Description of a new species of Nitrosococcus

Koops, Hans‐Peter; Böttcher, B.; Möller, U. C.; Pommerening‐Röser, Andreas; Stehr, G.

doi:10.1007/bf00248962

Cited by 71 publications

(57 citation statements)

References 11 publications

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“…These organisms were found to be closely related to each other (96.4% identity over 1304 bp of unambiguously aligned sequence), thus confirming the results of DNA-DNA hybridization experiments (Koops & Harms, 1985;Koops et al, 1990). The strains share a common ancestry with the photosynthetic organisms Chromatium and Ectothiorhodospira (Fig.…”

Section: Gamma-subdiv Is Ion Ammonia-oxidizing Bacteriasupporting

confidence: 79%

“…There have been a number of attempts at defining the taxonomic structure within the autotrophic ammonia oxidizers using DNA-DNA base pairing and mol% G + C determinations (Dodson et al, 1983;Koops & Harms, 1985;Koops et al, 1990. While groups of strains which could form the basis of species have been readily recognized using these approaches, they have proved of limited utility for the circumscription of genera.…”

Section: Introductionmentioning

confidence: 99%

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The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences

Head

Hiorns

Embley

et al. 1993

Journal of General Microbiology

347

232

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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.

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Section: Gamma-subdiv Is Ion Ammonia-oxidizing Bacteriasupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences

Head

Hiorns

Embley

et al. 1993

Journal of General Microbiology

347

232

View full text Add to dashboard Cite

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“…The now recognized diversity of genera and species of the ammonia oxidizers includes Nitrosomonas, with at least 10 species (19,23,53), Nitrosococcus (53), with 3 species (22,25,53), Nitrosospira, with 1 recognized species (44,54) and 4 other species indicated by DNA homology studies (24), Nitrosovibnio, with 1 described species (16) and 1 additional species indicated by DNA homology studies (24), and Nitrosolobus, with one described species (49) and 1 additional species indicated by DNA homology studies (24). The nitrite-oxidizing genera have received relatively less attention, and few have been examined by comparative sequence analysis.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria

Alm²,

et al. 1994

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Comparative 16S rRNA sequencing was used to evaluate phylogenetic relationships among selected strains of ammonia-and nitrite-oxidizing bacteria. All characterized strains were shown to be affiliated with the proteobacteria. The study extended recent 16S rRNA-based studies of phylogenetic diversity among nitrifiers by the comparison of eight strains of the genus Nitrobacter and representatives of the genera Nitrospira and Nitrospina. The later genera were shown to be affiliated with the delta subdivision of the proteobacteria but did not share a specific relationship to each other or to other members of the delta subdivision. All characterized Nitrobacter strains constituted a closely related assemblage within the alpha subdivision of the proteobacteria. As previously observed, all ammonia-oxidizing genera except Nitrosococcus oceanus constitute a monophyletic assemblage within the beta subdivision of the proteobacteria. Errors in the 16S rRNA sequences for two strains previously deposited in the databases by other investigators (Nitrosolobus multiformis C-71 and Nitrospira briensis C-128) were corrected. Consideration of physiology and phylogenetic distribution suggested that nitrite-oxidizing bacteria of the alpha and gamma subdivisions are derived from immediate photosynthetic ancestry. Each nitrifier retains the general structural features of the specific ancestor's photosynthetic membrane complex. Thus, the nitrifiers, as a group, apparently are not derived from an ancestral nitrifying phenotype.Biologists have been asking questions concerning the evolutionary origins of, and phylogenetic relationships among, chemolithotrophic microorganisms for well over a century. However, it has been only in the last decade that comparative molecular studies have provided the basis to shape an understanding of their phylogeny. Most notably, the use of comparative rRNA sequencing has provided an all-encompassing phylogenetic framework within which all the chemolithotrophs can be placed. The emerging phylogeny has, in turn, provided insights into their antiquity and the origins of lithotrophic metabolism. For example, sulfur oxidation and iron oxidation appear to be evolutionarily early and widespread metabolic modes that are not confined to a single phylogenetic assemblage of bacteria (27). An University, Evanston, with secondary consideration of cell shape and the highly characteristic cytoplasmic membrane structures (46). All known ammonia-oxidizing bacteria are obligate chemolithoautotrophs. In contrast, some nitrite-oxidizing bacteria are mixotrophs and also can grow heterotrophically (4, 26). Although the existing taxonomy assigns these bacteria to a single family, accumulating biochemical and molecular data do not support their phylogenetic coherence.Physiological and enzymatic data argue against a close relatedness between ammonia and nitrite oxidizers. They employ two very different key enzyme systems for the energygaining oxidation of ammonia and nitrite (5). Comparative sequencing studies based on 16S rRNA oli...

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“…The same strategy is probably used by the most halotolerant, ammonia oxidizer known to date, Nitrosococcus halophilus, which grows with up to 94 g NaCl l -1 (Koops et al, 1990). 'Ca.…”

Section: T R a N S P E P T Id A S E ( G G T ) M E T H Y Lp H O S P H mentioning

confidence: 99%

“…Although the upper salinity limit for autotrophic ammonia oxidation is still uncertain, nitrification appears to be constrained at salt concentrations exceeding 100 g l -1 (Oren, 2011). The obligately halotolerant AOB Nitrosococcus halophilus Nc4, grows optimally at 41 g NaCl l -1 (maximum at 94 g NaCl l -1 ) having been isolated from a salt lagoon (off Sardinia, Mediterranean Sea; Koops et al, 1990). This salinity range is within the values in the BSI habitats studied here (47-199 g NaCl l -1 ; Table 1).…”

Section: Bioenergetic Considerationsmentioning

confidence: 99%

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

et al. 2014

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The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares B54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

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Description of a new species of Nitrosococcus

Cited by 71 publications

References 11 publications

The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences

The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences

Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

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