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Book chapter

Book Chapters (5):

Two in English ( Imperial College Press and Springer) and Four in Chinese (BioProtocol and ChinaScience Publishing & Media Ltd )

1. Ju F*, Zhang L, Yao Y, WU L. (2024). Emerging biological pollutants and control. Chapter 10 of Environmental biosafety (in proof). China Science Publishing & Media Ltd.

2. Huang X, Zhang L, Yuan L, and Ju F*. (2021). Quantitative Metagenomics and Metatranscriptomics Methods of Microbiome. Microbiome Protocol eBook Bio-101: e2003693, BioProtocol. DOI: 10.21769/BioProtoc.2003693 (in Chinese).

3. Zhang L and Ju F*. (2021). RNA-Stable Isotope Probing for Microbial Communities. Microbiome Protocol eBook Bio-101: e2003692. BioProtocol. DOI: 10.21769/BioProtoc.2003692 (in Chinese).

4. Zhao Z and Ju F*. (2020). Isolation and Extraction of Intracellular Absorbed-extracellular and Free-extracellular Environmental DNA from Aquatic Microbial Community. Microbiome Protocol eBook Bio-101: e2003587. BioProtocol. DOI: 10.21769/BioProtoc.2003587 (in Chinese)

5. Zhang H, Zhou N, Ju F*. Immunoreaction-Based Sensors to Improve Bacterial Detection. Book chapter of “Handbook of Biochips”, Springer, May 2020. ISBN: 978-1-4614-6623-9.

6. Ju F, Fang H, Zhang T. Application of Metagenomics in Environmental Anaerobic Technology. Book chapter V of “Anaerobic Biotechnology: Environmental Protection and Resource Recovery”, Imperial College Press, October 2015. ISBN: 978-1-78326-790-3

Journal Publication

Journal Publication (87): Journal name (no. of articles): Nature Communication (1), The ISME Journal (6), Microbiome (2), Advanced Science (2), Environmental Science & Technology (12), Water Research (11), Science of the Total Environment (7), Applied Microbiology and Biotechnology (6), Environmental Microbiology (2), Journal of Hazardous Materials (4)

Publications at Westlake (* Denotes corresponding author)

1. Zhang L, Guo L, Cui Z, Ju F*. 2023. Exploiting predatory bacteria asbiocontrol agents across ecosystems. Trends in Microbiology. S0966-842X(23)00293-7 (Invited review)

2. Zhang L, Huang X, Zhou J, Ju F*. 2023. Active predation, phylogenetic diversity, and global prevalence of myxobacteriain wastewater treatment plants. The ISME Journal. 17(5):671-681

3. Yuan L, Ju F*. 2023. Potential auxiliary metabolic capabilities andactivities reveal biochemical impacts of viruses in municipal wastewater treatment plants. Environmental Science & Technology. 57(13):5485-5498

4. Zhu X, Zhu S, Zhao Z, Kang X, Ju F*. 2023. Microbiome dynamics duringanaerobic digestion of food waste and the genetic potential for poly (lacticacid) co-digestion. Chemical Engineering Journal. 473:145194

5. Zhu X, Li P, Ju F*. 2023. Microbiome dynamics and products profiles of biowaste fermentation underdifferent organic loads and additives. Engineering in Life Sciences. e2300216

6. Wang H, Wang Y, Zhang G, Zhao Z, Ju F*. 2023. Temporal dynamics andperformance association of the Tetrasphaera-enriched microbiome for enhancedbiological phosphorus removal. Engineering (InPress)

7.   Wang H, Lin L, Zhang L, Han P, Ju F*. 2023. Microbiome assembly mechanism and functionalpotential in enhanced biological phosphorus removal system enriched withTetrasphaera-related polyphosphate accumulating organisms. Environmental Research. 233:116494

8. Zhao Z, Zhang L, Zhang G, Gao H, Chen X, Li L, Ju F*. 2023. Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity andcommunity assembly within intertidal groundwater-surface water continuum. Water Research. 242:120236

9. Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F*. 2023. Deduplicationimproves cost-efficiency and yields of de novo assembly and binning of shotgun metagenomesin microbiome research. Microbiology Spectrum. 11(2). e04282-22

10. Lin L, Ju F*. 2023. Evaluation of different 16S rRNA genehypervariable regions and reference databases for profiling engineered microbiotastructure and functional guilds in a swine wastewater treatment plant. Interface Focus. 13(4):20230012

11. Lee J#, Ju F*#, Beck K, Bürgmann H*. 2023. Differential effects of wastewater treatment plant effluents on the antibioticresistomes of diverse river habitats. The ISME Journal. 17:1993-2002 (#equal contribution)

