Prophages in aquatic environments: From silent passengers to keystone regulators of biogeochemical cycles, biofilm dynamics, and antibiotic resistance dissemination

Abstract

Prophages, which are temperate bacteriophages integrated into bacterial chromosomes, serve as pervasive but understudied regulators of microbial ecology in aquatic environments. While they confer benefits such as enhanced virulence, stress resistance, and metabolic flexibility during lysogeny, environmental stressors can induce their lytic cycle, culminating in host cell lysis and phage dispersal. This review synthesizes current knowledge on prophage identification methodologies, environmental distribution patterns across diverse aquatic habitats (marine, freshwater, and wastewater systems), and their diverse roles in modulating environmental processes. Activation triggers and molecular pathways are systematically analyzed, alongside an assessment of their impacts on 1) biogeochemical cycling of C, N, P, and S; 2) dual regulation of biofilm dynamics; and 3) the dissemination and persistence of antibiotic resistance genes. The potential use of prophage derived endolysins as biocontrol agents is also discussed. By pinpointing key knowledge gaps—including in situ quantification of prophage induction, connecting prophage activity to community level processes, and validation under environmentally relevant conditions—this review proposes an integrated framework and priority research directions for aquatic prophage research, with cautious consideration of applications for water quality management and public-health protection.

Graphical abstract

Keywords

Prophage induction / Biogeochemical cycles / Antibiotic resistance genes / Biofilm dynamics / Aquatic ecosystems

Highlight

	● Establishes an integrated framework for aquatic prophage ecology.
	● Links environmental stressors to prophage induction and ecological effects.
	● Evaluates prophage effects on biogeochemical cycling and biofilm dynamics.
	● Clarifies constraints on prophage-mediated ARG transfer in aquatic systems.
	● Identifies priorities for prophage ecology and biosafety research.

References

[1] Abedon S T . (2017). Commentary: communication between viruses guides lysis–lysogeny decisions. Frontiers in Microbiology, 8: 983

[2] Aertsen A , Faster D , Michiels C W . (2005). Induction of Shiga toxin-converting prophage in Escherichia coli by high hydrostatic pressure. Applied and Environmental Microbiology, 71(3): 1155–1162

[3] Aframian N , Omer Bendori S , Kabel S , Guler P , Stokar-Avihail A , Manor E , Msaeed K , Lipsman V , Grinberg I , Mahagna A . et al. (2021). Dormant phages communicate via arbitrium to control exit from lysogeny. Nature Microbiology, 7(1): 145–153

[4] Alam K , Alhhazmi A , DeCoteau J F , Luo Y , Geyer C R . (2016). RecA inhibitors potentiate antibiotic activity and block evolution of antibiotic resistance. Cell Chemical Biology, 23(3): 381–391

[5] Andrade-Martínez J S , Camelo Valera L C , Chica Cárdenas L A , Forero-Junco L , López-Leal G , Moreno-Gallego J L , Rangel-Pineros G , Reyes A . (2022). Computational tools for the analysis of uncultivated phage genomes. Microbiology and Molecular Biology Reviews, 86(2): e0000421

[6] Arndt D , Grant J R , Marcu A , Sajed T , Pon A , Liang Y J , Wishart D S . (2016). PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Research, 44(W1): W16–W21

[7] Azulay G , Pasechnek A , Stadnyuk O , Ran-Sapir S , Fleisacher A M , Borovok I , Sigal N , Herskovits A A . (2022). A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response. Cell Reports, 39(3): 110723

[8] Babar T K , Glare T R , Hampton J G , Hurst M R H , Narciso J O . (2022). Isolation, purification, and characterisation of a phage tail-like bacteriocin from the insect pathogenic bacterium Brevibacillus laterosporus. Biomolecules, 12(8): 1154

[9] Bae T , Baba T , Hiramatsu K , Schneewind O . (2006). Prophages of Staphylococcus aureus Newman and their contribution to virulence. Molecular Microbiology, 62(4): 1035–1047

[10] Balarjishvili N , Kvachadze L , Tevdoradze E , Skhirtladze N , Leshkasheli L , Bolkvadze D , Pataridze T , Meskhi T , Chakraborty R , Kutateladze M . et al. (2021). Significance of lysogeny for the metabolism of Desulfovibrio spp. strains isolated from aquatic environments of Georgia. Journal of Applied Microbiology, 131(3): 1344–1359

[11] Balasubramanian S , Osburne M S , BrinJones H , Tai A K , Leong J M . (2019). Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagic E. coli infection. PLOS Pathogens, 15(1): e1007494

[12] Becker S C , Foster-Frey J , Donovan D M . (2008). The phage K lytic enzyme LysK and lysostaphin act synergistically to kill MRSA. FEMS Microbiology Letters, 287(2): 185–191

[13] Benoit G , James R , Raguideau S , Alabone G , Goodall T , Chikhi R , Quince C . (2026). High-quality metagenome assembly from nanopore reads with nanoMDBG. Nature Communications, 17(1): 3556

[14] Berger P , Kouzel I U , Berger M , Haarmann N , Dobrindt U , Koudelka G B , Mellmann A . (2019). Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization. BMC Genomics, 20(1): 504

[15] Binnenkade L , Teichmann L , Thormann K M . (2014). Iron triggers λSo prophage induction and release of extracellular DNA in Shewanella oneidensis MR-1 biofilms. Applied and Environmental Microbiology, 80(17): 5304–5316

[16] Bondy-Denomy J , Davidson A R . (2014). When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. Journal of Microbiology, 52(3): 235–242

[17] Borodovich T , Shkoporov A N , Ross R P , Hill C . (2022). Phage-mediated horizontal gene transfer and its implications for the human gut microbiome. Gastroenterology Report, 10: goac012

[18] Boyd E F , Brüssow H . (2002). Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends in Microbiology, 10(11): 521–529

[19] Braetz S , Schwerk P , Figueroa-Bossi N , Tedin K , Fulde M . (2023). Prophage Gifsy-1 induction in Salmonella enterica serovar Typhimurium reduces persister cell formation after ciprofloxacin exposure. Microbiology Spectrum, 11(4): e0187423

