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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Duffner C, Kublik S, Fösel B, Frostegård Å, Schloter M, Bakken L, Schulz S. Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers. Environ Microbiol 2022; 24:1887-1901. [PMID: 35106904 DOI: 10.1111/1462-2920.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel Fösel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lars Bakken
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
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3
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Bueno E, Mania D, Mesa S, Bedmar EJ, Frostegård Å, Bakken LR, Delgado MJ. Regulation of the Emissions of the Greenhouse Gas Nitrous Oxide by the Soybean Endosymbiont Bradyrhizobium diazoefficiens. Int J Mol Sci 2022; 23:1486. [PMID: 35163408 PMCID: PMC8836242 DOI: 10.3390/ijms23031486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
The greenhouse gas nitrous oxide (N2O) has strong potential to drive climate change. Soils are a major source of N2O, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model microorganism to study denitrification, a process that depends on a set of reductases, encoded by the napEDABC, nirK, norCBQD, and nosRZDYFLX genes, which sequentially reduce nitrate (NO3-) to nitrite (NO2-), nitric oxide (NO), N2O, and dinitrogen (N2). In this bacterium, the regulatory network and environmental cues governing the expression of denitrification genes rely on the FixK2 and NnrR transcriptional regulators. To understand the role of FixK2 and NnrR proteins in N2O turnover, we monitored real-time kinetics of NO3-, NO2-, NO, N2O, N2, and oxygen (O2) in a fixK2 and nnrR mutant using a robotized incubation system. We confirmed that FixK2 and NnrR are regulatory determinants essential for NO3- respiration and N2O reduction. Furthermore, we demonstrated that N2O reduction by B. diazoefficiens is independent of canonical inducers of denitrification, such as the nitrogen oxide NO3-, and it is negatively affected by acidic and alkaline conditions. These findings advance the understanding of how specific environmental conditions and two single regulators modulate N2O turnover in B. diazoefficiens.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Socorro Mesa
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Eulogio J. Bedmar
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - María J. Delgado
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
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4
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Mousavi SA, Gao Y, Penttinen P, Frostegård Å, Paulin L, Lindström K. Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules. Lett Appl Microbiol 2021; 74:204-211. [PMID: 34753197 DOI: 10.1111/lam.13599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022]
Abstract
To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.
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Affiliation(s)
- S A Mousavi
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Division of Ecology and Evolutionary Biology, Department of Biology, University of Turku, Turku, Finland
| | - Y Gao
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway.,International Research and Development Center, Kingenta Ecological Engineering Group Co. Ltd, Linyi, China
| | - P Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Å Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
| | - L Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - K Lindström
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland
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5
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Jonassen KR, Hagen LH, Vick SHW, Arntzen MØ, Eijsink VGH, Frostegård Å, Lycus P, Molstad L, Pope PB, Bakken LR. Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions. ISME J 2021; 16:580-590. [PMID: 34489539 PMCID: PMC8776835 DOI: 10.1038/s41396-021-01101-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Inoculating agricultural soils with nitrous oxide respiring bacteria (NRB) can reduce N2O-emission, but would be impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production are suitable substrates and vectors for NRB. We show that indigenous NRB in digestates grew to high abundance during anaerobic enrichment under N2O. Gas-kinetics and meta-omic analyses showed that these NRB’s, recovered as metagenome-assembled genomes (MAGs), grew by harvesting fermentation intermediates of the methanogenic consortium. Three NRB’s were isolated, one of which matched the recovered MAG of a Dechloromonas, deemed by proteomics to be the dominant producer of N2O-reductase in the enrichment. While the isolates harbored genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O sinks in soil, which was confirmed experimentally. The isolates were grown by aerobic respiration in digestates, and fertilization with these NRB-enriched digestates reduced N2O emissions from soil. Our use of digestates for low-cost and large-scale inoculation with NRB in soil can be taken as a blueprint for future applications of this powerful instrument to engineer the soil microbiome, be it for enhancing plant growth, bioremediation, or any other desirable function.
