Researcher biography
After obtaining a Master degree in soil microbiology from Shanghai Jiao Tong University (2012), I moved to Sydney and studied in the Centre for Marine Bio-innovation affiliated to the University of New South Wales. I obtained my PhD degree in Dec. 2016. My doctoral research focused on the bacterial diveristy on the surface of biochar, a emerging soil amendment. I developed a nanogold in situ hybridization method(link is external) that can specifically detect bacteria on the surface of biochar using electron microscopy. I also used 16S amplicon sequencing and environmental metagenomics to explore the bacterial compositions and functions on the surface of biochar.
I am now working with Prof. Gene Tyson in developing a novel in situ hybridization method combining with my previous skills and knowledge. My other topics of interest include soil micorbiome, sustainable agriculture and direct interspecies electron transfer.
Publications
Journal Articles
Qiu, Zhiguang, Paungfoo‐Lonhienne, Chanyarat, Ye, Jun, Gonzalez Garcia, Axa , Petersen, Ian, Di Bella, Lawrence, Hobbs, Richard, Ibanez, Minka, Heenan, Marijke, Wang, Weijin, Reeves, Steven and Schmidt, Susanne (2022). Biofertilizers can enhance nitrogen use efficiency of sugarcane. Environmental Microbiology, 24 (8), 3655-3671. doi: 10.1111/1462-2920.16027
Liu, Hongwei, Qiu, Zhiguang, Ye, Jun, Verma, Jay Prakash, Li, Jiayu and Singh, Brajesh K. (2022). Effective colonisation by a bacterial synthetic community promotes plant growth and alters soil microbial community. Journal of Sustainable Agriculture and Environment, 1 (1), 30-42. doi: 10.1002/sae2.12008
Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5
Wei, Xiaomeng, Hu, Yajun, Cai, Guan, Yao, Huaiying, Ye, Jun, Sun, Qi, Veresoglou, Stavros D., Li, Yaying, Zhu, Zhenke, Guggenberger, Georg, Chen, Xiangbi, Su, Yirong, Li, Yong, Wu, Jinshui and Ge, Tida (2021). Organic phosphorus availability shapes the diversity of phoD-harboring bacteria in agricultural soil. Soil Biology and Biochemistry, 161 108364, 108364. doi: 10.1016/j.soilbio.2021.108364
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 521-521. doi: 10.1038/s41587-021-00898-4
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39 (4), 499-509. doi: 10.1038/s41587-020-0718-6
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 520-520. doi: 10.1038/s41587-020-00769-4
Chen, Hui, Liu, Tao, Li, Jie, Mao, Likai, Ye, Jun, Han, Xiaoyu, Jetten, Mike S. M. and Guo, Jianhua (2020). Larger anammox granules not only harbor higher species diversity but also support more functional diversity. Environmental Science and Technology, 54 (22) acs.est.0c02609, 14664-14673. doi: 10.1021/acs.est.0c02609
Chen, Liang, Xiang, Wenhua, Wu, Huili, Ouyang, Shuai, Lei, Pifeng, Hu, Yajun, Ge, Tida, Ye, Jun and Kuzyakov, Yakov (2019). Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests. Applied Microbiology and Biotechnology, 103 (13), 5421-5433. doi: 10.1007/s00253-019-09867-z
You, Fang, Zhang, Liping, Ye, Jun and Huang, Longbin (2019). Microbial decomposition of biomass residues mitigated hydrogeochemical dynamics in strongly alkaline bauxite residues. Science of the Total Environment, 663, 216-226. doi: 10.1016/j.scitotenv.2019.01.317
Liao, Jianli, Ye, Jun, Liang, Yun, Khalid, Muhammad and Huang, Danfeng (2019). Pakchoi antioxidant improvement and differential rhizobacterial community composition under organic fertilization. Sustainability, 11 (8) 2424, 2424. doi: 10.3390/su11082424
Liu, Yalong, Ge, Tida, Ye, Jun, Liu, Shoulong, Shibistova, Olga, Wang, Ping, Wang, Jingkuan, Li, Yong, Guggenberger, Georg, Kuzyakov, Yakov and Wu, Jinshui (2019). Initial utilization of rhizodeposits with rice growth in paddy soils: rhizosphere and N fertilization effects. Geoderma, 338, 30-39. doi: 10.1016/j.geoderma.2018.11.040
Nielsen, Shaun, Joseph, Stephen, Ye, Jun, Chia, Chee, Munroe, Paul, Zwieten, Lukas van and Thomas, Torsten (2018). Crop-season and residual effects of sequentially applied mineral enhanced biochar and N fertiliser on crop yield, soil chemistry and microbial communities. Agriculture, Ecosystems and Environment, 255, 52-61. doi: 10.1016/j.agee.2017.12.020
Rafiq, Muhammad Khalid, Joseph, Stephen D., Li, Fei, Bai, Yanfu, Shang, Zhanhuan, Rawal, Aditya, Hook, James M., Munroe, Paul R., Donne, Scott, Taherymoosavi, Sara, Mitchell, David R. G., Pace, Ben, Mohammed, Mohanad, Horvat, Joseph, Marjo, Christopher E., Wagner, Avital, Wang, Yanlong, Ye, Jun and Long, Rui-Jun (2017). Pyrolysis of attapulgite clay blended with yak dung enhances pasture growth and soil health: Characterization and initial field trials. Science of the Total Environment, 607-608, 184-194. doi: 10.1016/j.scitotenv.2017.06.186
