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学者姓名：李香真
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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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Background Invasive plants often positively interact with nitrogen cycle microorganisms, but the key response species of nitrification community to plant invasion remain poorly understood. Additionally, the recent finding of complete ammonia oxidizing (comammox) bacterium Nitrospira has caused a heated debate on the relative importance of ammonia oxidizing bacteria (AOB), archaea (AOA) and comammox Nitrospira in environments. Methods We conducted a field study to explore the effect of the exotic plant Solidago canadensis invading the habitat of the native plant Humulus scandens on the soil communities of AOB, AOA and comammox Nitrospira in eastern China. The invasions were classified to low, medium and high levels (S. canadensis < 10%, similar to 50%, and > 90%, respectively). Results We found that comammox Nitrospira existed in all samples (0.36 to 1.33 x 10(7) copies g(-1) DW soil, n = 3), dominating over both AOB (0.29 to 8.52 x 10(6) copies g(-1) DW soil) and AOA (0.38 to 1.74 x 10(5) copies g(-1) DW soil) by 1-2 orders of magnitude. S. canadensis invasion decreased the abundance of AOB and AOA (p < 0.05) but increased the abundance of comammox Nitrospira in S. canadensis rhizosphere. All comammox Nitrospira detected in this study fall into Clade A rather than Clade B. S. canadensis invasion decreased the diversity of comammox Nitrospira (p < 0.05). Importantly, S. canadensis invasion changed the community structure of comammox Nitrospira in plant rhizospheres. Conclusion Our study suggests that comammox Nitrospira might be a crucial and beneficial N-cycler bacterium in S. canadensis invasion process.
Keyword ：
Ammonia-oxidizing microorganisms Ammonia-oxidizing microorganisms Comammox Nitrospira Comammox Nitrospira Plant invasion Plant invasion Plant-microbe interactions Plant-microbe interactions Solidago canadensis Solidago canadensis
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| GB/T 7714 | Qiao, Wen-Tao , Wang, Yong-Feng , Hou, Xue-Yan et al. Soil comammox Nitrospira dominates over ammonia-oxidizing archaea and bacteria in the invasion of Solidago canadensis [J]. | PLANT AND SOIL , 2025 , 513 (2) : 2417-2431 . |
| MLA | Qiao, Wen-Tao et al. "Soil comammox Nitrospira dominates over ammonia-oxidizing archaea and bacteria in the invasion of Solidago canadensis" . | PLANT AND SOIL 513 . 2 (2025) : 2417-2431 . |
| APA | Qiao, Wen-Tao , Wang, Yong-Feng , Hou, Xue-Yan , Li, Xiang-Zhen , Du, Dao-Lin , Dai, Zhi-Cong et al. Soil comammox Nitrospira dominates over ammonia-oxidizing archaea and bacteria in the invasion of Solidago canadensis . | PLANT AND SOIL , 2025 , 513 (2) , 2417-2431 . |
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Introduction One of the central aims in ecology is elucidating the mechanisms that shape community diversity. While biodiversity patterns across geographical gradients are often attributed both to local assembly processes and regional species pools, the distinct roles of these factors in shaping soil aerobic methanotrophic diversity remain underexplored.Methods Using amplicon sequencing and bioinformatics analysis, this study focuses on comparing the relative importance of species pool and community assembly processes in shaping soil methanotrophic communities across three distinct plateaus in China: the Loess Plateau, the Qinghai-Tibetan Plateau, and the Inner Mongolian Plateau. Each of these plateaus includes three distinct steppe habitats: desert, meadow, and typical steppe.Results Our findings reveal that pmoA beta (beta)-diversity followed a distance-decay pattern, which declined with geographical distance at different rates depending on the steppe type and area, potentially due to diverse mechanisms of community assembly. Moreover, a decoupling between beta-diversity and gamma-diversity observed, suggesting that local community assembly mechanisms primarily account for variations in beta-diversity patterns. Furthermore, the relative significance of these assembly processes (e.g., dispersal limitation, drift, environmental filtering, and biotic interactions) varies according to spatial scales and steppe types. Notably, the differential environmental conditions (such as soil pH, yearly average temperature, and precipitation) across scales and steppe habitats primarily modulate the intensity of these assembly processes, thereby influencing beta-diversity.Conclusion In summary, our study emphasizes the crucial role of local community assembly in changing soil methanotrophic beta-diversity's geographical patterns, highlighting the significance of a nuanced understanding of these processes for effective conservation and management strategies.
