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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2024.1368184</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Enhancing rice ecological production: synergistic effects of wheat-straw decomposition and microbial agents on soil health and yield</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Wen</surname>
<given-names>Yanfang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
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<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Ma</surname>
<given-names>Yangming</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Ziniu</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Yang</surname>
<given-names>Yonggang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Yuan</surname>
<given-names>Xiaojuan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2362708"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Kairui</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Luo</surname>
<given-names>Yongheng</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>He</surname>
<given-names>Ziting</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
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<contrib contrib-type="author">
<name>
<surname>Huang</surname>
<given-names>Xinhai</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author">
<name>
<surname>Deng</surname>
<given-names>Pengxin</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Congmei</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Yang</surname>
<given-names>Zhiyuan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Zongkui</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Ma</surname>
<given-names>Jun</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1736330"/>
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</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Sun</surname>
<given-names>Yongjian</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">*</xref>
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<aff id="aff1">
<sup>1</sup>
<institution>Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University</institution>, <addr-line>Wenjiang</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Patrizia Cesaro, University of Eastern Piedmont, Italy</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Flavio Anastasia, Universit&#xe0; del Piemonte Orientale, Italy</p>
<p>Xiaofeng Su, Chinese Academy of Agricultural Sciences, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Yongjian Sun, <email xlink:href="mailto:yongjians1980@163.com">yongjians1980@163.com</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>08</day>
<month>08</month>
<year>2024</year>
</pub-date>
<pub-date pub-type="collection">
<year>2024</year>
</pub-date>
<volume>15</volume>
<elocation-id>1368184</elocation-id>
<history>
<date date-type="received">
<day>10</day>
<month>01</month>
<year>2024</year>
</date>
<date date-type="accepted">
<day>25</day>
<month>07</month>
<year>2024</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2024 Wen, Ma, Wu, Yang, Yuan, Chen, Luo, He, Huang, Deng, Li, Yang, Chen, Ma and Sun</copyright-statement>
<copyright-year>2024</copyright-year>
<copyright-holder>Wen, Ma, Wu, Yang, Yuan, Chen, Luo, He, Huang, Deng, Li, Yang, Chen, Ma and Sun</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<sec>
<title>Aims</title>
<p>This study evaluated the impact of wheat straw return and microbial agent application on rice field environments.</p>
</sec>
<sec>
<title>Methods</title>
<p>Using Rice variety Chuankangyou 2115 and a microbial mix of <italic>Bacillus subtilis</italic> and <italic>Trichoderma harzianum</italic>. Five treatments were tested: T<sub>1</sub> (no straw return), T<sub>2</sub> (straw return), T<sub>3</sub>, T<sub>4</sub>, and T<sub>5</sub> (straw return with varying ratios of <italic>Bacillus subtilis</italic> and <italic>Trichoderma harzianum</italic>).</p>
</sec>
<sec>
<title>Results</title>
<p>Results indicated significant improvements in rice root length, surface area, dry weight, soil nutrients, and enzyme activity across T<sub>2</sub>-T<sub>5</sub> compared to T<sub>1</sub>, enhancing yield by 3.81-26.63%. T<sub>3</sub> (50:50 microbial ratio) was optimal, further increasing root dry weight, soil enzyme activity, effective panicle and spikelet numbers, and yield. Dominant bacteria in T<sub>3</sub> included <italic>MBNT15</italic>, <italic>Defluviicoccus</italic>, <italic>Ro</italic>kubacteriales, and <italic>Latescibacterota</italic>. Higher <italic>Trichoderma harzianum</italic> proportions (75% in T<sub>5</sub>) increased straw decomposition but slightly inhibited root growth. Correlation analysis revealed a significant positive relationship between yield and soil microorganisms like <italic>Gemmatimonadota</italic> and <italic>Firmicutes</italic> at the heading stage. Factors like dry root weight, straw decomposition rate post-jointing stage, and elevated soil enzyme activity and nutrient content from tiller to jointing stage contributed to increased panicle and spikelet numbers, boosting yield.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>The optimal <italic>Bacillus subtilis</italic> and <italic>Trichoderma harzianum</italic> ratio for straw return was 50:50, effectively improving soil health and synergizing high rice yield with efficient straw utilization.</p>
</sec>
</abstract>
<kwd-group>
<kwd>microbial treatment</kwd>
<kwd>rice yield</kwd>
<kwd>microbial combination</kwd>
<kwd>
<italic>Bacillus subtilis</italic>
</kwd>
<kwd>
<italic>Trichoderma harzianum</italic>
</kwd>
</kwd-group>
<counts>
<fig-count count="6"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="57"/>
<page-count count="14"/>
<word-count count="8224"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Plant Symbiotic Interactions</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<label>1</label>
<title>Introduction</title>
<p>Rice-wheat rotation, a typical flood and drought rotation pattern, is mainly distributed in the Yangtze River basin in China (<xref ref-type="bibr" rid="B25">Liu and Li, 2017</xref>). As a by-product of agricultural production, crop straw is rich in nutrients valuable for crop growth and reuse, such as organic carbon, nitrogen (N), phosphorus (P), and potassium (K), thereby aiding the improvement of soil quality (<xref ref-type="bibr" rid="B41">Song et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B16">Jin et&#xa0;al., 2020</xref>). However, returning straw to the field directly can result in incomplete decay, the propagation of pathogens and pests, and the subsequent reduction in crop yield (<xref ref-type="bibr" rid="B43">Song et&#xa0;al., 2023</xref>). As such, how to mitigate the adverse effects of straw returning has become a key area of research. The presence of beneficial microorganisms in soil supports the use of microbial agents as an eco-friendly and effective approach. Numerous studies have been conducted in this field. <xref ref-type="bibr" rid="B42">Song et&#xa0;al. (2022)</xref> discovered that the application of organic matrix and composite microbial preparations in conjunction with straw return to fields offers substantial benefits in terms of organic matter accumulation and alteration of the soil microbial community. <xref ref-type="bibr" rid="B7">Deng et&#xa0;al. (2021)</xref> observed that combining microbial agents with plants markedly increased the content of organic matter, alkali-hydrolyzed nitrogen, and invertase activity in the soil. <xref ref-type="bibr" rid="B38">Sarangi et&#xa0;al. (2021)</xref> demonstrated that microorganisms could facilitate the decomposition of rice straw and bolster the stress resistance of rice. Furthermore, <xref ref-type="bibr" rid="B57">Zhou et&#xa0;al. (2014)</xref> reported that adding a microbial agent enhanced the release of P from pulverized rice straw. Collectively, these findings suggest that the use of microbial agents in straw return processes accelerates straw decomposition, improves soil conditions, and significantly boosts crop yields.</p>
<p>Microbial agents encompass a diverse group, including bacteria and fungi. Numerous studies have been conducted on <italic>Bacillus subtilis</italic>, a bacterial species, and <italic>Trichoderma harzianum</italic>, a fungal species, and their roles in agriculture. Applying <italic>B. subtilis</italic> enhances soil contents of available N, P, and K; promotes N, P, and K-fixing capacities (<xref ref-type="bibr" rid="B5">Chowdappa et&#xa0;al., 2013</xref>); and improves soil enzyme activity (<xref ref-type="bibr" rid="B35">Ng et&#xa0;al., 2022</xref>). In comparison to applications of 50% urea, employing a microbial agent formulated with <italic>B. subtilis</italic> has been shown to reduce soil nitrogen loss by 54% (<xref ref-type="bibr" rid="B13">Hermosa et&#xa0;al., 2012</xref>). Moreover, <italic>B. subtilis</italic> can promote crop growth while inhibiting the proliferation of pathogenic bacteria. This is due to the ability of <italic>B. subtilis</italic> to produce antimicrobial metabolites, which can be used as an alternative to synthetic chemicals or as a supplement to biopesticides for the control of plant diseases, in addition to the ability of <italic>B. subtilis</italic> to activate induced systemic resistance (ISR) in the plant, which increases plant resistance to pathogens, and ISR induces the synthesis of jasmonic acid and ethylene in the plant (<xref ref-type="bibr" rid="B20">Li et&#xa0;al., 2017</xref>). <xref ref-type="bibr" rid="B5">Chowdappa et&#xa0;al. (2013)</xref> demonstrated that <italic>B. subtilis</italic> inhibits the mycelial growth of tomato late blight, while significantly enhancing root crown growth, leaf area, and the seedling