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Affiliation(s)
- Kjell Rune Jonassen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,VEAS WWTP, Slemmestad, Norway
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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6
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Gao Y, Mania D, Mousavi SA, Lycus P, Arntzen MØ, Woliy K, Lindström K, Shapleigh JP, Bakken LR, Frostegård Å. Competition for electrons favours N 2 O reduction in denitrifying Bradyrhizobium isolates. Environ Microbiol 2021; 23:2244-2259. [PMID: 33463871 DOI: 10.1111/1462-2920.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Bradyrhizobia are common members of soil microbiomes and known as N2 -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2 O. Inoculation with compatible rhizobia is often needed for optimal N2 -fixation, but the choice of inoculant may have consequences for N2 O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2 O. The N2 O-reducing isolates had strong preference for N2 O- over NO3 - -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3 - reductase) and Nos (N2 O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3 - reductase (Nar), reduced N2 O and NO3 - simultaneously. We propose that the control at the metabolic level, favouring N2 O reduction over NO3 - reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
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Affiliation(s)
- Yuan Gao
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kristina Lindström
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | | | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
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7
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Keuschnig C, Gorfer M, Li G, Mania D, Frostegård Å, Bakken L, Larose C. NO and N 2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains. Environ Microbiol 2020; 22:2182-2195. [PMID: 32157782 DOI: 10.1111/1462-2920.14980] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022]
Abstract
Fungal denitrification is claimed to produce non-negligible amounts of N2 O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO 2 - . Enzymatic reduction of NO 2 - (NIR) and NO (NOR) was assessed by correcting measured NO- and N2 O-kinetics for abiotic NO- and N2 O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2 O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2 O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2 O as a response to an abiotic NO production from the medium.
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Affiliation(s)
- Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
| | - Markus Gorfer
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Guofen Li
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
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8
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Woliy K, Degefu T, Frostegård Å. Host Range and Symbiotic Effectiveness of N 2O Reducing Bradyrhizobium Strains. Front Microbiol 2019; 10:2746. [PMID: 31849890 PMCID: PMC6896821 DOI: 10.3389/fmicb.2019.02746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Emissions of the potent greenhouse gas N2O is one of the environmental problems associated with intensive use of synthetic N fertilizers, and novel N2O mitigation strategies are needed to minimize fertilizer applications and N2O release without affecting agricultural efficiencies. Increased incorporation of legume crops in agricultural practices offers a sustainable alternative. Legumes, in their symbiosis with nitrogen fixing bacteria, rhizobia, reduce the need for fertilizers and also respond to the need for increased production of plant-based proteins. Not all combinations of rhizobia and legumes result in efficient nitrogen fixation, and legume crops therefore often need to be inoculated with compatible rhizobial strains. Recent research has demonstrated that some rhizobia are also very efficient N2O reducers. Several nutritionally and economically important legumes form root nodules in symbiosis with bacteria belonging to Bradyrhizobium. Here, the host-ranges of fourteen N2O reducing Bradyrhizobium strains were tested on six legume hosts; cowpea, groundnut, mung bean, haricot bean, soybean, and alfalfa. The plants were grown for 35 days in pots in sterile sand supplemented with N-free nutrient solution. Cowpea was the most promiscuous host nodulated by all test strains, followed by groundnut (11 strains) and mungbean (4 strains). Three test strains were able to nodulate all these three legumes, while none nodulated the other three hosts. For cowpea, five strains increased the shoot dry weight and ten strains the shoot nitrogen content (pairwise comparison; p < 0.05). For groundnut the corresponding results were three and nine strains. The symbiotic effectiveness for the different strains ranged from 45 to 98% in cowpea and 34 to 95% in groundnut, relative to fertilized controls. The N2O reduction capacity of detached nodules from cowpea plants inoculated with one of these strains confirmed active N2O reduction inside the nodules. When released from senescent nodules such strains are expected to also act as sinks for N2O produced by denitrifying organisms in the soil microbial community. Our strategy to search among known N2O-reducing Bradyrhizobium strains for their N2-fixation effectiveness successfully identified several strains which can potentially be used for the production of legume inoculants with the dual capacities of efficacious N2-fixation and N2O reduction.
