Publication

Lu Luan, Yuji Jiang*, Francisco Dini-Andreote, Thomas Crowther, Pengfa Li, Mohammad Bahram, Jie Zheng, Qinsong Xu, Xue-Xian Zhang*, Bo Sun* (2023) Integrating pH into the metabolic theory of ecology to predict bacterial diversity in soil. Proceedings of the National Academy of Sciences, 120(3): e2207832120  (doi link)

Achen Wang, Xuesong Luo, Xiang Li, Daqing Huang, Qiaoyun Huang, Xue-Xian Zhang, Wenli Chen* (2023) Bioaugmentation of woodchip bioreactors by Pseudomonas nicosulfuronedens D1-1 with functional species enrichment. Bioresource Technology, 385: 129309 (doi link).

Boying Wang, Kay Rutherfurd-Markwick, Naran Naren, Xue-Xian Zhang, Anthony Mutukumira* (2023) Microbiological and Physico-Chemical Characteristics of Black Tea Kombucha Fermented with a New Zealand Starter Culture. Foods, 12(12): 2314 (doi link)

Feng Xu, Sha Liu, Naran Naren, Lily Li, Lvyan Ma, and Xue-Xian Zhang* (2022) Experimental evolution of bacterial survival on metallic copper. Ecology and Evolution, 12(8): e9225  (doi link)

Feng Wei, Yuan Liu, Donglai Zhou, Wenlong Zhao, Zhennan Chen, Dasong Chen, Youguo Li*, and  Xue-Xian Zhang (2022) Transcriptomic identification of a unique set of nodule-specific cysteine  peptides expressed in the nitrogen-fixing root nodule of Astragalus sinicus. Molecular Plant-Microbe Interactions 35(10): 893-905 (doi link).

Boying Wang, Kay Rutherfund-Markwick, Xue-Xian Zhang, Anthony Mutukumira (2022) Isolation and characterisation of dominant acetic acid bacteria and yeast isolated from Kombucha samples at point of sale in New zealand. Current Research in Food Science 5: 835-844 (doi link).

Boying Wang, Kay Rutherfund-Markwick, Xue-Xian Zhang, Anthony Mutukumira (2022)  Kombucha: Production and Microbiological Research. Foods 11: 3456 (doi link).

Anming Xu, Di Wang, Yunhao Wang, Li Zhang, Zhensheng Xie, Yifan Cui, Pramod Bhamse, Haiying Yu, Xue-Xian Zhang, Defeng Li, Luyan Z Ma (2021) Mutations in surface-sensing receptor WspA lock the Wsp signal transduction system into a constitutively active state. Environmental Microbiology 24(3): 1150-1165 (doi link).

Naran Naren and Xue-Xian Zhang* (2021) Role of a local transcription factor in governing cellular carbon/nitrogen homeostasis in Pseudomonas fluorescens. Nucleic Acids Research, 49(6): 3204-3216  (doi link)

Amber R Paulson, Maureen O’Callaghan, Xue-Xian Zhang, Paul B Rainey, Mark RH Hurst (2021) In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella. G3: Genes | Genomes | Genetics 11(1): 1-11 (doi link)

Wenlong Zhao, Huixia Zhu, Feng Wei, Donglai Zhou, Youguo Li, and Xue-Xian Zhang (2021) Investigating the involvement of cytoskeletal proteins MreB and FtsZ in the origin of legume-rhizobial symbiosis. Molecular Plant-Microbe Interactions  (doi link)

Xue‐Xian Zhang, Stephen Ritchie, Hao Chang, Dawn Arnold, Robert Jackson, Paul Rainey (2020) Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet‐associated Pseudomonas in Oxford and Auckland. Ecology and Evolution 00:1-13 (doi link)

Naran Naren, Xue-Xian Zhang (2020) Global regulatory roles of the histidine-responsive transcriptional repressor HutC in Pseudomonas fluorescens SBW25. Journal of Bacteriology 202:e00792-19 (doi link)

Wenjuan Kang, Zhehao Jiang, Yonggang Chen, Fang Wu, Chang Liu, Haifang Wang, Shangli Shi, Xue-Xian Zhang (2020) Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level. BMC Plant Biology  20: 293 (doi link)