vitality index in tomatoes. In addition, the <italic>B. subtilis</italic> can secrete a variety of secondary metabolites that stimulate plant growth, increase disease resistance, and improve plant tolerance. A study found that cytokinins produced by <italic>Bacillus megaterium</italic> and <italic>B. subtilis</italic> on the surface of potato promote root cell growth and enhance root respiration, which in turn enhances the ability of the root system to absorb water, mineral elements, as well as increase potato tuber yield by increasing the net photosynthetic rate of potato leaves during the critical period of reproductive growth (<xref ref-type="bibr" rid="B8">Fan et&#xa0;al., 2021</xref>). <xref ref-type="bibr" rid="B21">Lima et&#xa0;al. (2019)</xref> revealed that inoculation of maize and soybeans with <italic>B. subtilis</italic> under water shortage conditions increases leaf water content and reduces leaf antioxidant activity to resist water stress. The effect of <italic>T. harzianum</italic> differs from that of <italic>B. subtilis</italic> in regulating the bacterial community and inhibiting pathogenic bacteria. It has been shown that seed germination and seedling growth rate of several crops, including wheat, tobacco, carrot and potato, were significantly enhanced and plant dry weight was increased by treatment with <italic>T. harzianum</italic> (<xref ref-type="bibr" rid="B6">da Silva Folli-Pereira et&#xa0;al., 2022</xref>), but too high a concentration may have an inhibitory effect (<xref ref-type="bibr" rid="B9">Gao et&#xa0;al., 2009</xref>). <xref ref-type="bibr" rid="B1">Abdenaceur et&#xa0;al. (2022)</xref> found that <italic>T. harzianum</italic> produces phosphatase and hydrogen cyanide, which contribute to promoting plant growth. <xref ref-type="bibr" rid="B32">Mironenka et&#xa0;al. (2021)</xref> reported that <italic>T. harzianum</italic> mitigates the adverse effects of the wheat pathogen <italic>Fusarium</italic> spp., and secretes cellulase to decompose organic matter. More than that, recent research advances have revealed that <italic>T. harzianum</italic> is able to enhance plant tolerance to abiotic stresses through interactions with plants (<xref ref-type="bibr" rid="B54">Yang et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B22">Lin et&#xa0;al., 2017</xref>). For example, treated cocoa seedlings not only grew faster but also demonstrated greater drought tolerance under drought conditions, which was reflected at the phenotypic, molecular and physiological levels of the plant. In addition, <italic>T. harzianum</italic> has the ability to be able to degrade straw. A research found that <italic>T. harzianum</italic> was able to produce cellulase, which was able to effectively degrade wheat straw (<xref ref-type="bibr" rid="B37">Radhakrishnan and Baek, 2017</xref>). While numerous studies have explored the functional mechanisms of <italic>B. subtilis</italic> and <italic>T. harzianum</italic> as individual microbial agents, research on the application of these two agents under straw-return conditions, especially in rice field soil environments, is still limited.</p>
<p>In this study, the effects of the combined application of <italic>B. subtilis</italic> and <italic>T. harzianum</italic> on the paddy soil environment, rice root system, straw decay, and rice yield were investigated to elucidate the underlying regulatory mechanisms of microorganisms in improving rice yield and soil fertility, facilitating efficient utilization of straw, and reducing environmental pollution. This study provides a theoretical and practical basis for green rice production.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Experimental site and materials</title>
<p>The experiment was conducted in 2022-2023 at the Rice Research Institute of Sichuan Agricultural University in Wenjiang, Chengdu, Sichuan Province, China (30&#xb0;43&#x2032;N, 103&#xb0;51&#x2032;E), building upon previous experiments (<xref ref-type="bibr" rid="B23">Liu et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B55">Yao et&#xa0;al., 2020</xref>). The previous crop was wheat, which was naturally air-dried and rolled into small pieces (about 4 cm) at a moisture content of 15% for straw mulching. 4710 kg/hm<sup>2</sup> of wheat straw (15.0% moisture content) was incorporated into the soil. The soil in the experimental field was sandy loam, with a topsoil depth of 0&#x2013;20 cm, containing 2.26 g/kg of total N, 20.45 g/kg of organic matter, 115.82 mg/kg of available N, 28.19 mg/kg of available P, and 87.88 mg/kg of available K. The tested rice variety was &#x201c;<italic>Chuankangyou 2115</italic>&#x201d; (provided by Sichuan Agricultural University, a three-line hybrid rice variety with a total growth period of 151.8 d). The microbial agents used were <italic>B. subtilis</italic> and <italic>T. harzianum</italic> (both provided by Sichuan Green Microbial Technology Co., Ltd.) at a concentration of 200 &#xd7; 10<sup>9</sup> CFU/g.</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Experimental design</title>
<p>The application rates of <italic>B. subtilis</italic> and <italic>T. harzianum</italic> were based on the method described by (<xref ref-type="bibr" rid="B27">Liu et&#xa0;al., 2018</xref>). The experiment used a completely randomized design with five treatments: T1 &#x2013; no wheat straw return; T2 &#x2013; return of wheat straw; T3 &#x2013; return of wheat straw with a combined application of microbial agents (<italic>B. subtilis</italic>: <italic>T. harzianum</italic>=50 g: 50 g); T4 &#x2013; return of wheat straw with a combined application of microbial agents (<italic>B. subtilis</italic>: <italic>T. harzianum</italic>=75 g: 25 g); and T5 &#x2013; return of wheat straw with a combined application of microbial agents (<italic>B. subtilis</italic>: <italic>T. harzianum</italic>=25 g: 75 g). Three replicates were conducted in a plot with an area of 4.0 m &#xd7; 5.0 m = 20.0 m&#xb2;. Wheat straw was fully incorporated into the soil, and one day before transplanting, a microbial agent was applied according to a prescribed ratio, with a total application rate of 50 kg/ha. On April 7, 2022, rice seeds were sown in a seeding field and covered with a film for seedling cultivation. By 15 May, the seedlings were transplanted to the experimental plots and planted at a spacing of 33.3 cm &#xd7; 16.7 cm between rows and plants, one plant per hole. 12 rows with 29 plants per row were finally planted in each plot. Raised beds (40 cm wide) were constructed between plots and covered with a plastic film. Fertilization and irrigation were consistently managed, and measures were taken to prevent and control diseases, pests, and weeds. The total amount of N applied was 150 kg/ha, with compound fertilizer (Urea- Phosphorus pentoxide - Potassium oxide:15-15-15) applied at a ratio of 5:2:3 for basal, tillering, and panicle fertilization; basal fertilizer was applied 1 d before transplanting, tillering fertilizer was applied 7 d after transplanting, and panicle fertilizer was applied at the booting and heading stages in equal amounts.</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>Measurement items and methods</title>
<sec id="s2_3_1">
<label>2.3.1</label>
<title>Soil nutrients</title>
<p>At 15 d after transplanting, tillering stage (36 d after transplanting), jointing, heading, and maturing stages, five points were taken from each plot according to the diagonal line, and the soil total N, alkali-hydrolyzed N, available P, and available K were determined after drying and grinding through a sieve with a mesh aperture of 250 &#x3bc;m.</p>
</sec>
<sec id="s2_3_2">
<label>2.3.2</label>
<title>Soil nutrients</title>
<p>Total N was determined using the Kaiser-type method, and available N was determined using the alkali-diffusion method; available P was determined using sulfuric acid-hydrochloric acid leaching spectrophotometry, and available K by ammonium acetate extraction using flame atomic absorption spectrophotometry (<xref ref-type="bibr" rid="B2">Bao, 2000</xref>).</p>
</sec>
<sec id="s2_3_3">
<label>2.3.3</label>
<title>Straw decay rate</title>
<p>Using the nylon net bag method (<xref ref-type="bibr" rid="B36">Ocio et&#xa0;al., 1991</xref>), intact crop straw of similar thickness and length was selected and cut into 3&#x2013;5 cm pieces. Exactly 30 g of the small pieces (N<sub>0</sub>) were weighed and placed in a net bag (25 cm x 35 cm, hole diameter of 425 &#x3bc;m nylon mesh bag), buried 5&#x2013;10 cm deep in the tillage layer. At 15 d after rice transplanting, tillering stage, jointing stage, heading stage, and maturing stage, five samples were randomly selected from each plot, rinsed with tap water until the water was colorless, dried in an 80&#xb0;C oven until they reached a constant weight, accurately weighed and the weight of each bag N<sub>x</sub> was recorded. Straw decay rate W<sub>x</sub> (%) = (N<sub>0</sub> &#x2212; N<sub>x</sub>)/N<sub>0</sub> &#xd7; 100.</p>
</sec>
<sec id="s2_3_4">
<label>2.3.4</label>
<title>Rice root system</title>
<p>At the rice tillering, jointing, heading, and maturing stages, 30 rice plants were randomly selected from each plot to calculate the average tillering number of each plot, and then the sampling of plants was carried out according to the average tillering number of the plot; roots were sampled by taking a 33.3 cm &#xd7; 16.7 cm &#xd7; 30 cm soil core around the plant. Intact root systems were obtained by washing the roots under running water and placing them in nylon nets with a pore size of 0.4 mm. Root morphology parameters, such as total root length and root surface area, were measured using WinRHIZO Pro v.2009c software and an Epson Expression 10000XL scanner. Next, the roots were fixed at 105&#xb0;C for 30 min and dried at 80&#xb0;C to a constant weight. Single-stem root length (cm) = total root length per plant/total number of stems per plant; single-stem root surface area (cm2) = total root volume per plant/total number of stems per plant; the root dry weight per hectare (kg/hm2) = the product of the dry weight of a single-stem root system &#xd7; the average number of tillers per plot &#xd7; the basic seedling number.</p>
