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Quelas JI, Cabrera JJ, Díaz-Peña R, Sánchez-Schneider L, Jiménez-Leiva A, Tortosa G, Delgado MJ, Pettinari MJ, Lodeiro AR, del Val C, Mesa S. Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism. Int J Mol Sci 2024; 25:2157. [PMID: 38396833 PMCID: PMC10888616 DOI: 10.3390/ijms25042157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this bacterium. To deeply uncover the function of PhaR, we applied a multipronged approach, including the expression profile of a phaR mutant at the transcriptional and protein levels under microaerobic conditions, and the identification of direct targets and of proteins associated with PHA granules. Our results confirmed a pleiotropic function of PhaR, affecting several phenotypes, in addition to PHA cycle control. These include growth deficiency, regulation of carbon and nitrogen allocation, and bacterial motility. Interestingly, PhaR may also modulate the microoxic-responsive regulatory network by activating the expression of fixK2 and repressing nifA, both encoding two transcription factors relevant for microaerobic regulation. At the molecular level, two PhaR-binding motifs were predicted and direct control mediated by PhaR determined by protein-interaction assays revealed seven new direct targets for PhaR. Finally, among the proteins associated with PHA granules, we found PhaR, phasins, and other proteins, confirming a dual function of PhaR in microoxia.
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Affiliation(s)
- Juan I. Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- YPF Tecnología S.A. (Y-TEC), Avenida. del Petróleo Argentino s/n (1923), Berisso 1923, Argentina
| | - Juan J. Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Rocío Díaz-Peña
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Lucía Sánchez-Schneider
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - María J. Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - M. Julia Pettinari
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Aníbal R. Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- Cátedra de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Coral del Val
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
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Baruah N, Haajanen R, Rahman MT, Pirttilä AM, Koskimäki JJ. Biosynthesis of polyhydroxybutyrate by Methylorubrum extorquens DSM13060 is essential for intracellular colonization in plant endosymbiosis. FRONTIERS IN PLANT SCIENCE 2024; 15:1302705. [PMID: 38390299 PMCID: PMC10883064 DOI: 10.3389/fpls.2024.1302705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Methylorubrum extorquens DSM13060 is an endosymbiont that lives in the cells of shoot tip meristems. The bacterium is methylotrophic and consumes plant-derived methanol for the production of polyhydroxybutyrate (PHB). The PHB provides protection against oxidative stress for both host and endosymbiont cells through its fragments, methyl-esterified 3-hydroxybutyrate (ME-3HB) oligomers. We evaluated the role of the genes involved in the production of ME-3HB oligomers in the host colonization by the endosymbiont M. extorquens DSM13060 through targeted genetic mutations. The strains with deletions in PHB synthase (phaC), PHB depolymerase (phaZ1), and a transcription factor (phaR) showed altered PHB granule characteristics, as ΔphaC had a significantly low number of granules, ΔphaR had a significantly increased number of granules, and ΔphaZ1 had significantly large PHB granules in the bacterial cells. When the deletion strains were exposed to oxidative stress, the ΔphaC strain was sensitive to 10 mM HO· and 20 mM H2O2. The colonization of the host, Scots pine (Pinus sylvestris L.), by the deletion strains varied greatly. The deletion strain ΔphaR colonized the host mainly intercellularly, whereas the ΔphaZ1 strain was a slightly poorer colonizer than the control. The deletion strain ΔphaC lacked the colonization potential, living mainly on the surfaces of the epidermis of pine roots and shoots in contrast to the control, which intracellularly colonized all pine tissues within the study period. In earlier studies, deletions within the PHB metabolic pathway have had a minor effect on plant colonization by rhizobia. We have previously shown the association between ME-3HB oligomers, produced by PhaC and PhaZ1, and the ability to alleviate host-generated oxidative stress during plant infection by the endosymbiont M. extorquens DSM13060. Our current results show that the low capacity for PHB synthesis leads to poor tolerance of oxidative stress and loss of colonization potential by the endosymbiont. Altogether, our findings demonstrate that the metabolism of PHB in M. extorquens DSM13060 is an important trait in the non-rhizobial endosymbiosis.
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Affiliation(s)
- Namrata Baruah
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roosa Haajanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mohammad Tanvir Rahman
- Disease Networks, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Julinová M, Šašinková D, Minařík A, Kaszonyiová M, Kalendová A, Kadlečková M, Fayyazbakhsh A, Koutný M. Comprehensive Biodegradation Analysis of Chemically Modified Poly(3-hydroxybutyrate) Materials with Different Crystal Structures. Biomacromolecules 2023; 24:4939-4957. [PMID: 37819211 PMCID: PMC10646986 DOI: 10.1021/acs.biomac.3c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/27/2023] [Indexed: 10/13/2023]
Abstract
This work presents a comprehensive analysis of the biodegradation of polyhydroxybutyrate (PHB) and chemically modified PHB with different chemical and crystal structures in a soil environment. A polymer modification reaction was performed during preparation of the chemically modified PHB films, utilizing 2,5-dimethyl-2,5-di(tert-butylperoxy)-hexane as a free-radical initiator and maleic anhydride. Films of neat PHB and chemically modified PHB were prepared by extrusion and thermocompression. The biological agent employed was natural mixed microflora in the form of garden soil. The course and extent of biodegradation of the films was investigated by applying various techniques, as follows: a respirometry test to determine the production of carbon dioxide through microbial degradation; scanning electron microscopy (SEM); optical microscopy; fluorescence microscopy; differential scanning calorimetry (DSC); and X-ray diffraction (XRD). Next-generation sequencing was carried out to study the microbial community involved in biodegradation of the films. Findings from the respirometry test indicated that biodegradation of the extruded and chemically modified PHB followed a multistage (2-3) course, which varied according to the spatial distribution of amorphous and crystalline regions and their spherulitic morphology. SEM and polarized optical microscopy (POM) confirmed that the rate of biodegradation depended on the availability of the amorphous phase in the interspherulitic region and the width of the interlamellar region in the first stage, while dependence on the size of spherulites and thickness of spherulitic lamellae was evident in the second stage. X-ray diffraction revealed that orthorhombic α-form crystals with helical chain conformation degraded concurrently with β-form crystals with planar zigzag conformation. The nucleation of PHB crystals after 90 days of biodegradation was identified by DSC and POM, a phenomenon which impeded biodegradation. Fluorescence microscopy evidenced that the crystal structure of PHB affected the physiological behavior of soil microorganisms in contact with the surfaces of the films.
