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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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Soil fungi are essential to ecosystem processes, yet their elevational distribution patterns and the ecological mechanisms shaping their communities remain poorly understood and actively debated, particularly in arid regions. Here, we investigated the diversity patterns and underlying mechanisms shaping soil fungal communities along an elevational gradient (1,707-3,548 m) on the northern slope of the Central Kunlun Mountains in northwest China. Results indicated that the dominant phyla identified across the seven elevational gradients were Basidiomycota and Ascomycota, displaying a unimodal pattern and a U-shaped pattern in relative abundance, respectively. Soil saprotroph and nectar/tap saprotroph were the dominant functional groups (>1.0%). Along the elevational gradients, soil fungal alpha-diversity demonstrated a generally decreasing trend, whereas beta-diversity showed a contrasting increasing trend. Among the environmental variables, altitude and climate (mean annual precipitation, MAP; mean annual temperature, MAT) were the strongest predictors for alpha-diversity. Partial least squares path modeling (PLSPM) analysis revealed that soil water content (Wat) was the most influential factor driving fungal alpha-diversity, while vegetation coverage (Veg) emerged as the primary determinant of soil fungal community composition. The influence of Wat on fungal alpha-diversity shifted from indirect to direct as elevation increased, transitioning from lower elevations (<= 2,448 m) to higher elevations (>= 2,746 m). Similarly, the impact of Veg on soil fungal community composition exhibited a comparable pattern. The null model analysis revealed that homogeneous selection and dispersal limitation dominated the soil fungal community assembly at elevations lower than 2,448 m and higher than 2,746 m, respectively. Variations in ecological processes may be linked to changes in key environmental factors that influence soil fungal communities in an elevation-dependent manner. These findings can enhance our ability to predict soil fungal diversity patterns and their responses to climate change in the ecosystems of the northern slope of the Central Kunlun Mountain.
Keyword ：
Central Kunlun Mountains Central Kunlun Mountains driving factors driving factors ecological processes ecological processes elevational gradients elevational gradients soil ecosystem soil ecosystem
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| GB/T 7714 | Zhang, Yongguang , Li, Chaonan , Zhang, Zhihao et al. Effects of soil water on fungal community composition along elevational gradients on the northern slope of the Central Kunlun Mountains [J]. | FRONTIERS IN MICROBIOLOGY , 2025 , 15 . |
| MLA | Zhang, Yongguang et al. "Effects of soil water on fungal community composition along elevational gradients on the northern slope of the Central Kunlun Mountains" . | FRONTIERS IN MICROBIOLOGY 15 (2025) . |
| APA | Zhang, Yongguang , Li, Chaonan , Zhang, Zhihao , Li, Chenhong , Zhang, Bo , Jiang, Hongchen et al. Effects of soil water on fungal community composition along elevational gradients on the northern slope of the Central Kunlun Mountains . | FRONTIERS IN MICROBIOLOGY , 2025 , 15 . |
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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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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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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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Biological soil crusts (biocrusts) are widely distributed in global drylands. Both the succession of biocrusts and increased precipitation levels have the capacity to augment soil water availability, thereby exerting significant influence on soil eukaryotic communities. Nonetheless, our understanding of the combined effects of biocrust succession and increasing precipitation on soil eukaryotic communities remains less comprehensive when compared to the well-documented impacts on soil prokaryotic and archaeal communities. In this study, we conducted a broad survey in Chinese deserts and collected biocrust samples in a transect with increasing precipitation. We obtained soil eukaryotic community data using high-throughput sequencing. Our statistical analyses revealed the following key findings: (1) In the absence of biocrusts (within bare soil), there existed a negative correlation between precipitation levels and eukaryotic diversity, as well as community similarity; however, within any of the biocrust successional stage, these patterns turned to be V-shaped, initially declined and then increased, with the nadir occurring at intermediate precipitation levels. (2) Biocrust succession markedly enhanced the abundances of mosses, and which were particularly higher under moderate than other precipitation levels. (3) The abundance of mosses emerged as the principal driver of soil eukaryotic community dynamics, wherein higher moss abundance correlated with diminished species diversity but complex species co-occurrence networks in late biocrust successional (the lichen and moss) stages and under moderate precipitation levels. (4) Soil C:P emerged as a pivotal factor mediating moss abundance and influencing the patterns observed in soil eukaryotic communities. In summary, our study concludes that biocrust succession alters the variation patterns of soil eukaryotic communities along the precipitation gradient.
Keyword ：
Biological soil crusts Biological soil crusts Fungi Fungi Metazoan Metazoan Microalgae Microalgae Protists Protists Succession Succession
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| GB/T 7714 | Xu, Lin , Kou, Yongping , Li, Xiangzhen et al. Succession of biological soil crusts modifies patterns of soil eukaryotic communities along a precipitation gradient [J]. | APPLIED SOIL ECOLOGY , 2025 , 213 . |
| MLA | Xu, Lin et al. "Succession of biological soil crusts modifies patterns of soil eukaryotic communities along a precipitation gradient" . | APPLIED SOIL ECOLOGY 213 (2025) . |
| APA | Xu, Lin , Kou, Yongping , Li, Xiangzhen , Li, Chaonan , Li, Jiabao , Zhang, Bingchang et al. Succession of biological soil crusts modifies patterns of soil eukaryotic communities along a precipitation gradient . | APPLIED SOIL ECOLOGY , 2025 , 213 . |
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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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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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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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