ДЕСТРУКЦИЯ ПЕРФТОРКАРБОНОВЫХ КИСЛОТ БАКТЕРИЯМИ РОДА PSEUDOMONAS ПОДТВЕРЖДЕНА ДАННЫМИ ОБ ИХ ГЕНОМАХ И МЕТАБОЛИТАХ

С.П. Четвериков, Г.Г. Худайгулов, Д.А. Шарипов, С.Н. Стариков

Аннотация


Изучен потенциал штаммов Pseudomonas sp. 2,4-D и P. mosselii 5(3) (UIB-53 и UIB-251 из коллекции микроорганизмов УИБ УФИЦ РАН), выделенных из загрязненных пестицидами и галогенорганическими соединениями почв, в качестве деструкторов перфторкарбоновых кислот (ПФКК) и выполнен анализ полных геномов этих штаммов. Геномы длиной 5,68 и 5,86 млн. пар нуклеотидов у штаммов 5(3) и 2,4-D соответственно содержат гены белков, потенциально участвующих в деструкции (дегалогенировании) фторорганических соединений: галоалкандегалогеназы (dhaA), галоацетатдегалогеназы H-1 (dehH1), переносчика ионов фтора (CrcB) и алкансульфонатмонооксигеназы (SsuE). Штаммы за 7 суток культивирования в жидкой среде с различными (C7-C10)-ПФКК в качестве единственного источника углерода и энергии полностью их утилизировали. Результаты анализа с помощью ЖХ-МС показали, что разложение ПФКК доходит до перфторгексановой кислоты с высвобождением, при различных стехиометрических соотношениях в зависимости от ПФКК, индикаторов минерализации ионов фтора, определяемых хроматографией с кондуктометрическим детектированием. Таким образом показано, что изученные штаммы бактерий рода Pseudomonas имеют большой генетически подтвержденный потенциал деструкции ПФКК.

Ключевые слова


перфторкарбоновые кислоты, деградация, Pseudomonas, геном

Полный текст:

PDF

Как процитировать материал

Литература


Ross I, McDonough J, Miles J, Storch J, Kochunarayanan PT, Kalve E, Hurst J, Dasgupta SS . A review of emerging technologies for remediation of PFASs. Remediation. 2018;28:101-26. doi: 10.1002/rem.21553

Fujii S, Tanaka S, Hong Lien NP, Qiu Y, Polprasert C. New POPs in the water environment: Distribution, bioaccumulation and treatment of perfluorinated compounds: A review paper. AQUA. 2007;56(5):313-26. doi: 10.2166/aqua.2007.005

Nascimento RA, Nunoo DBO, Bizkarguenaga E, Schultes L, Zabaleta I, Benskin JP, Spano S, Leonel J. Sulfluramid use in Brazilian agriculture: A source of per- and polyfluoroalkyl substances (PFASs) to the environment . Environ Pollut. 2018;242:1436-43. doi: 10.1016/j.envpol.2018.07.122

Xia C, Diamond ML, Peaslee GF, Peng H, Blum A, Wang Z, Shalin A, Whitehead HD, Green M, Schwartz-Narbonne H, Yang D, Venier M. Per- and polyfluoroalkyl substances in North American school uniforms. Environ Sci Technol. 2022;56:13845-57. doi: 10.1021/acs.est.2c02111.

Schaider LA, Balan SA, Blum A, Andrews DQ, Strynar MJ, Dickinson ME, Lunderberg DM, Lang JR, Peaslee GF. Fluorinated compounds in U.S. fast food packaging. Environ Sci Technol Lett. 2017;4:105-11. doi: 10.1021/acs.estlett.6b00435.

Pozo K, Moriera LB, Karaskova P, Pribylova P, Klanova J, de Carvalho MU, Maranho LA, de Souza Abessa DM. Using large amounts of firefighting foams releases per- and polyfluoroalkyl substances (PFAS) into estuarine environments: A baseline study in Latin America. Mar Pollut Bull. 2022;182:113938. doi: 10.1016/j.marpolbul.2022.113938.

Prevedouros K, Cousins IT, Buck RC, Korzeniowski SH. Sources, fate and transport of perfluorocarboxylates. Environ Sci Technol. 2006;40(1):32-44. doi: 10.1021/es0512475.