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Affiliation(s)
- Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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9
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Conthe M, Lycus P, Arntzen MØ, Ramos da Silva A, Frostegård Å, Bakken LR, Kleerebezem R, van Loosdrecht MCM. Denitrification as an N 2O sink. Water Res 2019; 151:381-387. [PMID: 30616050 DOI: 10.1016/j.watres.2018.11.087] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
The strong greenhouse gas nitrous oxide (N2O) can be emitted from wastewater treatment systems as a byproduct of ammonium oxidation and as the last intermediate in the stepwise reduction of nitrate to N2 by denitrifying organisms. A potential strategy to reduce N2O emissions would be to enhance the activity of N2O reductase (NOS) in the denitrifying microbial community. A survey of existing literature on denitrification in wastewater treatment systems showed that the N2O reducing capacity (VmaxN2O→N2) exceeded the capacity to produce N2O (VmaxNO3→N2O) by a factor of 2-10. This suggests that denitrification can be an effective sink for N2O, potentially scavenging a fraction of the N2O produced by ammonium oxidation or abiotic reactions. We conducted a series of incubation experiments with freshly sampled activated sludge from a wastewater treatment system in Oslo and found that the ratio α = VmaxN2O→N2/VmaxNO3→N2O fluctuated between 2 and 5 in samples taken at intervals over a period of 5 weeks. Adding a cocktail of carbon substrates resulted in increasing rates, but had no significant effect on α. Based on these results - complemented with qPCR and metaproteomic data - we discuss whether the overcapacity to reduce N2O can be ascribed to gene/protein abundance ratios (nosZ/nir), or whether in-cell competition between the reductases for electrons could be of greater importance.
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Affiliation(s)
- Monica Conthe
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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10
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Liu B, Zhang X, Bakken LR, Snipen L, Frostegård Å. Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell. Front Microbiol 2019; 9:3208. [PMID: 30671037 PMCID: PMC6331397 DOI: 10.3389/fmicb.2018.03208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/11/2018] [Indexed: 12/25/2022] Open
Abstract
Denitrification allows sustained respiratory metabolism during periods of anoxia, an advantage in soils with frequent anoxic spells. However, the gains may be more than evened out by the energy cost of producing the denitrification machinery, particularly if the anoxic spell is short. This dilemma could explain the evolution of different regulatory phenotypes observed in model strains, such as sequential expression of the four denitrification genes needed for a complete reduction of nitrate to N2, or a “bet hedging” strategy where all four genes are expressed only in a fraction of the cells. In complex environments such strategies would translate into progressive onset of transcription by the members of the denitrifying community. We exposed soil microcosms to anoxia, sampled for amplicon sequencing of napA/narG, nirK/nirS, and nosZ genes and transcripts after 1, 2 and 4 h, and monitored the kinetics of NO, N2O, and N2. The cDNA libraries revealed a succession of transcribed genes from active denitrifier populations, which probably reflects various regulatory phenotypes in combination with cross-talks via intermediates (NO2−, NO) produced by the “early onset” denitrifying populations. This suggests that the regulatory strategies observed in individual isolates are also displayed in complex communities, and pinpoint the importance for successive sampling when identifying active key player organisms.
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Affiliation(s)
- Binbin Liu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Snipen
- 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
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11
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Lycus P, Soriano-Laguna MJ, Kjos M, Richardson DJ, Gates AJ, Milligan DA, Frostegård Å, Bergaust L, Bakken LR. A bet-hedging strategy for denitrifying bacteria curtails their release of N 2O. Proc Natl Acad Sci U S A 2018; 115:11820-11825. [PMID: 30385636 PMCID: PMC6243289 DOI: 10.1073/pnas.1805000115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
When oxygen becomes limiting, denitrifying bacteria must prepare for anaerobic respiration by synthesizing the reductases NAR (NO3- → NO2-), NIR (NO2- → NO), NOR (2NO → N2O), and NOS (N2O → N2), either en bloc or sequentially, to avoid entrapment in anoxia without energy. Minimizing the metabolic burden of this precaution is a plausible fitness trait, and we show that the model denitrifier Paracoccus denitrificans achieves this by synthesizing NOS in all cells, while only a minority synthesize NIR. Phenotypic diversification with regards to NIR is ascribed to stochastic initiation of gene transcription, which becomes autocatalytic via NO production. Observed gas kinetics suggest that such bet hedging is widespread among denitrifying bacteria. Moreover, in response to oxygenation, P. denitrificans preserves NIR in the poles of nongrowing persister cells, ready to switch to anaerobic respiration in response to sudden anoxia. Our findings add dimensions to the regulatory biology of denitrification and identify regulatory traits that decrease N2O emissions.
