1 accounted for 92.21% of the variance among soil nutrients, enzyme activities, and fungal communities. Among them, QK, β-GC, and urease also had high correlations with fungal community changes. These results indicate that under the rice–Auricularia rotation system, the return of mushroom residue to the field significantly alters soil nutrients and enzyme activities, which are closely associated with shifts in microbial community structure.

3.5. Correlation Analysis of Soil Microbial Diversity with Soil Nutrients, Enzyme Activities, and Rice Yield

As shown in Figure 5a, significant correlations were observed between soil bacteria and soil fertility as well as rice yield. Specifically, the relative abundances of the genera Anaeromyxobacter, Geothrix, Haliangium, and Sideroxydans exhibited highly significant positive correlations with AN and yield, while the relative abundances of the genera Dokdonella, Holophaga, Nitrosospira, Pseudolabrys, Rhodanobacter, and Candidatus_Koribacter showed highly significant negative correlations with AN and yield. Additionally, Geothrix and Novosphingobium were positively correlated with TP; Sideroxydans was positively correlated with TK, TP, and yield; Anaeromyxobacter was positively correlated with TK, QK, and yield; and Haliangium was positively correlated with TK, TP, QK, and yield. In contrast, Candidatus_Koribacter, Dokdonella, Holophaga, Nitrosospira, Rhodanobacter, and Rhodoferax were negatively correlated with QK, while the relative abundances of Dokdonella, Holophaga, Nitrosospira, and Rhodanobacter showed significant negative correlations with TP.
Significant correlations were also found between soil bacteria and enzyme activities. Anaeromyxobacter, Haliangium, and Sideroxydans were positively correlated with β-GC and sucrase, Geothrix was positively correlated with NAG and urease, and Novosphingobium was positively correlated with β-GC and urease. Conversely, Dokdonella, Holophaga, Nitrosospira, and Rhodanobacter were negatively correlated with β-GC, NAG, and sucrase; Candidatus_Koribacter was negatively correlated with β-GC and sucrase; Pseudolabrys was negatively correlated with β-GC; and Rhodoferax was negatively correlated with NAG and NR.
As illustrated in Figure 5b, significant correlations were observed among soil fungi, soil fertility, and rice yield. Specifically, Hypholoma, Nigrospora, and Tetraplosphaeria exhibited highly significant positive correlations with QK, AN, and yield; Lecythophora and Tetraploa were positively correlated with QK, QP, and yield; Phaeosphaeria was positively correlated with AN, TK, TP, and yield; and Sarocladium was positively correlated with AN and yield. In contrast, Articulospora, Cystofilobasidium, Oidiodendron, and Penicillium showed highly significant negative correlations with AN and TK, while Fusicolla, Mortierella, Talaromyces, and Paraphaeosphaeria were negatively correlated with AN, TP, and yield.
Significant correlations were also found between soil fungi and enzyme activities. Funiliomyces, Hypholoma, Tetraplosphaeria, and Nigrospora were positively correlated with sucrase and β-GC, while Apiosordaria, Articulospora, Fusicolla, Mortierella, Paraphaeosphaeria, Penicillium, and Talaromyces were negatively correlated with sucrase and β-GC activities. Additionally, positive correlations were found for Hypholoma with NAG; Lecythophora with sucrase; Ochroconis with urease, NAG, and β-GC; and Tetraploa with sucrase. Conversely, negative correlations were found for Cystofilobasidium with NAG and β-GC; Mortierella with NAG; Oidiodendron with NAG and TN; and Paraphaeosphaeria, Penicillium, and Talaromyces with NAG.

