References
-
Tian, X. et al. Will reaching the maximum achievable yield potential meet future global food demand?. J. Clean. Prod. 294, 126285 (2021).
-
Rockstrom, J. et al. A safe operating space for humanity. Nature 461, 472–475 (2009).
-
Voets, J., Vanstaen, H. & Verstraete, W. Removal of Nitrogen From Highly Nitrogenous Wastewaters. J. Water Pollut. Control Fed. 47, 394–398 (1975).
-
Kartal, B., Kuenen, J. G. & van Loosdrecht, M. C. M. Sewage treatment with Anammox. Science 328, 702–703 (2010).
-
Oshiki, M., Shimokawa, M., Fujii, N., Satoh, H. & Okabe, S. Physiological characteristics of the anaerobic ammonium-oxidizing bacterium ‘Candidatus Brocadia sinica’. Microbiology 157, 1706–1713 (2011).
-
Wang, Z. et al. Unravelling adaptation of nitrite-oxidizing bacteria in mainstream PN/A process: Mechanisms and counter-strategies. Water Res. 200, 117239 (2021).
-
Feng, L. et al. Intracellular electron competition in response to the oxygen pressure of the aerobic denitrification process in an O2-based membrane biofilm reactor (MBfR) for nitrate removal. Sci. Total Environ. 875, 162592 (2023).
-
Huang, R., Meng, T., Liu, G., Gao, S. & Tian, J. Simultaneous nitrification and denitrification in membrane bioreactor: Effect of dissolved oxygen. J. Environ. Manag. 323, 116183 (2022).
-
Zhang, X. et al. Enhancement of nitrite production via addition of hydroxylamine to partial denitrification (PD) biomass: Functional genes dynamics and enzymatic activities. Bioresour. Technol. 318, 124274 (2020).
-
Zhao, J. et al. Selective Enrichment of Comammox Nitrospira in a Moving Bed Biofilm Reactor with Sufficient Oxygen Supply. Environ. Sci. Technol. 56, 13338–13346 (2022).
-
Zheng, M. et al. Predominance of comammox bacteria among ammonia oxidizers under low dissolved oxygen condition. Chemosphere 308, 136436 (2022).
-
Teklemariam, A. D. et al. The Battle between Bacteria and Bacteriophages: A Conundrum to Their Immune System. Antibiotics 12, 381 (2023).
-
Saw, P. E. & Song, E.-W. Phage display screening of therapeutic peptide for cancer targeting and therapy. Protein Cell 10, 787–807 (2019).
-
Karimi, M. et al. Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos. Adv. Drug Deliv. Rev. 106, 45–62 (2016).
-
Penades, J. R., Chen, J., Quiles-Puchalt, N., Carpena, N. & Novick, R. P. Bacteriophage-mediated spread of bacterial virulence genes. Curr. Opin. Microbiol. 23, 171–178 (2015).
-
Touchon, M., Moura de Sousa, J. A. & Rocha, E. P. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr. Opin. Microbiol. 38, 66–73 (2017).
-
Mathieu, J., Yu, P., Zuo, P., Da Silva, M. L. B. & Alvarez, P. J. J. Going viral: emerging opportunities for phage-based bacterial control in water treatment and reuse. Acc. Chem. Res. 52, 849–857 (2019).
-
Sohail, H. A. et al. Bacteriophages: emerging applications in medicine, food, and biotechnology. Phage 1, 75–82 (2020).
-
Wang, D. et al. Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system. Microbiome 12, 134 (2024).
-
Qi, H. et al. Symbiotic bacteriophages exhibit multiple adaptive strategies in activated sludge flocs and contribute to floc stability. Chem. Eng. J. 492, 152448 (2024).
-
Daims, H. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504 (2015).
-
Wang, Y. et al. Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling. Environ. Microbiome 17, 17 (2022).
-
Jin, M., Cai, L., Lu, L., Yu, M. & Zhang, R. Combined metabolomic and genomic analyses reveal phage-specific and infection stage-specific alterations to marine Roseobacter metabolism. ISME Commun. 5, ycaf047 (2025).
-
Duan, H., Ye, L., Lu, X. & Yuan, Z. Overcoming nitrite oxidizing bacteria adaptation through alternating sludge treatment with free nitrous acid and free ammonia. Environ. Sci. Technol. 53, 1937–1946 (2019).
-
Yu, L. et al. The differential proliferation of AOB and NOB during natural nitrifier cultivation and acclimation with raw sewage as seed sludge. RSC Adv. 10, 28277–28286 (2020).
-
Gruber-Dorninger, C. et al. Functionally relevant diversity of closely related Nitrospira in activated sludge. ISME J. 9, 643–655 (2015).
-
Ghimire-Kafle, S., Weaver, M. E. & Bollmann, A. Ecophysiological and genomic characterization of the freshwater complete ammonia oxidizer Nitrospira sp. Strain BO4. Appl. Environ. Microbiol. 89, (2023).
