The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity


Autoři: Mouna Mahjoubi aff001;  Habibu Aliyu aff002;  Simone Cappello aff003;  Mohamed Naifer aff001;  Yasmine Souissi aff001;  Don A. Cowan aff004;  Ameur Cherif aff001
Působiště autorů: Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, Ariana, Tunisia aff001;  Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany aff002;  Istituto per l’Ambiente Marino Costiero (IAMC)-CNR of Messina. Sp. San Raineri, Messina, Italy aff003;  Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa aff004
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0221574

Souhrn

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

Klíčová slova:

Comparative genomics – Crude oil – Genome annotation – Hydrocarbons – Pollution – Ribosomal RNA – Benzoates – Bioremediation


Zdroje

1. Jiang Z, Huang Y, Xu X, Liao Y, Shou L, Liu J, et al. Advance in the toxic effects of petroleum water accommodated fraction on marine plankton. Acta Ecologica Sinica. 2010;30(1):8–15. doi: 10.1016/j.chnaes.2009.12.002

2. Niazy Z, Hassanshahian M, Ataei A. Isolation and characterization of diesel-degrading Pseudomonas strains from diesel-contaminated soils in Iran (Fars province). Pollution. 2016;2(1):67–75. doi: 10.7508/PJ.2016.01.007

3. Cappello S, Genovese M, Denaro R, Santisi S, Volta A, Bonsignore M, et al. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS2003 on microcosm oil spill simulation. Brazilian Journal of Microbiology. 2014;45(4):1317–23. doi: 10.1590/s1517-83822014000400023 25763036

4. Crisafi F, Genovese M, Smedile F, Russo D, Catalfamo M, Yakimov M, et al. Bioremediation technologies for polluted seawater sampled after an oil-spill in Taranto Gulf (Italy): A comparison of biostimulation, bioaugmentation and use of a washing agent in microcosm studies. Marine pollution bulletin. 2016;106(1–2):119–26. doi: 10.1016/j.marpolbul.2016.03.017 26992747

5. Genovese M, Crisafi F, Denaro R, Cappello S, Russo D, Calogero R, et al. Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation. Frontiers in microbiology. 2014;5:162. doi: 10.3389/fmicb.2014.00162 24782850

6. Head IM, Jones DM, Röling WF. Marine microorganisms make a meal of oil. Nature Reviews Microbiology. 2006;4(3):173. doi: 10.1038/nrmicro1348 16489346

7. Joo H-S, Hirai M, Shoda M. Piggery wastewater treatment using Alcaligenes faecalis strain No. 4 with heterotrophic nitrification and aerobic denitrification. Water Research. 2006;40(16):3029–36. doi: 10.1016/j.watres.2006.06.021 16893560

8. Ju S, Zheng J, Lin J, Geng C, Zhu L, Guan Z, et al. The complete genome sequence of Alcaligenes faecalis ZD02, a novel potential bionematocide. Journal of biotechnology. 2016;218:73–4. doi: 10.1016/j.jbiotec.2015.12.001 26656226

9. Euzeby J. Subspecies Names Automatically Created by Rule 46. International Journal of Systematic and Evolutionary Microbiology. 1996;46(3):830–.

10. Schroll G, Busse H-J, Parrer G, Rölleke S, Lubitz W, Denner EB. Alcaligenes faecalis subsp. parafaecalis subsp. nov., a Bacterium Accumulating Poly-β-hydroxybutyrate from Acetone-butanol Bioprocess Residues. Systematic and applied microbiology. 2001;24(1):37–43. 11403397

11. Rehfuss M, Urban J. Alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor. Systematic and applied microbiology. 2005;28(5):421–9. doi: 10.1016/j.syapm.2005.03.003 16094869

12. Van Trappen S, Tan T-L, Samyn E, Vandamme P. Alcaligenes aquatilis sp. nov., a novel bacterium from sediments of the Weser Estuary, Germany, and a salt marsh on Shem Creek in Charleston Harbor, USA. International journal of systematic and evolutionary microbiology. 2005;55(6):2571–5. doi: 10.1099/ijs.0.63849–0

13. Lu C-Y, Li Y-Q, Tian Y, Han M-X, Rao MPN, Li Y-R, et al. Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium. International journal of systematic and evolutionary microbiology. 2017;67(4):939–43. doi: 10.1099/ijsem.0.001719 27959788

14. Abbas S, Ahmed I, Iida T, Lee Y-J, Busse H-J, Fujiwara T, et al. A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan. Antonie Van Leeuwenhoek. 2015;108(4):859–70. doi: 10.1007/s10482-015-0540-1 26238381