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Affiliation(s)
- Markéta Julinová
- Department
of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nad Ovčírnou 3685, 760 01, Zlín, Czech Republic
| | - Dagmar Šašinková
- Department
of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nad Ovčírnou 3685, 760 01, Zlín, Czech Republic
| | - Antonín Minařík
- Department
of Physics and Material Engineering, Faculty of Technology, Tomas Bata University in Zlín, Vavrečkova 5669, 760 01, Zlin, Czech Republic
| | - Martina Kaszonyiová
- Department
of Polymer Engineering, Faculty of Technology, Tomas Bata University in Zlín, Vavrečkova 5669, 760 01, Zlín, Czech Republic
| | - Alena Kalendová
- Department
of Polymer Engineering, Faculty of Technology, Tomas Bata University in Zlín, Vavrečkova 5669, 760 01, Zlín, Czech Republic
| | - Markéta Kadlečková
- Department
of Physics and Material Engineering, Faculty of Technology, Tomas Bata University in Zlín, Vavrečkova 5669, 760 01, Zlin, Czech Republic
| | - Ahmad Fayyazbakhsh
- Department
of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nad Ovčírnou 3685, 760 01, Zlín, Czech Republic
| | - Marek Koutný
- Department
of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nad Ovčírnou 3685, 760 01, Zlín, Czech Republic
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. FRONTIERS IN PLANT SCIENCE 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Martínez MDLÁM, Urzúa LS, Carrillo YA, Ramírez MB, Morales LJM. Polyhydroxybutyrate Metabolism in Azospirillum brasilense and Its Applications, a Review. Polymers (Basel) 2023; 15:3027. [PMID: 37514417 PMCID: PMC10383645 DOI: 10.3390/polym15143027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Gram-negative Azospirillum brasilense accumulates approximately 80% of polyhydroxybutyrate (PHB) as dry cell weight. For this reason, this bacterium has been characterized as one of the main microorganisms that produce PHB. PHB is synthesized inside bacteria by the polymerization of 3-hydroxybutyrate monomers. In this review, we are focusing on the analysis of the PHB production by A. brasilense in order to understand the metabolism during PHB accumulation. First, the carbon and nitrogen sources used to improve PHB accumulation are discussed. A. brasilense accumulates more PHB when it is grown on a minimal medium containing a high C/N ratio, mainly from malate and ammonia chloride, respectively. The metabolic pathways to accumulate and mobilize PHB in A. brasilense are mentioned and compared with those of other microorganisms. Next, we summarize the available information to understand the role of the genes involved in the regulation of PHB metabolism as well as the role of PHB in the physiology of Azospirillum. Finally, we made a comparison between the properties of PHB and polypropylene, and we discussed some applications of PHB in biomedical and commercial areas.
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Affiliation(s)
- María de Los Ángeles Martínez Martínez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Lucía Soto Urzúa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Yovani Aguilar Carrillo
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Mirian Becerril Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Luis Javier Martínez Morales
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
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Gorshkov AP, Kusakin PG, Borisov YG, Tsyganova AV, Tsyganov VE. Effect of Triazole Fungicides Titul Duo and Vintage on the Development of Pea ( Pisum sativum L.) Symbiotic Nodules. Int J Mol Sci 2023; 24:8646. [PMID: 37240010 PMCID: PMC10217885 DOI: 10.3390/ijms24108646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Triazole fungicides are widely used in agricultural production for plant protection, including pea (Pisum sativum L.). The use of fungicides can negatively affect the legume-Rhizobium symbiosis. In this study, the effects of triazole fungicides Vintage and Titul Duo on nodule formation and, in particular, on nodule morphology, were studied. Both fungicides at the highest concentration decreased the nodule number and dry weight of the roots 20 days after inoculation. Transmission electron microscopy revealed the following ultrastructural changes in nodules: modifications in the cell walls (their clearing and thinning), thickening of the infection thread walls with the formation of outgrowths, accumulation of poly-β-hydroxybutyrates in bacteroids, expansion of the peribacteroid space, and fusion of symbiosomes. Fungicides Vintage and Titul Duo negatively affect the composition of cell walls, leading to a decrease in the activity of synthesis of cellulose microfibrils and an increase in the number of matrix polysaccharides of cell walls. The results obtained coincide well with the data of transcriptomic analysis, which revealed an increase in the expression levels of genes that control cell wall modification and defense reactions. The data obtained indicate the need for further research on the effects of pesticides on the legume-Rhizobium symbiosis in order to optimize their use.
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Affiliation(s)
- Artemii P. Gorshkov
- Laboratory of Molecular and Cell Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg 196608, Russia; (A.P.G.); (P.G.K.); (A.V.T.)
| | - Pyotr G. Kusakin
- Laboratory of Molecular and Cell Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg 196608, Russia; (A.P.G.); (P.G.K.); (A.V.T.)
| | - Yaroslav G. Borisov
- Research Resource Centre “Molecular and Cell Technologies”, Saint Petersburg State University, Saint Petersburg 199034, Russia;
| | - Anna V. Tsyganova
- Laboratory of Molecular and Cell Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg 196608, Russia; (A.P.G.); (P.G.K.); (A.V.T.)
| | - Viktor E. Tsyganov
- Laboratory of Molecular and Cell Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg 196608, Russia; (A.P.G.); (P.G.K.); (A.V.T.)
- Saint Petersburg Scientific Center RAS, Universitetskaya Embankment 5, Saint Petersburg 199034, Russia
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Burghardt LT, diCenzo GC. The evolutionary ecology of rhizobia: multiple facets of competition before, during, and after symbiosis with legumes. Curr Opin Microbiol 2023; 72:102281. [PMID: 36848712 DOI: 10.1016/j.mib.2023.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 02/27/2023]
Abstract
Rhizobial bacteria have complex lifestyles that involve growth and survival in bulk soil, plant rhizospheres and rhizoplanes, legume infection threads, and mature and senescing legume nodules. In nature, rhizobia coexist and compete with many other rhizobial strains and species to form host associations. We review recent work defining competitive interactions across these environments. We highlight the use of sophisticated measurement tools and sequencing technologies to examine competition mechanisms in planta, and highlight environments (e.g. soil and senescing nodules) where we still know exceedingly little. We argue that moving toward an explicitly ecological framework (types of competition, resources, and genetic differentiation) will clarify the evolutionary ecology of these foundational organisms and open doors for engineering sustainable, beneficial associations with hosts.
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Affiliation(s)
- Liana T Burghardt
- The Pennsylvania State University, Department of Plant Science, University Park, PA 16802, United States; The Pennsylvania State University, Ecology Graduate Program, University Park, PA 16802, United States.
| | - George C diCenzo
- Queen's University, Department of Biology, Kingston, ON K7L 3N6, Canada
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Li S, Wu C, Liu H, Lyu X, Xiao F, Zhao S, Ma C, Yan C, Liu Z, Li H, Wang X, Gong Z. Systemic regulation of nodule structure and assimilated carbon distribution by nitrate in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1101074. [PMID: 36814755 PMCID: PMC9939697 DOI: 10.3389/fpls.2023.1101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The nitrate regulates soybean nodulation and nitrogen fixation systemically, mainly in inhibiting nodule growth and reducing nodule nitrogenase activity, but the reason for its inhibition is still inconclusive. METHODS The systemic effect of nitrate on nodule structure, function, and carbon distribution in soybean (Glycine max (L.) Merr.) was studied in a dual-root growth system, with both sides inoculated with rhizobia and only one side subjected to nitrate treatment for four days. The non-nodulating side was genetically devoid of the ability to form nodules. Nutrient solutions with nitrogen concentrations of 0, 100, and 200 mg L-1 were applied as KNO3 to the non-nodulating side, while the nodulating side received a nitrogen-free nutrient solution. Carbon partitioning in roots and nodules was monitored using 13C-labelled CO2. Other nodule responses were measured via the estimation of the nitrogenase activity and the microscopic observation of nodule ultrastructure. RESULTS Elevated concentrations of nitrate applied on the non-nodulating side caused a decrease in the number of bacteroids, fusion of symbiosomes, enlargement of the peribacteroid spaces, and onset of degradation of poly-β-hydroxybutyrate granules, which is a form of carbon storage in bacteroids. These microscopic observations were associated with a strong decrease in the nitrogenase activity of nodules. Furthermore, our data demonstrate that the assimilated carbon is more likely to be allocated to the non-nodulating roots, as follows from the competition for carbon between the symbiotic and non-symbiotic sides of the dual-root system. CONCLUSION We propose that there is no carbon competition between roots and nodules when they are indirectly supplied with nitrate, and that the reduction of carbon fluxes to nodules and roots on the nodulating side is the mechanism by which the plant systemically suppresses nodulation under nitrogen-replete conditions.
