† Present address: Newcastle Research Group in Fossil Fuels and Environmental Geochemistry, Drummond Building, The University, Newcastle-upon-Tyne NE1 7RU, UK.
Partial sequences of the 16S ribosomal RNA genes of eleven autotrophic ammonia-oxidizing bacteria were determined by PCR amplification from small amounts of heat-lysed biomass followed by direct sequencing of PCR products. The sequences were aligned with those of representative Proteobacteria and phylogenetic trees inferred using both parsimony and distance matrix methods. This confirmed that the autotrophic ammonia-oxidizers comprise two major lines of descent within the Proteobacteria. Nitrosomonas spp., Nitrosococcus mobilis, and strains of Nitrosovibrio, Nitrosospira and Nitrosolobus were located in the beta-subdivision. The recovery of Nitrosococcus oceanus strains as a deep branch in the gamma-subdivision supported the RNA catalogue data which had indicated that the genus Nitrosococcus is polyphyletic. The autotrophic ammonia-oxidizing bacteria of the beta-Proteobacteria formed a coherent group which is interpreted as representing a single family. Within this clade, the genera Nitrosovibrio, Nitrosospira and Nitrosolobus exhibited very high levels of homology in their 16S ribosomal RNA gene sequences and can be accommodated within a single genus. Separation of these genera is currently based entirely on gross morphological differences and these can now be considered more appropriate for the identification of species within this group. It is therefore proposed that Nitrosolobus, Nitrosovibrio and Nitrosospira strains be reclassified in a single genus for which the name Nitrosospira has priority.
BockE.,
KoopsH.-P.,
HarmsH.1986; Cell biology of nitrifying bacteria. In Nitrification Special Publication of the Society for General Microbiology 20 pp. 17–38 Edited by
ProsserJ. I.
Oxford: IRL Press;
De LeyJ.,
CattoirH.,
ReynaertsA.1970; The quantitative measurements of DNA hybridization from renaturation rates. European Journal of Biochemistry 12:133–142
DewhirstF. E.,
PasterB. F.,
BrightP. L.1989; Chromobacterium, Eikenella, Kingella, Neisseria, Simonsiella and Vitreoscilla species comprise a major branch of the beta group of Proteobacteria by 16S ribosomal ribonucleic acid sequence comparison : transfer of Eikenella and Simonsiella to the family Neisseriaceae (emend.). International Journal of Systematic Bacteriology 39:258–266
DodsonM. S.,
Mangan.J.,
WatsonS. W.1983; Comparison of deoxyribonucleotide acid homologies of six strains of ammonia-oxidizing bacteria. International Journal of Systematic Bacteriology 33:521–524
EdwardsU.,
RogallT.,
BlöckerH.,
EmdeM.,
BöttgerE. C.1989; Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Research 17:7843–7853
FreneyJ.,
BrunY.,
BesM.,
MeugnierH.,
GrimontF.,
GrimontP. A. D.,
NerviC.,
FleuretteJ.1988; Staphylococcus lugdunensis sp. nov. and Staphylococcus schleiferi sp. nov., two species from human clinical specimens. International Journal of Systematic Bacteriology 38:168–172
FryN. K.,
WarwickS.,
SaundersN. A.,
EmbleyT. M.1991; The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae
. Journal of General Microbiology 137:1215–1222
HallG. H.1986; Nitrification in lakes. In Nitrification Special Publication of the Society for General Microbiology 20 pp. 127–156 Edited by
ProsserJ. I.
Oxford: IRL Press;
HussV. A. R.,
FestlH.,
SchleiferK. H.1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Systematic and Applied Microbiology 4:184–192
JohnsonJ. L.1991; DNA reassociation experiments. In Nucleic Acid Techniques in Bacterial Systematics pp. 205–248 Edited by
StackebrandtE.,
GoodfellowM.
Chichester: John Wiley;
KoopsH.-P.,
MöllerU. C.1991; The lithotrophic ammonia-oxidizing bacteria. In The Prokaryotes, 2nd edn. pp. 2625–2637 Edited by
BalowsA.,
TruperH. G.,
DworkinM.,
HarderW.,
SchleiferK. H.
New York: Fischer-Verlag;
KoopsH.-P.,
BöttcherB.,
MöllerU. C.,
Pommerening-RöserA.,
StehrG.1990; Description of a new species of Nitrosococcus
. Archives of Microbiology 154:244–248
MordarskiM.,
GoodfellowM.,
WilliamsS. T.,
SneathP. H. A.1986; Evaluation of species groups in the genus Streptomyces
. In Biological, Biochemical and Biomedical Aspects of Actinomycetes pp. 517–526 Edited by
SzaboG.,
BiroS.,
GoodfellowM.
Budapest: Akademiai Kiado;
NeefsJ.-M.,
Van De PeerY.,
De RijkP.,
GorisA.,
De WachterR.1991; Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Research 19: (Suppl.) 1987–2015
SaikiR. K.,
GelfandD. H.,
StoffelS.,
ScharfS. J.,
HiguchiG. T.,
HornG. T.,
MullisK. B.,
ErlichH. A.1988; Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
StackebrandtE.1991; Unifying phylogeny and phenotypic diversity. In The Prokaryotes, 2nd edn. pp. 19–48 Edited by
BalowsA.,
TruperH. G.,
DworkinM.,
HarderW.,
SchleiferK. H.
New York: Fischer-Verlag;
SwoffordD.1991; PAUP: Phylogenetic analysis using parsimony, version 3.0. Computer program distributed by Illinois Natural History Survey, Champaign, Illinois, USA.
WatsonS. W.,
BockE.,
HarmsH.,
KoopsH.-P.,
HooperA. B.1989; Nitrifying bacteria. In Bergey’s Manual of Systematic Bacteriology3 pp. 1808–1834 Edited by
StaleyJ. T.,
BryantM. P.,
PfennigN.,
HoltJ. G.
Baltimore: Williams & Wilkins;
WayneL. G.,
BrennerD. J.,
ColwellR. R.,
GrimontP. A. D.,
KandlerO.,
KrichewskyM. I.,
MooreL. H.,
MooreW. E.,
MurrayE.,
StarrM. P.,
TruperH. G.1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 37:463–464
WinogradskyS.,
WinogradskyH.1933; Études sur la microbiologie du sol. VII. Nouvelles recherches sur les organismes de la nitrification. Annals de l’Institut Pasteur 50:350–432
WoeseC. R.,
WeisburgW. G.,
PasterB. J.,
HahnC. M.,
TannerR. S.,
KriegN. R.,
KoopsH.-P.,
HarmsH.,
StackebrandtE.1984b; The phylogeny of the purple bacteria: the beta subdivision. Systematic and Applied Microbiology 5:327–336
WoeseC. R.,
WeisburgW. G.,
HahnC. M.,
PasterB. J.,
ZablenL. B.,
LewisB. J.,
MackeT. J.,
LudwigW.,
StackebrandtE.1985; The phylogeny of the purple bacteria: the gamma subdivision. Systematic and Applied Microbiology 6:25–33