Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects

• Autorzy: Otlewska A. , Adamiak J. , Gutarowska B.
• Języki publikacji: EN

Abstrakty

EN

 As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2014
• Tom: 61
• Numer: 2
• Opis fizyczny: p.217-225,fig.,ref.

Twórcy

autor

Otlewska A.

• Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland

autor

Adamiak J.

• Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland

autor

Gutarowska B.

• Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland

Bibliografia

• Abdel-Haliem ME, Sakr AA, Ali MF, Ghaly MF, Sohlenkamp C (2013) Characterization of Streptomyces isolates causing colour changes of mural paintings in ancient Egyptian tombs. Microbiol Res 168: 428-437. 
• Alisi C (2011) Biodegradation and biorestoration of stone manufacts. Letture di Georisorse e Ambiente 3: 94-109.
• Atkins SD, Clark IM (2004) Fungal molecular diagnostics: a mini review. J Appl Genet 45: 3-15. 
• Cappitelli F, Abbruscato P, Foladori P, Zanardini E, Ranalli G, Principi P, Villa F, Polo A, Sorlini C (2009) Detection and elimination of cyanobacteria from frescoes: the case of the St. Brizio Chapel (Orvieto Cathedral, Italy). Microb Ecol 57: 633-639. 
• Capodicasa S, Fedi S, Porcelli AM, Zannoni D (2010) The microbial community dwelling on a biodeteriorated 16th century painting. Int Biodeterior Biodegradation 64: 727-733.
• Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70: 6147-6156. 
• Carmona N, Laiz L, Gonzalez JM, Garcia-Heras M, Villegas MA, Saiz-Jimenez C (2006) Biodeterioration of historic stained glasses from the Cartuja de Miraflores (Spain). Int Biodeterior Biodegradation 58: 155-161.
• Cetecioglu Z, Ince O, Ince B (2012) Gel electrophoresis based genetic fingerprinting techniques on environmental ecology. In Gel electrophoresis - advanced techniques. Magdeldin S, eds, pp 52-66. InTech, Croatia.
• Ciardo DE, Lucke K, Imhof A, Bloemberg GV, Bottger EC (2010) Systematic internal transcribed spacer sequence analysis for identification of clinical mold isolates in diagnostic mycology: a 5-year study. J Clin Microbiol 48: 2809-2813. 
• Ciardo DE, Schär G, Altwegg M, Böttger EC, Bosshard PP (2007) Identification of moulds in the diagnostic laboratory - an algorithm implementing molecular and phenotypic methods. Diagn Microbiol Infect Dis 59: 49-60. 
• Coutinho ML, Miller AZ, Gutierrez-Patricio S, Hernandez-Marine M, Gomez-Bolea A, Rogerio-Candelera MA, Philips AJL, Jurado V, Saiz-Jimenez C, Macedo MF (2013) Microbial communities on deteriorated artistic tiles from Pena National Palace (Sintra, Portugal). Int Biodeterior Biodegradation 84: 322-332.
• Cuzman OA, Ventura S, Sili C, Mascalchi C, Turchetti T, D'Acqui LP, Tiano P (2010) Biodiversity of phototrophic biofilms dwelling on monumental fountains. Microb Ecol 60: 81-95. 
• Dakal TC, Arora PK (2012) Evaluation of potential of molecular and physical techniques in studying biodeterioration. Rev Environ Sci Biotechnol 11: 71-104.
• De Felice B, Pasquale V, Tancredi N, Scherillo S, Guida M (2010) Genetic fingerprint of microorganisms associated with the deterioration of an historical tuff monument in Italy. J Genet 89: 253-257. 
• Deja-Sikora E, Sikora M, Gołębiewski M, Tretyn A (2007) Biblioteki metagenomowe jako źródło genów przydatnych w biotechnologii. Biotechnologia 4: 125-139 (in Polish).
• De Leo F, Iero A, Zammit G, Urzi CE (2012) Chemoorganotrophic bacteria isolated from biodeteriorated surfaces in cave and catacombs. Int J Speleol 41: 125-136.
• Fisher MM, Triplet EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65: 4630-4636. 
• Gaylarde CC, Rodriguez CH, Navarro-Noya YE, Ortega-Morales BO (2012) Microbial biofilms on the sandstone monuments of the Angkor Wat Complex, Cambodia. Curr Microbiol 64: 85-92. 
• Giacomucci L, Bertoncello R, Salvadori O, Martini I, Favaro M, Villa F, Sorlini C, Cappitelli F (2011) Microbial deterioration of artistic tiles from the façade of the Grande Albergo Ausonia and Hungaria (Venice, Italy). Microb Ecol 62: 287-298. 
• Gich FB, Amer E, Figueras JB, Abella CA, Balaguer MD, Poch M (2000) Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA). Int Microbiol 3: 103-106. 
