Ruifu Zhang

State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences

Affiliated withChinese Academy of Agricultural Sciences Nanjing Agricultural University

Research Area

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 1	2024
Publication title Cited by 2	2024

Other Publications

Article	Year
Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production. Frontiers in microbiology\| PubMed ID: 25484880	2014
Parental material and cultivation determine soil bacterial community structure and fertility. FEMS microbiology ecology\| PubMed ID: 25764534	2015
Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes. BMC genomics\| PubMed ID: 26076650	2015
Characterization and identification of the xylanolytic enzymes from Aspergillus fumigatus Z5. BMC microbiology\| PubMed ID: 26100973	2015
The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing. PloS one\| PubMed ID: 26317364	2015
Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9. Microbial cell factories\| PubMed ID: 26337367	2015
Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates. BMC genomics\| PubMed ID: 26346121	2015
Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in ... Environmental microbiology\| PubMed ID: 26486414	2016
Plant-Microbe Communication Enhances Auxin Biosynthesis by a Root-Associated Bacterium, Bacillus amyloliquefaciens SQR9. Molecular plant-microbe interactions : MPMI\| PubMed ID: 26808445	2016
Induced maize salt tolerance by rhizosphere inoculation of Bacillus amyloliquefaciens SQR9. Physiologia plantarum\| PubMed ID: 26932244	2016
Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea. Genome announcements\| PubMed ID: 26966209	2016
Draft Genome Sequences of Two Thiomicrospira Strains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea. Genome announcements\| PubMed ID: 26966216	2016
Characterization of extracellular polymeric substances of Bacillus amyloliquefaciens SQR9 induced by root exudates of cucumber. Journal of basic microbiology\| PubMed ID: 27254757	2016
Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion. Journal of microbiology (Seoul, Korea)\| PubMed ID: 27572510	2016
Amino Acids Hydrolyzed from Animal Carcasses Are a Good Additive for the Production of Bio-organic Fertilizer. Frontiers in microbiology\| PubMed ID: 27574521	2016
Two degradation strategies for overcoming the recalcitrance of natural lignocellulosic xylan by polysaccharides-binding GH10 and GH11 xylanases of filamentous fungi. Environmental microbiology\| PubMed ID: 27878934	2017
Haloprofundus marisrubri gen. nov., sp. nov., an extremely halophilic archaeon isolated from a brine-seawater interface. International journal of systematic and evolutionary microbiology\| PubMed ID: 27902200	2017
Identification of Root-Secreted Compounds Involved in the Communication Between Cucumber, the Beneficial Bacillus amyloliquefaciens, and the Soil-Borne Pathogen Fusarium oxysporum. Molecular plant-microbe interactions : MPMI\| PubMed ID: 27937752	2017
Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency. Frontiers in microbiology\| PubMed ID: 28066395	2016
Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system. Applied microbiology and biotechnology\| PubMed ID: 28197689	2017
Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 Induces Plant Salt Tolerance through Spermidine Production. Molecular plant-microbe interactions : MPMI\| PubMed ID: 28291380	2017
The unseen rhizosphere root-soil-microbe interactions for crop production. Current opinion in microbiology\| PubMed ID: 28433932	2017
Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae. International journal of systematic and evolutionary microbiology\| PubMed ID: 28984559	2017
Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. International journal of systematic and evolutionary microbiology\| PubMed ID: 29022541	2017
Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways. Molecular plant-microbe interactions : MPMI\| PubMed ID: 29309236	2018
ResDE Two-Component Regulatory System Mediates Oxygen Limitation-Induced Biofilm Formation by Bacillus amyloliquefaciens SQR9. Applied and environmental microbiology\| PubMed ID: 29427424	2018
FtsEX-CwlO regulates biofilm formation by a plant-beneficial rhizobacterium Bacillus velezensis SQR9. Research in microbiology\| PubMed ID: 29427638	2018
Effect of CBM1 and linker region on enzymatic properties of a novel thermostable dimeric GH10 xylanase (Xyn10A) from filamentous fungus Aspergillus fumigatus Z5. AMB Express\| PubMed ID: 29564574	2018
Identification of Chemotaxis Compounds in Root Exudates and Their Sensing Chemoreceptors in Plant-Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens SQR9. Molecular plant-microbe interactions : MPMI\| PubMed ID: 29714096	2018
Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation. Biochemical and biophysical research communications\| PubMed ID: 29913149	2018
Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe. Microbiome\| PubMed ID: 30236158	2018
Paracoccus salipaludis sp. nov., isolated from saline-alkaline soil. International journal of systematic and evolutionary microbiology\| PubMed ID: 30325298	2018
Recognition of dominant attractants by key chemoreceptors mediates recruitment of plant growth-promoting rhizobacteria. Environmental microbiology\| PubMed ID: 30421582	2019
Wall Teichoic Acids Are Required for Biofilm Formation and Root Colonization. Applied and environmental microbiology\| PubMed ID: 30552189	2019
Microbulbifer flavimaris sp. nov., a halophilic Gammaproteobacteria isolated from marine sediment of the Yellow Sea, China. International journal of systematic and evolutionary microbiology\| PubMed ID: 30777816	2019
Cloning and expression of a β-mannanase gene from Bacillus sp. MK-2 and its directed evolution by random mutagenesis. Enzyme and microbial technology\| PubMed ID: 30797481	2019
A genomic island in a plant beneficial rhizobacterium encodes novel antimicrobial fatty acids and a self-protection shield to enhance its competition. Environmental microbiology\| PubMed ID: 31106958	2019
Improvement of GH10 family xylanase thermostability by introducing of an extra α-helix at the C-terminal. Biochemical and biophysical research communications\| PubMed ID: 31160089	2019
Diversity-triggered deterministic bacterial assembly constrains community functions. Nature communications\| PubMed ID: 31444343	2019
Antibiotic Bacillomycin D Affects Iron Acquisition and Biofilm Formation in Bacillus velezensis through a Btr-Mediated FeuABC-Dependent Pathway. Cell reports\| PubMed ID: 31665633	2019
Root-Secreted Spermine Binds to SQR9 Histidine Kinase KinD and Modulates Biofilm Formation. Molecular plant-microbe interactions : MPMI\| PubMed ID: 31741422	2020
Induced root-secreted D-galactose functions as a chemoattractant and enhances the biofilm formation of Bacillus velezensis SQR9 in an McpA-dependent manner. Applied microbiology and biotechnology\| PubMed ID: 31813049	2020
A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Microbiome\| PubMed ID: 32252828	2020
Quorum sensing signal autoinducer-2 promotes root colonization of Bacillus velezensis SQR9 by affecting biofilm formation and motility. Applied microbiology and biotechnology\| PubMed ID: 32621125	2020
Specialized metabolic functions of keystone taxa sustain soil microbiome stability. Microbiome\| PubMed ID: 33517892	2021
Volatile compounds from beneficial rhizobacteria Bacillus spp. promote periodic lateral root development in Arabidopsis. Plant, cell & environment\| PubMed ID: 33548150	2021
Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9-based cyclical multiple genes coediting in filamentous fungi. Environmental microbiology\| PubMed ID: 33754479	2021
Bacillus velezensis tolerance to the induced oxidative stress in root colonization contributed by the two-component regulatory system sensor ResE. Plant, cell & environment\| PubMed ID: 33864643	2021
Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design. Applied microbiology and biotechnology\| PubMed ID: 34014347	2021
Chemotaxis of Beneficial Rhizobacteria to Root Exudates: The First Step towards Root-Microbe Rhizosphere Interactions. International journal of molecular sciences\| PubMed ID: 34206311	2021
Potassium Phosphite Enhances the Antagonistic Capability of to Manage Tomato Bacterial Wilt. Plant disease\| PubMed ID: 34491099	2022
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. The ISME journal\| PubMed ID: 34593997	2022
Identification of Adhesins in Plant Beneficial Rhizobacteria SQR9 and Their Effect on Root Colonization. Molecular plant-microbe interactions : MPMI\| PubMed ID: 34698535	2022
Rhizosphere microbiome: Functional compensatory assembly for plant fitness. Computational and structural biotechnology journal\| PubMed ID: 34712394	2021
The volatile cedrene from Trichoderma guizhouense modulates Arabidopsis root development through auxin transport and signalling. Plant, cell & environment\| PubMed ID: 34800291	2022
Nitrogen fertilization modulates beneficial rhizosphere interactions through signaling effect of nitric oxide. Plant physiology\| PubMed ID: 34865137	2022
Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus. Nature communications\| PubMed ID: 35197480	2022
Exploring the multi-level regulation of lignocellulases in the filamentous fungus Trichoderma guizhouense NJAU4742 from an omics perspective. Microbial cell factories\| PubMed ID: 35842666	2022
Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of to sense different ligands. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 35858353	2022
Identification of the core c-di-GMP turnover proteins responsible for root colonization of . iScience\| PubMed ID: 36300004	2022
Rhizosphere microbes enhance plant salt tolerance: Toward crop production in saline soil. Computational and structural biotechnology journal\| PubMed ID: 36467579	2022
Sustained Inhibition of Maize Seed-Borne Fusarium Using a Bacillus-Dominated Rhizospheric Stable Core Microbiota with Unique Cooperative Patterns. Advanced science (Weinheim, Baden-Wurttemberg, Germany)\| PubMed ID: 36529951	2023
Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes. Current opinion in microbiology\| PubMed ID: 36682279	2023
Plant commensal type VII secretion system causes iron leakage from roots to promote colonization. Nature microbiology\| PubMed ID: 37248429	2023
Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria. The New phytologist\| PubMed ID: 37357338	2023
Novel fatty acids-governed cannibalism in beneficial rhizosphere Bacillus enhances biofilm formation via a two-component system OmpS/R and toxin transporter. Science bulletin\| PubMed ID: 37402603	2023
Signal communication during microbial modulation of root system architecture. Journal of experimental botany\| PubMed ID: 37419655	2024
Investigating the effect of substrate binding on the catalytic activity of xylanase. Applied microbiology and biotechnology\| PubMed ID: 37715802	2023
Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture. Microbial biotechnology\| PubMed ID: 37837627	2023
Root colonization by beneficial rhizobacteria. FEMS microbiology reviews\| PubMed ID: 38093453	2024
[Isolation and characterization of a p-nitrophenol degradation Pseudomonas sp. strain P3 and construction of a genetically engineered bacterium]. Wei sheng wu xue bao = Acta microbiologica Sinica\| PubMed ID: 12557343	2002
[Degradation of methyl parathion in soil and Chinese chive by strain DLL-1]. Ying yong sheng tai xue bao = The journal of applied ecology\| PubMed ID: 15146643	2004
[Effect of organophosphorous insecticides on Chinese chive insect pests and their degradation by pesticide-degrading bacterium]. Ying yong sheng tai xue bao = The journal of applied ecology\| PubMed ID: 15574008	2004
Diversity of organophosphorus pesticide-degrading bacteria in a polluted soil and conservation of their organophosphorus hydrolase genes. Canadian journal of microbiology\| PubMed ID: 15980896	2005
[Horizontal transfer of environmental pollutant-degrading gene and application in bioremediation]. Yi chuan = Hereditas\| PubMed ID: 16257921	2005
Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene trans... Biodegradation\| PubMed ID: 16477356	2006
Long term effect of methylparathion contamination on soil microbial community diversity estimated by 16S rRNA gene cloning. Ecotoxicology (London, England)\| PubMed ID: 16816989	2006
Simultaneous biodegradation of methyl parathion and carbofuran by a genetically engineered microorganism constructed by mini-Tn5 transposon. Biodegradation\| PubMed ID: 17091349	2007
Expression, purification and characterization of two thermostable endoglucanases cloned from a lignocellulosic decomposing fungi Aspergillus fumigatus Z5 isolated from compost. Protein expression and purification\| PubMed ID: 21708265	2011
Changes in biochemical and microbiological parameters during the period of rapid composting of dairy manure with rice chaff. Bioresource technology\| PubMed ID: 21835612	2011
Optimization of survival and spore formation of Paenibacillus polymyxa SQR-21 during bioorganic fertilizer storage. Bioresource technology\| PubMed ID: 22264433	2012
Comparison of the spores of Paenibacillus polymyxa prepared at different temperatures. Biotechnology letters\| PubMed ID: 22294453	2012
Characterization of a thermostable β-glucosidase from Aspergillus fumigatus Z5, and its functional expression in Pichia pastoris X33. Microbial cell factories\| PubMed ID: 22340848	2012
A novel biochemical route for fuels and chemicals production from cellulosic biomass. PloS one\| PubMed ID: 22384058	2012
Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic acids research\| PubMed ID: 22422839	2012
High incidence of plasmids in marine Vibrio species isolated from Mai Po Nature Reserve of Hong Kong. Ecotoxicology (London, England)\| PubMed ID: 22684730	2012
Production and characterization of acidophilic xylanolytic enzymes from Penicillium oxalicum GZ-2. Bioresource technology\| PubMed ID: 22940308
