Structural and Kinetic Characteristics of 1,4-Dioxane-Degrading Bacterial Consortia Containing the Phylum TM7 |
Nam, Ji-Hyun
(Department of Environmental Engineering and Energy, Myongji University)
Ventura, Jey-R S. (Department of Engineering Science, College of Engineering and Agro-Industrial Technology, University of the Philippines) Yeom, Ick Tae (Department of Civil and Environmental Engineering, Sungkyunkwan University) Lee, Yongwoo (Department of Chemistry and Applied Chemistry, College of Science and Technology, Hanyang University) Jahng, Deokjin (Department of Environmental Engineering and Energy, Myongji University) |
1 | Dinis JM, Barton DE, Ghadiri J, Surendar D, Reddy K, Velasquez F, et al. 2011. In search of an uncultured humanassociated TM7 bacterium in the environment. PLoS One 6: e21280. DOI |
2 | Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. DOI |
3 | Findlay M, Smoler D, Fogel S. 2007. Dioxane-degrading propanotrophs for in-situ remediation. In: Battelle Conference: In Situ and On-Site Bioremediation Symposium, Baltimore, Maryland, USA. |
4 | Gedalanga PB, Pornwongthong P, Mora R, Chiang SY, Baldwin B, Ogles D, Mahendra S. 2014. Identification of biomarker genes to predict biodegradation of 1,4-dioxane. Appl. Environ. Microbiol. 80: 3209-3218. DOI |
5 | Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York, USA. |
6 | Parales RE, Adamus JE, White N, May HD. 1994. Degradation of 1,4-dioxane by an actinomycete in pure culture. Appl. Environ. Microbiol. 60: 4527-4530. |
7 | Popoola AV. 1992. Mechanism of reaction involving the formation of dioxane byproduct during the production of poly(ethylene terephthalate). J. Appl. Polym. Sci. 43: 1875-1877. |
8 | Roy D, Anagnostu G, Chaphalkar P. 1994. Biodegradation of dioxane and diglyme in industrial waste. J. Environ. Sci. Health A Environ. Sci. Eng. 29: 129-147. |
9 | Sei K, Miyagaki K, Kakinoki T, Fukugasako K, Inoue D, Ike M. 2013. Isolation and characterization of bacterial strains that have high ability to degrade 1,4-dioxane as a sole carbon and energy source. Biodegradation 24: 665-674. DOI |
10 | Sei K, Kakinoki T, Inoue D, Soda S, Fujita M, Ike M. 2010. Evaluation of the biodegradation potential of 1,4-dioxane in river, soil and activated sludge samples. Biodegradation 21: 585-591. DOI |
11 | So MH, Han JS, Han TH, Seo JW, Kim CG. 2009. Decomposition of 1,4-dioxane by photo-Fenton oxidation coupled with activated sludge in a polyester manufacturing process. Water Sci. Technol. 59: 1003-1009. DOI |
12 | 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. DOI |
13 | Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. DOI |
14 | Bernhardt D, Diekmann H. 1991. Degradation of dioxane, tetrahydrofuran and other cyclic ethers by an environmental Rhodococcus strain. Appl. Microbiol. Biotechnol. 36: 120-123. DOI |
15 | Grady CPL, Sock SM, Cowan RM. 1997. Biotreatability kinetics. Biotechnology in the Sustainable Environment. In Sayler GS, Sanseverino J, Davis KL (eds.). Plenum Press, New York, USA. |
16 | Gomez-Gil L, Kumar P, Barriault D, Bolin JT, Sylvestre M, Eltis LD. 2007. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J. Bacteriol. 189: 5705-5715. DOI |
17 | Garrity GM, Brenner DJ, Krieg NR, Staley JT. 2005. Bergey's Manual of Systematic Bacteriology; Volume Two: The Proteobacteria; Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. Springer, New York, USA. |
18 | Han JS, So MH, Kim CG. 2009. Optimization of biological wastewater treatment conditions for 1,4-dioxane decomposition in polyester manufacturing processes. Water Sci. Technol. 59: 995-1002. DOI |
19 | Alonso-Gutierrez J, Figueras A, Albaiges J, Jimenez N, Vinas M, Solanas AM, Novoa B. 2009. Bacterial communities from shoreline environments (Costa da Morte, Northwestern Spain) affected by the Prestige oil spill. Appl. Environ. Microbiol. 75: 3407-3418. DOI |
20 | Hanada A, Kurogi T, Giang NM, Yamada T, Kamimoto Y, Kiso Y, Hiraishi A. 2014. Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors. Microbes Environ. 29: 353-362. DOI |
21 | Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67: 411-419. DOI |
22 | Zenker MJ, Borden RC, Barlaz MA. 2003. Occurrence and treatment of 1,4-dioxane in aqueous environments. Environ. Eng. Sci. 20: 423-432. DOI |
23 | Vainberg S, McClay K, Masuda H, Root D, Condee C, Zylstra GJ, Steffan RJ. 2006. Biodegradation of ether pollutants by Pseudonocardia sp. strain ENV478. Appl. Environ. Microbiol. 72: 5218-5224. DOI |