• Gonzalez JM, Ortiz-Martinez A, Gonzalez-delValle MA, Laiz L, Saiz-Jimenez C (2003) An efficient strategy for screening large cloned libraries of amplified 16S rRNA sequences from complex environmental communities. J Microbiol Methods 55: 459-463. 
• Gonzalez JM, Saiz-Jimenez C (2005) Unknown microbial communities on rock art painting. Consequences for conservation and future perspectives. Coalition 10: 4-7.
• Gorbushina AA, Heyrman J, Dornieden T, Gonzalez-Delvalle M, Krumbein WM, Laiz L, Petersen K, Saiz-Jimenez C, Swings J (2004) Bacterial and fungal diversity and biodeterioration problems in mural painting environments of St. Martins church (Greene-Kreiensen, Germany). Int Biodeterior Biodegradation 53: 13-24.
• Gorbushina AA, Lialikova NN, Vlasov DI, Khizhniak TV (2002) Microbial communities on the monuments of Moscow and St. Petersburg: biodiversity and trophic relations. Mikrobiologiia 71: 409-417. 
• Gurtner C, Heyrman J, Piñar G, Lubitz W, Swings J, Rölleke S (2000) Comparative analyses of the bacterial diversity on two different biodeteriorated wall paintings by DGGE and 16S rDNA sequence analysis. Int Biodeterior Biodegradation 46: 229-239.
• Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685. 
• Heyrman J, Swings J (2001) 16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia Tomb (Necropolis of Carmona, Seville, Spain). Appl Microbiol 24: 417-422.
• Heyrman J, Balcaen AN, Rodriguez-Diaz M, Logan AN, Swings J, De Vos P (2003) Bacillus decolorationis sp. nov., isolated from biodeteriorated parts of the mural paintings at the Servilia tomb (Roman necropolis of Carmona Spain) and the Saint-Catherine chapel (Castle Herberstein, Austria). Int J Syst Evol Microbiol 53: 459-463. 
• Kiel G, Gaylarde CC (2006) Bacterial diversity in biofilms on external surfaces of historic buildings in Porto Alegre. World J Microbiol Biotechnol 22: 293-297.
• Lan W, Li H, Wang WD, Katayama Y, Gu JD (2010) Microbial community analysis of fresh and old microbial biofilms on Bayon temple sandstone of Angkor Thom, Cambodia. Microb Ecol 60: 105-115. 
• Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522. 
• McNamara CJ, Perry TD, Bearce KA, Hernandez-Duque G, Mitchell R (2006) Epilithic and endolithic bacterial communities in limestone from a Maya Archaeological Site. Microb Ecol 51: 51-64. 
• Mecler I, Nawrot U (2007) Techniki molekularne stosowane w diagnostyce mikrobiologicznej. Mikol Lek 14: 280-284 (in Polish).
• Michaelsen A, Pinzari F, Ripka K, Lubitz W, Piñar G (2006) Application of molecular techniques for identification of fungal communities colonizing paper material. Int Biodeterior Biodegradation 58: 133-141.
• Milanesi C, Baldi F, Borin S, Vignani R, Ciampolini F, Faleri C, Cresti M (2006) Biodeterioration of fresco by biofilm forming bacteria. Int Biodeterior Biodegradation 57: 168-173.
• Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-4724. 
• Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161: 497-505. 
• Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2: 317-322. 
• Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of 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. 
• Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127-141. 
• Neelakanta G, Sultana H (2013) The use of metagenomic approaches to analyze changes in microbial communities. Microbiol Insights 6: 37-48. 
• Nugari MP, Pietrini AM, Caneva G, Imperi F, Visca P (2009) Biodeterioration of mural paintings in a rocky habitat: The Crypt of the Original Sin (Matera, Italy). Int Biodeterior Biodegradation 63: 705-711.
• Ortega-Morales BO (2006) Cyanobacterial diversity and ecology on historic monuments in Latin America. Rev Latinoam Microbiol 48: 188-195. 
• Piñar G, Gurtner C, Lubitz W, Rölleke S (2001a) Identification of archaea in objects of art by denaturing gradient gel electrophoresis analysis and shotgun cloning. Methods Enzymol 336: 356-366. 
