Simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. after their exposure to petroleum hydrocarbons

Journal of Microbiological Methods

Volumn 94, Issue 2, 2013, Pages 135-140

  Kuyukina, Maria S ^a,b   Ivshina, Irena B ^a,b   Serebrennikova, Marina K ^a   Rubtsova, Ekaterina V ^a,b   Krivoruchko, Anastasiya V ^a,b  

^a INSTITUTE OF ECOLOGY AND GENETICS OF MICROORGANISMS   (Russian Federation)

^b PERM STATE UNIVERSITY   (Russian Federation)

Author keywords

16S rDNA targeted PCR; Cryogel immobilized bacteria; Petroleum hydrocarbons; Respirometry; Rhodococcus; Viability testing

Indexed keywords

ALCOHOL; DNA 16S; PETROLEUM DERIVATIVE; POLYVINYL ALCOHOL;

ARTICLE; BACTERIAL SURVIVAL; BACTERIAL VIABILITY; BACTERIUM DETECTION; CONTROLLED STUDY; CRYOGEL; NONHUMAN; OXIDATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESPIROMETRY; RHODOCOCCUS; RHODOCOCCUS OPACUS; RHODOCOCCUS RUBER; SPECTROPHOTOMETRY; STRAIN DIFFERENCE;

16S RDNA-TARGETED PCR; CRYOGEL-IMMOBILIZED BACTERIA; PETROLEUM HYDROCARBONS; RESPIROMETRY; RHODOCOCCUS; VIABILITY TESTING;

CELLS, IMMOBILIZED; HYDROCARBONS; MICROBIAL VIABILITY; PETROLEUM; POLYMERASE CHAIN REACTION; POLYVINYL ALCOHOL; RHODOCOCCUS; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); RHODOCOCCUS; RHODOCOCCUS OPACUS; RHODOCOCCUS RUBER;

EID: 84879712491     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2013.05.016     Document Type: Article

References (25)