24 | Winsley TJ, Snape I, McKinlay J, Stark J, van Dorst JM, Ji M, et al. 2014. The ecological controls on the prevalence of candidate division TM7 in polar regions. Front. Microbiol. 5: Article 345. |
25 | Xie S , Sun W, Luo C , Cupples AM. 2011. Novel a erobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation 22: 71-81. DOI |
26 | Zenker MJ, Borden RC, Barlaz MA. 2000. Mineralization of 1,4-dioxane in the presence of a structural analog. Biodegradation 11: 239-246. DOI |
27 | Zenker MJ, Borden RC, Barlaz MA. 2002. Modeling cometabolism of cyclic ethers. Environ. Eng. Sci. 19: 215-228. DOI |
28 | Zenker MJ, Borden RC, Barlaz MA. 2004. Biodegradation of 1,4-dioxane using trickling filter. J. Environ. Eng. 130: 926-931. DOI |
29 | Kim YM, Jeon JR, Murugesan K, Kim EJ, Chang YS. 2009. Biodegradation of 1,4-dioxane and transformation of related cyclic compounds by a newly isolated Mycobacterium sp. PH-06. Biodegradation 20: 511-519. DOI |
30 | Kampfer P, Kohlweyer U, Thiemer B, Andreesen JR. 2006. Pseudonocardia tetrahydrofuranoxydans sp. nov. Int. J. Syst. Evol. Microbiol. 56: 1535-1538. DOI |
31 | Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. DOI |
32 | Kohlweyer U, Thiemer B, Schrader T, Andreesen JR. 2000. Tetrahydrofuran degradation by a newly isolated culture of Pseudonocardia sp. strain K1. FEMS Microbiol. Lett. 186: 301-306. DOI |
33 | Krieg NR, Parte A, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, et al. 2011. Bergey's Manual of Systematic Bacteriology: Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer Science & Business Media. |
34 | Lane DJ. 1991. 16S/23S rRNA sequencing, pp. 115-175. In Stackebrandt E, Goodfellow M (eds.). Nucleic Acid Techniques In Bacterial Systematics. John Wiley and Sons, Chichester, UK. |
35 | Laplante K, Sebastien B, Derome N. 2013. Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation. Evol. Appl. 6: 643-659. DOI |
36 | Leahy JG, Batchelor PJ, Morcomb SM. 2003. Evolution of the soluble diiron monooxygenases. FEMS Microbiol. Rev. 27: 449-479. DOI |
37 | Li M, Mathieu J, Yang Y, Fiorenza S, Deng Y, He Z, et al. 2013. Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4- dioxane. Environ. Sci. Technol. 47: 9950-9958. DOI |
38 | Luo C, Xie S, Sun W, Li X, Cupples AM. 2009. Identification of a novel toluene-degrading bacterium from the candidate phylum TM7, as determined by DNA stable isotope probing. Appl. Environ. Microbiol. 75: 4644-4647. DOI |
39 | Lippincott D, Streger SH, Schaefer CE, Hinkle J, Stormo J, Steffan RJ. 2015. Bioaugmentation and propane biosparging for In Situ Biodegradation Of 1,4-dioxane. Ground Water Monit. Remediat. 35: 81-92. DOI |
40 | Liz JAZE, Jan-Roblero J, de la Serna JZD, de Leon AVP, Hernandez-Rodriguez C. 2009. Degradation of polychlorinated biphenyl (PCB) by a consortium obtained from a contaminated soil composed of Brevibacterium, Pandoraea and Ochrobactrum. World J. Microbiol. Biotechnol. 25: 165-170. DOI |
41 | Mahendra S, Alvarez-Cohen L. 2005. Pseudonocardia dioxanivorans sp nov., a novel actinomycete that grows on 1,4-dioxane. Int. J. Syst. Evol. Microbiol. 55: 593-598. DOI |
42 | Mahendra S, Alvarez-Cohen L. 2006. Kinetics of 1,4-dioxane biodegradation by monooxygenase-expressing bacteria. Environ. Sci. Technol. 40: 5435-5442. DOI |
43 | Mohr TKG. 2001. Solvent Stabilizers. Santa Clara Valley Water District, San Jose, California, USA. |
44 | Coleman NV, Bui NB, Holmes AJ. 2006. Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments. Environ. Microbiol. 8: 1228-1239. DOI |
45 | Mohr TKG, Stickney JA, DiGuiseppi WH. 2010. Environmental Investigation and Remediation: 1,4-Dioxane and Other Solvent Stabilizers. CRC Press, Boca Raton, Florida, USA. |
46 | Muyzer G, De Waal EC, Uitterlinden AG. 1993. Profiling o f complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700. |
47 | Nakamiya K, Hashimoto S, Ito H, Edmonds JS, Morita M. 2005. Degradation of 1,4-dioxane and cyclic ethers by an isolated fungus. Appl. Environ. Microbiol. 71: 1254-1258. DOI |
48 | Burback BL, Perry JJ. 1993. Biodegradation and biotransformation of groundwater pollutant mixtures by Mycobacterium vaccae. Appl. Environ. Microbiol. 59: 1025-1029. |
49 |
Coleman HM, Vimonses V, Leslie G, Amal R. 2007. Degradation of 1,4-dioxane in water using |
50 | Connon SA, Tovanabootr A, Dolan M, Vergin K, Giovannoni SJ, Semprini L. 2005. Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethenecontaminated groundwater. Environ. Microbiol. 7: 165-178. DOI |
51 | Ding GC, Heuer H, Smalla K. 2012. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Front. Microbiol. 3: Article 290. |
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