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Nowoczesne metody badania bioróżnorodności biocenoz bakteryjnych w środowisku

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Warianty tytułu
EN
Modern techniques used for biodiversity analysis in bacterial environmental communities
Konferencja
XIX Konferencja Przemysł Chemiczny : wyzwania i bariery z cyklu restrukturyzacja
Języki publikacji
PL EN
Abstrakty
PL
W analizach biocenoz bakteryjnych coraz powszechniej wykorzystywane są techniki biologii molekularnej. Wśród nich można wyróżnić metodę FISH – fluorescencyjnej hybrydyzacji in situ oraz jej modyfikacje (RING-FISH, Clone-FISH, CARDFISH i MAR-FISH). W artykule opisano też technikę elektroforezy w gradiencie denaturacji (DGGE), bazującą na bakteryjnym markerze molekularnym 16S rRNA oraz cystometrię przepływową. Ze względu na dużą przewagę tych metod nad klasycznymi metodami mikrobiologicznymi, wynikającą między innymi z możliwości analizowania próbek pobieranych bezpośrednio ze środowiska, są one stosowane w biotechnologii środowiskowej, np. w badaniach bakteryjnej biocenozy osadu czynnego, biorącej udział w biologicznym oczyszczaniu ścieków. Możliwe jest również użycie kilku metod, których rezultaty są komplementarne i pozwalają na stworzenie całościowego obrazu badanej biocenozy.
EN
Molecular techniques are very popular in microbial laboratories. Among them FISH- fluorescent in situ hybridization (with modifications like: CARD-FISH, MAR-FISH, RING-FISH, Clone- FISH), DGGE – denaturing gradient gel electrophoresis based on 16S rRNA molecular marker and flow cytometry, are the most popular. These analytical methods are commonly use in bacterial biodiversity research. The analysis can be performed directly on the environmental sample, so these procedures are simpler and faster that traditional ones. Therefore, molecular techniques can be used in aqueous bacterial biocenosis research, such as activated sludge, which takes part in biological wastewater treatment. It is also possible to use a set of molecular methods in order to obtain complimentary results to present total bacterial biocenosis picture.
Czasopismo
Rocznik
Strony
1105--1114
Opis fizyczny
Bibliogr. 44 poz., tab., rys.
Twórcy
autor
  • Katedra Biotechnologii Środowiskowej, Politechnika Śląska, Gliwice
  • Katedra Biotechnologii Środowiskowej, Politechnika Śląska, Gliwice
Bibliografia
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  • 3. Brown T.A.: Genomy. Wydawnictwo Naukowe PWN, 2009.
  • 4. Moraru C.L.: Development of protocols for in situ detection of genes in microorganisms. Master Thesis, University of Bremen and Max Planck International Research School for Marine Microbiology, Bremen 2006.
  • 5. Okabe S., Kinadichi T., Ito T.: MAR-FISH - An Ecophysiological Approach to Link Phylogenetic Affilliation and In Situ Metabolic Activity of Microorganisms at a Single-Cell Resolution. Microbes and Environments 2004, Vol. 19, No. 2, pp. 83-98.
  • 6. Cole J.R., Chai B., Marsh T.L., Farris R.K., Wang Q., Kulam SA, Chandra S., McGarrel D.M., Schmidt T.M., Garrity G., Tiedje J.M.: The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 2003, Vol. 31, No. I, pp. 442-443.
  • 7. Strunk O., Ludwig W: ARB, a software environmental for sequence data. Department of Microbiology, Technical University in Munich, Germany 1999.
  • 8. Van de Peer Y., De Rijk R, Wuyts L., Winkelmans T., De Wachter R: The European small subunit ribosomal RNA database. Nucleic Acids Research 2000, Vol. 28, No. I, pp. 175-176.
  • 9. Maidak B.L., Cole J.R., Parker Jr C.T., Garrity G.M., Larsen N., Li B., Librun T.G., McCaughey M.J., Olsen G.J., Overbeek R, PramanikS., SchmidtT.M., Tiedje J.M., Woese C.R: A new version of the RDP (Ribosomal Database Project). Nucleic Acids Research 1999, Vol. 27, No. I, pp. 171-173.
  • 10. Bohm-Hofstatter H., Tschernutter M., Kunert R.: Comparison of hybridization methods and real - time PCR: their value in animal cell line characterization. Applied Microbiology and Biotechnology 2010, Vol. 87, No. 2, pp. 419-425.
