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鋼筆

PUBLICATIONS

Google Scholar [publication number: 50; citations: 2,574; H-index: 25 Oct 2023 updated]:

https://scholar.google.com/citations?hl=en&user=9e0nrQIAAAAJ&view_op=list_works&sortby=pubdate

ORCID: https://orcid.org/0000-0002-9120-6762

Personal website: https://zczhou2017.wixsite.com/mysite

​Research Gate: https://www.researchgate.net/profile/Zhichao-Zhou-3

 

bioRxiv and proposed publications:

Zhichao Zhou#, Patricia Tran#, Elise S. Cowley, Elizabeth Trembath-Reichert, Karthik Anantharaman. Diversity and ecology of microbial sulfur metabolism (invited review to Nature Reviews Microbiology) *equal contribution

 

Zhichao Zhou et al. Longterm time-series study unravels seasonally and yearly viral-host association and ecogenomics of lake virus (draft finished, initially aiming to Nature Microbiology)

 

Zhichao Zhou et al. High-throughput sequencing for applications in petroleum reservoirs for enhanced oil recovery: methods, advances and future directions (in submission to Critical Reviews in Biotechnology)

 

Yang Liu, Zhichao Zhou, Yuchun Yang, Ji-Dong Gu, Meng Li. Genome-scale co-occurrence and co-transcription networks reveal key microbial taxa in mangrove sediments (in preparation)

 

Freeman Lan*, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, and Ophelia Venturelli*.  Massively parallel single-cell sequencing in diverse microbial populations (in submission to Nature Methods)

 

First author publications:

22. Zhichao Zhou, Patricia Q Tran, Alyssa M Adams, Kristopher Kieft, John A Breier, Caroline S Fortunato, Cody S Sheik, Julie A Huber, Meng Li, Gregory J Dick, Karthik Anantharaman*. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes.The ISME Journal 17(8):1194-1207 (2023). DOI: 10.1038/s41396-023-01421-0

 

21. Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman*. ViWrap: A modular pipeline to identify, bin, classify, and predict viral–host relationships for viruses from metagenomes. iMeta e118 (2023). DOI: 10.1002/imt2.118 (IF=N/A; new journal)

 

20. Zhichao Zhou#, Yang Liu#, Karthik Anantharaman, Meng Li*. The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis. mLife 1:374-381 (2022). DOI: 10.1002/mlf2.12048 (IF=N/A; new journal)

 

19. Zhichao Zhou#, Emily St. John#, Karthik Anantharaman*, Anna-Louise Reysenbach*. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. Microbiome 10(1):241 (2022). DOI: 10.1186/s40168-022-01424-7 (IF=16.837)

 

18. Zhichao Zhou, Han Meng, Wenjie Gu, Jing Li, Maocheng Deng, Ji-Dong Gu*. High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea. Marine Environmental Research 178:105641 (2022). DOI: 10.1016/j.marenvres.2022.105641 (IF=3.737)

 

17. Zhichao Zhou, Patricia Q. Tran, Yang Liu, Kristopher Kieft, Karthik Anantharaman*. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 10(1):33 (2022). DOI: 10.1186/s40168-021-01213-8 (IF=16.837) (Google citation: 85, in Mar 2023)

 

16. Kristopher Kieft#, Zhichao Zhou#, Rika E. Anderson, Alison Buchan, Barbara J. Campbell, Steven J. Hallam, Matthias Hess, Matthew B. Sullivan, David A. Walsh, Simon Roux, Karthik Anantharaman*. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications 12(1):3503 (2021). DOI: 10.1038/s41467-021-23698-5 (IF=17.694) (Editors’ Highlights in Earth Science)

 

15. Zhichao Zhou, Yang Liu, Jie Pan, Brandi R. Cron, Brandy M. Toner, Karthik Anantharaman, John A. Breier, Gregory J. Dick, Meng Li*. Gammaproteobacteria mediating utilization of methyl-, sulfur-and petroleum organic compounds in deep ocean hydrothermal plumes. The ISME Journal 14(12):3136-3148 (2020). DOI: 10.1038/s41396-020-00745-5 (IF=11.217)

 

14. Zhichao Zhou, Patricia Q. Tran, Kristopher Kieft, Karthik Anantharaman*. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. The ISME Journal 14(8):2060-2077 (2020). DOI: 10.1038/s41396-020-0669-4 (IF=11.217)

 

13. Zhichao Zhou, Jing Chen, Wenjie Gu, Ji-Dong Gu*. Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland. Applied Microbiology and Biotechnology 104(7):3167-3181 (2020). DOI: 10.1007/s00253-020-10415-3 (IF=5.560)

 

