Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015).
Liu, T. et al. Sustainable wastewater management through nitrogen-cycling microorganisms. Nat. Water 2, 936–952 (2024).
Ye, J. et al. Wastewater denitrification driven by mechanical energy through cellular piezo-sensitization. Nat. Water 2, 531–540 (2024).
Shi, H. et al. How β-cyclodextrin-functionalized biochar enhanced biodenitrification in low C/N conditions via regulating substrate metabolism and electron utilization. Environ. Sci. Technol. 57, 11122–11133 (2023).
Zhang, Y., Zhang, Z. & Chen, Y. Biochar mitigates N2O emission of microbial denitrification through modulating carbon metabolism and allocation of reducing power. Environ. Sci. Technol. 55, 8068–8078 (2021).
Yoshida, H., Mønster, J. & Scheutz, C. Plant-integrated measurement of greenhouse gas emissions from a municipal wastewater treatment plant. Water Res. 61, 108–118 (2014).
Du, W.-J. et al. Spatiotemporal pattern of greenhouse gas emissions in China’s wastewater sector and pathways towards carbon neutrality. Nat. Water 1, 166–175 (2023).
Daelman, M. R. J. et al. Methane emission during municipal wastewater treatment. Water Res. 46, 3657–3670 (2012).
Sun, Q. et al. Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system. Water Res. 267, 122502 (2024).
Ma, Y. et al. Comprehensive metagenomic and enzyme activity analysis reveals the negatively influential and potentially toxic mechanism of polystyrene nanoparticles on nitrogen transformation in constructed wetlands. Water Res. 202, 117420 (2021).
Zhou, J. et al. Unveiling the coupling mechanism between central carbon and nitrogen metabolism of Pseudomonas stutzeri. ACS EST Water 5, 230–241 (2025).
Mendonca, C. M. et al. Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soil Pseudomonas species. Proc. Natl Acad. Sci. USA 117, 32358–32369 (2020).
Inigo, M., Deja, S. & Burgess, S. C. Ins and outs of the TCA cycle: the central role of anaplerosis. Annu. Rev. Nutr. 41, 19–47 (2021).
Fischer, E. & Sauer, U. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem. 278, 46446–46451 (2003).
Krivoruchko, A. et al. Microbial acetyl-CoA metabolism and metabolic engineering. Metab. Eng. 28, 28–42 (2015).
Kim, D. H. et al. Optimum flux rerouting for efficient production of naringenin from acetate in engineered Escherichia coli. Biotechnol. Biofuels Bioprod. 15, 90 (2022).
Chen, J. & Strous, M. Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution. Biochim. Biophys. Acta, Bioenerg. 1827, 136–144 (2013).
Sparacino-Watkins, C., Stolz, J. F. & Basu, P. Nitrate and periplasmic nitrate reductases. Chem. Soc. Rev. 43, 676–706 (2014).
Zhou, S. et al. Use of acetate for the production of 3-hydroxypropionic acid by metabolically-engineered Pseudomonas denitrificans. Bioresour. Technol. 307, 123194 (2020).
Zheng, J. & Jia, Z. Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase. Nature 465, 961–965 (2010).
Novackova, I. et al. The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions. Int. J. Biol. Macromol. 206, 977–989 (2022).
Liu, Z. et al. Enhancing the insecticidal activity of new Bacillus thuringiensis X023 by copper ions. Microb. Cell Fact. 19, 195 (2020).
Thorgersen, M. P. et al. Molybdenum availability is key to nitrate removal in contaminated groundwater environments. Appl. Environ. Microbiol. 81, 4976–4983 (2015).
Kozaeva, E. et al. Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida. Metab. Eng. 67, 373–386 (2021).
Tovilla-Coutiño, D. B. et al. Engineered citrate synthase alters acetate accumulation in Escherichia coli. Metab. Eng. 61, 171–180 (2020).
Nie, M., Wang, J. & Zhang, K. Engineering a novel Acetyl-CoA pathway for efficient biosynthesis of acetyl-CoA-derived compounds. ACS Synth. Biol. 13, 358–369 (2024).
