Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Phân hủy benzen trong phản ứng sinh học biofilm khử nitrat: hoạt động và thành phần cộng đồng vi sinh vật
Tóm tắt
Benzen là một hợp chất thơm và có hại cho môi trường. Việc phân hủy sinh học benzen có thể giảm thiểu rủi ro độc hại sau khi xảy ra sự cố hoặc thải bỏ có kiểm soát hóa chất này vào môi trường. Trong nghiên cứu này, chúng tôi đã xác định thêm đặc điểm của một văn hóa biofilm liên tục kỵ khí được nuôi trồng trong hơn 14 năm trên benzen với nitrat làm chất nhận electron. Chúng tôi đã xác định tỷ lệ phân hủy ổn định, động lực thành phần cộng đồng vi sinh vật trong biofilm và các phản ứng phân hủy benzen kỵ khí ban đầu. Benzen đã được phân hủy với tỷ lệ 0,15 μmol/mg protein/ngày và hằng số tỷ lệ bậc nhất là 3,04/ngày, cao gấp bốn lần so với các tỷ lệ đã được báo cáo trước đó. Vi khuẩn thuộc họ Peptococcaceae được phát hiện đóng vai trò quan trọng trong văn hóa biofilm phân hủy benzen kỵ khí này, nhưng cũng có các thành viên của họ Anaerolineaceae được dự đoán tham gia vào quá trình phân hủy benzen hoặc phân hủy các sản phẩm chuyển hóa của benzen được dựa trên phân tích gene RNA ribosome 16S bằng công nghệ Illumina MiSeq. Việc giữ lại sinh khối trong bể phản ứng sử dụng ngón lọc đã dẫn đến sự giảm khả năng phân hủy benzen. Sự phát hiện gene mã hóa enzyme carboxylase benzen, abcA, và axit benzoic trong bể nuôi cấy cho thấy quá trình phân hủy benzen diễn ra thông qua một bước carboxyl hóa ban đầu.
Từ khóa
#benzen #phân hủy sinh học #biofilm kỵ khí #vi sinh vật #quần xã vi sinhTài liệu tham khảo
Abu Laban N, Selesi D, Jobelius C, Meckenstock RU (2009) Anaerobic benzene degradation by gram-positive sulfate-reducing bacteria. FEMS Microbiol Ecol 68:300–311. doi:10.1111/j.1574-6941.2009.00672.x
Abu Laban N, Selesi D, Rattei T, Tischler P, Meckenstock RU (2010) Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture. Environ Microbiol 12:2783–2796. doi:10.1111/j.1462-2920.2010.02248.x
Arai H, Akahira S, Ohishi T, Maeda M, Kudo T (1998) Adaptation of Comamonas testosteroni TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. Microbiology 144:2895–2903. doi:10.1099/00221287-144-10-2895
Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, JM Stams A, Springael D, Dejonghe W, Smidt H (2016) Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol. doi:10.1111/1462-2920.13531
Beller HR, Kane SR, Legler TC, Alvarez PJJ (2002) A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ Sci Technol 36:3977–3984. doi:10.1021/es025556w
Burland SM, Edwards EA (1999) Anaerobic benzene biodegradation linked to nitrate reduction. Appl Environ Microbiol 65:529–533
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303
Chakraborty R, Coates JD (2005) Hydroxylation and carboxylation—two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB. Appl Environ Microbiol 71:5427–5432. doi:10.1128/aem.71.9.5427-5432.2005
Chen K-F, Chang Y-C, Huang S-C (2012) Biodegradation potential of MTBE and BTEX under aerobic, nitrate reducing, and methanogenic conditions at a gasoline-contaminated site. Desalin Water Treat 48:278–284. doi:10.1080/19443994.2012.698825
Coates JD, Chakraborty R, Lack JG, O’Connor SM, Cole KA, Bender KS, Achenbach LA (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039–1043
Dou J, Liu X, Hu Z (2008a) Anaerobic BTEX degradation in soil bioaugmented with mixed consortia under nitrate reducing conditions. J Environ Sci 20:585–592. doi:10.1016/S1001-0742(08)62098-7
Dou J, Liu X, Hu Z, Deng D (2008b) Anaerobic BTEX biodegradation linked to nitrate and sulfate reduction. J Hazard Mater 151:720–729. doi:10.1016/j.jhazmat.2007.06.043
Dou J, Ding A, Liu X, Du Y, Deng D, Wang J (2010) Anaerobic benzene biodegradation by a pure bacterial culture of Bacillus cereus under nitrate reducing conditions. J Environ Sci 22:709–715. doi:10.1016/S1001-0742(09)60167-4
Ercan O, Bisschops MMM, Overkamp W, Jørgensen TR, Ram AF, Smid EJ, Pronk JT, Kuipers OP, Daran-Lapujade P, Kleerebezem M (2015) Physiological and transcriptional responses of different industrial microbes at near-zero specific growth rates. Appl Environ Microbiol 81:5662–5670. doi:10.1128/aem.00944-15
Faith DP (2006) The role of the phylogenetic diversity measure, PD, in bio-informatics: getting the definition right. Evol Bioinformatics Online 2:277–283