12. Zhu L, Yuan L, Shuai X, Lin Z, Sun Y, Zhou Z, Meng L, Ju F*, Chen H*. 2023. Deciphering basicand key traits of antibiotic resistome in influent and effluent of hospitalwastewater treatment systems. Water Research. 231:119614

13. Zhang H, Wang L, Zhang Z, Lin J, Ju F*. 2023. Cost-Efficient Micro-Well Array-Based Colorimetric AntibioticSusceptibility Testing (MacAST) for Bacteria from Culture or Community. Biosensors. 12(13),10.3390/bios13121028

14. Tang M, Chen Q, Zhong H, Ju F*, Sun W*, et al. 2023. Exploring diversity patterns and driving mechanisms of theantibiotic resistome and microbiome in saline groundwater. Journal of Hazardous Materials. 446:130734

15. Honda R, Kumar M, Wang R, Sabar M, Chaminda T, Ju F, et al. 2023. Recommendationsof key elements within an integrated monitoring framework of antimicrobialresistance for Asian countries. Environmental Science & Technology Letters (In Press).

16. Zhang J, Xu Z, Chu W, Ju F, Jin W, Li P, Xiao R. 2023. Residual chlorine persistently changes antibiotic resistance gene compositionand increases the risk of antibiotic resistance in sewer systems. Water Research. 245:120635

17. Jiang K, Li H, Liu W, Jiang Y, Zhang Z, Ju F, Song T, Li B, Wang X, Zhu C. 2023. Multiple antibiotic-resistant bacteria resistant to electrochemicaldisinfection with variation of key antibiotic resistance genes. ACS ES&T Water. 3(8):2096-2107

18. Gao S, Du Z, Ju F, Yan P, Niu B, Yao Y. 2023. Effect of rhizospheremicroorganisms on aflatoxin contamination of maize. Heliyon. 9(5):15949

19. Adyari B, Hou L, Zhang L, Chen N, Ju F, Zhu L, Yu C, Hu A. 2023. Seasonal hydrological dynamics governlifestyle preference of aquatic antibiotic resistome. Environmental Science & Ecotechnology. 13:100223

20. Xing W, Gai X, Ju F, Chen G. 2023. Microbial communities in tree root-compartment niches under Cdand Zn pollution: Structure, assembly process and co-occurrence relationship. Science of the Total Environment. 20:860:160273

21. Tang X, Li Y, Jin R, Yin G, Hou L, Liu M, Ju F, Han P. 2023. Communitypattern of potential phenanthrene (PHE) degrading bacteria in PHE contaminatedsoil revealed by 13C-DNA stable isotope probing. Chemosphere. 344:140377.

22. He Y, Jin H, Ju F*. 2023. Toxicological effects and underlying mechanisms of chlorination-derivedmetformin byproducts in Escherichia coli. Science of The Total Environment. 905:167281.

23. Zhang Y, Ju F*. 2023. Fighting caterpillar pestsand managing agricultural insecticide resistance with Lepidoptera-associated Enterococcuscasseliflavus. The Innovation Life. 3(1):100042

24. Zhang Z, Peng H, Yang D, Zhang G, Zhang J, Ju F*. 2022. Polyvinyl chloride degradation by a bacterium isolated fromthe gut of insect larvae. Nature Communication. 13: 5360

25. He Y, Zhang Y, Ju F*. 2022. Metformin contamination in global waters: biotic and abiotic transformation, byproduct generation and toxicity, and evaluation as a pharmaceutical indicator. Environmental Science & Technology. 56(19):13528-13545.

26. Zhang Z, Zhang G, Ju F*. 2022. Usingculture-enriched phenotypic metagenomics for targeted high-throughput monitoringof clinically-important fraction of the β-lactam resistome. EnvironmentalScience & Technology. 56(16):11429-11439

27. Shuai M, Zhang G, Zeng F, Fu Y, Ju F*, Ju-Sheng Zheng*, et al. 2022. Human gut antibiotic resistome andprogression of diabetes. Advanced Science. e2104965

28. Gao H, Zhao Z, Zhang L, Ju F*. 2022.Cyanopeptides restriction and degradation co-mediate microbiota assembly duringa freshwater cyanobacterial harmful algal bloom (CyanoHAB). Water Research. 220.118674

29. Yang X, Zhang L, Chen Y *, He Q, Liu T, Zhang G, Yuan L, Peng H, Wang H, Ju F*. 2022. Micro(nano)plasticsize and concentration co-differentiate nitrogen transformation, microbiotadynamics, and assembly patterns in constructed wetlands. Water Research. 220:118636

