[1] Chee-Sanford JC, Aminov RI, Krapac IJ, et al. Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities. Applied and Environmental Microbiology, 2001, 67: 1494-1502 [2] Knapp CW, Dolfing J, Ehlert PAI, et al. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environmental Science & Technology, 2010, 44: 580-587 [3] Binh CT, Heuer H, Kaupenjohann M, et al. Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiology Ecology, 2008, 66: 25-37 [4] Kenzaka T, Tani K, Sakotani A, et al. High-frequency phage-mediated gene transfer among Escherichia coli cells, determined at the single-cell level. Applied and Environmental Microbiology, 2007, 73: 3291-3299 [5] Subirats J, Sanchez-Melsio A, Borrego CM, et al. Meta-genomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes. International Journal of Antimicrobial Agents, 2016, 48: 163-167 [6] Krupovic M, Dolja VV, Koonin EV. Origin of viruses: Primordial replicators recruiting capsids from hosts. Nature Reviews Microbiology, 2019, 17: 449-458 [7] Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiology Reviews, 2004, 28: 127-181 [8] Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology, 2020, 18: 125-138 [9] Shousha A, Awaiwanont N, Sofka D, et al. Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes. Applied and Environmental Microbiology, 2015, 81: 4600-4606 [10] Haaber J, Leisner JJ, Cohn MT, et al. Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells. Nature Communications, 2016, 7: 13333, doi: 10.1038/ncomms13333 [11] Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: Metagenomic analysis of composition and dynamics. Mobile DNA, 2017, 8: 12 [12] Shkoporov AN, Hill C. Bacteriophages of the human gut: The “known unknown” of the microbiome. Cell Host & Microbe, 2019, 25: 195-209 [13] Moon K, Jeon JH, Kang I, et al. Freshwater viral meta-genome reveals novel and functional phage-borne antibiotic resistance genes. Microbiome, 2020, 8: 75 [14] Sander M, Schmieger H. Method for host-independent detection of generalized transducing bacteriophages in natural habitats. Applied and Environmental Microbiology, 2001, 67: 1490-1493 [15] Lang AS, Zhaxybayeva O, Beatty JT. Gene transfer agents: Phage-like elements of genetic exchange. Nature Reviews Microbiology, 2012, 10: 472-482 [16] Kimura M, Jia ZJ, Nakayama N, et al. Ecology of viruses in soils: Past, present and future perspectives. Soil Science and Plant Nutrition, 2008, 54: 1-32 [17] Wilhelm SW, Weinbauer MG, Suttle CA, et al. The role of sunlight in the removal and repair of viruses in the sea. Limnology and Oceanography, 1998, 43: 586-592 [18] 王德铭. 环境介质中病毒生态的研究. 应用生态学报, 1990, 1(3): 277-286 [Wang D-M. Studies on the ecology of virus in environmental media. Chinese Journal of Applied Ecology, 1990, 1(3): 277-286] [19] Goyal SM, Gerba CP. Comparative adsorption of human enteroviruses, simian rotavirus, and selected bacteriophages to soils. Applied and Environmental Microbiology, 1979, 38: 241-247 [20] Güemes AGC, Youle M, Cantú VA, et al. Viruses as winners in the game of life. Annual Review of Virology, 2016, 3: 197-214 [21] Williamson KE, Fuhrmann JJ, Wommack KE, et al. Viruses in soil ecosystems: An unknown quantity within an unexplored territory. Annual Review of Virology, 2017, 4: 201-219 [22] Gonzalez-Martin C, Teigell-Perez N, Lyles M, et al. Epiflurescent direct counts of bacteria and viruses from topsoil of various desert dust storm regions. Research in Microbiology, 2013, 164: 17-21 [23] Williamson KE, Radosevich M, Smith DW, et al. Incidence of lysogeny within temperate and extreme soil environments. Environmental Microbiology, 2007, 9: 2563-2574 [24] Williamson KE, Corzo KA, Drissi CL, et al. Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods. Biology and Fertility of Soils, 2013, 49: 857-869 [25] Williamson KE, Radosevich M, Wommack KE. Abundance and diversity of viruses in six Delaware soils. Applied and Environmental Microbiology, 2005, 71: 3119-3125 [26] Helsley KR, Brown TM, Furlong K, et al. Applications and limitations of tea extract as a virucidal agent to assess the role of phage predation in soils. Biology and Fertility of Soils, 2014, 50: 263-274 [27] Chen L, Xun WB, Sun L, et al. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of Southern China. European Journal of Soil Biology, 2014, 62: 121-126 [28] Zablocki O, Adriaenssens EM, Cowan D. Diversity and ecology of viruses in hyperarid desert soils. Applied and Environmental Microbiology, 2016, 82: 770-777 [29] Marie T, Moura de Sousa JA, Rocha EP. Embracing the enemy: The diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Current Opinion in Microbiology, 2017, 38: 66-73 [30] King AMQ, Adams MJ, Carstens EB, et al. Virus Taxo-nomy: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, CA, USA: Elsevier Academic Press, 2012: 1261-1291 [31] Walker PJ, Siddell SG, Lefkowitz EJ, et al. Changes to virus taxonomy and the international code of virus classification and nomenclature ratified by the international committee on taxonomy of viruses. Archives of Virology, 2019, 164: 2417-2429 [32] Adriaenssens EM, Kramer R, Van Goethem MW, et al. Environmental drivers of viral community composition in antarctic soils identified by viromics. Microbiome, 2017, 5: 83 [33] Bi L, Yu DT, Du S, et al. Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils. Environmental Microbiology, 2020, 22, doi: 10.1111/1462-2920.15010 [34] Sun GW, Xiao JZ, Wang HM, et al. Efficient purification and concentration of viruses from a large body of high turbidity seawater. MethodsX, 2014, 1: 197-206 [35] Thurber RV, Haynes M, Breitbart M, et al. Laboratory procedures to generate viral metagenomes. Nature Protocols, 2009, 4: 470-483 [36] Trubl G, Solonenko N, Chittick L, et al. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ, 2016, 4: e1999 [37] Emerson JB. Soil viruses: A new hope. mSystems, 2019, 4: e00120-19 [38] Emerson JB, Roux S, Brum JR, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 2018, 3: 870-880 [39] Sun MM, Ye M, Jiao WT, et al. Changes in tetracycline partitioning and bacteria/phage-comediated ARGs in microplastic-contaminated greenhouse soil facilitated by sophorolipid. Journal of Hazardous Materials, 2018, 345: 131-139 [40] Larrañaga O, Brown-Jaque M, Quirós P, et al. Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil. Environment International, 2018, 115: 133-141 [41] Narr A, Nawaz A, Wick LY, et al. Soil viral communities vary temporally and along a land use transect as revealed by virus-like particle counting and a modified community fingerprinting approach (fRAPD). Frontiers in Microbiology, 2017, 8: 1975 [42] Quiros P, Muniesa M. Contribution of cropland to the spread of Shiga toxin phages and the emergence of new Shiga toxin-producing strains. Scientific Reports, 2017, 7: 7796 [43] Williamson KE, Wommack KE, Radosevich M. Sampling natural viral communities from soil for culture-independent analyses. Applied and Environmental Microbiology, 2003, 69: 6628-6633 [44] Lasobras J, Dellunde J, Jofre J, et al. Occurrence and levels of phages proposed as surrogate indicators of enteric viruses in different types of sludges. Journal of Applied Microbiology, 1999, 86: 723-729 [45] Araujo RM, Lasobras J, Lucena F, et al. Methodological improvements for the recovery of bacteroides fragilis phages and coliphages from environmental samples. Water Science and Technology, 1993, 27: 119-122 [46] Danovaro R, Dell’Anno A, Trucco A, et al. Determination of virus abundance in marine sediments. Applied and Environmental Microbiology, 2001, 67: 1384-1387 [47] Zablocki O, Zyl LV, Adriaenssens EM, et al. High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils. Applied and Environmental Microbiology, 2014, 80: 6888-6897 [48] Goller PC, Haro-Moreno JM, Rodriguez-Valera F, et al. Uncovering a hidden diversity: Optimized protocols for the extraction of dsDNA bacteriophages from soil. Microbiome, 2020, 8: 17 [49] 张辉, 赵炳梓, 张佳宝. 