</sec>
<sec id="s2_3_5">
<label>2.3.5</label>
<title>Soil enzyme activities</title>
<p>At 15 days after rice transplanting, tillering, jointing, heading and ripening stages, 5 points were selected from the diagonal of each plot and samples were collected at a depth of 0-20 cm using a soil sampler. After natural air drying, the soil samples were ground and screened with a diameter of 250 &#x3bc;m to determine the activities of sucrase, urease and acid phosphatase. Soil sucrase activity was determined using the 3,5-dinitro salicylic acid colorimetric method. Soil urease activity was determined using the phenol sodium hypochlorite colorimetric method, and acid phosphatase activity was determined using the sodium phenyl phosphate colorimetric method (<xref ref-type="bibr" rid="B11">Guan, 1986</xref>).</p>
</sec>
<sec id="s2_3_6">
<label>2.3.6</label>
<title>Soil bacterial microbial community</title>
<p>2 g of fresh soil removed from rice roots, and immediately put into a sterile EP tube, frozen in liquid nitrogen, and stored at -80&#xb0;C. DNA was extracted from soil samples using Soil DNA Kit (Omega), and then the bacterial 16S rRNA was amplified and sequenced by Shanghai Piceno Biotechnology Co., LTD. The sequences were compared in Silva library (<ext-link ext-link-type="uri" xlink:href="https://www.arb-silva.de/">https://www.arb-silva.de/</ext-link>) to determine the classification and abundance of strains. The Chao index represents the richness, and the higher the index value, the higher the richness of the community. Shannon index represents species diversity, and the higher the index value, the higher the diversity of the community. PCoA (Principal Coordinates Analysis), also known as principal coordinate analysis, is a non-binding data dimensionality reduction analysis method that can be used to study the similarity or divergence of sample community composition.</p>
</sec>
<sec id="s2_3_7">
<label>2.3.7</label>
<title>Actual yield and its constituent factors</title>
<p>At the maturation stage, 50 plant-effective panicles were investigated in each plot, and 10 plants were randomly selected based on the average spike number. The evaluated traits included the number of empty grains, number of filled grains, and 1000-grain weight. Additionally, the seed-set rate and total&#xa0;floret number were calculated. The yield was calculated based on the actual number of plants at harvest (13.5 a moisture content).</p>
</sec>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Data analysis</title>
<p>Data were processed using Microsoft Excel 2019, and Sigma Plot 14.0 was used for graphical representation. Statistical analysis was performed using SPSS 24.0, one-way analysis of variance and Duncan&#x2019;s multiple range test were used, and the least significant difference method was employed to determine significant differences between treatment means at P&lt;0.05. Additionally, as the experimental results over two years show a consistent trend, the comprehensive report will primarily focus on the experiments conducted in 2022.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results and analysis</title>
<sec id="s3_1">
<label>3.1</label>
<title>Effects of microbial agents on rice yield and its components under rice-wheat rotation</title>
<p>
<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref> shows that all treatments significantly affect rice yield and its components, except for grains per ear and 1000-grain weight in year 2022, and 1000-grain weight in year 2023. The results from the two-year experiment were consistent. Compared with T<sub>1</sub> treatment, the rice yield of T<sub>2</sub>, T<sub>3</sub>, T<sub>4</sub> and T<sub>5</sub> treatment increased by 3.81%, 17.15%, 10.63% and 10.38% in 2022, and 12.75%, 26.63%, 15.45% and 13.76% in 2023, respectively. T3 treatment, which had the highest yield, was identified as the optimal treatment for combined microbial agent application under wheat straw return conditions. In 2022, from the perspective of yield components, the T<sub>1</sub> treatment had a higher setting rate, which was significantly higher than that of other treatments, but this could not compensate for the lack of effective panicle number and total spikelet number. Compared to the T<sub>1</sub> treatment, the T<sub>2</sub> treatment significantly increased the number of spikelets per panicle by 4.26%; the application of microbial agents in treatments T<sub>3</sub>-T<sub>5</sub> could further increase the effective panicle number and total spikelet number, showing a significant increase of 6.97 ~ 11.54% and 9.67 ~ 15.23% compared to T<sub>1</sub>, respectively. In 2023, compared to the T<sub>1</sub> treatment, the T<sub>2</sub> treatment significantly increased the effective panicle number by 9.85%; the combined application of microbial agents (T<sub>3</sub>-T<sub>5</sub> treatments) significantly increased the effective panicle number by 3.86-33.12% and the total spikelet number by 3.87-23.74%, ensuring an increase in yield. Overall, the two-year data, compared with T<sub>4</sub> and T<sub>5</sub> treatments, T<sub>3</sub> treatment could further increase the number of effective panicle and total spikelets of rice, thus increasing the yield of rice. In this study, T<sub>3</sub> treatment combined with wheat stalk return to the field (<italic>Bacillus subtilis: Trichoderma harzia</italic> = 50 g: 50 g) was the appropriate treatment.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Effects of combined application of microbial agents on rice yield and its components.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center">Season</th>
<th valign="middle" align="center">Treatment</th>
<th valign="middle" align="center">Effective panicle<break/>/(&#xd7;10<sup>4</sup>/hm<sup>2</sup>)</th>
<th valign="middle" align="center">Spikelets per panicle</th>
<th valign="top" align="center">Spikelets number<break/>/(&#xd7;10<sup>6</sup>/hm<sup>2</sup>)</th>
<th valign="middle" align="center">Seed-setting rate/%</th>
<th valign="middle" align="center">1000-grain weight/g</th>
<th valign="middle" align="center">grain yield<break/>/(kg/hm<sup>2</sup>)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" rowspan="6" align="center">
<bold>2022</bold>
</td>
<td valign="middle" align="center">T<sub>1</sub>
</td>
<td valign="middle" align="center">227.73c</td>
<td valign="middle" align="center">162.01a</td>
<td valign="middle" align="center">368.95d</td>
<td valign="middle" align="center">87.13a</td>
<td valign="middle" align="center">35.33a</td>
<td valign="middle" align="center">9270.37c</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>2</sub>
</td>
<td valign="middle" align="center">232.80c</td>
<td valign="middle" align="center">165.60a</td>
<td valign="middle" align="center">385.37c</td>
<td valign="middle" align="center">84.97b</td>
<td valign="middle" align="center">34.58a</td>
<td valign="middle" align="center">9623.47c</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>3</sub>
</td>
<td valign="middle" align="center">254.00a</td>
<td valign="middle" align="center">167.43a</td>
<td valign="middle" align="center">425.15a</td>
<td valign="middle" align="center">80.45c</td>
<td valign="middle" align="center">34.44a</td>
<td valign="middle" align="center">10860.02a</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>4</sub>
</td>
<td valign="middle" align="center">249.60ab</td>
<td valign="middle" align="center">168.25a</td>
<td valign="middle" align="center">419.77ab</td>
<td valign="middle" align="center">81.29c</td>
<td valign="middle" align="center">34.42a</td>
<td valign="middle" align="center">10256.13b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>5</sub>
</td>
<td valign="middle" align="center">243.60b</td>
<td valign="middle" align="center">166.17a</td>
<td valign="middle" align="center">404.62b</td>
<td valign="middle" align="center">81.10c</td>
<td valign="middle" align="center">35.08a</td>
<td valign="middle" align="center">10232.76b</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>
<italic>F</italic> value</bold>
</td>
<td valign="middle" align="center">20.87**</td>
<td valign="middle" align="center">2.51</td>
<td valign="middle" align="center">81.41**</td>
<td valign="middle" align="center">20.55**</td>
<td valign="middle" align="center">2.34</td>
<td valign="middle" align="center">18.16**</td>
</tr>
<tr>
<td valign="middle" rowspan="6" align="center">
<bold>2023</bold>
</td>
<td valign="middle" align="center">T<sub>1</sub>
</td>
<td valign="middle" align="center">186.60d</td>
<td valign="middle" align="center">175.55b</td>
<td valign="middle" align="center">327.74b</td>
<td valign="middle" align="center">75.82b</td>
<td valign="middle" align="center">33.88a</td>
<td valign="middle" align="center">8482.05c</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>2</sub>
</td>
<td valign="middle" align="center">207.00b</td>
<td valign="middle" align="center">168.76bc</td>
<td valign="middle" align="center">349.36b</td>
<td valign="middle" align="center">76.56b</td>
<td valign="middle" align="center">34.57a</td>
<td valign="middle" align="center">9436.26b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>3</sub>
</td>
<td valign="middle" align="center">248.40a</td>
<td valign="middle" align="center">163.35c</td>
<td valign="middle" align="center">405.54a</td>
