Synergistic nitrogen-sulfur metabolism driving biodeterioration revealed by metagenomic and DNA-SIP analyses at the Chen Cihong residence
Source abstract
Abstract
Abstract Acid attack on stone cultural heritage is intrinsically linked to microbially driven nitrogen and sulfur cycling, yet the precise acid-producing metabolic machinery remains elusive. By integrating amplicon sequencing, DNA-stable isotope probing (DNA-SIP) and metagenomics, this study unveils a novel synergistic mechanism. A predominance of Candidatus Nitrocosmicus (AOA) and Nitrosospira (NOB) was found on the stone. Following 15 N incubation, active nitrification was confirmed by increased amoA and nxrB gene abundance and the production of 15 NO 2 ⁻ and 15 NO 3 ⁻. Furthermore, elevated norB and nosZ gene levels, alongside 15 NO 2 ⁻ and 15 NO 3 ⁻ depletion, confirmed an active denitrification. Concurrently, Dissimilatory Nitrate Reduction to Ammonium (DNRA) supplied the substrate by ammonia-oxidization, driving an internal nitrogen cycle. Crucially, metagenomics revealed coupling between denitrification and sulfur oxidation, demonstrating a synergistic cycle that accelerates acid production and salt damage. These findings establish a probable link between coupled nitrification-denitrification-sulfur oxidation and stone decay, providing a new conceptual framework for developing targeted biostatic strategies.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Building materials and conservation · Mine drainage and remediation techniques · Microbial Applications in Construction Materials
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (77)
Show source-provided references
1. Patil, S. M. & Kasthurba, A. K. Weathering of stone monuments: damage assessment of basalt and laterite. Mater. Today. 43, 1647–1658 (2021).
2. Liu, X., Meng, H., Wang, Y., Katayama, Y. & Gu, J.-D. Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments. Int. Biodeterior. Biodegrad. 133, 9–16 (2018).10.1016/j.ibiod.2018.05.011 ↗
3. Wang, L. et al. Water determines geomicrobiological impact on stone heritage. Nat. Geosci. 18, 108–111 (2025).10.1038/s41561-024-01631-x ↗
4. Yang, X. et al. The mechanisms of salt weathering responsible for sandstone deterioration in the Yungang Grottoes. China. Eng. Geol. 350, 107989 (2025).10.1016/j.enggeo.2025.107989 ↗
5. Wu, F. et al. Community structures of bacteria and archaea associated with the biodeterioration of sandstone sculptures at the Beishiku Temple. Int. Biodeterior. Biodegrad. 164, 105290 (2021).10.1016/j.ibiod.2021.105290 ↗
6. Meng, S. et al. Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments. Sci. Total. Environ. 876, 162665 (2023).10.1016/j.scitotenv.2023.162665 ↗
7. Bridier, A. et al. Spatial organization plasticity as an adaptive driver of surface microbial communities. Front. Microbiol. 8, 1364 (2017).10.3389/fmicb.2017.01364 ↗
8. Mu, B., Gui, Z., Lu, F., Petropoulos, E. & Yu, Y. Microbial-induced carbonate precipitation improves physical and structural properties of Nanjing ancient city walls. Materials 14, 5665 (2021).10.3390/ma14195665 ↗
9. Liu, X., Koestler, R. J., Warscheid, T., Katayama, Y. & Gu, J.-D. Microbial deterioration and sustainable conservation of stone monuments and buildings. Nat. Sustain. 3, 991–1004 (2020).10.1038/s41893-020-00602-5 ↗
10. Louati, M. et al. Elucidating the ecological networks in stone-dwelling microbiomes. Environ. Microbiol. 22, 1467–1480 (2020).10.1111/1462-2920.14700 ↗
11. Schröer, L., Boon, N., Kock, T. D. & Cnudde, V. The capabilities of bacteria and archaea to alter natural building stones—a review. Int. Biodeterior. Biodegrad. 165, 105329 (2021).10.1016/j.ibiod.2021.105329 ↗
12. Skipper, P. J. A., Skipper, L. K. & Dixon, R. A. A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces. Sci. Rep. 12, 4877 (2022).10.1038/s41598-022-08851-4 ↗
