The Experts below are selected from a list of 162 Experts worldwide ranked by ideXlab platform
Eva Spieck - One of the best experts on this subject based on the ideXlab platform.
-
Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea.
Frontiers in microbiology, 2020Co-Authors: Eva Spieck, Sebastian Lücker, Sabine Keuter, Katharina Sass, Sophia Hirschmann, Michael Spohn, Daniela Indenbirken, Linnea F. M. Kop, Alejandra GiavenoAbstract:Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially Nitrite oxidation – the second step of nitrification – is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic Nitrite-Oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex Nitrite-Oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and Nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high Nitrite concentrations. Growth was optimal at temperatures of 35 - 37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of Nitrite and ammonium, with an optimal incubation temperature of 37°C.
-
Low Temperature and Neutral pH Define "Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii.
Applied and environmental microbiology, 2019Co-Authors: Simone Wegen, Boris Nowka, Eva SpieckAbstract:ABSTRACT Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and Nitrite. Besides Nitrospira, “Candidatus Nitrotoga” has been identified as a key Nitrite-Oxidizing Bacterium (NOB) performing the second step of nitrification, Nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii. Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM Nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii. Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species. IMPORTANCE “Ca. Nitrotoga” is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low Nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the Nitrite-Oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
-
The draft genome sequence of "Nitrospira lenta" strain BS10, a Nitrite Oxidizing Bacterium isolated from activated sludge.
Standards in genomic sciences, 2018Co-Authors: Dimitra Sakoula, Eva Spieck, Holger Daims, Boris Nowka, Sebastian LückerAbstract:The genus Nitrospira is considered to be the most widespread and abundant group of Nitrite-Oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of “Nitrospira lenta” strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of “N. lenta” has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the “N. lenta” core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and “N. defluvii”, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of “N. lenta” provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.
-
Longterm Monitoring of Nitrification and Nitrifying Communities during Biofilter Activation of Two Marine Recirculation Aquaculture Systems (RAS)
International Journal of Aquaculture and Fishery Sciences - Peertechz Publications, 2017Co-Authors: Sabine Keuter, Stefanie Beth, Gerrit Quantz, Carsten Schulz, Eva SpieckAbstract:Biofilters are crucial and costly components in marine recirculating aquaculture systems. However, not much is known about the settlement of nitrifying organisms and developing nitrification rates during the start-up phases of these reactors. The nitrifying microorganisms in moving bed biofilters of two marine recirculation aquaculture systems identical in construction were monitored for 388 and 477 days by PCR based methods, accompanied by laboratory nitrifying activity tests. Ammonia and Nitrite were added to the recirculating aquaculture system 1, while system 2 was spiked with fish feed. On day 88, system 1 was stocked with turbot (at 17 °C) and on day 126 system 2 was stocked with sea bass cultivated at 22 °C. The potential nitrification rates corresponded well to the conditions in the operating systems, and in both systems slowly developing Nitrite oxidation rates led to high Nitrite peaks. However, after 218 (biofilter 1) and 286 (biofilter 2) days, potential rates of Nitrite Oxidizing bacteria outreached those of ammonia Oxidizing bacteria. The Nitrite Oxidizing bacteria were remarkably diverse on the genus level, and for the first time Nitrotoga was detected in marine biofilter systems. Nitrospira was assumed to be the most dominant Nitrite Oxidizing Bacterium, also confirmed by electron microscopy. The ammonia Oxidizing organisms belong almost exclusively to Nitrosomonas, of which dominant species shifted in both systems over time. The high similarities of some 16S rRNA gene sequences of Nitrospira and Nitrosomonas to sequences found previously in other marine recirculating aquaculture systems suggested that the species are characteristic for this artificial ecosystem.
-
Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.
Genome announcements, 2017Co-Authors: Brett L. Mellbye, Eva Spieck, Peter J. Bottomley, Edward W. Davis, Jeff H. Chang, Luis A. Sayavedra-sotoAbstract:Here, we present the 3.9-Mb draft genome sequence of Nitrobacter vulgaris strain Ab1, which was isolated from a sewage system in Hamburg, Germany. The analysis of its genome sequence will contribute to our knowledge of Nitrite-Oxidizing bacteria and acyl-homoserine lactone quorum sensing in nitrifying bacteria.