30. He L#,Huang X#, Zhang G, Yuan L, Shen E, Zhang L, Zhang X, Zhang T, Tao L*, Ju F*. 2022. Distinctive signatures of pathogenic and antibiotic resistant potentials in thehadal microbiome. Environmental Microbiome. 25.17(1): 19

31. Freudenthal J, Ju F, Bürgmann H, Dumack K. 2022. Microeukaryotic gut parasites inwastewater treatment plants: Diversity, activity and removal. Microbiome. 10(1): 27

32. Jiang C, Chen H, Grossart HP, Zhang Q, Stoks R, Zhao Y, Ju F, Liu W,Yang Y. 2022. Frequency of occurrence andhabitat selection shape the spatial variation in the antibiotic resistome inriverine ecosystems in eastern China. Environmental Microbiomes. 17(1):53

33. Lin D, Huang D, Zhang J, Yao Y, Zhang G, Ju F, Xu B, Wang M. 2022. Reduction ofantibiotic resistance genes (ARGs) in swine manure-fertilized soil viafermentation broth from fruit and vegetable waste. Environmental Research. 214: 113835

34. Zhu L, Lian Y, Lin D, Huang D, Yao Y, Ju F, Wang M. 2022. Insights intomicrobial contamination in multi-type manure-amended soils: The profile ofhuman bacterial pathogens, virulence factor genes and antibiotic resistancegenes. Journal of Hazardous Materials. 437: 129356

35. Wang C, Wang Y, Wang Y, Liu L, Wang D, Ju F, Xia Y, Zhang T. 2022. Impacts offood waste to sludge ratios on microbial dynamics and functional traits inthermophilic digesters. Water Research. 2022. 219.118590

36. Zhang Z, Liu C, Zhang H, Xu Z, Ju F, Yu C,Xu Y. 2022. Ultrafast interfacial self-assemblytoward supramolecular metal-organic films for water desalination. Advanced Science. 9(24):e2201624

37. Liang J, Liu J, Wang X, Sun H, Zhang Y, Ju F, et al. 2022. Genomic analysisreveals adaptation of Vibrio campbellii to the hadal ocean. Appliedand Environmental Microbiology. 88(16):e00575-22

38. Zhou J, Wang D, Ju F, Hu W, Liang J, Bai Y, Liu H, Qu J. 2022. Profiling microbial removal ofmicropollutants in sand filters: Biotransformation pathways and associatedbacteria. Journal of Hazardous Materials. 423:127167

39. He Y, Jin H, Gao H, Zhang G, Ju F*. 2022. Prevalence, production, and ecotoxicity ofchlorination-derived metformin byproducts in Chinese urban water systems. Science of the Total Environment. 151665

40. Zhang R, He Y, Yao L, Chen J, Zhu S, Rao X, Tang P, You J, Hua G, Zhang L, Ju F*, Wu L*. 2021. Metformin chlorination byproducts in drinking water exhibit markedtoxicities of a potential health concern. Environment International. 146:106244

41. Yuan L, Wang Y, Zhang L, Alejandro P, Zhou J, Smets B, Bürgmann H, Ju F*. 2021. Pathogenic andindigenous denitrifying bacteria are transcriptionally active and key multi-antibioticresistant players in wastewater treatment plants. Environmental Science& Technology. 55(15):10862-10874

42. Zhang L, Yin W, Wang C, Zhang A, Zhang H, Ju F*. 2021. Untanglingmicrobiota diversity and assembly patterns in the world's largest waterdiversion canal. Water Research. 117617.

43. Zhang H, Yao Y, Hui Y, Zhou N*, Ju F*. 2021. A3D-printed microfluidic gradient concentration chip for rapid antibioticsusceptibility testing. Bio-Design and Manufacturing. 174:1-10

44. Yang X, Wang H, Zhang L, Kong L, Chen Y*, He Q, Li L, Grossart H, Ju F*. 2021. Marinealgae facilitate transfer of microplastics and associated pollutants into foodwebs. Science of The Total Environment. 787: 147535

45. Wang H, Liu W, Haider M, Ju F, Yu Z, Shi Y, Cai W, Wang A. 2021. Waste activated sludgelysate treatment: resource recovery and refractory organics degradation. Journalof Hazardous Materials. 416: 126206

46. Lee J, Ju F, MaileMoskowitz A, Beck K, Maccagnan A, McArdell C, et al. 2021. Unraveling theriverine antibiotic resistome: the downstream fate of anthropogenic inputs. Water Research. 197:117050