Gottschal JC (1993) Growth kinetics and competition —some contemporary comments. Antonie Van Leeuwenhoek 63:299–313. doi:10.1007/bf00871225
Helmus R, Brock OP, Carboni A, Prantl SM, van Leeuwen JA, Gerritse J, Parsons JR, de Voogt P (2016) Identification strategy for transformation products of environmental pollutants using UHPLC-QTOF. In: Nontarget 2016, Ascona
Herrmann S, Kleinsteuber S, Chatzinotas A, Kuppardt S, Lueders T, Richnow H-H, Vogt C (2010) Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol 12:401–411. doi:10.1111/j.1462-2920.2009.02077.x
Kasai Y, Takahata Y, Manefield M, Watanabe K (2006) RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater. Appl Environ Microbiol 72:3586–3592. doi:10.1128/aem.72.5.3586-3592.2006
Kjelleberg S, Albertson N, Flärdh K, Holmquist L, Jouper-Jaan Å, Marouga R, Östling J, Svenblad B, Weichart D (1993) How do non-differentiating bacteria adapt to starvation? Antonie Van Leeuwenhoek 63:333–341. doi:10.1007/bf00871228
Kleinsteuber S, Schleinitz KM, Breitfeld J, Harms H, Richnow HH, Vogt C (2008) Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions. FEMS Microbiol Ecol 66:143–157. doi:10.1111/j.1574-6941.2008.00536.x
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–1291. doi:10.1093/bioinformatics/btm091
Kümmel S, Herbst F-A, Bahr A, Duarte M, Pieper DH, Jehmlich N, Seifert J, von Bergen M, Bombach P, Richnow HH, Vogt C (2015) Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers. FEMS Microbiol Ecol 91. doi:10.1093/femsec/fiv006
Kunapuli U, Lueders T, Meckenstock RU (2007) The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J 1:643–653
Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics:115–175
Liang B, Wang L-Y, Mbadinga SM, Liu J-F, Yang S-Z, Gu J-D, Mu B-Z (2015) Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation. AMB Express 5:37. doi:10.1186/s13568-015-0117-4
Liou JSC, DeRito CM, Madsen EL (2008) Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ Microbiol 10:1964–1977. doi:10.1111/j.1462-2920.2008.01612.x
Lovley DR (1997) Potential for anaerobic bioremediation of BTEX in petroleum-contaminated aquifers. J Ind Microbiol Biotechnol 18:75–81. doi:10.1038/sj.jim.2900246
Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275
Lueders T (2017) The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. FEMS Microbiol Ecol 93. doi:10.1093/femsec/fiw220
Luo F, Gitiafroz R, Devine CE, Gong Y, Hug LA, Raskin L, Edwards EA (2014) Metatranscriptome of an anaerobic benzene-degrading, nitrate-reducing enrichment culture reveals involvement of carboxylation in benzene ring activation. Appl Environ Microbiol 80:4095–4107. doi:10.1128/aem.00717-14
Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM (2016) Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. J Mol Microbiol Biotechnol 26:92–118
Milo R (2013) What is the total number of protein molecules per cell volume? A call to rethink some published values. BioEssays 35:1050–1055. doi:10.1002/bies.201300066
Muyzer G, Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci Technol 32:1–9. doi:10.1016/0273-1223(96)00001-7
Nales M, Butler BJ, Edwards EA (1998) Anaerobic benzene biodegradation: a microcosm survey. Bioremediat J 2:125–144. doi:10.1080/10889869891214268
Nielsen PH (1987) Biofilm dynamics and kinetics during high-rate sulfate reduction under anaerobic conditions. Appl Environ Microbiol 53:27–32
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41:D590–D596. doi:10.1093/nar/gks1219
Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A (2013) Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J 7:2178–2191. doi:10.1038/ismej.2013.83
Ramiro-Garcia J, Hermes G, Giatsis C, Sipkema D, Zoetendal E, Schaap P, Smidt H (2016) NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes [version 1; referees: 2 approved with reservations, 1 not approved] vol 5. vol 1791
Rittmann BE, McCarty PL (1980) Model of steady-state-biofilm kinetics. Biotechnol Bioeng 22:2343–2357. doi:10.1002/bit.260221110
da Rocha UN, van Elsas JD, van Overbeek LS (2010) Real-time PCR detection of Holophagae (Acidobacteria) and Verrucomicrobia subdivision 1 groups in bulk and leek (Allium porrum) rhizosphere soils. J Microbiol Methods 83:141–148. doi:10.1016/j.mimet.2010.08.003