4. Discussion

After rice harvest, rice fields remain idle during the winter. The winter climate is suitable for growing A. auricula in the southern regions of China. Using idle paddy fields for cultivating A. auricula can increase the utilization rate of the land, further enabling farmers to harvest A. auricula and achieve higher profits. The main components of the A. auricula culture substrate are cellulose, hemicellulose, and lignin. Before the growth of A. auricula, the fresh culture substrate has completed formation of the tubular fiber structure. After the growth of A. auricula, the biomass structure in the residue is decomposed by microorganisms and the fiber structure is damaged, while retaining abundant nutrients such as mycelium, proteins, and amino acids [28]. Returning the A. auricula residue to the field can not only improve the soil but also provides rich nutrients for the growth of rice. In the following year’s rice cultivation, the A. auricula residue can replace part of the chemical fertilizers otherwise required while achieving similar rice yields. This is very beneficial for both agricultural production and environmental protection.
Changes in soil physico-chemical properties and nutrient content are closely associated with the return of mushroom residue to the field. Following mushroom residue application, significant increases were observed in soil organic matter, TN, TP, TK, QK, QP, and AN. Hao et al. [29] demonstrated that the return of Stropharia rugosoannulata residue effectively enhanced soil organic carbon, nitrogen, and potassium contents, aligning with our findings. Additionally, Chen et al. [30] noted that mushroom residue, which is rich in lignin and polysaccharides, can slowly release nutrients through microbial degradation, consistent with the 59.29% increase in organic matter observed in the F2 treatment in this study. Mushroom residue contains substantial organic matter and nutrients, and its appropriate application not only significantly improves the soil nutrient content and structure but also enhances the water retention capacity and mitigates soil acidity or alkalinity 20. Indeed, the soil pH in the F1 and F2 treatments was significantly higher than that in the K0 treatment, consistent with findings reported by Frąc et al. [31]. This indicates that mushroom residue application effectively alleviates soil acidification and its adverse effects, thereby promoting nutrient uptake and improving crop yield and nutritional status. Overall, the results of this study highlight that the rational application of A. auricula residue in rice-cultivated soils significantly enhances the soil nutrient content, offering substantial benefits for improving soil quality and increasing rice yield.
Enzyme activity has been proposed as a biological indicator of soil quality and is closely linked to soil functions. The significant increases in β-GC, urease, and NAG activities found in this study indicate that mushroom residue input accelerates carbon and nitrogen cycling [32]. During the decomposition of mushroom residue returned to the field, soil aggregate and pore structures are altered, enhancing the buffering capacity and water retention, thereby providing carriers for various enzymes. Additionally, the mushroom residue supplies abundant energy substrates for soil microorganisms, optimizing their habitat and stimulating metabolic activities. This in turn promotes the secretion of enzymes involved in carbon, nitrogen, and phosphorus cycling, which enter the soil through vigorous root exudation and microbial activity, leading to increased enzyme activity and faster carbon and nitrogen turnover [33]. Nannipieri et al. [32] emphasized that soil enzyme activity is directly related to substrate availability, further suggesting that the cellulose and chitin in mushroom residue may provide specific substrates for β-GC. Furthermore, in paddy field experiments, Zhang et al. [34] found that sucrase activity was significantly positively correlated with the QP content, supporting the synergistic effect observed in this study, where the sucrase activity increased by 407.78% alongside a 38.84% rise in QP.
In this study, the activities of sucrase, NAG, catalase, urease, LAP, and β-GC all increased after A. auricula residue application, with urease, β-GC, sucrase, and NAG activities rising with higher mushroom residue application levels. These findings further demonstrate that the return of A. auricula residue to the field effectively promotes the transformation of enzyme activities related to carbon and nitrogen cycling, facilitating the decomposition of slow-release nutrients into readily available forms for plant uptake. This process provides additional nutrients for plant growth, playing a significant role in soil nutrient cycling and ecosystem stability.
Soil microorganisms play a pivotal role in soil ecosystems, driving nutrient cycling and organic matter degradation; therefore, soil microbes are recognized as key indicators of soil health [35]. The results of this study demonstrate that the return of mushroom residue to the field significantly influences the diversity and community structure of soil bacteria and fungi. Specifically, mushroom residue application notably enhanced bacterial diversity and richness while reducing fungal diversity and richness, consistent with the findings of Su et al. [36]. In addition, Six et al. [37] suggested that bacteria, compared to fungi, preferentially utilize readily decomposable resources. The addition of mushroom residue provides heterotrophic bacteria with exogenous organic materials and nutrients, promoting their proliferation, reducing intercommunity competition, and thereby enhancing bacterial diversity in paddy soils [38]. Although the return of A. auricula residue to the field impacted fungal diversity and richness, it significantly increased the relative abundance of Sarocladium, with antifungal properties and ability to promote the growth of rice [39], while reducing the relative abundances of some fungi with the ability to invade plant roots, such as Trichoderma, Fusarium, and Fusicolla [40], thereby modulating the fungal community structure and composition.