[20] Bruce J B , Lion S , Buckling A , Westra E R , Gandon S . (2021). Regulation of prophage induction and lysogenization by phage communication systems. Current Biology, 31(22): 5046–5051.e7

[21] Bruder K , Malki K , Cooper A , Sible E , Shapiro J W , Watkins S C , Putonti C . (2016). Freshwater metaviromics and bacteriophages: a current assessment of the state of the art in relation to bioinformatic challenges. Evolutionary Bioinformatics, 12(S1): 25–33

[22] Brüssow H , Canchaya C , Hardt W D . (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiology and Molecular Biology Reviews, 68(3): 560–602

[23] Canchaya C , Proux C , Fournous G , Bruttin A , Brüssow H . (2003). Prophage genomics. Microbiology and Molecular Biology Reviews, 67(2): 238–276

[24] Carrolo M , Frias M J , Pinto F R , Melo-Cristino J , Ramirez M . (2010). Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae. PLoS One, 5(12): e15678

[25] Casjens S . (2003). Prophages and bacterial genomics: what have we learned so far?. Molecular Microbiology, 49(2): 277–300

[26] Chatterjee A , Duerkop B A . (2019). Sugar and fatty acids Ack-celerate prophage induction. Cell Host & Microbe, 25(2): 175–176

[27] Chen L X , Zhao Y L , McMahon K D , Mori J F , Jessen G L , Nelson T C , Warren L A , Banfield J F . (2019). Wide distribution of phage that infect freshwater SAR11 bacteria. mSystems, 4(5): e00410–19

[28] Chen Y Q , Wang Y L , Paez-Espino D , Polz M F , Zhang T . (2021). Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature Communications, 12(1): 5398

[29] Choi J , Kotay S M , Goel R . (2010). Various physico-chemical stress factors cause prophage induction in Nitrosospira multiformis 25196- an ammonia oxidizing bacteria. Water Research, 44(15): 4550–4558

[30] Choi J , Kotay S M , Goel R . (2011). Bacteriophage-based biocontrol of biological sludge bulking in wastewater. Bioengineered Bugs, 2(4): 214–217

[31] Christie G E , Calendar R . (2016). Bacteriophage P2. Bacteriophage, 6(1): e1145782

[32] Christie G E , Dokland T . (2012). Pirates of the caudovirales. Virology, 434(2): 210–221

[33] Chu T C , Murray S R , Hsu S F , Vega Q , Lee L H . (2011). Temperature-induced activation of freshwater Cyanophage AS-1 prophage. Acta Histochemica, 113(3): 294–299

[34] Chung I Y , Jang H J , Bae H W , Cho Y H . (2014). A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly. Proceedings of the National Academy of Sciences of the United States of America, 111(31): 11503–11508

[35] Cirz R T , Chin J K , Andes D R , De Crécy-Lagard V , Craig W A , Romesberg F E . (2005). Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biology, 3(6): e176

[36] Cirz R T , Jones M B , Gingles N A , Minogue T D , Jarrahi B , Peterson S N , Romesberg F E . (2007). Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin. Journal of Bacteriology, 189(2): 531–539

[37] Cochran P K , Kellogg C A , Paul J H . (1998). Prophage induction of indigenous marine lysogenic bacteria by environmental pollutants. Marine Ecology Progress Series, 164: 125–133

[38] Coclet C , Roux S . (2021). Global overview and major challenges of host prediction methods for uncultivated phages. Current Opinion in Virology, 49: 117–126

[39] Cook R , Brown N , Redgwell T , Rihtman B , Barnes M , Clokie M , Stekel D J , Hobman J , Jones M A , Millard A . (2021). INfrastructure for a PHAge reference database: identification of large-scale biases in the current collection of cultured phage genomes. PHAGE: Therapy, Applications, and Research, 2(4): 214–223

[40] Cornuault J K , Moineau S . (2021). Induction and elimination of prophages using CRISPR interference. The CRISPR Journal, 4(4): 549–557

[41] Couvin D , Bernheim A , Toffano-Nioche C , Touchon M , Michalik J , Néron B , Rocha E P C , Vergnaud G , Gautheret D , Pourcel C . (2018). CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Research, 46(W1): W246–W251

[42] Crispim J S , Dias R S , Laguardia C N , Araújo L C , da Silva J D , Vidigal P M P , de Sousa M P , da Silva C C , Santana M F , de Paula S O . (2019). Desulfovibrio alaskensis prophages and their possible involvement in the horizontal transfer of genes by outer membrane vesicles. Gene, 703: 50–57

[43] Czyz A , Los M , Wrobel B , Wegrzyn G . (2001). Inhibition of spontaneous induction of lambdoid prophages in Escherichia coli cultures: simple procedures with possible biotechnological applications. BMC Biotechnology, 1(1): 1

[44] Danovaro R , Dell’Anno A , Corinaldesi C , Rastelli E , Cavicchioli R , Krupovic M , Noble R T , Nunoura T , Prangishvili D . (2016). Virus-mediated archaeal hecatomb in the deep seafloor. Science Advances, 2(10): e1600492

[45] Davies D G , Parsek M R , Pearson J P , Iglewski B H , Costerton J W , Greenberg E P . (1998). The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science, 280(5361): 295–298

[46] Dávila-Ramos S , Castelán-Sánchez H G , Martínez-Ávila L , del Rayo Sánchez-Carbente M , Peralta R , Hernández-Mendoza A , Dobson A D W , Gonzalez R A , Pastor N , Batista-García R A . (2019). A review on viral metagenomics in extreme environments. Frontiers in Microbiology, 10: 2403

[47] Dedrick R M , Jacobs-Sera D , Bustamante C A G , Garlena R A , Mavrich T N , Pope W H , Reyes J C C , Russell D A , Adair T , Alvey R . et al. (2017). Prophage-mediated defence against viral attack and viral counter-defence. Nature Microbiology, 2(3): 16251

[48] Deng X H , Yuan J , Chen L P , Chen H , Wei C H , Nielsen P H , Wuertz S , Qiu G L . (2023). CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. Water Research, 235: 119906