Rosenkranz F, Cabrol L, Carballa M, Donoso-Bravo A, Cruz L, Ruiz-Filippi G, Chamy R, Lema JM (2013) Relationship between phenol degradation efficiency and microbial community structure in an anaerobic SBR. Water Res 47:6739–6749. doi:10.1016/j.watres.2013.09.004
Ruan M-Y, Liang B, Mbadinga SM, Zhou L, Wang L-Y, Liu J-F, Gu J-D, Mu B-Z (2016) Molecular diversity of bacterial bamA gene involved in anaerobic degradation of aromatic hydrocarbons in mesophilic petroleum reservoirs. Int Biodeterior Biodegradation 114:122–128. doi:10.1016/j.ibiod.2016.06.005
Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G, Lapidus A (2009) Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics 10:351–351. doi:10.1186/1471-2164-10-351
Schut F, de Vries EJ, Gottschal JC, Robertson BR, Harder W, Prins RA, Button DK (1993) Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl Environ Microbiol 59:2150–2160
Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851. doi:10.1099/ijs.0.02699-0
Staats M, Braster M, Röling WFM (2011) Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume. Environ Microbiol 13:1216–1227. doi:10.1111/j.1462-2920.2010.02421.x
Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. BioTechniques 28(1102):1104
Strous M, Heijnen JJ, Kuenen JG, Jetten MSM (1998) The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms. Appl Microbiol Biotechnol 50:589–596. doi:10.1007/s002530051340
Suarez MP, Rifai HS (1999) Biodegradation rates for fuel hydrocarbons and chlorinated solvents in groundwater. Bioremediat J 3:337–362. doi:10.1080/10889869991219433
Sun W, Cupples AM (2012) Diversity of five anaerobic toluene-degrading microbial communities investigated using stable isotope probing. Appl Environ Microbiol 78:972–980. doi:10.1128/aem.06770-11
Sutton NB, Maphosa F, Morillo JA, Abu Al-Soud W, Langenhoff AAM, Grotenhuis T, Rijnaarts HHM, Smidt H (2013) Impact of long-term diesel contamination on soil microbial community structure. Appl Environ Microbiol 79:619–630. doi:10.1128/aem.02747-12
Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, Buscot F, Richnow H-H, von Bergen M, Seifert J (2012) Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J 6:2291–2301 http://www.nature.com/ismej/journal/v6/n12/suppinfo/ismej201268s1.html
Tian L, Scholte J, Borewicz K, van den Bogert B, Smidt H, Scheurink AJW, Gruppen H, Schols HA (2016) Effects of pectin supplementation on the fermentation patterns of different structural carbohydrates in rats. Mol Nutr Food Res:n/a-n/a doi:10.1002/mnfr.201600149
Ulrich AC, Edwards EA (2003) Physiological and molecular characterization of anaerobic benzene-degrading mixed cultures. Environ Microbiol 5:92–102. doi:10.1046/j.1462-2920.2003.00390.x
Ulrich AC, Beller HR, Edwards EA (2005) Metabolites detected during biodegradation of 13C6-benzene in nitrate-reducing and methanogenic enrichment cultures. Environ Sci Technol 39:6681–6691. doi:10.1021/es050294u
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucl Acids Res 40:e115. doi:10.1093/nar/gks596
Van Verseveld HW, De Hollander JA, Frankena J, Braster M, Leeuwerik FJ, Stouthamer AH (1986) Modeling of microbial substrate conversion, growth and product formation in a recycling fermentor. Antonie Van Leeuwenhoek 52:325–342. doi:10.1007/bf00428644
Vogt C, Kleinsteuber S, Richnow HH (2011) Anaerobic benzene degradation by bacteria. Microb Biotechnol 4:710–724. doi:10.1111/j.1751-7915.2011.00260.x
Weelink S (2008) Degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria. Wageningen University, Dissertation
Winderl C, Anneser B, Griebler C, Meckenstock RU, Lueders T (2008) Depth-resolved quantification of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl Environ Microbiol 74:792–801. doi:10.1128/aem.01951-07
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56:1331–1340. doi:10.1099/ijs.0.64169-0
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134. doi:10.1186/1471-2105-13-134
van der Zaan BM, Saia FT, Stams AJ, Plugge CM, de Vos WM, Smidt H, Langenhoff AA, Gerritse J (2012) Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae as dominant benzene degraders and evidence for a syntrophic process. Environ Microbiol 14:1171–1181. doi:10.1111/j.1462-2920.2012.02697.x