  • 11. Zwirglmaier K., Ludwig W., Schleifer K.H.: Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization - RING-FISH. Molecular Microbiology 2004, Vol. 51, No. I, pp. 89-96.
  • 12. Pernthaler A., Pernthaler J., Amman R.: Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria. Applied and Environmental Microbiology 2002, Vol. 68, No. 6, pp. 3094-3101.
  • 13. Raszka A., Ziembińska A., Wiechetek A.: Metody i techniki biologii molekularnej w biotechnologii środowiskowej. Czasopismo Techniczne 2009, vol. 106, nr. 2, ss. 101-114
  • 14. Schramm A., Fuchs B.M., Nielsen J.L., Tonolla M., Stahl D.A.: Fluorescence in situ hybridization of I6S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environmental Microbiology 2002, Vol. 4, No. 11, pp. 713-720.
  • 15. Peng Y., Zhang S., Zeng W., Zheng S., Mino T., Satoh H.: Organic removal by denitritation and methanogenesis and nitrogen removal by nitritation from landfill leachate. Water Research 2008, Vol. 42, No. 4-5, pp. 883-892.
  • 6. Guerrero J., Guisasola A., Baeza J.A.: The nature of the carbon source rules the competition between PAO and denitriflers in systems for simultaneous biological nitrogen and phosphorus removal. Water Research 2011, Vol. 45, No. 16, pp. 479-4802.
  • 17. Winkler M.-K.H., Bassin J.R, Kleerebezem R., De Bruin L.M.M., Van den Brand T.RH., van Loosdrecht M.C.M.: Selective sludge removal in a segregated aerobic granular biomass system as a strategy to control PAO-GAO competition at high temperatures. Water Research 2011, Vol. 45, pp.3291-3299.
  • 18. Wilén B.-M., Onuki M., Hermansson M., Lumley D., Mino T.: Microbial community structure in activated sludge floe analysed by fluorescence in situ hybridization and its relation to floe stability. Water Research 2008, Vol. 42, pp. 2300-2308.
  • 19. Chelliapan S., Wiłby T., Yuzir A., Sallis RJ.: Influence of organic loading on the performance and microbial community structure of an anaerobic stage reactor treating pharmaceutical wastewater. Desalination 201 I, Vol. 271, pp. 257-264.
  • 20. Degenaar A.R, Ismail A., Bux R: Comparative evaluation of the microbial community in biological processes treating industrial and domestic wastewaters. Journal of Applied Microbiology 2008, Vol. 104, No. 2, pp. 353-363.
  • 21. Phuong K., Hanzaki S., Kakii K., NikataT.: Involvement of Acinetobacter sp. in the floe - formation in activated sludge process. Journal of Biotechnology 2012, Vol. 157, pp. 505-511.
  • 22. De Roy K., Clement L., Thas O., Wang Y., Boon N.: Flow cytometry for fast microbial community fingerprinting. Water Research 2012, Vol. 46, No. 3, pp. 907-919.
  • 23. Lisiecka U., Kostro K., Jarosz L: Cytometria przepływowa jako nowoczesna metoda w diagnostyce i prognozowaniu chorób. Medycyna Weterynaryjna 2006, vol. 62, nr. 9, ss. 998-1001.
  • 24. Álvarez-Barrientos A., Arroyo J., Cantón R., Nombela C., Sánchez-Pérez M: Applications of F'.jw Cytometry to Clinical Microbiology. Clinical Microbiology Reviews 2000, Vol. 13, No. 2, pp. 167-195.
  • 25. Wallner G., Amman R., Beisker W: Optimizing Fluorescent In Situ Hybridization With rRNA-Targeted Oligonucleotide Probes for Flow Cytometric Identification of Microorganisms. Cytometry 1993, Vol. 14, No. 2, pp. 136-43.
  • 26. Michels C.A.: Genetic Techniques for Biological Research. John Wiley & Sons, 2002.
  • 27. Ziglio G., Andreottola G., Barbesti S., Boschetti G., Bruni L., Foladori R, Villa R.: Assessment of activated sludge viability with flow cytometry. Water Research 2002, Vol. 36, No. 2, pp. 460-468.
  • 28. Lencastre Fernandez R., Nierychlo M., Lundin L., Pedersen A.E., Puentes Tellez RE., Dutta A., Carlquist M., Bolic A., Schápper D., Brunetti A.C., Helmark S., Heins A.-L, Jensen A.D., Nopens I., Rottwitt K., Szita N., Van ElsasJ.D., Nielsen RH., MartinussenJ., Sorensen S.J., LantzA.E., Gernaey K.V.: Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnology Advances 2011, Vol. 29, No. 6, pp. 575-599.