15. Liu X, Huang D, Wu J, Yu C, Zhou R, Liu C, et al. The genome sequence of Alcaligenes faecalis NBIB-017 contains genes with potentially high activities against Erwinia carotovora. Genome announcements. 2016;4(2):e00222–16. doi: 10.1128/genomeA.00222-16 27056227

16. Nakano M, Niwa M, Nishimura N. Development of a PCR-based method for monitoring the status of Alcaligenes species in the agricultural environment. Biocontrol science. 2014;19(1):23–31. doi: 10.4265/bio.19.23 24670615

17. Pan X, Lin D, Zheng Y, Zhang Q, Yin Y, Cai L, et al. Biodegradation of DDT by Stenotrophomonas sp. DDT-1: characterization and genome functional analysis. Scientific reports. 2016;6:21332. doi: 10.1038/srep21332 26888254

18. Magthalin CJ, Varadharajan A, Swarnalatha S, Sekaran G. Cationic dispersant immobilized matrix for sequestering Cr (III) from contaminated soil. Materials Today: Proceedings. 2016;3(10):3697–702. doi: 10.1016/j.matpr.2016.11.015

19. Durán RE, Barra-Sanhueza B, Salvà-Serra F, Méndez V, Jaén-Luchoro D, Moore ERB, et al. Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile. Microbiology Resource Announcements. 2019;8(5):e01664–18. doi: 10.1128/MRA.01664-18 30714040

20. Durán RE, Méndez V, Rodríguez-Castro L, Barra-Sanhueza B, Salvà-Serra F, Moore ER, et al. Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors. Frontiers in microbiology. 2019;10:528. doi: 10.3389/fmicb.2019.00528 31024465

21. Santisi S, Cappello S, Catalfamo M, Mancini G, Hassanshahian M, Genovese L, et al. Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium. Brazilian Journal of Microbiology. 2015;46(2):377–87. doi: 10.1590/S1517-838246120131276 26273252

22. Hassanshahian M, Emtiazi G, Caruso G, Cappello S. Bioremediation (bioaugmentation/biostimulation) trials of oil polluted seawater: a mesocosm simulation study. Marine environmental research. 2014;95:28–38. doi: 10.1016/j.marenvres.2013.12.010 24388285

23. Pinzon NM, Ju L-K. Analysis of rhamnolipid biosurfactants by methylene blue complexation. Applied microbiology and biotechnology. 2009;82(5):975–81. doi: 10.1007/s00253-009-1896-9 19214498

24. Youssef NH, Duncan KE, Nagle DP, Savage KN, Knapp RM, McInerney MJ. Comparison of methods to detect biosurfactant production by diverse microorganisms. Journal of microbiological methods. 2004;56(3):339–47. doi: 10.1016/j.mimet.2003.11.001 14967225

25. Mahjoubi M, Jaouani A, Guesmi A, Amor SB, Jouini A, Cherif H, et al. Hydrocarbonoclastic bacteria isolated from petroleum contaminated sites in Tunisia: isolation, identification and characterization of the biotechnological potential. New biotechnology. 2013;30(6):723–33. doi: 10.1016/j.nbt.2013.03.004 23541698

26. Stanton S, Meyer JJM, Van der Merwe CF. An evaluation of the endophytic colonies present in pathogenic and non-pathogenic Vanguerieae using electron microscopy. South African journal of botany. 2013;86:41–5. doi: 10.1016/j.sajb.2013.01.007

27. Kalman S, Kiehne KL, Libs JL, Yamamoto T. Cloning of a novel cryIC-type gene from a strain of Bacillus thuringiensis subsp. galleriae. Appl Environ Microbiol. 1993;59(4):1131–7. 8476286

28. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology. 2012;19(5):455–77. doi: 10.1089/cmb.2012.0021 22506599

29. Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8. doi: 10.1093/nar/gkm160 17452365

30. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International journal of systematic and evolutionary microbiology. 2017;67(5):1613–7. doi: 10.1099/ijsem.0.001755 28005526

31. Katoh K, Standley DM. MAFFT: iterative refinement and additional methods. Multiple Sequence Alignment Methods: Springer; 2014. p. 131–46.