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Affiliation(s)
- Pawel Lycus
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | | | - Morten Kjos
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - David John Richardson
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom
| | - Andrew James Gates
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom
| | - Daniel Aleksanteri Milligan
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Linda Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway;
| | - Lars Reier Bakken
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway;
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12
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Bakken LR, Frostegård Å. Sources and sinks for N2
O, can microbiologist help to mitigate N2
O emissions? Environ Microbiol 2017; 19:4801-4805. [DOI: 10.1111/1462-2920.13978] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 11/27/2022]
Affiliation(s)
- 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
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13
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Wang Y, Tian H, Huang F, Long W, Zhang Q, Wang J, Zhu Y, Wu X, Chen G, Zhao L, Bakken LR, Frostegård Å, Zhang X. Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline. Sci Rep 2017; 7:14778. [PMID: 29116183 PMCID: PMC5677008 DOI: 10.1038/s41598-017-15122-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 10/23/2017] [Indexed: 11/08/2022] Open
Abstract
Quinoline is biodegradable under anaerobic conditions, but information about the degradation kinetics and the involved microorganisms is scarce. Here, the dynamics of a quinoline-degrading bacterial consortium were studied in anoxic batch cultures containing nitrate. The cultures removed 83.5% of the quinoline during the first 80 hours, which were dominated by denitrification, and then switched to methanogenesis when the nitrogen oxyanions were depleted. Time-resolved community analysis using pyrosequencing revealed that denitrifiying bacteria belonging to the genus Thauera were enriched during the denitrification stage from 12.2% to 38.8% and 50.1% relative abundance in DNA and cDNA libraries, respectively. This suggests that they are key organisms responsible for the initial attack on quinoline. Altogether, 13 different co-abundance groups (CAGs) containing 76 different phylotypes were involved, directly or indirectly, in quinoline degradation. The dynamics of these CAGs show that specific phylotypes were associated with different phases of the degradation. Members of Rhodococcus and Desulfobacterium, as well as Rhodocyclaceae- and Syntrophobacteraceae-related phylotypes, utilized initial metabolites of the quinoline, while the resulting smaller molecules were used by secondary fermenters belonging to Anaerolineae. The concerted action by the different members of this consortium resulted in an almost complete anaerobic mineralization of the quinoline.
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Affiliation(s)
- Yun Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, P.R. China
| | - Hao Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Fei Huang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Wenmin Long
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Qianpeng Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Jing Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Ying Zhu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Xiaogang Wu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Guanzhou Chen
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, N-1432, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, N-1432, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China.
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14
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Hink L, Lycus P, Gubry-Rangin C, Frostegård Å, Nicol GW, Prosser JI, Bakken LR. Kinetics of NH 3 -oxidation, NO-turnover, N 2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environ Microbiol 2017; 19:4882-4896. [PMID: 28892283 DOI: 10.1111/1462-2920.13914] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/26/2017] [Indexed: 11/28/2022]
Abstract
Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N2 O) than ammonia oxidising archaea (AOA), due to their higher N2 O yield under oxic conditions and denitrification in response to oxygen (O2 ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N2 O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH3 + NH4+) and O2 . Half-saturation constants for O2 and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N2 O production reached maxima near O2 half-saturation constant concentration (2-10 μM O2 ) and decreased to zero in response to complete O2 -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O2 concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration.