[49] Dieppa-Colón E , Martin C , Kosmopoulos J C , Anantharaman K . (2025). Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages. Environmental Microbiome, 20(1): 5

[50] Duerkop B A , Clements C V , Rollins D , Rodrigues J L M , Hooper L V . (2012). A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proceedings of the National Academy of Sciences of the United States of America, 109(43): 17621–17626

[51] Enwemeka C S , Williams D , Enwemeka S K , Hollosi S , Yens D . (2009). Blue 470-nm light kills methicillin-resistant Staphylococcus aureus (MRSA) in vitro. Photobiomodulation, Photomedicine, and Laser Surgery, 27(2): 221–226

[52] Erdogdu B , Dokuz S , Sarigode E , Karabasoglu C , Ozbek T . (2026). Prophage: agent provocateur?. Archives of Microbiology, 208(4): 183

[53] Erez Z , Steinberger-Levy I , Shamir M , Doron S , Stokar-Avihail A , Peleg Y , Melamed S , Leavitt A , Savidor A , Albeck S . et al. (2017). Communication between viruses guides lysis–lysogeny decisions. Nature, 541(7638): 488–493

[54] Fang Y , Mercer R G , McMullen L M , Gänzle M G . (2017). Induction of Shiga toxin-encoding prophage by abiotic environmental stress in food. Applied and Environmental Microbiology, 83(19): e01378–17

[55] Feiner R , Argov T , Rabinovich L , Sigal N , Borovok I , Herskovits A A . (2015). A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nature Reviews Microbiology, 13(10): 641–650

[56] Flowers J J , He S M , Malfatti S , del Rio T G , Tringe S G , Hugenholtz P , McMahon K D . (2013). Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal. The ISME Journal, 7(12): 2301–2314

[57] Fortier L C , Sekulovic O . (2013). Importance of prophages to evolution and virulence of bacterial pathogens. Virulence, 4(5): 354–365

[58] Gabig-Ciminska M , Los M , Holmgren A , Albers J , Czyz A , Hintsche R , Wegrzyn G , Enfors S O . (2004). Detection of bacteriophage infection and prophage induction in bacterial cultures by means of electric DNA chips. Analytical Biochemistry, 324(1): 84–91

[59] Gallego Del Sol F , Penadés J R , Marina A . (2019). Deciphering the molecular mechanism underpinning phage arbitrium communication systems. Molecular Cell, 74(1): 59–72.e3

[60] García-López R , Vázquez-Castellanos J F , Moya A . (2015). Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations. Frontiers in Bioengineering and Biotechnology, 3: 141

[61] Geng Y C , Nguyen T V P , Homaee E , Golding I . (2024). Using bacterial population dynamics to count phages and their lysogens. Nature Communications, 15(1): 7814

[62] Gödeke J , Paul K , Lassak J , Thormann K M . (2011). Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1. The ISME Journal, 5(4): 613–626

[63] Gomes I B . (2025). The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health. Journal of Applied Microbiology, 136(4): lxaf064

[64] Gu X , Huang D , Chen J H , Li X , Zhou Y Q , Huang M H , Liu Y N , Yu P F . (2022). Bacterial inactivation and biofilm disruption through indigenous prophage activation using low-intensity cold atmospheric plasma. Environmental Science & Technology, 56(12): 8920–8931

[65] Guan N Z , Li J H , Shin H D , Du G C , Chen J , Liu L . (2017). Microbial response to environmental stresses: from fundamental mechanisms to practical applications. Applied Microbiology and Biotechnology, 101(10): 3991–4008

[66] Guan Z Y , Pei K , Wang J , Cui Y Q , Zhu X , Su X , Zhou Y B , Zhang D L , Tang C , Yin P . et al. (2019). Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage. Cell Discovery, 5(1): 29

[67] Guffey J S , Wilborn J . (2006). In vitro bactericidal effects of 405-nm and 470-nm blue light. Photobiomodulation, Photomedicine, and Laser Surgery, 24(6): 684–688

[68] Guo J H , Gao S H , Lu J , Bond P L , Verstraete W , Yuan Z G . (2017). Copper oxide nanoparticles induce lysogenic bacteriophage and metal-resistance genes in Pseudomonas aeruginosa PAO1. ACS Applied Materials & Interfaces, 9(27): 22298–22307

[69] Guo J R , Bolduc B , Zayed A A , Varsani A , Dominguez-Huerta G , Delmont T O , Pratama A A , Gazitúa M C , Vik D , Sullivan M B . et al. (2021). VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome, 9(1): 37

[70] Guo M T , Yuan Q B , Yang J . (2015). Distinguishing effects of ultraviolet exposure and chlorination on the horizontal transfer of antibiotic resistance genes in municipal wastewater. Environmental Science & Technology, 49(9): 5771–5778

[71] Guo Y X , Lin S T , Chen R , Gu J Y , Tang K H , Nie Z L , Huang Z X , Weng J H , Lin J Z , Liu T L . et al. (2024a). A reverse transcriptase controls prophage genome reduction to promote phage dissemination in Pseudomonas aeruginosa biofilms. Cell Reports, 43(11): 114883

[72] Guo Y X , Tang K H , Sit B , Gu J Y , Chen R , Shao X Q , Lin S T , Huang Z X , Nie Z L , Lin J Z . et al. (2024b). Control of lysogeny and antiphage defense by a prophage-encoded kinase-phosphatase module. Nature Communications, 15(1): 7244

[73] Hafeezunnisa M , Chhakchhuak P I R , Krishnakumar J , Sen R . (2021). Rho-dependent transcription termination regulates the toxin–antitoxin modules of cryptic prophages to silence their expression in Escherichia coli. FEBS Letters, 595(15): 2057–2067

[74] Han J , Aljahdali N , Zhao S H , Tang H L , Harbottle H , Hoffmann M , Frye J G , Foley S L . (2024). Infection biology of Salmonella enterica. EcoSal Plus, 12(1): eesp00012023

[75] Hare J M , Ferrell J C , Witkowski T A , Grice A N . (2014). Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi. PLoS One, 9(4): e93861

