Bacterial diversity associated with archaeological waterlogged wood: Ribosomal RNA clone libraries and denaturing gradient gel electrophoresis (DGGE)

International Biodeterioration and Biodegradation

Volumn 61, Issue 1, 2008, Pages 106-116

  Landy, Eleanor T ^a,b   Mitchell, Julian I ^a   Hotchkiss, Sarah ^a   Eaton, Rod A ^a  

^a UNIVERSITY OF PORTSMOUTH   (United Kingdom)

^b UNIVERSITY OF SURREY   (United Kingdom)

Author keywords

Archaeological; Bacteria; Denaturing gradient gel electrophoresis (DGGE); Diversity; Waterlogged wood

Indexed keywords

BIODIVERSITY; CLONING; DENATURATION; ELECTROPHORESIS; RNA; WOOD;

DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE); WATERLOGGED WOOD;

BACTERIA;

ARCHAEOLOGY; BACTERIUM; CLONE; DNA FINGERPRINTING; ELECTROKINESIS; GEL; MICROBIAL COMMUNITY; RNA; WATERLOGGING; WOOD;

BACTERIA; BIODIVERSITY; DENATURATION; ELECTROPHORESIS; NUCLEIC ACIDS; WOOD;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); BREVUNDIMONAS; CELLVIBRIO; CYTOPHAGA; FLAVOBACTERIUM; PSEUDOMONAS;

EID: 36849077624     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2007.07.007     Document Type: Article

References (44)