Yuhua Zhan, Zhiping Deng, Yongliang Yan, Hongyang Zhang, Chao Lu, Zhimin Yang, Liguo Shang, Yi Huang, Fanyang Lv, Yaqun Liu, Yichao Liu, Shanshan Wang, Sanfeng Chen, Xue-Xian Zhang, Qi Cheng, Min Lin (2019) NfiR, a new regulatory noncoding RNA (ncRNA), is required in concert with the NfiS ncRNA for optimal expression of nitrogenase genes in Pseudomonas stutzeri A1501. Applied and Environmental Microbiology 85(14):e00762-19 (doi link)

PRJ Yulo, Nicolas Desprat, Monica L Gerth, Yunhao Liu, Xue-Xian Zhang, Paul B Rainey, Heather L Hendricksona (2018) Experimental evolution of cell shape in bacteria. BioRxiv doi: https://doi.org/10.1101/263681.

Liu YH, Gokhale CS, Rainey PB, Zhang XX* (2017) Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25.  Molecular Microbiology 105 (4): 589-605 (doi link)

Jiang Y, Liu M, Zhang J, Chen Y, Chen X, Chen L, Li H, Zhang XX*, Sun B (2017) Nematode grazing promotes bacterial community dynamics in soil at the aggregate level. The ISME Journal 11: 2705-2717 (doi link)

Gerth ML*, Liu YH, Jiao W, Zhang XX, Baker EN, Lott JS, Rainey PB, Johnston JM (2017) Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.  Proteins: Structure, Function Bioinformatics 85: 1580-1588 (doi link)

Liu S and Zhang XX* (2016) Small colony variants are more susceptible to copper-mediated contact killing for Pseudomonas aeruginosa and Staphylococcus aureus. Journal of Medical Microbiology 65 (10): 1143-1151.  (doi link)

Liu YH, Rainey PB and Zhang XX* (2015) Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol. Molecular Microbiology 98 (3): 553-570.  (doi link)

Zhang XX*, Gauntlett JC, Oldenburg DG, Cook GM and Rainey PB (2015) Role of the transporter-like sensor kinase CbrA in histidine uptake and signal transduction. Journal of Bacteriology 197 (17): 2867-2878.  (doi link)

Sun RB, Zhang XX, Guo XS, Wang DZ and Chu HY* (2015) Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biology & Biochemistry 88: 9-18.   (doi link)

Zhang XX*, Ritchie SR and Rainey PB (2014) Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts. Cellular & Molecular Life Sciences 71(4): 541-547.  (doi link)

Liu YH, Rainey PB and Zhang XX* (2014) Mini-Tn7 vectors for studying post-transcriptional gene expression in Pseudomonas. Journal of Microbiological Methods 107: 182-185. (doi link)

Rainey PB*, Desprat N, Driscoll WW, Zhang XX (2014) Microbes are not bound by sociobiology: response to Kümmerli and Ross‐Gillespie (2013). Evolution 68 (11): 3344-3355.  (doi link)

Sun B, Wang F, Jiang Y, Li Y, Dong Z, Li Z, Zhang XX* (2014) A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure. Ecology and Evolution 4(7): 1073-1087.  (doi link)

Alsohim AS, Taylor TB, Barrett GA, Gallie J, Zhang XX, Altamirano‐Junqueira AE, Johnson LJ, Rainey PB, Jackson RW* (2014) The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 aids spreading motility and plant growth promotion. Environmental Microbiology 16(7): 2267-2281.  (doi link)

Xue-Xian Zhang and Paul B Rainey* (2013) Exploring the sociobiology of pyoverdin-producing Pseudomonas. Evolution 67:3161-3174.  (doi link)

Jackson RW, XX Zhang, MW Silby (2013) Identification and Mutational Activation of Niche‐Specific Genes Provide Insight into Regulatory Networks and Bacterial Function in Complex Environments. Molecular Microbial Ecology of the Rhizosphere 1:875-882. (doi link)

Sun B., Wang X., Wang F., Jiang Y and Zhang XX* (2013) Assessing the relative effects of geographic location and soil type on microbial communities associated with straw decomposition. Applied and Environmental Microbiology 79: 3327-35.  (doi link)