Furthermore, the composition of bacterial and fungal communities varied among treatments [41]. In this study, the return of A. auricula residue to the field increased the relative abundances of beneficial bacterial phyla such as Acidobacteriota, Proteobacteria, Chloroflexi, Myxococcota, and Desulfobacterota. Proteobacteria play a crucial role in soil carbon, nitrogen, and sulfur cycling and exhibit strong resistance to heavily polluted soils [42], particularly under heavy metal stress [43]. Acidobacteriota can degrade cellulose [44] and participate in iron cycling and other ecosystem functions [45]. Chloroflexi generates energy through photosynthesis and facilitates carbon transformation and utilization under low nutrient availability [46]. With mushroom residue addition, the relative abundances of Myxococcota and Desulfobacterota significantly increased, accelerating organic matter decomposition [47], providing more nutrients for plant growth, and preventing sulfide accumulation that could harm plants. Chen et al. [29] also found that organic waste application significantly increased the relative abundances of Proteobacteria and Acidobacteriota, which was directly linked to the input of carbon and nitrogen sources from the residue. These microorganisms play key roles in carbon and nitrogen cycling, further validating the promotion of functional microbes by mushroom residue return to the field.
Compared to those found in the K0 treatment, the F1 and F2 treatments exhibited higher relative abundances of the genera Anaeromyxobacter, Haliangium, Candidatus_Koribacter, and Rhodanobacter. Anaeromyxobacter, an anaerobic bacterium, participates in the redox processes of multivalent heavy metals, stabilizes radioactive elements, and metabolizes organic halides [48]. Haliangium enhances soil carbon cycling, accelerates organic matter decomposition, and provides nutrients for plants [49]. Candidatus_Koribacter is essential for degrading various organic compounds, including cellulose, hemicellulose, starch, and chitin [50]. Rhodanobacter promotes nitrification pathways and utilizes Fe2+ for denitrification [51]. Li et al. [52] reported that the return of organic material to the field can suppress the proliferation of pathogenic fungi (e.g., Fusarium) while promoting the colonization of beneficial fungi (e.g., Trichoderma) by regulating the soil pH and carbon-to-nitrogen ratio, consistent with the observed trends in fungal community structure in this study. The increase in beneficial microorganisms in the soil can promote plant growth and enhance yield [53]. Therefore, the diverse microbial community formed by the return of A. auricula residue to the field contributes to soil improvement and the maintenance of high soil functionality.
Soil nutrients, enzyme activities, and microbial communities are key factors maintaining the rhizosphere microenvironment, interacting with and constraining one another. The utilization of fungal residues is a major factor driving soil nutrients, enzyme activity, and microbial communities, as evidenced by the regulation of multiple measured chemical and biological indicator parameters. In a life-cycle assessment, Dorr et al. [54] highlighted that the return of mushroom residue to the field reduces the risk of nitrogen leaching by regulating microbial functions, validating the positive correlation between AN and bacterial abundance observed in this study. Spearman correlation heatmaps indicated that after the return of A. auricula residue to the field, bacterial genera such as Geothrix, Novosphingobium, Promicromonospora, Anaeromyxobacter, Haliangium, and Sideroxydans significantly and positively influenced soil properties, including QP, TP, pH, QK, AN, TK, and organic matter, as well as the activities of soil enzymes such as urease, sucrase, β-GC, and NAG.
A systematic review [32] emphasized the central role of soil enzymes in carbon, nitrogen, and phosphorus cycling, noting that β-GC and urease activities are significantly positively correlated with organic matter decomposition rates, providing a theoretical basis for the observed increase in enzyme activities observed in this study. Soil organic matter supplies ample substrates for enzymes such as urease and sucrase, thereby enhancing their activities. Urease catalyzes urea hydrolysis to produce ammonia and carbon dioxide, providing nitrogen and carbon sources for Geothrix. During metabolism, Geothrix generates organic acids, whose carboxyl and hydroxyl groups bind with calcium ions in calcium phosphate, forming soluble complexes that promote phosphate dissolution and increase soil-available phosphorus. Sucrase catalyzes the hydrolysis of sucrose into glucose and fructose; therefore, the enhanced activity of sucrase increases available carbon sources in the soil, providing more energy for bacterial growth. In a paddy field experiment, Huang et al. [55] found that increased sucrase activity is closely linked to higher soil-available phosphorus, indicating that enzyme activities improve phosphorus availability by promoting organic phosphorus mineralization, corroborating the findings of the present study. Bacteria such as Geothrix and Novosphingobium utilize nutrients released by the activities of these enzymes for their growth and metabolism. Additionally, the fungal residue may contain certain metabolites with antifungal properties, which can effectively reduce the abundance of pathogenic fungi. In summary, the return of A. auricula residue to the field can foster sustainable and healthy soil ecosystems through interactions between microorganisms and soil physicochemical properties.

