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Yoon S, Heo H, Han H, Song DU, Bakken LR, Frostegård Å, Yoon S. Suggested role of NosZ in preventing N 2O inhibition of dissimilatory nitrite reduction to ammonium. mBio 2023; 14:e0154023. [PMID: 37737639 PMCID: PMC10653820 DOI: 10.1128/mbio.01540-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.
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Affiliation(s)
- Sojung Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hokwan Heo
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Dong-Uk Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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2
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Cheng Y, Elrys AS, Merwad ARM, Zhang H, Chen Z, Zhang J, Cai Z, Müller C. Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3791-3800. [PMID: 35226464 DOI: 10.1021/acs.est.1c07997] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg-1 day-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N2O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N2O emissions.
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Affiliation(s)
- Yi Cheng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing 210023, China
| | - Ahmed S Elrys
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Abdel-Rahman M Merwad
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Huimin Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Zhaoxiong Chen
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, Giessen 35392, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin 4, Ireland
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3
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Broman E, Zilius M, Samuiloviene A, Vybernaite-Lubiene I, Politi T, Klawonn I, Voss M, Nascimento FJA, Bonaglia S. Active DNRA and denitrification in oxic hypereutrophic waters. WATER RESEARCH 2021; 194:116954. [PMID: 33667950 DOI: 10.1016/j.watres.2021.116954] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Baltic Sea Centre, Stockholm University, 106 91 Stockholm, Sweden.
| | - Mindaugas Zilius
- Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania
| | | | | | - Tobia Politi
- Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania
| | - Isabell Klawonn
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Baltic Sea Centre, Stockholm University, 106 91 Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania; Department of Biology, University of Southern Denmark, 5230 Odense, Denmark; Department of Marine Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden.
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4
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Involvement of NO 3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method. Appl Environ Microbiol 2020; 86:AEM.01054-20. [PMID: 32631862 DOI: 10.1128/aem.01054-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO3 --reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N2O reduction. A common prominent physiological feature observed in the isolates was NO2 - accumulation before NH4 + production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO2 --to-NH4 + reduction at submillimolar NO3 - concentrations and downregulation of nrfA or nirB transcription when NO3 - was being reduced to NO2 - In batch and chemostat experiments, both isolates produced NH4 + from NO3 - reduction when incubated with excess organic electron donors, while incubation with excess NO3 - resulted in NO2 - buildup but no substantial NH4 + production, presumably due to inhibitory NO3 - concentrations. This previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO3 - and NO2 - Unlike denitrification, which leads to nitrogen loss and N2O emission, DNRA reduces NO3 - and NO2 - to NH4 +, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.
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5
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Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions. Adv Microb Physiol 2019; 75:137-175. [PMID: 31655736 DOI: 10.1016/bs.ampbs.2019.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologically catalyzed nitrous oxide (N2O, laughing gas) reduction to dinitrogen gas (N2) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N2O reductase (NosZ), which is the only known enzyme that converts N2O to N2. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N2O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N2O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N2O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N2O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N2O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.
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6
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7
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Significance of MccR, MccC, MccD, MccL and 8-methylmenaquinone in sulfite respiration of Wolinella succinogenes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:12-21. [DOI: 10.1016/j.bbabio.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/26/2018] [Accepted: 10/13/2018] [Indexed: 11/17/2022]
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8
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Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase Genes nirS and nirK. Appl Environ Microbiol 2018; 84:AEM.01985-17. [PMID: 29196287 DOI: 10.1128/aem.01985-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/27/2017] [Indexed: 11/20/2022] Open
Abstract
The versatile soil bacterium Anaeromyxobacter dehalogenans lacks the hallmark denitrification genes nirS and nirK (encoding NO2 -→NO reductases) and couples growth to NO3 - reduction to NH4 + (respiratory ammonification) and to N2O reduction to N2 A. dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2 - to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3 - or NO2 - to Fe(III)-grown axenic cultures of A. dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3 - to N2 in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology of A. dehalogenans The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lacking nirS or nirK but with Fe(III) reduction potential and genes for NO3 - and N2O reduction are not rare, indicating that NO3 - reduction to N2 through linked biotic-abiotic reactions is not limited to A. dehalogenans Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3 - reducers, denitrification independent of NO-forming NO2 - reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux.IMPORTANCE Current attempts to gauge N loss from soils rely on the quantitative measurement of nirK and nirS genes and/or transcripts. In the presence of iron, the common soil bacterium Anaeromyxobacter dehalogenans is capable of denitrification and the production of N2 without the key denitrification genes nirK and nirS Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.
