Abstract
A novel enrofloxacin-degrading fungus was isolated from a rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L.. The isolate, designated KC0924g, was identified as a member of the genus Humicola based on morphological characteristics and tandem conserved sequence analysis. The optimal temperature and pH for enrofloxacin degradation by strain KC0924g were 28 °C and 9.0, respectively. Under such condition, 98.2% of enrofloxacin with an initial concentration of 1 mg L−1 was degraded after 72 h of incubation, with nine possible degradation products identified. Four different metabolic pathways were proposed, which were initiated by cleavage of the piperazine moiety, hydroxylation of the aromatic ring, oxidative decarboxylation, or defluorination. In addition to enrofloxacin, strain KC0924g also degraded other fluoroquinolone antibiotics (ciprofloxacin, norfloxacin, and ofloxacin), malachite green (an illegal additive in aquaculture), and leucomalachite green. Pretreatment of cells of strain KC0924g with Cu2+ accelerated ENR degradation. Furthermore, it was speculated that a flavin-dependent monooxygenase was involved in ENR degradation, based on the increased transcriptional levels of these two genes after Cu2+ induction. This work enriches strain resources for enrofloxacin remediation and, more importantly, would facilitate studies on the molecular mechanism of ENR degradation with degradation-related transcriptome available.
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References
Abd El-Monaem EM, Eltaweil AS, Elshishini HM, Hosny M, Abou Alsoaud MM, Attia NF, El-Subruiti GM, Omer AM (2022) Sustainable adsorptive removal of antibiotic residues by chitosan composites: An insight into current developments and future recommendations. Arab J Chem 15(5):103743. https://doi.org/10.1016/j.arabjc.2022.103743
Alexandrino DAM, Mucha AP, Almeida CMR, Gao W, Jia Z, Carvalho MF (2017) Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics. Sci Total Environ 581–582:359–368. https://doi.org/10.1016/j.scitotenv.2016.12.141
Ashiq A, Vithanage M, Sarkar B, Kumar M, Bhatnagar A, Khan E, Xi Y, Ok YS (2021) Carbon-based adsorbents for fluoroquinolone removal from water and wastewater: a critical review. Environ Res 197:111091. https://doi.org/10.1016/j.envres.2021.111091
Barko JW, Hardin DG, Matthews MS (1982) Growth and morphology of submersed freshwater macrophytes in relation to light and temperature. Can J Bot 60(6):877–887. https://doi.org/10.1139/b82-113
Bergwerff AA, Scherpenisse P (2003) Determination of residues of malachite green in aquatic animals. J Chromatogr B Analyt Technol Biomed Life Sci 788(2):351–359. https://doi.org/10.1016/s1570-0232(03)00042-4
Bhatt S, Chatterjee S (2022) Fluoroquinolone antibiotics: OCCURRENCE, mode of action, resistance, environmental detection, and remediation - a comprehensive review. Environ Pollut 315:120440. https://doi.org/10.1016/j.envpol.2022.120440
Blake SL, Walker SH, Muddiman DC, Hinks D, Beck KR (2011) Spectral accuracy and sulfur counting capabilities of the LTQ-FT-ICR and the LTQ-Orbitrap XL for small molecule analysis. J Am Soc Mass Spectrom 22(12):2269–2275. https://doi.org/10.1007/s13361-011-0244-3
Boonsaner M, Hawker DW (2010) Accumulation of oxytetracycline and norfloxacin from saline soil by soybeans. Sci Total Environ 408(7):1731–1737. https://doi.org/10.1016/j.scitotenv.2009.12.032
Chen X, Ji J, Zhao L, Qiu J, Dai C, Wang W, He J, Jiang J, Hong Q, Yan X (2017) Molecular mechanism and genetic determinants of buprofezin degradation. Appl Environ Microbiol. 83(18). https://doi.org/10.1128/aem.00868-17
Crous PW, Verkley GJM, Groenewald JZ (2009) Fungal biodiversity. In: CBS Laboratory Manual Series, 1. CBS-KNAW Fungal Biodeiversity Centre. Utrecht, pp 1–269
Čvančarová M, Moeder M, Filipová A, Cajthaml T (2015) Biotransformation of fluoroquinolone antibiotics by ligninolytic fungi – metabolites, enzymes and residual antibacterial activity. Chemosphere 136:311–320. https://doi.org/10.1016/j.chemosphere.2014.12.012