12. Zhichao Zhou, Yang Liu, Wei Xu, Jie Pan, Zhu-Hua Luo*, Meng Li*. Genome and community-level interaction insights on wide carbon utilizing and element cycling function of Hydrothermarchaeota from hydrothermal sediment. mSystems 5(1):e00795-19 (2020). DOI: 10.1128/mSystems.00795-19 (mSystems® Top Cited Collection; Editor-selected, highly cited articles; 5 papers in the last 2 years in Nov 2021) (IF=7.324)

 

11. Zhichao Zhou, Bo Liang, Li-Ying Wang, Jin-Feng Liu, Bo-Zhong Mu*, Hojae Shim, Ji-Dong Gu*. Identifying the core bacterial microbiome of hydrocarbon degradation and a shift of dominant methanogenesis pathways in the oil and aqueous phases of petroleum reservoirs of different temperatures from China. Biogeosciences 16:4229-4241 (2019). DOI: 10.5194/bg-16-4229-2019 (IF=5.092)

 

10. Zhichao Zhou, Yang Liu, Karen G. Lloyd, Jie Pan, Yuchun Yang, Ji-Dong Gu*, Meng Li*. Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea). The ISME Journal 13(4):885-901 (2019). DOI: 10.1038/s41396-018-0321-8 (IF=11.217)

 

9. Zhichao Zhou, Guo-Xia Zhang, Yan-Bin Xu, Ji-Dong Gu*. Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Applied Microbiology and Biotechnology 102:8035-8048 (2018). DOI: 10.1007/s00253-018-9147-6 (IF=5.560)

 

8. Zhichao Zhou#, Qiaoyan Wei#, Yuchun Yang, Meng Li*, Ji-Dong Gu*. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Applied Microbiology and Biotechnology 102:5859-5871 (2018). DOI: 10.1007/s00253-018-9078-2 (IF=5.560)

 

7. Zhichao Zhou, Jie Pan, Fengping Wang, Ji-Dong Gu, Meng Li*. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiology Reviews 42(5):639-655 (2018). DOI: 10.1093/femsre/fuy023 (IF=15.177)

 

6. Zhichao Zhou#, Yang Liu#, Meng Li*, Ji-Dong Gu. Two or three domains: a new view of tree of life in the genomics era. Applied Microbiology and Biotechnology 102(7):3049-3058 (2018). DOI: 10.1007/s00253-018-8831-x (IF=5.560)

 

5. Zhichao Zhou, Han Meng, Yang Liu, Ji-Dong Gu*, Meng Li*. Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing. Frontiers in Microbiology 8:2148 (2017). DOI: 10.3389/fmicb.2017.02148 (IF=6.064)

 

4. Zhichao Zhou, Jing Chen, Han Meng, Volodymyr Dvornyk, Ji-Dong Gu*. New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria. Applied Microbiology and Biotechnology 101(3):1267-1287 (2017). DOI: 10.1007/s00253-016-8013-7 (IF=5.560)

 

3. Zhichao Zhou, Jing Chen, Huiluo Cao, Ping Han, Ji-Dong Gu*. Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes. Frontiers in Microbiology 5:789 (2015). DOI: 10.3389/fmicb.2014.00789 (IF=6.064)

 

2. Zhichao Zhou, Ping Han, Ji-Dong Gu*. New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments. Applied Microbiology and Biotechnology 98(10):4663-70 (2014). DOI: 10.1007/s00253-014-5599-5 (IF=5.560)

 

1. Zhichao Zhou, Fan Jiang, Shaohua Wang, Fang Peng*, Jun Dai, Wenxin Li, Chengxiang Fang. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. International Journal of Systematic and Evolutionary Microbiology 62:1963-1969 (2012). DOI: 10.1099/ijs.0.031104-0 (IF=2.689)

 

2nd and other author publications:

28. Dinesh Kumar Kuppa Baskaran#, Shreyansh Umale#, Zhichao Zhou, Karthik Raman*, Karthik Anantharaman*. Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. ISME communications 3(1):42 (2023). DOI: 10.1038/s43705-023-00242-8

 

27. Yu-Yu Cheng, Zhichao Zhou, James M. Papadopoulos, Jason D. Zuke, Tanya G. Falbel, Karthik Anantharaman, Briana M. Burton, and Ophelia S. Venturelli. Efficient plasmid transfer via natural competence in a microbial co-culture. Molecular Systems Biology e11406 (2023). DOI: 10.15252/msb.202211406 (IF=12.74)

 

26. Jing Chen, Zhichao Zhou, Ji-Dong Gu*. Seasonal variations of n-damo bacterial community in the subtropical Mai Po mangrove wetland of Hong Kong. International Biodeterioration & Biodegradation 175:105503 (2022). DOI: 10.1016/j.ibiod.2022.105503 (IF=4.32)

 