Contribution of bacillomycin D in Bacillus amyloliquefaciens SQR9 to antifungal activity and biofilm formation. Applied and environmental microbiology\| PubMed ID: 23160135	2013
Enhanced root colonization and biocontrol activity of Bacillus amyloliquefaciens SQR9 by abrB gene disruption. Applied microbiology and biotechnology\| PubMed ID: 23196984	2013
Development of a specific real-time PCR assay targeting the poly-γ-glutamic acid synthesis gene, pgsB, for the quantification of Bacillus amyloliquefaciens in solid-state fermentation. Bioresource technology\| PubMed ID: 23266849	2013
Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. The Journal of biological chemistry\| PubMed ID: 23293028	2013
The supernatant of Bacillus pumilus SQR-N43 has antifungal activity towards Rhizoctonia solani. Journal of basic microbiology\| PubMed ID: 23417338	2013
Promoter analysis and transcription regulation of fus gene cluster responsible for fusaricidin synthesis of Paenibacillus polymyxa SQR-21. Applied microbiology and biotechnology\| PubMed ID: 24072159	2013
Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources. Biotechnology for biofuels\| PubMed ID: 24131596	2013
Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times. PloS one\| PubMed ID: 24465530	2014
Enhanced control of cucumber wilt disease by Bacillus amyloliquefaciens SQR9 by altering the regulation of Its DegU phosphorylation. Applied and environmental microbiology\| PubMed ID: 24584252	2014
Enhanced rhizosphere colonization of beneficial Bacillus amyloliquefaciens SQR9 by pathogen infection. FEMS microbiology letters\| PubMed ID: 24612247	2014
Complete Genome Sequence of Paenibacillus polymyxa SQR-21, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity and Rhizosphere Colonization Ability. Genome announcements\| PubMed ID: 24723719	2014
Comparative proteomics analysis of Bacillus amyloliquefaciens SQR9 revealed the key proteins involved in in situ root colonization. Journal of proteome research\| PubMed ID: 25299960	2014
Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing. Microbial ecology\| PubMed ID: 25391237	2015
The neutral metallopeptidase NMP1 of Trichoderma guizhouense is required for mycotrophy and self-defence. Environmental microbiology\| PubMed ID: 26118314	2016
Manipulating the banana rhizosphere microbiome for biological control of Panama disease. Scientific reports\| PubMed ID: 26242751	2015
Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei. Genome announcements\| PubMed ID: 26272569	2015
Success evaluation of the biological control of Fusarium wilts of cucumber, banana, and tomato since 2000 and future research strategies. Critical reviews in biotechnology\| PubMed ID: 26810104	2017
pheS , an effective host-genotype-independent counter-selectable marker for marker-free chromosome deletion in Bacillus amyloliquefaciens. Applied microbiology and biotechnology\| PubMed ID: 27730334	2017
Comparative Genomic Analysis of and Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats. Frontiers in microbiology\| PubMed ID: 28066362	2016
Enhanced Control of Plant Wilt Disease by a Xylose-Inducible degQ Gene Engineered into Bacillus velezensis Strain SQR9XYQ. Phytopathology\| PubMed ID: 29927357	2019
Participating mechanism of a major contributing gene ysnE for auxin biosynthesis in Bacillus amyloliquefaciens SQR9. Journal of basic microbiology\| PubMed ID: 33914927	2021
Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study. AMB Express\| PubMed ID: 36287351	2022
A toxin-mediated policing system in optimizes division of labor via penalizing cheater-like nonproducers. eLife\| PubMed ID: 37096874	2023
Bacillus velezensis SQR9 inhibition to fungal denitrification responsible for decreased NO emissions from acidic soils. The Science of the total environment\| PubMed ID: 37146817	2023
Beneficial Rhizobacterium Triggers Induced Systemic Resistance of Maize to Gibberella Stalk Rot via Calcium Signaling. Molecular plant-microbe interactions : MPMI\| PubMed ID: 37188493	2023
Metabolic interactions affect the biomass of synthetic bacterial biofilm communities. mSystems\| PubMed ID: 37971263	2023
Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant "cry for help" response to assemble disease suppressing and growth promoting rhizomicrobiome. Nature communications\| PubMed ID: 38429257	2024
Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. The New phytologist\| PubMed ID: 38494698	2024
Beneficial rhizobacterium Bacillus velezensis SQR9 regulates plant nitrogen uptake via endogenous signaling pathway. Journal of experimental botany\| PubMed ID: 38497798	2024
Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling. Cell reports\| PubMed ID: 38551966	2024