Dai Y, Tang H, Chang J, Wu Z, Liang W (2014) What’s better, Ceratophyllum demersum L. or Myriophyllum verticillatum L., individual or combined? Ecol Eng 70:397–401. https://doi.org/10.1016/j.ecoleng.2014.06.009
Doorslaer VX, Dewulf J, Langenhove HV, Demeestere K (2014) Fluoroquinolone antibiotics: an emerging class of environmental micropollutants. Sci Total Environ 500–501:250–269. https://doi.org/10.1016/j.scitotenv.2014.08.075
Fang L, Chen C, Li S, Ye P, Shi Y, Sharma G, Sarkar B, Shaheen SM, Lee SS, Xiao R (2023) A comprehensive and global evaluation of residual antibiotics in agricultural soils: accumulation, potential ecological risks, and attenuation strategies. Ecotoxicol Environ Saf 262:115175. https://doi.org/10.1016/j.ecoenv.2023.115175
Gong Z, Xie J, Liu J, Liu T, Chen J, Li J, Gan J (2023) Oxidation towards enrofloxacin degradation over nanoscale zero-valent copper: mechanism and products. Environ Sci Pollut Res Int 30:38700–38712. https://doi.org/10.1007/s11356-022-24984-5
Hoang TT, Tu LT, Le Nga P, Dao QP (2013) A preliminary study on the phytoremediation of antibiotic contaminated sediment. Int J Phytoremediation 15(1):65–76. https://doi.org/10.1080/15226514.2012.670316
Hoshino Y, Fujii S, Shinonaga H, Arai K, Saito F, Fukai T, Satoh H, Miyazaki Y, Ishikawa J (2010) Monooxygenation of rifampicin catalyzed by the rox gene product of Nocardia farcinica: structure elucidation, gene identification and role in drug resistance. J Antibiot (tokyo) 63(1):23–28. https://doi.org/10.1038/ja.2009.116
Huijbers MME, Montersino S, Westphal AH, Tischler D, van Berkel WJH (2014) Flavin dependent monooxygenases. Arch Biochem Biophys 544:2–17. https://doi.org/10.1016/j.abb.2013.12.005
Hwang WC, Xu Q, Wu B, Godzik A (2018) Retraction: crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50, William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik. Proteins 86(2):269. https://doi.org/10.1002/prot.24661
Ibrahim SRM, Mohamed SGA, Altyar AE, Mohamed GA (2021) Natural products of the fungal genus humicola: diversity, biological activity, and industrial importance. Curr Microbiol 78(7):2488–2509. https://doi.org/10.1007/s00284-021-02533-6
Jensen KA Jr, Houtman CJ, Ryan ZC, Hammel KE (2001) Pathways for extracellular Fenton chemistry in the brown rot basidiomycete Gloeophyllum trabeum. Appl Environ Microbiol 67(6):2705–2711. https://doi.org/10.1128/aem.67.6.2705-2711.2001
Karl W, Schneider J, Wetzstein HG (2006) Outlines of an “exploding” network of metabolites generated from the fluoroquinolone enrofloxacin by the brown rot fungus Gloeophyllum striatum. Appl Microbiol Biotechnol 71(1):101–113. https://doi.org/10.1007/s00253-005-0177-5
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 23(21):2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Li Y, Niu J, Wang W (2011) Photolysis of Enrofloxacin in aqueous systems under simulated sunlight irradiation: kinetics, mechanism and toxicity of photolysis products. Chemosphere 85(5):892–897. https://doi.org/10.1016/j.chemosphere.2011.07.008
Li W, Shi Y, Gao L, Liu J, Cai Y (2012) Occurrence of antibiotics in water, sediments, aquatic plants, and animals from Baiyangdian Lake in North China. Chemosphere 89(11):1307–1315. https://doi.org/10.1016/j.chemosphere.2012.05.079
Lin ZZ, Zhang HY, Peng AH, Lin YD, Li L, Huang ZY (2016) Determination of malachite green in aquatic products based on magnetic molecularly imprinted polymers. Food Chem 200:32–37. https://doi.org/10.1016/j.foodchem.2016.01.001
Liu Z, Wang T (2012) Effects of pH on aquaculture. China Anim Husb Vet Digest 12:99
Liu J, Sun Z, Chen L (2020) Isolation and characterisation of a malachite green-degrading bacterium, Citrobacter sp. D3, and its degradation properties. Fujian J Agric Sci (in Chinese) 35(6):8. https://doi.org/10.19303/j.issn.1008-0384.2020.06.012