5. Conclusions

Under the rice–A. auricula rotation mode, the return of mushroom residue to the field can effectively increase the soil nutrient content, soil enzyme activity, and diversity and abundance of soil microorganisms. High-throughput sequencing technology showed that the return of mushroom residue to the field could significantly increase the Chao1 and Shannon diversity indices of soil bacteria and decrease those of fungi. The dominant bacterial phyla were Acidobacteria and Proteobacteria, while Ascomycota and Basidiomycota were identified as the major fungal taxa, with soil organic matter, QK, β-GC, and urease activity being the main factors affecting the composition of soil bacterial and fungal communities in the farmland under rice–A. auricula rotation. In conclusion, under the rice–A. auricula rotation pattern, the return of 67.5 tons/ha (149,925 bags) of A. auricula residue to the field can substantially improve soil quality and agricultural production. As the advantages and yield-increasing principles of the rice–A. auricula rotation mode are gradually clarified, the application scope of this mode will expand significantly, thereby greatly enhancing soil fertility and rice yield.

Author Contributions

Conceptualization, W.Y., J.S. and L.M.; methodology, J.S. and W.Y.; software, W.Y., J.L. and Q.Q.; validation, T.Z., B.Y. and Y.X.; writing—original draft preparation, W.Y., J.L. and Q.Q.; writing—review and editing, L.M. and W.Y.; funding acquisition, L.M. and W.Y. W.Y., T.Z. and B.Y. contributed to the work equally and should be regarded as co-first authors. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Project of Collaborative Extension of Major Agricultural Technologies of Zhejiang (2021XTTGSYJ02-1) and the China Agriculture Research System of MOF and MARA (CARS-20).

Data Availability Statement

The raw sequence data of microorganisms reported in this paper have been deposited in the Genome Sequence Archive (GSA) database under accession numbers CRA026195.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
TNTotal nitrogen
TKTotal phosphorus
NNNitrate nitrogen
ANAmmonium nitrogen
QKAvailable potassium
QP Available phosphorus
TP Total phosphorus
OMTOrganic matter
WATWater content
ECElectrical conductivity
LAPLeucine aminopeptidase
SCSucrase
NRNitrate reductase
CATCatalase
UEUrease
β-GCβ-Glucosidase
NAGAcetyl-β-D-glucosaminidase
RDARedundancy analysis

