Evaluating the assignment of alkB terminal restriction fragments and sequence types to distinct bacterial taxa

Appl Environ Microbiol. 2013 May;79(9):3129-32. doi: 10.1128/AEM.04028-12. Epub 2013 Mar 1.

Abstract

Sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses revealed multiple alkB gene copies/cell in soil bacterial isolates and an apparently high genetic mobility among various phylogenetic groups. Identifying alkane degraders by alkB terminal restriction fragments (T-RFs) and sequences is strongly biased, as the phylogenetic trees based on 16S rRNA and alkB gene sequences were highly inconsistent.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification*
  • Bacteria / enzymology
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bacterial Proteins / genetics
  • Cytochrome P-450 CYP4A / genetics*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Genetic Variation*
  • Phylogeny
  • Polymorphism, Restriction Fragment Length
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil
  • Soil Microbiology*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Ribosomal, 16S
  • Soil
  • Cytochrome P-450 CYP4A