Liu C, Pan K, Xu H, Song Y, Qi X, Lu Y, Jiang X, Liu H (2024) The effects of enrofloxacin exposure on responses to oxidative stress, intestinal structure and intestinal microbiome community of largemouth bass (Micropterus salmoides). Chemosphere 348:140751. https://doi.org/10.1016/j.chemosphere.2023.140751
Ma R, Fang W, Yang Z, Hu K (2019) Liver proteome analysis of grass carp (Ctenopharyngodon idellus) following treatment with enrofloxacin. Fish Physiol Biochem 45(6):1941–1952. https://doi.org/10.1007/s10695-019-00690-x
Ma B, Wang D, Mei X, Lei C, Li C, Wang H (2023) Effect of enrofloxacin on the microbiome, metabolome, and abundance of antibiotic resistance genes in the chicken cecum. Microbiol Spectr 11:e0479522. https://doi.org/10.1128/spectrum.04795-22
Minerdi D, Zgrablic I, Castrignanò S, Catucci G, Medana C, Terlizzi ME, Gribaudo G, Gilardi G, Sadeghi SJ (2016) Escherichia coli overexpressing a Baeyer-Villiger monooxygenase from Acinetobacter radioresistens becomes resistant to imipenem. Antimicrob Agents Chemother 60(1):64–74. https://doi.org/10.1128/aac.01088-15
Moreira VR, Lebron YAR, da Silva MM, de Souza Santos LV, Jacob RS, de Vasconcelos CKB, Viana MM (2020) Graphene oxide in the remediation of norfloxacin from aqueous matrix: simultaneous adsorption and degradation process. Environ Sci Pollut Res Int 27(27):34513–34528. https://doi.org/10.1007/s11356-020-09656-6
Orimolade BO, Oladipo AO, Idris AO, Usisipho F, Azizi S, Maaza M, Lebelo SL, Mamba BB (2023) Advancements in electrochemical technologies for the removal of fluoroquinolone antibiotics in wastewater: A review. Sci Total Environ 881:163522. https://doi.org/10.1016/j.scitotenv.2023.163522
Pan LJ, Li J, Li CX, Tang XD, Yu GW, Wang Y (2018) Study of ciprofloxacin biodegradation by a Thermus sp. isolated from pharmaceutical sludge. J Hazard Mater 343:59–67. https://doi.org/10.1016/j.jhazmat.2017.09.009
Parshikov IA, Sutherland JB (2012) Microbial transformations of antimicrobial quinolones and related drugs. J Ind Microbiol Biotechnol 39(12):1731–1740. https://doi.org/10.1007/s10295-012-1194-x
Pedersen O, Colmer TD, Sand-Jensen K (2013) Underwater photosynthesis of submerged plants - recent advances and methods. Front Plant Sci 4:140. https://doi.org/10.3389/fpls.2013.00140
Rayner RW (1970) A mycological colour chat. Commonwealth Mycological Institute and British Mycological Society. Kew, Surrey
Reis RAG, Li H, Johnson M, Sobrado P (2021) New frontiers in flavin-dependent monooxygenases. Arch Biochem Biophys 699:108765. https://doi.org/10.1016/j.abb.2021.108765
Riaz L, Mahmood T, Khalid A, Rashid A, Ahmed Siddique MB, Kamal A, Coyne MS (2018) Fluoroquinolones (FQs) in the environment: a review on their abundance, sorption and toxicity in soil. Chemosphere 191:704–720. https://doi.org/10.1016/j.chemosphere.2017.10.092
Ricken B, Kolvenbach BA (2017) FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp. strain BR1 subsisting on sulfonamide antibiotics. Sci Rep 7(1):15783. https://doi.org/10.1038/s41598-017-16132-8
Sangare L, Zhao Y, Folly YME, Chang J, Li J, Selvaraj JN, Xing F, Zhou L, Wang Y, Liu Y (2014) Aflatoxin B1 Degradation by a Pseudomonas Strain. Toxins 6(10):3028–3040
Santamaría L, Van Vierssen W (1997) Photosynthetic temperature responses of fresh- and brackish-water macrophytes: a review. Aquat Bot 58(2):135–150. https://doi.org/10.1016/S0304-3770(97)00015-6
Santos F, Almeida CMR, Ribeiro I, Ferreira AC, Mucha AP (2019) Removal of veterinary antibiotics in constructed wetland microcosms – response of bacterial communities. Ecotoxicol Environ Saf 169:894–901. https://doi.org/10.1016/j.ecoenv.2018.11.078
Srivastava S, Sinha R, Roy D (2004) Toxicological effects of malachite green. Aquat Toxicol 66(3):319–329. https://doi.org/10.1016/j.aquatox.2003.09.008
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. https://doi.org/10.1093/molbev/msr121
Tripathi P, Khare P, Barnawal D, Shanker K, Srivastava PK, Tripathi RD, Kalra A (2020) Bioremediation of arsenic by soil methylating fungi: role of Humicola sp. strain 2WS1 in amelioration of arsenic phytotoxicity in Bacopa monnieri L. Sci Total Environ 716:136758. https://doi.org/10.1016/j.scitotenv.2020.136758