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Affiliation(s)
- Linda Hink
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully CEDEX 69134, France
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
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15
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Zhu Y, Zhang X, Wu X, Chen G, Bakken LR, Zhao L, Frostegård Å, Zhang X. Carbon-driven enrichment of the crucial nitrate-reducing bacteria in limed peat soil microcosms. Lett Appl Microbiol 2017; 65:159-164. [PMID: 28517029 DOI: 10.1111/lam.12756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/28/2022]
Abstract
Bacteria of Dechloromonas were recognized as potential functional important denitrifiers in a long-term shell sand-amended peat soil. Different microcosms in a solid matrix and slurry systems with the addition of carbon and nitrogen sources, for example, clover leaves, glutamate and nitrate, were established. The bacterial community structures were analysed by pyrosequencing of the 16S rRNA gene to select the conditions for enriching bacteria of Dechloromonas. The results showed that a relatively even bacterial community in the initial soil shifted to communities dominated by a few types of nitrate-reducing bacteria after the incubation, which strongly responded to the carbon substrates addition and consumption. The bacteria of several genera including Dechloromonas, Pseudomonas, Clostridium, Aeromonas and Ferribacterium were significantly enriched after a certain period of time. The bacteria of Dechloromonas became one of the most predominant bacteria in the incubated community. Especially when added the mixed carbon substrates into the solid soil matrix, as high as 34% of abundance was detected. This study proved that the functional important bacteria from the genus of Dechloromonas could be enriched to an extremely high abundance by using proper culture condition which will benefit to the isolation or direct metagenomics study for Dechloromonas. SIGNIFICANCE AND IMPACT OF THE STUDY The study of key players in a microbial community is always of important. In this study, the functional important denitrifiers in a shell sand-amended peat soil were investigated. Using different carbon sources in the incubation, we found the bacteria from the genus of Dechloromonas were enriched to an abundance of higher than 34% with several other denitrifiers together. This work provides us helpful insights not only for knowing the diversity of denitrifiers in the studied peat soil, but also for understanding their response to the carbon sources and the culture conditions.
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Affiliation(s)
- Y Zhu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - X Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - X Wu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - G Chen
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - L R Bakken
- Department of Environmental Science, Norwegian University of Life Sciences, Ås, Norway
| | - L Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Å Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - X Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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16
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Degefu T, Wolde-meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40:205-214. [DOI: 10.1016/j.syapm.2017.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
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17
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Lim NYN, Roco CA, Frostegård Å. Transparent DNA/RNA Co-extraction Workflow Protocol Suitable for Inhibitor-Rich Environmental Samples That Focuses on Complete DNA Removal for Transcriptomic Analyses. Front Microbiol 2016; 7:1588. [PMID: 27803690 PMCID: PMC5067521 DOI: 10.3389/fmicb.2016.01588] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/22/2016] [Indexed: 12/04/2022] Open
Abstract
Adequate comparisons of DNA and cDNA libraries from complex environments require methods for co-extraction of DNA and RNA due to the inherent heterogeneity of such samples, or risk bias caused by variations in lysis and extraction efficiencies. Still, there are few methods and kits allowing simultaneous extraction of DNA and RNA from the same sample, and the existing ones generally require optimization. The proprietary nature of kit components, however, makes modifications of individual steps in the manufacturer’s recommended procedure difficult. Surprisingly, enzymatic treatments are often performed before purification procedures are complete, which we have identified here as a major problem when seeking efficient genomic DNA removal from RNA extracts. Here, we tested several DNA/RNA co-extraction commercial kits on inhibitor-rich soils, and compared them to a commonly used phenol-chloroform co-extraction method. Since none of the kits/methods co-extracted high-quality nucleic acid material, we optimized the extraction workflow by introducing small but important improvements. In particular, we illustrate the need for extensive purification prior to all enzymatic procedures, with special focus on the DNase digestion step in RNA extraction. These adjustments led to the removal of enzymatic inhibition in RNA extracts and made it possible to reduce genomic DNA to below detectable levels as determined by quantitative PCR. Notably, we confirmed that DNase digestion may not be uniform in replicate extraction reactions, thus the analysis of “representative samples” is insufficient. The modular nature of our workflow protocol allows optimization of individual steps. It also increases focus on additional purification procedures prior to enzymatic processes, in particular DNases, yielding genomic DNA-free RNA extracts suitable for metatranscriptomic analysis.
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Affiliation(s)
- Natalie Y N Lim
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas Norway
| | - Constance A Roco
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, AasNorway; Department of Microbiology, Cornell University, Ithaca, NYUSA
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas Norway
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18
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Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. Front Microbiol 2016; 7:73. [PMID: 26903960 PMCID: PMC4748112 DOI: 10.3389/fmicb.2016.00073] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany
| | - Wafa Achouak
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Spiros N Agathos
- Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador
| | - Mark Bailey
- Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic
| | - Dominique Brunel
- Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France
| | - Åsa Frostegård
- NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
| | - Thierry Heulin
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel
| | - Kristiina L Kruus
- Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland
| | - George A Kowalchuk
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Antonio Lagares
- Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina
| | | | - Philippe Lemanceau
- Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France
| | - Denis Le Paslier
- CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia Norwich, UK
| | - David D Myrold
- Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA
| | | | - Paolo Nannipieri
- Department of Agrifood and Environmental Science, University of Florence Florence, Italy
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia
| | - John J Parnell
- National Ecological Observatory Network Boulder, CO, USA
| | - Alfred Pühler
- Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | | | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Alexander Sczyrba
- Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany
| | - Angela Sessitsch
- Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden
| | - Jan Sørensen
- Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Geertje van Keulen
- Institute of Life Science, Medical School, Swansea University Swansea, UK
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China
| | - Xiaojun Zhang
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liping Zhao
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Pascal Simonet
- Institute of Life Science, Medical School, Swansea University Swansea, UK
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19
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Qu Z, Bakken LR, Molstad L, Frostegård Å, Bergaust LL. Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions. Environ Microbiol 2016; 18:2951-63. [PMID: 26568281 DOI: 10.1111/1462-2920.13128] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 11/27/2022]
Abstract
Oxygen is known to repress denitrification at the transcriptional and metabolic levels. It has been a common notion that nitrous oxide reductase (N2 OR) is the most sensitive enzyme among the four N-oxide reductases involved in denitrification, potentially leading to increased N2 O production under suboxic or fluctuating oxygen conditions. We present detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of e(-) -flow to O2 and N2 O under various O2 regimes. Transcription of nosZ took place concomitantly with that of narG under suboxic conditions, whereas transcription of nirS and norB was inhibited until O2 levels approached 0 μM in the liquid. Catalytically functional N2 OR was synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2 O reduction rates were 10 times higher when anaerobic pre-cultures were subjected to the same conditions. Upon oxygen exposure, there was an incomplete and transient inactivation of N2 OR that could be ascribed to its lower ability to compete for electrons compared with terminal oxidases. The demonstrated reduction of N2 O at high O2 partial pressure and low N2 O concentrations by a bacterium not known as a typical aerobic denitrifier may provide one clue to the understanding of why some soils appear to act as sinks rather than sources for atmospheric N2 O.
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Affiliation(s)
- Zhi Qu
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars R Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars Molstad
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Linda L Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway.
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20
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Mania D, Heylen K, van Spanning RJM, Frostegård Å. Regulation of nitrogen metabolism in the nitrate-ammonifying soil bacteriumBacillus viretiand evidence for its ability to grow using N2O as electron acceptor. Environ Microbiol 2016; 18:2937-50. [DOI: 10.1111/1462-2920.13124] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Daniel Mania
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
| | - Kim Heylen
- Laboratory of Microbiology; Department of Biochemistry and Microbiology; University of Ghent; Gent Belgium
| | - Rob J. M. van Spanning
- Department of Molecular Cell Biology; Faculty of Earth and Life Science; VU University; Amsterdam The Netherlands
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
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Mania D, Heylen K, van Spanning RJM, Frostegård Å. The nitrate-ammonifying andnosZ-carrying bacteriumBacillus viretiis a potent source and sink for nitric and nitrous oxide under high nitrate conditions. Environ Microbiol 2014; 16:3196-210. [DOI: 10.1111/1462-2920.12478] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/13/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Mania