Ye, Jun, Perez, Pablo Gonzalez, Zhang, Rui, Nielsen, Shaun, Huang, Danfeng and Thomas, Torsten (2017). Effects of different C/N ratios on bacterial compositions and processes in an organically managed soil. Biology and Fertility of Soils, 54 (1), 1-11. doi: 10.1007/s00374-017-1246-5
Williams, Timothy J., Liao, Yan, Ye, Jun, Kuchel, Rhiannon P., Poljak, Anne, Raftery, Mark J. and Cavicchioli, Ricardo (2017). Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi. Environmental Microbiology, 19 (6), 2210-2227. doi: 10.1111/1462-2920.13705
Ye, Jun, Joseph, Stephen D., Ji, Mukan, Nielsen, Shaun, Mitchell, David R. G., Donne, Scott, Horvat, Joseph, Wang, Jianli, Munroe, Paul and Thomas, Torsten (2017). Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars. Isme Journal, 11 (5), 1087-1101. doi: 10.1038/ismej.2016.187
Liao, Y., Williams, T. J., Ye, J., Charlesworth, J., Burns, B. P., Poljak, A., Raftery, M. J. and Cavicchioli, R. (2016). Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Scientific Reports, 6. doi: 10.1038/srep37454
Ye, Jun, Zhang, Rui, Nielsen, Shaun, Joseph, Stephen D., Huang, Danfeng and Thomas, Torsten (2016). A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties. Frontiers in Microbiology, 7 (APR) 372. doi: 10.3389/fmicb.2016.00372
Joseph, Stephen, Pow, Doug, Dawson, Kathy, Mitchell, David R.G., Rawal, Aditya, Hook, James, Taherymoosavi, Sarasadat, Van Zwieten, Lukas, Rust, Joshua, Donne, Scott, Munroe, Paul, Pace, Ben, Graber, Ellen, Thomas, Torsten, Nielsen, Shaun, Ye, Jun, Lin, Yun, Pan, Genxing, Li, Lianqing and Solaiman, Zakaria M. (2015). Feeding Biochar to Cows: An Innovative Solution for Improving Soil Fertility and Farm Productivity. Pedosphere, 25 (5), 666-679. doi: 10.1016/S1002-0160(15)30047-3
Yao, Chunxue, Joseph, Stephen, Li, Lianqing, Pan, Genxing, Lin, Yun, Munroe, Paul, Pace, Ben, Taherymoosavi, Sarasadat, Van Zwieten, Lukas, Thomas, Torsten, Nielsen, Shaun, Ye, Jun and Donne, Scott (2015). Developing more effective enhanced biochar fertilisers for improvement of pepper yield and quality. Pedosphere, 25 (5), 703-712. doi: 10.1016/s1002-0160(15)30051-5
Joseph, Stephen, Husson, Olivier, Graber, Ellen Ruth, van Zwieten, Lukas, Taherymoosavi, Sara, Thomas, Torsten, Nielsen, Shaun, Ye, Jun, Pan, Genxing, Chia, Chee, Munroe, Paul, Allen, Jessica, Lin, Yun, Fan, Xiaorong and Donne, Scott (2015). The Electrochemical Properties of Biochars and How They Affect Soil Redox Properties and Processes. Agronomy, 5 (3), 322-340. doi: 10.3390/agronomy5030322
Ye, Jun, Nielsen, Shaun, Joseph, Stephen and Thomas, Torsten (2015). High-Resolution and Specific Detection of Bacteria on Complex Surfaces Using Nanoparticle Probes and Electron Microscopy. PLoS ONE, 10 (5). doi: 10.1371/journal.pone.0126404
Perez, Pablo Gonzalez, Zhang, Rui, Wang, Xiaoli, Ye, Jun and Huang, Danfeng (2015). Characterization of the amino acid composition of soils under organic and conventional management after addition of different fertilizers. Journal of Soils and Sediments, 15 (4), 890-901. doi: 10.1007/s11368-014-1049-3
Perez, Pablo Gonzalez, Ye, Jun, Wang, Shu, Wang, XiaoLi and Huang, DanFeng (2014). Analysis of the occurrence and activity of diazotrophic communities in organic and conventional horticultural soils. Applied Soil Ecology, 79, 37-48. doi: 10.1016/j.apsoil.2014.03.006
Wang, Xiao-Li, Ye, Jun, Gonzalez Perez, Pablo, Tang, Dong-Mei and Huang, Dan-Feng (2013). The impact of organic farming on the soluble organic nitrogen pool in horticultural soil under open field and greenhouse conditions: a case study. Soil Science and Plant Nutrition, 59 (2), 237-248. doi: 10.1080/00380768.2013.770722
Wang, Xiaoli, Gonzalez Perez, Pablo, Ye, Jun and Huang, Danfeng (2012). 土壤宏蛋白质组学蛋白质提取方法及其应用. Chinese Journal of Applied and Environmental Biology, 18 (4), 691-696. doi: 10.3724/SP.J.1145.2012.00691
Wang, Shu, Pablo, Gonzalez Perez, Ye, Jun and Huang, Danfeng (2012). Abundance and diversity of nitrogen-fixing bacteria in rhizosphere and bulk paddy soil under different duration of organic management. World Journal of Microbiology & Biotechnology, 28 (2), 493-503. doi: 10.1007/s11274-011-0840-1
Wang, Shu, Ye, Jun, Perez, Pablo Gonzalez and Huang, Dan-Feng (2011). Abundance and diversity of ammonia-oxidizing bacteria in rhizosphere and bulk paddy soil under different duration of organic management. African Journal of Microbiology Research, 5 (31), 5560-5568. doi: 10.5897/AJMR10.749