1
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Saghaï A, Hallin S. Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol 2024; 32:602-613. [PMID: 38462391 DOI: 10.1016/j.tim.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024]
Abstract
Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2
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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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3
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Wilkens D, Simon J. Biosynthesis and function of microbial methylmenaquinones. Adv Microb Physiol 2023; 83:1-58. [PMID: 37507157 DOI: 10.1016/bs.ampbs.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany; Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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4
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Identification of nosZ-expressing microorganisms consuming trace N 2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales. THE ISME JOURNAL 2022; 16:2087-2098. [PMID: 35676322 PMCID: PMC9381517 DOI: 10.1038/s41396-022-01260-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022]
Abstract
Microorganisms possessing N2O reductases (NosZ) are the only known environmental sink of N2O. While oxygen inhibition of NosZ activity is widely known, environments where N2O reduction occurs are often not devoid of O2. However, little is known regarding N2O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h−1) of N2O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O2 sustained dissolved oxygen concentration above 4 µM; however, complete N2O reduction of influent N2O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N2O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N2O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N2O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.
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5
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Liu H, Li Y, Pan B, Zheng X, Yu J, Ding H, Zhang Y. Pathways of soil N 2O uptake, consumption, and its driving factors: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:30850-30864. [PMID: 35092587 DOI: 10.1007/s11356-022-18619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N2O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N2O uptake and consumption. N2O emissions at the soil surface are the result of gross N2O production, uptake, and consumption, which are co-occurring processes. Soil N2O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N2O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N2O uptake and consumption and their driving factors and measurement techniques. This systematic review of N2O uptake and consumption will help to further understand N transformations and soil N2O emissions.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China.
| | - Baobao Pan
- School of Agriculture and Food, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China.
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6
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Durand S, Guillier M. Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria. Front Mol Biosci 2021; 8:667758. [PMID: 34026838 PMCID: PMC8139620 DOI: 10.3389/fmolb.2021.667758] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.
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Affiliation(s)
- Sylvain Durand
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Maude Guillier
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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7
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Fukushi M, Mino S, Tanaka H, Nakagawa S, Takai K, Sawabe T. Biogeochemical Implications of N 2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov. iScience 2020; 23:101462. [PMID: 32866828 PMCID: PMC7476070 DOI: 10.1016/j.isci.2020.101462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/21/2020] [Accepted: 08/12/2020] [Indexed: 01/02/2023] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.
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Affiliation(s)
- Muneyuki Fukushi
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Hirohisa Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
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8
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Stein LY. The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases. Trends Microbiol 2020; 28:500-511. [DOI: 10.1016/j.tim.2020.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
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9
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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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10
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van der Stel AX, Wösten MMSM. Regulation of Respiratory Pathways in Campylobacterota: A Review. Front Microbiol 2019; 10:1719. [PMID: 31417516 PMCID: PMC6682613 DOI: 10.3389/fmicb.2019.01719] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
The Campylobacterota, previously known as Epsilonproteobacteria, are a large group of Gram-negative mainly, spiral-shaped motile bacteria. Some members like the Sulfurospirillum spp. are free-living, while others such as Helicobacter spp. can only persist in strict association with a host organism as commensal or as pathogen. Species of this phylum colonize diverse habitats ranging from deep-sea thermal vents to the human stomach wall. Despite their divergent environments, they share common energy conservation mechanisms. The Campylobacterota have a large and remarkable repertoire of electron transport chain enzymes, given their small genomes. Although members of recognized families of transcriptional regulators are found in these genomes, sofar no orthologs known to be important for energy or redox metabolism such as ArcA, FNR or NarP are encoded in the genomes of the Campylobacterota. In this review, we discuss the strategies that members of Campylobacterota utilize to conserve energy and the corresponding regulatory mechanisms that regulate the branched electron transport chains in these bacteria.