47. Niederdorfer R, Fragner L, Yuan L, Hausherr D, Wei J, Magyar P, Joss A, Lehmann MF, Ju F, Helmut Bürgmann. 2021. Distinct growth stages controlled by the interplay ofdeterministic and stochastic processes in functional anammox biofilms. Water Research. 200:117225

48. Wang Y, Ye J, Ju F, Liu L, Boyd J, Deng Y, Parks D, Jiang X, Yin X, Woodcroft B, Tyson G, Hugenholtz P, Polz M. 2021. Successional dynamics and alternative stable states in asaline activated sludge microbial community over 9 years. Microbiome. 9(1):1-15

49. Wang Y, Qin W, Jiang X, Ju F, Mao Y, Zhang A, Stahl D, Zhang T. 2021. easonalprevalence of ammonia-oxidizing archaea in a full-scale municipal wastewater treatmentplant treating saline wastewater revealed by a 6-year time-series analysis. Environmental Science &Technology. 55(4):2662-2673

50. Gao C, Cao H, Ju F, Xiao K, Cai P, Wu Y, Huang Q. 2021. Emergent transcriptional adaption facilitatesconvergent succession within a synthetic community. ISME Communications. 1(1):1-5

51. Cao Y, Yu X, Ju F, Zhan H, Jiang B, Kang H, Xie Z. 2021. Airborne bacterial communitydiversity, source and function along the antarctic coast. Science of the Total Environment. 765:142700

52. Zhu G, Wang X, Yang T, Gillings M, Wang C, Ju F, et al. 2021. Air pollution could driveglobal dissemination of antibiotic resistance genes. The ISME Journal. 15:270-281

53. Zhong H, Sun H, Liu R, Zhan Y, Huang X, Ju F, and Zhang X. 2021. Comparative genomic analysis of labrenzia aggregata (Alphaproteobacteria)strains isolated from a trench: insights into the metabolic potentials andbiogeochemical functions. Frontiers in Microbiology. 12:770370

54. Ni Y, Yu G, Chen H, Deng Y, Wells P, Steves C, Ju F, Fu J. 2020. M2IA: A web serverfor microbiome and metabolome integrative analysis. Bioinformatics. 36(11):3493-3498

55. Hu W, Liang J, Ju F, Wang Q, Liu R, Bai Y, Liu H, Qu J. 2020. Metagenomics unravelsdifferential microbiome composition and metabolic potential in rapid sandfilters purifying surface water versus groundwater. Environmental Science & Technology. 54(8):5197-5206

56. Wang C, Wang Y, Wang Y, Cheung K, Ju F, Xia Y, Zhang T. 2020. Genome-centric microbiome analysis reveals solid retention time(SRT)-shaped species interactions and niche differentiation in food waste andsludge co-digesters. Water Research. 15(181):115858

Publications Prior to Westlake University

Postdoctoral research: Environmental Resistome and Microbiome of Wastewater Treatment Plant

57. Ju F, Beck K, Yin X, McArdell C, Singer H, Johnson D, Zhang T, Buergmann H. 2019. Wastewater treatment plant resistomes are shaped by bacterial composition,genetic exchange and upregulated expression in the effluent. The ISME Journal. 13(2):346-360

Postgraduate research: Environmental Microbiome of Activated Sludge and Anaerobic Digestion

58. Zhao F#, Ju F#, Huang K, Mao Y, Zhang X, Ren H, Zhang T. 2019. Comprehensive insights into the key components of bacterial assemblages inpharmaceutical wastewater treatment plants. Science of The Total Environment. 651:2148-2157. (#equalcontribution)

59. Guo F, Zhang T, Li B, Wang Z, Ju F, Liang Y. 2019. Mycobacterial species and their contribution to cholesterol degradation in wastewater treatmentplants. Scientific Reports. 9(1):836

60. Ju F, Wang Y, Zhang T. 2018. Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveledwith genome-resolved metagenomics. Biotechnology for Biofuels. 11(1):135

61. Jiang X, Ye L, Ju F, Wang Y, Zhang T. 2018. Toward an intensive longitudinal understanding of activated sludge bacterial assembly and dynamics. Environmental Science & Technology. 52 (15): 8224-8232

62. Jiang X, Ye L, Ju F, Li B, Ma L, Zhang T. 2018. Temporal dynamics of activated sludge bacterial communities in two diversity variantfull-scale sewage treatment plants. Applied Microbiology and Biotechnology. 1-10

63. Huang K, Mao Y, Zhao F, Zhang X, Ju F, Ye L, Wang Y, Li B, Ren H, Zhang T. 2018. Free-living bacteria and potential bacterial pathogens in sewage treatment plants. Applied Microbiology and Biotechnology.102(5):2455-2464

64. Ju F, Lau F, Zhang T. 2017. Linking microbial community, environmental variables and methanogenesis in anaerobic biogas digesters of chemically enhanced primary treatment sludge. Environmental Science & Technology. 51(7):3982-3992

65. Hu A, Ju F, Hou L, Li J, Yang X, Wang H, Mulla S, Sun Q, Bürgmann H*,Yu C*.2017. Strong impactof anthropogenic contamination on the cooccurrencepatterns of a riverine microbial community. Environmental Microbiology. 19(12):4993-5009.

