PCR for direct detection of indigenous uncultured magnetic cocci in sediment and phylogenetic analysis of amplified 16S ribosomal DNA

R. H. Thornhill, J. G. Burgess, Tadashi Matsunaga

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

PCR primers specific to the 16S ribosomal DNA (rDNA) of magnetic cocci were designed and used to amplify DNA from magnetically isolated magnetic cocci. The PCR products were subcloned by ligation into plasmid vector pCRII, and five clones containing approximately 270-bp fragments of amplified DNA were sequenced. The specific primers were also used to detect magnetic coccus 16S rDNA in environmental samples. Magnetic coccus 16S rDNA was amplified from the water column above sediment kept in an anoxic environment in the laboratory, but little was amplified from a water column kept in an oxic environment. These results suggest that magnetic cocci in the water column in an anoxic environment had migrated there from the sediment as a response to the microoxic or anoxic conditions, rather than having been present previously in a nonmagnetic form and having become magnetic due to these conditions. The specific primers were also used to detect magnetic cocci in aquatic sediment. DNA was extracted from sediment by direct lysis and purified for use as a PCR template by electrophoresis on an agarose- polyvinylpyrrolidone gel. 16S rDNA was then amplified and subcloned, and two clones were sequenced. The clones were screened for chimeric DNA by comparing sections of each with the GenBank database.

Original languageEnglish
Pages (from-to)495-500
Number of pages6
JournalApplied and Environmental Microbiology
Volume61
Issue number2
Publication statusPublished - 1995
Externally publishedYes

Fingerprint

Coccus
Ribosomal DNA
ribosomal DNA
phylogenetics
DNA
Polymerase Chain Reaction
sediments
Clone Cells
phylogeny
sediment
Water
clones
clone
Povidone
water column
Nucleic Acid Databases
Sepharose
Ligation
Electrophoresis
plasmid vectors

ASJC Scopus subject areas

  • Biotechnology
  • Environmental Science(all)
  • Microbiology

Cite this

PCR for direct detection of indigenous uncultured magnetic cocci in sediment and phylogenetic analysis of amplified 16S ribosomal DNA. / Thornhill, R. H.; Burgess, J. G.; Matsunaga, Tadashi.

In: Applied and Environmental Microbiology, Vol. 61, No. 2, 1995, p. 495-500.

Research output: Contribution to journalArticle

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