[76] Hargreaves K R , Kropinski A M , Clokie M R J . (2014). What does the talking?: quorum sensing signalling genes discovered in a bacteriophage genome. PLoS One, 9(1): e85131

[77] He F , Bhoobalan-Chitty Y , Van L B , Kjeldsen A L , Dedola M , Makarova K S , Koonin E V , Brodersen D E , Peng X . (2018). Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nature Microbiology, 3(4): 461–469

[78] Hornbeck P V . (2015). Enzyme-linked immunosorbent assays. Current Protocols in Immunology, 110(1): 2.1.1–2.1.23

[79] Howard-Varona C , Hargreaves K R , Abedon S T , Sullivan M B . (2017). Lysogeny in nature: mechanisms, impact and ecology of temperate phages. The ISME Journal, 11(7): 1511–1520

[80] Hu Y Q , Zeng Y X , Du Y , Zhao W , Li H R , Han W , Hu T , Luo W . (2023). Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments. BMC Genomics, 24(1): 534

[81] Huang D , Xia R , Chen C Y , Liao J Q , Chen L X , Wang D S , Alvarez P J J , Yu P F . (2024). Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends in Microbiology, 32(9): 902–916

[82] Huang D , Yu P F , Ye M , Schwarz C , Jiang X , Alvarez P J J . (2021). Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. Microbiome, 9(1): 150

[83] Huang D , Yuan M M , Chen J H , Zheng X X , Wong D , Alvarez P J J , Yu P F . (2023a). The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME Communications, 3(1): 46

[84] Huang H N , Feng G Q , Wang M , Liu C , Wu Y , Dong L , Feng L Y , Zheng X , Chen Y G . (2022a). Nitric oxide: a neglected driver for the conjugative transfer of antibiotic resistance genes among wastewater microbiota. Environmental Science & Technology, 56(10): 6466–6478

[85] Huang H N , Lin L , Bu F , Su Y L , Zheng X , Chen Y G . (2022b). Reductive stress boosts the horizontal transfer of plasmid-borne antibiotic resistance genes: the neglected side of the intracellular redox spectrum. Environmental Science & Technology, 56(22): 15594–15606

[86] Huang H N , Lin L , Liu Q M , Li X Y , Liao J Q , Dong L , Zhang J Y , Su Y L , Luo J Y , Feng L Y . et al. (2025). Hydrogen sulfide drives horizontal transfer of plasmid-borne antibiotic resistance genes in wastewater ecosystems. Nature Water, 3(11): 1268–1280

[87] Huang J H , Dai X Y , Wu Z W , Hu X , Sun J J , Tang Y J , Zhang W Q , Han P Z , Zhao J Q , Liu G J . et al. (2023b). Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. The ISME Journal, 17(9): 1467–1481

[88] Hynes A P , Moineau S . (2017). Phagebook: the social network. Molecular Cell, 65(6): 963–964

[89] Igler C , Brockhurst M . (2023). Bacteriophage ecology: getting a head start on genomic competitors. Current Biology, 33(19): R1011–R1013

[90] Imamovic L , Muniesa M . (2012). Characterizing RecA-independent induction of Shiga toxin2-encoding phages by EDTA treatment. PLoS One, 7(2): e32393

[91] Jancheva M , Böttcher T . (2021). A metabolite of Pseudomonas triggers prophage-selective lysogenic to lytic conversion in Staphylococcus aureus. Journal of the American Chemical Society, 143(22): 8344–8351

[92] Jiang S C , Paul J H . (1996). Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Marine Ecology Progress Series, 142: 27–38

[93] Kanamaru S , Leiman P G , Kostyuchenko V A , Chipman P R , Mesyanzhinov V V , Arisaka F , Rossmann M G . (2002). Structure of the cell-puncturing device of bacteriophage T4. Nature, 415(6871): 553–557

[94] Kant P , Petersen B , Sicheritz-Pontén T , Kondabagil K . (2026). On the low abundance of antibiotic resistance genes in bacteriophage genomes and their random acquisition via specialized transduction. Genome Biology and Evolution, 18(5): evag079

[95] Kawaguchi T, Watanabe S, Liu Y, Aiba Y, Tan X E, Veeranarayanan S, Miyanaga K, Sasahara T, Shimamori Y, Alessa O, et al. (2025). Gene-specific reversal of carbapenem-resistant Pseudomonas aeruginosa via phage-delivered CRISPR-Cas13a. npj Antimicrobials and Resistance, 3(1): 98

[96] Kieft K , Anantharaman K . (2022). Deciphering active prophages from metagenomes. mSystems, 7(2): e0008422

[97] Kieft K , Zhou Z C , Anderson R E , Buchan A , Campbell B J , Hallam S J , Hess M , Sullivan M B , Walsh D A , Roux S . et al. (2021). Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications, 12(1): 3503

[98] Kintz E , Davies M R , Hammarlöf D L , Canals R , Hinton J C D , van der Woude M W . (2015). A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide. Molecular Microbiology, 96(2): 263–275

[99] Koonin E V , Makarova K S . (2024). CRISPR in mobile genetic elements: counter-defense, inter-element competition and RNA-guided transposition. BMC Biology, 22(1): 295

[100] Krause H M , Higgins N P . (1986). Positive and negative regulation of the mu operator by mu repressor and Escherichia coli integration host factor. The Journal of Biological Chemistry, 261(8): 3744–3752

[101] Kreuzer K N . (2013). DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harbor Perspectives in Biology, 5(11): a012674

[102] Laganenka L , Sander T , Lagonenko A , Chen Y , Link H , Sourjik V . (2019). Quorum sensing and metabolic state of the host control lysogeny-lysis switch of bacteriophage T1. mBio, 10(5): e01884–19

[103] Lakshminarasimhan A . (2022). Prophage induction therapy: activation of the lytic phase in prophages for the elimination of pathogenic bacteria. Medical Hypotheses, 169: 110980

[104] Lamy-Besnier Q , Bignaud A , Garneau J R , Titecat M , Conti D E , Von Strempel A , Monot M , Stecher B , Koszul R , Debarbieux L . et al. (2023). Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria. Microbiome, 11(1): 111