-
Wei, Y., Chen, Y., Xia, W., Ye, M. & Li, Y.-Y. Dynamic pulse approach to enhancing mainstream Anammox process stability: Integrating sidestream support and tackling nitrite-oxidizing bacteria challenges. Bioresour. Technol. 395, 130327 (2024).
-
Duan, H. et al. Nitrite oxidizing bacteria (NOB) contained in influent deteriorate mainstream NOB suppression by sidestream inactivation. Water Res. 162, 331–338 (2019).
-
Ali, M. et al. Physiological characterization of anaerobic ammonium oxidizing bacterium ‘Candidatus Jettenia caeni’. Environ. Microbiol. 17, 2172–2189 (2015).
-
Cui, B. et al. The effect of dissolved oxygen concentration on long-term stability of partial nitrification process. J. Environ. Sci. 90, 343–351 (2020).
-
Al-Hazmi, H. E., Yin, Z., Grubba, D., Majtacz, J. B. & Makinia, J. Comparison of the Efficiency of Deammonification under Different DO Concentrations in a Laboratory-Scale Sequencing Batch Reactor. Water 14, 368 (2022).
-
Yuan, Y., Xie, Y., Xu, P. & Li, X. Verification of inhibition effects of anoxic/aerobic alternation on NOB in nitrosation system under mainstream conditions. J. Water Process Eng. 45, 102479 (2022).
-
Qiu, J., Li, X., Peng, Y. & Jiang, H. Advanced nitrogen removal from landfill leachate via a two-stage combined process of partial nitrification-Anammox (PNA) and partial denitrification-Anammox (PDA). Sci. Total Environ. 810, 151186 (2022).
-
Hubaux, N., Wells, G. & Morgenroth, E. Impact of coexistence of flocs and biofilm on performance of combined nitritation-anammox granular sludge reactors. Water Res. 68, 127–139 (2015).
-
Dong, W., Lu, G., Yan, L., Zhang, Z. & Zhang, Y. Characteristics of pellets with immobilized activated sludge and its performance in increasing nitrification in sequencing batch reactors at low temperatures. J. Environ. Sci. 42, 202–209 (2016).
-
Seuntjens, D. et al. Mainstream partial nitritation/anammox with integrated fixed-film activated sludge: Combined aeration and floc retention time control strategies limit nitrate production. Bioresour. Technol. 314, 123711 (2020).
-
Li, J. et al. A critical review of one-stage anammox processes for treating industrial wastewater: Optimization strategies based on key functional microorganisms. Bioresour. Technol. 265, 498–505 (2018).
-
Wang, Z. et al. Nitrite accumulation in comammox-dominated nitrification-denitrification reactors: Effects of DO concentration and hydroxylamine addition. J. Hazard. Mater. 384, 121375 (2020).
-
Wu, W. et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 12, 485–494 (2018).
-
Winkler, M.-K. H. et al. An integrative review of granular sludge for the biological removal of nutrients and recalcitrant organic matter from wastewater. Chem. Eng. J. 336, 489–502 (2018).
-
Chamblee, J. et al. Endolysin Regulation in Phage Mu Lysis. mBio 13, (2022).
-
Nair, G. & Jain, V. An intramolecular cross-talk in D29 mycobacteriophage endolysin governs the lytic cycle and phage-host population dynamics. Sci. Adv. 10, eadh9812 (2024).
-
Voigt, E., Rall, B. C., Chatzinotas, A., Brose, U. & Rosenbaum, B. Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 9, e12194 (2021).
-
Lee, S., Hazard, C. & Nicol, G. W. Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation. ISME J. 18, wrae205 (2024).
-
Quiros, P. et al. Identification of a virulent phage infecting species of Nitrosomonas. ISME J. 17, 645–648 (2023).
-
Kotay, S. M., Datta, T., Choi, J. & Goel, R. Biocontrol of biomass bulking caused by Haliscomenobacter hydrossis using a newly isolated lytic bacteriophage. Water Res. 45, 694–704 (2011).
-
Petrovski, S., Seviour, R. J. & Tillett, D. Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7. Appl. Environ. Microbiol. 77, 7864–7867 (2011).
-
Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).
-
Paez-Espino, D. et al. IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. Nucleic Acids Res. 47, D678–D686 (2019).
-
Baquero, D. P. et al. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nat. Commun. 15, 7702 (2024).
-
Rodriguez-Brito, B. et al. Viral and microbial community dynamics in four aquatic environments. ISME J. 4, 739–751 (2010).
-
Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466–470 (2016).
-
Silveira, C. B. & Rohwer, F. L. Piggyback-the-Winner in host-associated microbial communities. npj Biofilms Microbiomes 2, 16010 (2016).
-
Silveira, C. B. & Rohwer, F. L. Piggyback-the-Winner in host-associated microbial communities. npj Biofilms Microbomes 2, 16010 (2016).