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Affiliation(s)
- Sha Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Chengbin Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hao Liu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaochen Lyu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Fengsheng Xiao
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shuhong Zhao
- College of Engineering, Northeast Agricultural University, Harbin, China
| | - Chunmei Ma
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chao Yan
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhilei Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hongyu Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xuelai Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenping Gong
- College of Agriculture, Northeast Agricultural University, Harbin, China
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Lee J, Um S, Kim SH. Metabolomic analysis of halotolerant endophytic bacterium Salinivibrio costicola isolated from Suaeda maritima (L.) dumort. Front Mol Biosci 2022; 9:967945. [PMID: 36120548 PMCID: PMC9478568 DOI: 10.3389/fmolb.2022.967945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, the Salinivibrio costicola strain was isolated from Suaeda maritima (L.) Dumort. collected in Sinan, Republic of Korea. The endophytic characteristics of the Gram-negative bacterium S. costicola were verified with metagenomics sequencing of S. maritima. S. costicola was cultivated for 3 days in a liquid medium with 3.3% sea salt and analyzed the metabolites produced by the strain cultured in five different bacterial cultivation media. From the bacterial cultures, polyhydroxybutyrate derivatives were detected using high-resolution mass spectrometry, and three major compounds were isolated by high-performance liquid chromatography. The chemical structures of the compounds were elucidated using nuclear magnetic resonance and MS analyses. The relationship between the compounds was confirmed with Global Natural Product Social Molecular Networking, which showed clustering of the compounds. From the S. maritima extract, polyhydroxybutyrate derivatives produced by S. costicola were detected as being accumulated in the host plant.
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Optimization of Production of Polyhydroxyalkanoates (PHAs) from Newly Isolated Ensifer sp. Strain HD34 by Response Surface Methodology. Processes (Basel) 2022. [DOI: 10.3390/pr10081632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Petroleum-based plastics have become a big problem in many countries because of their non-degradability and that they become microplastics in the environment. This study focused on the optimization of production medium and conditions of polyhydroxyalkanoates (PHAs), which are biodegradable bioplastics and are accumulated in microbial cells. Among 341 isolates from 40 composted soil samples, the best isolate was the HD34 strain, which was identified using morphological, molecular, and biochemical methods. The results showed that the strain was most closely related to Ensifer adhaerens LMG20216T, with 99.6% similarity. For optimization of production medium and conditions using response surface methodology, it exhibited an optimal medium containing 3.99% (w/v) of potato dextrose broth (PDB) and 1.54% (w/v) of D-glucose with an adjusted initial pH of 9.0. The optimum production was achieved under culture conditions of a temperature of 28 °C, inoculum size of 2.5% (v/v), and a shaking speed of 130 rpm for 5 days. The results showed the highest PHA content, total cell dry weight, and PHA yield as 72.96% (w/w) of cell dry weight, 9.30 g/L, and 6.78 g/L, respectively. The extracted PHA characterization was studied using gas chromatography, 1H NMR, FTIR, and XRD. The results found that the polymer was a polyhydroxybutyrate (PHB) with a melting temperature (Tm) and degradation temperature (Td) of 173.5 °C and 260.8 °C, respectively.
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11
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Yang Z, Du H, Xing X, Li W, Kong Y, Li X, Zhang C. A small heat shock protein, GmHSP17.9, from nodule confers symbiotic nitrogen fixation and seed yield in soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:103-115. [PMID: 34487637 PMCID: PMC8710831 DOI: 10.1111/pbi.13698] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 05/27/2023]
Abstract
Legume-rhizobia symbiosis enables biological nitrogen fixation to improve crop production for sustainable agriculture. Small heat shock proteins (sHSPs) are involved in multiple environmental stresses and plant development processes. However, the role of sHSPs in nodule development in soybean remains largely unknown. In the present study, we identified a nodule-localized sHSP, called GmHSP17.9, in soybean, which was markedly up-regulated during nodule development. GmHSP17.9 was specifically expressed in the infected regions of the nodules. GmHSP17.9 overexpression and RNAi in transgenic composite plants and loss of function in CRISPR-Cas9 gene-editing mutant plants in soybean resulted in remarkable alterations in nodule number, nodule fresh weight, nitrogenase activity, contents of poly β-hydroxybutyrate bodies (PHBs), ureide and total nitrogen content, which caused significant changes in plant growth and seed yield. GmHSP17.9 was also found to act as a chaperone for its interacting partner, GmNOD100, a sucrose synthase in soybean nodules which was also preferentially expressed in the infected zone of nodules, similar to GmHSP17.9. Functional analysis of GmNOD100 in composite transgenic plants revealed that GmNOD100 played an essential role in soybean nodulation. The hsp17.9 lines showed markedly more reduced sucrose synthase activity, lower contents of UDP-glucose and acetyl coenzyme A (acetyl-CoA), and decreased activity of succinic dehydrogenase (SDH) in the tricarboxylic acid (TCA) cycle in nodules due to the missing interaction with GmNOD100. Our findings reveal an important role and an unprecedented molecular mechanism of sHSPs in nodule development and nitrogen fixation in soybean.