[105] Lee L H , Lui D , Platner P J , Hsu S F , Chu T C , Gaynor J J , Vega Q C , Lustigman B K . (2006). Induction of temperate cyanophage AS-1 by heavy metal-copper. BMC Microbiology, 6(1): 17

[106] Leitner L , Ujmajuridze A , Chanishvili N , Goderdzishvili M , Chkonia I , Rigvava S , Chkhotua A , Changashvili G , McCallin S , Schneider M P . et al. (2021). Intravesical bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate: a randomised, placebo-controlled, double-blind clinical trial. The Lancet Infectious Diseases, 21(3): 427–436

[107] Lemire S , Figueroa-Bossi N , Bossi L . (2011). Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genetics, 7(6): e1002149

[108] Li J , Wang D P , Zhang Q F , He X W , Liu P , Ye L , Ren H Q , Zhang X X . (2025). Prevalence and functional impact of the interactions between lysogenic phages and hosts in activated sludge systems: insights from large-scale metagenomics and experimental evidence. Water Research, 286: 124270

[109] Li Z K , Chen L , Huang S X , Zhang Y , Yao F , Huang P H , Shang Y Y , Yuan X M , Xie X Q , Li Y . et al. (2026). Helicobacter pylori phages: resource landscape, translational challenges, and engineered antibacterial strategies. Archives of Microbiology, 208(9): 441

[110] Liao H P , Liu C , Zhou S G , Liu C Q , Eldridge D J , Ai C F , Wilhelm S W , Singh B K , Liang X L , Radosevich M . et al. (2024). Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments. Nature Communications, 15(1): 8315

[111] Liebmann J , Born M , Kolb-Bachofen V . (2010). Blue-light irradiation regulates proliferation and differentiation in human skin cells. Journal of Investigative Dermatology, 130(1): 259–269

[112] Lin Z J , Ruan C J , Xia R , Liao J Q , Zhu L , Wang D S , Alvarez P J J , Yu P F . (2025). Bacterium–phage interactions enhance biofilm resilience during membrane filtration biofouling under oxidative and hydraulic stresses. Environmental Science & Technology, 59(17): 8614–8628

[113] Little J W , Mount D W . (1982). The SOS regulatory system of Escherichia coli. Cell, 29(1): 11–22

[114] Liu R Y , Qi R , Wang J , Zhang Y , Liu X C , Rossetti S , Tandoi V , Yang M . (2017). Phage-host associations in a full-scale activated sludge plant during sludge bulking. Applied Microbiology and Biotechnology, 101(16): 6495–6504

[115] Liu X , Ye Y , Zhang Z S , Rensing C , Zhou S G , Nealson K H . (2023). Prophage induction causes Geobacter electroactive biofilm decay. Environmental Science & Technology, 57(15): 6196–6204

[116] Liu Z Y , Tang K H , Zhou Y Q , Liu T L , Guo Y X , Wu D T , Wang X X . (2024). Active prophages in coral-associated Halomonas capable of lateral transduction. The ISME Journal, 18(1): wrae085

[117] López-Leal G , Camelo-Valera L C , Hurtado-Ramírez J M , Verleyen J , Castillo-Ramírez S , Reyes-Muñoz A . (2022). Mining of thousands of prokaryotic genomes reveals high abundance of prophages with a strictly narrow host range. mSystems, 7(4): e0032622

[118] Lu J , Guo J H . (2024). Prophage induction by non-antibiotic compounds promotes transformation of released antibiotic resistance genes from cell lysis. Water Research, 263: 122200

[119] Lunde M , Aastveit A H , Blatny J M , Nes I F . (2005). Effects of diverse environmental conditions on φLC3 prophage stability in Lactococcus lactis. Applied and Environmental Microbiology, 71(2): 721–727

[120] Luo Q X , Chang M R , Lu P , Guo Q , Jiang X Q , Xiao T T , Zhang H Y , Ma Y Y , Zhang Y , Yu W . et al. (2025). Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China. Nature Communications, 16(1): 3536

[121] Lymer D , Lindström E S . (2010). Changing phosphorus concentration and subsequent prophage induction alter composition of a freshwater viral assemblage. Freshwater Biology, 55(9): 1984–1996

[122] Ma R J , Xu B , Chen X W , Sun Q , Li Y Y , Zheng Q , Jiao N Z , Zhang R . (2025). Prophages in marine Citromicrobium: diversity, activity, and interaction with the host. ISME Communications, 5(1): ycaf148

[123] Mallawaarachchi V , Roach M J , Decewicz P , Papudeshi B , Giles S K , Grigson S R , Bouras G , Hesse R D , Inglis L K , Hutton A L K . et al. (2023). Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinformatics, 39(10): btad586

[124] Mäntynen S , Laanto E , Oksanen H M , Poranen M M , Díaz-Muñoz S L . (2021). Black box of phage–bacterium interactions: exploring alternative phage infection strategies. Open Biology, 11(9): 210188

[125] McDaniel L , Paul J H . (2005). Effect of nutrient addition and environmental factors on prophage induction in natural populations of marine Synechococcus species. Applied and Environmental Microbiology, 71(2): 842–850

[126] McDonald J E , Smith D L , Fogg P C M , McCarthy A J , Allison H E . (2010). High-throughput method for rapid induction of prophages from lysogens and its application in the study of Shiga toxin-encoding Escherichia coli strains. Applied and Environmental Microbiology, 76(7): 2360–2365

[127] McGannon C M , Fuller C A , Weiss A A . (2010). Different classes of antibiotics differentially influence Shiga toxin production. Antimicrobial Agents and Chemotherapy, 54(9): 3790–3798

[128] Melechen N E , Go G . (1980). Induction of lambdoid prophages by amino acid deprivation: differential inducibility; Role of recA. Molecular and General Genetics MGG, 180(1): 147–155

[129] Middelboe M , Traving S J , Castillo D , Kalatzis P G , Glud R N . (2025). Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments. The ISME Journal, 19(1): wraf004

[130] Miller C , Thomsen L E , Gaggero C , Mosseri R , Ingmer H , Cohen S N . (2004). SOS response induction by ß-lactams and bacterial defense against antibiotic lethality. Science, 305(5690): 1629–1631