13. Büdel, B. et al. Reshaping of sandstone surfaces by cryptoendolithic cyanobacteria: bioalkalization causes chemical weathering in arid landscapes. Geobiology 2, 261–268 (2004).10.1111/j.1472-4677.2004.00040.x ↗
14. Ding, X. et al. An internal recycling mechanism between ammonia/ammonium and nitrate driven by ammonia-oxidizing archaea and bacteria (AOA, AOB, and Comammox) and DNRA on Angkor sandstone monuments. Int. Biodeterior. Biodegrad. 165, 105328 (2021).10.1016/j.ibiod.2021.105328 ↗
15. Li, Y. & Gu, J.-D. A more accurate definition of water characteristics in stone materials for an improved understanding and effective protection of cultural heritage from biodeterioration. Int. Biodeterior. Biodegrad. 166, 105338 (2022).10.1016/j.ibiod.2021.105338 ↗
16. Wang, L., Ma, C., Wu, F. & Liu, X. Identification and screening of acid-secreting bacterial strains isolated from limestone of the Longmen Grottoes monuments. Int. Biodeterior. Biodegrad. 208, 106255 (2025).10.1016/j.ibiod.2025.106255 ↗
17. Wu, F. et al. Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China. Sci. Total. Environ. 893, 164616 (2023).10.1016/j.scitotenv.2023.164616 ↗
18. Meng, H., Luo, L., Chan, H., Katayama, Y. & Gu, J.-D. Higher diversity and abundance of ammonia-oxidizing archaea than bacteria detected at the Bayon Temple of Angkor Thom in Cambodia. Int. Biodeterior. Biodegrad. 115, 234–243 (2016).10.1016/j.ibiod.2016.08.021 ↗
19. Hu, P. & Gu, J.-D. New insights on nitrogen transformation and attack on world stone monuments. Trends Microbiol. 33, 260–263 (2025).10.1016/j.tim.2025.01.002 ↗
20. Hu, P. et al. Diverse virome and microbiome and their interactions for biodeterioration of Angkorian Bayon Temple in Cambodia. Total. Environ. Microbiol. 1, 100018 (2025).10.1016/j.temicr.2025.100018 ↗
21. Qian, Y., Liu, X., Hu, P., Gao, L. & Gu, J.-D. Identifying the major metabolic potentials of microbial driven carbon, nitrogen and sulfur cycling on stone cultural heritage worldwide. Sci. Total. Environ. 954, 176757 (2024).10.1016/j.scitotenv.2024.176757 ↗
22. He, J. et al. From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China. Sci. Total. Environ. 805, 150395 (2022).10.1016/j.scitotenv.2021.150395 ↗
23. Liang, X. et al. Higher abundance of ammonia-oxidizing bacteria than archaea in biofilms and the microbial community composition of Kaiping Diaolou of China. Int. Biodeterior. Biodegrad. 184, 105647 (2023).10.1016/j.ibiod.2023.105647 ↗
24. Ding, X. et al. Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses. Appl. Microbiol. Biotechnol. 104, 9823–9837 (2020).10.1007/s00253-020-10886-4 ↗
25. Zanardini, E., May, E., Purdy, K. J. & Murrell, J. C. Nutrient cycling potential within microbial communities on culturally important stoneworks. Environ. Microbiol. Rep. 11, 147–154 (2019).10.1111/1758-2229.12707 ↗
26. Myllykangas, J. P., Rissanen, A. J., Hietanen, S. & Jilbert, T. Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary. Biogeochem 148, 291–309 (2020).10.1007/s10533-020-00660-z ↗
27. Neina, D. The role of soil pH in plant nutrition and soil remediation. Appl. Environ. Soil. Sci. 2019, 5794869 (2019).10.1155/2019/5794869 ↗
28. Handley, K. M. et al. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J. 7, 800–816 (2013).10.1038/ismej.2012.148 ↗
29. Sahinkaya, E. & Dursun, N. Use of elemental sulfur and thiosulfate as electron sources for water denitrification. Bioprocess. Biosyst. Eng. 38, 531–541 (2015).10.1007/s00449-014-1293-3 ↗
30. Hu, Y., Wu, G., Li, R., Xiao, L. & Zhan, X. Iron sulphides mediated autotrophic denitrification: An emerging bioprocess for nitrate pollution mitigation and sustainable wastewater treatment. Water Res. 179, 115914 (2020).10.1016/j.watres.2020.115914 ↗
31. Lin, S. et al. Biological sulfur oxidation in wastewater treatment: A review of emerging opportunities. Water Res. 43, 399–415 (2018).10.1016/j.watres.2018.06.051 ↗
32. Marzocchi, U. et al. Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment. ISME J. 8, 1682–1690 (2014).10.1038/ismej.2014.19 ↗
33. Shao, M. F., Zhang, T. & Fang, H. H. Sulfur-driven autotrophic denitrification: diversity, biochemistry, and engineering applications. Appl. Microbiol. Biotechnol. 88, 1027–1042 (2010).10.1007/s00253-010-2847-1 ↗
34. Qian, L. et al. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. Microbiome. 11, 71 (2023).10.1186/s40168-023-01501-5 ↗
35. Bary, B., Le Bescop, P., Leterrier, N. & Deville, E. Coupled chemo-transport-mechanical modelling and numerical simulation of external sulfate attack in mortar. Cem. Concr. Comp. 49, 70–83 (2014).10.1016/j.cemconcomp.2013.12.010 ↗
36. Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322 (1996).10.1128/aem.62.2.316-322.1996 ↗
37. Zhang, M. et al. Time-dependent shifts in populations and activity of bacterial and archaeal ammonia oxidizers in response to liming in acidic soils. Soil Biol. Biochem. 112, 77–89 (2017).10.1016/j.soilbio.2017.05.001 ↗
38. Zhang, M. et al. Characterization of nitrate-dependent As(III)-oxidizing communities in arsenic-contaminated soil and investigation of their metabolic potentials by the combination of DNA-stable isotope probing and metagenomics. Environ. Sci. Technol. 54, 7366–7377 (2020).10.1021/acs.est.0c01601 ↗
39. Jiang, R. et al. Use of newly designed primers for quantification of complete ammonia-oxidizing (Comammox) bacterial clades and strict nitrite oxidizers in the genus Nitrospira. Appl. Environ. Microbiol. 86, e01775–20 (2020).10.1128/AEM.01775-20 ↗
40. Arshad, Z., Shin, K. H. & Hur, J. Utilization and applications of stable isotope analysis for wastewater treatment systems: a review. Environ. Res. 264, 120347 (2025).10.1016/j.envres.2024.120347 ↗
41. Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).10.1038/s41587-019-0209-9 ↗
42. Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).10.1093/bioinformatics/bty560 ↗
43. Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 31, 1674–1676 (2015).10.1093/bioinformatics/btv033 ↗
44. Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 11, 119 (2010).10.1186/1471-2105-11-119 ↗
45. Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).10.1093/molbev/msab293 ↗
46. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25, 1754–1760 (2009).10.1093/bioinformatics/btp324 ↗
47. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).10.1093/bioinformatics/btp352 ↗
48. Kang, D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).10.7717/peerj.7359 ↗
49. Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).10.1101/gr.186072.114 ↗
50. Zhao, M. et al. Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China. Front. Microbiol. 15, 1453430 (2024).10.3389/fmicb.2024.1453430 ↗
51. Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).10.1038/nature04983 ↗
52. Verhamme, D. T., Prosser, J. I. & Nicol, G. W. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J. 5, 1067–1071 (2011).10.1038/ismej.2010.191 ↗
53. Jung, M. Y. et al. Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283 (2022).10.1038/s41396-021-01064-z ↗
54. Meng, H., Katayama, Y. & Gu, J.-D. More wide occurrence and dominance of ammonia-oxidizing archaea than bacteria at three Angkor sandstone temples of Bayon, Phnom Krom and Wat Athvea in Cambodia. Int. Biodeterior. Biodegrad. 117, 78–88 (2017).10.1016/j.ibiod.2016.11.012 ↗
55. Kowalchuk, G. A. & Stephen, J. R. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55, 485–529 (2001).10.1146/annurev.micro.55.1.485 ↗
56. Gadd, G. M. Geomicrobiology of the built environment. Nat. Microbiol. 2, 16275 (2017).10.1038/nmicrobiol.2016.275 ↗
57. Kuypers, M. M. M., Marchant, H. K. & Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol. 16, 263–276 (2018).10.1038/nrmicro.2018.9 ↗
58. Chen, Y. & Wang, F. Insights on nitrate respiration by Shewanella. Front. Mar. Sci. 1, 80 (2015).10.3389/fmars.2014.00080 ↗