Keyword ：
community assembly community assembly deterministic processes deterministic processes soil methanotrophic communities soil methanotrophic communities species pool species pool stochastic processes stochastic processes
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| GB/T 7714 | Kou, Yongping , Feng, Zhe , Li, Huan et al. Assembly mechanisms, not species pool, shape β-diversity of soil methanotrophic communities in steppes of China [J]. | FRONTIERS IN MICROBIOLOGY , 2025 , 15 . |
| MLA | Kou, Yongping et al. "Assembly mechanisms, not species pool, shape β-diversity of soil methanotrophic communities in steppes of China" . | FRONTIERS IN MICROBIOLOGY 15 (2025) . |
| APA | Kou, Yongping , Feng, Zhe , Li, Huan , Liu, Yanjiao , Xu, Lin , Li, Xiangzhen . Assembly mechanisms, not species pool, shape β-diversity of soil methanotrophic communities in steppes of China . | FRONTIERS IN MICROBIOLOGY , 2025 , 15 . |
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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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Maintaining a dynamic balance among various life-history traits is crucial for survival in a warming world, yet the underlying mechanisms remain enigmatic. In this study, we employed the western clawed frog (Xenopus tropicalis) as a model and conducted a long-tern experiment from zygotes to adult stage. We find that even within the previously considered normal temperature range, a 5 degrees C increase in ambient temperature can establish a new metabolic state, resulting in elevated oxidative stress and a shift in energy allocation towards immune defense at the expense of sexual development. This conceptual framework of temperature-dependent trade-off strategy suggests that, while some studies observed that warm temperature reduces the risk of infection, it is important to note that this change may present challenges in the form of accelerated aging and reduced fertility, especially in ectotherms. These results not only indicate a far more complex adaptive response to future climate change than previously anticipated, but also provide a concise method for constructing animal models to explore diseases related to homeostatic disorders.
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| GB/T 7714 | Li, Jiaying , Zhu, Jiahao , Budian, Ayi et al. Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis [J]. | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
| MLA | Li, Jiaying et al. "Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis" . | COMMUNICATIONS BIOLOGY 8 . 1 (2025) . |
| APA | Li, Jiaying , Zhu, Jiahao , Budian, Ayi , Zeng, Yiwei , Wang, Shouhong , Gong, Yuzhou et al. Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis . | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
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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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Introduction Flavonoids are the most abundant secondary metabolites in plants and play important roles in plant growth, environmental adaptation, and human health. Tobacco serves as a vital cash crop and key source of flavonoids. Given tobacco's high nitrogen demand and the particular sensitivity of flavonoid synthesis to nitrogen supply, understanding the regulatory mechanisms of flavonoid biosynthesis under varying nitrogen conditions is essential.Methods and results We systematically investigated the flavonoid biosynthesis pathways in the cigar tobacco cultivar Haiyan 204 under different nitrogen application rates using integrated transcriptomic and metabolomic analyses. This study identified 694 differentially expressed metabolites (DEMs) and 6,114 differentially expressed genes (DEGs). Integrated analyses revealed significant enrichment in the flavonoid biosynthesis and phenylpropanoid biosynthesis pathways. A regulatory network of flavonoid biosynthesis in response to nitrogen was constructed. Weighted gene co-expression network analysis (WGCNA) identified CHS2 as a key gene strongly associated with flavonoid biosynthesis, alongside its potential regulatory transcription factors MYB7, MYB9, bHLH14, and MYB_related1. The reliability of transcriptome data was validated via qPCR.Discussion These results provide a scientific basis for elucidating the biosynthesis mechanisms of tobacco flavonoids and identifying key nitrogen-responsive genes. The constructed regulatory network and identified transcriptional regulators offer critical insights into nitrogen-modulated flavonoid synthesis in cigar tobacco.
Keyword ：
cigar tobacco cigar tobacco flavonoids flavonoids metabolomics metabolomics nitrogen nitrogen transcriptomics transcriptomics
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| GB/T 7714 | Jia, Kai , Shi, Juanjuan , Bai, Lingli et al. Integrated transcriptomic and metabolomic analysis of flavonoid biosynthesis in cigar tobacco leaves under variable nitrogen regimes [J]. | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
| MLA | Jia, Kai et al. "Integrated transcriptomic and metabolomic analysis of flavonoid biosynthesis in cigar tobacco leaves under variable nitrogen regimes" . | FRONTIERS IN PLANT SCIENCE 16 (2025) . |
| APA | Jia, Kai , Shi, Juanjuan , Bai, Lingli , Wang, Xueren , Wang, Yuemin , Li, Xiangzhen et al. Integrated transcriptomic and metabolomic analysis of flavonoid biosynthesis in cigar tobacco leaves under variable nitrogen regimes . | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
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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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