scholarly journals Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genusNitrospira

2015 ◽  
Vol 112 (36) ◽  
pp. 11371-11376 ◽  
Author(s):  
Hanna Koch ◽  
Sebastian Lücker ◽  
Mads Albertsen ◽  
Katharina Kitzinger ◽  
Craig Herbold ◽  
...  
Keyword(s):  
Niche Partitioning ◽  
Wide Distribution ◽  
Key Factors ◽  
Nitrite Oxidation ◽  
Ecophysiological Traits ◽  
Metabolic Versatility ◽  
Nitrite Oxidizing Bacteria ◽  
Freshwater Habitats ◽  
Ecological Success ◽  
Nitrite Oxidizers

Nitrospiraare a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data fromNitrospira moscoviensisrepresenting the ubiquitousNitrospiralineage II, we identified ecophysiological traits that contribute to the ecological success ofNitrospira. Unexpectedly,N. moscoviensispossesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enablesN. moscoviensisto supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes inNitrospira lentafrom activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allowsN. moscoviensisto use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared withNitrospira defluviifrom lineage I,N. moscoviensisshares theNitrospiracore metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity ofNitrospirain natural and engineered ecosystems.

scholarly journals Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

2020 ◽  
Author(s):  
Barbara Bayer ◽  
Mak A. Saito ◽  
Matthew R. McIlvin ◽  
Sebastian Lücker ◽  
Dawn M. Moran ◽  
...  
Keyword(s):  
Alternative Energy ◽  
Uv Light ◽  
Niche Differentiation ◽  
Nitrite Oxidation ◽  
Metabolic Potential ◽  
Metabolic Versatility ◽  
Test Genome ◽  
Nitrite Oxidizing Bacteria ◽  
Obligate Chemolithoautotroph ◽  
Proteomic Response

AbstractThe genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T 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 pCO2, and requires exogenous vitamin B12. 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) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 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.

scholarly journals Characterization of the First “CandidatusNitrotoga” Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Katharina Kitzinger ◽  
Hanna Koch ◽  
Sebastian Lücker ◽  
Christopher J. Sedlacek ◽  
Craig Herbold ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Nitrogen Cycle ◽  
Alternative Energy ◽  
Carbon Fixation ◽  
Metagenomic Data ◽  
Nitrite Oxidation ◽  
Metabolic Versatility ◽  
Nitrite Oxidizing Bacteria ◽  
Genes Encoding

ABSTRACTNitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “CandidatusNitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “Ca. Nitrotoga” culture was available. Here we obtained the first “Ca. Nitrotoga” isolate from activated sludge. This organism, “CandidatusNitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “Ca. Nitrotoga” enrichments, which were described as cold-adapted NOB. “Ca. Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO2−) and nitrate (up to 25 mM NO3−). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparentKm(Km(app)) of ~89 µM nitrite and aVmaxof ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “Ca. Nitrotoga fabula” were reconstructed from the closed genome. “Ca. Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “Ca. Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “Ca. Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “Ca. Nitrotoga fabula” to survive nitrite depletion and colonize new niches.IMPORTANCENitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus “CandidatusNitrotoga” and performed a detailed physiological and genomic characterization of this organism (“CandidatusNitrotoga fabula”). Differences between key phenotypic properties of “Ca. Nitrotoga fabula” and those of previously enriched “Ca. Nitrotoga” members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that “Ca. Nitrotoga” are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in “Ca. Nitrotoga fabula” expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.

scholarly journals Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

2020 ◽  
Author(s):  
Barbara Bayer ◽  
Mak A. Saito ◽  
Matthew R. McIlvin ◽  
Sebastian Lücker ◽  
Dawn M. Moran ◽  
...  
Keyword(s):  
Alternative Energy ◽  
Metabolic Response ◽  
Uv Light ◽  
Niche Differentiation ◽  
Marine Environments ◽  
Nitrite Oxidation ◽  
Metabolic Versatility ◽  
Test Genome ◽  
Nitrite Oxidizing Bacteria ◽  
Pyruvate:Ferredoxin Oxidoreductase

AbstractThe genus Nitrospira is the most widespread group of chemolithoautotrophic nitrite-oxidizing bacteria that thrive in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T represents the type genus and was isolated from the oceanic water column over 30 years ago, however, its genome has not yet been analyzed. Here, we analyzed the complete genome sequence of N. marina and performed select physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to combat oxidative, osmotic and UV-light induced stress and low dissolved pCO2, and is able to grow chemoorganotrophically on formate. We further investigated the metabolic response of N. marina to low (∼5.6 µM) O2 concentrations commonly encountered in marine environments with high nitrite concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation. Additionally, a Cu/Zn-binding superoxide dismutase increased in abundance potentially protecting this putatively more O2-sensitive POR complex from oxidative damage. An increase in abundance of proteins involved in alternative energy metabolisms, including type 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 important insights into the metabolic diversity and niche differentiation of NOB in marine environments.

scholarly journals Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

2021 ◽  
Author(s):  
Xin Sun ◽  
Claudia Frey ◽  
Emilio Garcia-Robledo ◽  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Nitrogen Loss ◽  
Niche Differentiation ◽  
Nitrite Reduction ◽  
Nitrite Oxidation ◽  
Fixed Nitrogen ◽  
Anoxic Waters ◽  
Biogeochemical Models ◽  
Nitrite Oxidizing Bacteria ◽  
Oxygen Addition ◽  
Oxygen Minimum

AbstractNitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.

scholarly journals Keeping a Completely Autotrophic Nitrogen Removal over Nitrite System Effective in Treating Low Ammonium Wastewater by Adopting an Alternative Low and High Ammonium Influent Regime

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Qinglong Chang ◽  
Weigang Wang ◽  
Jie Chen ◽  
Yayi Wang
Keyword(s):  
High Throughput ◽  
Nitrogen Removal ◽  
High Throughput Sequencing ◽  
Operating Mode ◽  
Ammonium Concentration ◽  
Nitrite Oxidation ◽  
Time Control ◽  
Nitrite Oxidizing Bacteria ◽  
Excessive Proliferation ◽  
Autotrophic Nitrogen Removal

An alternative low and high ammonium influent regime was proposed and adopted to keep a completely autotrophic nitrogen removal over nitrite (CANON) effective when treating low ammonium wastewater. Results show that, by cyclic operating at an alternative low and high ammonium concentration for 10 days and 28 days, the CANON system could effectively treat low ammonium wastewater. Excessive proliferation of nitrite oxidizing bacteria (NOB) under low ammonium environment was still the challenge for the stable CANON operation; but with 28 days of a high ammonium treatment combined with a sludge retention time control, the NOB overproliferated in the low ammonium operational period could be under control. Specifically, when the nitrite oxidation rate reached 8 g N/m3/h, the CANON system should enter the high ammonium influent operating mode. 16S rDNA high-throughput sequencing results show that the appropriate sludge discharging provided an environment favoring Candidatus Jettenia.

Inhibition of Nitrification of Ammonia-Rich Wastewater in Immobilized Nitrifiers System

2011 ◽  
Vol 183-185 ◽  
pp. 197-200 ◽  
Author(s):  
Zhi Rong Li ◽  
Zhi Zhang ◽  
Zhen Jia Zhang
Keyword(s):  
Ammonia Oxidation ◽  
High Strength ◽  
Ammonia Solution ◽  
Ammonia Oxidizing Bacteria ◽  
Inhibition Kinetics ◽  
Nitrite Oxidation ◽  
Haldane Model ◽  
Nitrite Oxidizing Bacteria ◽  
Inhibition Of Nitrification ◽  
Kinetics Of

Inhibition of ammonia oxidation and nitrite oxidation was studied in an immobilized biomass system. Ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) suffered different inhibition in ammonia-rich wastewater. NOB started to be inhibited when FA (free ammonia) was 2mg/L, and was totally inhibited when FA was 8mg/L. AOB started to be inhibited when FA was 22mg/L, and tended to lose activity when FA was higher than 170mg/L. Inhibition kinetics of ammonia oxidation and nitrite oxidation could be described by Haldane model. Immobilization alleviated inhibition of FA to nitrifiers, maintaining high activity even at high strength ammonia solution. Partial nitrification could be achieved by varying degrees of inhibition of FA to AOB and NOB.

Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records

Zootaxa ◽  
2019 ◽  
Vol 4588 (1) ◽  
pp. 1
Author(s):  
RONALD FRICKE ◽  
GERALD R. ALLEN ◽  
DIETMAR AMON ◽  
SERGE ANDRÉFOUËT ◽  
WEI-JEN CHEN ◽  
...  
Keyword(s):  
New Records ◽  
Fish Fauna ◽  
Wide Distribution ◽  
Estuarine Fish ◽  
Western Pacific Ocean ◽  
Transitional Waters ◽  
Estuarine Fishes ◽  
Marine Habitats ◽  
Freshwater Habitats ◽  
Wide Distribution Range

A checklist of the marine and estuarine fishes of New Ireland Province is presented, with special emphasis on Kavieng District, combining both previous and new records. After the recent KAVIENG 2014 expedition, a total of 1325 species in 153 families were recorded from the region. The largest families are the Gobiidae, Pomacentridae, Labridae, Serranidae, Apogonidae, Lutjanidae, Chaetodontidae, Blenniidae, Carangidae, Acanthuridae, Scaridae, Holocentridae, Syn-gnathidae, Lethrinidae and Scorpaenidae. A total of 810 fish species (61.1 % of the total marine and estuarine fish fauna) are recorded from New Ireland for the first time.The fish fauna of New Ireland includes 142 species in transitional waters and 1264 species in marine habitats, and 54 species species in freshwater habitats. Zoogeographically, 1179 species have a wide distribution range, most frequently a broad Indo-West Pacific distribution. Among the remaining species, just 12 are endemic to New Ireland. 

Nitrite oxidation inhibition by hydroxylamine: experimental and model evaluation

2004 ◽  
Vol 50 (6) ◽  
pp. 295-304 ◽  
Author(s):  
P. (Lek) Noophan ◽  
L.A. Figueroa ◽  
J. Munakata-Marr
Keyword(s):  
Oxidation Rate ◽  
Biological Nitrogen Removal ◽  
Ammonia Oxidizers ◽  
Batch Experiments ◽  
Nitrite Oxidation ◽  
Ph Values ◽  
Initial Ph ◽  
Nitrogen Concentrations ◽  
Biological Nitrogen ◽  
Nitrite Oxidizers

A proposed approach for biological nitrogen removal significantly reduces cost by reducing biomass production and carbon requirements via inhibition of nitrite oxidation (NO2− to NO3−). Batch experiments were conducted to examine the effect of hydroxylamine (HM) on nitrite oxidizers, ammonia oxidizers, and nitrite reducers. Hydroxylamine effect experiments were done at initial pH values of 7.4-8.4, nitrogen concentrations of 100 mg N/L, biomass concentrations of 100-400 mg VSS/L and HM dosages up to 43 mg/L. Nitrite oxidizer activity was completely inhibited by HM at dosages of 7.0 and 8.9 mg/L for pH values of 8.4 and 7.6, respectively. Relatively low HM concentrations (0.35-5.5 mg/L) can be used to completely inhibit nitrite oxidation, but do not significantly affect ammonia oxidizers and nitrite reducers. A model developed to describe the effect of pH on nitrite oxidation rate fits the data well (R2 = 0.89) with values for Vmax of 0.372 (mg N/mg VSS-hr), pH* of 7.72, and the inhibition constant Kh of 0.154. Incorporation of HM inhibition into the model provided a good fit to relative nitrite oxidation rate as a function of undissociated HM concentration (R2 = 0.80, Vmax = 0.028 mg N/mg VSS-hr, pH* = 7.89, Kh * 0.302, a * 0.195, and Ki = 0.277 mg/L).

scholarly journals NcPuf1 Is a Key Virulence Factor in Neospora caninum

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1019
Author(s):  
Chenrong Wang ◽  
Congshan Yang ◽  
Jing Liu ◽  
Qun Liu
Keyword(s):  
Neospora Caninum ◽  
Wide Distribution ◽  
Key Factors ◽  
Processing Bodies ◽  
Puf Proteins ◽  
P Bodies ◽  
Intracellular Parasites ◽  
Binding Factor ◽  
Puf Protein

Background: Neospora caninum is an apicomplexan parasite that infects many mammals and particularly causes abortion in cattle. The key factors in its wide distribution are its virulence and ability to transform between tachyzoite and bradyzoite forms. However, the factors are not well understood. Although Puf protein (named after Pumilio from Drosophila melanogaster and fem-3 binding factor from Caenorhabditis elegans) have a functionally conserved role in promoting proliferation and inhibiting differentiation in many eukaryotes, the function of the Puf proteins in N. caninum is poorly understood. Methods: The CRISPR/CAS9 system was used to identify and study the function of the Puf protein in N. caninum. Results: We showed that N. caninum encodes a Puf protein, which was designated NcPuf1. NcPuf1 is found in the cytoplasm in intracellular parasites and in processing bodies (P-bodies), which are reported for the first time in N. caninum in extracellular parasites. NcPuf1 is not needed for the formation of P-bodies in N. caninum. The deletion of NcPuf1 (ΔNcPuf1) does not affect the differentiation in vitro and tissue cysts formation in the mouse brain. However, ΔNcPuf1 resulted in decreases in the proliferative capacity of N. caninum in vitro and virulence in mice. Conclusions: Altogether, the disruption of NcPuf1 does not affect bradyzoites differentiation, but seriously impairs tachyzoite proliferation in vitro and virulence in mice. These results can provide a theoretical basis for the development of attenuated vaccines to prevent the infection of N. caninum.

scholarly journals Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting

2020 ◽  
Author(s):  
Anna J. Mueller ◽  
Man-Young Jung ◽  
Cameron R. Strachan ◽  
Craig W. Herbold ◽  
Rasmus H. Kirkegaard ◽  
...  
Keyword(s):  
Cell Sorting ◽  
Alternative Energy ◽  
Niche Differentiation ◽  
Organic N ◽  
Nitrite Oxidation ◽  
Terminal Oxidases ◽  
Half Saturation Constant ◽  
Nitrite Oxidizing Bacteria ◽  
Activity Screening ◽  
Shed Light

Abstract Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named “Candidatus Nitrohelix vancouverensis” and “Candidatus Nitronauta litoralis”, shed light on the niche differentiation and potential ecological roles of Nitrospinae.

Sign in / Sign up

Export Citation Format

Share Document