Advertisement

Ecotoxicology

, Volume 25, Issue 1, pp 234–247 | Cite as

Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C

  • Wenyang Wu
  • Haiying Huang
  • Zhenmin Ling
  • Zhengsheng Yu
  • Yiming Jiang
  • Pu Liu
  • Xiangkai LiEmail author
Article

Abstract

Strain LZ-C, isolated from a petrochemical wastewater discharge site, was found to be resistant to heavy metals and to degrade various aromatic compounds, including naphenol, naphthalene, 2-methylnaphthalene and toluene. Data obtained from 16S rRNA gene sequencing showed that this strain was closely related to Delftia lacustris. The 5,889,360 bp genome of strain LZ-C was assembled into 239 contigs and 197 scaffolds containing 5855 predicted open reading frames (ORFs). Among these predicted ORFs, 464 were different from the type strain of Delftia. The minimal inhibitory concentrations were 4 mM, 30 µM, 2 mM and 1 mM for Cr(VI), Hg(II), Cd(II) and Pb(II), respectively. Both genome sequencing and quantitative real-time PCR data revealed that genes related to Chr, Czc and Mer family genes play important roles in heavy metal resistance in strain LZ-C. In addition, the Na+/H+ antiporter NhaA is important for adaptation to high salinity resistance (2.5 M NaCl). The complete pathways of benzene and benzoate degradation were identified through KEGG analysis. Interestingly, strain LZ-C also degrades naphthalene but lacks the key naphthalene degradation gene NahA. Thus, we propose that strain LZ-C exhibits a novel protein with a function similar to NahA. This study is the first to reveal the mechanisms of heavy metal resistance and salinity tolerance in D. lacustris and to identify a potential 2-methylnaphthalene degradation protein in this strain. Through whole-genome sequencing analysis, strain LZ-C might be a good candidate for the bioremediation of heavy metals and polycyclic aromatic hydrocarbons.

Keywords

Delftia lacustris Genome sequencing Heavy metal resistance Polycyclic aromatic hydrocarbons 

Notes

Acknowledgments

This research was supported by a National Natural Science Foundation Grants 31470224, 31200085, MOST international cooperation Grant 2014DFA91340 and Gansu Provincial International Cooperation Grant 134WCGA176.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10646_2015_1583_MOESM1_ESM.tif (958 kb)
Cell growth over a range of temperatures (A) and pH values (B) (TIFF 957 kb)
10646_2015_1583_MOESM2_ESM.tif (40.2 mb)
COG functional classification. The total number of classification is based on the 5204 COG assignments across the 5179 protein-coding genes with at least one COG assignment. Within the COG category, not comprises hypothetical protein-coding and RNA genes (TIFF 41213 kb)
10646_2015_1583_MOESM3_ESM.tif (22.8 mb)
Global gene conservation in Delftia. Each circle represents the total number of gene types in each genome. Overlapping regions depict the number of genes types shared between the respective genomes. The numbers outside the circles indicate the total number of genes identified in each genome, including paralogs and gene duplications. Abbreviations: CCUG 15835, Delftia acidovorans CCUG 15835; CCUG 274B, Delftia acidovorans CCUG 274B; Cs1-4, Delftia sp. Cs1-4; SPH-1, Delftia acidovorans SPH-1 (TIFF 23312 kb)
10646_2015_1583_MOESM4_ESM.tif (25.4 mb)
The LZ-C genome was compared with other Delftia genomes. Dot plots were constructed using MUMmer 3.22 software, and nucleotide-based alignments were performed with MUMmer. The dot plots were generated using the MUMmerplot script and the gnuplot program (www.gnuplot.info/docs_4.0/gnuplot.html). The aligned segments are represented as dots or lines. Forward matches are shown in red, and reverse complement matches are shown in blue. Abbreviations: CCUG 15835, Delftia acidovorans CCUG 15835; CCUG 274B, Delftia acidovorans CCUG 274B; Cs1-4, Delftia sp. Cs1-4; SPH-1, Delftia acidovorans SPH-1 (TIFF 26060 kb)
10646_2015_1583_MOESM5_ESM.xlsx (25 kb)
The unique genes in LZ-C compared to other Delftia strains (XLSX 25 kb)
10646_2015_1583_MOESM6_ESM.xlsx (10 kb)
High salt tolerance genes identified in strain LZ-C (XLSX 9 kb)
10646_2015_1583_MOESM7_ESM.xlsx (13 kb)
Heavy metal resistance genes identified in strain LZ-C (XLSX 13 kb)

