Community structure of ammonia-oxidizing bacteria within anoxic marine sediments

Thomas Erich Freitag, James Ivor Prosser

Research output: Contribution to journalArticle

123 Citations (Scopus)

Abstract

The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and beta- and gamma-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and beta-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for gamma-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of beta-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized beta-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.

Original languageEnglish
Pages (from-to)1359-1371
Number of pages12
JournalApplied and Environmental Microbiology
Volume69
Issue number3
DOIs
Publication statusPublished - Mar 2003

Keywords

  • 16S RIBOSOMAL-RNA
  • GRADIENT GEL-ELECTROPHORESIS
  • POLYMERASE CHAIN-REACTION
  • BETA-SUBDIVISION
  • CLASS PROTEOBACTERIA
  • MOLECULAR ANALYSIS
  • NITROSOMONAS-EUTROPHA
  • NATURAL ENVIRONMENTS
  • NITRIFYING BACTERIA
  • DNA FRAGMENTS

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