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学者姓名：姚敏杰
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Background and aimsIn agriculture, cropping and fertilization practices can significantly affect the soil microbial community, which in turn affects crop growth. Nevertheless, it remains uncertain how cropping and fertilization treatments influence the structure, function, and metabolic characteristics of microbial communities from bulk soil to rhizosphere soil.MethodHere, a dual-factor experiment was carried out in the black soil of Northeast China, involving cropping (soybean-maize rotation and continuous maize cultivation) and fertilization (no fertilizer control, chemical fertilizer, and chemical fertilizer plus straw incorporation) treatments. After 10 years of experimentation, we collected the maize non-rhizosphere and rhizosphere soil and maize root samples, and conducted the quantification and amplicon sequencing of the 16S rRNA gene and ITS region, as well as metagenomic sequencing and metabolome analysis of soil samples.ResultsOur results revealed that fertilization exerts a greater influence than cropping practices on microbial community structures from soil to maize root by largely altering soil chemical properties, and on various metabolic genes and pathways. Crop rotation primarily mediated microbial community assembly by influencing specific functional groups. Compared to continuous cropping, crop rotation enriches beneficial bacteria, fungi and mycovirus, suppresses fungal pathogen abundance, and lowers fungal species diversity in the maize rhizosphere through balancing metabolites originating from a variety of plant and microbial sources. Crop rotation also imposes stronger homogeneous selections on the prokaryotic community than continuous cropping.ConclusionIn summary, cropping and fertilization treatments shape the maize root-microbiome relationships with distinct mechanisms.
Keyword ：
Crop rotation Crop rotation Fertilization Fertilization Maize microbiome Maize microbiome Metabolome Metabolome Metagenomics Metagenomics Straw incorporation Straw incorporation
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| GB/T 7714 | Liu, Chi , Wang, Jialong , Wang, Yaosheng et al. Crop rotation and fertilization shape the microbiomes of maize rhizosphere soil with distinct mechanisms [J]. | PLANT AND SOIL , 2025 , 507 (1-2) : 89-108 . |
| MLA | Liu, Chi et al. "Crop rotation and fertilization shape the microbiomes of maize rhizosphere soil with distinct mechanisms" . | PLANT AND SOIL 507 . 1-2 (2025) : 89-108 . |
| APA | Liu, Chi , Wang, Jialong , Wang, Yaosheng , Li, Lujun , Feng, Zhihan , Xian, Yuchen et al. Crop rotation and fertilization shape the microbiomes of maize rhizosphere soil with distinct mechanisms . | PLANT AND SOIL , 2025 , 507 (1-2) , 89-108 . |
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center dot Soil CO2 emissions show distinct regional patterns in steppe ecosystems. center dot Altitude, soil carbon, and nitrogen availability drive regional CO2 emission variability. center dot Nitrogen addition enhances CO2 emissions in nitrogen-limited regions, with saturation effects in nitrogen-rich soils. Soil respiration is a pivotal component of the global carbon cycle, yet the regional-scale variations in CO2 emissions across steppe ecosystems, especially under anthropogenic nitrogen deposition, remain poorly understood. Here, we investigated soil CO2 emissions from 30 sites spanning three major steppe regions (Inner Mongolia Plateau, Loess Plateau, and Tibetan Plateau) to elucidate regional patterns and underlying drivers. Our results show that desert steppes emitted 50%-90% less CO2 than meadow steppes, primarily due to differences in soil organic carbon (SOC). Simulated nitrogen deposition via nitrate (NO3-) addition significantly enhanced CO2 emissions in nitrogen-limited regions (Loess and Tibetan Plateaus), while nitrogen-rich soils (Inner Mongolia Plateau) showed saturation effects. Random forest and partial least squares path modeling (PLSPM) analyses showed that nitrogen availability, climate, and elevation jointly regulated CO2 fluxes, with distinct regional pathways. These findings highlight the importance of spatial heterogeneity in regulating carbon emissions and suggest region-specific strategies. Protecting high-carbon steppes and regulating nitrogen inputs are vital for mitigating climate feedbacks in China grasslands.
