Biodiversity of streptomycetes isolated from a succession sequence at a post-mining site and their evidence in Miocene lacustrine sediment

Microbiological Research

Volumn 165, Issue 7, 2010, Pages 594-608

  Chroňáková, Alica ^a,b   Krištůfek, Václav ^a   Tichý, Martin ^c   Elhottová, Dana ^a  

^a INSTITUTE OF SOIL BIOLOGY   (Czech Republic)

^b UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^c INSTITUTE OF MICROBIOLOGY   (Czech Republic)

Author keywords

16S rDNA ITS; Actinomycetes; Antibiotics; Primary succession; Subsurface

Indexed keywords

16S RDNA; ACTINOMYCETES; AMOXICILLIN; ANTIBIOTIC RESISTANCE GENES; BIOLOGICALLY ACTIVE COMPOUNDS; COMMUNITY DEVELOPMENT; CZECH REPUBLIC; GENETIC DIVERSITY; GENETIC ELEMENTS; INTERNAL TRANSCRIBED SPACERS; LACUSTRINE SEDIMENTS; LATE STAGE; MINING SITES; MIOCENE; MIOCENE SEDIMENTS; NONRIBOSOMAL PEPTIDE; PATTERN ANALYSIS; PIONEER SPECIES; PLATE ASSAY; POLYKETIDE SYNTHASES; PRIMARY SUCCESSION; PRISTINE ENVIRONMENTS; SAMPLING SITE; STREPTOMYCETES; SUBSURFACE; SYNTHASES;

BACTERIA; BACTERIOLOGY; BIODIVERSITY; SEDIMENTOLOGY; SEDIMENTS;

ANTIBIOTICS;

ANTIINFECTIVE AGENT; BACTERIAL DNA; RNA 16S;

ANTIBIOTIC RESISTANCE; BACTERIUM; BIOACTIVITY; BIODIVERSITY; LACUSTRINE DEPOSIT; MINING; MIOCENE; PRIMARY SUCCESSION; PRISTINE ENVIRONMENT; SPOIL HEAP; SUBSTRATE;

ARTICLE; BIODIVERSITY; CLASSIFICATION; CZECH REPUBLIC; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MINING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEDIMENT; STREPTOMYCES;

ANTI-BACTERIAL AGENTS; BIODIVERSITY; CZECH REPUBLIC; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; MINING; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; STREPTOMYCES;

CZECH REPUBLIC; SOKOLOV BASIN;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); STREPTOMYCES; STREPTOMYCES MICROFLAVUS; STREPTOMYCES SPORORAVEUS; STREPTOMYCETACEAE; STREPTOMYCINEAE;

EID: 77956405169     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2009.10.002     Document Type: Article

References (50)

