A molecular approach to search for diversity among bacteria in the environment
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Molecular 16S rDNA-based techniques were applied to a peat sample from northern Germany in order to investigate the bacterial diversity present and compare the clone sequences with those obtained from similar studies on other terrestrial samples. Genomic DNA was extracted from the peat matrix by a direct lysis procedure. 16S rRNA genes were amplified using PCR primers targeting conserved regions of bacterial 16S rDNA. 16S rDNA fragments were blunt end cloned into a plasmid vector and the resulting clone library of 262 sequences was screened by hybridization with different oligonucleotide probes and sequence analysis of randomly selected clones. The 16S rDNA insert of 76 clones was partially sequenced. Clones identified either by hybridization or by sequence analysis fell into three phyla. As judged by hybridization with a specific oligonucleotide probe, 42% of the clones represented members of the alpha subclass of Proteobacteria. Twenty-five of these clones were selected randomly for sequence analysis; none could be assigned to any of the known genera of this subclass. The second largest clone group comprises 15% of the clones and clusters aroundAcidimicrobium ferrooxidans andRubrobacter radiotolerans, both of which are remotely related to members of the order Actinomycetales. The third major clone cluster (10%) was moderately to remotely related to theAcidobacterium capsulatum phylum. Of the additional clones sequenced, a few could be assigned to other subclasses ofProteobacteria, theVerrucomicrobium phylum and the phylum of spirochetes. Comparison of the results presented here with those from other environments reveals a significant number of common clone clusters. As the vast majority of sequences retrieved from any of the marine and terrestrial samples investigated so far by molecular methods indicate the presence of novel bacterial species it can be assumed that a huge, as yet untapped biotechnological potential is present in the environment.
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- Blackall LL, EM Seviour, MA Cunningham, RJ Seviour and P Hugenholtz. 1994. ‘Microthrix parvicella’ is a novel, deep branching member of theActinomyces subphylum. Syst Appl Microbiol 17: 513–518.
- Blackall LL, H Stratton, D Bradford, T Del Dot, C Sjörup, EM Seviour and RJ Seviour. 1996. ‘Candidatus Microthrix parvicella’, a filamentous bacterium from activated sludge sewage treatment plants. Int J Syst Bacteriol 46: 344–346.
- Cabot EL and AT Beckenbach. 1989. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comp Appl Biosci 5: 233–234.
- Choi KB, BJ Paster, FE Dewhirst and UB Göbel. 1994. Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis. Infect Immun 62: 1889–1895.
- Clark DA and PR Norris. 1996.Acidimicrobium ferrooxidans gen nov, sp nov: mixed culture ferrous iron oxidation withSulfobacillus species. Microbiology 142: 785–790.
- Felsenstein J. 1993. PHYLIP Phylogeny Inference Package, version 3.5.1. Seattle: Department of Genetics, University of Washington.
- Fuhrman JA, K McCallum and AA Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl Environ Microbiol 59: 1294–1302.
- Goebel B and E Stackebrandt. 1994. Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleach environments. Appl Environ Microbiol 60: 1614–1621.
- Hiraishi A, N Kishimoto, Y Kosako, N Wakao and T Tano. 1995. Phylogenetic position of the menaquinone-containing acidophilic chemo-organotrophAcidobacterium capsulatum. FEMS Microbiol Lett 132: 91–94.
- Jukes TH and CR Cantor. 1969. Evolution of protein molecules. In: Mammalian protein metabolism (Munro HN, ed), pp 21–132, Academic Press, New York.
- Liesack W and E Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174: 5072–5078.
- Liesack W and E Stackebrandt. 1992. Unculturable microbes detected by molecular sequences and probes. Biodivers Conser 1: 250–262.
- Liesack W, K-J Chin, U Hengstmann, R Großkopf and PH Janssen. 1995. Characterization of microbial populations of rice microcosms using traditional cultivation and molecular techniques. 7th International Symposium on Microbial Ecology, Santos, Brazil. Abstract S4-5.1. Brazilian Society for Microbiology, Santos.
- Maidak BL, N Larsen, MJ McCaughey, R Overbeck, GJ Olsen, K Fogel, J Blandy and CR Woese. 1994. The ribosomal database project. Nucleic Acids Res 22: 3483–3487.
- Mullins TD, TB Britschgi, RL Krest and SJ Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40: 148–158.
- Muyzer G, E de Waal and A Uitterlinde. 1993. Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695–700.
- Muyzer G and EC de Waal. 1994. Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA. In: Structure, Development and Environmental Significance of Microbial Mats (Stal LJ and P Caumette, eds), pp 207–214, NATO ASI Series, vol G35, Springer-Verlag, Berlin.
- Rainey FA, NL Ward and E Stackebrandt. 1993. Molecular ecology study of a New Zealand acidothermal soil. Thermophiles '93, Hamilton, New Zealand. Abstract A7. University of Waikato, Hamilton.
- Rheims H, C Spröer, FA Rainey and E Stackebrandt. 1996. Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiology 142: 2863–2870.
- Ruff-Roberts AL, GJ Kuenen and DM Ward. 1994. Distribution of cultivated and uncultivated cyanobacteria andChloroflexus-like bacteria in hot spring microbial mats. Appl Environ Microbiol 60: 697–704.
- Saano A, K Lindström and JD Van Elsas. 1995 Eubacterial diversity in Finnish forest soil. 7th International Symposium on Microbial Ecology, Santos, Brazil. Abstract P1-3.9. Brazilian Society for Microbiology, Santos.
- Schlesner H. 1994. The development of media suitable for the micro-organisms morphologically resemblingPlanctomyces spp,Pirellula spp, and otherPlanctomycetales from various aquatic habitats using dilute media. Syst Appl Microbiol 17: 135–145.
- Stackebrandt E, W Liesack and BM Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB 7: 232–236.
- Ueda T, Y Suga and T Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur J Soil Sci 46: 415–421.
- Von Wintzingerode F. 1994. Phylogenetische und chemotaxonomische Hinweise auf die Anwesenheit neuer Bakterienarten in einer Torflagerstätte in Ost-Niedersachsen. Diploma Thesis. Technical University, Braunschweig.
- Wagner C, A Grießhammer and HL Drake. 1996. Acetogenic capacities and the anaerobic turnover of carbon in a Kansas prairie soil. Appl Environ Microbiol 62: 494–500.
- Ward N, FA Rainey, B Goebel and E Stackebrandt. 1995. Identifying and culturing the ‘unculturables’—a challenge for microbiologists. In: Microbial Diversity and Ecosystem Function (Allsopp D, RR Colwell and DL Hawksworth, eds), pp 89–110, CAB International, Wallingford.
- Ward N, FA Rainey, E Stackebrandt and H Schlesner. 1995. Unraveling the extent of diversity within the orderPlanctomycetales. Appl Environ Microbiol 61: 2270–2275.
- Ward-Rainey N, FA Rainey, H Schlesner and E Stackebrandt. 1995. Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria. Microbiology 141: 3247–3250.
About this Article
- A molecular approach to search for diversity among bacteria in the environment
Journal of Industrial Microbiology
Volume 17, Issue 3-4 , pp 159-169
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- molecular ecology
- 16S rDNA
- gene library
- oligonucleotide probes
- uncultured organisms
- Industry Sectors