Keyword ：
nitrogen deposition nitrogen deposition regional-scale regional-scale soil CO2 emission soil CO2 emission steppe ecosystems steppe ecosystems
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| GB/T 7714 | Song, Wei , He, Xiaodong , Qin, Shuping et al. Regional-scale patterns and drivers of soil CO2 emissions in steppe ecosystems [J]. | SOIL ECOLOGY LETTERS , 2025 , 7 (4) . |
| MLA | Song, Wei et al. "Regional-scale patterns and drivers of soil CO2 emissions in steppe ecosystems" . | SOIL ECOLOGY LETTERS 7 . 4 (2025) . |
| APA | Song, Wei , He, Xiaodong , Qin, Shuping , Yao, Minjie , Li, Xiangzhen . Regional-scale patterns and drivers of soil CO2 emissions in steppe ecosystems . | SOIL ECOLOGY LETTERS , 2025 , 7 (4) . |
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The increasing complexity of experimental designs and the volume of data in the microbiome field, along with the diversification of omics data types, pose substantial challenges to statistical analysis and visualization. Here we present a step-by-step protocol based on the R microeco package (https://github.com/ChiLiubio/microeco) that details the statistical analysis and visualization of microbiome data. The omics data types shown consist of amplicon sequencing data, metagenomic sequencing data and nontargeted metabolomics data. The analysis of amplicon sequencing data specifically involves data preprocessing and normalization, core taxa, alpha diversity, beta diversity, differential abundance testing and machine learning. We consider various data analysis scenarios in each section to exhibit the comprehensiveness of the protocol. We emphasize that different normalized data produced by various methods are selected for subsequent analysis of each part based on the best analytical practices. Additionally, in the differential abundance test analysis, we adopt parametric community simulation to enable the performance evaluation of various testing approaches. For the analysis of metagenomic data, the focus is on how bioinformatic analysis data are read and preprocessed, which refers to the major usage differences from amplicon sequencing data. For metabolomics data, we mainly demonstrate the differential test, machine learning and association analysis with microbial abundances. To address some complex analyses, this protocol extensively combines different types of methods to build an analysis pipeline. This protocol is more comprehensive and scalable compared with alternative methods. The provided R codes can run in about 6 h on a laptop computer.
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| GB/T 7714 | Liu, Chi , Mansoldo, Felipe R. P. , Li, Hankang et al. A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package [J]. | NATURE PROTOCOLS , 2025 . |
| MLA | Liu, Chi et al. "A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package" . | NATURE PROTOCOLS (2025) . |
| APA | Liu, Chi , Mansoldo, Felipe R. P. , Li, Hankang , Vermelho, Alane Beatriz , Zeng, Raymond Jianxiong , Li, Xiangzhen et al. A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package . | NATURE PROTOCOLS , 2025 . |
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Applying organic fertilizers can improve soil quality, promote the growth of nitrogen-fixing bacteria, and reduce dependence on chemical fertilizers. Here we investigated the effects of different organic fertilization treatments (organic fertilizer substituting 20 %, 40 % or 60 % of chemical nitrogen fertilizer and increased organic fertilizers at the rate of 45, 90 and 135 t ha(-1)) on soil diazotrophic communities at different growth stages (seedling, flowering, fruiting and maturity) of tomato. The results indicated that both organic fertilizer treatments and growth stages significantly affected the diversity and compositions of soil diazotrophic community, and organic fertilizer had a greater effect than growth stages. Compared to chemical fertilizer, the organic substitution overall increased the relative abundances of Bradyrhizobium, Skermanella, Paenibacillus and Azospirillum. Increased organic fertilizers raised the relative abundances of Methylocaldum and Hyphomicrobium. Organic substitution treatments increased the network complexity and microbial interactions of diazotrophic communities, but increased organic fertilizers reduced the alpha diversity and network complexity. Organic fertilizer affected the diazotrophic community structure and key taxa mainly through altering soil available nutrients and pH. The key diazotrophic genera varied at different growth stages. Azospirilum and Skermanella played an important role in diazotrophic community assembly in the flowering stage, additionally, Sinorhizobium, Paenibacillus, and Zoogloea were important in the fruiting stage. This study provided a deep understanding of the roles of organic fertilizer in regulating soil diazotrophic communities in tomato field.