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Affiliation(s)
- Zhanwu Yang
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Hui Du
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Xinzhu Xing
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Wenlong Li
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Youbin Kong
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Xihuan Li
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Caiying Zhang
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
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12
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Crang N, Borah K, James EK, Jorrín B, Green P, Tkacz A, East AK, Poole PS. Role and Regulation of Poly-3-Hydroxybutyrate in Nitrogen Fixation in Azorhizobium caulinodans. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1390-1398. [PMID: 34875178 DOI: 10.1094/mpmi-06-21-0138-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
An Azorhizobium caulinodans phaC mutant (OPS0865) unable to make poly-3-hydroxybutyrate (PHB), grows poorly on many carbon sources and cannot fix nitrogen in laboratory culture. However, when inoculated onto its host plant, Sesbania rostrata, the phaC mutant consistently fixed nitrogen. Upon reisolation from S. rostrata root nodules, a suppressor strain (OPS0921) was isolated that has significantly improved growth on a variety of carbon sources and also fixes nitrogen in laboratory culture. The suppressor retains the original mutation and is unable to synthesize PHB. Genome sequencing revealed a suppressor transition mutation, G to A (position 357,354), 13 bases upstream of the ATG start codon of phaR in its putative ribosome binding site (RBS). PhaR is the global regulator of PHB synthesis but also has other roles in regulation within the cell. In comparison with the wild type, translation from the phaR native RBS is increased approximately sixfold in the phaC mutant background, suggesting that the level of PhaR is controlled by PHB. Translation from the phaR mutated RBS (RBS*) of the suppressor mutant strain (OPS0921) is locked at a low basal rate and unaffected by the phaC mutation, suggesting that RBS* renders the level of PhaR insensitive to regulation by PHB. In the original phaC mutant (OPS0865), the lack of nitrogen fixation and poor growth on many carbon sources is likely to be due to increased levels of PhaR causing dysregulation of its complex regulon, because PHB formation, per se, is not required for effective nitrogen fixation in A. caulinodans.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nick Crang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Patrick Green
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Alison K East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
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13
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Mandon K, Nazaret F, Farajzadeh D, Alloing G, Frendo P. Redox Regulation in Diazotrophic Bacteria in Interaction with Plants. Antioxidants (Basel) 2021; 10:antiox10060880. [PMID: 34070926 PMCID: PMC8226930 DOI: 10.3390/antiox10060880] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/23/2022] Open
Abstract
Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance nutrient acquisition. Nitrogen-fixing bacteria, either as endophytes or as endosymbionts, specifically improve the growth and development of plants by supplying them with nitrogen, a key macro-element. Survival and proliferation of these bacteria require their adaptation to the rhizosphere and host plant, which are particular ecological environments. This adaptation highly depends on bacteria response to the Reactive Oxygen Species (ROS), associated to abiotic stresses or produced by host plants, which determine the outcome of the plant-bacteria interaction. This paper reviews the different antioxidant defense mechanisms identified in diazotrophic bacteria, focusing on their involvement in coping with the changing conditions encountered during interaction with plant partners.
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Affiliation(s)
- Karine Mandon
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Fanny Nazaret
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Davoud Farajzadeh
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz 5375171379, Iran;
- Center for International Scientific Studies and Collaboration (CISSC), Ministry of Science, Research and Technology, Tehran 158757788, Iran
| | - Geneviève Alloing
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Pierre Frendo
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
- Correspondence:
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14
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Müller-Santos M, Koskimäki JJ, Alves LPS, de Souza EM, Jendrossek D, Pirttilä AM. The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol Rev 2021; 45:fuaa058. [PMID: 33118006 DOI: 10.1093/femsre/fuaa058] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Therefore, it is widely believed that the function of PHB is to serve as a mobilizable carbon repository when bacteria face carbon limitation, supporting their survival. However, recent findings indicate that bacteria switch from PHB synthesis to mobilization under stress conditions such as thermal and oxidative shock. The mobilization products, 3-hydroxybutyrate and its oligomers, show a protective effect against protein aggregation and cellular damage caused by reactive oxygen species and heat shock. Thus, bacteria should have an environmental monitoring mechanism directly connected to the regulation of the PHB metabolism. Here, we review the current knowledge on PHB physiology together with a summary of recent findings on novel functions of PHB in stress resistance. Potential applications of these new functions are also presented.
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Affiliation(s)
- Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Luis Paulo Silveira Alves
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
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15
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Samarah LZ, Tran TH, Stacey G, Vertes A. Mass Spectrometry Imaging of Bio‐oligomer Polydispersity in Plant Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Laith Z. Samarah
- Department of Chemistry George Washington University Washington DC 20052 USA
| | - Tina H. Tran
- Department of Chemistry George Washington University Washington DC 20052 USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry C. S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA
| | - Akos Vertes
- Department of Chemistry George Washington University Washington DC 20052 USA
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16
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Samarah LZ, Tran TH, Stacey G, Vertes A. Mass Spectrometry Imaging of Bio-oligomer Polydispersity in Plant Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays. Angew Chem Int Ed Engl 2021; 60:9071-9077. [PMID: 33529427 DOI: 10.1002/anie.202015251] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/30/2020] [Indexed: 12/17/2023]
Abstract
Mass spectrometry imaging (MSI) enables simultaneous spatial mapping for diverse molecules in biological tissues. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) has been a mainstream MSI method for a wide range of biomolecules. However, MALDI-MSI of biological homopolymers used for energy storage and molecular feedstock is limited by, e.g., preferential ionization for certain molecular classes. Matrix-free nanophotonic ionization from silicon nanopost arrays (NAPAs) is an emerging laser desorption ionization (LDI) platform with ultra-trace sensitivity and molecular imaging capabilities. Here, we show complementary analysis and MSI of polyhydroxybutyric acid (PHB), polyglutamic acid (PGA), and polysaccharide oligomers in soybean root nodule sections by NAPA-LDI and MALDI. For PHB, number and weight average molar mass, polydispersity, and oligomer size distributions across the tissue section and in regions of interest were characterized by NAPA-LDI-MSI.
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Affiliation(s)
- Laith Z Samarah
- Department of Chemistry, George Washington University, Washington, DC, 20052, USA
| | - Tina H Tran
- Department of Chemistry, George Washington University, Washington, DC, 20052, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Akos Vertes
- Department of Chemistry, George Washington University, Washington, DC, 20052, USA
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17
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Amadu AA, Qiu S, Ge S, Addico GND, Ameka GK, Yu Z, Xia W, Abbew AW, Shao D, Champagne P, Wang S. A review of biopolymer (Poly-β-hydroxybutyrate) synthesis in microbes cultivated on wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143729. [PMID: 33310224 DOI: 10.1016/j.scitotenv.2020.143729] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
The large quantities of non-degradable single use plastics, production and disposal, in addition to increasing amounts of municipal and industrial wastewaters are among the major global issues known today. Biodegradable plastics from biopolymers such as Poly-β-hydroxybutyrates (PHB) produced by microorganisms are potential substitutes for non-degradable petroleum-based plastics. This paper reviews the current status of wastewater-cultivated microbes utilized in PHB production, including the various types of wastewaters suitable for either pure or mixed culture PHB production. PHB-producing strains that have the potential for commercialization are also highlighted with proposed selection criteria for choosing the appropriate PHB microbe for optimization of processes. The biosynthetic pathways involved in producing microbial PHB are also discussed to highlight the advancements in genetic engineering techniques. Additionally, the paper outlines the factors influencing PHB production while exploring other metabolic pathways and metabolites simultaneously produced along with PHB in a bio-refinery context. Furthermore, the paper explores the effects of extraction methods on PHB yield and quality to ultimately facilitate the commercial production of biodegradable plastics. This review uniquely discusses the developments in research on microbial biopolymers, specifically PHB and also gives an overview of current commercial PHB companies making strides in cutting down plastic pollution and greenhouse gases.