-
Mara, P. et al. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME J. 14, 3079–3092 (2020).
-
Hurwitz, B. L. & U’Ren, J. M. Viral metabolic reprogramming in marine ecosystems. Curr. Opin. Microbiol. 31, 161–168 (2016).
-
Sun, M., Yuan, S., Xia, R., Ye, M. & Balcázar, J. L. Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance. Environ. Microbiol. 25, 800–810 (2023).
-
Yuan, L. & Ju, F. Potential auxiliary metabolic capabilities and activities reveal biochemical impacts of viruses in municipal wastewater treatment plants. Environ. Sci. Technol. 57, 5485–5498 (2023).
-
Wang, D. et al. Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor. Water Res. 225, 119137 (2022).
-
Fuhrman, J. A. Marine viruses and their biogeochemical and ecological effects. Nature 399, 541–548 (1999).
-
Weitz, J. S. & Wilhelm, S. W. Ocean viruses and their effects on microbial communities and biogeochemical cycles. F1000 Biol. Rep. 4, 17 (2012).
-
Weitz, J. S. et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. 9, 1352–1364 (2015).
-
Shelford, E. J., Middelboe, M., Møller, E. F. & Suttle, C. A. Virus-driven nitrogen cycling enhances phytoplankton growth. Aquat. Microb. Ecol. 66, 41–46 (2012).
-
Pourtois, J., Tarnita, C. E. & Bonachela, J. A. Impact of Lytic Phages on Phosphorus- vs. Nitrogen-Limited Marine Microbes. Front. Microbiol. 11, (2020).
-
Suttle, C. A. Viruses in the sea. Nature 437, 356–361 (2005).
-
Bolsan, A. C. et al. Bacteriophages in wastewater treatment: can they be an approach to optimize biological treatment processes?. Environ. Sci. Pollut. Res. Int 29, 89889–89898 (2022).
-
Lood, C. et al. Digital phagograms: predicting phage infectivity through a multilayer machine learning approach. Curr. Opin. Virol. 52, 174–181 (2022).
-
Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
-
Shalem, O., Sanjana, N. E. & Zhang, F. High-throughput functional genomics using CRISPR-Cas9. Nat. Rev. Genet. 16, 299–311 (2015).
-
Carlson, H. K. et al. Geochemical constraints on bacteriophage infectivity in terrestrial environments. ISME Commun. 3, 78 (2023).
-
Bacteriophage application in inhibiting corrosion- producing bacteria | BMC Microbiology | Full Text. https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-03952-2.
-
Zhang, G. et al. Bacteriophage application in inhibiting corrosion-producing bacteria. BMC Microbiol. 25, 241 (2025).
-
Huang, D. et al. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol. 32, 902–916 (2024).
-
Letten, A. D. & Ludington, W. B. Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities. ISME J. 17, 641–644 (2023).
-
Chen, L., Zhao, X., Wongso, S., Lin, Z. & Wang, S. Trade-offs between receptor modification and fitness drive host-bacteriophage co-evolution leading to phage extinction or co-existence. ISME J. 18, wrae214 (2024).
-
Borin, J. M., Avrani, S., Barrick, J. E., Petrie, K. L. & Meyer, J. R. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc. Natl. Acad. Sci. 118, e2104592118 (2021).
-
Costa, P., Pereira, C., Romalde, J. L. & Almeida, A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 599, 110209 (2024).
-
Reisch, C. R. & Prather, K. L. J. The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. Sci. Rep. 5, 15096 (2015).
-
Yehl, K. et al. Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis. Cell 179, 459 (2019).
-
Meile, S., Du, J., Dunne, M., Kilcher, S. & Loessner, M. J. Engineering therapeutic phages for enhanced antibacterial efficacy. Curr. Opin. Virol. 52, 182–191 (2022).
-
Peng, H., Chen, I. A. & Qimron, U. Engineering phages to fight multidrug-resistant bacteria. Chem. Rev. 125, 933–971 (2024).
-
Chaudhary, N. et al. CRISPR-Cas-assisted phage engineering for personalized antibacterial treatments. Indian J. Med. Microbiol. 53, 100771 (2025).
-
Steiner, L. X. et al. Phage-induced disturbance of a marine sponge microbiome. Environ. Microbiome 19, 97 (2024).
-
Balleste, E. et al. Bacteriophages in sewage: abundance, roles, and applications. FEMS Microbes 3, xtac009 (2022).
-
Pfeifer, E., Bonnin, R. A. & Rocha, E. P. C. Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion. mBio 13, (2022).
-
Shi, L.-D. et al. A mixed blessing of viruses in wastewater treatment plants. Water Res. 215, 118237 (2022).
-
Jiang, S. et al. Generic Diagramming Platform (GDP): a comprehensive database of high-quality biomedical graphics. Nucleic Acids Res. 53, D1670–D1676 (2024).