Keyword ：
Co-occurrence network Co-occurrence network Diazotrophs Diazotrophs Increased organic fertilizer Increased organic fertilizer Organic fertilizer substitution Organic fertilizer substitution Tomato Tomato
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| GB/T 7714 | Lu, Chunmiao , Luo, Jiahui , Sheng, Tianlong et al. Diazotrophic communities shift with organic fertilizer substitution and growth stages in tomato field soil [J]. | EUROPEAN JOURNAL OF SOIL BIOLOGY , 2025 , 126 . |
| MLA | Lu, Chunmiao et al. "Diazotrophic communities shift with organic fertilizer substitution and growth stages in tomato field soil" . | EUROPEAN JOURNAL OF SOIL BIOLOGY 126 (2025) . |
| APA | Lu, Chunmiao , Luo, Jiahui , Sheng, Tianlong , Xie, Yuebin , Xian, Yuchen , Jiang, Yanqiong et al. Diazotrophic communities shift with organic fertilizer substitution and growth stages in tomato field soil . | EUROPEAN JOURNAL OF SOIL BIOLOGY , 2025 , 126 . |
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R mecoturn package is developed for microbial turnover analysis.Linear mixed-effects model is implemented for beta diversity analysis.The shift profiles of taxonomic abundances can be fitted with multiple models.The combination of different approaches can address complex turnover cases.One of the most critical studies on microbial ecology is to reveal microbial turnover patterns along spatial, temporal, or environmental gradients. In such studies, it is often necessary to select appropriate statistical methods based on the experimental design, especially when considering random effects. However, there are few tools that can be readily applied to such cases. In this study, we present a mecoturn R package, designed to support various statistical analyses of microbial turnover along gradients. Two R6 classes (betaturn and taxaturn) have been developed to investigate the beta diversity of microbial communities and the shift profiles of taxonomic abundances, respectively. In each category, several fundamental functions and approaches were encapsulated to enable data preparation, data conversion and filtering, model fitting and visualization. Each analytical component can be implemented with the consideration of random effects, such as (generalized) linear mixed-effects model. Especially in the analysis of beta diversity, the application of linear mixed-effects model fills a gap in the field of related methodologies. To demonstrate the efficacy of two classes and their diverse methodologies, we employed microbial community datasets of bulk soil, rhizosphere soil, and root endophytes of wheat from varying regions of China to conduct a comparative analysis for different pipelines. We found that reasonable analysis considering the heterogeneity of plants can strengthen the reliability of statistical hypothesis testing. The mecoturn package can be freely installed from CRAN (The Comprehensive R Archive Network) or GitHub repository (accessible at: github.com/ChiLiubio/mecoturn).
Keyword ：
beta diversity beta diversity ecology ecology gradient gradient microbial community microbial community taxonomic abundance taxonomic abundance
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| GB/T 7714 | Liu, Chi , Luo, Jiahui , Lu, Chunmiao et al. mecoturn: An R package for deciphering microbial turnover patterns along gradients [J]. | SOIL ECOLOGY LETTERS , 2025 , 7 (4) . |
| MLA | Liu, Chi et al. "mecoturn: An R package for deciphering microbial turnover patterns along gradients" . | SOIL ECOLOGY LETTERS 7 . 4 (2025) . |
| APA | Liu, Chi , Luo, Jiahui , Lu, Chunmiao , Sheng, Tianlong , Zeng, Raymond Jianxiong , Li, Xiangzhen et al. mecoturn: An R package for deciphering microbial turnover patterns along gradients . | SOIL ECOLOGY LETTERS , 2025 , 7 (4) . |
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phoD richness and abundance was higher on the southeastern than northwestern plateau.phoD richness first increased, then decreased with rising temperatures.phoD richness increased consistently with higher humidity.Warm, humid conditions led to soil acidification, driving phoD taxa distribution.The alkaline phosphatase (phoD) gene-encoding bacterial communities (phoD-harbouring communities, hereafter) play crucial roles in organic phosphorus (Po) mineralisation across global terrestrial ecosystems. However, their geographic distribution and driving factors remain unclear, largely due to the mosaic temperature and humidity patterns and the lack of comprehensive high-resolution sampling data across the Qinghai-Tibet Plateau. We addressed this gap using amplicon sequencing techniques and analyses of soil properties as well as plant biomass. Plant biomass, soil organic carbon (C), Po content, C:P ratio, alkaline phosphatase (ALP) activity, and the richness and abundance of key soil phoD-harbouring taxa were higher in warmer, more humid regions, such as the southeastern plateau than the northeastern plateau, while soil pH followed an inverse trend. Soil pH and Po content emerged as the key factors shaping the geographic distribution of phoD-harbouring communities. Acidic soils were associated with higher C:P ratios, community richness, ALP activity, and Po content than alkaline soils. Our findings suggest that warmer, more humid regions promote soil acidification, which in turn drive changes in phoD-harbouring communities, enhance ALP activity, and stimulate Po mineralisation. This study provides new insights into the geographic distribution of phoD-harbouring communities and their role in Po mineralisation across the Qinghai-Tibet Plateau.
