Journal ArticleDOI
Genetic diversity in Sargasso Sea bacterioplankton.
TLDR
The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.Abstract:
BACTERIOPLANKTON are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species1–3. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction4. The analysis indicates the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs—cyanobacteria, prochlorophytes and chloroplasts—was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.read more
Citations
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Journal ArticleDOI
Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic
TL;DR: In this paper, the authors investigated bacterioplankton assemblage composition using a sensitive DNA fingerprinting technique -ARISA-over vertical profiles from surface waters to 1200 m depth.
Book ChapterDOI
Nucleic Acid Probes and Their Application in Environmental Microbiology
TL;DR: It is routine to start the classification of a newly isolated microorganism with the determination and comparative analysis of at least one nucleic acid sequence, the most commonly used molecule is the ribonucleic acid of the small subunit of the ribosome, the 16S rRNA of Bacteria and Archaea.
Book ChapterDOI
Non-Culturable Bacteria in Complex Commensal Populations
TL;DR: This chapter focuses on the commensal microflora of the mouth and large intestine and examines its relationship with disease, and discusses the problems inherent in its study and molecular methods developed to investigate its unculturable component.
Journal ArticleDOI
Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of endodontic infections.
TL;DR: Application of the PCR-DGGE method in endodontic research has revealed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases and suggests that the structure of the bacterial community can play a role in the development of symptoms.
Journal ArticleDOI
Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis.
Ingo Bergmann,Ingo Bergmann,Edith Nettmann,Edith Nettmann,K. Mundt,K. Mundt,Michael Klocke,Michael Klocke +7 more
TL;DR: Both approaches detected similar archaeal groups and revealed nearly the same abundance, pointing to a predominance of hydrogenotrophic methanogens in the biogas plant.
References
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DNA sequencing with chain-terminating inhibitors
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Randall Keichi Saiki,David H. Gelfand,Susanne Stoffel,Stephen J. Scharf,Russell Higuchi,Glenn Thomas Horn,Kary B. Mullis,Henry A. Erlich +7 more
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.
Journal ArticleDOI
Site-directed mutagenesis by overlap extension using the polymerase chain reaction.
TL;DR: In this paper, complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends, and these fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the three' extension of the complementary strand.
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