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
| | - Kim Heylen
- Laboratory of Microbiology; Department of Biochemistry and Microbiology; University of Ghent; Gent Belgium
| | - Rob J. M. van Spanning
- Department of Molecular Cell Biology; Faculty of Earth and Life Science; VU University; Amsterdam The Netherlands
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
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Luckmann M, Mania D, Kern M, Bakken LR, Frostegård Å, Simon J. Production and consumption of nitrous oxide in nitrate-ammonifying Wolinella succinogenes cells. Microbiology (Reading) 2014; 160:1749-1759. [PMID: 24781903 DOI: 10.1099/mic.0.079293-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Global warming is moving more and more into the public consciousness. Besides the commonly mentioned carbon dioxide and methane, nitrous oxide (N2O) is a powerful greenhouse gas in addition to its contribution to depletion of stratospheric ozone. The increasing concern about N2O emission has focused interest on underlying microbial energy-converting processes and organisms harbouring N2O reductase (NosZ), such as denitrifiers and ammonifiers of nitrate and nitrite. Here, the epsilonproteobacterial model organism Wolinella succinogenes is investigated with regard to its capacity to produce and consume N2O during growth by anaerobic nitrate ammonification. This organism synthesizes an unconventional cytochrome c nitrous oxide reductase (cNosZ), which is encoded by the first gene of an atypical nos gene cluster. However, W. succinogenes lacks a nitric oxide (NO)-producing nitrite reductase of the NirS- or NirK-type as well as an NO reductase of the Nor-type. Using a robotized incubation system, the wild-type strain and suitable mutants of W. succinogenes that either produced or lacked cNosZ were analysed as to their production of NO, N2O and N2 in both nitrate-sufficient and nitrate-limited growth medium using formate as electron donor. It was found that cells growing in nitrate-sufficient medium produced small amounts of N2O, which derived from nitrite and, most likely, from the presence of NO. Furthermore, cells employing cNosZ were able to reduce N2O to N2. This reaction, which was fully inhibited by acetylene, was also observed after adding N2O to the culture headspace. The results indicate that W. succinogenes cells are competent in N2O and N2 production despite being correctly grouped as respiratory nitrate ammonifiers. N2O production is assumed to result from NO detoxification and nitrosative stress defence, while N2O serves as a terminal electron acceptor in anaerobic respiration. The ecological implications of these findings are discussed.
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Affiliation(s)
- Monique Luckmann
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Daniel Mania
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr Falsens vei 1, N1432 Ås, Norway
| | - Melanie Kern
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Lars R Bakken
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N1432 Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr Falsens vei 1, N1432 Ås, Norway
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
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Liu B, Mao Y, Bergaust L, Bakken LR, Frostegård Å. Strains in the genusThaueraexhibit remarkably different denitrification regulatory phenotypes. Environ Microbiol 2013; 15:2816-28. [DOI: 10.1111/1462-2920.12142] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Binbin Liu
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; N-1432; Norway
| | | | | | - Lars R. Bakken
- Department of Plant and Environmental Sciences; Norwegian University of Life Sciences; Ås; N-1432; Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; N-1432; Norway
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Degefu T, Wolde-meskel E, Frostegård Å. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia. Syst Appl Microbiol 2013; 36:272-80. [PMID: 23643092 DOI: 10.1016/j.syapm.2013.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/16/2013] [Accepted: 03/25/2013] [Indexed: 11/17/2022]
Abstract
The taxonomic diversity of thirty-seven Rhizobium strains, isolated from nodules of leguminous trees and herbs growing in Ethiopia, was studied using multilocus sequence analyses (MLSA) of six core and two symbiosis-related genes. Phylogenetic analysis based on the 16S rRNA gene grouped them into five clusters related to nine Rhizobium reference species (99-100% sequence similarity). In addition, two test strains occupied their own independent branches on the phylogenetic tree (AC86a2 along with R. tibeticum; 99.1% similarity and AC100b along with R. multihospitium; 99.5% similarity). One strain from Milletia ferruginea was closely related (>99%) to the genus Shinella, further corroborating earlier findings that nitrogen-fixing bacteria are distributed among phylogenetically unrelated taxa. Sequence analyses of five housekeeping genes also separated the strains into five well-supported clusters, three of which grouped with previously studied Ethiopian common bean rhizobia. Three of the five clusters could potentially be described into new species. Based on the nifH genes, most of the test strains from crop legumes were closely related to several strains of Ethiopian common bean rhizobia and other symbionts of bean plants (R. etli and R. gallicum sv. phaseoli). The grouping of the test strains based on the symbiosis-related genes was not in agreement with the housekeeping genes, signifying differences in their evolutionary history. Our earlier studies revealing a large diversity of Mesorhizobium and Ensifer microsymbionts isolated from Ethiopian legumes, together with the results from the present analysis of Rhizobium strains, suggest that this region might be a potential hotspot for rhizobial biodiversity.
