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Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil

Yi ZHONG, Jian WANG, Yizhi SONG, Yuting LIANG, Guanghe LI

《环境科学与工程前沿（英文）》 2012年 第6卷 第6期   页码 797-805 doi: 10.1007/s11783-012-0405-z

摘要： A rhizobox system constructed with crude oil-contaminated soil was vegetated with alfalfa ( L.) to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to explore the potential mechanisms by which plants enhance the removal of crude oil in soil. During the 80-day experiment, 31.6% of oil was removed from the adjacent rhizosphere (AR); this value was 27% and 53% higher than the percentage of oil removed from the far rhizosphere (FR) and from the non-rhizosphere (NR), respectively. The populations of heterotrophic bacteria and hydrocarbon-degrading bacteria were higher in the AR and FR than in the NR. However, the removal rate of crude oil was positively correlated with the proportion of hydrocarbon-degrading bacteria in the rhizosphere. In total, 796, 731, and 379 functional genes were detected by microarray in the AR, FR, and NR, respectively. Higher proportions of functional genes related to carbon degradation and organic remediation, were found in rhizosphere soil compared with NR soil, suggesting that the rhizosphere selectively increased the abundance of these specific functional genes. The increase in water-holding capacity and decrease in pH as well as salinity of the soil all followed the order of AR>FR>NR. Canonical component analysis showed that salinity was the most important environmental factor influencing the microbial functional structure in the rhizosphere and that salinity was negatively correlated with the abundance of carbon and organic degradation genes.

关键词： crude oil-contaminated soil     phytoremediation     rhizosphere effects     rhizobox     functional genes    

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The diazotrophic community in oat rhizosphere: effects of legume intercropping and crop growth stage

Yadong YANG, Xiaomin FENG, Yuegao HU, Zhaohai ZENG

《农业科学与工程前沿（英文）》 2019年 第6卷 第2期   页码 162-171 doi: 10.15302/J-FASE-2018212

摘要：

In this study, the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil in three cropping systems and at two oat growth stages were investigated using real-time PCR and Illumina MiSeq sequencing. The gene abundance in oat-soybean intercropping (OSO) and oat-mungbean intercropping (OMO) was significantly greater than that in sole oat (O), but the gene abundance significantly decreased at the later stage in all the treatments. Alpha diversity indices in OSO and OMO were higher at the heading stage, but lower at the maturity stage than that in O. and were the dominant genera identified in all samples, with an average proportion of 35.8% and 12.4%, respectively. The proportion of dominant genera showed significant differences and varied with cropping system and growth stage. Principal component analysis showed that growth stage had a stronger effect than intercropping on the diazotrophic community structure. However, Mantel test and redundancy analysis showed there was no environmental factor significantly correlated to the diazotrophic community structure. Our results demonstrate that intercropping had a weaker effect than growth stage on the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil.

关键词： community composition     Illumina MiSeq sequencing     nifH gene     oat-legume intercropping     rhizosphere soil    

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Effect of rhizosphere on soil microbial community and pyrene biodegradation

SU Yuhong, YANG Xueyun, CHIOU Cary

《环境科学与工程前沿（英文）》 2008年 第2卷 第4期   页码 468-474 doi: 10.1007/s11783-008-0078-9

摘要： To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and pyrene (PYR) biodegradation. The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting. With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 34.0%, 28.4%, 27.7%, and 9.9%, respectively. However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue. The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere. Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers. The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR. Total PLFAs in planted soils were all higher than those in non-planted soils. PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did.
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Sulfur mediated heavy metal biogeochemical cycles in coastal wetlands: From sediments, rhizosphere to

《环境科学与工程前沿（英文）》 2022年 第16卷 第8期 doi: 10.1007/s11783-022-1523-x

摘要：

• In sediments, the transformation of sulfides may lead to the release of heavy metals.