1. Ames R.N. Chitin decomposing actinomycetes associated with VAM fungus from a calcareous soil. New Phytol 1989, 111:67-71.
2. Ayuso-Sacido A., Genilloud O. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microbial Ecol 2004, 49:10-24.
3. Baldrian P., Trögl J., Frouz J., Šnajdr J., Valášková V., Merhautová V., et al. Enzyme activities and microbial biomass in topsoil layer during spontaneous succession in spoil heaps after brown coal mining. Soil Biol Biochem 2008, 40:2107-2115.
4. Bell A.A., Wheeler M.H. Biosynthesis and function of fungal melanins. Annu Rev Phytopathol 1986, 24:411-451.
5. Challis G.L., Hopwood D.A. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Natl Acad Sci USA 2003, 100:14555-14561.
6. Cano R.J., Borucki M.K. Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber. Science 1995, 268:1060-1064.
7. Davelos A.L., Kinkel L.L., Samac D.A. Spatial variation in frequency and intensity of antibiotic interactions among Streptomycetes from prairie soil. Appl Environ Microbiol 2004, 70:1051-1058.
8. Edwards U., Rogall T., Blöcker H., Emde M., Böttger E.C. Isolation and direct complete nucleotide determination of entire genes. Characterisation of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989, 17:7843-7853.
9. Elhottová D., Krištůfek V., Frouz J., Nováková A., Chroňáková A. Screening for microbial markers in Miocene sediment exposed during open-cast brown coal mining. Antonie Van Leeuwenhoek 2006, 89:459-463.
10. Elhottová D., Krištůfek V., Frouz J., Malý S. Rhizosphere effect of colonizer plant species on the development of soil microbial community dutiny primary succession on post mining sites. Commun Soil Sci Plan 2009, 40:758-770.
11. Fajardo A., Martínez J.L. Antibiotics as signals that trigger specific bacterial responses. Curr Opin Microbiol 2008, 11:161-167.
12. Fajardo-Cavazos P., Nicholson W. Bacillus endospores isolated from granite: close molecular relationships to globally distributed Bacillus spp. from endolithic and extreme environments. Appl Environ Microbiol 2006, 72:2856-2863.
13. Fliermans C.B., Balkwill D.L. Microbial life in deep terrestrial subsurfaces. BioScience 1989, 39:370-377.
14. Frouz J., Pižl V., Tajovský K., Balík V., Háněl L., Starý J., et al. Soil development and succession of soil biota in afforested and non-reclaimed sites in post mining landscape - preliminary results 2002, 621-626. Proceedings SWEP 2002, Cagliary. R. Ciccu (Ed.).
15. Frouz J., Nováková A. Development of soil microbial properties in topsoil layer during spontaneous succession in heaps after brown coal mining in relation to humus microstructure development. Geoderma 2005, 129:54-64.
16. Frouz J., Elhottová D., Kuráž V., Šourková M. Effects of soil macrofauna on other soil biota and soil formation in reclaimed and unreclaimed post mining sites: results of a field microcosm experiment. Appl Soil Ecol 2006, 33:308-320.
17. Frouz J., Pižl V., Cienciala E., Kalčík J. Carbon storage in post-mining forest soil, the role of tree biomass and soil bioturbation. Biogeochemistry 2009, 94:111-121.
18. Gemma J.N., Koske R.E., Carreiro M. Seasonal dynamics of selected species of VAM in a sand dune. Mycol Res 1989, 92:317-321.
19. Guindon S., Gascuel O. Simple, fast and accurate algorithm to estimate large phylogenies by maximal likelihood. Syst Biol 2003, 52:696-704.
20. Hall T.A. Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
21. Heuer H., Krsek M., Baker P., Smalla K. Wellington EMH. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 1997, 63:3233-3241.
22. Hodkinson I.D., Webb N.R., Coulson S.J. Primary community assembly on land - the missing stages: why are the heterotrophic organisms always there first?. J Ecol 2002, 90:569-577.
23. ISO ISO/DIS 10390: soil quality - determination of pH 1992, International Organization for Standardization.
24. Johnson S.S., Hebsgaard M.B., Christensen T.R., Mastepanov M., Nielsen R., Munch K., et al. Ancient bacteria show evidence of DNA repair. Proc Natl Acad Sci USA 2007, 104:14401-14405.