1. Bell K.S., Kuyukina M.S., Heidbrink S., Philp J.C., Aw D.W.J., Ivshina I.B., Christofi N. Identification and environmental detection of Rhodococcus species by 16S rDNA-targeted PCR. J. Appl. Microbiol. 1999, 87:472-480.
2. Caravelli A., Giannuzzi L., Zaritzky N. Effect of chlorine on filamentous microorganisms present in activated sludge as evaluated by respirometry and INT-dehydrogenase activity. Water Res. 2004, 38:2395-2405.
3. Cassidy M.B., Lee H., Trevors J.T. Environmental applications of immobilized microbial cells: a review. J. Ind. Microbiol. 1996, 16:79-101.
4. Clifford R.J., Milillo M., Prestwood J., Quintero R., Zurawski D.V., Kwak Y.I., Waterman P.E., Lesho E.P., Mc Gann P. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PLoS One 2012, 7(11):e48558. 10.1371/journal.pone.0048558.
5. De Vos P., Bučko M., Gemeiner P., Navrátil M., Švitel J., Faas M., Strand B.L., Skjak-Braek G., Morch Y.A., Vikartovská A., Lacík I., Kolláriková G., Orive G., Poncelet D., Pedraz J.L., Ansorge-Schumacher M.B. Multiscale requirements for bioencapsulation in medicine and biotechnology. Biomaterials 2009, 30:2559-2570.
6. Errampalli D., Tresse O., Lee H., Trevors J.T. Bacterial survival and mineralization of p-nitrophenol in soil by green fluorescent protein-marked Moraxella sp. G21 encapsulated cells. FEMS Microbiol. Ecol. 1999, 30:229-236.
7. Hiura T., Hashidoko Y., Kobayashi Y., Tahara S. Effective degradation of tannic acid by immobilized rumen microbes of a sika deer (Cervus nippon yesoensis) in winter. Anim. Feed Sci. Technol. 2010, 155:1-8.
8. Jézéquel K., Lebeau T. Soil bioaugmentation by free and immobilized bacteria to reduce potentially phytoavailable cadmium. Bioresour. Technol. 2008, 99:690-698.
9. Khattak S.F., Spatara M., Roberts L., Roberts S.C. Application of colorimetric assays to assess viability, growth and metabolism of hydrogel-encapsulated cells. Biotechnol. Lett. 2006, 28:1361-1370.
10. Kim C.-W., Koopman B., Bitton G. INT-dehydrogenase activity test for assessing chlorine and hydrogen peroxide inhibition of filamentous pure cultures and activated sludge. Water Res. 1994, 28:1117-1121.
11. Kuyukina M.S., Ivshina I.B. Application of Rhodococcus in bioremediation of contaminated environments. Microbiology Monographs 2010, vol. 16:231-262. Springer-Verlag, Berlin, Heidelberg. H.M. Alvarez (Ed.).
12. Kuyukina M.S., Ivshina I.B., Gavrin A.Yu., Podorozhko E.A., Lozinsky V.I., Jeffree C.E., Philp J.C. Immobilization of hydrocarbon-oxidizing bacteria in poly(vinyl alcohol) cryogels hydrophobized using a biosurfactant. J. Microbiol. Methods 2006, 65:596-603.
13. Kuyukina M.S., Ivshina I.B., Serebrennikova M.K., Krivorutchko A.V., Podorozhko E.A., Ivanov R.V., Lozinsky V.I. Petroleum-contaminated water treatment in a fluidized-bed bioreactor with immobilized Rhodococcus cells. Int. Biodeterior. Biodegrad. 2009, 63:427-432.
14. Kuyukina M.S., Ivshina I.B., Kamenskikh T.N., Bulicheva M.V., Stukova G.I. Survival of cryogel-immobilized Rhodococcus cells in crude oil-contaminated soil and their impact on biodegradation efficiency. Int. Biodeterior. Biodegrad. 2012, 10.1016/j.ibiod.2012.05.035.
15. Larcher S., Yargeau V. Biodegradation of sulfamethoxazole by individual and mixed bacteria. Appl. Microbiol. Biotechnol. 2011, 91:211-218.
16. Larkin M.J., Kulakov L.A., Allen C.C.R. Biodegradation and Rhodococcus - masters of catabolic versatility. Curr. Opin. Biotechnol. 2005, 16:282-290.
17. Lozinsky V.I. Cryogels on the basis of natural and synthetic polymers: preparation, properties and areas of implementation. Russ. Chem. Rev. 2002, 71:489-511.
18. Matsuki T., Watanabe K., Fujimoto J., Kado Y., Takada T., Matsumoto K., Tanaka R. Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl. Environ. Microbiol. 2004, 70:167-173.
19. Mikesková H., Novotný Č., Svobodová K. Interspecific interactions in mixed microbial cultures in a biodegradation perspective. Appl. Microbiol. Biotechnol. 2012, 95:861-870.
20. Rathore S., Desai P.M., Liew C.V., Chan L.W., Heng P.W.S. Microencapsulation of microbial cells. J. Food Eng. 2013, 116:369-381.
21. Rodrigues J.L.M., Aiello M.R., Urbance J.W., Tsoi T.V., Tiedje J.M. Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. J. Microbiol. Methods 2002, 51:181-189.
22. Van der Geize R., Dijkhuizen L. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 2004, 7:255-261.
23. Walker J.D., Colwell R.R. Microbial petroleum degradation: use of mixed hydrocarbon substrates. Appl. Environ. Microbiol. 1974, 27:1053-1060.
24. Warhurst A.M., Fewson C.A. Biotransformations catalyzed by the genus Rhodococcus. Crit. Rev. Biotechnol. 1994, 14:29-73.
25. Wrenn B.A., Venosa A.D. Selective enumeration of aromatic and aliphatic hydrocarbon-degrading bacteria by a most-probable number procedure. Can. J. Microbiol. 1996, 42:252-258.