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Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
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Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A, Frostegård Å. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2012; 63:1746-1753. [PMID: 22941297 DOI: 10.1099/ijs.0.044032-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.
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Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Endalkachew Wolde-Meskel
- School of Plant and Horticultural Sciences, Hawassa University, PO Box 5, Hawassa, Ethiopia.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Binbin Liu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
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Bergaust L, van Spanning RJM, Frostegård Å, Bakken LR. Expression of nitrous oxide reductase in Paracoccus denitrificans is regulated by oxygen and nitric oxide through FnrP and NNR. Microbiology (Reading) 2011; 158:826-834. [PMID: 22174385 PMCID: PMC3541799 DOI: 10.1099/mic.0.054148-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The reductases performing the four steps of denitrification are controlled by a network of transcriptional regulators and ancillary factors responding to intra- and extracellular signals, amongst which are oxygen and N oxides (NO and NO2–). Although many components of the regulatory network have been identified, there are gaps in our understanding of their role(s) in controlling the expression of the various reductases, in particular the environmentally important N2O reductase (N2OR). We investigated denitrification phenotypes of Paracoccus denitrificans mutants deficient in: (i) regulatory proteins (three FNR-type transcriptional regulators, NarR, NNR and FnrP, and NirI, which is involved in transcription activation of the structural nir cluster); (ii) functional enzymes (NO reductase and N2OR); or (iii) ancillary factors involved in N2O reduction (NirX and NosX). A robotized incubation system allowed us to closely monitor changes in concentrations of oxygen and all gaseous products during the transition from oxic to anoxic respiration. Strains deficient in NO reductase were able to grow during denitrification, despite reaching micromolar concentrations of NO, but were unable to return to oxic respiration. The FnrP mutant showed linear anoxic growth in a medium with nitrate as the sole NOx, but exponential growth was restored by replacing nitrate with nitrite. We interpret this as nitrite limitation, suggesting dual transcriptional control of respiratory nitrate reductase (NAR) by FnrP and NarR. Mutations in either NirX or NosX did not affect the phenotype, but the double mutant lacked the potential to reduce N2O. Finally, we found that FnrP and NNR are alternative and equally effective inducers of N2OR.
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Affiliation(s)
- Linda Bergaust
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Rob J. M. van Spanning
- Department of Molecular Cell Biology, Faculty of Earth and Life Science, VU University, Amsterdam, The Netherlands
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R. Bakken
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
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Degefu T, Wolde-meskel E, Frostegård Å. Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban trees in Southern regions of Ethiopia. Syst Appl Microbiol 2011; 34:216-26. [DOI: 10.1016/j.syapm.2010.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 08/14/2010] [Accepted: 09/28/2010] [Indexed: 11/17/2022]
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Wolde-Meskel E, Terefework Z, Frostegård Å, Lindström K. Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 2005; 55:1439-1452. [PMID: 16014464 DOI: 10.1099/ijs.0.63534-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR-RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500-1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR-RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100% similar to those of previously described species and 34 were novel sequences with 94-99% similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.
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Affiliation(s)
- Endalkachew Wolde-Meskel
- Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Science, PO Box 5040, N-1432 Ås, Norway
| | - Zewdu Terefework
- Department of Applied Chemistry and Microbiology, Biocenter 1, FIN-0014 University of Helsinki, Finland
| | - Åsa Frostegård
- Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Science, PO Box 5040, N-1432 Ås, Norway
| | - Kristina Lindström
- Department of Applied Chemistry and Microbiology, Biocenter 1, FIN-0014 University of Helsinki, Finland
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