66. Ju F#, Li B#, Ma L, Wang Y, Huang D, Zhang T. 2016. Antibiotic resistance genes and human bacterial pathogens: co-occurrence, removal, and enrichmentin municipal sewage sludge digesters. Water Research. 91:1-10 (#equal contribution)

67. Ju F, Wang Y, Lau F, Fung W, Huang D, Xia Y, Zhang T. 2016. Anaerobic digestion of chemically enhanced primary treatment (CEPT) sludge and themicrobial community structure. Applied Microbiology and Biotechnology. 100(20):8975-8982

68. Ju F, Zhang T. 2015. Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant. The ISME Journal. 9:683-695

69. Li B, Yang Y, Ma L, Ju F, Guo F, Tiedje J. Zhang T. 2015. Metagenomic and networkanalysis reveal wide distribution and co-occurrenceof environmental antibiotic resistance genes. The ISME Journal. 9(11): 2490-2502

70. Ju F, Zhang T. 2015. Experimental design and bioinformatics analysis for the application of metagenomics in environmental sciences and biotechnology. Environmental Science &Technology. 49(21):12628-12640

71. Ju F, Zhang T. 2015. 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions. Applied Microbiology and Biotechnology. 99(10):4119-4129

72. Wang Y, Xia Y, Ju F, Zhang T. 2015. Metagenome approaches revealed abiological prospect for improvement on mesophilic cellulose degradation. Applied Microbiology and Biotechnology. 99(24):10871-10879

73. Li B#, Ju F#, Cai L, Zhang T. 2015. Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-throughput metagenomic approach. Environmental Science &Technology. 49(17):10492–10502 (#equalcontribution)

74. Chao Y, Ma L, Yang Y, Ju F, Zhang X, Wu, W, Zhang T. 2014. Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment. Scientific Reports. srep03550

75. Liu L, Wang Z, Ju F, Zhang T. 2014. Co-occurrence correlations of heavy metals in sediments revealed using network analysis. Chemosphere. 119:1305-1313

76. Ju F, Zhang T. 2014. Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing. Microbial Ecology. 68(2):235-246

77. Xia Y, Ju F, Fang H, Zhang T*. 2013. Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortiumby metagenomics. PLoS ONE. 8(1):e53779

78. Fang H, Cai L, Yang Y, Ju F, Li X, Yu Y, Zhang T. 2014. Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments. Science ofthe Total Environment. 470-471:983-992

79. Peng X, Guo F, Ju F, Zhang T. 2014. Shiftsin the microbial community, nitrifiers and denitrifiers in the biofilm in afull-scale rotating biological contactor. Environmental Science & Technology. 48(14):8044-8052

80. Cai L, Ju F, Zhang T. 2014. Tracking human sewage microbiome in a municipal wastewater treatment plant. Applied Microbiology and Biotechnology. 98(7):3317-3326

81. Yang Y, Li B, Ju F, Zhang T. 2013. Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environmental Science &Technology. 18(47): 10197-10205

82. Guo F, Ju F, Cai L, Zhang T. 2013. Taxonomic precision of different hypervariable regions of 16SrRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PLoS ONE. 8(10):e7618

83. Ju F, Guo F, Ye L, Xia Y, Zhang T. 2014. Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over four years. Environmental Microbiology Reports. 6(1):80-89

84. Ju F, Xia Y, Guo F, Wang Z, Zhang T. 2014. Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environmental Microbiology. 16(8):2421-2432

Graduate research: WastewaterTreatment and Environmental Engineering

85. Lan S, Ju F, Wu X. 2012. Treatment of wastewater containing EDTA-Cu(II) using the combined process of interior microelectrolysis and Fenton oxidation-coagulation. Separationand Purification Technology.89:117-124

86. Ju F, Hu Y, Cheng J. 2011. Removal of chelatedCu (II) from aqueous solution by adsorption–coprecipitation with ironhydroxides prepared from microelectrolysis process. Desalination. 274(1):130-135   

87. Ju F, Hu Y. 2011. Removal of EDTA-chelatedcopper from aqueous solution by interior microelectrolysis. Separation and Purification Technology. 78(1):33-41