References

  1. Aguilar-Barajas E, Paluscio E, Cervantes C, Rensing C (2008) Expression of chromate resistance genes from Shewanella sp. strain ANA-3 in Escherichia coli. FEMS Microbiol Lett 285:97–100CrossRefGoogle Scholar
  2. Alisi C, Musella R, Tasso F, Ubaldi C, Manzo S, Cremisini C, Sprocati AR (2009) Bioremediation of diesel oil in a co-contaminated soil by bioaugmentation with a microbial formula tailored with native strains selected for heavy metals resistance. Sci Total Environ 407(8):3024–3032CrossRefGoogle Scholar
  3. Antonio Ventosa JJN, Oren Aharon (1998) Biology of Moderately Halophilic Aerobic Bacteria. Microbiol Mol Biol Rev 62(2):504–544Google Scholar
  4. Banerjee A, Ghoshal AK (2011) Phenol degradation performance by isolated Bacillus cereus immobilized in alginate. Int Biodeterior Biodegrad 65(7):1052–1060. doi: 10.1016/j.ibiod.2011.04.011 CrossRefGoogle Scholar
  5. Baquero F, Martínez J-L, Cantón R (2008) Antibiotics and antibiotic resistance in water environments. Curr Opin Biotechnol 19(3):260–265CrossRefGoogle Scholar
  6. Bautista-Hernández DA (2012) Zinc and Lead biosorption by Delftia tsuruhatensis: A bacterial strain resistant to metals isolated from mine tailings. J Water Res Prot. doi: 10.4236/jwarp.2012.44023 Google Scholar
  7. Boscha Rafael, García-Valdés E, Moore ERB (1999) Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene 236(1):149–157CrossRefGoogle Scholar
  8. Brown N, Shih Y, Leang C, Glendinning K, Hobman J, Wilson J (2002) Mercury transport and resistance. Biochem Soc Trans 30(4):715CrossRefGoogle Scholar
  9. Busenlehner LS, Pennella MA, Giedroc DP (2003) The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance. FEMS Microbiol Rev 27:131–143. doi: 10.1016/S0168-6445(03)00054-8 CrossRefGoogle Scholar
  10. Calo D, Guan Z, Naparstek S, Eichler J (2011) Different routes to the same ending: comparing the N-glycosylation processes of Haloferax volcanii and Haloarcula marismortui, two halophilic archaea from the Dead Sea. Mol Microbiol 81(5):1166–1177CrossRefGoogle Scholar
  11. Choudhury R, Srivastava S (2001) Zinc resistance mechanisms in bacteria. Curr Sci 81(7):768–775Google Scholar
  12. Delcher AL, Salzberg SL, Phillippy AM (2003) Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinform. doi: 10.1002/0471250953.bi1003s00 Google Scholar
  13. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6):673–679. doi: 10.1093/bioinformatics/btm009 CrossRefGoogle Scholar
  14. Derraik JG (2002) The pollution of the marine environment by plastic debris: a review. Mar Pollut Bull 44(9):842–852CrossRefGoogle Scholar
  15. Dua M, Singh A, Sethunathan N, Johri AK (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59:143–152. doi: 10.1007/s00253-002-1024-6 CrossRefGoogle Scholar
  16. Fu B, Chen L (1995) Landscape diversity types and their ecological significance. Di li xue bao/Chung-kuo ti li hsueh hui pien chi 51:454–462Google Scholar
  17. Gao H, Zhou L, Ma M-Q, Chen X-G, Hu Z-D (2004) Composition and source of unknown organic pollutants in atmospheric particulates of the Xigu District, Lanzhou, People’s Republic of China. Bull Environl Contam Toxicol 72(5):923–930Google Scholar
  18. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA (2014) Human and environmental impacts on river sediment microbial communities. PloS One. doi: 10.1371/journal.pone.0097435 Google Scholar
  19. Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11(3):236–243CrossRefGoogle Scholar
  20. Giller KE, Witter E, Mcgrath SP (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol Biochem 30(10):1389–1414CrossRefGoogle Scholar