Ahmad, H. A. et al. Multi-omics analysis revealed the selective enrichment of partial denitrifying bacteria for the stable coupling of partial-denitrification and anammox process under the influence of low strength magnetic field. Water Res. 245, 120619 (2023).
Dolan, S. K. & Welch, M. The glyoxylate shunt, 60 years on. Annu. Rev. Microbiol. 72, 309–330 (2018).
Fang, J. et al. Impact of Cr(VI) on P removal performance in enhanced biological phosphorus removal (EBPR) system based on the anaerobic and aerobic metabolism. Bioresour. Technol. 121, 379–385 (2012).
Wang, X. & Wang, W.-X. Intracellular biotransformation of Cu(II)/Cu(I) explained high Cu toxicity to phytoplankton Chlamydomonas reinhardtii. Environ. Sci. Technol. 55, 14772–14781 (2021).
Arguello, J. M. et al. Mechanisms of copper homeostasis in bacteria. Front. Cell. Infect. Microbiol. https://doi.org/10.3389/fcimb.2013.00073 (2013).
González-Guerrero, M. & Argüello, J. M. Mechanism of Cu+-transporting ATPases. Proc. Natl Acad. Sci. USA 105, 5992–5997 (2008).
Tsvetkov, P. et al. Copper induces cell death by targeting lipoylated TCA cycle proteins. Science 375, 1254–1261 (2022).
Wan, R. et al. Effect of CO2 on microbial denitrification via inhibiting electron transport and consumption. Environ. Sci. Technol. 50, 9915–9922 (2016).
Liu, J. et al. Siderophores as a selective regulator for enhancing anaerobic ammonium oxidation bacteria. Nat. Water 3, 806–817 (2025).
Jiang, M. et al. Bio-denitrification performance enhanced by graphene-facilitated iron acquisition. Water Res. 180, 115916 (2020).
Pan, Y. et al. Electron competition among nitrogen oxides reduction during methanol-utilizing denitrification in wastewater treatment. Water Res. 47, 3273–3281 (2013).
Müller, C. et al. Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature 608, 626–631 (2022).
Dong, B. et al. A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar. Environ. Int. 183, 108435 (2024).
Liao, Y. et al. From mechanism to application: decrypting light-regulated denitrifying microbiome through geometric deep learning. iMeta 3, e162 (2024).
Hao, S. et al. Awakening a latent phosphoenolpyruvate–oxaloacetate–glyceraldehyde carbon-fixation pathway for cost-effective nitrogen removal. Chem. Eng. J. 488, 151065 (2024).
Xu, D. et al. Selective genes expression and metabolites transformation drive a robust nitrite accumulation during nitrate reduction under alternating feast-famine condition. Water Res. 255, 121520 (2024).
Wan, H. et al. Algal-mediated nitrogen removal and sustainability of algal-derived dissolved organic matter supporting denitrification. Bioresour. Technol. 407, 131083 (2024).
Burow, L. C. et al. Anaerobic glyoxylate cycle activity during simultaneous utilization of glycogen and acetate in uncultured Accumulibacter enriched in enhanced biological phosphorus removal communities. ISME J. 2, 1040–1051 (2008).
Luo, Y. et al. Cr(VI) reduction and Fe(II) regeneration by Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron. Environ. Sci. Technol. 57, 11313–11324 (2023).
Hubenova, Y. et al. The glyoxylate pathway contributes to enhanced extracellular electron transfer in yeast-based biofuel cell. Bioelectrochemistry 116, 10–16 (2017).
Qi, Z. et al. Glyoxylate cycle maintains the metabolic homeostasis of Pseudomonas aeruginosa in viable but nonculturable state induced by chlorine stress. Microbiol. Res. 270, 127341 (2023).
Jia, F. et al. FeO might be more suitable than Fe2+ for the construction of anammox-dominated Fe–N coupling system. Water Res. 274, 123097 (2025).
An, Z. et al. Synchronous achievement of advanced nitrogen removal and N2O reduction in the anoxic zone in the AOA process for low C/N municipal wastewater. Environ. Sci. Technol. 58, 2335–2345 (2024).