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Affiliation(s)
- Ayesha Algade Amadu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China.
| | - Gloria Naa Dzama Addico
- Council for Scientific and Industrial Research (CSIR) - Water Research Institute (WRI), P.O. Box AH 38, Achimota Greater Accra, Ghana
| | - Gabriel Komla Ameka
- Department of Botany, University of Ghana, P.O. Box LG55, Legon, Accra, Ghana
| | - Ziwei Yu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Wenhao Xia
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Abdul-Wahab Abbew
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Dadong Shao
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, PR China
| | - Pascale Champagne
- Department of Civil Engineering, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Sufeng Wang
- School of Economics and Management, Anhui Jianzhu University, Hefei, Anhui 230601, PR China
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18
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Quides KW, Salaheldine F, Jariwala R, Sachs JL. Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs. Evolution 2021; 75:1189-1200. [PMID: 33521949 DOI: 10.1111/evo.14173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/31/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Current Institution: Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Fathi Salaheldine
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Ruchi Jariwala
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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Abstract
There is growing interest in the use of associative, plant growth-promoting bacteria (PGPB) as biofertilizers to serve as a sustainable alternative for agriculture application. While a variety of mechanisms have been proposed to explain bacterial plant growth promotion, the molecular details of this process remain unclear. The plant rhizosphere harbors a diverse population of microorganisms, including beneficial plant growth-promoting bacteria (PGPB), that colonize plant roots and enhance growth and productivity. In order to specifically define bacterial traits that contribute to this beneficial interaction, we used high-throughput transposon mutagenesis sequencing (TnSeq) in two model root-bacterium systems associated with Setaria viridis: Azoarcus olearius DQS4T and Herbaspirillum seropedicae SmR1. This approach identified ∼100 significant genes for each bacterium that appeared to confer a competitive advantage for root colonization. Most of the genes identified specifically in A. olearius encoded metabolism functions, whereas genes identified in H. seropedicae were motility related, suggesting that each strain requires unique functions for competitive root colonization. Genes were experimentally validated by site-directed mutagenesis, followed by inoculation of the mutated bacteria onto S. viridis roots individually, as well as in competition with the wild-type strain. The results identify key bacterial functions involved in iron uptake, polyhydroxybutyrate metabolism, and regulation of aromatic metabolism as important for root colonization. The hope is that by improving our understanding of the molecular mechanisms used by PGPB to colonize plants, we can increase the adoption of these bacteria in agriculture to improve the sustainability of modern cropping systems.
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The Fungicide Tetramethylthiuram Disulfide Negatively Affects Plant Cell Walls, Infection Thread Walls, and Symbiosomes in Pea ( Pisum sativum L.) Symbiotic Nodules. PLANTS 2020; 9:plants9111488. [PMID: 33158267 PMCID: PMC7694270 DOI: 10.3390/plants9111488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/26/2022]
Abstract
In Russia, tetramethylthiuram disulfide (TMTD) is a fungicide widely used in the cultivation of legumes, including the pea (Pisum sativum). Application of TMTD can negatively affect nodulation; nevertheless, its effect on the histological and ultrastructural organization of nodules has not previously been investigated. In this study, the effect of TMTD at three concentrations (0.4, 4, and 8 g/kg) on nodule development in three pea genotypes (laboratory lines Sprint-2 and SGE, and cultivar 'Finale') was examined. In SGE, TMTD at 0.4 g/kg reduced the nodule number and shoot and root fresh weights. Treatment with TMTD at 8 g/kg changed the nodule color from pink to green, indicative of nodule senescence. Light and transmission electron microscopy analyses revealed negative effects of TMTD on nodule structure in each genotype. 'Finale' was the most sensitive cultivar to TMTD and Sprint-2 was the most tolerant. The negative effects of TMTD on nodules included the appearance of a senescence zone, starch accumulation, swelling of cell walls accompanied by a loss of electron density, thickening of the infection thread walls, symbiosome fusion, and bacteroid degradation. These results demonstrate how TMTD adversely affects nodules in the pea and will be useful for developing strategies to optimize fungicide use on legume crops.
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Liu S, Liao LL, Nie MM, Peng WT, Zhang MS, Lei JN, Zhong YJ, Liao H, Chen ZC. A VIT-like transporter facilitates iron transport into nodule symbiosomes for nitrogen fixation in soybean. THE NEW PHYTOLOGIST 2020; 226:1413-1428. [PMID: 32119117 DOI: 10.1111/nph.16506] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Effective legume-rhizobia symbiosis depends on efficient nutrient exchange. Rhizobia need to synthesize iron-containing proteins for symbiotic nitrogen fixation (SNF) in nodules, which depends on host plant-mediated iron uptake into the symbiosome. We functionally investigated a pair of vacuolar iron transporter like (VTL) genes, GmVTL1a/b, in soybean (Glycine max) and evaluated their contributions to SNF, including investigations of gene expression patterns, subcellular localization, and mutant phenotypes. Though both GmVTL1a/b genes were specifically expressed in the fixation zone of the nodule, GmVTL1a was the lone member to be localized at the tonoplast of tobacco protoplasts, and shown to facilitate ferrous iron transport in yeast. GmVTL1a targets the symbiosome in infected cells, as verified by in situ immunostaining. Two vtl1 knockout mutants had lower iron concentrations in nodule cell sap and peribacteroid units than in wild-type plants, suggesting that GmVTL1 knockout inhibited iron import into symbiosomes. Furthermore, GmVTL1 knockout minimally affected soybean growth under nonsymbiotic conditions, but dramatically impaired nodule development and SNF activity under nitrogen-limited and rhizobia-inoculation conditions, which eventually led to growth retardation. Taken together, these results demonstrate that GmVTL1a is indispensable for SNF in nodules as a transporter of ferrous iron from the infected root cell cytosol to the symbiosome.
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Affiliation(s)
- Sheng Liu
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li Li Liao
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Miao Miao Nie
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Ting Peng
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng Shi Zhang
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia Ning Lei
- Vector-borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Jia Zhong
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Chang Chen
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Tran TT, Charles TC. Lactic acid containing polymers produced in engineered Sinorhizobium meliloti and Pseudomonas putida. PLoS One 2020; 15:e0218302. [PMID: 32191710 PMCID: PMC7082056 DOI: 10.1371/journal.pone.0218302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
This study demonstrates that novel polymer production can be achieved by introducing pTAM, a broad-host-range plasmid expressing codon-optimized genes encoding Clostridium propionicum propionate CoA transferase (PctCp, Pct532) and a modified Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1Ps6-19, PhaC1400), into phaC mutant strains of the native polymer producers Sinorhizobium meliloti and Pseudomonas putida. Both phenotypic analysis and gas chromatography analysis indicated the synthesis and accumulation of biopolymers in S. meliloti and P. putida strains. Expression in S. meliloti resulted in the production of PLA homopolymer up to 3.2% dried cell weight (DCW). The quaterpolymer P (3HB-co-LA-co-3HHx-co-3HO) was produced by expression in P. putida. The P. putida phaC mutant strain produced this type of polymer the most efficiently with polymer content of 42% DCW when cultured in defined media with the addition of sodium octanoate. This is the first report, to our knowledge, of the production of a range of different biopolymers using the same plasmid-based system in different backgrounds. In addition, it is the first time that the novel polymer (P(3HB-co-LA-co-3HHx-co-3HO)), has been reported being produced in bacteria.