[131] Miller-Ensminger T , Garretto A , Stark N , Putonti C . (2020). Mimicking prophage induction in the body: induction in the lab with pH gradients. PeerJ, 8: e9718

[132] Motlagh A M , Bhattacharjee A S , Goel R . (2015). Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR). Water Research, 81: 1–14

[133] Muniesa M , Imamovic L , Jofre J . (2011). Bacteriophages and genetic mobilization in sewage and faecally polluted environments. Microbial Biotechnology, 4(6): 725–734

[134] Nakayama K , Takashima K , Ishihara H , Shinomiya T , Kageyama M , Kanaya S , Ohnishi M , Murata T , Mori H , Hayashi T . (2000). The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Molecular Microbiology, 38(2): 213–231

[135] Newton G J , Daniels C , Burrows L L , Kropinski A M , Clarke A J , Lam J S . (2001). Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Molecular Microbiology, 39(5): 1237–1247

[136] Oppenheim A B , Kobiler O , Stavans J , Court D L , Adhya S . (2005). Switches in bacteriophage lambda development. Annual Review of Genetics, 39: 409–429

[137] Palomo A , Dechesne A , Smets B F , Zheng Y . (2023). Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters. Water Research, 245: 120655

[138] Park D W , Park J H . (2020). Characterization of endolysin LysECP26 derived from rV5-like phage vB_EcoM-ECP26 for inactivation of Escherichia coli O157:H7. Journal of Microbiology and Biotechnology, 30(10): 1552–1558

[139] Payne A T , Davidson A J , Kan J J , Peipoch M , Bier R , Williamson K . (2020). Widespread cryptic viral infections in lotic biofilms. Biofilm, 2: 100016

[140] Pei Z M , Liu Y F , Chen Y T , Pan T , Sun X H , Wang H C , Ross R P , Lu W W , Chen W . (2024). A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology. Gut Microbes, 16(1): 2309684

[141] Pelludat C , Mirold S , Hardt W D . (2003). The SopEΦ phage integrates into the ssrA gene of Salmonella enterica serovar Typhimurium A36 and is closely related to the Fels-2 prophage. Journal of Bacteriology, 185(17): 5182–5191

[142] Philippot L , Griffiths B S , Langenheder S . (2021). Microbial community resilience across ecosystems and multiple disturbances. Microbiology and Molecular Biology Reviews, 85(2): e00026–20

[143] Pleška M , Lang M , Refardt D , Levin B R , Guet C C . (2018). Phage–host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology & Evolution, 2(2): 359–366

[144] Press R , Glansdorff N , Miner P , De Vries J , Kadner R , Maas W K . (1971). Isolation of transducing particles of φ80 bacteriophage that carry different regions of the Escherichia coli genome. Proceedings of the National Academy of Sciences of the United States of America, 68(4): 795–798

[145] Quirós P , Sala-Comorera L , Gómez-Gómez C , Ramos-Barbero M D , Rodríguez-Rubio L , Vique G , Yance-Chávez T , Atarés S , García-Gutierrez S , García-Marco S . et al. (2023). Identification of a virulent phage infecting species of Nitrosomonas. The ISME Journal, 17(5): 645–648

[146] Reisoglu Ş , Aydin S . (2023). Bacteriophages as a promising approach for the biocontrol of antibiotic resistant pathogens and the reconstruction of microbial interaction networks in wastewater treatment systems: a review. Science of the Total Environment, 890: 164291

[147] Reyneke B , Havenga B , Waso-Reyneke M , Khan S , Khan W . (2024). Benefits and challenges of applying bacteriophage biocontrol in the consumer water cycle. Microorganisms, 12(6): 1163

[148] Rossi A , Morlino M S , Gaspari M , Basile A , Kougias P , Treu L , Campanaro S . (2022). Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. Microbiome, 10(1): 125

[149] Rostøl J T , Chmielowska C , Marina A , Penadés J R . (2026). Revisiting the life cycle of temperate phages. Nature Reviews Microbiology, 24(10): 702–714

[150] Rostøl J T , Quiles-Puchalt N , Iturbe-Sanz P , Lasa Í , Penadés J R . (2024). Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles. Nature Microbiology, 9(5): 1312–1324

[151] Roux S , Adriaenssens E M , Dutilh B E , Koonin E V , Kropinski A M , Krupovic M , Kuhn J H , Lavigne R , Brister J R , Varsani A . et al. (2019). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37(1): 29–37

[152] Roux S , Enault F , Hurwitz B L , Sullivan M B . (2015). VirSorter: mining viral signal from microbial genomic data. PeerJ, 3: e985

[153] Salmond G P C , Fineran P C . (2015). A century of the phage: past, present and future. Nature Reviews Microbiology, 13(12): 777–786

[154] Sayid R , van den Hurk A W M , Rothschild-Rodriguez D , Herrema H , de Jonge P A , Nobrega F L . (2024). Characteristics of phage-plasmids and their impact on microbial communities. Essays in Biochemistry, 68(5): 583–592

[155] Schmidt A K , Schwartzkopf C M , Pourtois J D , Burgener E B , Faith D R , Joyce A , Lamma T , Kumar G , Bollyky P L , Secor P R . (2024). Targeted deletion of Pf prophages from diverse Pseudomonas aeruginosa isolates has differential impacts on quorum sensing and virulence traits. Journal of Bacteriology, 206(5): e0040223

[156] Schuch R , Nelson D , Fischetti V A . (2002). A bacteriolytic agent that detects and kills Bacillus anthracis. Nature, 418(6900): 884–889

[157] Schuster H , Beyersmann D , Mikolajczyk M , Schlicht M . (1973). Prophage induction by high temperature in thermosensitive dna mutants lysogenic for bacteriophage lambda. Journal of Virology, 11(6): 879–885

[158] Shkilnyj P , Colon M , Koudelka G . (2013). Bacteriophage 434 Hex protein prevents RecA-mediated repressor autocleavage. Viruses, 5(1): 111–126