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9
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Hein S, Witt S, Simon J. Clade II nitrous oxide respiration of Wolinella succinogenes depends on the NosG, -C1, -C2, -H electron transport module, NosB and a Rieske/cytochrome bc complex. Environ Microbiol 2017; 19:4913-4925. [PMID: 28925551 DOI: 10.1111/1462-2920.13935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 01/20/2023]
Abstract
Microbial reduction of nitrous oxide (N2 O) is an environmentally significant process in the biogeochemical nitrogen cycle. However, it has been recognized only recently that the gene encoding N2 O reductase (nosZ) is organized in varying genetic contexts, thereby defining clade I (or 'typical') and clade II (or 'atypical') N2 O reductases and nos gene clusters. This study addresses the enzymology of the clade II Nos system from Wolinella succinogenes, a nitrate-ammonifying and N2 O-respiring Epsilonproteobacterium that contains a cytochrome c N2 O reductase (cNosZ). The characterization of single non-polar nos gene deletion mutants demonstrated that the NosG, -C1, -C2, -H and -B proteins were essential for N2 O respiration. Moreover, cells of a W. succinogenes mutant lacking a putative menaquinol-oxidizing Rieske/cytochrome bc complex (QcrABC) were found to be incapable of N2 O (and also nitrate) respiration. Proton motive menaquinol oxidation by N2 O is suggested, supported by the finding that the molar yield for W. succinogenes cells grown by N2 O respiration using formate as electron donor exceeded that of fumarate respiration by about 30%. The results demand revision of the electron transport chain model of clade II N2 O respiration and challenge the assumption that NosGH(NapGH)-type iron-sulfur proteins are menaquinol-reactive.
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Affiliation(s)
- Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Samantha Witt
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
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10
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Haase D, Hermann B, Einsle O, Simon J. Epsilonproteobacterial hydroxylamine oxidoreductase (
ε
Hao): characterization of a ‘missing link’ in the multihaem cytochrome
c
family. Mol Microbiol 2017; 105:127-138. [DOI: 10.1111/mmi.13690] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Doreen Haase
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
| | - Bianca Hermann
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Oliver Einsle
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
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Nolan JV, Godwin IR, de Raphélis-Soissan V, Hegarty RS. Managing the rumen to limit the incidence and severity of nitrite poisoning in nitrate-supplemented ruminants. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an15324] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Inclusion of nitrate (NO3−) in ruminant diets is a means of increasing non-protein nitrogen intake while at the same time reducing emissions of enteric methane (CH4) and, in Australia, gaining carbon credits. Rumen microorganisms contain intracellular enzymes that use hydrogen (H2) released during fermentation to reduce NO3− to nitrite (NO2−), and then reduce the resulting NO2− to ammonia or gaseous intermediates such as nitrous oxide (N2O) and nitric oxide (NO). This diversion of H2 reduces CH4 formation in the rumen. If NO2− accumulates in the rumen, it may inhibit growth of methanogens and other microorganisms and this may further reduce CH4 production, but also lower feed digestibility. If NO2− is absorbed and enters red blood cells, methaemoglobin is formed and this lowers the oxygen-carrying capacity of the blood. Nitric oxide produced from absorbed NO2− reduces blood pressure, which, together with the effects of methaemoglobin, can, at times, lead to extreme hypoxia and death. Nitric oxide, which can be formed in the gut as well as in tissues, has a variety of physiological effects, e.g. it reduces primary rumen contractions and slows passage of digesta, potentially limiting feed intake. It is important to find management strategies that minimise the accumulation of NO2−; these include slowing the rate of presentation of NO3– to rumen microbes or increasing the rate of removal of NO2−, or both. The rate of reduction of NO3− to NO2− depends on the level of NO3− in feed and its ingestion rate, which is related to the animal’s feeding behaviour. After NO3− is ingested, its peak concentration in the rumen depends on its rate of solubilisation. Once in solution, NO3− is