Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens

Kiyoshi Tajima, Takafumi Nagamine, Hiroki Matsui, Mutsumi Nakamura, Rustam Aminov

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Abstract

Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other - with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea. © 2001 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.
Original languageEnglish
JournalFEMS Microbiology Letters
Volume200
Issue number1
Pages (from-to)67-72
Number of pages6
ISSN0378-1097
DOIs
Publication statusPublished - 2001
Externally publishedYes

Keywords

  • Animals
  • Archaea
  • Bacteria
  • Cattle
  • Eukaryotic Cells
  • Euryarchaeota
  • Evolution, Molecular
  • Gene Library
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Archaeal
  • RNA, Ribosomal, 16S
  • Rumen
  • Sequence Analysis, DNA
  • primer DNA
  • ribosome RNA
  • anaerobic bacterium
  • article
  • bacterium
  • cattle
  • controlled study
  • feces analysis
  • gene amplification
  • gene library
  • Methanobacterium
  • methanobrevibacter
  • molecular cloning
  • nonhuman
  • nucleotide sequence
  • phylogeny
  • polymerase chain reaction
  • priority journal
  • RNA sequence
  • ruminant stomach
  • sequence analysis
  • swine
  • Thermoplasma
  • Bovinae
  • Methanobrevibacter
  • Methanomicrobium mobile
  • Sus scrofa
  • Molecular diversity
  • Archaeobacteria Bacteria Microorganisms (Archaeobacteria, Bacteria, Microorganisms) - Cell Wall-less Archaeobacteria [09800] Thermoplasma
  • Archaeobacteria Bacteria Microorganisms (Archaeobacteria, Bacteria, Microorganisms) - Methanogenic Archaeobacteria [09500] methanogen
  • Bacteria Microorganisms (Archaeobacteria, Bacteria, Microorganisms) - Archaeobacteria [09400] archaea
  • Methanobacteriales Methanogenic Archaeobacteria Archaeobacteria Bacteria Microorganisms (Archaeobacteria, Bacteria, Microorganisms) - Methanobacteriaceae [09511] Methanobrevibacter spp.
  • Methanomicrobiales Methanogenic Archaeobacteria Archaeobacteria Bacteria Microorganisms (Archaeobacteria, Bacteria, Microorganisms) - Methanomicrobiaceae [09531] Methanomicrobium mobile
  • Microorganisms (Microorganisms) - Microorganisms [01000] Euryarchaeota
  • archaeal 16S rRNA library archaeal 16S ribosomal RNA library
  • D30 primer
  • D33 primer
  • 03502, Genetics - General
  • 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
  • 14004, Digestive system - Physiology and biochemistry
  • 31000, Physiology and biochemistry of bacteria
  • 31500, Genetics of bacteria and viruses
  • Biochemistry and Molecular Biophysics
  • rumen digestive system
  • PCR polymerase chain reaction DNA amplification method
  • phylogenetic analysis analytical method, molecular genetics method
  • AB304182 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304183 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304184 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304185 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304186 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304187 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304188 Genbank, EMBL, DDBJ nucleotide sequence
  • AB304189 Genbank, EMBL, DDBJ nucleotide sequence
  • Molecular Genetics

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