{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T06:58:09Z","timestamp":1788332289877,"version":"build-2803163510"},"reference-count":76,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,7]],"date-time":"2024-11-07T00:00:00Z","timestamp":1730937600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"The National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22276146"],"award-info":[{"award-number":["22276146"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"The National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2021JQ-053"],"award-info":[{"award-number":["2021JQ-053"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007128","name":"Natural Science Foundation of Shaanxi Province","doi-asserted-by":"publisher","award":["22276146"],"award-info":[{"award-number":["22276146"]}],"id":[{"id":"10.13039\/501100007128","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007128","name":"Natural Science Foundation of Shaanxi Province","doi-asserted-by":"publisher","award":["2021JQ-053"],"award-info":[{"award-number":["2021JQ-053"]}],"id":[{"id":"10.13039\/501100007128","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The contribution of denitrifying anaerobic methane oxidation (DAMO) as a methane sink across different habitats, especially those affected by anthropogenic activities, remains unclear. Mining and industrial and domestic use of metals\/metal-containing compounds can all cause metal contamination in freshwater ecosystems. Precipitation of metal ions often limits their toxicity to local microorganisms, yet microbial activity may also cause the redissolution of various precipitates. In contrast to most other studies that apply soluble metal compounds, this study investigated the responses of enriched DAMO culture to model insoluble copper compounds, malachite and covellite, in simulated sedimentary environments. Copper \u2264 0.22 \u00b5m from covellite appeared to cause immediate inhibition in 10 h. Long-term tests (54 days) showed that apparent methane consumption was less impacted by various levels of malachite and covellite than soluble copper. However, the medium-\/high-level malachite and covellite caused a 46.6\u201377.4% decline in denitrification and also induced significant death of the representative DAMO microorganisms. Some enriched species, such as Methylobacter tundripaludum, may have conducted DAMO or they may have oxidized methane aerobically using oxygen released by DAMO bacteria. Quantitative polymerase chain reaction analysis suggests that Candidatus Methanoperedens spp. were less affected by covellite as compared to malachite while Candidatus Methylomirabilis spp. responded similarly to the two compounds. Under the stress induced by copper, DAMO archaea, Planctomycetes spp. or Phenylobacterium spp. synthesized PHA\/PHB-like compounds, rendering incomplete methane oxidation. Overall, the findings suggest that while DAMO activity may persist in ecosystems previously exposed to copper pollution, long-term methane abatement capability may be impaired due to a shift of the microbial community or the inhibition of representative DAMO microorganisms.<\/jats:p>","DOI":"10.3390\/microorganisms12112259","type":"journal-article","created":{"date-parts":[[2024,11,7]],"date-time":"2024-11-07T12:12:13Z","timestamp":1730981533000},"page":"2259","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The Effects of Model Insoluble Copper Compounds in a Sedimentary Environment on Denitrifying Anaerobic Methane Oxidation (DAMO) Enrichment"],"prefix":"10.3390","volume":"12","author":[{"given":"Longfei","family":"Xia","sequence":"first","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Shaanxi Provincial Land Engineering Construction Group, Xi\u2019an 710075, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peiru","family":"Yao","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6992-2519","authenticated-orcid":false,"given":"Hodon","family":"Ryu","sequence":"additional","affiliation":[{"name":"United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengzhong","family":"Dong","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4625-5952","authenticated-orcid":false,"given":"Shihai","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongjian","family":"Liao","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3251-436X","authenticated-orcid":false,"given":"Yaohuan","family":"Gao","sequence":"additional","affiliation":[{"name":"School of Human Settlements and Civil Engineering, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"},{"name":"Institute of Global Environmental Change, Xi\u2019an Jiaotong University, 19-3027 iHarbour Campus, Xi\u2019an 710115, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"4495","DOI":"10.1073\/pnas.1318393111","article-title":"Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands","volume":"111","author":"Hu","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7477","DOI":"10.1038\/ncomms8477","article-title":"High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions","volume":"6","author":"Segarra","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zheng, Y., Hou, L., Chen, F., Zhou, J., Liu, M., Yin, G., Gao, J., and Han, P. (2020). Denitrifying anaerobic methane oxidation in intertidal marsh soils: Occurrence and environmental significance. Geoderma, 357.","DOI":"10.1016\/j.geoderma.2019.113943"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Yang, W.-T., Wang, W.-Q., Shen, L.-D., Bai, Y.-N., Liu, X., Tian, M.-H., Wang, C., Feng, Y.-F., Liu, Y., and Yang, Y.-L. (2022). Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields. Sci. Total Environ., 838.","DOI":"10.1016\/j.scitotenv.2022.156534"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1038\/ismej.2015.262","article-title":"NC10 bacteria in marine oxygen minimum zones","volume":"10","author":"Padilla","year":"2016","journal-title":"ISME J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.5194\/bg-14-1631-2017","article-title":"Effects of low oxygen concentrations on aerobic methane oxidation in seasonally hypoxic coastal waters","volume":"14","author":"Steinle","year":"2017","journal-title":"Biogeosciences"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Yang, Y., Chen, J., Tong, T., Xie, S., and Liu, Y. (2020). Influences of eutrophication on methanogenesis pathways and methanogenic microbial community structures in freshwater lakes. Environ. Pollut., 260.","DOI":"10.1016\/j.envpol.2020.114106"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Jilbert, T., Cowie, G., Lintum\u00e4ki, L., Jokinen, S., Asmala, E., Sun, X., M\u00f6rth, C.-M., Norkko, A., and Humborg, C. (2021). Anthropogenic Inputs of Terrestrial Organic Matter Influence Carbon Loading and Methanogenesis in Coastal Baltic Sea Sediments. Front. Earth Sci., 9.","DOI":"10.3389\/feart.2021.716416"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nature04617","article-title":"A microbial consortium couples anaerobic methane oxidation to denitrification","volume":"440","author":"Raghoebarsing","year":"2006","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nature08883","article-title":"Nitrite-driven anaerobic methane oxidation by oxygenic bacteria","volume":"464","author":"Ettwig","year":"2010","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/nature12375","article-title":"Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage","volume":"500","author":"Haroon","year":"2013","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1039\/D2VA00091A","article-title":"Significance of anaerobic oxidation of methane (AOM) in mitigating methane emission from major natural and anthropogenic sources: A review of AOM rates in recent publications","volume":"1","author":"Gao","year":"2022","journal-title":"Environ. Sci. Adv."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Yang, W.-T., Shen, L.-D., and Bai, Y.-N. (2023). Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems. Environ. Res., 219.","DOI":"10.1016\/j.envres.2022.115174"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Wang, J., Yao, X., Jia, Z., Zhu, L., Zheng, P., Kartal, B., and Hu, B. (2022). Nitrogen input promotes denitrifying methanotrophs\u2019 abundance and contribution to methane emission reduction in coastal wetland and paddy soil. Environ. Pollut., 302.","DOI":"10.1016\/j.envpol.2022.119090"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Chen, F., Zheng, Y., Hou, L., Niu, Y., Gao, D., An, Z., Zhou, J., Yin, G., Dong, H., and Han, P. (2021). Microbial abundance and activity of nitrite\/nitrate-dependent anaerobic methane oxidizers in estuarine and intertidal wetlands: Heterogeneity and driving factors. Water Res., 190.","DOI":"10.1016\/j.watres.2020.116737"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1111\/1462-2920.16102","article-title":"Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils","volume":"24","author":"Yang","year":"2022","journal-title":"Environ. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"16138","DOI":"10.1007\/s11356-021-16914-8","article-title":"NO3\u2212 is an important driver of nitrite-dependent anaerobic methane oxidation bacteria and CH4 fluxes in the reservoir riparian zone","volume":"29","author":"Song","year":"2022","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.envint.2014.08.010","article-title":"Effects of sediment geochemical properties on heavy metal bioavailability","volume":"73","author":"Zhang","year":"2014","journal-title":"Environ. Int."