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Hernández-Oaxaca D, Claro K, Rogel MA, Rosenblueth M, Martinez-Romero J, Martinez-Romero E. Novel symbiovars ingae, lysilomae and lysilomaefficiens in bradyrhizobia from tree-legume nodules. Syst Appl Microbiol 2023; 46:126433. [PMID: 37207476 DOI: 10.1016/j.syapm.2023.126433] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/16/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Inga vera and Lysiloma tree legumes form nodules with Bradyrhizobium spp. from the japonicum group that represent novel genomospecies, for which we describe here using genome data, symbiovars lysilomae, lysilomaefficiens and ingae. Genes encoding Type three secretion system (TTSS) that could affect host specificity were found in ingae but not in lysilomae nor in lysilomaefficiens symbiovars and uptake hydrogenase hup genes (that affect nitrogen fixation) were observed in bradyrhizobia from the symbiovars ingae and lysilomaefficiens. nolA gene was found in the symbiovar lysilomaefficiens but not in strains from lysilomae. We discuss that multiple genes may dictate symbiosis specificity. Besides, toxin-antitoxin genes were found in the symbiosis islands in bradyrhizobia from symbiovars ingae and lysilomaefficiens. A limit (95%) to define symbiovars with nifH gene sequences was proposed here.
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Affiliation(s)
| | - Karen Claro
- Genomic Science Center, UNAM Cuernavaca México, México
| | - Marco A Rogel
- Genomic Science Center, UNAM Cuernavaca México, México
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Hakobyan A, Zhu J, Glatter T, Paczia N, Liesack W. Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. Metab Eng 2020; 61:181-196. [PMID: 32479801 DOI: 10.1016/j.ymben.2020.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/29/2019] [Revised: 03/20/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
Methane, a non-expensive natural substrate, is used by Methylocystis spp. as a sole source of carbon and energy. Here, we assessed whether Methylocystis sp. strain SC2 is able to also utilize hydrogen as an energy source. The addition of 2% H2 to the culture headspace had the most significant positive effect on the growth yield under CH4 (6%) and O2 (3%) limited conditions. The SC2 biomass yield doubled from 6.41 (±0.52) to 13.82 (±0.69) mg cell dry weight per mmol CH4, while CH4 consumption was significantly reduced. Regardless of H2 addition, CH4 utilization was increasingly redirected from respiration to fermentation-based pathways with decreasing O2/CH4 mixing ratios. Theoretical thermodynamic calculations confirmed that hydrogen utilization under oxygen-limited conditions doubles the maximum biomass yield compared to fully aerobic conditions without H2 addition. Hydrogen utilization was linked to significant changes in the SC2 proteome. In addition to hydrogenase accessory proteins, the production of Group 1d and Group 2b hydrogenases was significantly increased in both short- and long-term incubations. Both long-term incubation with H2 (37 d) and treatments with chemical inhibitors revealed that SC2 growth under hydrogen-utilizing conditions does not require the activity of complex I. Apparently, strain SC2 has the metabolic capacity to channel hydrogen-derived electrons into the quinone pool, which provides a link between hydrogen oxidation and energy production. In summary, H2 may be a promising alternative energy source in biotechnologically oriented methanotroph projects that aim to maximize biomass yield from CH4, such as the production of high-quality feed protein.
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Affiliation(s)
- Anna Hakobyan
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jing Zhu
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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Torres AR, Brito B, Imperial J, Palacios JM, Ciampitti IA, Ruiz-argüeso T, Hungria M. Hydrogen-uptake genes improve symbiotic efficiency in common beans (Phaseolus vulgaris L.). Antonie van Leeuwenhoek 2020; 113:687-96. [DOI: 10.1007/s10482-019-01381-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/26/2019] [Indexed: 01/20/2023]
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Degli Esposti M, Martinez Romero E. A survey of the energy metabolism of nodulating symbionts reveals a new form of respiratory complex I. FEMS Microbiol Ecol 2016; 92:fiw084. [DOI: 10.1093/femsec/fiw084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
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Ikuta T, Takaki Y, Nagai Y, Shimamura S, Tsuda M, Kawagucci S, Aoki Y, Inoue K, Teruya M, Satou K, Teruya K, Shimoji M, Tamotsu H, Hirano T, Maruyama T, Yoshida T. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME J 2015; 10:990-1001. [PMID: 26418631 PMCID: PMC4796938 DOI: 10.1038/ismej.2015.176] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction. The host individual harbours heterogeneous symbiont subpopulations that either possess or lack the gene clusters encoding hydrogenase or nitrate reductase. The proportions of the different symbiont subpopulations in a host appeared to vary with the environment or with the host's development. Furthermore, the symbiont subpopulations were distributed in patches to form a mosaic pattern in the gill. Genomic heterogeneity in an endosymbiont population may enable differential utilization of diverse substrates and confer metabolic flexibility. Our findings open a new chapter in our understanding of how symbiotic organisms alter their metabolic capabilities and expand their range of habitats.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Miwako Tsuda
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Koji Inoue
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Morimi Teruya
- Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan.,Okinawa Science and Technology Promotion Center (OSTC), 112-18 Asahimachi, Naha, Okinawa, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
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Roumagnac P, Richaud P, Barakat M, Ortet P, Roncato MA, Heulin T, Peltier G, Achouak W, Cournac L. Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat. Microbiologyopen 2012; 1:349-61. [PMID: 23233392 PMCID: PMC3535381 DOI: 10.1002/mbo3.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 12/03/2022] Open
Abstract
Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 μmol/L O2 concentration or within soluble protein extracts up to 25–30 μmol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.