Keyword ：
alkaline phosphatase alkaline phosphatase geographic distribution geographic distribution organic phosphorus mineralisation organic phosphorus mineralisation phoD-harbouring community phoD-harbouring community phosphorus fractions phosphorus fractions Qinghai-Tibet Plateau Qinghai-Tibet Plateau
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| GB/T 7714 | Xu, Lin , Li, Jiabao , Li, Chaonan et al. The distribution of soil alkaline phosphatase (phoD) gene harbouring bacteria across Qinghai-Tibet Plateau [J]. | SOIL ECOLOGY LETTERS , 2025 , 7 (2) . |
| MLA | Xu, Lin et al. "The distribution of soil alkaline phosphatase (phoD) gene harbouring bacteria across Qinghai-Tibet Plateau" . | SOIL ECOLOGY LETTERS 7 . 2 (2025) . |
| APA | Xu, Lin , Li, Jiabao , Li, Chaonan , Kou, Yongping , Yao, Minjie , Wang, Changting et al. The distribution of soil alkaline phosphatase (phoD) gene harbouring bacteria across Qinghai-Tibet Plateau . | SOIL ECOLOGY LETTERS , 2025 , 7 (2) . |
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Root-associated fungal communities of wheat have a great impact on plant health, crop productivity and quality. However, little is known about the relationships among wheat varieties, fungal communities, and wheat productivity. In this study, we analyzed fungal communities in the endosphere and rhizosphere across 95 wheat varieties during two important wheat growth stages, i.e., the regreening stage and the heading stage. The results showed that abundant and core subcommunities played a prominent role in shaping the overall fungal community composition and structure. Stochastic processes including undominated process and dispersal limitation were the main assembly mechanisms in both endosphere and rhizosphere. Rhizosphere fungi at the regreening stage contained the most low-abundance keystone taxa, which contributed to maintaining community stability and functionality. Wheat quality and yield were positively affected by rare taxa in the rhizosphere at the regreening stage. Wheat yield showed significant positive correlations with keystone taxa and Glomeromycota at the heading stage. Abundant and core taxa exhibited higher heritability than rare and non-core taxa. In the rhizosphere, abundant subcommunity was enriched with taxa of low/moderate heritability at regreening stage, while rare subcommunity recruited taxa with higher heritability at heading stage. While abundant and core taxa strongly influenced overall community structure and composition, the importance of less abundant rhizosphere species should be emphasized for the keystone status, the relationships with wheat quality/yield, and the higher heritability. This study enhances our understanding of wheat-fungal interactions and their implications for sustainable agriculture, guiding wheat breeding and management practices to improve productivity.