  21. Gristina AG (1987) Biomaterial-centered infection: microbial adhesion versus tissue integration. Science 237:1588–1595CrossRefGoogle Scholar
  22. Groning JA, Eulberg D, Tischler D, Kaschabek SR, Schlomann M (2014) Gene redundancy of two-component (chloro)phenol hydroxylases in Rhodococcus opacus 1CP. FEMS Microbiol Lett 361(1):68–75. doi: 10.1111/1574-6968.12616 CrossRefGoogle Scholar
  23. Guzik U, Hupert-Kocurek K, Sitnik M, Wojcieszyńska D (2013) High activity catechol 1, 2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis, cis-muconic acid production. Antonie van Leeuwenhoek 103:1297–1307CrossRefGoogle Scholar
  24. Hobman JL, Julian DJ, Brown NL (2012) Cysteine coordination of Pb(II) is involved in the PbrR-dependent activation of the lead-resistance promoter, PpbrA, from Cupriavidus metallidurans CH34. BMC Microbiol 12(1):109. doi: 10.1186/1471-2180-12-109 CrossRefGoogle Scholar
  25. Huaiman C, Chunrong Z, Shenqiang W and Cong T (2000) Combined pollution and pollution index of heavy metals in red soil. PedosphereGoogle Scholar
  26. Huyuan Zhang QZ, Yang Bo, Wang Jinfang (2014) Compacted Sewage sludge as a barrier for tailings: the heavy metal speciation and total organic carbon content in the compacted sludge specimen. PloS One. doi: 10.1371/journal.pone.0100932.t001 Google Scholar
  27. Intorne AC, de Oliveira MVV, de M Pereira L, de Souza Filho GA (2012) Essential role of the czc determinant for cadmium, cobalt and zinc resistance in Gluconacetobacter diazotrophicus PAl 5. Int Microbiol 15(2):69–78. doi: 10.2436/20.1501.01.160 Google Scholar
  28. Jain S, Bhatt A (2013) Molecular and in situ characterization of cadmium-resistant diversified extremophilic strains of Pseudomonas for their bioremediation potential. 3Biotech 4(3):297–304. doi: 10.1007/s13205-013-0155-z Google Scholar
  29. Jinlong N, Faqiang L, Lin H, Yuanyuan J, Xuehong D, Yuanjun S (2012) Advanced treatment technology of the COD of chemical outward-discharged wastewater. Ind Water Treat 8:021Google Scholar
  30. Joutey NT, Bahafid W, Sayel H, Ananou S, El Ghachtouli N (2014) Hexavalent chromium removal by a novel Serratia proteamaculans isolated from the bank of Sebou River (Morocco). Environ Sci Pollut Res Int 21(4):3060–3072. doi: 10.1007/s11356-013-2249-x CrossRefGoogle Scholar
  31. Jurelevicius D, Alvarez VM, Peixoto R, Rosado AS, Seldin L (2012) Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHD) encoding genes in different soils from King George Bay, Antarctic Peninsula. Appl Soil Ecol 55:1–9. doi: 10.1016/j.apsoil.2011.12.008 CrossRefGoogle Scholar
  32. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:109–114Google Scholar
  33. Kauppi B (1998) Structure of an aromatic-ring-hydroxylation dioxygenase-naphthalene 1, 2-dioxygenases. Structure 6(5):571–586CrossRefGoogle Scholar
  34. Korf I, Gish W (2000) MPBLAST: improved BLAST performance with multiplexed queries. Bioinformatics 16(11):1052–1053CrossRefGoogle Scholar
  35. Kulkarni M, Chaudhari A (2007) Microbial remediation of nitro-aromatic compounds: an overview. J Environ Manag 85(2):496–512CrossRefGoogle Scholar
  36. Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9(4):299–306. doi: 10.1093/Bib/Bbn017 CrossRefGoogle Scholar
  37. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108. doi: 10.1093/nar/gkm160 CrossRefGoogle Scholar
  38. Lalitha S (2000) Primer premier 5. Biotech Softw Internet Rep 1(6):270–272CrossRefGoogle Scholar
  39. Lee S-W, Glickmann E, Cooksey DA (2001) Chromosomal locus for cadmium resistance in Pseudomonas putida consisting of a cadmium-transporting ATPase and a MerR family response regulator. Appl Environ Microbiol 67(4):1437–1444CrossRefGoogle Scholar
