Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay

Microbial Ecology

Volumn 70, Issue 4, 2015, Pages 912-921

  Jung, Jaejoon ^a   Jang, In ae ^a   Ahn, Sungeun ^a   Shin, Bora ^a   Kim, Jisun ^a   Park, Chulwoo ^a   Jee, Seung Cheol ^b   Sung, Jung Suk ^b   Park, Woojun ^a  

^a Korea University   (South Korea)

^b Dongguk University   (South Korea)

Author keywords

Alkane; Bioremediation; Diesel; Red clay; Transcriptome

Indexed keywords

ALKANE; ALUMINUM SILICATE; CARBON; CLAY; N-HEXADECANE; RNA 16S; SOIL POLLUTANT;

ACINETOBACTER; BIOREMEDIATION; BIOTA; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; OXIDATIVE STRESS; SEQUENCE ANALYSIS; SOIL POLLUTANT;

ACINETOBACTER; ALKANES; ALUMINUM SILICATES; BIODEGRADATION, ENVIRONMENTAL; BIOTA; CARBON; OXIDATIVE STRESS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

EID: 84946474082     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-015-0624-5     Document Type: Article

References (41)

1. Throne-Holst M, Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB (2007) Identification of novel genes involved in long-chain n-alkane degradation by Acinetobacter sp. strain DSM 17874. Appl Environ Microbiol 73(10):3327–3332
2. Marín MM, Yuste L, Rojo F (2003) Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa. J Bacteriol 185:3232–3237
3. Liu C, Wang W, Wu Y, Zhou Z, Lai Q, Shao Z (2011) Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5. Environ Microbiol 13:1168–1178
4. Tani A, Ishige T, Sakai Y, Kato N (2001) Gene structures and regulation of the alkane hydroxylase complex in Acinetobacter sp. strain M-1. J Bacteriol 183:1819–1823
5. Hamamura N, Yeager CM, Arp DJ (2001) Two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8. Appl Environ Microbiol 67:4992–4998
6. Smits TH, Balada SB, Witholt B, van Beilen JB (2002) Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. J Bacteriol 184:1733–1742
7. van Beilen JB, Kingma J, Witholt B (1994) Substrate specificity of the alkane hydroxylase system of Pseudomonas oleovorans GPo1. Enzyme Microb Technol 16:904–911
8. van Beilen JB, Neuenschwander M, Smits TH, Roth C, Balada SB, Witholt B (2002) Rubredoxins involved in alkane oxidation. J Bacteriol 184:1722–1732
9. Maier T, Förster HH, Asperger O, Hahn U (2001) Molecular characterization of the 56-kDa CYP153 from Acinetobacter sp. EB104. Biochem Biophys Res Commun 286:652–658
10. Balba MT, Al-Awadhi N, Al-Daher R (1998) Bioremediation of oil-contaminated soil: microbiological methods for feasibility assessment and field evaluation. J Microbiol Methods 32:155–164
11. Jimenez N, Vinas M, Sabate J, Diez S, Bayona JM, Solanas AM, Albaiges J (2006) The Prestige oil spill. 2. Enhanced biodegradation of a heavy fuel oil under field conditions by the use of an oleophilic fertilizer. Environ Sci Technol 40:2578–2585
12. Tyagi M, da Fonseca MM, de Carvalho CC (2011) Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 22:234–241
13. Jung J, Choi S, Hong H, Sung JS, Park W (2014) Effect of red clay on diesel bioremediation and soil bacterial community. Microb Ecol 68:314–323
14. Kang YS, Jung J, Jeon CO, Park W (2011) Acinetobacter oleivorans sp. nov. is capable of adhering to and growing on diesel-oil. J Microbiol 49:29–34
15. Kang YS, Park W (2010) Protection against diesel oil toxicity by sodium chloride-induced exopolysaccharides in Acinetobacter sp. strain DR1. J Biosci Bioeng 109:118–123
16. Kang YS, Park W (2010) Contribution of quorum-sensing system to hexadecane degradation and biofilm formation in Acinetobacter sp. strain DR1. J Appl Microbiol 109:1650–1659
17. Jung J, Noh J, Park W (2011) Physiological and metabolic responses for hexadecane degradation in Acinetobacter oleivorans DR1. J Microbiol 49:208–215