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Affiliation(s)
| | - Marc M. S. M. Wösten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
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11
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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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12
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Taylor AJ, Kelly DJ. The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen. Adv Microb Physiol 2019; 74:239-329. [PMID: 31126532 DOI: 10.1016/bs.ampbs.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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Affiliation(s)
- Aidan J Taylor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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13
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Conthe M, Wittorf L, Kuenen JG, Kleerebezem R, van Loosdrecht MCM, Hallin S. Life on N 2O: deciphering the ecophysiology of N 2O respiring bacterial communities in a continuous culture. ISME JOURNAL 2018; 12:1142-1153. [PMID: 29416125 PMCID: PMC5864245 DOI: 10.1038/s41396-018-0063-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/19/2017] [Accepted: 12/29/2017] [Indexed: 01/04/2023]
Abstract
Reduction of the greenhouse gas N2O to N2 is a trait among denitrifying and non-denitrifying microorganisms having an N2O reductase, encoded by nosZ. The nosZ phylogeny has two major clades, I and II, and physiological differences among organisms within the clades may affect N2O emissions from ecosystems. To increase our understanding of the ecophysiology of N2O reducers, we determined the thermodynamic growth efficiency of N2O reduction and the selection of N2O reducers under N2O- or acetate-limiting conditions in a continuous culture enriched from a natural community with N2O as electron acceptor and acetate as electron donor. The biomass yields were higher during N2O limitation, irrespective of dilution rate and community composition. The former was corroborated in a continuous culture of Pseudomonas stutzeri and was potentially due to cytotoxic effects of surplus N2O. Denitrifiers were favored over non-denitrifying N2O reducers under all conditions and Proteobacteria harboring clade I nosZ dominated. The abundance of nosZ clade II increased when allowing for lower growth rates, but bacteria with nosZ clade I had a higher affinity for N2O, as defined by μmax/Ks. Thus, the specific growth rate is likely a key factor determining the composition of communities living on N2O respiration under growth-limited conditions.
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Affiliation(s)
- Monica Conthe
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J Gijs Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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14
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Stein LY. Resolving N2
O respiration pathways: a tale of two NosZ clades. Environ Microbiol 2017; 19:4806-4807. [DOI: 10.1111/1462-2920.13969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/21/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lisa Y. Stein
- Department of Biological Sciences; Univ. Alberta; Edmonton T6G 2E9 Canada
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15
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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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16
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Goris T, Schenz B, Zimmermann J, Lemos M, Hackermüller J, Schubert T, Diekert G. The complete genome of the tetrachloroethene-respiring Epsilonproteobacterium Sulfurospirillum halorespirans. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.1197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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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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Hein S, Klimmek O, Polly M, Kern M, Simon J. A class C radicalS-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Mol Microbiol 2017; 104:449-462. [DOI: 10.1111/mmi.13638] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Oliver Klimmek
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Markus Polly
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - 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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Phylogenetic and functional potential links pH and N 2O emissions in pasture soils. Sci Rep 2016; 6:35990. [PMID: 27782174 PMCID: PMC5080606 DOI: 10.1038/srep35990] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/10/2016] [Indexed: 01/18/2023] Open
Abstract
Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.
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Yoon S, Nissen S, Park D, Sanford RA, Löffler FE. Nitrous Oxide Reduction Kinetics Distinguish Bacteria Harboring Clade I NosZ from Those Harboring Clade II NosZ. Appl Environ Microbiol 2016; 82:3793-800. [PMID: 27084012 PMCID: PMC4907195 DOI: 10.1128/aem.00409-16] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/12/2016] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Bacteria capable of reduction of nitrous oxide (N2O) to N2 separate into clade I and clade II organisms on the basis of nos operon structures and nosZ sequence features. To explore the possible ecological consequences of distinct nos clusters, the growth of bacterial isolates with either clade I (Pseudomonas stutzeri strain DCP-Ps1, Shewanella loihica strain PV-4) or clade II (Dechloromonas aromatica strain RCB, Anaeromyxobacter dehalogenans strain 2CP-C) nosZ with N2O was examined. Growth curves did not reveal trends distinguishing the clade I and clade II organisms tested; however, the growth yields of clade II organisms exceeded those of clade I organisms by 1.5- to 1.8-fold. Further, whole-cell half-saturation constants (Kss) for N2O distinguished clade I from clade II organisms. The apparent Ks values of 0.324 ± 0.078 μM for D. aromatica and 1.34 ± 0.35 μM for A. dehalogenans were significantly lower than the values measured for P. stutzeri (35.5 ± 9.3 μM) and S. loihica (7.07 ± 1.13 μM). Genome sequencing demonstrated that Dechloromonas denitrificans possessed a clade II nosZ gene, and a measured Ks of 1.01 ± 0.18 μM for N2O was consistent with the values determined for the other clade II organisms tested. These observations provide a plausible mechanistic basis for why the relative activity of bacteria with clade I nos operons compared to that of bacteria with clade II nos operons may control N2O emissions and determine a soil's N2O sink capacity. IMPORTANCE Anthropogenic activities, in particular fertilizer application for agricultural production, increase N2O emissions to the atmosphere. N2O is a strong greenhouse gas with ozone destruction potential, and there is concern that nitrogen may become the major driver of climate change. Microbial N2O reductase (NosZ) catalyzes N2O reduction to environmentally benign dinitrogen gas and represents the major N2O sink process. The observation that bacterial groups with clade I nosZ versus those with clade II nosZ exhibit distinct affinities to N2O has implications for N2O flux models, and these distinct characteristics may provide opportunities to curb N2O emissions from relevant soil ecosystems.
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Affiliation(s)
- Sukhwan Yoon
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Silke Nissen
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Doyoung Park
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
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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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