Sebastian Lücker - One of the best experts on this subject based on the ideXlab platform.
-
Metabolic versatility of the Nitrite-Oxidizing Bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions
The ISME Journal, 2020Co-Authors: Barbara Bayer, Sebastian Lücker, Mak A. Saito, Matthew R. Mcilvin, Dawn M. Moran, Thomas S. Lankiewicz, Christopher L. Dupont, Alyson E. SantoroAbstract:The genus Nitrospira is the most widespread group of Nitrite-Oxidizing bacteria and thrives in diverse natural and engineered ecosystems . Nitrospira marina Nb-295^T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved p CO_2, and requires exogenous vitamin B_12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O_2 concentrations. The abundance of a potentially more efficient CO_2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb _ 3 -type terminal oxidase increased under O_2 limitation, suggesting a role in sustaining Nitrite oxidation-driven autotrophy. This putatively more O_2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O_2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic Nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
-
Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea.
Frontiers in microbiology, 2020Co-Authors: Eva Spieck, Sebastian Lücker, Sabine Keuter, Katharina Sass, Sophia Hirschmann, Michael Spohn, Daniela Indenbirken, Linnea F. M. Kop, Alejandra GiavenoAbstract:Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially Nitrite oxidation – the second step of nitrification – is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic Nitrite-Oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex Nitrite-Oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and Nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high Nitrite concentrations. Growth was optimal at temperatures of 35 - 37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of Nitrite and ammonium, with an optimal incubation temperature of 37°C.
-
The draft genome sequence of "Nitrospira lenta" strain BS10, a Nitrite Oxidizing Bacterium isolated from activated sludge.
Standards in genomic sciences, 2018Co-Authors: Dimitra Sakoula, Eva Spieck, Holger Daims, Boris Nowka, Sebastian LückerAbstract:The genus Nitrospira is considered to be the most widespread and abundant group of Nitrite-Oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of “Nitrospira lenta” strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of “N. lenta” has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the “N. lenta” core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and “N. defluvii”, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of “N. lenta” provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.
-
Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic Nitrite-Oxidizing Bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Dimitry Y. Sorokin, Sebastian Lücker, Dana Vejmelkova, W.i.c. Rijpstra, Gerard Muyzer, Galina M. Streshinskaya, Jaap S. Sinninghe Damsté, Robbert Kleerbezem, Mark C.m. Van Loosdrecht, Holger DaimsAbstract:A novel Nitrite-Oxidizing Bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with Nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing Nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with Nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).
-
Nitrification expanded: discovery, physiology and genomics of a Nitrite-Oxidizing Bacterium from the phylum Chloroflexi
The ISME Journal, 2012Co-Authors: Dimitry Y. Sorokin, Sebastian Lücker, Dana Vejmelkova, Nadezhda A. Kostrikina, Robbert Kleerebezem, W.i.c. Rijpstra, D. Le Paslier, Gerard Muyzer, Jaap S. Sinninghe Damsté, Michael WagnerAbstract:Nitrite-Oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic Nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus , was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for Nitrite ( K _s=1 m M ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known Nitrite oxidizers. N. hollandicus grows on Nitrite and CO_2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO_2 fixation by the Calvin cycle and a Nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial Nitrite oxidizers, Nitrobacter and Nitrococcus . Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from Nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.
Holger Daims - One of the best experts on this subject based on the ideXlab platform.
-
The draft genome sequence of "Nitrospira lenta" strain BS10, a Nitrite Oxidizing Bacterium isolated from activated sludge.
Standards in genomic sciences, 2018Co-Authors: Dimitra Sakoula, Eva Spieck, Holger Daims, Boris Nowka, Sebastian LückerAbstract:The genus Nitrospira is considered to be the most widespread and abundant group of Nitrite-Oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of “Nitrospira lenta” strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of “N. lenta” has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the “N. lenta” core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and “N. defluvii”, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of “N. lenta” provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.
-
Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic Nitrite-Oxidizing Bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Dimitry Y. Sorokin, Sebastian Lücker, Dana Vejmelkova, W.i.c. Rijpstra, Gerard Muyzer, Galina M. Streshinskaya, Jaap S. Sinninghe Damsté, Robbert Kleerbezem, Mark C.m. Van Loosdrecht, Holger DaimsAbstract:A novel Nitrite-Oxidizing Bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with Nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing Nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with Nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).