Van Caekenberghe DL, Pattyn SR (1984) In vitro activity of ciprofloxacin compared with those of other new fluorinated piperazinyl-substituted quinoline derivatives. Antimicrob Agents Chemother 25(4):518–521. https://doi.org/10.1128/AAC.25.4.518
Van Berkel WJH, Kamerbeek NM, Fraaije MW (2006) Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J Biotechnol 124(4):670–689. https://doi.org/10.1016/j.jbiotec.2006.03.044
Volkers G, Palm GJ, Weiss MS, Wright GD, Hinrichs W (2011) Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase. FEBS Lett 585(7):1061–1066. https://doi.org/10.1016/j.febslet.2011.03.012
Wang XW, Houbraken J, Groenewald JZ, Meijer M, Andersen B, Nielsen KF, Crous PW, Samson RA (2016) Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments. Stud Mycol 84:145–224. https://doi.org/10.1016/j.simyco.2016.11.005
Wang XW, Yang FY, Meijer M, Kraak B, Sun BD, Jiang YL, Wu YM, Bai FY, Seifert KA, Crous PW, Samson RA, Houbraken J (2019) Redefining Humicola sensu stricto and related genera in the Chaetomiaceae. Stud Mycol 93:65–153. https://doi.org/10.1016/j.simyco.2018.07.001
Wang L, Hu T, Li Y, Zhao Z, Zhu M (2023) Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture. Environ Pollut 339:122734. https://doi.org/10.1016/j.envpol.2023.122734
Wetzstein HG, Schmeer N, Karl W (1997) Degradation of the fluoroquinolone enrofloxacin by the brown rot fungus Gloeophyllum striatum. Appl Environ Microbiol 63(11):4272–4281. https://doi.org/10.1128/aem.63.11.4272-4281
Wetzstein HG, Stadler M, Tichy HV, Dalhoff A, Karl W (1999) Degradation of ciprofloxacin by basidiomycetes and identification of metabolites generated by the brown rot fungus Gloeophyllum striatum. Appl Environ Microbiol 65(4):1556–1563. https://doi.org/10.1128/aem.65.4.1556-1563.1999
Wetzstein HG, Schneider J, Karl W (2006) Patterns of metabolites produced from the fluoroquinolone enrofloxacin by basidiomycetes indigenous to agricultural sites. Appl Microbiol Biotechnol 71(1):90–100. https://doi.org/10.1007/s00253-005-0178-4
Xie Z, Saad A, Shang Y, Wang Y, Luo S, Wei Z (2023) Enhanced degradation of micropollutants by visible light photocatalysts with strong oxygen activation ability. Water Res 247:120785. https://doi.org/10.1016/j.watres.2023.120785
Xu G, Wang J (2014) Biodegradation of decabromodiphenyl ether (BDE-209) by white-rot fungus Phlebia lindtneri. Chemosphere 110:70–77. https://doi.org/10.1016/j.chemosphere.2014.03.052
Zhang H, Huang CH (2007) Adsorption and oxidation of fluoroquinolone antibacterial agents and structurally related amines with goethite. Chemosphere 66(8):1502–1512. https://doi.org/10.1016/j.chemosphere.2006.08.024
Zhang L, Zhang Y, Liu L (2019) Effect of submerged macrophytes Vallisneria spiralis L. on restoring the sediment contaminated by enrofloxacin in aquaculture ponds. Ecol Eng 140:105596. https://doi.org/10.1016/j.ecoleng.2019.105596
Zhang M, Fan D, Pan L, Su C, Li Z, Liu C, He Q (2023) Characterization and removal mechanism of a novel enrofloxacin-degrading microorganism, Microbacterium proteolyticum GJEE142 capable of simultaneous removal of enrofloxacin, nitrogen and phosphorus. J Hazard Mater 454:131452. https://doi.org/10.1016/j.jhazmat.2023.131452
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This research was supported by the Shanghai Agriculture Applied Technology Development Program, China (Grant No. 2020–02-08–00-07-F01483), the National Natural Science Foundation of China (31900097), and the Natural Science Foundation of Shanghai (20ZR1450800).
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Chen, X., Zhang, Y. & Liu, J. A novel enrofloxacin-degrading fungus, Humicola sp. KC0924g, isolated from the rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L.. Int Microbiol (2024). https://doi.org/10.1007/s10123-024-00513-x
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DOI: https://doi.org/10.1007/s10123-024-00513-x