scholarly journals Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Christopher J. Sedlacek ◽  
Andrew T. Giguere ◽  
Michael D. Dobie ◽  
Brett L. Mellbye ◽  
Rebecca V. Ferrell ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Agricultural Soils ◽  
Nitrosomonas Europaea ◽  
Oxygen Limitation ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Effect Of Oxygen

ABSTRACT Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria. IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

scholarly journals Transcriptomic response of Nitrosomonas europaea transitioned from ammonia- to oxygen-limited steady-state growth

2019 ◽  
Author(s):  
Christopher J. Sedlacek ◽  
Andrew T. Giguere ◽  
Michael D. Dobie ◽  
Brett L. Mellbye ◽  
Rebecca V Ferrell ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Agricultural Soils ◽  
Nitrosomonas Europaea ◽  
Oxygen Limitation ◽  
Ammonia Oxidizing Bacteria ◽  
Limited Growth ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Effect Of Oxygen

AbstractAmmonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g. by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia to nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regards to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other AOB.ImportanceNitrification is a ubiquitous, microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments increasing the eutrophication of downstream aquatic ecosystems and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their response to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here we investigate the physiology of the best characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

scholarly journals Comparison of different two-pathway models for describing the combined effect of DO and nitrite on the nitrous oxide production by ammonia-oxidizing bacteria

2016 ◽  
Vol 75 (3) ◽  
pp. 491-500 ◽  
Author(s):  
Longqi Lang ◽  
Mathieu Pocquet ◽  
Bing-Jie Ni ◽  
Zhiguo Yuan ◽  
Mathieu Spérandio
Keyword(s):  
Nitrous Oxide ◽  
Combined Effect ◽  
Ammonia Oxidizing Bacteria ◽  
N2o Production ◽  
Mathematical Structures ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Pathway Models ◽  
Microbial Systems ◽  
Electron Carriers

The aim of this work is to compare the capability of two recently proposed two-pathway models for predicting nitrous oxide (N2O) production by ammonia-oxidizing bacteria (AOB) for varying ranges of dissolved oxygen (DO) and nitrite. The first model includes the electron carriers whereas the second model is based on direct coupling of electron donors and acceptors. Simulations are confronted to extensive sets of experiments (43 batches) from different studies with three different microbial systems. Despite their different mathematical structures, both models could well and similarly describe the combined effect of DO and nitrite on N2O production rate and emission factor. The model-predicted contributions for nitrifier denitrification pathway and hydroxylamine pathway also matched well with the available isotopic measurements. Based on sensitivity analysis, calibration procedures are described and discussed for facilitating the future use of those models.

scholarly journals Revision of N2O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718

2014 ◽  
Vol 80 (16) ◽  
pp. 4930-4935 ◽  
Author(s):  
Jessica A. Kozlowski ◽  
Jennifer Price ◽  
Lisa Y. Stein
Keyword(s):  
Nitric Oxide ◽  
Nitrite Reductase ◽  
Nitrosomonas Europaea ◽  
Ammonia Oxidizers ◽  
Nitric Oxide Reductase ◽  
Wild Type ◽  
Content Type ◽  
Resting Cell ◽  
Nitrifier Denitrification ◽  
Cell Assays

ABSTRACTNitrite reductase (NirK) and nitric oxide reductase (NorB) have long been thought to play an essential role in nitrous oxide (N2O) production by ammonia-oxidizing bacteria. However, essential gaps remain in our understanding of how and when NirK and NorB are active and functional, putting into question their precise roles in N2O production by ammonia oxidizers. The growth phenotypes of theNitrosomonas europaeaATCC 19718 wild-type and mutant strains deficient in expression of NirK, NorB, and both gene products were compared under atmospheric and reduced O2tensions. Anoxic resting-cell assays and instantaneous nitrite (NO2−) reduction experiments were done to assess the ability of the wild-type and mutantN. europaeastrains to produce N2O through the nitrifier denitrification pathway. Results confirmed the role of NirK for efficient substrate oxidation ofN. europaeaand showed that NorB is involved in N2O production during growth at both atmospheric and reduced O2tensions. Anoxic resting-cell assays and measurements of instantaneous NO2−reduction using hydrazine as an electron donor revealed that an alternate nitrite reductase to NirK is present and active. These experiments also clearly demonstrated that NorB was the sole nitric oxide reductase for nitrifier denitrification. The results of this study expand the enzymology for nitrogen metabolism and N2O production byN. europaeaand will be useful to interpret pathways in other ammonia oxidizers that lack NirK and/or NorB genes.