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Affiliation(s)
- Tam T. Tran
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- * E-mail:
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Kosmachevskaya OV, Osipov EV, Van Chi T, Mai PTT, Topunov AF. Effect of Cultivation Conditions on Poly(3-hydroxybutyrate) Synthesis by Nodule Bacteria Rhizobium phaseoli. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s000368382001010x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Xu X, Shao M, Yin C, Mao Z, Shi J, Yu X, Wang Y, Sun F, Zhang Y. Diversity, Bacterial Symbionts, and Antimicrobial Potential of Termite-Associated Fungi. Front Microbiol 2020; 11:300. [PMID: 32231643 PMCID: PMC7082625 DOI: 10.3389/fmicb.2020.00300] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
The phylogenetic diversity of fungi isolated from the Odontotermes formosanus was investigated by dilution-plate method, combined with morphological characteristics and 5.8S rDNA sequencing. Thirty-nine fungi were isolated and purified from O. formosanus, which were belonging to two phyla and four classes (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Agaricomycetes). Furthermore, nine bacterial 16S rRNA sequences were obtained from total fungal genomic DNA. All bacterial symbionts were segmented into four genera: Bacillus, Methylobacterium, Paenibacillus, and Trabulsiella. The antimicrobial activities of all endophytic fungi extracts were tested by using the filter paper method against Escherichia coli (ATCC 8739), Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 6538), and Canidia albicans (ATCC 10231). The results exhibited that 25 extracts (64%) exhibited antibacterial activity against at least one of the tested bacterial strains. Furthermore, the secondary metabolites 1 [5-hydroxyramulosin (1a):biatriosporin M (1b) = 2:1] from the Pleosporales sp. BYCDW4 exhibited potent antimicrobial activities against E. coli, C. albicans, B. subtilis, and S. aureus with the inhibition zone diameter (IZD) of 13.67, 14.33, 12.17, and 11.33 mm, respectively, which were comparable with those of the positive control. 1-(2,5-Dihydroxyphenyl)-3-hydroxybutan-1-one (2) from the Microdiplodia sp. BYCDW8 showed medium inhibitory activities against B. subtilis and S. aureus, with the IZD range of 8.32–9.13 mm. In conclusion, the study showed the diversity of insect symbionts could be expected to develop the resource of new species and antibiotics.
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Affiliation(s)
- Xiao Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Mingwei Shao
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Caiping Yin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingjing Shi
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Xinyuan Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Ying Wang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Feifei Sun
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Yinglao Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
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25
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Kandelinskaya OL, Grischenko HR, Кhripach VA, Zhabinskii VN, Kartizhova LE, Shashko YK, Kosmachevskaya OV, Nasybullina EI, Topunov AF. Anabolic/anticatabolic and adaptogenic effects of 24-epibrassinolide on Lupinus angustifolius: Causes and consequences. Steroids 2020; 154:108545. [PMID: 31758963 DOI: 10.1016/j.steroids.2019.108545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/19/2019] [Accepted: 11/14/2019] [Indexed: 11/19/2022]
Abstract
Lupinus angustifolius L. is a legume culture known as a source of valuable feed protein and the N2-fixator for improving soil fertility. However, its low ecological resistance does not allow for a stable yield of the crop. Earlier, we have shown that steroid phytohormone 24-epibrassinolide (EBR) increases the tolerance of lupine to chlorine ions by activating the protective proteins in ripening seeds (such as proteinase inhibitors that prevent protein breakdown) and lectins. Here we investigated the effect of EBR on the functional status of the N2-fixing system in root nodules, protein synthesis in ripening seeds and the resistance of lupine plants to various pathogens. It was found that EBR enhanced the nodulation process, N2-fixing activity of nitrogenase and the accumulation of poly-β-hydroxybutirate in the bacteroides, increased the leghemoglobin content in the nodules as well as the metabolic activity of bacteroides. According to data on the inclusion of 14C-leucine in maturing seed proteins, EBR increased the accumulation of protein in them against the background of a short-term decrease in protein synthesis and its subsequent regeneration to the control level. Gradual inhibition of protein synthesis, characteristic of other legumes, was observed in control variants of lupine. EBR increased lupine resistance to phytopathogenic fungi of Colletotrichum genus and insects of Noctuidae and Scarabaeidae families. We concluded that a more complete implementation of the potential productivity and sustainability of lupine under the action of EBR was achieved due to the anabolic/anti-catabolic effect on the N2 fixation system in root nodules, as well as on protein synthesis in ripening seeds.
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Affiliation(s)
- Olga L Kandelinskaya
- Kuprevich Institute of Experimental Botany of the National Academy of Sciences of Belarus, 220072 Minsk, Akademicheskaya, 27, Belarus.
| | - Helena R Grischenko
- Kuprevich Institute of Experimental Botany of the National Academy of Sciences of Belarus, 220072 Minsk, Akademicheskaya, 27, Belarus
| | - Vladimir A Кhripach
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 2200141 Minsk, Kuprevich st, 5/2, Belarus
| | - Vladimir N Zhabinskii
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 2200141 Minsk, Kuprevich st, 5/2, Belarus
| | - Lylia E Kartizhova
- Institute of Microbiology of the National Academy of Sciences of Belarus, 2200141 Minsk, Kuprevich st, 2, Belarus
| | - Yuriy K Shashko
- Research and Practical Center of the National Academy of Sciences of Belarus for Arable Farming, 222160 Zhodino, Timiriyazeva, 1, Belarus
| | - Olga V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Elvira I Nasybullina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Alexey F Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
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26
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Pastor-Bueis R, Sánchez-Cañizares C, James EK, González-Andrés F. Formulation of a Highly Effective Inoculant for Common Bean Based on an Autochthonous Elite Strain of Rhizobium leguminosarum bv. phaseoli, and Genomic-Based Insights Into Its Agronomic Performance. Front Microbiol 2019; 10:2724. [PMID: 31920999 PMCID: PMC6927923 DOI: 10.3389/fmicb.2019.02724] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Common bean is a poor symbiotic N-fixer, with a low response to inoculation owing to its promiscuous nodulation with competitive but inefficient resident rhizobia. Consequently, farmers prefer to fertilize them rather than rely on their capacity for Biological Nitrogen Fixation (BNF). However, when rhizobial inoculants are based on autochthonous strains, they often have superior BNF performance in the field due to their genetic adaptations to the local environment. Nevertheless, there is scant information at the genomic level explaining their superiority or on how their genomes may influence the inoculant performance. This information is especially important in technologically advanced agri-systems like Europe, where environmental concerns and increasingly stringent fertilizer regulations are encouraging a return to the use of rhizobial inoculants, but based upon strains that have been thoroughly characterized in terms of their symbiotic performance and their genetics. The aim of this study was to design an inoculant formulation based on a superior autochthonous strain, Rhizobium leguminosarum bv. phaseoli LCS0306, to assess its performance in the field, and to determine the genomic features contributing to the high effectiveness of its symbiosis with common bean. Plants inoculated with the autochthonous strain LCS0306 fixed significantly more nitrogen than those with the allochthonous strains R. phaseoli ATCC 14482T and R. etli CFN42T, and had grain yield similar to the nitrogen-fertilized controls. Inoculation with LCS0306 was particularly efficacious when formulated with a carrier based upon a mixture of perlite and biochar. Whole genome comparisons revealed no differences in the classical symbiotic genes of strain LCS0306 within the symbiovar phaseoli. However, its symbiotic superior performance might be due to its genomic versatility, as it harbors a large assortment of genes contributing to fitness and competitiveness. It is concluded that inoculation with elite rhizobia formulated with perlite-biochar carriers might constitute a step-change in the sustainable cultivation of common bean in Spanish soils.