Wang Y, Munir U, Huang Q. Occurrence of per- and polyfluoroalkyl substances (PFAS) in soil: Sources, fate, and remediation. Soil Environl Health. 2023;1(1):100004. doi: 10.1016/j.seh.2023.100004.

Bin J, Yaqian Z. World profile of foreseeable strategies for the removal of per- and polyfluoroalkyl substances (PFASs) from water. In: Persistant Pollutants in Water and Advanced Treatment Technology. 2023. P. 47-69

Sung-Hee S. Health risk of human exposure to perfluorinated compounds (PFASs) in Hyeongsan River, Pohang. Jf Environ Analysis Health Toxicol. 2022;3:77-84. doi: 10.36278/jeaht.25.3.77

Calvert L, Green MP, De Iuliis GN, Dun M, Turner BD, Clarke BO, Eamens AL, Roman SD, Nixon B. Assessment of the emerging threat posed by perfluoroalkyl and polyfluoroalkyl substances to mrle Reproduction in humans. Front Endocrinol. 2022;12:799043. doi: 10.3389/fendo.2021.799043.

Cheng J, Vecitis CD, Park H, Mader BT, Hoffmann MR. Sonochemical degradation of perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) in landfill groundwater: environmental matrix effects. Environ Sci Technol. 2008;42:8057-63. doi: 10.1021/es8013858

Wang F, Shih K, Lu X, Liu C. Mineralization behavior of fluorine in perfluorooctanesulfonate (PFOS) during thermal treatment of lime-conditioned sludge. Environ Sci Technol. 2013; 47: 2621-27. doi: 10.1021/ es305352p

Marquínez-Marquínez AN, Loor-Molina NS, Quiroz-Fernández LS, Maddela NR, Luque R, Rodríguez-Díaz JM. Recent advances in the remediation of perfluoroalkylated and polyfluoroalkylated contaminated sites. Environ Res. 2023;219:115152. doi: 10.1016/j.envres.2022.115152.

Kabiri S, Navarro DA, Hamad SA, Grimison C, Higgins CP, Mueller JF, Kookana RS, McLaughlin MJ. Physical and chemical properties of carbon-based sorbents that affect the removal of per- and polyfluoroalkyl substances from solution and soil. Sci Total Environ. 2023;875:162653. doi: 10.1016/j.scitotenv.2023.162653.

Mayer-Blackwell K, Sewell H, Fincker M, Spormann AM. Comparative physiology of organohalide-respiring bacteria. In: Adrian BTL, Löffler FE, eds. Organohalide-Respiring Bacteria. Berlin Heidelberg: Springer; 2016. P.. 259-80.

Wackett LP, McMahon K. Why Is the biodegradation of polyfluorinated compounds so rare? mSphere. 2021; 6(5):Article e00721-21. doi: 10.1128/mSphere.00721-21.

Chetverikov SP, Sharipov DA, Korshunova TY, Loginov ON. Degradation of perfluorooctanyl sulfonate by strain Pseudomonas plecoglossicida 2.4-D. Appl Biochem Microbiol. 2017;53(5):533-8. doi: 10.1134/S0003683817050027

Shaw DMJ, Munoz G, Bottos EM, Duy SV, Sauve S, Liu J, Van Hamme JD. Degradation and defluorination of 6:2 fluorotelomer sulfonamidoalkyl betaine and 6:2 fluorotelomer sulfonate by Gordonia sp. strain NB4-1Y under sulfur-limiting conditions. Sci Total Environ. 2019;647:690-8. doi: 10.1016/j.scitotenv.2018.08.012.

Huang S, Jaffé PR. Defluorination of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) by Acidimicrobium sp. Strain A6. Environ Sci Technol. 2019;53(19):11410-19. doi: 10.1021/acs.est.9b04047.

Yu Y, Zhang K, Li Z, Ren C, Chen J, Lin Y.-H, Liu J, Men Y. Microbial cleavage of c–f bonds in two C6 Per- and polyfluorinated compounds via reductive defluorination. Environ Sci Technol. 2020;54(22):14393-402. doi: 10.1021/acs.est.0c04483.

Ruiz-Urigüen M, Shuai W., Huang S, Jaffé PR. Biodegradation of PFOA in microbial electrolysis cells by Acidimicrobiaceae sp. strain A6. Chem. 2022;292:133506. doi: 10.1016/j.chemosphere.2021.133506.