25. Jing Chen, Zhichao Zhou, Ji-Dong Gu*. Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments. Marine Environmental Research 181:105739 (2022). DOI: 10.1016/j.marenvres.2022.105739 (IF=3.74)

 

24. Jie Pan#, Wei Xu#, Zhichao Zhou, Zongze Shao, Chunming Dong, Lirui Liu, Zhunhua Luo*, Meng Li*. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. Microbiome 10(1):8 (2022). DOI: 10.1186/s40168-021-01202-x (IF=16.837)

 

23. Jun Feng, Yili Qian, Zhichao Zhou, Sarah Ertmer, Eugenio I. Vivas, Freeman Lan, Joshua J. Hamilton, Federico E. Rey, Karthik Anantharaman and Ophelia S. Venturelli*. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host & Microbe 30(2):200-215.e12 (2022). DOI: 10.1016/j.chom.2021.12.006 (IF=31.316)

 

22. Kristopher Kieft, Adam M. Breister, Phil Huss, Alexandra M. Linz, Elizabeth Zanetakos, Zhichao Zhou, Janina Rahlff, Sarah P. Esser, Alexander J. Probst, Srivatsan Raman, Simon Roux, Karthik Anantharaman*. Virus-associated organosulfur metabolism in human and environmental systems. Cell Reports 36(5):109471 (2021). DOI: 10.1016/j.celrep.2021.109471 (IF=9.995)

 

21. Lin Xu, Bingjian Zhu, Chaonan Li, Zhichao Zhou, Minjie Yao, Xiaobing Zhou, Junming Wang, Bingchang Zhang*, Xiangzhen Li*. Increasing relative abundance of non-cyanobacterial photosynthetic organisms drives ecosystem multifunctionality during the succession of biological soil crusts. Geoderma 395:115052 (2021). DOI: 10.1016/j.geoderma.2021.115052 (IF=7.422)

 

20. Adam M. Breister#, Muhammad A. Imam#, Zhichao Zhou, Md Ariful Ahsan, Juan C. Noveron, Karthik Anantharaman*, Pavana Prabhakar*. Soil microbiomes mediate degradation of vinyl ester-based polymer composites. Communications Materials 1:101 (2020). DOI: 10.1038/s43246-020-00102-1 (IF=N/A; new journal)

 

19. Xiuran Yin#, Mingwei Cai#, Yang Liu, Guowei Zhou, Tim Richter-Heitmann, David A. Aromokeye, Ajinkya C. Kulkarni, Rolf Nimzyk, Henrik Cullhed, Zhichao Zhou, Jie Pan, Yuchun Yang, Ji-Dong Gu, Marcus Elvert, Meng Li*, Michael W. Friedrich*. Subgroup level differences of physiological activities in marine Lokiarchaeota. The ISME Journal 15(3):848-861 (2021). DOI: 10.1038/s41396-020-00818-5 (IF=11.217)

 

18. Meng Han*, Xiaowei Zhang, Zhichao Zhou, Ling Luo, Wensheng Lan, Jih-Gaw Lin, Xiao-Yan Li, and Ji-Dong Gu*. Simultaneous occurrence and analysis of both anammox and n-damo bacteria in five full-scale wastewater treatment plants. International Biodeterioration & Biodegradation 156:105112 (2020). DOI: 10.1016/j.ibiod.2020.105112 (IF=4.907)

 

17. Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman*. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8(1):90 (2020). DOI: 10.1186/s40168-020-00867-0 (Google citation: 301, in Mar 2023) (IF=16.837)

 

16. Jie Pan, Zhichao Zhou, Oded Béjà, Mingwei Cai, Yuchun Yang, Yang Liu, Ji-Dong Gu, Meng Li*. Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota. Microbiome 8(1):43 (2020). DOI: 10.1186/s40168-020-00820-1 (IF=16.837)

 

15. Mingwei Cai#, Yang Liu#, Xiuran Yin, Zhichao Zhou, Michael W. Friedrich, Tim Richter-Heitmann, Rolf Nimzyk, Ajinkya Kulkarni, Xiaowen Wang, Wenjin Li, Jie Pan, Yuchun Yang, Ji-Dong Gu, Meng Li*. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Science China Life Sciences 63(6):886-897 (2020). DOI: 10.1007/s11427-020-1679-1 (IF=10.372)

 

14. Yongming Wang, Jie Pan, Jun Yang, Zhichao Zhou, Yueping Pan, Meng Li*. Patterns and processes of free‐living and particle‐associated bacterioplankton and archaeaplankton communities in a subtropical river‐bay system in South China. Limnology and Oceanography 65:S161-S179 (2020). DOI: 10.1002/lno.11314 (IF=5.019)

 