• Piñar G, Gurtner C, Ramos C, Lubitz W, Rölleke S (2001b) Identification of archaea in deteriorated ancient wall paintings by DGGE and FISH analysis. In Protection and conservation of the cultural heritage of the Mediterranean cities. Galan E, Zezza E, eds, pp 209-214. Balkema/Swets and Zeitlinger.
• Piñar G, Ripka K, Weber J, Sterflinger K (2009) The microbiota of a subsurface monument the medieval chapel of St. Virgil (Vienna, Austria). Int Biodeterior Biodegradation 63: 851-859.
• Piñar G, Garcia-Valles M, Gimeno-Torrente D, Fernandez-Turiel JL, Ettenauer J, Sterflinger K (2013) Microscopic, chemical, and molecular-biological investigation of the decayed medieval stained window glasses of two Catalonian churches. Int Biodeterior Biodegradation 84: 388-400. 
• Popa R, Mashall MJ, Nguyen H, Tebo BM, Brauer S (2009) Limitations and benefits of ARISA intra-genomic diversity fingerprinting. J Microbiol Methods 78: 111-118. 
• Portillo MC, Saiz-Jimenez C, Gonzalez JM (2009) Molecular characterization of total and metabolically active bacterial communities of ''white colonizations'' in the Altamira Cave, Spain. Res Microbiol 160: 41-47. 
• Rastogi G, Sani RS (2011) Molecular techniques to asses microbial community structure, function and dynamics in the environment. In Microbes and microbial technology: agricultural and environmental applications. Ahmad I, Ahmad F, Pichtel J, eds, pp 29-57. Springer, New York.
• Raszka A, Ziembinska A, Wiechetek A (2009) Techniki molekularne stosowane w diagnostyce mikrobiologicznej. Środowisko 2: 101-114.
• Ripka K, Denner EBM, Michaelsen A, Lubitz W, Piñar G (2006) Molecular characterization of Halobacillus strains isolated from different medieval wall paintings and building materials in Austria. Int Biodeterior Biodegradation 58: 124-132.
• Ronaghi M (2013) Pyrosequencing sheds light on DNA sequencing. Genome Res 11: 3-11. 
• Rölleke S, Muyzer G, Wawer C, Wanner G, Lubitz W (1996) Identification of bacteria in the biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 62: 2059-2065. 
• Rölleke S, Witte A, Wanner G, Lubitz W (1998) Medieval wall painting-a habitat for archaea: identification of archaea by denaturing gradient gel electrophoresis (DGGE) of PCR amplified gene fragments coding 16S rRNA in a medieval wall painting. Int Biodeterior Biodegradation 41: 85-92.
• Shah N, Tang H, Doak TG, Ye Y (2011) Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput 2011: 165-176. 
• Saiz-Jimenez C, Laiz L (2000) Occurrence of halotolerant and halophilic bacterial communities in deteriorated monuments. Int Biodeterior Biodegradation 46: 319-326.
• Saiz-Jimenez C, Miller AZ, Martin-Sanchez PM, Hernandez-Marine M (2012) Uncovering the origin of the black stains in Lascaux Cave in France. Environ Microbiol 14: 3220-3231. 
• Schabereiter-Gurtner C, Pinar G, Lubitz W, Rölleke S (2001) An advanced molecular strategy to identify bacterial communities on art objects. J Microbiol Methods 45: 77-87. 
• Simon C, Rolf D (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77: 1153-1161. 
• Sklarz MY, Angel R, Gillor O, Soares IM (2011) Amplified rDNA restriction analysis (ARDRA) for identification and phylogenetic placement of 16S rDNA clones. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. de Bruijn FJ, eds, pp 59-60. John Wiley & Sons, Inc., Hoboken, New Jersey. 
• Smerda J, Sedlácek I, Pácová Z, Krejcí E, Havel L (2006) Paenibacillus sepulcri sp. nov., isolated from biodeteriorated mural paintings in the Servilia tomb. Int J Syst Evol Microbiol 56: 2341-2344. 
• Stomeo F, Portillo MC, Gonzalez JM, Laiz L, Saiz-Jimenez C (2008) Pseudonocardia in white colonization in two caves with Paleolithic paintings. Int Biodeterior Biodegradation 62: 483-486.
• Streit WR, Schmitz RA (2004) Metagenomics - the key to the uncultured microbes. Curr Opin Microbiol 7: 492-498. 
• Tatusova TA, Madden TL (1999) BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250. 
• Tomaselli L, Lamenti G, Bosco M, Tiano P (2000) Biodiversity of photosynthetic microorganisms dwelling on stone monuments. Int Biodeterior Biodegradation 46: 251-258.
• Więckowicz M (2009) Molekularne metody identyfikacji mikroorganizmów w złożonych ekosystemach. Post Mikrobiol 48: 67-73 (in Polish).