-
unexpected diversity of chlorite dismutases a catalytically efficient dimeric enzyme from nitrobacter winogradskyi
Journal of Bacteriology, 2011Co-Authors: Georg Mlynek, Michael Wagner, Frank Maixner, Bjorn Sjoblom, Julius Kostan, Stephanie Fureder, Kira Gysel, Paul G Furtmuller, Christian Obinger, Holger DaimsAbstract:ABSTRACT Chlorite dismutase (Cld) is a unique heme enzyme catalyzing the conversion of ClO2− to Cl− and O2. Cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a Nitrite-Oxidizing Bacterium of the genus Nitrospira. Here we characterized a novel Cld-like protein from the chemolithoautotrophic Nitrite oxidizer Nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. Its three-dimensional (3D) crystal structure revealed a dimer of two identical subunits, which sharply contrasts with the penta- or hexameric structures of other chlorite dismutases. Despite a truncated N-terminal domain in each subunit, this novel enzyme turned out to be a highly efficient chlorite dismutase (Km = 90 μM; kcat = 190 s−1; kcat/Km = 2.1 × 106 M−1 s−1), demonstrating a greater structural and phylogenetic diversity of these enzymes than was previously known. Based on comparative analyses of Cld sequences and 3D structures, signature amino acid residues that can be employed to assess whether uncharacterized Cld-like proteins may have a high chlorite-dismutating activity were identified. Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other Nitrite oxidizers.
-
Isolation and characterization of a moderately thermophilic Nitrite-Oxidizing Bacterium from a geothermal spring.
FEMS Microbiology Ecology, 2010Co-Authors: Elena V. Lebedeva, Sebastian Lücker, Holger Daims, Frank Maixner, Sandra Off, Sabine Zumbrägel, Myriam Kruse, Ayvi Shagzhina, André Lipski, Eva SpieckAbstract:Geothermal environments are a suitable habitat for nitrifying microorganisms. Conventional and molecular techniques indicated that chemolithoautotrophic Nitrite-Oxidizing bacteria affiliated with the genus Nitrospira are widespread in environments with elevated temperatures up to 55 °C in Asia, Europe, and Australia. However, until now, no thermophilic pure cultures of Nitrospira were available, and the physiology of these bacteria was mostly uncharacterized. Here, we report on the isolation and characterization of a novel thermophilic Nitrospira strain from a microbial mat of the terrestrial geothermal spring Gorjachinsk (pH 8.6; temperature 48 °C) from the Baikal rift zone (Russia). Based on phenotypic properties, chemotaxonomic data, and 16S rRNA gene phylogeny, the isolate was assigned to the genus Nitrospira as a representative of a novel species, for which the name Nitrospira calida is proposed. A highly similar 16S rRNA gene sequence (99.6% similarity) was detected in a Garga spring enrichment grown at 46 °C, whereas three further thermophilic Nitrospira enrichments from the Garga spring and from a Kamchatka Peninsula (Russia) terrestrial hot spring could be clearly distinguished from N. calida (93.6–96.1% 16S rRNA gene sequence similarity). The findings confirmed that Nitrospira drive Nitrite oxidation in moderate thermophilic habitats and also indicated an unexpected diversity of heat-adapted Nitrospira in geothermal hot springs.
-
structural and functional characterisation of the chlorite dismutase from the Nitrite Oxidizing Bacterium candidatus nitrospira defluvii identification of a catalytically important amino acid residue
Journal of Structural Biology, 2010Co-Authors: Julius Kostan, Michael Wagner, Holger Daims, Frank Maixner, Georg Mlynek, Bjorn Sjoblom, Paul G Furtmuller, Christian Obinger, Kristina DjinoviccarugoAbstract:Abstract Chlorite dismutase (Cld) is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen (reaction: ClO 2 - → Cl - + O 2 ). Since bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment, it is of high interest to understand the molecular mechanism of chlorite detoxification. Here we investigate a highly active Cld from Candidatus Nitrospira defluvii (NdCld), a key nitrifier in biological wastewater treatment, using a comprehensive structural, biochemical and bioinformatics approach. We determined the crystal structure of Cld from Candidatus Nitrospira defluvii and showed that functional NdCld is a homopentamer possessing a fold found in other Clds and Cld-like enzymes. To investigate the Cld function in more detail, site-directed mutagenesis of a catalytically important residue (Arg173) was performed and two enzyme mutants were structurally and biochemically characterized. Arginine 173 is demonstrated to play a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation. Furthermore, using a structure-based sequence alignment, we show that the residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins. Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor.