  • 29. Foladori R, Bruni L., Tamburini S., Ziglio G.: Direct quantification of bacterial biomass in influent, effluent and activated sludge of wastewater treatment plants by using flow cytometry, Water Research 2010, Vol. 44, pp.3807-3818.
  • 30. Foladori R, Bruni L., Tamburini S.: Bacteria permeabilisation and disruption caused by sludge reduction technologies evaluated by flow cytometry. Water Research 2010, Vol. 44, No. 17, pp. 4888-4899.
  • 31. Muela A., Orruńo M., Alonso M.L., Pazos M., Arana I., Alonso R.M., Jiménez Rosa M., Garaizabal I., Maguregui M.I., Barcina I.: Microbiological parameters as and additional tool to improve wastewater treatment plant monitoring. Ecological Indicators 2011, Vol. 11, No. 2, pp. 431-437.
  • 32. Muyzer G., Smalla K.: Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 1998, Vol. 73, No. I, pp. 127-141.
  • 33. Sheffiled V.C., Cox D.R., Lerman L.S., Myers R.M.: Attachment of a 40-base-pair G+Crich sequence (GC-clamp) to genomic DNA fragments
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  • 34. Muyzer G.: DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology 1999, Vol. 2, No. 3, pp. 317-322.
  • 35. Snaidr J., Amman R., Huber I., Ludwig W., Schleifer K.H.: Phylogenetic Analysis and In Situ Identification of Bacteria in Activated Sludge. Applied and Environmental Microbiology 1997, Vol. 63, No. 7, pp. 2884-2896.
  • 36. Purkhold U., Pommerening-Roser A., Juretschko S., Schmid M.C., Ko-ops H.R, Wagner M.: Phytogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative I6S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys. Applied and Environmental Microbiology 2000, Vol. 66, No. 12, pp. 5368-5382.
  • 37. Crocetti G.R., Hugenholtz R, Bond RL., Schuer A., Keller J., Jenkins D., Blackall L.L.: Identification of Polyphosphate - Accumulating Organisms and Design of 16S rRNA - Directed Probes for Their Detection and Quantitation. Applied and Environmental Microbiology, Vol. 66, No. 3, pp. 1175-1182.
  • 38. Yan S.-T., Zheng H., Li A., Zhang H., Xing X.-H., Chu L.-B., Ding G., Sun X.-L., Jurcik B.: Systematic analysis of biochemical performance and the microbial community of an activated sludge process using ozone - treated sludge for sludge retention. Bioresource Technology 2009, Vol. 100, No. 21, pp. 5002-5009.
  • 39. Laurent J., Jaziri K., Guignard R., Casellas M., Dagot C.: Comprehenisive insight of the performances of excess sludge reduction by 90°C thermal treatment coupled with activated sludge at pilot scale: COD and N removal, bacterial populations, fate of heavy metals. Process Biochemistry 2011, Vol. 46, pp. 1808-1816.
  • 40. Yao Y., Guan J., Tang R, Jiao H., Lin Ch., WangJ., Lu Z., Min H.,Gao H.: Assessment of toxicity of tetrahydrofuran on the microbial community in activated sludge. Bioresource Technology 2010, Vol. 101, No. 14, pp. 523-5221.
  • 41. Chang L., Ali S.W., Li-Bo G., Fang-Bo Y., Shun-Peng L., Wong M.H.: Biotreatment of o-nitrobenzaldehyde manufacturing wastewater and changes in activated sludge floes in a sequencing batch reactor. Bioresource Technology 2012, Vol. 104, pp. 228-234.
  • 42. Hesham A.E-L., Qi R., Yang M.: Comparison of bacterial community structures in two systems of a sewage treatment plant using PCR-DGGE analysis. Journal of Environmental Sciences 2011, Vol. 23, No. 12, pp. 2049-2054.
  • 43. Bin Z., Zhe Ch., Zhigang Q., Min J., Zhigiang Ch., Zhaoli Ch., Junwen L., Xuan W., Jingfeng W.: Dynamic and distribution of ammonia-oxidizing bacteria communities during sludge granulation in an anaerobic-aerobic sequencing batch reactor. Water Research 2011, Vol. 45, pp. 6207%2I6.
  • 44. www.cyto.purdue.edu, 16.12.12.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-e3f1fb3d-20f8-40c7-ad3c-f7fc5a3532db
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