32. Silla-Martínez JM, Capella-Gutiérrez S, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–3. doi: 10.1093/bioinformatics/btp348 19505945

33. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013;14(1):1–14. doi: 10.1186/1471-2105-14-60 23432962

34. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016;66(2):1100–3. doi: 10.1099/ijsem.0.000760 26585518

35. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC genomics. 2008;9(1):75. doi: 10.1186/1471-2164-9-75 18261238

36. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic acids research. 2008;36(suppl_2):W181–W4. doi: 10.1093/nar/gkn179 18411202

37. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9. doi: 10.1093/bioinformatics/btu153 24642063

38. Afgan E, Baker D, Van den Beek M, Blankenberg D, Bouvier D, Čech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic acids research. 2016;44(W1):W3–W10. doi: 10.1093/nar/gkw343 27137889

39. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009–10. doi: 10.1093/bioinformatics/btr039 21278367

40. Abd-Elsalam HE, Hafez EE, Hussain AA, Ali AG, El-Hanafy AA. Isolation and identification of three-rings polyaromatic hydrocarbons (anthracene and phenanthrene) degrading bacteria. Am Eurasian J Agric Environ Sci. 2009;5:31–8.

41. Singha LP, Kotoky R, Pandey P. Draft Genome Sequence of Alcaligenes faecalis BDB4, a Polyaromatic Hydrocarbon-Degrading Bacterium Isolated from Crude Oil-Contaminated Soil. Genome announcements. 2017;5(48):e01346–17. doi: 10.1128/genomeA.01346-17 29192081

42. Pal S, Kundu A, Banerjee TD, Mohapatra B, Roy A, Manna R, et al. Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment. Genomics. 2017;109(5–6):374–82. doi: 10.1016/j.ygeno.2017.06.002 28625866

43. Rocha EP, Cornet E, Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS genetics. 2005;1(2):e15. doi: 10.1371/journal.pgen.0010015 16132081

44. Almagro G, Viale AM, Montero M, Rahimpour M, Muñoz FJ, Baroja-Fernández E, et al. Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales. PLOS ONE. 2015;10(1):e0115516. doi: 10.1371/journal.pone.0115516 25607991

45. Paliwal V, Raju SC, Modak A, Phale PS, Purohit HJ. Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation. PLoS One. 2014;9(1):e84000. doi: 10.1371/journal.pone.0084000 24475028

46. Rani S, Jeon WJ, Koh H-W, Kim Y-E, Kang M-S, Park S-J. Genomic potential of Marinobacter salinus Hb8 T as sulfur oxidizing and aromatic hydrocarbon degrading bacterium. Marine Genomics. 2017;34:19–21. doi: 10.1016/j.margen.2017.02.005

47. Macchi M, Martinez M, Tauil RN, Valacco M, Morelli I, Coppotelli B. Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation. World Journal of Microbiology and Biotechnology. 2018;34(1):7. doi: 10.1007/s11274-017-2391-6 29214360

48. Seo J-S, Keum Y-S, Li QX. Bacterial degradation of aromatic compounds. International journal of environmental research and public health. 2009;6(1):278–309. doi: 10.3390/ijerph6010278 19440284

49. Yamanashi T, Kim S-Y, Hara H, Funa N. In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1. Bioscience, biotechnology, and biochemistry. 2015;79(5):830–5. doi: 10.1080/09168451.2014.993915 25558786

50. Serrano AE, Escudero LV, Tebes-Cayo C, Acosta M, Encalada O, Fernández-Moroso S, et al. First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. Standards in genomic sciences. 2017;12(1):43. doi: 10.1186/s40793-017-0252-4 28770028


Článek vyšel v časopise

PLOS One


2019 Číslo 9

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Léčba bolesti v ordinaci praktického lékaře
nový kurz
Autoři: MUDr. PhDr. Zdeňka Nováková, Ph.D.

Revmatoidní artritida: včas a k cíli
Autoři: MUDr. Heřman Mann

Jistoty a nástrahy antikoagulační léčby aneb kardiolog - neurolog - farmakolog - nefrolog - právník diskutují
Autoři: doc. MUDr. Štěpán Havránek, Ph.D., prof. MUDr. Roman Herzig, Ph.D., doc. MUDr. Karel Urbánek, Ph.D., prim. MUDr. Jan Vachek, MUDr. et Mgr. Jolana Těšínová, Ph.D.

Léčba akutní pooperační bolesti
Autoři: doc. MUDr. Jiří Málek, CSc.

Nové antipsychotikum kariprazin v léčbě schizofrenie
Autoři: prof. MUDr. Cyril Höschl, DrSc., FRCPsych.

Všechny kurzy
Kurzy Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se