References

  1. Qiao, Y.L.; Tie, J.Z.; Wang, X.H.; Wei, B.H.; Zhang, W.B.; Liu, Z.C.; Zhang, G.B.; Lyu, J.; Liao, W.B.; Hu, L.L.; et al. Comprehensive evaluation on effect of planting and breeding waste composts on the yield, nutrient utilization, and soil environment of baby cabbage. J. Environ. Manag. 2023, 341, 117941. [Google Scholar] [CrossRef]
  2. Hu, L.J.; Li, Y.; Tian, S.B.; Wei, J.Y.; Liao, D.X.; Feng, M.Y.; Zhang, H.; Zou, M.; Hang, X.N. Fungi Residue Returning: Effects on Soil Physicochemical Characters, Microorganisms and Enzyme Activity in Vegetable Field. Chin. Agric. Sci. Bull. 2020, 36, 98–104. [Google Scholar] [CrossRef]
  3. Zhang, L.; Sun, X. Changes in physical, chemical, and microbiological properties during the two-stage co-composting of green waste with spent mushroom compost and biochar. Bioresour. Technol. 2014, 171, 274–284. [Google Scholar] [CrossRef] [PubMed]
  4. Chen, L.D.; Zhou, W.; Luo, L.; Li, Y.R.; Chen, Z.; Gu, Y.F.; Chen, Q.; Deng, O.P.; Xu, X.X.; Lan, T.; et al. Short-term responses of soil nutrients, heavy metals and microbial community to partial substitution of chemical fertilizer with spent mushroom substrates (SMS). Sci. Total Environ. 2022, 844, 157064. [Google Scholar] [CrossRef] [PubMed]
  5. Xiao, J.; Wang, C.J.; Huang, M.; Sun, N.; Zhang, W.J.; Xu, M.G. Meta-analysis of biochar application effects on soil fertility and yieldsof fruit and vegetables in greenhouse. J. Plant Nutr. Fertil. 2018, 24, 228–236. [Google Scholar] [CrossRef]
  6. Li, X.L.; Xu, K.Q.; Xiao, R.; Li, J.J.; Chen, X.M.; Wang, X.Y. Effects of Fertilizer with Gypsum Application on Growing Development and Nutrient Uptake of Potting Corn in Coastal Saline Soil. J. Anhui Sci. Technol. Univ. 2011, 25, 23–28. [Google Scholar] [CrossRef]
  7. Zhang, N.; Pan, X.; Liu, J.; Yu, H.J.; Zhang, B.; Du, H.L.; Liu, F.M.; Hao, S. Response of Soil Nutrients and Microbial Communities to Increased Application of Mushroom Dreg in Albic Soil. Chin. Agric. Sci. Bull. 2025, 41, 49–55. [Google Scholar] [CrossRef]
  8. Tang, Q.; Liu, W.; Huang, H.; Peng, Z.; Deng, L. Responses of Crop Yield, Soil Fertility, and Heavy Metals to Spent Mushroom Residues Application. Plants 2024, 13, 663. [Google Scholar] [CrossRef]
  9. Zhang, H.Y.; Zhang, M.; Wang, J.; Wang, C.Y.; Zhou, W.; Deng, L.J. Effects of Combined Application of Chemical Fertilizers with Different Mushroom Residues on Soil Fertility and Enzymes Activities. J. Soil Water Conserv. 2022, 36, 364–370. [Google Scholar] [CrossRef]
  10. Li, Y.; Zhang, L.P.; Fang, S.Z.; Tian, Y.; Guo, J. Variation of soil enzyme activity and microbial biomass in poplar plantations of different genotypes and stem spacings. J. For. Res. 2018, 29, 963–972. [Google Scholar] [CrossRef]
  11. Li, F.L.; Wang, H.P.; Zhang, Q.; Wang, Q.Y.; Lin, Q.; Luo, T. Effect of Mushroom Residue on Soil Property and Crop and Research Progress in its Recycling. J. Agric. Sci. Technol. 2015, 17, 100–106. [Google Scholar] [CrossRef]
  12. Wang, Q.F.; Jiang, X.; Guan, D.W.; Wei, D.; Zhao, B.S.; Ma, M.C.; Chen, S.F.; Li, L.; Cao, F.M.; Li, J. Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere of Chinese Mollisols. Appl. Soil Ecol. 2018, 125, 88–96. [Google Scholar] [CrossRef]
  13. Peng, X.H.; Chen, X.T.; He, H.; Dai, J.C.; Hu, J.; Dai, D.; Sun, P.; Wang, Z.; Wei, Z.; Wei, Y.H. Effects of Returning Stropharia rugosoannulata Cultivation Residue to Paddy Fields on Rice growth and Soil Environment. Acta Agric. Univ. Jiangxiensis 2023, 45, 349–360. [Google Scholar] [CrossRef]
  14. Yang, Y.H.; Ma, J.W.; Ye, Z.Q.; Di, C.Y.; Wang, X.D. Effects of continous application of edibe fungus residue on soil fertility preperties under rice-edible fungus rotation system. J. Soil Water Conserv. 2013, 27, 172–176. [Google Scholar] [CrossRef]
  15. Li, Y.; Li, C.Y.; Fu, X.J.; Zhan, C.S.; Shi, Z.J.; Mao, X.Q.; Xu, N.C.; Wang, H.H. Performance and high-yielding cultural techniques of high-quality indica-japonica hybrid rice combination Yongyou 1540 planted as double-cropping late rice in Quzhou. Hybrid Rice 2022, 37, 125–128. [Google Scholar] [CrossRef]
  16. Norman, R.J.; Stucki, J.W. The Determination of Nitrate and Nitrite in Soil Extracts by Ultraviolet Spectrophotometry. Soil Sci. Soc. Am. J. 1981, 45, 347–353. [Google Scholar] [CrossRef]
  17. Rhine, E.D.; Mulvaney, R.L.; Pratt, E.J.; Sims, G.K. mproving the Berthelot reaction for determining ammonium in soil extracts and water. Soil Sci. Soc. Am. J. 1998, 62, 473–480. [Google Scholar] [CrossRef]
  18. Ying, B.; Xiao, S.Z.; Xiong, K.N.; Cheng, Q.W.; Luo, J.S. Comparative studies of the distribution characteristics of rocky desertification and land use/land cover classes in typical areas of Guizhou province, China. Environ. Earth Sci. 2014, 71, 631–645. [Google Scholar] [CrossRef]
