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学者姓名：李香真
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Abstract ：
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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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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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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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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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 landscape of the drylands is characterized by patches of shrub plants and various successional stages of biocrusts, creating microhabitats that influence soil microbial communities. While previous studies have primarily focused on soil prokaryotes and a limited subset of eukaryotes-mainly fungi-a critical knowledge gap remains: the intrinsic effects of different microhabitat types on the diversity, community composition, and assembly processes of total soil eukaryotes are still poorly understood. To address this gap, we investigated how soil depth, biocrust succession, and shrub cover influence the structure and assembly of total soil eukaryotic communities in the Gurbantunggut Desert, China. 18S rRNA gene-based high-throughput sequencing was used to analyze variations in soil eukaryotic communities among different microhabitats. All three microhabitat factors significantly influenced soil eukaryotic communities. Specifically, alpha diversity was higher in the subsoil layer, early-stage biocrusts, and in areas without shrub cover compared to the top crust layer, late-stage biocrusts, and areas with shrub cover, respectively. Archaeplastida and Opisthokonta emerged as the dominant eukaryotic groups. Network complexity was greater in the top crust, late biocrust stages, and under shrub-free conditions than in the subsoil, early-stage biocrusts, and areas with shrub cover. Community assembly processes shifted from homogeneous to heterogeneous selection from the subsoil to the surface crust and from early to late biocrust stages, whereas a shift from homogeneous selection to ecological drift occurred from shrub-covered to shrub-free areas. Soil pH, total organic carbon, and total phosphorus were identified as key drivers of eukaryotic community variation. Overall, our findings highlight that microhabitat heterogeneity, through its influence on soil nutrient status, plays a critical role in structuring soil eukaryotic communities in desert ecosystems. This study advances our understanding of how multiple microhabitat factors jointly shape microbial community dynamics in drylands.
Keyword ：
biological soil crust biological soil crust community assembly community assembly community composition community composition eukaryotes eukaryotes microhabitats microhabitats
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| GB/T 7714 | Tang, Xin , Liu, Jiahui , Mao, Qian et al. Environmental Heterogeneity Among Microhabitats Shapes the Diversity and Community Composition of Soil Eukaryotes in the Gurbantunggut Desert [J]. | LAND DEGRADATION & DEVELOPMENT , 2025 . |
| MLA | Tang, Xin et al. "Environmental Heterogeneity Among Microhabitats Shapes the Diversity and Community Composition of Soil Eukaryotes in the Gurbantunggut Desert" . | LAND DEGRADATION & DEVELOPMENT (2025) . |
| APA | Tang, Xin , Liu, Jiahui , Mao, Qian , Fang, Binyu , Li, Xiangzhen , Xu, Lin . Environmental Heterogeneity Among Microhabitats Shapes the Diversity and Community Composition of Soil Eukaryotes in the Gurbantunggut Desert . | LAND DEGRADATION & DEVELOPMENT , 2025 . |
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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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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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