  40. Leedjärv A, Ivask A, Virta M (2008) Interplay of different transporters in the mediation of divalent heavy metal resistance in Pseudomonas putida KT2440. J Bacteriol 190(8):2680–2689CrossRefGoogle Scholar
  41. Liu C, Xu J, Liu C, Zhang P, Dai M (2009) Heavy metals in the surface sediments in Lanzhou Reach of Yellow River, China. Bull Environ Contam Toxicol 82(1):26–30CrossRefGoogle Scholar
  42. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964CrossRefGoogle Scholar
  43. Ma Y, Galinski EA, Grant WD, Oren A, Ventosa A (2010) Halophiles 2010: life in saline environments. Appl Environ Microbiol 76(21):6971–6981. doi: 10.1128/AEM.01868-10 CrossRefGoogle Scholar
  44. Mager T, Rimon A, Padan E, Fendler K (2011) Transport mechanism and pH regulation of the Na+/H+ antiporter NhaA from Escherichia coli: an electrophysiological study. J Biol Chem 286(26):23570–23581. doi: 10.1074/jbc.M111.230235 CrossRefGoogle Scholar
  45. Margesin R, Schinner F (2001) Biodegradation and bioremediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol 56:650–663. doi: 10.1007/s002530100701 CrossRefGoogle Scholar
  46. Monsieurs P, Moors H, Van Houdt R, Janssen PJ, Janssen A, Coninx I, Mergeay M, Leys N (2011) Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 24(6):1133–1151CrossRefGoogle Scholar
  47. Morais PV, Branco R, Francisco R (2011) Chromium resistance strategies and toxicity: what makes Ochrobactrum tritici 5bvl1 a strain highly resistant. Biometals 24(3):401–410. doi: 10.1007/s10534-011-9446-1 CrossRefGoogle Scholar
  48. Morel MA, Ubalde MC, Braña V, Castro-Sowinski S (2011) Delftia sp. JD2: a potential Cr(VI)-reducing agent with plant growth-promoting activity. Arch Microbiol 193(1):63–68CrossRefGoogle Scholar
  49. Mueller-Spitz S, Crawford K (2014) Silver nanoparticle inhibition of polycyclic aromatic hydrocarbons degradation by Mycobacterium species RJGII-135. Lett Appl Microbiol 58(4):330–337CrossRefGoogle Scholar
  50. Qixing Z (1999) Combined chromium and phenol pollution in a marine prawn fishery. Bull Environl Contam Toxicol 62(4):476–482CrossRefGoogle Scholar
  51. Ramírez-Díaz MI, Díaz-Pérez C, Vargas E, Riveros-Rosas H, Campos-García J, Cervantes C (2008) Mechanisms of bacterial resistance to chromium compounds. Biometals 21(3):321–332CrossRefGoogle Scholar
  52. Saa L, Jaureguibeitia A, Largo E, Llama MJ, Serra JL (2010) Cloning, purification and characterization of two components of phenol hydroxylase from Rhodococcus erythropolis UPV-1. Appl Microbiol Biotechnol 86(1):201–211. doi: 10.1007/s00253-009-2251-x CrossRefGoogle Scholar
  53. Sánchez-Andrea I, Triana D, Sanz JL (2012) Bioremediation of acid mine drainage coupled with domestic wastewater treatment. Water Sci Technol 66(11):2425–2431CrossRefGoogle Scholar
  54. Sedlmeier R, Altenbuchner J (1992) Cloning and DNA-sequence analysis of the mercury resistance genes of Streptomyces-lividans. Mol Gen Genet 236(1):76–85Google Scholar
  55. Shen G, Lu Y, Wang M, Sun Y (2005) Status and fuzzy comprehensive assessment of combined heavy metal and organo-chlorine pesticide pollution in the Taihu Lake region of China. J Environ Manag 76(4):355–362CrossRefGoogle Scholar
  56. Silver S, Phung LT (1996) Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50(1):753–789CrossRefGoogle Scholar
  57. Stearman R, Yuan DS, Yamaguchi-Iwai Y, Klausner RD, Dancis A (1996) A permease-oxidase complex involved in high-affinity iron uptake in yeast. Science 27:1552–1557CrossRefGoogle Scholar