scholarly journals Low nitrous oxide production through nitrifier-denitrification in intermittent-feed high-rate nitritation reactors

2017 ◽  
Vol 123 ◽  
pp. 429-438 ◽  
Author(s):  
Qingxian Su ◽  
Chun Ma ◽  
Carlos Domingo-Félez ◽  
Anne Sofie Kiil ◽  
Bo Thamdrup ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
High Rate ◽  
Oxide Production ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production

scholarly journals Response to Comment on “Oxygen Regulates Nitrous Oxide Production Directly in Agricultural Soils”

2020 ◽  
Vol 54 (4) ◽  
pp. 2556-2557
Author(s):  
Xiaotong Song ◽  
Xiaotang Ju ◽  
Cairistiona F.E. Topp ◽  
Robert M. Rees
Keyword(s):  
Nitrous Oxide ◽  
Agricultural Soils ◽  
Oxide Production ◽  
Nitrous Oxide Production

scholarly journals Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils

2016 ◽  
Vol 82 (10) ◽  
pp. 2919-2928 ◽  
Author(s):  
Steven A. Higgins ◽  
Allana Welsh ◽  
Luis H. Orellana ◽  
Konstantinos T. Konstantinidis ◽  
Joanne C. Chee-Sanford ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Agricultural Soils ◽  
Agricultural Practices ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Amino Acid Identity ◽  
N Loss ◽  
Content Type ◽  
Denitrification Potential ◽  
Fungal Isolates

ABSTRACTMembers of the Fungi convert nitrate (NO3−) and nitrite (NO2−) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3−or NO2−in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2−. Novel PCR primers targeting thep450norgene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novelp450noramplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylumAscomycotaand expand the known fungal P450nor sequence diversity.p450norwas detected in all fungal isolates that produced N2O from NO2−, whereasnirK(encoding the NO-forming NO2−reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separatenirKprimer sets. Collectively, our findings demonstrate the value ofp450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.IMPORTANCEA comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungalp450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.

scholarly journals Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

2016 ◽  
Vol 82 (11) ◽  
pp. 3310-3318 ◽  
Author(s):  
Brett L. Mellbye ◽  
Andrew Giguere ◽  
Frank Chaplen ◽  
Peter J. Bottomley ◽  
Luis A. Sayavedra-Soto
Keyword(s):  
Nitrous Oxide ◽  
Steady State ◽  
Greenhouse Gas ◽  
Gene Cluster ◽  
Inorganic Carbon ◽  
Nitrosomonas Europaea ◽  
Carbon Limitation ◽  
Content Type ◽  
State Growth ◽  
Inorganic Carbon Limitation

ABSTRACTNitrosomonas europaeais a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses ofN. europaeato conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3to nitrite, depending on the dilution rate and Na2CO3concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1metabolism, including the genes for RuBisCO (cbbgene cluster), carbonic anhydrase, folate-linked metabolism of C1moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest thatN. europaeaadapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3oxidation from growth and increased N2O production.IMPORTANCENitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO2) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome ofNitrosomonas europaea, a model ammonia-oxidizing bacterium, and report on increased production of N2O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N2O emissions from nitrification in soils and wastewater treatment.

scholarly journals Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

2015 ◽  
Vol 82 (1) ◽  
pp. 51-61 ◽  
Author(s):  
Brian J. Vaccaro ◽  
Michael P. Thorgersen ◽  
W. Andrew Lancaster ◽  
Morgan N. Price ◽  
Kelly M. Wetmore ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Electron Acceptor ◽  
Pseudomonas Stutzeri ◽  
Basic Function ◽  
Nitric Oxide Reductase ◽  
Content Type ◽  
Nitric Oxide Release ◽  
Peripheral Proteins ◽  
Cofactor Biosynthesis

ABSTRACTEnzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library fromPseudomonas stutzeristrain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.

Sign in / Sign up

Export Citation Format

Share Document