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1126\/science.adg6704","article-title":"Impacts of metal mining on river systems: A global assessment","volume":"381","author":"Macklin","year":"2023","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.1002\/etc.4440","article-title":"The Fate of Copper Added to Surface Water: Field, Laboratory, and Modeling Studies","volume":"38","author":"Rader","year":"2019","journal-title":"Environ. Toxicol. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1007\/s00253-010-2847-1","article-title":"Sulfur-driven autotrophic denitrification: Diversity, biochemistry, and engineering applications","volume":"88","author":"Shao","year":"2010","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.chemgeo.2003.09.001","article-title":"Mineral stimulation of subsurface microorganisms: Release of limiting nutrients from silicates","volume":"203","author":"Rogers","year":"2004","journal-title":"Chem. Geol."},{"key":"ref_23","unstructured":"Scott, R.A. (2005). Copper Enzymes in Denitrification. Encyclopedia of Inorganic Chemistry, JohnWiley and Sons."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/01490451003614971","article-title":"Stimulation of Methanotroph Activity by Cu-Substituted Borosilicate Glass","volume":"28","author":"Kulczycki","year":"2011","journal-title":"Geomicrobiol. J."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.jhazmat.2014.04.031","article-title":"Enrichment of denitrifying methanotrophic bacteria from municipal wastewater sludge in a membrane bioreactor at 20 \u00b0C","volume":"274","author":"Kampman","year":"2014","journal-title":"J. Hazard. Mater."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.watres.2015.08.040","article-title":"Improvement of the trace metal composition of medium for nitrite-dependent anaerobic methane oxidation bacteria: Iron (II) and copper (II) make a difference","volume":"85","author":"He","year":"2015","journal-title":"Water Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1007\/s41742-018-0118-7","article-title":"Effects of Copper and PQQ on the Denitrification Activities of Microorganisms Facilitating Nitrite- and Nitrate-Dependent DAMO Reaction","volume":"12","author":"Hatamoto","year":"2018","journal-title":"Int. J. Environ. Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1016\/j.watres.2015.11.011","article-title":"Iron reduction in the DAMO\/Shewanella oneidensis MR-1 coculture system and the fate of Fe(II)","volume":"88","author":"Fu","year":"2016","journal-title":"Water Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.watres.2016.06.065","article-title":"Cr(VI) reduction coupled with anaerobic oxidation of methane in a laboratory reactor","volume":"102","author":"Lu","year":"2016","journal-title":"Water Res."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Liang, L., Sun, C., Jin, Z., Wang, M., Yu, Q., Zhao, Z., and Zhang, Y. (2022). Magnetite-mediated electrically connected community for shortening startup of methane-dependent denitrification in a membrane biofilm reactor. Chem. Eng. J., 428.","DOI":"10.1016\/j.cej.2021.132004"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Zhang, M., Lu, G., Li, Z., Xu, F., Yang, N., Sun, X., Xu, R., and Sun, W. (2021). Effects of antimony on anaerobic methane oxidization and microbial community in an antimony-contaminated paddy soil: A microcosm study. Sci. Total Environ., 784.","DOI":"10.1016\/j.scitotenv.2021.147239"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Cervi, E.C., Clark, S., Boye, K.E., Gustafsson, J.P., Baken, S., and Burton, G.A. (2021). Copper transformation, speciation, and detoxification in anoxic and suboxic freshwater sediments. Chemosphere, 282.","DOI":"10.1016\/j.chemosphere.2021.131063"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/s12665-019-8080-z","article-title":"Ecological risk by heavy metal contents in sediments within the Wei River Basin, China","volume":"78","author":"Yang","year":"2019","journal-title":"Environ. Earth Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1038\/s41396-018-0109-x","article-title":"A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction","volume":"12","author":"Cai","year":"2018","journal-title":"ISME J."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3656","DOI":"10.1128\/AEM.00067-09","article-title":"Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum","volume":"75","author":"Ettwig","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"407","DOI":"10.2175\/106143013X13807328848216","article-title":"Physical Extraction of Microorganisms from Water-Saturated, Packed Sediment","volume":"86","author":"Ugolini","year":"2014","journal-title":"Water Environ. Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1016\/S0038-0717(97)00232-0","article-title":"Extraction of microorganisms from soil: Evaluation of the efficiency by counting methods and activity measurements","volume":"30","author":"Riis","year":"1998","journal-title":"Soil Biol. Biochem."