25. Kämpfer P. The family Streptomycetaceae, part I: taxonomy. The prokaryotes 2006, 538-604. Springer Science+Business Media, LLC, New York. 3rd ed. M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, E. Stackebrandt (Eds.).
26. Kandeler E., Deiglmayr K., Tscherko D., Bru D., Philippot L. Abundance of narG, nirS, nirK and nosZ genes of denitrifying bacteria during primary succession of a glacier foreland. Appl Environ Microbiol 2006, 72:5957-5962.
27. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT version 5.25: multiple sequence alignment program. Nucleic Acids Res 2002, 30:3059-3066.
28. Katsifas E.A., Giannoutsou E.P., Karagouni A.D. Diversity of streptomycetes among specific Greek terrestrial ecosystems. Lett Appl Microbiol 1999, 29:48-51.
29. Kilbertus, Mangenot Origine et composition des matières organiques impliquées dans la formation des agrégats organominéraux. Colloques Internationaux du CNRS 1981, 303:103-111.
30. Krištůfek V., Ravasz K., Pižl V. Actinomycete communities in earthworm guts and surrounding soil. Pedobiologia 1993, 37:379-384.
31. Krištůfek V., Elhottová D., Chroňáková A., Dostálková I., Picek T., Kalčík J. Growth strategy of heterotrophic bacterial population along successional sequence on spoil of brown coal colliery substrate. Folia Microbiol 2005, 50:427-435.
32. Kříbek B., Strnad M., Boháček Z., Sýkorová J., Čejka J., Sobalík Z. Geochemistry of Miocene lacustrine sediments from the Sokolov Coal Basin (Czech Republic). Int J Coal Geol 1998, 37:207-233.
33. Kurtböke D.I., Neller R.J., Bellgard S.E. Mesophilic actinomycetes in natural and reconstructed sand dune vegetation zones of Fraser Island, Australia. Microb Ecol 2007, 54:332-340.
34. Lanoot B., Vancanneyt M., Hoste B., Vandemeulebroecke K., Cnockaert M.C., Dawyndt P., et al. Grouping of streptomycetes using 16S-ITS RFLP fingerprinting. Res Microbiol 2005, 156:755-762.
35. Lavelle P., Spain A.V. Soil ecology 2001, Kluwer Academic Publishers, Dordrecht.
36. Lewis K., Epstein S., Godoy V.G., Hong S.H. Intact DNA in ancient permafrost. Trends Microbiol 2008, 16:92-94.
37. Madigan M.T., Martinko J.M. Brock biology of microorganisms 2006, Pearson Education, Upper Saddle River, New Jersey. 11th ed.
38. Mindlin S.Z., Soina V.S., Petrova M.A., Gorlenko Z.M. Isolation of antibiotic resistance bacterial strains from eastern Siberia permafrost sediments. Russ J Genet 2008, 44:36-44.
39. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
40. Riedlinger J., Schrey S.D., Tarkka M.T., Happ R., Kapur M., Fiedler H.P. Auxofuran, a novel metabolite that stimulates the growth of fly agaric, is produced by mycorrhiza helper bacterium Streptomyces strain AcH 505. Appl Environ Microbiol 2006, 72:3550-3557.
41. Schrey S.D., Tarkka M.T. Friends and foes: Streptomycetes as modulators of plant disease and symbiosis. Antonie Van Leeuwenhoek 2008, 94:11-19.
42. Schillawski S., Petsch S. Release of biodegradable dissolved organic matter from ancient sedimentary rocks. Global Geochem Cycles 2008, 22:GB3002.
43. Schipper L.A., Degens B.P., Sparling G.P., Duncan L.C. Changes in microbial heterotrophic diversity along five plant successional sequences. Soil Biol Biochem 2001, 33:2093-2103.
44. Shirling E.B., Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966, 16:313-340.
45. Shrestha P.M., Noll M., Liesack W. Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession. Environ Microbiol 2007, 9:2464-2474.
46. Sigler W.V., Zeyer J. Microbial diversity and activity along the forefields of two receding glaciers. Microb Ecol 2002, 43:397-407.
47. Swindell S.R., Plasterer T.N. SEQMAN. Contig assembly. Meth Mol Biol 1997, 70:75-89.
48. Swofford D.L. PAUP*: Phylogenetic Analysis using Parsimony (and other methods) 2002, Sinauer Associates, Sunderland.
49. Vance E.D., Brookers P.C., Jenkinson D.S. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 1987, 9:703-707.
50. Vreeland R., Rosenzweig W., Powers D. Isolation of a 250 million year old halotolerant bacterium from a primary salt crystal. Nature 2000, 407:897-900.