关键词： Coastal wetland     Heavy metal     Sulfur     Biogeochemical cycle    

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Changes in bulk soil affect the disease-suppressive rhizosphere microbiome against Fusarium wilt disease

Lin FU, Wu XIONG, Francisco DINI-ANDREOTE, Beibei WANG, Chengyuan TAO, Yunze RUAN, Zongzhuan SHEN, Rong LI, Qirong SHEN

《农业科学与工程前沿（英文）》 2020年 第7卷 第3期   页码 307-316 doi: 10.15302/J-FASE-2020328

摘要：

Harnessing disease-suppressive microbiomes constitutes a promising strategy for optimizing plant growth. However, relatively little information is available about the relationship between bulk and rhizosphere soil microbiomes. Here, the assembly of banana bulk soil and rhizosphere microbiomes was investigated in a monoculture system consisting of bio-organic (BIO) and organic management practices. Applying BIO practice in newly reclaimed fields resulted in a high-efficiency biocontrol rate, thus providing a promising strategy for pre-control of Fusarium wilt disease. The soil microbiota was further characterized by MiSeq sequencing and quantitative PCR. The results indicate that disease suppression was mediated by the structure of a suppressive rhizosphere microbiome with respect to distinct community composition, diversity and abundance. Overall microbiome suppressiveness was primarily related to a particular set of enriched bacterial taxa affiliated with s, , , , and . Finally, structural equation modeling was used to show that the changes in bulk soil bacterial community determined its induced rhizosphere bacterial community, which serves as an important and direct factor in restraining the pathogen. Collectively, this study provides an integrative approach to disentangle the biological basis of disease-suppressive microbiomes in the context of agricultural practice and soil management.

关键词： agricultural practice     bulk soil     disease suppression     rhizosphere ecology    

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Improving the efficiency and effectiveness of global phosphorus use: focus on root and rhizosphere levels

null

《农业科学与工程前沿（英文）》 2019年 第6卷 第4期   页码 357-365 doi: 10.15302/J-FASE-2019275

摘要：

Phosphorus (P) is essential for life and for efficient crop production, but global P use with limited recycling is inefficient in several sectors, including agronomy. Unfortunately, plant physiologists, agronomists, farmers and end users employ different measures for P use efficiency (PUE), which often masks their values at different scales. The term P use effectiveness, which also considers energetic and sustainability measures in addition to P balances, is also a valuable concept. Major physiological and genetic factors for plant P uptake and utilization have been identified, but there has been limited success in genetically improving PUE of modern crop cultivars. In maize, studies on root architectural and morphological traits appear promising. Rhizosphere processes assist in mobilizing and capturing sparingly soluble phosphate from rock phosphate. Combinations of phosphate-solubilizing microorganisms with ammonium-based nitrogen fertilizer, as well as strategies of fertilizer placement near the roots of target crops, can moderately enhance PUE. The desired concentration of P in the products differs, depending on the final use of the crop products as feed, food or for energy conversion, which should be considered during crop production.

关键词： acquisition efficiency     plant growth promoting rhizobacteria     phosphate     use efficiency     utilization efficiency    

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Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

Yang SONG, Chen ZHU, Waseem RAZA, Dongsheng WANG, Qiwei HUANG, Shiwei GUO, Ning LING, Qirong SHEN

《农业科学与工程前沿（英文）》 2019年 第6卷 第2期   页码 206-206 doi: 10.15302/J-FASE-2018234

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Moving policy and regulation forward for single-use plastic alternatives

《环境科学与工程前沿（英文）》 2021年 第15卷 第3期 doi: 10.1007/s11783-021-1423-5

摘要： Single-use plastics are often used once or cannot be reused for extended periods. They are widely consumed with the rapid development of social economy. The waste generated by single-use plastics threatens ecosystem health by entering the environment and ultimately restricts sustainable human development. The innovation of sustainable and environmentally friendly single-use plastic alternative materials and the joint participation of governments, enterprises and the public are promising technologies and management approaches that can solve the problem of single-use plastics wastes. The development of single-use plastic alternative products can be promoted fundamentally only by improving relevant legislation and standards, providing differentiated industrial policies, encouraging scientific and technological innovation and expanding public participation.