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Affiliation(s)
- Raquel Pastor-Bueis
- Institute of Environment, Natural Resources and Biodiversity, Universidad de León, León, Spain
| | | | - Euan K James
- The James Hutton Institute, Dundee, United Kingdom
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27
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Nouwen N, Gargani D, Giraud E. The Modification of the Flavonoid Naringenin by Bradyrhizobium sp. Strain ORS285 Changes the nod Genes Inducer Function to a Growth Stimulator. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1517-1525. [PMID: 31265361 DOI: 10.1094/mpmi-05-19-0133-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As inducers of nodulation (nod) genes, flavonoids play an important role in the symbiotic interaction between rhizobia and legumes. However, in addition to the control of expression of nod genes, many other effects of flavonoids on rhizobial cells have been described. Here, we show that the flavonoid naringenin stimulates the growth of the photosynthetic Bradyrhizobium sp. strain ORS285. This growth-stimulating effect was still observed for strain ORS285 with nodD1, nodD2, or the naringenin-degrading fde operon deleted. Phenotypic microarray analysis indicates that in cells grown in the presence of naringenin, the glycerol and fatty acid metabolism is activated. Moreover, electron microscopic and enzymatic analyses show that polyhydroxy alkanoate metabolism is altered in cells grown in the presence of naringenin. Although strain ORS285 was able to degrade naringenin, a fraction was converted into an intensely yellow-colored molecule with an m/z (+) of 363.0716. Further analysis indicates that this molecule is a hydroxylated and O-methylated form of naringenin. In contrast to naringenin, this derivative did not induce nod gene expression, but it did stimulate the growth of strain ORS285. We hypothesize that the growth stimulation and metabolic changes induced by naringenin are part of a mechanism to facilitate the colonization and infection of naringenin-exuding host plants.
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Affiliation(s)
- Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
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28
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Kumar G, Ponnusamy VK, Bhosale RR, Shobana S, Yoon JJ, Bhatia SK, Rajesh Banu J, Kim SH. A review on the conversion of volatile fatty acids to polyhydroxyalkanoates using dark fermentative effluents from hydrogen production. BIORESOURCE TECHNOLOGY 2019; 287:121427. [PMID: 31104939 DOI: 10.1016/j.biortech.2019.121427] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
The production of bio/microbial-based polymers, polyhydroxyalkanoates (PHAs) from volatile fatty acids (VFAs) of dark fermentative effluents in the bio-H2 reactor is being paid attention, owing to their commercial demand, applications and as carbon as well as energy storage source. Since, they are the cheap precursors for such valuable renewable biopolymers which all possess the properties; those are analogous to the petro-derived plastics. Several studies were stated, related to the consumption of both individual and mixed VFAs for the potential PHAs production. Their biodegradability nature makes them extremely desirable alternative to fossil-derived synthetic polymers. In this regard, this review summarizes the use of bio-based PHAs production via both microbial and biochemical pathways using dark fermentative bio-H2 production from waste streams as feedstock. Furthermore, this review deals the characteristics, synthesis and production of the bio-based PHAs along with their co-polymers and applications to give an outlook on future research.
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Affiliation(s)
- Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus, 4036 Stavanger, Norway; School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City 807, Taiwan; Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City 807, Taiwan
| | - Rahul R Bhosale
- Department of Chemical Engineering, College of Engineering, Qatar University, P.O Box 2713, Doha, Qatar
| | - Sutha Shobana
- Department of Chemistry and Research Centre, Aditanar College of Arts and Science, Virapandianpatnam, Tiruchendur, Tamil Nadu, India
| | - Jeong-Jun Yoon
- Intelligent Sustainable Materials R&BD Group, Korea Institute of Industrial Technology (KITECH), Cheonan, Chungnam 31056, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - J Rajesh Banu
- Department of Civil Engineering, Anna University Regional Campus, Tirunelveli, India
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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29
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Krishnan HB, Oehrle NW, Alaswad AA, Stevens WG, Maria John KM, Luthria DL, Natarajan SS. Biochemical and Anatomical Investigation of Sesbania herbacea (Mill.) McVaugh Nodules Grown under Flooded and Non-Flooded Conditions. Int J Mol Sci 2019; 20:E1824. [PMID: 31013805 PMCID: PMC6514687 DOI: 10.3390/ijms20081824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/26/2023] Open
Abstract
Sesbania herbacea, a native North American fast-growing legume, thrives in wet and waterlogged conditions. This legume enters into symbiotic association with rhizobia, resulting in the formation of nitrogen-fixing nodules on the roots. A flooding-induced anaerobic environment imposes a challenge for the survival of rhizobia and negatively impacts nodulation. Very little information is available on how S. herbacea is able to thrive and efficiently fix N2 in flooded conditions. In this study, we found that Sesbania plants grown under flooded conditions were significantly taller, produced more biomass, and formed more nodules when compared to plants grown on dry land. Transmission electron microscopy of Sesbania nodules revealed bacteroids from flooded nodules contained prominent polyhydroxybutyrate crystals, which were absent in non-flooded nodules. Gas and ion chromatography mass spectrometry analysis of nodule metabolites revealed a marked decrease in asparagine and an increase in the levels of gamma aminobutyric acid in flooded nodules. 2-D gel electrophoresis of nodule bacteroid proteins revealed flooding-induced changes in their protein profiles. Several of the bacteroid proteins that were prominent in flooded nodules were identified by mass spectrometry to be members of the ABC transporter family. The activities of several key enzymes involved in nitrogen metabolism was altered in Sesbania flooded nodules. Aspartate aminotransferase (AspAT), an enzyme with a vital role in the assimilation of reduced nitrogen, was dramatically elevated in flooded nodules. The results of our study highlight the potential of S. herbacea as a green manure and sheds light on the morphological, structural, and biochemical adaptations that enable S. herbacea to thrive and efficiently fix N2 in flooded conditions.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO 65211, USA.
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
| | - Nathan W Oehrle
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO 65211, USA.
| | - Alaa A Alaswad
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
| | - William Gene Stevens
- Plant Science Division, University of Missouri, Delta Center, Portageville, MO 63873, USA.
| | - K M Maria John
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD 20705, USA.
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD 20705, USA.