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Affiliation(s)
- Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, F-34398, Montpellier Cedex-5, France
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Annan H, Golding AL, Zhao Y, Dong Z. Choice of hydrogen uptake (Hup) status in legume-rhizobia symbioses. Ecol Evol 2012; 2:2285-90. [PMID: 23139886 PMCID: PMC3488678 DOI: 10.1002/ece3.325] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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: 04/05/2012] [Revised: 06/07/2012] [Accepted: 06/18/2012] [Indexed: 11/30/2022] Open
Abstract
The H2 is an obligate by-product of N-fixation. Recycling of H2 through uptake hydrogenase (Hup) inside the root nodules of leguminous plants is often considered an advantage for plants. However, many of the rhizobium-legume symbioses found in nature, especially those used in agriculture are shown to be Hup−, with the plants releasing H2 produced by nitrogenase activity from root nodules into the surrounding rhizosphere. Recent studies have suggested that, H2 induces plant-growth-promoting rhizobacteria, which may explain the widespread of Hup− symbioses in spite of the low energy efficiency of such associations. Wild legumes grown in Nova Scotia, Canada, were surveyed to determine if any plant-growth characteristics could give an indication of Hup choice in leguminous plants. Out of the plants sampled, two legumes, Securigera varia and Vicia cracca, showed Hup+ associations. Securigera varia exhibited robust root structure as compared with the other plants surveyed. Data from the literature and the results from this study suggested that plants with established root systems are more likely to form the energy-efficient Hup+ symbiotic relationships with rhizobia. Conversely, Hup− associations could be beneficial to leguminous plants due to H2-oxidizing plant-growth-promoting rhizobacteria that allow plants to compete successfully, early in the growing season. However, some nodules from V. cracca tested Hup+, while others were Hup−. This was similar to that observed in Glycine max and Pisum sativum, giving reason to believe that Hup choice might be affected by various internal and environmental factors.
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Affiliation(s)
- Henry Annan
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, Canada, B3H 3C3
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Abstract
This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zülpicher Str. 47b, D-50923 Cologne, Germany.
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Antolín MC, Muro I, Sánchez-Díaz M. Sewage sludge application can induce changes in antioxidant status of nodulated alfalfa plants. Ecotoxicol Environ Saf 2010; 73:436-442. [PMID: 19959231 DOI: 10.1016/j.ecoenv.2009.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 06/16/2009] [Accepted: 08/30/2009] [Indexed: 05/28/2023]
Abstract
A greenhouse experiment was conducted to investigate the oxidative stress produced by sewage sludge addition on nodulated alfalfa (Medicago sativa L. cv. Aragón) plants. Two types of sludge were incorporated into substrate: anaerobic mesophilic digested (AM) and autothermal thermophilic aerobic digested (ATAD) sludge. Pots without sludge but with inoculated plants were used as control treatment for comparison. Results showed that sludge amended plants had increased tissue accumulation of heavy metals that induced oxidative stress. This is characterized by induction of the antioxidant enzymatic activities and alterations in the redox state of ascorbate. ATAD sludge application produced a reduction in nodulation, increased nodule antioxidant enzyme activities and decreased ascorbate/dehydroascorbate ratio. As a consequence, nodules of ATAD treatment suffered from oxidative damages as evidenced by high malondialdehyde levels. By contrast, AM application enhanced plant growth and no deleterious effects on nodulation were found. Nodules developed in AM sludge had increased antioxidant enzyme activities, ascorbate/dehydroascorbate ratio and improved capacity for thiol synthesis. Results clearly showed that nodulated alfalfa performed better in AM than in ATAD sludge and suggest that differential response appears to be mediated by plant ability to thiol synthesis and to maintenance of a more equilibrated antioxidant status.
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Affiliation(s)
- M Carmen Antolín
- Dpto. Biología Vegetal, Sección Biología Vegetal (Unidad Asociada al CSIC, EEAD, Zaragoza), Facultades de Ciencias y Farmacia, Universidad de Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain.
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Cytryn EJ, Jitacksorn S, Giraud E, Sadowsky MJ. Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains. ISME J 2008; 2:158-70. [DOI: 10.1038/ismej.2007.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
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