关键词： Single-use plastic alternatives     Policy     Regulation     Sustainable development    

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Phase transition regulation and caloric effect

《能源前沿（英文）》 2023年 第17卷 第4期   页码 463-477 doi: 10.1007/s11708-023-0860-1

摘要： Solid state refrigeration based on caloric effect is regarded as a potential candidate for replacing vapor-compression refrigeration. Numerous methods have been proposed to optimize the refrigeration properties of caloric materials, of which single field tuning as a relatively simple way has been systemically studied. However, single field tuning with few tunable parameters usually obtains an excellent performance in one specific aspect at the cost of worsening the performance in other aspects, like attaining a large caloric effect with narrowing the transition temperature range and introducing hysteresis. Because of the shortcomings of the caloric effect driven by a single field, multifield tuning on multicaloric materials that have a coupling between different ferro-orders came into view. This review mainly focuses on recent studies that apply this method to improve the cooling performance of materials, consisting of enlarging caloric effects, reducing hysteresis losses, adjusting transition temperatures, and widening transition temperature spans, which indicate that further progress can be made in the application of this method. Furthermore, research on the sign of lattice and spin contributions to the magnetocaloric effect found new phonon evolution mechanisms, calling for more attention on multicaloric effects. Other progress including improving cyclability of FeRh alloys by introducing second phases and realizing a large reversible barocaloric effect by hybridizing carbon chains and inorganic groups is described in brief.

关键词： phase transition regulation     caloric effect     solid state refrigeration    

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The function and regulation of OTU deubiquitinases

Jiansen Du, Lin Fu, Yingli Sui, Lingqiang Zhang

《医学前沿（英文）》 2020年 第14卷 第5期   页码 542-563 doi: 10.1007/s11684-019-0734-4

摘要： Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.

关键词： ubiquitin     OTU deubiquitinases     structure     function     regulation    

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Rhizosphere immunity: targeting the underground for sustainable plant health management

Zhong WEI, Ville-Petri FRIMAN, Thomas POMMIER, Stefan GEISEN, Alexandre JOUSSET, Qirong SHEN

《农业科学与工程前沿（英文）》 2020年 第7卷 第3期   页码 317-328 doi: 10.15302/J-FASE-2020346

摘要：

Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between plants, microbiota and the surrounding soil matrix. These interactions can potentially extend the innate plant immune system to a point where the rhizosphere immunity can fulfil all four core functions of a full immune system: pathogen prevention, recognition, response and homeostasis. We suggest that considering plant health from a meta-organism perspective will help in developing multidisciplinary pathogen management strategies that focus on steering the whole plant-microbe-soil networks instead of individual components. This might be achieved by bringing together the latest discoveries in phytopathology, microbiome research, soil science and agronomy to pave the way toward more sustainable and productive agriculture.

关键词： rhizosphere     soil microbiome     plant immunity     microbial ecology     plant health     soilborne pathogens    

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RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Fruit ripening is a complex developmental process made up of genetically programmed physiological and biochemical activities. It culminates in desirable changes in the structural and textural properties and is governed by a complex regulatory network. Much is known about ethylene, one of the most important metabolites promoting the ripening of climacteric fruits. However, the dynamic interplay between phytohormones also plays an important part. Additional regulatory factors such as transcription factors (TFs) and epigenetic modifications also play vital role in the regulation of climacteric fruit ripening. Here, we review and evaluate the complex regulatory network comprising interactions between hormones and the action of TFs and epigenetic modifications during climacteric fruit ripening.

 

关键词： climacteric fruit ripening / phytohormones / TFs / epigenetic modifications    

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Molecular regulation and genetic improvement of seed oil content in

Wei HUA,Jing LIU,Hanzhong WANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第3期   页码 186-194 doi: 10.15302/J-FASE-2016107

摘要： As an important oil crop and a potential bioenergy crop, L. is becoming a model plant for basic research on seed lipid biosynthesis as well as seed oil content, which has always been the key breeding objective. In this review, we present current progress in understanding of the regulation of oil content in , including genetics, biosynthesis pathway, transcriptional regulation, maternal effects and QTL analysis. Furthermore, the history of breeding for high oil content in is summarized and the progress in breeding ultra-high oil content lines is described. Finally, prospects for breeding high oil content cultivars are outlined.