<td valign="middle" align="center">81.59a</td>
<td valign="middle" align="center">33.78a</td>
<td valign="middle" align="center">10474.18a</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>4</sub>
</td>
<td valign="middle" align="center">208.80b</td>
<td valign="middle" align="center">186.58a</td>
<td valign="middle" align="center">389.62a</td>
<td valign="middle" align="center">72.53c</td>
<td valign="middle" align="center">34.00a</td>
<td valign="middle" align="center">9638.25b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>5</sub>
</td>
<td valign="middle" align="center">193.80c</td>
<td valign="middle" align="center">175.67b</td>
<td valign="middle" align="center">340.43b</td>
<td valign="middle" align="center">76.57b</td>
<td valign="middle" align="center">35.05a</td>
<td valign="middle" align="center">9511.69b</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>
<italic>F</italic> value</bold>
</td>
<td valign="middle" align="center">141.94**</td>
<td valign="middle" align="center">10.51**</td>
<td valign="middle" align="center">25.42**</td>
<td valign="middle" align="center">12.73**</td>
<td valign="middle" align="center">1.84</td>
<td valign="middle" align="center">60.88**</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>Data in the same column with different letters are significantly different at the 5% level. *, ** indicate significant differences at the 0.05 and 0.01 levels, respectively. T<sub>1</sub>: no wheat straw return; T<sub>2</sub>: wheat straw return; T<sub>3</sub>: T<sub>2</sub> + (Bacillus subtilis: Trichoderma harzianum=50:50); T<sub>4</sub>: T<sub>2</sub> +(<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=75:25); T<sub>5</sub>: T<sub>2</sub> + (<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=25:75).</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Effects of microbial agent on rice root growth under rice-wheat rotation</title>
<p>As shown in <xref ref-type="table" rid="T2">
<bold>Tables&#xa0;2</bold>
</xref> and <xref ref-type="table" rid="T3">
<bold>3</bold>
</xref>, the root morphology of rice followed a pattern of an initial increase before decreasing during the growth stages, peaking at the heading stage. During the tillering stage, the differences in single-stem root length and root surface area were not significant. However, in other growth stages, significant differences in these two indicators and population root dry weight were observed among the treatments. Compared to the T<sub>1</sub> treatment, the T<sub>2</sub>, T<sub>3</sub>, T<sub>4</sub>, and T<sub>5</sub> treatments increased the single-stem root length (RLS) by 0.88&#x2013;1.99%, 4.77&#x2013;10.38%, 5.18&#x2013;7.77%, and 2.24&#x2013;8.41%, respectively, from the jointing to the maturing stages. Single-stem root surface area (RAS) increased by 2.12&#x2013;22.50%, 10.68&#x2013;23.56%, 3.31&#x2013;11.06%, and 3.18&#x2013;15.87% in the T<sub>2</sub>, T<sub>3</sub>, T<sub>4</sub>, and T<sub>5</sub> treatments, respectively, compared with the T<sub>1</sub> treatment; the microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) showed the best performance regarding the RLS and RAS under the T<sub>3</sub> treatment. During the tillering stage, the T<sub>1</sub> treatment had the highest population root dry weight (RWP), significantly higher than the wheat straw return (T<sub>2</sub>) and microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>). However, from the heading to maturing stages, the microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) were higher than the T<sub>1</sub> treatment, with the T<sub>3</sub> treatment showing the best performance, increasing RWP by 4.80&#x2013;6.55% compared to the T<sub>1</sub> treatment. In summary, while wheat straw return (T<sub>2</sub>) can promote root growth in rice from the jointing stage onwards, the combined application of microbial agents (T<sub>3</sub>&#x2013;T<sub>5</sub>) based on straw return demonstrates a more pronounced effect, with the T<sub>3</sub> treatment showing the most significant improvement in root growth.</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Effects of combined application of microbial agents on root morphology at the tillering and jointing stages.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="center">Treatment</th>
<th valign="middle" colspan="3" align="center">Tillering stage</th>
<th valign="top" colspan="3" align="center">Jointing stage</th>
</tr>
<tr>
<th valign="middle" align="center">RLS/cm</th>
<th valign="middle" align="center">RAS/cm<sup>2</sup>
</th>
<th valign="middle" align="center">RWP/(kg/hm<sup>2</sup>)</th>
<th valign="middle" align="center">RLS/cm</th>
<th valign="middle" align="center">RAS/cm<sup>2</sup>
</th>
<th valign="middle" align="center">RWP/(kg/hm<sup>2</sup>)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">T<sub>1</sub>
</td>
<td valign="middle" align="center">403.13a</td>
<td valign="middle" align="center">88.58a</td>
<td valign="middle" align="center">431.00a</td>
<td valign="middle" align="center">507.98b</td>
<td valign="middle" align="center">103.98b</td>
<td valign="middle" align="center">403.20b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>2</sub>
</td>
<td valign="middle" align="center">391.06a</td>
<td valign="middle" align="center">86.52a</td>
<td valign="middle" align="center">409.80b</td>
<td valign="middle" align="center">518.10b</td>
<td valign="middle" align="center">127.38a</td>
<td valign="middle" align="center">438.40a</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>3</sub>
</td>
<td valign="middle" align="center">402.47a</td>
<td valign="middle" align="center">85.76a</td>
<td valign="middle" align="center">366.40c</td>
<td valign="middle" align="center">536.91a</td>
<td valign="middle" align="center">128.47a</td>
<td valign="middle" align="center">440.60a</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>4</sub>
</td>
<td valign="middle" align="center">400.43a</td>
<td valign="middle" align="center">84.96a</td>
<td valign="middle" align="center">397.20b</td>
<td valign="middle" align="center">536.71a</td>
<td valign="middle" align="center">120.48a</td>
<td valign="middle" align="center">410.80b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>5</sub>
</td>
<td valign="middle" align="center">399.62a</td>
<td valign="middle" align="center">84.34a</td>
<td valign="middle" align="center">366.40c</td>
<td valign="middle" align="center">519.34b</td>
<td valign="middle" align="center">108.93b</td>
<td valign="middle" align="center">390.20c</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>F value</bold>
</td>
<td valign="middle" align="center">0.51</td>
<td valign="middle" align="center">0.62</td>
<td valign="middle" align="center">42.26**</td>
<td valign="middle" align="center">12.31*</td>
<td valign="middle" align="center">15.01**</td>
<td valign="middle" align="center">46.83**</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>RLS, Single stem root length; RAS, Single stem root surface area; RWP, Population root dry weight. Data in the same column with different letters are significantly different at the 5% level. *, ** indicate significant differences at the 0.05 and 0.01 levels, respectively. T<sub>1</sub>: no wheat straw return; T<sub>2</sub>: wheat straw return; T<sub>3</sub>: T<sub>2</sub> + (<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=50:50); T<sub>4</sub>: T<sub>2</sub> +(<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=75:25); T<sub>5</sub>: T<sub>2</sub> + (Bacillus subtilis: Trichoderma harzianum=25:75).</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Effects of combined application of microbial agents on root morphology at the heading and maturing stages.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="center">Treatment</th>
<th valign="middle" colspan="3" align="center">Heading stage</th>
<th valign="top" colspan="3" align="center">Maturing stage</th>
</tr>
<tr>
<th valign="middle" align="center">RLS/cm</th>
<th valign="middle" align="center">RAS/cm<sup>2</sup>
</th>
<th valign="middle" align="center">RWP/(kg/hm<sup>2</sup>)</th>
<th valign="middle" align="center">RLS/cm</th>
<th valign="middle" align="center">RAS/cm<sup>2</sup>
</th>
<th valign="middle" align="center">RWP/(kg/hm<sup>2</sup>)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">T<sub>1</sub>
</td>
<td valign="middle" align="center">732.20b</td>
<td valign="middle" align="center">151.56b</td>
<td valign="middle" align="center">458.60d</td>
<td valign="middle" align="center">688.14c</td>
<td valign="middle" align="center">140.08b</td>
<td valign="middle" align="center">427.40b</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>2</sub>
</td>
<td valign="middle" align="center">773.02a</td>
<td valign="middle" align="center">157.52ab</td>
<td valign="middle" align="center">482.60b</td>
<td valign="middle" align="center">694.19c</td>
<td valign="middle" align="center">143.06b</td>
<td valign="middle" align="center">456.00ab</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>3</sub>
</td>
<td valign="middle" align="center">767.15a</td>
<td valign="middle" align="center">167.75a</td>
<td valign="middle" align="center">526.80a</td>
<td valign="middle" align="center">759.58a</td>
<td valign="middle" align="center">160.78a</td>
<td valign="middle" align="center">477.20a</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>4</sub>
</td>
<td valign="middle" align="center">770.11a</td>
<td valign="middle" align="center">156.58ab</td>
<td valign="middle" align="center">480.60bc</td>
<td valign="middle" align="center">741.64b</td>
<td valign="middle" align="center">155.57a</td>
<td valign="middle" align="center">455.40ab</td>
</tr>
<tr>
<td valign="middle" align="center">T<sub>5</sub>
</td>