imported by bacteria and protozoa and quickly reduced to NO2−. One management option is to encapsulate the NO3− supplement to lower its solubility. Acclimating animals to NO3− is an established management strategy that appears to limit NO2− accumulation in the rumen by increasing microbial nitrite reductase activity more than nitrate reductase activity; however, it does not guarantee complete protection from NO2− poisoning. Adding concentrates into nitrate-containing diets also helps reduce the risk of poisoning and inclusion of microbial cultures with enhanced NO2−-reducing properties is another potential management option. A further possibility is to inhibit NO2− absorption. Animals differ in their tolerance to NO3− supplementation, so there may be opportunities for breeding animals more tolerant of dietary NO3−. Our review aims to integrate current knowledge of microbial processes responsible for accumulation of NO2− in rumen fluid and to identify management options that could minimise the risks of NO2− poisoning while reducing methane emissions and maintaining or enhancing livestock production.
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12
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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13
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Kern M, Simon J. Three transcription regulators of the Nss family mediate the adaptive response induced by nitrate, nitric oxide or nitrous oxide in Wolinella succinogenes. Environ Microbiol 2015; 18:2899-912. [PMID: 26395430 DOI: 10.1111/1462-2920.13060] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/16/2015] [Indexed: 12/30/2022]
Abstract
Sensing potential nitrogen-containing respiratory substrates such as nitrate, nitrite, hydroxylamine, nitric oxide (NO) or nitrous oxide (N2 O) in the environment and subsequent upregulation of corresponding catabolic enzymes is essential for many microbial cells. The molecular mechanisms of such adaptive responses are, however, highly diverse in different species. Here, induction of periplasmic nitrate reductase (Nap), cytochrome c nitrite reductase (Nrf) and cytochrome c N2 O reductase (cNos) was investigated in cells of the Epsilonproteobacterium Wolinella succinogenes grown either by fumarate, nitrate or N2 O respiration. Furthermore, fumarate respiration in the presence of various nitrogen compounds or NO-releasing chemicals was examined. Upregulation of each of the Nap, Nrf and cNos enzyme systems was found in response to the presence of nitrate, NO-releasers or N2 O, and the cells were shown to employ three transcription regulators of the Crp-Fnr superfamily (homologues of Campylobacter jejuni NssR), designated NssA, NssB and NssC, to mediate the upregulation of Nap, Nrf and cNos. Analysis of single nss mutants revealed that NssA controls production of the Nap and Nrf systems in fumarate-grown cells, while NssB was required to induce the Nap, Nrf and cNos systems specifically in response to NO-generators. NssC was indispensable for cNos production under any tested condition. The data indicate dedicated signal transduction routes responsive to nitrate, NO and N2 O and imply the presence of an N2 O-sensing mechanism.
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Affiliation(s)
- Melanie Kern
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany.
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14
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Abstract
The global biogeochemical nitrogen cycle is essential for life on Earth. Many of the underlying biotic reactions are catalyzed by a multitude of prokaryotic and eukaryotic life forms whereas others are exclusively carried out by microorganisms. The last century has seen the rise of a dramatic imbalance in the global nitrogen cycle due to human behavior that was mainly caused by the invention of the Haber-Bosch process. Its main product, ammonia, is a chemically reactive and biotically favorable form of bound nitrogen. The anthropogenic supply of reduced nitrogen to the biosphere in the form of ammonia, for example during environmental fertilization, livestock farming, and industrial processes, is mandatory in feeding an increasing world population. In this chapter, environmental ammonia pollution is linked to the activity of microbial metalloenzymes involved in respiratory energy metabolism and bioenergetics. Ammonia-producing multiheme cytochromes c are discussed as paradigm enzymes.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287, Darmstadt, Germany,
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