关键词： breeding     maternal effects     oilseed rape     QTL    

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Regulation of exogenous bFGF gene mediated by recombinant adeno-associated virus

Ke SONG, Nianjing RAO, Meiling CHEN, Yingguang CAO

《医学前沿（英文）》 2009年 第3卷 第2期   页码 158-163 doi: 10.1007/s11684-009-0042-5

摘要： The regulatory effect of basic fibroblast growth factor (bFGF) mediated by recombinant adeno-associated virus (AAV) was investigated. Recombinant plasmid pAAV-S3-bFGF, and pSVneo were co-transfected into BHK-21 cells, then the recombinant AAV genome was replicated and packaged with the helper virus HSV1-rc/ΔUL2. The titer of the recombinant rAAV2-tet-off-bFGF was determined by dot-blot assay. MC3T3-E1 cells were infected with rAAV2-tet-off-bFGF. Regulatory effects of Doxycycline (Dox) on bFGF and osteogenic factors were assayed quantitatively by real-time reverse transcription-polymerase chain reaction (RT-PCR) and Western blot. The physical particle titer of rAAV2-tet-off-bFGF successfully constructed was 1.8×10 vector genomes/mL, and the virus could infect MC3T3-E1 cells effectively. In MC3T3-E1 cells treated with Dox, the expression levels of exogenous bFGF and osteogenic factors declined to varying degrees. It was concluded that rAAV2-tet-off-bFGF could infect MC3T3 cells efficiently, and this recombinant system could be regulated successfully by Dox .

关键词： tetracycline regulatory system     adeno-associated virus     basic fibroblast growth factor     gene regulation    

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RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

Yinglin JI, Mingyang XU, Aide WANG

《农业科学与工程前沿（英文）》   页码 314-334 doi: 10.15302/J-FASE-2021386

摘要： Fruit ripening is a complex developmental process made up of genetically programmed physiological and biochemical activities. It culminates in desirable changes in the structural and textural properties and is governed by a complex regulatory network. Much is known about ethylene, one of the most important metabolites promoting the ripening of climacteric fruits. However, the dynamic interplay between phytohormones also plays an important part. Additional regulatory factors such as transcription factors (TFs) and epigenetic modifications also play vital role in the regulation of climacteric fruit ripening. Here, we review and evaluate the complex regulatory network comprising interactions between hormones and the action of TFs and epigenetic modifications during climacteric fruit ripening.

关键词： climacteric fruit ripening     phytohormones     TFs     epigenetic modifications    

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标题 作者 时间 类型 操作

Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil

Yi ZHONG, Jian WANG, Yizhi SONG, Yuting LIANG, Guanghe LI

期刊论文

The diazotrophic community in oat rhizosphere: effects of legume intercropping and crop growth stage

Yadong YANG, Xiaomin FENG, Yuegao HU, Zhaohai ZENG

期刊论文

Effect of rhizosphere on soil microbial community and pyrene biodegradation

SU Yuhong, YANG Xueyun, CHIOU Cary

期刊论文

Sulfur mediated heavy metal biogeochemical cycles in coastal wetlands: From sediments, rhizosphere to

期刊论文

Changes in bulk soil affect the disease-suppressive rhizosphere microbiome against Fusarium wilt disease

Lin FU, Wu XIONG, Francisco DINI-ANDREOTE, Beibei WANG, Chengyuan TAO, Yunze RUAN, Zongzhuan SHEN, Rong LI, Qirong SHEN

期刊论文

Improving the efficiency and effectiveness of global phosphorus use: focus on root and rhizosphere levels

null

期刊论文

Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

Yang SONG, Chen ZHU, Waseem RAZA, Dongsheng WANG, Qiwei HUANG, Shiwei GUO, Ning LING, Qirong SHEN

期刊论文

Moving policy and regulation forward for single-use plastic alternatives

期刊论文

Phase transition regulation and caloric effect

期刊论文

The function and regulation of OTU deubiquitinases

Jiansen Du, Lin Fu, Yingli Sui, Lingqiang Zhang

期刊论文

Rhizosphere immunity: targeting the underground for sustainable plant health management

Zhong WEI, Ville-Petri FRIMAN, Thomas POMMIER, Stefan GEISEN, Alexandre JOUSSET, Qirong SHEN

期刊论文

RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

期刊论文

Molecular regulation and genetic improvement of seed oil content in

Wei HUA,Jing LIU,Hanzhong WANG

期刊论文

Regulation of exogenous bFGF gene mediated by recombinant adeno-associated virus

Ke SONG, Nianjing RAO, Meiling CHEN, Yingguang CAO

期刊论文

RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

Yinglin JI, Mingyang XU, Aide WANG

期刊论文