<td valign="middle" align="center">756.20a</td>
<td valign="middle" align="center">156.37ab</td>
<td valign="middle" align="center">463.00cd</td>
<td valign="middle" align="center">746.00b</td>
<td valign="middle" align="center">158.98a</td>
<td valign="middle" align="center">441.20b</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>F value</bold>
</td>
<td valign="middle" align="center">8.222*</td>
<td valign="middle" align="center">1.64</td>
<td valign="middle" align="center">21.54**</td>
<td valign="middle" align="center">57.90**</td>
<td valign="middle" align="center">15.96**</td>
<td valign="middle" align="center">4.76*</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>RLS, Single stem root length; RAS, Single stem root surface area; RWP, Population root dry weight. Data in the same column with different letters are significantly different at the 5% level. *, ** indicate significant differences at the 0.05 and 0.01 levels, respectively. T<sub>1</sub>: no wheat straw return; T<sub>2</sub>: wheat straw return; T<sub>3</sub>: T<sub>2</sub> + (<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=50:50); T<sub>4</sub>: T<sub>2</sub> +(<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=75:25); T<sub>5</sub>: T<sub>2</sub> + (<italic>Bacillus subtilis</italic>: <italic>Trichoderma harzianum</italic>=25:75).</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Effects of microbial agent on straw decay and soil enzyme activities under rice-wheat rotation</title>
<p>As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>, the straw decay rate gradually increased with time, reaching 62.16&#x2013;74.89% at the rice maturing stage. Compared to the T<sub>2</sub> treatment, the microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) significantly increased the straw decay rate by 12.64&#x2013;45.97% during all rice growth stages, with the T<sub>5</sub> treatment showing the highest increase in straw decay rate, which was 1.54&#x2013;10.12% and 5.10&#x2013;15.75% more than that of the T<sub>3</sub> and T<sub>4</sub> treatments, respectively.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Effects of combined application of microbial agents on straw decay rate <bold>(A)</bold>, soil sucrase <bold>(B)</bold>, soil phosphatase <bold>(C)</bold> and soil urease <bold>(D)</bold> at main growth period of rice. 15d, at 15 days after rice transplanting; TS, tillering stage; JS, jointing stage; HS, heading stage; MS, Maturing stage. One-way analysis of variance and Duncan&#x2019;s multiple range test were used. Different lowercase letters indicate significant difference in P&lt;0.05 level between different treatments in the same growth period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g001.tif"/>
</fig>
<p>As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>, soil sucrase activity in all treatments showed a similar trend, reaching a maximum at the tillering stage and then decreasing. Compared to the T<sub>1</sub> treatment, the T<sub>2</sub>&#x2013;T<sub>5</sub> treatments increased soil sucrase activity by 3.33&#x2013;13.39%, 35.79&#x2013;64.62%, 21.40&#x2013;58.21%, and 10.80&#x2013;47.64%, respectively, with T<sub>3</sub> treatment showing the most significant increase.</p>
<p>As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1C</bold>
</xref>, the soil phosphatase activity in all treatments followed a trend of increasing and then decreasing, reaching a maximum during the jointing stage. Compared to the T<sub>1</sub> treatment, the T<sub>2</sub>&#x2013;T<sub>5</sub> treatments increased soil phosphatase activity by 2.58&#x2013;8.24%, 19.68&#x2013;30.89%, 11.67&#x2013;25.53%, and 1.83&#x2013;17.33%, respectively, with the T<sub>3</sub> treatment showing the most significant increase, followed by the T<sub>4</sub> treatment; the T<sub>5</sub> treatment showed no significant increase in the soil phosphatase activity.</p>
<p>As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1D</bold>
</xref>, the soil urease activity of all treatments showed a similar trend of increasing and then decreasing, reaching a peak during the jointing stage. Compared to the T<sub>1</sub> treatment, the T<sub>2</sub> treatment significantly increased soil urease activity by 9.80&#x2013;13.48% from 15 d after transplanting to the tillering stage, while the microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) significantly increased soil urease activity by 19.25&#x2013;52.21%, 11.76&#x2013;41.42%, and 8.91&#x2013;37.25%, respectively, during all rice growth stages. These results indicate that wheat straw return combined with microbial agent application can increase the straw decay rate and soil enzyme activity; the T<sub>5</sub> treatment showed the best effect on straw decay, the T<sub>3</sub> treatment showed the best effect on soil sucrase and phosphatase activities, and the T<sub>3</sub>&#x2013;T<sub>5</sub> treatments showed a significant effect on soil urease activity, with T<sub>3</sub> &gt; T<sub>4</sub> &gt; T<sub>5</sub>.</p>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Effects of microbial agents on soil available nutrients under rice-wheat rotation</title>
<p>As shown in <xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>, except for the heading stage, the total soil N of the T<sub>3</sub> and T<sub>4</sub> treatments was significantly higher than that of the T<sub>1</sub> treatment during all other growth stages, with increases ranging from 8.54% to 16.92% for T<sub>3</sub> and from 7.31% to 12.48% for T<sub>4</sub>. There was no significant difference in total soil N between the T<sub>2</sub> and T<sub>5</sub> treatments and the T<sub>1</sub> treatment during all rice growth stages. According to <xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>, the T<sub>2</sub> treatment of straw returning was significantly higher than T<sub>1</sub> in TS; the microbial agent-combined application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) significantly increased soil available nitrogen content compared with T<sub>1</sub> and T<sub>2</sub> at day 15 and HS (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). T<sub>3</sub> treatment showed the highest content in all periods, which significantly increased by 4.85%-12.46% compared with T<sub>1</sub>. These results indicate that combining microbial agents can significantly increase the soil available N content, with T<sub>3</sub> showing the best effect, followed by T<sub>4</sub>. The soil available N content showed a decreasing trend during the rice growth stages, and the decrease in the soil available N content of the combined microbial agent application treatments (T<sub>3</sub>&#x2013;T<sub>5</sub>) was higher than that of the T<sub>1</sub> treatment, with the T<sub>3</sub> treatment showing the most significant decrease. As shown in <xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2C</bold>
</xref>, the available phosphorus content in soil treated with microbial agents (T<sub>3</sub>-T<sub>5</sub>) was significantly higher than that in the T<sub>1</sub> treatment from 15 d after transplanting to TS, with the T<sub>3</sub> treatment showing the greatest increase, which was 6.35 ~ 29.81% higher than the T<sub>1</sub> treatment. Compared to the T<sub>1</sub> treatment without straw return, the soil available phosphorus content in the straw return T<sub>2</sub> treatment significantly increased during the periods 15 days after transplanting, TS, and JS. Within the treatments using microbial agents (T<sub>3</sub>-T<sub>5</sub>), the T<sub>3</sub> treatment further increased the soil available phosphorus content compared to T<sub>2</sub>. The T<sub>5</sub> treatment, which involved the application of microbial agents, showed the lowest soil available phosphorus content during the JS and HS periods. Soil available K (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2D</bold>
</xref>) in all treatments showed a decreasing trend during all rice growth stages. Except during the HS period when the available potassium content in the soil of T<sub>1</sub> was higher than that of T<sub>2</sub>, the available potassium content in T<sub>2</sub> was higher than that in T<sub>1</sub> during the rest of the periods. However, it is important to note that the differences in soil available potassium content between T<sub>1</sub> and T<sub>2</sub> were not significant in any of the growth stages. The available potassium content in the soil of the microbial agent combined treatment (T<sub>3</sub>-T<sub>5</sub>) was significantly higher than that in treatments T<sub>1</sub> and T<sub>2</sub> at 15 days after transplanting and during the TS period; the T<sub>3</sub> treatment showed the highest available potassium content in the soil at all growth stages, which was 9.15 ~ 13.14% higher than that in treatments T<sub>1</sub> and T<sub>2</sub>.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Effects of combined application of microbial agents on soil total nitrogen content <bold>(A)</bold>, soil alkali-hydrolyzed nitrogen content <bold>(B)</bold>, soil available phosphorus content <bold>(C)</bold> and soil available kalium content <bold>(D)</bold> at main growth period of rice. 15d, at 15 days after rice transplanting; TS, tillering stage; JS, jointing stage; HS, heading stage; MS, Maturing stage. One-way analysis of variance and Duncan&#x2019;s multiple range test were used. Different lowercase letters indicate significant difference in P&lt;0.05 level between different treatments in the same growth period.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g002.tif"/>
</fig>
</sec>
<sec id="s3_5">
<label>3.5</label>
<title>Effects of microbial agent on soil bacterial diversity in rice heading stage under rice-wheat rotation</title>