  19. Vance, E.D.; Brookes, P.C.; Jenkinson, D.S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 1987, 19, 703–707. [Google Scholar] [CrossRef]
  20. Cambardella, C.A.; Elliott, E.T. Particulate soil organic-matter changes across a grassland cultivation sequence. Soil Sci. Soc. Am. J. 1992, 56, 777–783. [Google Scholar] [CrossRef]
  21. Dai, L.; Liu, C.; Yu, L.; Song, C.; Peng, L.; Li, X.; Tao, L.; Li, G. Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds. Front. Microbiol. 2018, 9, 2290. [Google Scholar] [CrossRef] [PubMed]
  22. Zhang, Q.Q.; Du, Y.; Zhang, Y.L.; Zhang, Z.H.; Zhang, B.; Lu, Y.; Zeng, F.J. Effects of Different Irrigation Levels on the Yield and Quality of theCyperus esculentusL. at Tuber Stage. Acta Agrestia Sin. 2024, 32, 3636–3645. [Google Scholar] [CrossRef]
  23. Chen, F.; Zhao, J.; Ma, J.; Zhu, Y.F.; Luo, Z.B. Effects of vegetation restoration on functional groups related to soil carbon, nitrogen and phosphorus cycles in open-pit mining area of the Loess Plateau. Acta Pedol. Sin. 2023, 60, 1507–1519. [Google Scholar] [CrossRef]
  24. Du, Y.Y.; Bao, Y.Y.; Liu, X.Y.; Zhang, X.Y. Effects of Tartary Buckwheat Rotation on Enzyme Activities and Microorganisms in Rhizosphere Soil of Cultivated Potato in Yunnan Province. J. Agric. Sci. Technol. 2024, 26, 192–200. [Google Scholar] [CrossRef]
  25. Wang, L.H.; He, Z.X.; Li, J.; Zhang, J.; Xie, J.M.; Zhang, X.D. Effects of bio-organic fertilizer with microbial inoculants on the growth, physiological characteristics, yield and quality of garlic seedlings. J. Gansu Agric. Univ. 2022, 58, 63–70. [Google Scholar] [CrossRef]
  26. Li, D.S.; Cheng, X.M.; Jiang, Z.; Qu, C.; Yan, H.; Wu, Q.N. Effects of Crop Rotation on the Growth, Quality and Soil Environment of Euryale ferox. J. Chin. Med. Mater. 2024, 47, 12–21. [Google Scholar] [CrossRef]
  27. Eivazi, F.; Tabatabai, M.A. Factors affecting glucosidase and galactosidase activities in soils. Soil Biol. Biochem. 1990, 22, 891–897. [Google Scholar] [CrossRef]
  28. Zhao, Q.X.; Wang, H.X.; Wang, L.Y.; Song, Y.Z.; Li, X.; Yang, C.; Li, F.J. Effects of combined application of bacterial residue and chemical fertilizer on soil nutrients and enzyme activities in paddy field. Jiangsu Agric. Sci. 2024, 52, 191–197. [Google Scholar] [CrossRef]
  29. Hao, H.B.; Yue, Y.H.; Wang, Q.; Xiao, T.T.; Zhao, Z.L.; Zhang, J.J.; Chen, H. Effects of the rice-mushroom rotation pattern on soil properties and microbial community succession in paddy fields. Front. Microbiol. 2024, 15, 1449922. [Google Scholar] [CrossRef]
  30. Chen, Y.; Sun, R.B.; Sun, T.T.; Liang, Y.T.; Jiang, Y.J.; Sun, B. Organic amendments shift the phosphorus-correlated microbial co-occurrence pattern in the peanut rhizosphere network during long-term fertilization regimes. Appl. Soil Ecol. 2018, 124, 229–239. [Google Scholar] [CrossRef]
  31. Frąc, M.; Pertile, G.; Panek, J.; Gryta, A.; Oszust, K.; Lipiec, J.; Usowicz, B. Mycobiome composition and diversity under the long-term application of spent mushroom substrate and chicken manure. Agronomy 2021, 11, 410. [Google Scholar] [CrossRef]
  32. Nannipieri, P.; Trasar-Cepeda, C.; Dick, R.P. Soil enzyme activity: A brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biol. Fertil. Soils 2017, 54, 11–19. [Google Scholar] [CrossRef]
  33. Borase, D.N.; Nath, C.P.; Hazra, K.K.; Senthilkumar, M.; Singh, S.S.; Praharaj, C.S.; Singh, U.; Kumar, N. Long-term impact of diversified crop rotations and nutrient management practices on soil microbial functions and soil enzymes activity. Ecol. Indic. 2020, 114, 106322. [Google Scholar] [CrossRef]
  34. Zhang, W.; Rong, F.L.; Zhu, H.Y.; Cao, F.B.; Chen, J.N.; Chen, F.L. Effects of adding vermicompost on soil fertility and enzyme activity of acidic paddy soil. J. Nucl. Agric. Sci. 2025, 39, 615–623. [Google Scholar]
  35. Zhao, J.; Liu, J.; Liang, H.; Huang, J.; Chen, Z.; Nie, Y.; Wang, C.; Wang, Y. Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health. PLoS ONE 2018, 13, e0192967. [Google Scholar] [CrossRef]
  36. Su, Y.; He, Z.C.; Yang, Y.H.; Jia, S.Q.; Yu, M.; Chen, X.J.; Shen, A.L. Linking soil microbial community dynamics to straw-carbon distribution in soil organic carbon. Sci. Rep. 2020, 10, 5526. [Google Scholar] [CrossRef]
  37. Six, J.; Frey, S.D.; Thiet, R.K.; Batten, K.M. Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems. Soil Sci. Soc. Am. J. 2006, 70, 555–569. [Google Scholar] [CrossRef]
  38. Subhashini, D. Growth Promotion and Increased Potassium Uptake of Tobacco by Potassium-Mobilizing Bacterium Frateuria aurantia Grown at Different Potassium Levels in Vertisols. Commun. Soil Sci. Plant Anal. 2014, 46, 210–220. [Google Scholar] [CrossRef]
  39. Kemp, N.D.; Vaughan, M.M.; McCormick, S.P.; Brown, J.A.; Bakker, M.G. Sarocladium zeae is a systemic endophyte of wheat and an effective biocontrol agent against Fusarium head blight. Biol. Control 2020, 149, 104329. [Google Scholar] [CrossRef]
