title: The phylogenetic affiliation of an uncultured population of ammonia-oxidizing bacteria harboring environmental sequences of amoA cluster-3.
abstract: We investigated the phylogenetic diversity of ammonia-oxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by the cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster- 1 could carry amoA sequences of environmental amoA cluster-3.
authors.affiliation: Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea.
authors.forename: Jin-Kyung
authors.initials: JK
authors.lastname: Hong
authors.forename: Jae-Chang
authors.initials: JC
authors.lastname: Cho
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D003001:Cloning, Molecular; D004275:DNA, Ribosomal / Q000235:genetics; D017753:Ecosystem; D020459:Genes, rRNA; D019015:Geologic Sediments / Q000382:microbiology*; D005810:Multigene Family; D009792:Oceans and Seas; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D020560:Proteobacteria / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase