scholarly journals Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

2020 ◽  
Author(s):  
Anne Daebeler ◽  
Katharina Kitzinger ◽  
Hanna Koch ◽  
Craig W. Herbold ◽  
Michaela Steinfeder ◽  
...  
Keyword(s):  
Alternative Energy ◽  
Amplicon Sequencing ◽  
Extreme Environment ◽  
Survival Strategies ◽  
Alkaline Ph ◽  
Nitrite Oxidation ◽  
Nadh:Quinone Oxidoreductase ◽  
Cation Homeostasis ◽  
Nitrite Oxidizing Bacteria ◽  
Lineage Iv

AbstractNitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members of Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

scholarly journals Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

2020 ◽  
Vol 14 (12) ◽  
pp. 2967-2979 ◽  
Author(s):  
Anne Daebeler ◽  
Katharina Kitzinger ◽  
Hanna Koch ◽  
Craig W. Herbold ◽  
Michaela Steinfeder ◽  
...  
Keyword(s):  
Alternative Energy ◽  
Amplicon Sequencing ◽  
Extreme Environment ◽  
Survival Strategies ◽  
Alkaline Ph ◽  
Nitrite Oxidation ◽  
Nadh:Quinone Oxidoreductase ◽  
Cation Homeostasis ◽  
Nitrite Oxidizing Bacteria ◽  
Lineage Iv

Abstract Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3–12.8 g salt/l), highly alkaline (pH 8.9–10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from  Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

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.

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

AbstractChemolithoautotrophic 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.

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 AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Arnold Y Seo ◽  
Pick-Wei Lau ◽  
Daniel Feliciano ◽  
Prabuddha Sengupta ◽  
Mark A Le Gros ◽  
...  
Keyword(s):  
Energy Source ◽  
Energy Production ◽  
Alternative Energy ◽  
Yeast Cells ◽  
Survival Strategies ◽  
Glucose Starvation ◽  
Term Survival ◽  
Long Term Survival ◽  
Glucose Depletion

Dietary restriction increases the longevity of many organisms, but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy (µ-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger µ-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interacted with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating µ-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate µ-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms.

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.

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.

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