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3877","DOI":"10.1128\/AEM.02960-10","article-title":"pmoA primers for detection of anaerobic methanotrophs","volume":"77","author":"Luesken","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1007\/s00253-016-8065-8","article-title":"McrA primers for the detection and quantification of the anaerobic archaeal methanotroph Candidatus Methanoperedens nitroreducens","volume":"101","author":"Vaksmaa","year":"2017","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/s41396-018-0302-y","article-title":"Active pathways of anaerobic methane oxidation across contrasting riverbeds","volume":"13","author":"Shen","year":"2019","journal-title":"ISME J."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Gao, Y., Lee, J., Neufeld, J.D., Park, J., Rittmann, B.E., and Lee, H.-S. (2017). Anaerobic oxidation of methane coupled with extracellular electron transfer to electrodes. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-05180-9"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2905","DOI":"10.1039\/D2EW00152G","article-title":"Release and migration of Pb from Pb(ii) and Pb(iv) compounds in the presence of microbiological activity","volume":"8","author":"Gao","year":"2022","journal-title":"Environ. Sci. Water Res. Technol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"8344","DOI":"10.1073\/pnas.0812808106","article-title":"The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity","volume":"106","author":"Macomber","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/s10646-014-1355-y","article-title":"Direct and indirect effects of copper-contaminated sediments on the functions of model freshwater ecosystems","volume":"24","author":"Gardham","year":"2015","journal-title":"Ecotoxicology"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1007\/s11356-014-3406-6","article-title":"Remediation of sediment and water contaminated by copper in small-scaled constructed wetlands: Effect of bioaugmentation and phytoextraction","volume":"22","author":"Huguenot","year":"2015","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.envpol.2018.07.020","article-title":"Denitrifier communities impacted by heavy metal contamination in freshwater sediment","volume":"242","author":"Guo","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"349","DOI":"10.2166\/wst.1999.0181","article-title":"Impact of heavy metals on denitrification in surface wetland sediments receiving wastewater","volume":"40","author":"Sakadevan","year":"1999","journal-title":"Water Sci. Technol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.2134\/jeq2007.0666","article-title":"Impact of Elevated Copper on the Rate and Gaseous Products of Denitrification in Freshwater Sediments","volume":"38","author":"Jacinthe","year":"2009","journal-title":"J. Environ. Qual."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1111\/j.1574-6941.2011.01107.x","article-title":"Impact of copper on the diversity, abundance and transcription of nitrite and nitrous oxide reductase genes in an urban European estuary","volume":"77","author":"Machado","year":"2011","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_50","first-page":"421","article-title":"Increased copper levels inhibit denitrification in urban soils","volume":"109","author":"Li","year":"2018","journal-title":"Earth Environ. Sci. Trans. R. Soc. Edinb."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1111\/1751-7915.12352","article-title":"Influence of copper on expression of nirS, norB and nosZ and the transcription and activity of NIR, NOR and N2OR in the denitrifying soil bacteria Pseudomonas stutzeri","volume":"9","author":"Black","year":"2016","journal-title":"Microb. Biotechnol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.biortech.2018.07.139","article-title":"Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium","volume":"268","author":"Jiang","year":"2018","journal-title":"Bioresour. Technol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Wang, Y., Lai, C.-Y., Wu, M., Lu, X., Hu, S., Yuan, Z., and Guo, J. (2022). Copper stimulation on methane-supported perchlorate reduction in a membrane biofilm reactor. J. Hazard. Mater., 425.","DOI":"10.1016\/j.jhazmat.2021.127917"},{"key":"ref_54","first-page":"380","article-title":"Toxicity of copper(II) ions to microorganisms in biological wastewater treatment systems","volume":"412\u2013413","author":"Banihani","year":"2011","journal-title":"Sci. Total Environ."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/s43705-023-00246-4","article-title":"Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings","volume":"3","author":"Li","year":"2023","journal-title":"ISME Commun."