18. Jung J, Madsen EL, Jeon CO, Park W (2011) Comparative genomic analysis of Acinetobacter oleivorans DR1 to determine strain-specific genomic regions and gentisate biodegradation. Appl Environ Microbiol 77:7418–7424
19. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
20. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc., Newark
21. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
22. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
23. Huang Y, Niu B, Gao Y, Fu L, Li W (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26:680–682
24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
25. Han J, Jung J, Hyun S, Park H, Park W (2012) Effects of nutritional input and diesel contamination on soil enzyme activities and microbial communities in Antarctic soils. J Microbiol 50(6):916–924
26. Jung J, Baek JH, Park W (2010) Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1. J Bacteriol 192:4794–4795
27. van Beilen JB, Eggink G, Enequist H, Bos R, Witholt B (1992) DNA sequence determination and functional characterization of the OCT-plasmid-encoded alkJKL genes of Pseudomonas oleovorans. Mol Microbiol 6:3121–3136
28. Hummerjohann J, Küttel E, Quadroni M, Ragaller J, Leisinger T, Kertesz MA (1998) Regulation of the sulfate starvation response in Pseudomonas aeruginosa: role of cysteine biosynthetic intermediates. Microbiology 144:1375–1386
29. Naether A, Foesel BU, Naegele V, Wüst PK, Weinert J, Bonkowski M, Alt F, Oelmann Y, Polle A, Lohaus G, Gockel S, Hemp A, Kalko EK, Linsenmair KE, Pfeiffer S, Renner S, Schöning I, Weisser WW, Wells K, Fischer M, Overmann J, Friedrich MW (2012) Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ Microbiol 78:7398–7406
30. Ponsin V, Coulomb B, Guelorget Y, Maier J, Höhener P (2014) In situ biostimulation of petroleum hydrocarbon degradation by nitrate and phosphate injection using a dipole well configuration. J Contam Hydrol 171C:22–31
31. da Silva AC, de Oliveira FJ, Bernardes DS, de França FP (2009) Bioremediation of marine sediments impacted by petroleum. Appl Biochem Biotechnol 153:58–66
32. Pramanik P, Kim PJ (2013) Effect of limited nickel availability on methane emission from EDTA treated soils: coenzyme M an alternative biomarker for methanogens. Chemosphere 90:873–876
33. Sikora AE, Beyhan S, Bagdasarian M, Yildiz FH, Sandkvist M (2009) Cell envelope perturbation induces oxidative stress and changes in iron homeostasis in Vibrio cholerae. J Bacteriol 191:5398–5408
34. van Beilen JB, Panke S, Lucchini S, Franchini AG, Röthlisberger M, Witholt B (2001) Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147:1621–1630
35. van Beilen JB, Marín MM, Smits TH, Röthlisberger M, Franchini AG, Witholt B, Rojo F (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 6:264–273
36. Kato T, Miyanaga A, Kanaya S, Morikawa M (2009) Alkane inducible proteins in Geobacillus thermoleovorans B23. BMC Microbiol 9:60
37. Allgood GS, Perry JJ (1985) Oxygen defense systems in obligately thermophilic bacteria. Can J Microbiol 31:1006–1010
38. Broadbent JR, Larsen RL, Deibel V, Steele JL (2010) Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress. J Bacteriol 192:2445–2458
39. Pini CV, Bernal P, Godoy P, Ramos JL, Segura A (2009) Cyclopropane fatty acids are involved in organic solvent tolerance but not in acid stress resistance in Pseudomonas putida DOT-T1E. Microb Biotechnol 2:253–261
40. Mykytczuk NC, Trevors JT, Ferroni GD, Leduc LG (2010) Cytoplasmic membrane fluidity and fatty acid composition of Acidithiobacillus ferrooxidans in response to pH stress. Extremophiles 14:427–441
41. Ramos JL, Duque E, Gallegos MT, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A (2002) Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 56:743–768