13. Yuchun Yang, Jie Pan, Zhichao Zhou, Jiapeng Wu, Yang Liu, Jih-Gaw Lin, Yiguo Hong, Xiaoyan Li, Meng Li*, Ji-Dong Gu*. Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems. Water Research 168:115142 (2020). DOI: 10.1016/j.watres.2019.115142 (IF=13.400)

 

12. Lei Zhou, Zhichao Zhou, Yu-Wei Lu, Lei Ma, Yang Bai, Xiao-Xiao Li, Serge Maurice Mbadinga, Yi-Fan Liu, Xin-Chen Yao, Yi-Jie Qiao, Zi-Rui Zhang, Jin-Feng Liu, Shi-Zhong Yang, Wei-Dong Wang, Ji-Dong Gu, Bo-Zhong Mu*. The newly proposed TACK and DPANN archaea detected in the production waters from a high-temperature petroleum reservoir. International Biodeterioration & Biodegradation 143:104729 (2019). DOI: 10.1016/j.ibiod.2019.104729 (IF=4.907)

 

11. Qian-Qian Hu, Zhi-Chao Zhou, Yi-Fan Liu, Lei Zhou, Serge Maurice Mbadinga, Jin-Feng Liu, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu*. High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene. International Biodeterioration & Biodegradation 143:104708 (2019). DOI: 10.1016/j.ibiod.2019.05.025 (IF=4.907)

 

10. Jin-Feng Liu, Kai Zhang, Bo Liang, Zhi-Chao Zhou, Shi-Zhong Yang, Wei Li, Zhao-Wei Hou, Xiao-Lin Wu*, Ji-Dong Gu, Bo-Zhong Mu*. Key players in the methanogenic biodegradation of n-hexadecane identified by DNA-Stable isotope probing. International Biodeterioration & Biodegradation 143:104709 (2019). DOI: 10.1016/j.ibiod.2019.05.026 (IF=4.907)

 

9. Han Meng, Zhichao Zhou, Ruonan Wu, Yongfeng Wang, Ji-Dong Gu*. Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene. Applied Microbiology and Biotechnology 103(2):995-1005 (2019). DOI: 10.1007/s00253-018-9466-7 (IF=5.560)

 

8. Jie Pan, Yulian Chen, Yongming Wang, Zhichao Zhou, Meng Li*. Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Lifestyle of Bathyarchaeota Subgroup-6. Microbial Ecology 77(2):417-428 (2019). DOI: 10.1007/s00248-018-1309-7 (IF=4.192)

 

7. Yang Liu, Zhichao Zhou, Jie Pan, Brett J. Baker, Ji-Dong Gu, Meng Li*. Comparative genomic inference reveals mixotrophic lifestyle of Thorarchaeota. The ISME Journal 12(4):1021-1031 (2018). DOI: 10.1038/s41396-018-0060-x (IF=11.217)

 

6. Xiaobo Liu, Meng Li*, Cindy J. Castelle, Alexander J. Probst, Zhichao Zhou, Jie Pan, Yang Liu, Jillian F. Banfield, Ji-Dong Gu*. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome 6(1):102 (2018). DOI: 10.1186/s40168-018-0488-2 (IF=16.837)

 

5. Bo Liang, Li-Ying Wang, Zhichao Zhou, Serge M. Mbadinga, Lei Zhou, Jin-Feng Liu, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu*. High frequency of Thermodesulfovibrio spp. and Anaerolineaceae in association with Methanoculleus spp. in a long-term incubation of n-alkanes-degrading methanogenic enrichment culture. Frontiers in Microbiology 7:1431 (2016). DOI: 10.3389/fmicb.2016.01431 (IF=6.064)

 

4. Ling Luo, Zhi-Chao Zhou, Ji-Dong Gu*. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem. Ecotoxicology 24:1508-1516 (2015). DOI: 10.1007/s10646-015-1452-6 (IF=2.935)

 

3. Jing Chen, Zhichao Zhou, Ji-Dong Gu*. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes. Applied Microbiology and Biotechnology 99:1463-1473 (2015). DOI: 10.1007/s00253-014-6051-6 (IF=5.560)

 

2. Jing Chen, Zhi-Chao Zhou, Ji-Dong Gu*. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes. Applied Microbiology and Biotechnology 98:5685-5696 (2014). DOI: 10.1007/s00253-014-5733-4 (IF=5.560)

 

1. Wei Su, Zhichao Zhou, Fan Jiang, XuLu Chang, Ying Liu, Shaohua Wang, Wenjing Kan, Mengchen Xiao, Ming Shao, Fang Peng*, Chengxiang Fang. Iodobacter limnosediminis sp nov., isolated from Arctic lake sediment. International Journal of Systematic and Evolutionary Microbiology 63:1464-1470 (2013). DOI: 10.1099/ijs.0.039982-0 (IF=2.689)

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