<p>A total of 3,363,677 valid reads and 93,761 OTUs were obtained by 16S rRNA amplicon sequencing of soil bacteria. The average amplicon length was 420 bp. The number of valid sequences detected in each soil sample exceeded 40,000, and the sparse curve was flat, indicating that the genetic data was sufficient to reasonably estimate bacterial OTUs in the soil samples (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>). The analysis of microbial community diversity index of each treatment found that the Alpha diversity Chao richness index (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>) showed significant differences between T<sub>1</sub> and T<sub>2</sub>, T<sub>3</sub>, T<sub>4</sub> and T<sub>5</sub> among treatments, while the Shannon diversity index (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4B</bold>
</xref>) showed no significant differences among treatments. PCoA was used to analyze the relative contributions of straw returning to field and microorganisms to soil bacterial diversity. From the <xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>, it can be observed that there is a certain degree of separation among the soil bacterial communities across different treatments. The community in T<sub>1</sub> (no straw return to the field) is significantly separated from the other treatments along the PCo1 axis, indicating that the soil bacterial community composition without straw return differs greatly from those with straw return. Additionally, T<sub>2</sub> (straw return) compared to treatments with different proportions of microbial inoculants (T<sub>3</sub>-T<sub>5</sub>) shows that the latter are closer to each other but also display some degree of separation, especially in the T<sub>4</sub> treatment, which was significantly different from T<sub>3</sub> and T<sub>5</sub> in that it was biased more upwards in the PCo2. Thus, this suggests that the application of microbial agents alters the soil bacterial community and that different microbial agent ratios do alter the bacterial community of the soil. The proximity or overlap of T<sub>3</sub>, T<sub>4</sub>, and T<sub>5</sub>, which involve different proportions of microbial inoculants, in the PCoA plot may indicate that although the proportions of the inoculants differ, the trend in their impact on the bacterial community might have certain similarities. Interestingly, the distance between T<sub>3</sub> and T<sub>4</sub> treatments and T<sub>2</sub> (straw return) is closer, whereas T<sub>5</sub> is further from T<sub>2</sub>, indicating that T<sub>5</sub> may have a more distinct microbial community change.</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Dilution curves for different treatments. The abscissa represents the amount of sequencing data; The ordinate indicates the number of species.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g003.tif"/>
</fig>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Changes in chao index <bold>(A)</bold> for alpha diversity and shannon index <bold>(B)</bold> for beta diversity of soil bacteria at the OTU level. Beta diversity using Primary coordinate Analysis (PCoA) based on OUT Level weighted UniFrac distance measures <bold>(C)</bold>. One-way analysis of variance and Duncan&#x2019;s multiple range test were used. Different lowercase letters indicate significant difference between different treatments at P&lt;0.05 level.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g004.tif"/>
</fig>
</sec>
<sec id="s3_6">
<label>3.6</label>
<title>Effects of microbial agent on composition of soil bacterial community in rice heading stage under rice-wheat rotation</title>
<p>
<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref> shows that the top 10 bacterial phyla include <italic>Proteobacteria</italic>, <italic>Acidobacteriota</italic>, <italic>Chloroflexi</italic>, <italic>Actinobacteriota</italic>, <italic>Gemmatimonadota</italic>, <italic>Chloroflexi Desulfobacterota</italic>, <italic>Myxococcota</italic>, <italic>Nitrospirota</italic>, <italic>Methylomirabilota</italic>, and <italic>Firmicutes</italic>. In <xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>, the average proportion of total soil bacteria among different treatments was 85.56%. Some bacterial groups such as <italic>Proteobacteria</italic>, <italic>Chloroflexi</italic>, and <italic>Myxococcota</italic> maintained stable abundance at the phylum level, but the relative abundance of <italic>Actinobacteriota</italic> in treatment T<sub>3</sub> was higher than the other treatments, and reached significant levels with treatments T<sub>1</sub>, T<sub>2</sub> and T<sub>4</sub>.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Heatmap analysis of the relative abundance of bacteria at the level of phylum <bold>(A)</bold> and species <bold>(B)</bold> under different treatments. Different colours in <bold>(A)</bold> refer to different bacterial phylums. The red colour in <bold>(B)</bold> refers to the increase in relative abundance and the blue colour indicates the decrease in relative abundance; the shade of the colour represents the degree of increase or decrease.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g005.tif"/>
</fig>
<p>To further compare the differences in genera composition between samples and illustrate the trends in species abundance distribution, a heatmap analysis was conducted. A clustered heatmap was drawn using the abundance data of the top 20 genera in terms of average abundance (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>). Soil bacteria under different treatments exhibited different abundances at the genus level. Compared to T<sub>1</sub>, treatment T<sub>2</sub> had higher abundances of <italic>4-29-1</italic> and <italic>Anaeromyxobacter</italic>; in treatments T<sub>3</sub>-T<sub>5</sub>, where microbial agents were applied, the abundances of <italic>Defluviicoccus</italic> and <italic>MBNT15</italic> were relatively higher than in T<sub>1</sub> and T<sub>2</sub>; compared to T<sub>1</sub> and T<sub>2</sub>, treatment T<sub>3</sub> had a higher abundance of <italic>MBNT15</italic>, <italic>Defluviicoccus</italic> and <italic>Rokubacteriales.</italic>
</p>
</sec>
<sec id="s3_7">
<label>3.7</label>
<title>Correlation analysis between root traits and yield and its components</title>
<p>There was no significant correlation between RLS and RAS and yield components at TS, while there was significant negative correlation between RWP and effective panicle, spikelets number and total yield (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). However, RLS, RAS and RWP were positively correlated with effective panicle, spikelet number and yield at maturity stages. In addition, RLS was positively correlated with effective panicle number, spikelets number and yield during the whole growth period. In conclusion, root quality and morphological traits significantly affected the increase of effective panicle number and effective spikelets after wheat straw was returned to the field, which ensured the increase of yield.</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Relationship between root morphology <bold>(A)</bold>, straw decay and soil enzyme activity <bold>(B)</bold>, soil nutrient characteristics <bold>(C)</bold>, microbial at phylum level <bold>(D)</bold> and yield characteristics under combined application of microbial agent. TS, Tillering stage; JS, Jointing stage; HS, Heading stage; MS, Maturing stage; RLS, RLS: Single stem root length; RAS, Single stem root surface area; RWP, Population root dry weight; SDR, Straw decay rate; SS, Soil sucrase; SU, Soil urease; SP, Soil phosphatase; STN, Soil total nitrogen; SAN, Soil alkali-hydrolyzable nitrogen; SAP, Soil available phosphorus; SAK, Soil available kalium; *, ** indicate significant differences at the 0.05 and 0.01 levels. Red means increased abundance, blue means decreased abundance; The darker the color, the greater the increase/decrease.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1368184-g006.tif"/>
</fig>
<p>SDR is significantly positively correlated with effective panicle, spikelets number, and yield during all stages (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref>). <xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref> also shows that during the tillering and jointing stages, SS, SU, and SP are significantly positively correlated with the effective panicles and spikelets number and yield. As shown in <xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6C</bold>
</xref>, during the jointing and maturity stages, STN is highly significantly positively correlated with the effective panicles and spikelets number; SAN and SAK are significantly positively correlated with the effective panicles, the spikelets number, and yield at all stages; SAP is mainly significantly positively correlated with the effective panicles, spikelets per panicle, spikelets number, and yield during the heading stage. In <xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>, during the heading stage, soil microorganisms at the phylum level are mostly positively correlated with yield, with <italic>MBNT15</italic>, <italic>Rokubacteriales</italic>, and <italic>Latescibacterota</italic> genera showing significant positive correlations with the spikelets per panicle, spikelets number, and yield.</p>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<sec id="s4_1">
<label>4.1</label>
<title>Effects of microbial agent on wheat straw decay and soil enzyme activity under wheat straw return</title>
<p>In our study, the combined application of microbial agents under straw returning can significantly enhance the root growth, straw decomposition, soil available nutrients from jointing to heading stage of rice, and improve soil microbial community at heading stage of rice, contributing to a significant increase in the number of effective panicles and total spikelets, thereby increasing rice yield.</p>