  40. Clocchiatti, A.; Hannula, S.E.; Van den Berg, M.; Hundscheid, M.P.J.; De Boer, W. Evaluation of Phenolic Root Exudates as Stimulants of Saptrophic Fungi in the Rhizosphere. Front. Microbiol. 2021, 12, 644046. [Google Scholar] [CrossRef]
  41. Brenzinger, K.; Costa, O.Y.A.; Ho, A.; Koorneef, G.; Robroek, B.; Molenaar, D.; Korthals, G.; Bodelier, P.L.E. Steering microbiomes by organic amendments towards climate-smart agricultural soils. Biol. Fertil. Soils 2021, 57, 1053–1074. [Google Scholar] [CrossRef]
  42. Rampelotto, P.H.; de Siqueira Ferreira, A.; Barboza, A.D.; Roesch, L.F. Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems. Microb. Ecol. 2013, 66, 593–607. [Google Scholar] [CrossRef]
  43. Li, X.M.; Zhang, W.; Liu, T.X.; Chen, L.X.; Chen, P.C.; Li, F.B. Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil. Soil Biol. Biochem. 2016, 94, 70–79. [Google Scholar] [CrossRef]
  44. Lee, S.H.; Ka, J.O.; Cho, J.C. Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol. Lett. 2008, 285, 263–269. [Google Scholar] [CrossRef]
  45. Wang, Y.; Sheng, H.F.; He, Y.; Wu, J.Y.; Jiang, Y.X.; Fung-Yee, T.N.; Zhou, H.W. Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Appl. Environ. Microbiol. 2012, 78, 8264–8271. [Google Scholar] [CrossRef]
  46. Fullerton, H.; Moyer, C.L. Comparative single-cell genomics of Chloroflexi from the Okinawa trough deep-subsurface biosphere. Appl. Environ. Microbiol. 2016, 82, 3000–3008. [Google Scholar] [CrossRef]
  47. Guan, Y.P.; Wu, M.K.; Che, S.H.; Yuan, S.; Yang, X.; Li, S.Y.; Tian, P.; Wu, L.; Yang, M.Y.; Wu, Z.H. Effects of continuous straw returning on soil functional microorganisms and microbial communities. J. Microbiol. 2023, 61, 49–62. [Google Scholar] [CrossRef]
  48. Prakash, O.; Gihring, T.M.; Dalton, D.D.; Chin, K.J.; Green, S.J.; Akob, D.M.; Wanger, G.; Kostka, J.E. Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. Int. J. Syst. Evol. Microbiol. 2010, 60 Pt 3, 546–553. [Google Scholar] [CrossRef] [PubMed]
  49. Dai, W.; Liu, Y.; Yao, D.; Wang, N.; Ye, X.; Cui, Z.; Wang, H. Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils. Sci. Total Environ. 2023, 871, 161680. [Google Scholar] [CrossRef] [PubMed]
  50. Zhang, X.; Gao, G.; Wu, Z.; Wen, X.; Zhong, H.; Zhong, Z.; Yang, C.; Bian, F.; Gai, X. Responses of soil nutrients and microbial communities to intercropping medicinal plants in moso bamboo plantations in subtropical China. Environ. Sci. Pollut. Res. Int. 2020, 27, 2301–2310. [Google Scholar] [CrossRef] [PubMed]
  51. Cao, X.; Zheng, H.; Liao, Y.; Feng, L.; Jiang, L.; Liu, C.; Mao, Y.; Shen, Q.; Zhang, Q.; Ji, F. Effects of iron-based substrate on coupling of nitrification, aerobic denitrification and Fe(II) autotrophic denitrification in tidal flow constructed wetlands. Bioresour. Technol. 2022, 361, 127657. [Google Scholar] [CrossRef]
  52. Li, J.; Yang, Y.; Wen, J.L.; Mo, F.; Liu, Y. Continuous manure application strengthens the associations between soil microbial function and crop production: Evidence from a 7-year multisite field experiment on the Guanzhong Plain. Agric. Ecosyst. Environ. 2022, 338, 108082. [Google Scholar] [CrossRef]
  53. Garbeva, P.; van Veen, J.A.; van Elsas, J.D. Microbial diversity in soil: Selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu. Rev. Phytopathol. 2004, 42, 243–270. [Google Scholar] [CrossRef]
  54. Erica, D.; Maximilien, K.; Benoît, G.; Christine, A. Life cycle assessment of a circular, urban mushroom farm. J. Clean. Prod. 2020, 288, 125668. [Google Scholar] [CrossRef]
  55. Huang, M.; Peng, Y.M.; Zhao, W.X.; Gao, X.; Wu, S.W.; Zhang, J.; Li, S.; Li, W.N.; Cui, X.Q.; Wu, J.Z.; et al. Effects of different tillage measures during summer fallow seasonontents and enzyme activities in dryland wheat field. Soil Fertil. Sci. China 2024, 30–42. [Google Scholar] [CrossRef]
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Figure 1. Effect of mushroom residues returned to the field on soil nutrients, physico-chemical properties, extracellular enzyme activities, and rice yield. (a) Effect of mushroom residues returned to the field on soil nitrate nitrogen (NN), ammonium nitrogen (AN), available potassium (QK), and available phosphorus (QP). (b) Effect of mushroom residues returned to the field on soil total nitrogen (TN), total phosphorus (TK), total phosphorus (TP), and organic matter (OMT). (c) Effect of mushroom residues returned to the field on soil water content (WAT), pH, and electrical conductivity (EC). (d) Effect of mushroom residues returned to the field on soil leucine aminopeptidase (LAP), acetyl-β-D-glucosaminidase (NAG), sucrase (SC), nitrate reductase (NR), and catalase (CAT). (e) Effect of mushroom residues returned to the field on soil urease (UE) and β-glucosidase (β-GC). (f) Effect of mushroom residues returned to the field on rice yield. Different letters indicate significant differences (p < 0.05, Duncan’s multiple range test).