不同提取方法对土壤中病毒回收率的比较. 土壤学报, 2008, 45(3): 452-458 [Zhang H, Zhao B-Z, Zhang J-B. Soil virus recovery effeciency of various methods. Acta Pedologica Sinica, 2008, 45(3): 452-458] [50] Conceição-Neto N, Zeller M, Lefrère H, et al. Modular approach to customise sample preparation procedures for viral metagenomics: A reproducible protocol for virome analysis. Scientific Reports, 2015, 5: 16532 [51] Ross J, Topp E. Abundance of antibiotic resistance genes in bacteriophage following soil fertilization with dairy manure or municipal biosolids, and evidence for potential transduction. Applied and Environmental Microbiology, 2015, 81: 7905-7913 [52] Duhaime MB, Deng L, Poulos BT, et al. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: A rigorous assessment and optimization of the linker amplification method. Environmental Microbiology, 2012, 14: 2526-2537 [53] Han LL, Yu DT, Zhang LM, et al. Genetic and functional diversity of ubiquitous DNA viruses in selected chinese agricultural soils. Scientific Reports, 2017, 7: 45142 [54] Hoeijmakers WA, Bartfai R, Francoijs KJ, et al. Linear amplification for deep sequencing. Nature Protocols, 2011, 6: 1026-1036 [55] Kim KH, Bae JW. Amplification methods bias meta-genomic libraries of uncultured single-stranded and double-stranded DNA viruses. Applied and Environmental Microbiology, 2011, 77: 7663-7668 [56] Yilmaz S, Allgaier M, Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods, 2010, 7: 943-944 [57] Hatfull GF. Dark matter of the biosphere: The amazing world of bacteriophage diversity. Journal of Virology, 2015, 89: 8107-8110 [58] Zhu YG, Johnson TA, Su JQ, et al. Diverse and abundant antibiotic resistance genes in chinese swine farms. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110: 3435-3440 [59] Debroas D, Siguret C. Viruses as key reservoirs of antibiotic resistance genes in the environment. The ISME Journal, 2019, 13: 2856-2867 [60] Lindell D, Jaffe JD, Johnson ZI, et al. Photosynthesis genes in marine viruses yield proteins during host infection. Nature, 2005, 438: 86-89 [61] Oliver KM, Degnan PH, Hunter MS, et al. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science, 2009, 325: 992-994 [62] Chen J, Novick RP. Phage-mediated intergeneric transfer of toxin genes. Science, 2009, 323: 139-141 [63] Song S, Guo Y, Kim JS, et al. Phages mediate bacterial self-recognition. Cell Reports, 2019, 27: 737-749 [64] Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, et al. Uncovering earth’s virome. Nature, 2016, 536: 425-430 [65] Lekunberri I, Subirats J, Borrego CM, et al. Exploring the contribution of bacteriophages to antibiotic resis-tance. Environmental Pollution, 2017, 220: 981-984 [66] Calero-Caceres W, Muniesa M. Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater. Water Research, 2016, 95: 11-18 [67] Lekunberri I, Villagrasa M, Balcazar JL, et al. Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges. Science of the Total Environment, 2017, 601-602: 206-209 [68] Wang MZ, Liu P, Zhou Q, et al. Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces. Environmental Pollution, 2018, 238: 291-298 [69] Yang YX, Xie XJ, Tang MJ, et al. Exploring the profile of antimicrobial resistance genes harboring by bacteriophage in chicken feces. Science of the Total Environment, 2020, 700: 134446 [70] Ye M, Sun MM, Huang D, et al. A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment. Environment International, 2019, 129: 488-496 |