Luis A. Sayavedra-soto - One of the best experts on this subject based on the ideXlab platform.
-
Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi
American Society for Microbiology, 2018Co-Authors: Brett L. Mellbye, Andrew T. Giguere, Ganti S. Murthy, Peter J. Bottomley, Luis A. Sayavedra-soto, Frank W. R. ChaplenAbstract:Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH4+). Up to 60% of NH4+-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO3−), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO2], and nitrous oxide [N2O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.Nitrification, the aerobic oxidation of ammonia to nitrate via Nitrite, emits nitrogen (N) oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-Oxidizing Bacterium Nitrosomonas europaea and the Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1
-
Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.
Genome announcements, 2017Co-Authors: Brett L. Mellbye, Eva Spieck, Peter J. Bottomley, Edward W. Davis, Jeff H. Chang, Luis A. Sayavedra-sotoAbstract:Here, we present the 3.9-Mb draft genome sequence of Nitrobacter vulgaris strain Ab1, which was isolated from a sewage system in Hamburg, Germany. The analysis of its genome sequence will contribute to our knowledge of Nitrite-Oxidizing bacteria and acyl-homoserine lactone quorum sensing in nitrifying bacteria.
-
Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification
mBio, 2016Co-Authors: Brett L. Mellbye, Andrew T. Giguere, Peter J. Bottomley, Luis A. Sayavedra-sotoAbstract:ABSTRACT Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via Nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO 2 , and N 2 O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing Nitrite oxidizer, Nitrobacter winogradskyi. We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes ( ncgABC ) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi . Production and consumption of NO x increased and production of N 2 O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable. IMPORTANCE Bacterial cell-cell signaling, or quorum sensing (QS), is a method of bacterial communication and gene regulation that is well studied in bacteria. However, little is known about the purpose of QS in many environmentally important bacteria. Here, we demonstrate quorum quenching coupled with mRNA-Seq to identify QS-controlled genes and phenotypes in Nitrobacter winogradskyi, a Nitrite-Oxidizing Bacterium. Nitrite oxidizers play an important role in the nitrogen cycle though their participation in nitrification, the aerobic oxidation of ammonia to nitrate via Nitrite. Our quorum quenching approach revealed that QS influences production and consumption of environmentally important nitrogen oxide gases (NO, NO 2 , and N 2 O) in N. winogradskyi . This study demonstrated a novel technique for studying QS in difficult-to-work-with microorganisms and showed that Nitrite oxidizers might also contribute to nitrification-dependent production of nitrogen oxide gases that contribute to global warming.
-
Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers
Applied and environmental microbiology, 2015Co-Authors: Brett L. Mellbye, Peter J. Bottomley, Luis A. Sayavedra-sotoAbstract:ABSTRACT Nitrobacter winogradskyi is a chemolithotrophic Bacterium that plays a role in the nitrogen cycle by Oxidizing Nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this Bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS.
-
Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations.
FEMS microbiology letters, 2015Co-Authors: Luis A. Sayavedra-soto, Brett L. Mellbye, Peter J. Bottomley, Frank W. R. Chaplen, Jeff H. Chang, Rebecca V. Ferrell, Michael D. Dobie, Alex Buchanan, Daniel J. ArpAbstract:Nitrobacter winogradskyi Nb-255 is a Nitrite-Oxidizing Bacterium that can grow solely on Nitrite (NO2−) as a source of energy and nitrogen. In most natural situations, NO2− oxidation is coupled closely to ammonium (NH4+) oxidation by bacteria and archaea and, conceptually, N. winogradskyi can save energy using NH4+ to meet its N -biosynthetic requirements. Interestingly, NH4+ delayed the growth of N. winogradskyi when at concentrations higher than 35 mM, but grew well at concentrations below 25 mM NH4+ while adjusting the expression of 24% of its genes. Notable genes that changed in expression included those with roles in nitrogen and carbon assimilation. Contrary to expectations, higher expression of glutamate synthase (GOGAT), instead of glutamate dehydrogenase, was detected at higher NH4+ concentration. Genes in assimilatory NO2− metabolism and the degradation of glycogen and biofilm/motility were downregulated when N. winogradskyi was grown in the presence of NH4+. Nitrobacter winogradsky i grown in medium with 25 mM NH4+ upregulated genes in post-translational modification, protein turnover, biogenesis and chaperons. The data suggest that N. winogradskyi physiology is modified in the presence of NH4+ and is likely to be modified during coupled nitrification with NH3 oxidizers.