Kwon BG, Lim H-J, Na S-H, Choi B-I, Shin D-S, Chung S-Y. Biodegradation of perfluorooctanesulfonate (PFOS) as an emerging contaminant. Chemosphere. 2014;109:221-5. doi: 10.1016/j.chemosphere.2014.01.072.

Yi LB, Chai LY, Xie Y, Peng QJ, Peng QZ. Isolation, identification, and degradation performance of a PFOA-degrading strain. Genet Mol Res. 2016;15:235-46. doi: 10.4238/gmr.15028043.

Beškoski VP, Yamamoto A, Nakano T, Yamamoto K, Matsumura C, Motegi M, Beškoski LS, Inui H. Defluorination of perfluoroalkyl acids is followed by production of monofluorinated fatty acids. Sci Total Environ. 2018;636:355-59. doi: 10.1016/j.scitotenv.2018.04.243.

Chiriac FL, Stoica C, Iftode C, Pirvu F, Petre VA, Paun I, Pascu LF, Vasile GG, Nita-Lazar M. Bacterial biodegradation of perfluorooctanoic acid (PFOA) and perfluorosulfonic acid (PFOS) using pure Pseudomonas strains. Sustainability. 2023;15(18):14000. doi: 10.3390/su151814000.

Zhang Z, Sarkar D, Biswas JK, Datta R. Biodegradation of per- and polyfluoroalkyl substances (PFAS): a review. Bioresource Technol. 2022;344:126223. doi: 10.1016/j.biortech.2021.126223.

Kiel M, Engesser KH. The biodegradation vs. biotransformation of fluorosubstituted aromatics. App Microbiol Biotechnol. 2015;99:7433-64. doi: 10.1007/s00253-015-6817-5.

Nogales J, García JL, Díaz E. Degradation of aromatic compounds in Pseudomonas: A systems biology view. In: Rojo F, ed. Aerobic Utilization of Hydrocarbons, Oils and Lipids: Handbook of Hydrocarbon and Lipid Microbiology. Cham, Switzerland: Springer: 2017. P. 1-49.

Yi L, Tang C, Peng Q , Peng Q, Chai L. Draft genome sequence of perfluorooctane acid-degrading bacterium Pseudomonas parafulva YAB-1. Genome Announc. 2015; 3: e00935–e00915. doi: 10.1128/genomeA.00935-15.

Harris J, Gross M, Kemball J, Farajollahi S, Dennis P, Sitko J, Steel JJ, Almand E, Kelley-Loughnane N, Varaljay VA. Draft genome sequence of the bacterium Delftia acidovorans Strain D4B isolated from soil. Microbiol Resour Announc. 2021;10(44):e0063521. doi: 10.1128/MRA.00635-21.

Spaan KM, van Noordenburg C, Plassmann MM, Schultes L, Shaw S, Berger M, Heide-Jørgensen MP, Rosing-Asvid A, Granquist SM, Dietz R, Sonne C, Rigét F, Roos A, Benskin JP. Fluorine mass balance and suspect screening in marine mammals from the northern hemisphere. Environ Sci Technol. 2020;54(7):4046-8. doi: 10.1021/acs.est.9b06773.

Brendel S, Fetter É, Staude C, Vierke L, Biegel-Engler A. Short-chain perfluoroalkyl acids: environmental concerns and a regulatory strategy under REACH. Environ Sci Eur. 2018;30(1): 9. doi: 10.1186/s12302-018-0134-4.

Li F, Duan J, Tian S, Ji H, Zhu Y, Wei Z, Zhao D. Short-chain per- and polyfluoroalkyl substances in aquatic systems: occurrence, impacts and treatment. Chem Engen J. 2020; 380:122506. doi: 10.1016/j.cej.2019.122506.

Sambrook J, Russell DW. Purification of nucleic acids by extraction with phenol:chloroform. Cold Spring Harb Protoc. 2006; 2006(1):pdb.prot4455. doi: 10.1101/pdb.prot4455.

Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014;30(15):2114-20. doi: 10.1093/bioinformatics/btu170.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, Lesin V, Nikolenko S, Pham S, Prjibelski A, Pyshkin A, Sirotkin A, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455-77. doi: 10.1089/cmb.2012.0021.

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9:357-359. doi: 10.1038/nmeth.1923.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014; 9: e112963. doi: 10.1371/journal.pone.0112963. eCollection 2014.

Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antoine Van Leeuwenhoek. 2017;110(10):1281-6. doi: 10.1007/s10482-017-0844-4.