Figure 1. Effect of mushroom residues returned to the field on soil nutrients, physico-chemical properties, extracellular enzyme activities, and rice yield. (a) Effect of mushroom residues returned to the field on soil nitrate nitrogen (NN), ammonium nitrogen (AN), available potassium (QK), and available phosphorus (QP). (b) Effect of mushroom residues returned to the field on soil total nitrogen (TN), total phosphorus (TK), total phosphorus (TP), and organic matter (OMT). (c) Effect of mushroom residues returned to the field on soil water content (WAT), pH, and electrical conductivity (EC). (d) Effect of mushroom residues returned to the field on soil leucine aminopeptidase (LAP), acetyl-β-D-glucosaminidase (NAG), sucrase (SC), nitrate reductase (NR), and catalase (CAT). (e) Effect of mushroom residues returned to the field on soil urease (UE) and β-glucosidase (β-GC). (f) Effect of mushroom residues returned to the field on rice yield. Different letters indicate significant differences (p < 0.05, Duncan’s multiple range test).
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Figure 2. Species richness and diversity of soil bacteria and fungi after returning mushroom residues to the field. (a) ACE, Chao1, Shannon, and Simpson indices for bacteria. (b) ACE, Chao1, Shannon, and Simpson indices for fungi. Numbers on box plots represent the significance based on the p-value.
Figure 2. Species richness and diversity of soil bacteria and fungi after returning mushroom residues to the field. (a) ACE, Chao1, Shannon, and Simpson indices for bacteria. (b) ACE, Chao1, Shannon, and Simpson indices for fungi. Numbers on box plots represent the significance based on the p-value.
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Figure 3. Effect of mushroom residues returned to the field on soil bacterial and fungal community composition. (a) Bacterial community composition at the phylum level. (b) Bacterial community composition at the genus level. (c) Fungal community composition at the phylum level. (d) Fungal community composition at the genus level.
Figure 3. Effect of mushroom residues returned to the field on soil bacterial and fungal community composition. (a) Bacterial community composition at the phylum level. (b) Bacterial community composition at the genus level. (c) Fungal community composition at the phylum level. (d) Fungal community composition at the genus level.
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Figure 4. Redundancy analysis of soil nutrients, enzyme activities, and microbial community for bacteria (a) and fungi (b).
Figure 4. Redundancy analysis of soil nutrients, enzyme activities, and microbial community for bacteria (a) and fungi (b).
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Figure 5. Correlations of dominant soil microbial taxa with indicators of soil fertility and enzyme activities for bacteria (a) and fungi (b). Red indicates a significant positive correlation, and blue indicates a significant negative correlation. * p < 0.05; ** p < 0.01.
Figure 5. Correlations of dominant soil microbial taxa with indicators of soil fertility and enzyme activities for bacteria (a) and fungi (b). Red indicates a significant positive correlation, and blue indicates a significant negative correlation. * p < 0.05; ** p < 0.01.
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Yuan, W.; Zong, T.; Yu, B.; Xin, Y.; Lu, J.; Qiu, Q.; Ma, L.; Song, J. Effects of Auricularia auricula Residue on Soil Physicochemical Properties, Microbial Community Composition, Diversity, and Rice Yield. Agronomy 2025, 15, 2313. https://doi.org/10.3390/agronomy15102313

AMA Style

Yuan W, Zong T, Yu B, Xin Y, Lu J, Qiu Q, Ma L, Song J. Effects of Auricularia auricula Residue on Soil Physicochemical Properties, Microbial Community Composition, Diversity, and Rice Yield. Agronomy. 2025; 15(10):2313. https://doi.org/10.3390/agronomy15102313

Chicago/Turabian Style

Yuan, Weidong, Tingxuan Zong, Bin Yu, Ya Xin, Jia Lu, Qin Qiu, Lin Ma, and Jiling Song. 2025. "Effects of Auricularia auricula Residue on Soil Physicochemical Properties, Microbial Community Composition, Diversity, and Rice Yield" Agronomy 15, no. 10: 2313. https://doi.org/10.3390/agronomy15102313

APA Style

Yuan, W., Zong, T., Yu, B., Xin, Y., Lu, J., Qiu, Q., Ma, L., & Song, J. (2025). Effects of Auricularia auricula Residue on Soil Physicochemical Properties, Microbial Community Composition, Diversity, and Rice Yield. Agronomy, 15(10), 2313. https://doi.org/10.3390/agronomy15102313

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