<p>Crop straw is a valuable and recyclable biological resource, rich in cellulose, lignin, N, P, K, and trace elements (<xref ref-type="bibr" rid="B33">Mishra et&#xa0;al., 2023</xref>). The decay of crop straw is a complex biochemical process in which microorganisms play important roles. Extensive studies have been conducted on the microbial decay of straw. <xref ref-type="bibr" rid="B28">Liu et&#xa0;al. (2016)</xref> showed that microbial agents accelerated the decay rate of wheat straw in the soil and influenced its final mineralization degree. <xref ref-type="bibr" rid="B31">Mehmood et&#xa0;al. (2020)</xref> and <xref ref-type="bibr" rid="B34">Moon (2022)</xref> also proved that adjusting the microbial diversity in soil by increasing certain microbial members is an effective method to improve the efficacy of soil-beneficial flora, which can improve the decomposition of substances such as straw, promote the removal of harmful substances and improve soil fertility. These studies indicated that microbial agents can significantly promote the decay of crop straw and nutrient release. This is consistent with the results of this study, where straw return to the field (with microbial inoculant application) treatments T<sub>3</sub>-T<sub>5</sub> showed significantly enhanced straw decomposition and nutrient release compared to the straw return treatment without inoculant (T<sub>2</sub>). However, it is important to note that different ratios of microbial inoculants had varying effects on straw decomposition (<xref ref-type="bibr" rid="B17">Li et&#xa0;al., 2024</xref>). Our study indicates that the decomposition rate of wheat straw was highest under the T<sub>5</sub> treatment, with a microbial agent application ratio of <italic>B. subtilis</italic> (25 g): <italic>T. harzianum</italic> (75 g). This suggests that a 1:3 ratio might be more suitable for straw decomposition. This may be due to the fact that <italic>T. harzianum</italic> secretes cellulase, which plays a more critical role in straw decomposition (<xref ref-type="bibr" rid="B18">Li et&#xa0;al., 2016</xref>).</p>
<p>This is consistent with the results of this study, where straw return to the field (with microbial agent application) treatments T<sub>3</sub>-T<sub>5</sub> showed significantly enhanced straw decomposition and nutrient release compared to the straw return treatment without microbial agent (T<sub>2</sub>). However, it is important to note that different ratios of microbial agent had varying effects on straw decomposition. Our study indicates that the decomposition rate of wheat straw was highest under the T<sub>5</sub> treatment, with a microbial agent application ratio of 25 g:75 g. This suggests that a 25:75 ratio might be more suitable for straw decomposition. This may be due to the fact that a significant amount of <italic>T. harzianum</italic> secretes more cellulase, playing a more crucial role in straw decomposition (<xref ref-type="bibr" rid="B18">Li et&#xa0;al., 2016</xref>).</p>
<p>Soil enzymes act as catalysts for biochemical reactions and are closely related to the physicochemical properties, nutrient status, and biological activity of the soil. These enzymes are essential indicators for evaluating soil fertility and environmental quality (<xref ref-type="bibr" rid="B30">Marx et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B4">Chen et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B15">Humberto et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B14">Hu et&#xa0;al., 2022</xref>). <xref ref-type="bibr" rid="B56">Zhang et&#xa0;al. (2023)</xref> showed that the application of exogenous microbial agents reshaped the rhizosphere bacterial community structure of bananas and improved the activity of soil enzymes, such as soil catalase and dehydrogenase. Notably, different agents have varying effects.</p>
<p>
<xref ref-type="bibr" rid="B29">Ma et&#xa0;al. (2023)</xref> applied four kinds of bacteria (<italic>XF-5C</italic>, <italic>Clostridium L13</italic>, <italic>Bacillus licheniformis PB3</italic>, <italic>Methylbacterium B0021</italic>), the four microbial agents significantly increased the activities of soil urease, soil phosphatase and soil peroxidase to varying degrees, <italic>XF-5C</italic> and <italic>L13</italic> significantly increased soil urease activity, while <italic>B0021</italic> significantly increased soil phosphatase activity. <xref ref-type="bibr" rid="B26">Liu A. et&#xa0;al. (2022)</xref> demonstrated that after the application of <italic>Bacillus</italic>, the activities of sucrase, urease, phosphatase, and other enzymes in the soil were significantly improved. <xref ref-type="bibr" rid="B10">Gong et&#xa0;al. (2013)</xref> also found that inoculating <italic>T. harzianum</italic> in rice seedbeds can enhance the activity of soil urease, sucrase, and phosphatase. The results of our study are consistent with previous findings, showing that the soil enzyme activity in the straw return treatment T<sub>2</sub> was relatively higher compared to the no straw return treatment T<sub>1</sub>. Moreover, upon the application of different ratios of <italic>B. subtilis</italic> and <italic>T. harzianum</italic> on top of straw return, the activities of soil sucrase, phosphatase, and urease in all treatment groups were further increased to varying degrees. However, the degree of improvement varied with different ratios, with the best being a <italic>B. subtilis</italic> to <italic>T. harzianum</italic> ratio of 1:1 (T<sub>3</sub>). The application of microbial agents can increase the activity of soil enzymes, and the increased activity of soil enzymes can provide more nutrients for the growth of microorganisms, thus promoting the reproduction of microorganisms, which can form a kind of benign cycle for soil ecology (<xref ref-type="bibr" rid="B51">Wu et&#xa0;al., 2023a</xref>). Therefore, microbial agents can be used to regulate soil microbial diversity. In this experiment, all three ratios of microbial agents improved soil enzyme activity in the rice field, with a <italic>B. subtilis</italic>: <italic>T. harzianum</italic> of 50 g: 50 g being the most effective in enhancing soil enzyme activity. This experiment was conducted in the ecological area of Sichuan, with a wheat straw return rate of 4710 kg/hm<sup>2</sup> and a water content of 15.0% for agent application. However, the suitability of the optimal microbial agent ratio identified in this study for different ecological areas and soil conditions remains to be further validated.</p>
</sec>
<sec id="s4_2">
<label>4.2</label>
<title>Effects of microbial agent application on rice root system, soil nutrients, and yield under wheat straw return</title>
<p>This study showed that applying microbial agents could accelerate straw decay, increase soil nutrients, and promote the growth of rice root systems, thereby improving rice yields. It is noteworthy that the root phenotypes of the wheat straw-returned treatment (T<sub>2</sub>) were mostly weaker than those of the non-returned treatment (T<sub>1</sub>) during the early stages of rice growth. The reason for this phenomenon may be due to the incomplete decomposition of wheat straw in the early stage affecting the root growth, while the root phenotypes were lower in the straw-returned treatment with the application of microbial agents (T<sub>3</sub>-T<sub>5</sub>) compared to the wheat straw-returned treatment (T<sub>2</sub>), which may be due to the fact that nutrients in the wheat straw stimulate the activity of soil microorganisms (<xref ref-type="bibr" rid="B12">Guo et&#xa0;al., 2015</xref>), increasing the nutrient conversion rate of soil microorganisms, which results in microorganisms competing for nutrients with the rice root system to compete for nutrients, temporarily inhibiting the growth of the rice root system (<xref ref-type="bibr" rid="B39">Singh et&#xa0;al., 2004</xref>).</p>
<p>In addition, root length, root surface area and root dry weight were higher in the wheat straw-returned treatment (T<sub>2</sub>) than in the control (T<sub>1</sub>) during the remaining growth period due to nutrient release from the decomposition of wheat straw; and some of the root phenotypes were further increased in the microbial agents applied on top of the wheat straw-returned treatment (T<sub>3</sub>-T<sub>5</sub>).This is consistent with the results of <xref ref-type="bibr" rid="B52">Xu et&#xa0;al. (2018)</xref>, indicating that adding microbial agents could promote plant growth, possibly because the beneficial flora in the microbial inoculants improved the microbial community in the soil (<xref ref-type="bibr" rid="B24">Liu L. et&#xa0;al., 2022</xref>). The application of microbial agents increased soil enzyme activity, making nutrients in the soil more easily absorbed by rice and promoting nutrient release from straw decay (<xref ref-type="bibr" rid="B50">Wu et&#xa0;al., 2023b</xref>), which is beneficial for the growth of the rice root system. The results of this experiment showed that rice yield, effective panicles, spikelet number, single-stem root length, single-stem root surface area, and root dry weight were significantly correlated. This is consistent with the results of <xref ref-type="bibr" rid="B39">Singh et&#xa0;al. (2004)</xref>, indicating that better root morphology can contribute to the formation of effective panicles and spikelet numbers, thereby benefiting yield.</p>