Zhang XX*, Chang H, Tran SL, Gauntlett JC, Cook GM and Rainey PB (2012) Variation in transport explains polymorphism of histidine and urocanate utilization in a natural Pseudomonas population. Environmental Microbiology 14: 1941-1951.  (doi link)

Rainey PB, Beaumont HJE, Ferguson GC, Gallie J, Kost C, Libby E and Zhang XX (2011). The evolutionary emergence of stochastic phenotype switching.  BMC Microbial Cell Factories 10(S1): S14.  (doi link)

Sun B, Dong ZX, Zhang XX, Li Y, Xao H, Cui ZL (2011) Rice to vegetables: short- versus long-term impact of land use change on the indigenous soil microbial community. Microbial Ecology 62: 474-485.  (doi link)

Zhang XX*, Liu YH and Rainey PB (2010) CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environmental Microbiology 12: 1674-1683.  (doi link)

Knight CG, Zhang XX, Gunn A, Brenner T, Jackson RW, Giddens SR, Sripardi P, Zitzmann N and Rainey PB (2010) Testing temperature-induced proteomic changes in the plant-associated bacterium Pseudomonas fluorescens SBW25. Environmental Microbiology Reports 2: 396-402.  (doi link)

Zhang XX*, Rainey PB (2010) Bet hedging in the underworld. Genome Biology 11(10): 137.  (doi link)

McDonald MJ, Gehrig SM, Meintjes PL, Zhang XX and Rainey PB* (2009) Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183: 1041-1053.  (doi link)

Silby MW*, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey, SAC, Knight CG Malone JG et al (2009) Genomic and functional analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10(5): R51.  (doi link)

Zhang XX* and Rainey PB (2008) Dual involvement of CbrAB and NtrBC in the regulation of histidine utilization in Pseudomonas fluorescens SBW25. Genetics 178: 185–195. (doi link)

Zhang XX* and Rainey PB (2008) Regulation of copper homeostasis in Pseudomonas fluorescens SBW25. Environmental Microbiology 10: 3284-3294.  (doi link)

CD Moon, SR Giddens, XX Zhang, RW Jackson (2008) Molecular Mechanisms Underpinning Colonization of a Plant by Plant Growth‐Promoting Rhizobacteria. Plant-Bacteria Interactions: Strategies and Techniques to Promote Plant Growth. https://doi.org/10.1002/9783527621989.ch6.

Moon CD*, Zhang XX, Matthijs S, Schafer M, Budzikiewicz H, Rainey PB (2008) Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. BMC Microbiology 8: 7.  (doi link)

Zhang XX* and Rainey PB (2007) Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176: 2165-2176.  (doi link)

Zhang XX*, Scott K, Meffin R, Rainey PB (2007) Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BMC Microbiology 7: 114.  (doi link)

Zhang XX*, Rainey PB (2007) Construction and validation of a neutrally-marked strain of Pseudomonas fluorescensSBW25. J. of Microbiol Methods 71:78-81.  (doi link)

Zhang XX* and Rainey PB (2007) The role of a P1-type ATPase from Pseudomonas fluorescens SBW25 in copper homeostasis and plant colonization. Molecular Plant-Microbe Interactions 20: 581-588.  (doi link)

Fukami T*, Beaumont HJ, Zhang XX, Rainey PB (2007) Immigration history controls diversification in experimental adaptive radiation. Nature 446: 436-439.  (doi link)

Giddens SR, Jackson RW*, Moon CD, Jacobs MA, Zhang XX, Gehrig SM, Rainey PB (2007) Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proc. Natl. Acad. Sci. USA 104: 18247-18252.  (doi link)

Tett A, Spiers AJ, Crossman LC, Ager D, Ciric L, Dow JM, Fry JC, Harris D, Lilley A, Oliver A, Parkhill J, Quail MA, Rainey PB, Saunders NJ, Seeger K, Snyder LA, Squares R, Thomas CM, Turner SL, Zhang XX, Field D, Bailey MJ. (2007) Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. The ISME Journal 1(4): 331-340.  (doi link)