Keyword ：
Heritability Heritability Rare taxa Rare taxa Root-associated fungi Root-associated fungi Wheat varieties Wheat varieties Wheat yield Wheat yield
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| GB/T 7714 | Kang, Xia , Zheng, Yuyin , Feng, Zhihan et al. Contrasting roles of abundant and rare root-associated fungi in wheat: Community assembly, heritability and agronomic impacts [J]. | APPLIED SOIL ECOLOGY , 2025 , 209 . |
| MLA | Kang, Xia et al. "Contrasting roles of abundant and rare root-associated fungi in wheat: Community assembly, heritability and agronomic impacts" . | APPLIED SOIL ECOLOGY 209 (2025) . |
| APA | Kang, Xia , Zheng, Yuyin , Feng, Zhihan , Yao, Minjie , Li, Xiangzhen , Han, Dejun et al. Contrasting roles of abundant and rare root-associated fungi in wheat: Community assembly, heritability and agronomic impacts . | APPLIED SOIL ECOLOGY , 2025 , 209 . |
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Studying the physioecological mechanisms behind the high daily productivity of ratoon rice is essential for improving farming strategies and maintaining stable yields in intensive cropping systems. This study compared the physiological traits of main crop rice (MR), ratooning season rice (RSR), and single-cropping mid-late rice (LR) with the same genotype and flowering time as RSR, from 2021 to 2022. The results demonstrated that RSR maintained higher leaf SPAD values than both MR and LR at the heading stage. Moreover, the translocation efficiency of stem-stored non-structural carbohydrates (NSC) to grains was significantly greater in RSR compared to MR (24.18-58.1%) and LR (24.59-63.5%). C-13 isotope labeling confirmed that RSR exhibited superior assimilate allocation to grain pools, with values 13.7% and 14.74% higher than those of MR and LR, respectively. Anatomical analysis of vascular bundles at panicle-stem nodes showed an increased phloem area proportion in RSR. Furthermore, RSR exhibited elevated expression levels of genes associated with nitrogen uptake and metabolism regulation (AMTs, NRTs, and NRFs), sucrose transport (SUTs, SWEET11, and INVs), and stress tolerance (TPSs and TPPs), particularly within its grain parts, relative to MR and LR. Enzymatic activities of sucrose synthase (SS), sucrose phosphate synthase (SPS), and invertase in RSR grains were also significantly higher than in MR and LR. Further analysis indicated that these advantageous physiological traits in RSR arise from the elevated gene expression and enzyme activities, which are positively modulated by endogenous hormones including zeatin riboside (ZR), abscisic acid (ABA), and indole-3-acetic acid (IAA). These hormones serve as key factors for the efficient coordination of matter production and translocation in rice ratooning. This study provides important theoretical and practical insights into the formation and regulation mechanisms of high and stable yield in ratoon rice.
Keyword ：
Dry matter accumulation Dry matter accumulation Enzymatic activity Enzymatic activity Material transport Material transport Phytohormone Phytohormone Ratoon rice Ratoon rice Translocation Translocation
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| GB/T 7714 | Xie, Yuebin , Zou, Jingnan , Cao, Shuying et al. The Higher Average Daily Grain Yield and Its Formation Mechanisms Underlying the Efficient Photo-Assimilate Transport in Rice Ratooning [J]. | RICE , 2025 , 18 (1) . |
| MLA | Xie, Yuebin et al. "The Higher Average Daily Grain Yield and Its Formation Mechanisms Underlying the Efficient Photo-Assimilate Transport in Rice Ratooning" . | RICE 18 . 1 (2025) . |
| APA | Xie, Yuebin , Zou, Jingnan , Cao, Shuying , Lan, Chaojie , Qin, Bin , Xu, Hailong et al. The Higher Average Daily Grain Yield and Its Formation Mechanisms Underlying the Efficient Photo-Assimilate Transport in Rice Ratooning . | RICE , 2025 , 18 (1) . |
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One of the key goals of ecology is to understand how communities are assembled. The species co-existence theory suggests that community beta-diversity is influenced by species pool and community assembly processes, such as environmental filtering, dispersal events, ecological drift and biotic interactions. However, it remains unclear whether there are similar beta-diversity patterns among different soil microbial groups and whether all these mechanisms play significant roles in mediating beta-diversity patterns. By conducting a broad survey across Chinese deserts, we aimed to address these questions by investing biological soil crusts (biocrusts). Through amplicon-sequencing, we acquired beta-diversity data for multiple microbial groups, that is, soil total bacteria, diazotrophs, phoD-harbouring taxa, and fungi. Our results have shown varying distance decay rates of beta-diversity across microbial groups, with soil total bacteria showing a weaker distance-decay relationship than other groups. The impact of the species pool on community beta-diversity varied across microbial groups, with soil total bacteria and diazotrophs being significantly influenced. While the contributions of specific assembly processes to community beta-diversity patterns varied among different microbial groups, significant effects of local community assembly processes on beta-diversity patterns were consistently observed across all groups. Homogenous selection and dispersal limitation emerged as crucial processes for all groups. Precipitation and soil C:P were the key factors mediating beta-diversity for all groups. This study has substantially advanced our understanding of how the communities of multiple microbial groups are structured in desert biocrust systems.