[159] Shuai X Y , Zhou Z C , Ba X L , Lin Y H , Lin Z J , Liu Z , Yu X , Zhou J Y , Zeng G S , Ge Z Y . et al. (2024). Bacteriophages: vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?. Water Research, 248: 120833

[160] Silpe J E , Bassler B L . (2019). A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell, 176(1−2): 268–280.e13

[161] Silpe J E , Duddy O P , Bassler B L . (2023). Induction mechanisms and strategies underlying interprophage competition during polylysogeny. PLoS Pathogens, 19(5): e1011363

[162] Silpe J E , Wong J W H , Owen S V , Baym M , Balskus E P . (2022). The bacterial toxin colibactin triggers prophage induction. Nature, 603(7900): 315–320

[163] Stefanic P , Stare E , Floccari V A , Kovac J , Hertel R , Rocha U , Kovács Á T , Mandić-Mulec I , Strube M L , Dragoš A . (2025). Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales. Cell Reports, 44(1): 115197

[164] Stiffler A K , Hesketh-Best P J , Varona N S , Zagame A , Wallace B A , Lapointe B E , Silveira C B . (2024). Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses. Microbiome, 12(1): 143

[165] Stokar-Avihail A , Tal N , Erez Z , Lopatina A , Sorek R . (2019). Widespread utilization of peptide communication in phages infecting soil and pathogenic bacteria. Cell Host & Microbe, 25(5): 746–755.e5

[166] Struk M , Grygorcewicz B , Nawrotek P , Augustyniak A , Konopacki M , Kordas M , Rakoczy R . (2017). Enhancing effect of 50 Hz rotating magnetic field on induction of Shiga toxin-converting lambdoid prophages. Microbial Pathogenesis, 109: 4–7

[167] Svenningsen S L , Costantino N , Court D L , Adhya S . (2005). On the role of Cro in λ prophage induction. Proceedings of the National Academy of Sciences of the United States of America, 102(12): 4465–4469

[168] Sweet T Jr , Sindi S , Sistrom M . (2023). Going through phages: a computational approach to revealing the role of prophage in Staphylococcus aureus. Access Microbiology, 5(6): acmi000424

[169] Tan X L , Zhang M J , Liu S Z , Xiao X , Zhang Y , Jian H H . (2024). Prophage enhances the ability of deep-sea bacterium Shewanella psychrophila WP2 to utilize D-amino acid. Microbiology Spectrum, 12(2): e03263–23

[170] Tang A X , Zhang J Y , Huang J , Deng Y , Wang D , Yu P F , Zhao R X , Wang Y L , Chen Z H , Zhang T . et al. (2024). Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater. Water Research, 265: 122253

[171] Taveira I , Bazylinski D , Abreu F . (2021). Release the iron: does the infection of magnetotactic bacteria by phages play a role in making iron available in aquatic environments?. Journal of Oceanology and Limnology, 39(6): 2063–2069

[172] Taylor V L , Fitzpatrick A D , Islam Z , Maxwell K L . (2019). The diverse impacts of phage morons on bacterial fitness and virulence. Advances in Virus Research, 101: 1–31

[173] Thabet M A . (2026). Targeting phage-mediated gene transfer: a novel C3-symmetric polymer (PTriAce-1) inhibits temperate phage replication in Staphylococcus aureus. International Journal of Drug Delivery Technology, 16(8s): 784–793

[174] Tong D , Wang Y J , Yu H D , Shen H J , Dahlgren R A , Xu J M . (2023). Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil. The ISME Journal, 17(8): 1247–1256

[175] Toyofuku M , Cárcamo-Oyarce G , Yamamoto T , Eisenstein F , Hsiao C C , Kurosawa M , Gademann K , Pilhofer M , Nomura N , Eberl L . (2017). Prophage-triggered membrane vesicle formation through peptidoglycan damage in Bacillus subtilis. Nature Communi-cations, 8(1): 481

[176] Trofeit L , Sattler E , Künz J , Hilbert F . (2023). Salmonella prophages, their propagation, host specificity and antimicrobial resistance gene transduction. Antibiotics, 12(3): 595

[177] Vázquez R , Díez-Martínez R , Domingo-Calap P , García P , Gutiérrez D , Muniesa M , Ruiz-Ruigómez M , Sanjuán R , Tomás M , Tormo-Mas M Á . et al. (2022). Essential topics for the regulatory consideration of phages as clinically valuable therapeutic agents: a perspective from Spain. Microorganisms, 10(4): 717

[178] Vercoe R B , Chang J T , Dy R L , Taylor C , Gristwood T , Clulow J S , Richter C , Przybilski R , Pitman A R , Fineran P C . (2013). Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genetics, 9(4): e1003454

[179] Vilas Boas D , Almeida C , Sillankorva S , Nicolau A , Azeredo J , Azevedo N F . (2016). Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH). Biofouling, 32(2): 179–190

[180] Vilas-Boas D, Melo L D R (2021). Monitoring bacteriophage infection on bacterial cells using FISH. In: Azevedo N F, Almeida C, eds. Fluorescence In-Situ Hybridization (FISH) for Microbial Cells. New York: Humana Press: 157–168

[181] von Boeselager R F , Pfeifer E , Frunzke J . (2018). Cytometry meets next-generation sequencing – RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum. Scientific Reports, 8(1): 14856

[182] Wagner P L , Neely M N , Zhang X P , Acheson D W K , Waldor M K , Friedman D I . (2001). Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. Journal of Bacteriology, 183(6): 2081–2085

[183] Waldor M K , Mekalanos J J . (1996). Lysogenic conversion by a filamentous phage encoding cholera toxin. Science, 272(5270): 1910–1914

[184] Walker M W G , Richard E , Wiegand T , Wang J , Yang Z F , Casas-Ciniglio A A , Hoffmann F T , Shahnawaz H , Gaudet R G , Arpaia N . et al. (2026). Temperate phages enhance bacterial host fitness via RNA-guided flagellar remodelling. Nature Microbiology, 11(7): 1815–1832

[185] Wang D , Liu L , Xu X Q , Wang C X , Wang Y L , Deng Y , Zhang T . (2024). Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system. Microbiome, 12(1): 134