Meier-Kolthoff JP, Sardà Carbasse J, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucl Acid Res. 2022;50(D1):D801-7. doi: 10.1093/nar/gkab902.

Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068-9. doi: 10.1093/bioinformatics/btu153.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10. doi: 10.1016/S0022-2836(05)80360-2.

Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol. 2015;32:2798-800. doi: 10.1093/molbev/msv150.

Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat. 1972;6:645-67.

Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucl Acids Res. 2021;49:W293-6. doi: 10.1093/nar/gkab301.

Meier-Kolthoff JP, Goker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10:2182. doi: 10.1038/s41467-019-10210-3.

Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk H-P. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genom Sci. 2014;9:2. doi: 10.1186/1944-3277-9-2. eCollection 2014.

Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016;66:1100-3. doi: 10.1099/ijsem.0.000760.

Raymond RL. Microbial oxidation of n-paraffinic hydrocarbons. Dev Ind Microbiol. 1961;2:23-54.

Bertani G. Studies on lysogenesis I. J Bacteriol. 1951;62:293-300. doi: 10.1128/jb.62.3.293-300.1951.

Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M , Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, Van Oeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL. Introducing the bacterial and viral bioinformatics resource center (BV-BRC): A resource combining PATRIC, IRD and ViPR. Nucl Acids Res. 2023; 51:D678-89. doi: 10.1093/nar/gkac1003.

Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018;68:461-6. doi: 10.1099/ijsem.0.002516.

Marchetto F, Roverso M, Righetti D, Bogialli S, Filippini F, Bergantino E, Sforza E. Bioremediation of per- and poly-fluoroalkyl substances (PFAS) by Synechocystis sp. PCC 6803: A chassis for a synthetic biology approach. Life. 2021;11:1300. /doi: 10.3390/life11121300.

Li Y, Yue Y, Zhang H, Yang Z, Wang H, Tian S, Wang J, Zhang Q, Wang W. Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: In silico and in vitro approach. Environ Int. 2019;131: 104999. doi: 10.1016/j.envint.2019.104999.

Trang B, Li Y, Xue XS, Ateia M, Houk KN, Dichtel WR. Low-temperature mineralization of perfluorocarboxylic acids. Science. 2022;377(6608):839-45. doi: 10.1126/science.abm8868.

Park C, Shin B, Park W. Protective role of bacterial alkanesulfonate monooxygenase under oxidative stress. App Environ Microbiol. 2020;86(15):e00692-20. doi: 10.1128/AEM.00692-20.

Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol. 2022;24(11):5082-104. doi: 10.1111/1462-2920.16110.

Wackett LP. Pseudomonas: versatile biocatalysts for PFAS. Environ Microbiol. 2022;24(7):2882-9. doi: 10.1111/1462-2920.15990.

Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS. Pseudomonas genome database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucl Acids Res. 2009; 37:D483-8. doi: 10.1093/nar/gkn861.

Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA, Brinkman FS. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucl Acids Res. 2016;44:D646-53. doi: 10.1093/nar/gkv1227.

Luz AL, Anderson JK, Goodrum P, Durda J. Perfluorohexanoic acid toxicity, part I: Development of a chronic human health toxicity value for use in risk assessment. Regul Toxicol Pharmacol. 2019;103:41-55. doi: 10.1016/j.yrtph.2019.01.019.

Zango ZU, Ethiraj B, Al-Mubaddel FS, Alam MM, Lawal MA, Kadir HA, Khoo KS, Garba ZN, Usman F, Zango MU, Lim JW. An overview on human exposure, toxicity, solid-phase microextraction and adsorptive removal of perfluoroalkyl carboxylic acids (PFCAs) from water matrices. Environ Res. 2023;231(Pt.2):116102. doi: 10.1016/j.envres.2023.116102.

Han JS, Jang S, Son HY, Kim YB, Kim Y, Noh JH, Kim MJ, Lee BS. Subacute dermal toxicity of perfluoroalkyl carboxylic acids: comparison with different carbon-chain lengths in human skin equivalents and systemic effects of perfluoroheptanoic acid in Sprague Dawley rats. Arch Toxicol. 2020;94(2):523-39. doi: 10.1007/s00204-019-02634-z.




DOI: http://dx.doi.org/10.24855/biosfera.v17i1.955

© ФОНД НАУЧНЫХ ИССЛЕДОВАНИЙ "XXI ВЕК"