Selective enrichment and molecular characterization of a previously uncultured <i>Nitrospira</i>‐like bacterium from activated sludge

Spieck, Eva; Hartwig, Christina; McCormack, Iris; Maixner, Frank; Wagner, Michael; Lipski, André; Daims, Holger

doi:10.1111/j.1462-2920.2005.00905.x

Cited by 143 publications

(168 citation statements)

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“…Selective enrichment of nitrite oxidizing bacteria was successfully performed from all nine soils of a polygon transect with incubation temperatures of Nitrite oxidation at low temperature M Alawi et al 41C, 101C and 171C using 0.3 mM nitrite. Following the protocol for the enrichment of a slow-growing Nitrospira strain (Spieck et al, 2006), permafrost cultures were regularly supplemented with additional substrate, when it was consumed. The highest degree of enrichment of nitrite oxidizing bacteria in relation to the total cell number was achieved in culture 6680, which was purified by plating on lithoautotrophic nitrite agar.…”

Section: Resultsmentioning

confidence: 99%

“…Recently, chemotaxonomic analysis was successful in separating a new species of Nitrospira enriched from activated sludge (Spieck et al, 2006) from known species of this genus. Here, this method was used for the initial characterization of nitrite oxidizing enrichments originating from the Siberian Arctic.…”

Section: Chemotaxonomic Analysismentioning

confidence: 99%

“…For observation by electron microscopy cells were collected at 13 000 r.p.m., fixed with 2.5% (v/v), glutaraldehyde and 2% (w/v) osmium tetroxide and embedded in Epon 812 (Serva) according to a previously published protocol (Spieck et al, 2006). Examination was carried out with a transmission electron microscope (Zeiss model Leo 906E with a CCD camera model 794).…”

Section: Electron Microscopymentioning

confidence: 99%

“…When dense flocs of nitrite oxidizing bacteria had developed, cells were harvested by centrifugation, washed in 0.9% (w/v) NaCl and stored at À201C. Preparation of fatty acid methyl esters and gas chromatographic analyses of the extracts were performed as described previously (Spieck et al, 2006).…”

Section: Analysis Of the Fatty Acidsmentioning

confidence: 99%

“…Consumption of nitrite was regularly checked by the Griess-Ilosavay spot test and replaced in the case of growth. Upscaling was performed as described (Spieck et al, 2006) to get a sufficient cell amount for further analysis. Purity tests were performed and modified by Steinmü ller and Bock (1976).…”

Section: Culturingmentioning

confidence: 99%

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Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

et al. 2007

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Permafrost-affected soils of the Siberian Arctic were investigated with regard to identification of nitrite oxidizing bacteria active at low temperature. Analysis of the fatty acid profiles of enrichment cultures grown at 41C, 101C and 171C revealed a pattern that was different from that of known nitrite oxidizers but was similar to fatty acid profiles of Betaproteobacteria. Electron microscopy of two enrichment cultures grown at 101C showed prevalent cells with a conspicuous ultrastructure. Sequence analysis of the 16S rRNA genes allocated the organisms to a so far uncultivated cluster of the Betaproteobacteria, with Gallionella ferruginea as next related taxonomically described organism. The results demonstrate that a novel genus of chemolithoautotrophic nitrite oxidizing bacteria is present in polygonal tundra soils and can be enriched at low temperatures up to 171C. Cloned sequences with high sequence similarities were previously reported from mesophilic habitats like activated sludge and therefore an involvement of this taxon in nitrite oxidation in nonarctic habitats is suggested. The presented culture will provide an opportunity to correlate nitrification with nonidentified environmental clones in moderate habitats and give insights into mechanisms of cold adaptation. We propose provisional classification of the novel nitrite oxidizing bacterium as 'Candidatus Nitrotoga arctica'.

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Section: Resultsmentioning

confidence: 99%

Section: Chemotaxonomic Analysismentioning

confidence: 99%

Section: Electron Microscopymentioning

confidence: 99%

Section: Analysis Of the Fatty Acidsmentioning

confidence: 99%

Section: Culturingmentioning

confidence: 99%

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Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

et al. 2007

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Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real‐time quantitative PCR

Kindaichi

Kawano²,

Ito

et al. 2006

Biotech & Bioengineering

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Population dynamics of ammonia-oxidizing bacteria (AOB) and uncultured Nitrospira-like nitrite-oxidizing bacteria (NOB) dominated in autotrophic nitrifying biofilms were determined by using real-time quantitative polymerase chain reaction (RTQ-PCR) and fluorescence in situ hybridization (FISH). Although two quantitative techniques gave the comparable results, the RTQ-PCR assay was easier and faster than the FISH technique for quantification of both nitrifying bacteria in dense microcolony-forming nitrifying biofilms. Using this RTQ-PCR assay, we could successfully determine the maximum specific growth rate (mu = 0.021/h) of uncultured Nitrospira-like NOB in the suspended enrichment culture. The population dynamics of nitrifying bacteria in the biofilm revealed that once they formed the biofilm, the both nitrifying bacteria grew slower than in planktonic cultures. We also calculated the spatial distributions of average specific growth rates of both nitrifying bacteria in the biofilm based on the concentration profiles of NH4+, NO2-, and O2, which were determined by microelectrodes, and the double-Monod model. This simple model estimation could explain the stratified spatial distribution of AOB and Nitrospira-like NOB in the biofilm. The combination of culture-independent molecular techniques and microelectrode measurements is a very powerful approach to analyze the in situ kinetics and ecophysiology of nitrifying bacteria including uncultured Nitrospira-like NOB in complex biofilm communities.

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Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

et al. 2021

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The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammoniaoxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

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Selective enrichment and molecular characterization of a previously uncultured Nitrospira‐like bacterium from activated sludge

Cited by 143 publications

References 50 publications

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real‐time quantitative PCR

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

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