59. Martínez-Espinosa, C. et al. Denitrification in wetlands: A review towards a quantification at global scale. Sci. Total. Environ. 754, 142398 (2021).10.1016/j.scitotenv.2020.142398 ↗
60. Zhou, M. et al. Synthetic phylogenetically diverse communities promote denitrification and stability. Environ. Res. 231, 116184 (2023).10.1016/j.envres.2023.116184 ↗
61. Gao, H. et al. Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. Water Res. 155, 275–287 (2019).10.1016/j.watres.2019.02.020 ↗
62. Ma, L. et al. Temperature-dependent regulation of denitrification intermediates in high-temperature ecosystems. Environ. Sci. Technol. 59, 12630–12641 (2025).10.1021/acs.est.5c00174 ↗
63. Williamson, T. & Juenger, M. The role of activating solution concentration on alkali-silica reaction in alkali-activated fly ash concrete. Cem. Concr. Res. 83, 124–130 (2016).10.1016/j.cemconres.2016.02.008 ↗
64. Yang, M., Paudel, S. R. & Asa, E. Comparison of pore structure in alkali activated fly ash geopolymer and ordinary concrete due to alkali-silica reaction using micro-computed tomography. Constr. Build. Mater. 236, 117524 (2020).10.1016/j.conbuildmat.2019.117524 ↗
65. Ranalli, G., & Zanardini, E. in Microorganisms in the Deterioration and Preservation of Cultural Heritage. (ed. Joseph, E.) 263–279 (Springer, Cham, 2021).10.1007/978-3-030-69411-1_12 ↗
66. He, D. et al. Insights into the bacterial and fungal communities and microbiome that causes a microbe outbreak on ancient wall paintings in the Maijishan Grottoes. Int. Biodeterior. Biodegrad. 163, 105250 (2021).10.1016/j.ibiod.2021.105250 ↗
67. Fan, Y. et al. The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes. Water Res. 262, 122113 (2024).10.1016/j.watres.2024.122113 ↗
68. Zhou, Z. et al. Diversity and ecology of microbial sulfur metabolism. Nat. Rev. Microbiol. 23, 122–140 (2025).10.1038/s41579-024-01104-3 ↗
69. Francesco, D. C., Stefano, P., Piet, N. L. L. & Giovanni, E. Chemolithotrophic denitrification in biofilm reactors. Chem. Eng. J. 280, 643–657 (2015).10.1016/j.cej.2015.05.131 ↗
70. Francesco, D. C., Francesco, P., Piet, N. L. L. & Giovanni, E. Electron donors for autotrophic denitrification. Chem. Eng. J. 362, 922–937 (2019).10.1016/j.cej.2019.01.069 ↗
71. He, Y., Wang, Y. & Song, X. High-effective denitrification of low C/N wastewater by combined constructed wetland and biofilm-electrode reactor (CW–BER). Bioresour. Technol. 203, 245–251 (2016).10.1016/j.biortech.2015.12.060 ↗
72. Hao, R., Meng, C. & Li, J. An integrated process of three-dimensional biofilm-electrode with sulfur autotrophic denitrification (3DBER-SAD) for wastewater reclamation. Appl. Microbiol. Biotechnol. 100, 7339–7348 (2016).10.1007/s00253-016-7534-4 ↗
73. Furumai, H., Tagui, H., Fujita, K. & Fujita Effects of pH and alkalinity on sulfur-denitrification in a biological granular filter. Water Sci. Technol. 34, 355–362 (1996).10.2166/wst.1996.0391 ↗
74. Gadekar, S., Nemati, M. & Hill, G. A. Batch and continuous biooxidation of sulphide by Thiomicrospira sp. CVO: Reaction kinetics and stoichiometry. Water Res. 40, 2436–2446 (2006).10.1016/j.watres.2006.04.007 ↗
75. Kimura, K., Nakamura, M. & Watanabe, Y. Nitrate removal by a combination of elemental sulfur-based denitrification and membrane filtration. Water Res. 36, 1758–1766 (2002).10.1016/S0043-1354(01)00376-1 ↗
76. Pan, J. et al. Simultaneous nitrite and ammonium production in an autotrophic partial denitrification and ammonification of wastewaters containing thiocyanate. Bioresour. Technol. 252, 20–27 (2018).10.1016/j.biortech.2017.12.059 ↗
77. Yi, Q. et al. Elemental sulfur and organic matter amendment drive alkaline pH neutralization and mineral weathering in iron ore tailings through inducing sulfur oxidizing bacteria. Environ. Sci. Technol. 57, 21744–21756 (2023).10.1021/acs.est.3c05749 ↗