Takashi Yamaguchi - One of the best experts on this subject based on the ideXlab platform.
-
effluent treatment in an aquaponics based closed aquaculture system with single stage nitrification denitrification using a down flow hanging sponge reactor
International Biodeterioration & Biodegradation, 2018Co-Authors: Daisuke Tanikawa, Hiromi Tokuzawa, Yuga Hirakata, Masashi Hatamoto, Yuka Nakamura, Takashi YamaguchiAbstract:Abstract A laboratory-scale demonstration of the aquaculture effluent treatment was conducted in a system that combined a down-flow hanging sponge (DHS) reactor and a hydroponic cultivation bed (HCB). Cyprinus carpio was used as a model aquaculture fish and Cupsicum frutescens was used as a model hydroponic plant. The aquarium water was circulated through the HCB and DHS using a submerged pump. The experiment was divided into six phases in which the sodium acetate solution was supplied using different feeding patterns. The sodium acetate solution acted as a carbon source and not only eliminated nitrogen through denitrification but also increased the alkalinity through biological degradation of the acetate. Denitrification was observed to eliminate 7.7% of the total nitrogen at the inlet out of which 53.5% was converted by C. frutescens to form a fruit. The microbial community in the sludge that was retained in the DHS contained both nitrifying and denitrifying bacteria. Nitrososhaera was the dominant ammonia-Oxidizing Bacterium, whereas Nitrospira was the dominant Nitrite-Oxidizing Bacterium. Further, Opitutus acted as the dominant denitrifying Bacterium. No major bacterial pathogen was detected in the DHS–HCB system. The study confirmed that the DHS system provided single-stage nitrification–denitrification and that the overall DHS–HCB system provided a low-cost and high-performance aquaculture effluent treatment system that is capable of being used for safe food production.
-
Effluent treatment in an aquaponics-based closed aquaculture system with single-stage nitrification–denitrification using a down-flow hanging sponge reactor
International Biodeterioration & Biodegradation, 2018Co-Authors: Daisuke Tanikawa, Hiromi Tokuzawa, Yuga Hirakata, Masashi Hatamoto, Yuka Nakamura, Takashi YamaguchiAbstract:Abstract A laboratory-scale demonstration of the aquaculture effluent treatment was conducted in a system that combined a down-flow hanging sponge (DHS) reactor and a hydroponic cultivation bed (HCB). Cyprinus carpio was used as a model aquaculture fish and Cupsicum frutescens was used as a model hydroponic plant. The aquarium water was circulated through the HCB and DHS using a submerged pump. The experiment was divided into six phases in which the sodium acetate solution was supplied using different feeding patterns. The sodium acetate solution acted as a carbon source and not only eliminated nitrogen through denitrification but also increased the alkalinity through biological degradation of the acetate. Denitrification was observed to eliminate 7.7% of the total nitrogen at the inlet out of which 53.5% was converted by C. frutescens to form a fruit. The microbial community in the sludge that was retained in the DHS contained both nitrifying and denitrifying bacteria. Nitrososhaera was the dominant ammonia-Oxidizing Bacterium, whereas Nitrospira was the dominant Nitrite-Oxidizing Bacterium. Further, Opitutus acted as the dominant denitrifying Bacterium. No major bacterial pathogen was detected in the DHS–HCB system. The study confirmed that the DHS system provided single-stage nitrification–denitrification and that the overall DHS–HCB system provided a low-cost and high-performance aquaculture effluent treatment system that is capable of being used for safe food production.