<p>This study demonstrated that the application of microbial agents in combination wheat straw return could increase the soil nutrient content, especially before the jointing stage of rice growth. <xref ref-type="bibr" rid="B3">Chen et&#xa0;al. (2021)</xref> reported that microbial agents can increase the content of available N and P in soil; <xref ref-type="bibr" rid="B46">Wang et&#xa0;al. (2023)</xref> found that microbial agents can not only promote the proliferation of beneficial microorganisms in continuous cropping soil but also change the physical and chemical properties of the soil, such as increasing available phosphorus. Furthermore, <xref ref-type="bibr" rid="B49">Wu and Lin (2003)</xref> revealed that microorganisms have a unique impact on nutrient transformation and can release nutrients from insoluble mineral substances, as observed with microbial agents like <italic>Bacillus</italic> spp. and <italic>Pseudomonas</italic> spp. with phosphate-solubilizing capabilities. This indicates that microbial agents can convert soil-insoluble nutrients into available nutrients that are easily absorbed by plants, thus promoting plant growth, and this finding is similar to the results of this study. In addition, the soil nutrient results of this experiment showed that wheat straw return could significantly increase the available N and P in the soil, which differs from the results of <xref ref-type="bibr" rid="B27">Liu et&#xa0;al. (2018)</xref> and may be attributable to the type of straw and the soil environment. <xref ref-type="bibr" rid="B44">Wang (2006)</xref> reported that the combination of microbial residue and organic fertilizer resulted in higher effective panicles and grain-setting rates, showing an increase of 9.30% in effective panicles and 16.66% in grain-setting rate compared to conventional fertilization, indicating that microbial residue combined with organic fertilizer can stabilize tillering and promote panicles; which is consistent with the results of this study, where the application of microbial agents increased the number of effective panicles by 6.97&#x2013;11.54%. The results of this experiment indicated that the T3 treatment (50g of <italic>B. subtilis</italic> and <italic>T. harzianum</italic> respectively) yielded the best results, significantly increasing soil nutrient content, improving root dry weight, optimizing root morphology, promoting effective tillering of rice, and consequently increasing yield.</p>
</sec>
<sec id="s4_3">
<label>4.3</label>
<title>Effects of microbial agent application on soil bacteria at heading stage of rice under wheat straw return</title>
<p>Rhizosphere soil microbial community is one of the indexes to evaluate soil quality. In general, the richer the soil microbial species and the more active the metabolism, the healthier the soil is and the more suitable it is for plant growth (<xref ref-type="bibr" rid="B53">Xue et&#xa0;al., 2011</xref>). The role and application of microorganisms in agricultural production have been increasingly recognized. The booting stage of rice is a critical period for its nutritional growth and coincides with the peak demand for water and nutrients. Analyzing bacterial communities in the soil during this stage is essential for understanding the structure of microbial communities in the rhizosphere of rice (<xref ref-type="bibr" rid="B48">Wei et&#xa0;al., 2010</xref>). In this study, there were no significant differences in the Simpson index among different treatments, but the Chao1 index was lowest in the T<sub>1</sub> treatment, indicating a significant difference from other treatments. This suggests that straw return and microbial inoculant application can affect the diversity and richness indices of bacterial communities in the rhizosphere of rice, impacting the microbial community structure. The results of the phylum-level richness index shown that the dominant phyla are <italic>Proteobacteria</italic>, followed by <italic>Acidobacteria</italic>, <italic>Chloroflexi</italic>, <italic>Actinobacteria</italic>, and <italic>Firmicutes</italic>. Previous research has indicated that <italic>Proteobacteria</italic> generally thrive in nutrient-rich environments, suggesting that the application of microbial agents has increased the nutrient content in the soil (<xref ref-type="bibr" rid="B40">Solank et&#xa0;al., 2020</xref>). Moreover, <italic>Acidobacteria</italic>, an important group of bacteria in soil, involved in the degradation of plant residues, iron cycling, one-carbon compound metabolism, and photosynthesis, contributing to material cycling and ecological environment construction (<xref ref-type="bibr" rid="B45">Wang et&#xa0;al., 2016</xref>). Research by <xref ref-type="bibr" rid="B19">Li et&#xa0;al. (2020)</xref> on the combined application of organic fertilizers also showed that the most abundant phyla under different treatments are <italic>Proteobacteria</italic>, <italic>Chloroflexi</italic>, and <italic>Actinobacteria</italic>. Additionally, variations in geographic location, soil types, and cultivation methods can lead to differences in bacterial communities in rice fields. Among several treatments, T<sub>3</sub> had the highest yield and, compared to other treatments, also had the highest abundance of <italic>Actinobacteria</italic>, which are widely considered biocontrol agents for plants and effective against rice sheath blight (<xref ref-type="bibr" rid="B47">Wang et&#xa0;al., 2012</xref>). Heatmap analysis indicates that fertilization methods can influence the abundance of microbial communities in the rhizosphere soil, with differences observed at the genus level among treatments. The genus <italic>MBNT15</italic> was dominant in the T<sub>3</sub> treatment, and its role in enhancing rice production requires further research.</p>
</sec>
</sec>
<sec id="s5" sec-type="conclusion">
<label>5</label>
<title>Conclusion</title>
<p>From the results of this experiment, it can be concluded that returning wheat straw to the soil can effectively increase both the alkali-hydrolyzed N and available P in the soil, compared to no returning wheat straw. The application of microbial agents to the returned wheat straw can accelerate straw decay, increase soil enzyme activity and nutrient content, promote the growth of the rice root system, and ultimately increase rice yield. Furthermore, the combination of 50 g of <italic>B. subtilis</italic> and 50 g of <italic>T. harzianum</italic>, applied with a full return of wheat straw, showed the best effect. The dominant bacteria genera of T<sub>3</sub> treatment were <italic>MBNT15</italic>, <italic>Defluviicoccus</italic>, <italic>Rokubacteriales</italic> and <italic>Latescibacterota</italic>. Correlation analysis revealed that soil microorganisms present during the heading stage were significantly positive correlated with yield at the phylum level, including <italic>Gemmatimonadota</italic> and <italic>Firmicutes</italic>. There was a positive correlation between the genus level and the yield of <italic>MBNT15</italic>, <italic>Rokubacteriales</italic> and <italic>Latescibacterota</italic>. In addition, correlation analysis indicated that the straw decay rate, the group root dry weight, soil enzyme, and nutrient content were all positively correlated with effective panicles and total spikelet number of rice, particularly the high group root dry weight of rice after jointing. A high wheat straw decay rate, soil enzyme activity, and enhanced nutrient content from tillering to jointing are key factors in increasing effective panicles and total spikelet number, consequently leading to an increase in rice yield.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data availability statement</title>
<p>The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author contributions</title>
<p>YW: Writing &#x2013; original draft, Methodology, Investigation. YM: Software, Formal analysis, Writing &#x2013; original draft, Methodology, Investigation. ZW: Writing &#x2013; review &amp; editing, Software, Data curation. YY: Writing &#x2013; review &amp; editing, Software, Data curation. XY: Writing &#x2013; review &amp; editing, Visualization. KC: Writing &#x2013; review &amp; editing, Visualization. YL: Writing &#x2013; review &amp; editing, Visualization. ZH: Writing &#x2013; review &amp; editing, Formal analysis. XH: Writing &#x2013; review &amp; editing, Formal analysis. PD: Writing &#x2013; review &amp; editing, Formal analysis. CL: Writing &#x2013; review &amp; editing, Software. ZY: Writing &#x2013; review &amp; editing, Supervision. ZC: Writing &#x2013; review &amp; editing, Supervision. JM: Writing &#x2013; review &amp; editing, Supervision. YS: Writing &#x2013; review &amp; editing, Writing &#x2013; original draft, Visualization, Supervision, Project administration, Methodology, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization.</p>
</sec>
</body>
<back>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Key Research and Development Program Foundation of Ministry of Science and Technology of China (Grant No. 2023YFD2301903); the National Key Research and Development Program Foundation of Ministry of Science and Technology of China (Grant No. 2022YFD1100204); the Project Foundation of the State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (Grant No. SKL-ZY202228); the Research Program Foundation of Key Laboratory of Sichuan Province, China, the Cultivation of Green and Efficient Super Rice Varieties (Grant No. 2022ZDZX0012); Sichuan agricultural machinery R&amp;D manufacturing promotion and application integration pilot project (Hilly area rice intelligent transplanted R&amp;D manufacturing promotion and application); the Rice Breeding Project Foundation of Sichuan Provincial Science and Technology Department (Grant No. 2021YFYZ0005).</p>
</sec>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
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