[186] Wang J , Zhang Y B , Meng Q Y , Hu Z Y , Fu J , Dang C Y . (2025a). New perspectives on bacterial chlorine resistance: phages encoding chlorine resistance genes improve bacterial adaptation. Water Research, 282: 123607

[187] Wang Q , Wang M , Yang Q X , Feng L R , Zhang H , Wang R F , Wang R M . (2025b). The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants. Water Research, 268: 122776

[188] Wang X J , Ruan C J , Shen C F , Liao J Q , Wang D S , Alvarez P J J , Yu P F . (2025c). Synergistic treatment of reverse osmosis membrane biofouling with quorum quenching bacteria and hitchhiking phages. Environmental Science & Technology, 59(11): 5647–5660

[189] Ward T E , Bruhn D F , Shean M L , Watkins C S , Bulmer D , Winston V . (1993). Characterization of a new bacteriophage which infects bacteria of the genus Acidiphilium. Journal of General Virology, 74(11): 2419–2425

[190] Wdowiak M , Paczesny J , Raza S . (2022). Enhancing the stability of bacteriophages using physical, chemical, and nano-based approaches: a review. Pharmaceutics, 14(9): 1936

[191] Wilhelm S W , Suttle C A . (1999). Viruses and nutrient cycles in the sea: viruses play critical roles in the structure and function of aquatic food webs. BioScience, 49(10): 781–788

[192] Williamson S J , Houchin L A , McDaniel L , Paul J H . (2002). Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Applied and Environmental Microbiology, 68(9): 4307–4314

[193] Wood T L , Guha R , Tang L , Geitner M , Kumar M , Wood T K . (2016). Living biofouling-resistant membranes as a model for the beneficial use of engineered biofilms. Proceedings of the National Academy of Sciences of the United States of America, 113(20): E2802–E2811

[194] Wu Z Q , Guo L Y , Wu Y , Yang M Y , Du S , Shao J B , Zhang Z F , Zhao Y L . (2024). Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family. mSphere, 9(7): e0045824

[195] Xia R , Sun M M , Balcázar J L , Yu P F , Hu F , Alvarez P J J . (2023). Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes. The ISME Journal, 17(7): 1004–1014

[196] Xie T , Lin D , Cai X D , Ma L J , Wang L , Cai T G , Ye Y Q , Shen L Q , Sun M M , Ye M . et al. (2025). Nano-biochar regulates phage–host interactions, reducing antibiotic resistance genes in vermicomposting systems. Proceedings of the National Academy of Sciences of the United States of America, 122(34): e2511986122

[197] Xu R Y , Ge T D , Fan Y C , Yang L , Zhang Y , Han S Q , Radosevich M , Liang X L . (2025). Mitomycin C-induced prophage activation for exploring the Lysogeny-lysis functional dynamics in situ. Applied Soil Ecology, 215: 106436

[198] Xu Y M . (2021). Phage and phage lysins: new era of bio-preservatives and food safety agents. Journal of Food Science, 86(8): 3349–3373

[199] Yang G Q , Lin A N , Wu X , Lin C F , Zhu S Y , Zhuang L . (2024). Geobacter-associated prophages confer beneficial effect on dissimilatory reduction of Fe(III) oxides. Fundamental Research, 4(6): 1568–1575

[200] Yang P G , Wang N , Wang C , Yao Y F , Fu X J , Yu W R , Cai R , Yao M . (2017). 460 nm visible light irradiation eradicates MRSA via inducing prophage activation. Journal of Photochemistry and Photobiology B: Biology, 166: 311–322

[201] Zamora-Caballero S , Chmielowska C , Quiles-Puchalt N , Brady A , Del Sol F G , Mancheño-Bonillo J , Felipe-Ruíz A , Meijer W J J , Penadés J R , Marina A . (2024). Antagonistic interactions between phage and host factors control arbitrium lysis–lysogeny decision. Nature Microbiology, 9(1): 161–172

[202] Zang B , Zhou H , Nan H K , Li Y , Li Q , Sano D , Chen R . (2025). Exploring the potential positive impact of phage-bacterium interactions on membrane fouling mitigation. Frontiers of Environmental Science & Engineering, 19(10): 139

[203] Zhang H M , Buttaro B A , Fouts D E , Sanjari S , Evans B S , Stevens R H . (2019). Bacteriophage φEf11 ORF28 endolysin, a multifunctional lytic enzyme with properties distinct from all other identified Enterococcus faecalis phage endolysins. Applied and Environmental Microbiology, 85(13): e00555–19

[204] Zhang J Z , Dou T , Shen Y , Wang W R , Wang L K , Wu X H , Zhang M , Wang D S , Yu P F . (2024a). Application of nanozymes in problematic biofilm control: progress, challenges and prospects. Frontiers of Environmental Science & Engineering, 18(11): 136

[205] Zhang M H , Zhang T Y , Yu M S , Chen Y L , Jin M . (2022). The life cycle transitions of temperate phages: regulating factors and potential ecological implications. Viruses, 14(9): 1904

[206] Zhang P J , Wang Y H , Lin H , Liang J S , Wang J T , Bai Y H , Qu J H , Wang A J . (2024b). Bacterial evolution in Biofiltration of drinking water treatment plant: different response of phage and plasmid to varied water sources. Water Research, 259: 121887

[207] Zhong Z P , Tian F N , Roux S , Gazitúa M C , Solonenko N E , Li Y F , Davis M E , Van Etten J L , Mosley-Thompson E , Rich V I . et al. (2021). Glacier ice archives nearly 15,000-year-old microbes and phages. Microbiome, 9(1): 160

[208] Zhou S , Xiong C , Su Y L , Wang Y Y , Gao Y Y , Tang Z P , Liu B Y , Wu Y Y , Duan Y . (2022). Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: distribution and influencing factors. Environmental Pollution, 304: 119158

[209] Zimmerman A E , Howard-Varona C , Needham D M , John S G , Worden A Z , Sullivan M B , Waldbauer J R , Coleman M L . (2020). Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nature Reviews Microbiology, 18(1): 21–34

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