  58. Sundar K, Vidya R, Mukherjee A, Chandrasekaran N (2010) High chromium tolerant bacterial strains from Palar River Basin: Impact of tannery pollution. Res J Environ Earth Sci 2(2):112–117Google Scholar
  59. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62(2):625–630Google Scholar
  60. Swaathy S, Kavitha V, Pravin AS, Mandal AB, Gnanamani A (2014) Microbial surfactant mediated degradation of anthracene in aqueous phase by marine Bacillus licheniformis MTCC 5514. Biotechnol Rep 4:161–170. doi: 10.1016/j.btre.2014.10.004 CrossRefGoogle Scholar
  61. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33–36CrossRefGoogle Scholar
  62. Tikilili PV, Nkhalambayausi-Chirwa EM (2011) Characterization and biodegradation of polycyclic aromatic hydrocarbons in radioactive wastewater. J Hazard Mater 192(3):1589–1596CrossRefGoogle Scholar
  63. Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vlcek C, Cardenas E, Mackova M, Macek T (2012) Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PloS One 7(7):e40653. doi: 10.1371/journal.pone.0040653 CrossRefGoogle Scholar
  64. Umrania VV (2006) Bioremediation of toxic heavy metals using acidothermophilic autotrophes. Bioresour Technol 97(10):1237–1242. doi: 10.1016/j.biortech.2005.04.048 CrossRefGoogle Scholar
  65. Vimont S, Berche P (2000) NhaA, an Na+/H+ antiporter involved in environmental survival of Vibrio cholerae. J Bacteriol 182(10):2937–2944CrossRefGoogle Scholar
  66. Wasay S, Barrington S, Tokunaga S (1998) Remediation of soils polluted by heavy metals using salts of organic acids and chelating agents. Environ Technol 19(4):369–379CrossRefGoogle Scholar
  67. Wu G, Sun M, Liu P, Zhang X, Yu Z, Zheng Z, Chen Y, Li X (2014) Enterococcus faecalis strain LZ-11 isolated from Lanzhou reach of the Yellow River is able to resist and absorb cadmium. J Appl Microbiol 116(5):1172–1180. doi: 10.1111/jam.12460 CrossRefGoogle Scholar
  68. Xu X, Hu H, Dailey AB, Kearney G, Talbott EO, Cook RL (2013) Potential health impacts of heavy metals on HIV-infected population in USA. PloS One. doi: 10.1371/journal.pone.0074288 Google Scholar
  69. Yang LF, Jiang JQ, Zhao BS, Zhang B, Feng DQ, Lu WD, Wang L, Yang SS (2006) A Na+/H+ antiporter gene of the moderately halophilic bacterium Halobacillus dabanensis D-8T: cloning and molecular characterization. FEMS Microbiol Lett 255(1):89–95CrossRefGoogle Scholar
  70. Yu Z, Li J, Li Y, Wang Q, Zhai X, Wu G, Liu P, Li X (2014) A mer operon confers mercury reduction in a Staphylococcus epidermidis strain isolated from Lanzhou reach of the Yellow River. Int Biodeterior Biodegrad 90:57–63CrossRefGoogle Scholar
  71. Yuka Sone RN, Pan-Hou Hidemitsu, Itoh Tomoo, Kiyono Masako (2013) Role of MerC, MerE, MerF, MerT, and/or MerP in resistance to mercurials and the transport of mercurials in Escherichia coli. Biol Pharm Bull 36(11):1835–1841CrossRefGoogle Scholar
  72. Zhang X, Krumholz LR, Yu Z, Chen Y, Liu P, Li X (2013) A novel subspecies of Staphylococcus aureus from sediments of Lanzhou reach of the yellow river aerobically reduces hexavalent chromium. J Biorem Biodegrad 4:4Google Scholar
  73. Zhang X, Wu W, Virgo N, Zou L, Liu P, Li X (2014) Global transcriptome analysis of hexavalent chromium stress responses in Staphylococcus aureus LZ-01. Ecotoxicology 23(8):1534–1545. doi: 10.1007/s10646-014-1294-7 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Wenyang Wu
    • 1
  • Haiying Huang
    • 1
  • Zhenmin Ling
    • 1
  • Zhengsheng Yu
    • 1
  • Yiming Jiang
    • 1
  • Pu Liu
    • 1
  • Xiangkai Li
    • 1
    Email author
  1. 1.MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life SciencesLanzhou UniversityLanzhouPeople’s Republic of China

Personalised recommendations