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/MRA.00824-18","article-title":"Draft Genome Sequences of Obligate Methylotrophs Methylovorus sp. Strain MM2 and Methylobacillus sp. Strain MM3, Isolated from Grassland Soil","volume":"7","author":"Macey","year":"2018","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1099\/ijs.0.066175-0","article-title":"Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria","volume":"64","author":"Kulichevskaya","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1038\/ismej.2016.14","article-title":"Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge","volume":"10","author":"McIlroy","year":"2016","journal-title":"ISME J."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1038\/s41396-020-0716-1","article-title":"Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog","volume":"14","author":"Castelle","year":"2020","journal-title":"ISME J."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1111\/1758-2229.12078","article-title":"Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment","volume":"5","author":"Dumont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"6418","DOI":"10.1128\/JB.05380-11","article-title":"Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96","volume":"193","author":"Svenning","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Lichtenberg, M., Line, L., Schrameyer, V., Jakobsen, T.H., Rybtke, M.L., Toyofuku, M., Nomura, N., Kolpen, M., Tolker-Nielsen, T., and K\u00fchl, M. (2021). Nitric-oxide-driven oxygen release in anoxic Pseudomonas aeruginosa. iScience, 24.","DOI":"10.1016\/j.isci.2021.103404"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1016\/j.cell.2016.08.007","article-title":"Toward Accurate and Quantitative Comparative Metagenomics","volume":"166","author":"Nayfach","year":"2016","journal-title":"Cell"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Shen, J., McFarland, A.G., Young, V.B., Hayden, M.K., and Hartmann, E.M. (2021). Toward Accurate and Robust Environmental Surveillance Using Metagenomics. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.600111"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Zhang, L., Dumont, M.G., Bodelier, P.L.E., Adams, J.M., He, D., and Chu, H. (2020). DNA stable-isotope probing highlights the effects of temperature on functionally active methanotrophs in natural wetlands. Soil Biol. Biochem., 149.","DOI":"10.1016\/j.soilbio.2020.107954"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"7371","DOI":"10.1021\/acs.est.9b00077","article-title":"Acetate Production from Anaerobic Oxidation of Methane via Intracellular Storage Compounds","volume":"53","author":"Cai","year":"2019","journal-title":"Environ. Sci. Technol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"M\u00fcller-Santos, M., Koskim\u00e4ki, J.J., Alves, L.P.S., de Souza, E.M., Jendrossek, D., and Pirttil\u00e4, A.M. (2020). The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol. Rev., 45.","DOI":"10.1093\/femsre\/fuaa058"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Macey, M.C., Pratscher, J., Crombie, A.T., and Murrell, J.C. (2020). Impact of plants on the diversity and activity of methylotrophs in soil. Microbiome, 8.","DOI":"10.1186\/s40168-020-00801-4"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Gao, Y., Trueman, B.F., and Gagnon, G.A. (2022). Early phase effects of silicate and orthophosphate on lead (Pb) corrosion scale development and Pb release. J. Environ. Manag., 321.","DOI":"10.1016\/j.jenvman.2022.115947"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1080\/03067319308027619","article-title":"Speciation of Heavy Metals in Soils and Sediments. An Account of the Improvement and Harmonization of Extraction Techniques Undertaken Under the Auspices of the BCR of the Commission of the European Communities","volume":"51","author":"Ure","year":"1993","journal-title":"Int. J. Environ. Anal. Chem."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Hu, S., Hu, J., Sun, Y., Zhu, Q., Wu, L., Liu, B., Xiao, K., Liang, S., Yang, J., and Hou, H. (2021). Simultaneous heavy metal removal and sludge deep dewatering with Fe(II) assisted electrooxidation technology. J. Hazard. Mater., 405.","DOI":"10.1016\/j.jhazmat.2020.124072"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/s11270-007-9564-0","article-title":"A Review of the Different Methods Applied in Environmental Geochemistry for Single and Sequential Extraction of Trace Elements in Soils and Related Materials","volume":"189","author":"Rao","year":"2008","journal-title":"Water Air Soil Pollut."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1016\/j.biortech.2017.06.053","article-title":"Quantification of the methane concentration using anaerobic oxidation of methane coupled to extracellular electron transfer","volume":"241","author":"Gao","year":"2017","journal-title":"Bioresour. Technol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"Qin","year":"2012","journal-title":"Nature"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. 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