Keyword ：
beta-diversity beta-diversity biological soil crusts biological soil crusts community assembly processes community assembly processes drylands drylands soil microbial community soil microbial community species coexistence theory species coexistence theory
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| GB/T 7714 | Xu, Lin , Li, Xiangzhen , Tang, Xin et al. Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems [J]. | MOLECULAR ECOLOGY , 2024 , 33 (13) . |
| MLA | Xu, Lin et al. "Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems" . | MOLECULAR ECOLOGY 33 . 13 (2024) . |
| APA | Xu, Lin , Li, Xiangzhen , Tang, Xin , Kou, Yongping , Li, Chaonan , Li, Jiabao et al. Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems . | MOLECULAR ECOLOGY , 2024 , 33 (13) . |
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The pmoA gene serves as a biomarker of the methane-oxidizing communities in soils. Therefore, much effort has been directed at quantifying the pmoA gene to quantify the abundances of methanotrophs at the local or regional scale, however, the abundances of methane-oxidizing bacteria as well as factors shaping the abundance of methane-oxidizing bacteria at the global scale remains poorly understood. To fill this knowledge gap, we per-formed a quantitative analysis of peer-reviewed publications to assess the distribution of the pmoA gene abundances across various biomes, climatic zones, land use, and between forest and grassland biomes, with 114 observations collected from 27 peer-reviewed articles. Results showed that the abundance of pmoA genes increased significantly with latitude, whereas a higher pmoA gene abundance was observed in the boreal forest than in cold grassland, dry grassland, temperate forest, and temperate grassland, while tropical grassland and the tropical forest did not differ significantly from other biomes in pmoA gene abundance. The PCA indicated that pmoA abundance was positively correlated with MAT and MAP but negatively correlated with pH. The TOC was as a key driver of pmoA gene abundance at a global scale. The abundance of the pmoA gene in tropical and boreal forests increased with TOC, while the pmoA gene abundance in temperate forests and grasslands decreased with TOC. The pmoA gene abundance in the tropical and subtropical zones increased with TOC while pmoA gene abundance in the temperate climatic zones decreased with TOC. The path model revealed a direct effect of vegetation cover on the pmoA gene abundance, but indirect effect of climate and soil properties on pmoA gene abundance via their direct effect on vegetation cover. We suggest that the changes of TOC and C:N ratio due changes of vegetation and climate across biomes may serve as a possible mechanism underlying the idiosyncratic effects of TOC on the abundance of methanotrophs in soils.
Keyword ：
Humid and arid climate Humid and arid climate Land use Land use Linear mixed-effect model pmoA gene Linear mixed-effect model pmoA gene PLS-PM model PLS-PM model Quantitative review Quantitative review
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| GB/T 7714 | Hedenec, Petr , Alias, Amirah , Almahasheer, Hanan et al. Global assessment of soil methanotroph abundances across biomes and climatic zones: The role of climate and soil properties [J]. | APPLIED SOIL ECOLOGY , 2024 , 195 . |
| MLA | Hedenec, Petr et al. "Global assessment of soil methanotroph abundances across biomes and climatic zones: The role of climate and soil properties" . | APPLIED SOIL ECOLOGY 195 (2024) . |
| APA | Hedenec, Petr , Alias, Amirah , Almahasheer, Hanan , Liu, Chi , Chee, Poh Seng , Yao, Minjie et al. Global assessment of soil methanotroph abundances across biomes and climatic zones: The role of climate and soil properties . | APPLIED SOIL ECOLOGY , 2024 , 195 . |
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