1. Amann R., Fuchs B., and Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Current Opinions in Biotechnology 12 (2001) 231-236
2. Barbieri E., Potenza L., Rossi I., Sisti D., Giomaro G., Rossetti S., Beimfohr C., and Stocchi V. Phylogenetic characterization and in situ detection of a Cytophaga-Flexibacter-Bacteroides phylogroup bacterium in Tuber borchii Vittad. Ectomycorrhizal mycelium. Applied and Environmental Microbiology 66 (2000) 5035-5042
3. Bjordal, C.G., Nilsson, T., 2002. Decomposition of waterlogged archaeological wood. In: Hoffman, P., Spriggs, J.A., Grant, T., Cook, C., Recht, A., (Eds.), Proceedings of the Eighth ICOM Group on Wet Organic Archaeological Materials Conference, Stockholm, pp. 235-247.
4. Björdal C.G., Nilsson T., and Daniel G. Microbial decay of waterlogged archaeological wood found in Sweden. Applicable to archaeology and conservation. International Biodeterioration & Biodegradation 43 (1999) 63-71
5. Björdal C.G., Daniel G., and Nilsson T. Depth of burial, an important factor in controlling bacterial decay of waterlogged archaeological poles. International Biodeterioration & Biodegradation 45 (2000) 15-26
6. Blanchette R.A. A review of microbial deterioration found in archaeological wood from different environments. International Biodeterioration & Biodegradation 46 (2000) 189-204
7. Boutelje J.B., and Bravery A.F. Observations on the bacterial attack of piles supporting a Stockholm building. Journal Institute of Wood Science 20 (1968) 47-57
8. Boutelje J.B., and Kiessling H. On water-stored oak timber and its decay by fungi and bacteria. Archiv fur Mikrobiologie 49 (1964) 305-314
9. Clarke A.M., Kirby R., and Rose P.D. Molecular microbial ecology of lignocellulose mobilisation as a carbon source in mine drainage wastewater treatment. Water SA 30 (2004) 658-661
10. Clausen C.A. Bacterial associations with decaying wood: a review. International Biodeterioration & Biodegradation 37 (1996) 101-107
11. Cottrell M.T., and Kirchman D.L. Community composition of marine picoplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridisation. Applied Environmental Microbiology 66 (2000) 5116-5122
12. Cottrell M.T., and Kirchman D.L. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Applied and Environmental Microbiology 66 (2000) 1692-1697
13. Daniel, G., Nilsson, T., 1986. Ultrastructural observations on wood degrading erosion bacteria. International Research Group on Wood Preservation No. IRG/WP/1283.
14. Daniel G.F., Nilsson T., and Singh A.P. Degradation of lignocellulosics by unique tunnel-forming bacteria. Canadian Journal of Microbiology 33 (1987) 943-948
15. Eslyn W.E., and Moore W.G. Bacteria and accompanying deterioration in river pilings. Materials and Organisms Suppl. 4 (1984) 263-282
16. Fandino L.B., Riemann L., Steward G.F., Long R.A., and Azam F. Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquatic Microbial Ecology 23 (2001) 119-130
17. Ferrera I.R., Massana R., Casamayor E.O., Balagué V., Pedrós-Alió C., and Mas J. High diversity biofilm for the oxidation of sulfide-containing effluents. Applied Microbiology and Biotechnology 64 (2004) 726-734
18. Fuhrman J.A., and Campbell L. Microbial microdiversity. Nature 393 (1998) 410-411
19. Giraffa G., and Nevianai E. DNA-based, culture independent strategies for evaluating microbial communities in food-associated ecosystems. International Journal of Food Microbiology 6 (2001) 19-34
20. Harmsen L., and Nissen T.V. Timber decay caused by bacteria. Nature 266 (1965) 319
21. Helms A.C., Martiny A.C., Hofman-Bang J., Ahring B.K., and Kilstrup M. Identification of bacterial cultures from archaeological wood using molecular biological techniques. International Biodeterioration & Biodegradation 53 (2004) 79-88
22. Hengstmann U., Chin K.-J., Janssen P.H., and Liesack W. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Applied and Environmental Microbiology 65 (1999) 5050-5058
23. Higgins D.G., Thompson J.D., and Gibson T.J. Using CLUSTAL for multiple sequence alignments. Methods in Enzymology 266 (1996) 384-402
24. Höfle M.G., and Brettar I. Genotyping of heterotrophic bacteria from the central Baltic Sea by use of low-molecular-weight RNA profiles. Applied and Environmental Microbiology 62 (1996) 1383-1390
25. Kim Y.S., and Singh A.P. Micromorphological characteristics of wood biodegradation in wet environments: a review. International Association of Wood Anatomists Journal 21 (2000) 135-155
26. Kindaichi T., Ito T., and Okabe S. Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. Applied and Environmental Microbiology 70 (2004) 1641-1650
27. Landy E.T., Bjordal C.G., Nilsson T., Mitchell J.I., and Eaton R.A. Estimation of the diversity of bacterial communities in wooden foundation poles across Europe using molecular biology techniques. Biomolecular Archaeology Symposium (2004)
28. Lau W.W.Y., Jumars P.A., and Armbrust E.V. Genetic diversity of attached bacteria in the hind-gut of deposit-feeding shrimp Neotrypaea (formerly Callianassa) californiensis (Decapoda: Thalassinidae). Microbial Ecology 43 (2002) 455-466
29. Levy J.F., Millbank J.W., Dwyer G., and Baines E.F. The role of bacteria in wood decay (1974), Record of the 1974 Annual Convention of the British Wood Preserving Association pp. 3-13
30. Line M.A. A nitrogen fixing consortia associated with the bacterial decay of a wooden pipeline. Letters in Applied Microbiology 25 (1997) 220-224
31. Llobet-Brossa E., Roselló-Mora R., and Amann R. Microbial community composition of Wadden sea sediments as revealed by fluorescence in situ hybridisation. Applied and Environmental Microbiology 64 (1998) 2691-2696
32. MacGregor B.J. Molecular approaches to the study of aquatic microbial communities. Current Opinion in Biotechnology 10 (1999) 220-224
33. McCammon S.A., and Bowman J.P. Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisae sp. nov., Flavobacterium tegetincola sp. nov. and Flavobacterium xanthum sp. nov. mon. rev. and re-classification of [Flavobacterium] salengens as Salegentibacter salegens gen. nov., comb. nov. International Journal of Systematic Bacteriology 50 (2000) 1055-1063
34. Muyzer G., De Waal E.C., and Uitterlinden A.G. Profiling of complex microbial populations by denaturing-gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied Environmental Microbiology 59 (1993) 695-700
35. O'Sullivan L.A., Weightman A.J., and Fry J.C. New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in river Taff epilithon. Applied and Environmental Microbiology 68 (2002) 201-210
36. Powell K.L., Pedley S., Daniel G., and Corfield M. Ultrastructural observations of microbial succession and decay of wood buried at a Bronze Age archaeological site. International Biodeterioration & Biodegradation 47 (2001) 165-173
37. Rambaut, A., 1996. Se-Al: Sequence Alignment Editor, Available at 〈http://evolve.zoo.ox.ac.uk/〉.
38. Robinson-Cox J.F., Bateson M.M., and Ward D.M. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Applied and Environmental Microbiology 61 (1995) 1240-1245
39. Shafer H., and Muyzer G. Denaturing gradient gel electrophoresis in marine microbial ecology. In: Paul J.H. (Ed). Methods in Microbiology vol. 30 (2001), Academic Press Ltd, New York 425-468
40. Swofford, D., 2000. PAUP* Phylogenetic Analysis using parsimony (* and other methods), Sinauer Associates, Sutherland, MA Version 4.
41. Theron J., and Cloete T.E. Molecular techniques for determining microbial diversity and community structure in natural environments. Critical Reviews in Microbiology 26 (2000) 37-57
42. Tiano, P., 2002. Biodegradation of cultural heritage: decay mechanisms and control methods. Ninth ARIADNE Workshop "Historic Material and their Diagnostic", ARCCHIP, Prague, 22-28 April 2002. 〈http://www.arcchip.cz/w09/w09_tiano.pdf〉.
43. Vainio E.J., and Hantula J. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycological Research 104 (2000) 927-936
44. von Wintzingerode F., Göbel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. Federation of European Microbiology Societies Microbiology Reviews 21 (1997) 213-229