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30
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Importance of Poly-3-Hydroxybutyrate Metabolism to the Ability of Herbaspirillum seropedicae To Promote Plant Growth. Appl Environ Microbiol 2019; 85:AEM.02586-18. [PMID: 30610076 PMCID: PMC6414382 DOI: 10.1128/aem.02586-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/22/2018] [Indexed: 01/21/2023] Open
Abstract
The application of bacteria as plant growth promoters is a sustainable alternative to mitigate the use of chemical fertilization in agriculture, reducing negative economic and environmental impacts. Several plant growth-promoting bacteria synthesize and accumulate the intracellular polymer polyhydroxybutyrate (PHB). However, the role of PHB in plant-bacterium interactions is poorly understood. In this study, applying the C4 model grass Setaria viridis and several mutants in the PHB metabolism of the endophyte Herbaspirillum seropedicae yielded new findings on the importance of PHB for bacterial colonization of S. viridis roots. Taken together, the results show that deletion of genes involved in the synthesis and degradation of PHB reduced the ability of the bacteria to enhance plant growth but with little effect on overall root colonization. The data suggest that PHB metabolism likely plays an important role in supporting specific metabolic routes utilized by the bacteria to stimulate plant growth. Herbaspirillum seropedicae is an endophytic bacterium that establishes an association with a variety of plants, such as rice, corn, and sugarcane, and can significantly increase plant growth. H. seropedicae produces polyhydroxybutyrate (PHB), stored in the form of insoluble granules. Little information is available on the possible role of PHB in bacterial root colonization or in plant growth promotion. To investigate whether PHB is important for the association of H. seropedicae with plants, we inoculated roots of Setaria viridis with H. seropedicae strain SmR1 and mutants defective in PHB production (ΔphaP1, ΔphaP1 ΔphaP2, ΔphaC1, and ΔphaR) or mobilization (ΔphaZ1 ΔphaZ2). The strains producing large amounts of PHB colonized roots, significantly increasing root area and the number of lateral roots compared to those of PHB-negative strains. H. seropedicae grows under microaerobic conditions, which can be found in the rhizosphere. When grown under low-oxygen conditions, only the parental strain and ΔphaP2 mutant exhibited normal growth. The lack of normal growth under low oxygen correlated with the inability to stimulate plant growth, although there was no effect on the level of root colonization. The data suggest that PHB is produced in the root rhizosphere and plays a role in maintaining normal metabolism under microaerobic conditions. To confirm this, we screened for green fluorescent protein (GFP) expression under the control of the H. seropedicae promoters of the PHA synthase and PHA depolymerase genes in the rhizosphere. PHB synthesis is active on the root surface and later PHB depolymerase expression is activated. IMPORTANCE The application of bacteria as plant growth promoters is a sustainable alternative to mitigate the use of chemical fertilization in agriculture, reducing negative economic and environmental impacts. Several plant growth-promoting bacteria synthesize and accumulate the intracellular polymer polyhydroxybutyrate (PHB). However, the role of PHB in plant-bacterium interactions is poorly understood. In this study, applying the C4 model grass Setaria viridis and several mutants in the PHB metabolism of the endophyte Herbaspirillum seropedicae yielded new findings on the importance of PHB for bacterial colonization of S. viridis roots. Taken together, the results show that deletion of genes involved in the synthesis and degradation of PHB reduced the ability of the bacteria to enhance plant growth but with little effect on overall root colonization. The data suggest that PHB metabolism likely plays an important role in supporting specific metabolic routes utilized by the bacteria to stimulate plant growth.
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31
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Mangaraj S, Yadav A, Bal LM, Dash SK, Mahanti NK. Application of Biodegradable Polymers in Food Packaging Industry: A Comprehensive Review. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s41783-018-0049-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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32
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Nishihata S, Kondo T, Tanaka K, Ishikawa S, Takenaka S, Kang CM, Yoshida KI. Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation. BMC Microbiol 2018; 18:156. [PMID: 30355296 PMCID: PMC6201568 DOI: 10.1186/s12866-018-1317-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulation is orchestrated by not only the enzymes for PHB synthesis but also PHB-binding phasin proteins (PhaPs) stabilizing the PHB granules. The transcription factor PhaR controls the phaP genes. Results Inactivation of phaR led to decreases in PHB accumulation, less cell yield, increases in exopolysaccharide (EPS) production, some improvement in heat stress tolerance, and slightly better growth under microaerobic conditions. Changes in the transcriptome upon phaR inactivation were analyzed. PhaR appeared to be involved in the repression of various target genes, including some PHB-degrading enzymes and others involved in EPS production. Furthermore, in vitro gel shift analysis demonstrated that PhaR bound to the promoter regions of representative targets. For the phaP1 and phaP4 promoter regions, PhaR-binding sites were determined by DNase I footprinting, allowing us to deduce a consensus sequence for PhaR-binding as TGCRNYGCASMA (R: A or G, Y: C or T, S: C or G, M: A or C). We searched for additional genes associated with a PhaR-binding sequence and found that some genes involved in central carbon metabolism, such as pdhA for pyruvate dehydrogenase and pckA for phosphoenolpyruvate carboxykinase, may be regulated positively and directly by PhaR. Conclusions These results suggest that PhaR could regulate various genes not only negatively but also positively to coordinate metabolism holistically in response to PHB accumulation. Electronic supplementary material The online version of this article (10.1186/s12866-018-1317-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shogo Nishihata
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Takahiko Kondo
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Choong-Min Kang
- Department of Biological Science, California State University, Stanislaus, Turlock, CA, 95382, USA
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan.
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33
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Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FDO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R, Müller-Santos M. PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Front Microbiol 2018; 9:472. [PMID: 29599762 PMCID: PMC5862806 DOI: 10.3389/fmicb.2018.00472] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.
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Affiliation(s)
- Marcelo B Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Cícero S Teixeira
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z T Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luis P S Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Glaucio Valdameri
- Department of Clinical Analysis, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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Klonowska A, Melkonian R, Miché L, Tisseyre P, Moulin L. Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history. BMC Genomics 2018; 19:105. [PMID: 29378510 PMCID: PMC5789663 DOI: 10.1186/s12864-018-4487-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099-111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. RESULTS In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. CONCLUSION The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica.
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Affiliation(s)
| | - Rémy Melkonian
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France
| | - Lucie Miché
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France.,Present address: Aix Marseille University, University of Avignon, CNRS, IRD, IMBE, Marseille, France
| | | | - Lionel Moulin
- IRD, Cirad, University of Montpellier, IPME, Montpellier, France.
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Bourion V, Heulin-Gotty K, Aubert V, Tisseyre P, Chabert-Martinello M, Pervent M, Delaitre C, Vile D, Siol M, Duc G, Brunel B, Burstin J, Lepetit M. Co-inoculation of a Pea Core-Collection with Diverse Rhizobial Strains Shows Competitiveness for Nodulation and Efficiency of Nitrogen Fixation Are Distinct traits in the Interaction. FRONTIERS IN PLANT SCIENCE 2018; 8:2249. [PMID: 29367857 PMCID: PMC5767787 DOI: 10.3389/fpls.2017.02249] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/21/2017] [Indexed: 05/07/2023]
Abstract
Pea forms symbiotic nodules with Rhizobium leguminosarum sv. viciae (Rlv). In the field, pea roots can be exposed to multiple compatible Rlv strains. Little is known about the mechanisms underlying the competitiveness for nodulation of Rlv strains and the ability of pea to choose between diverse compatible Rlv strains. The variability of pea-Rlv partner choice was investigated by co-inoculation with a mixture of five diverse Rlv strains of a 104-pea collection representative of the variability encountered in the genus Pisum. The nitrogen fixation efficiency conferred by each strain was determined in additional mono-inoculation experiments on a subset of 18 pea lines displaying contrasted Rlv choice. Differences in Rlv choice were observed within the pea collection according to their genetic or geographical diversities. The competitiveness for nodulation of a given pea-Rlv association evaluated in the multi-inoculated experiment was poorly correlated with its nitrogen fixation efficiency determined in mono-inoculation. Both plant and bacterial genetic determinants contribute to pea-Rlv partner choice. No evidence was found for co-selection of competitiveness for nodulation and nitrogen fixation efficiency. Plant and inoculant for an improved symbiotic association in the field must be selected not only on nitrogen fixation efficiency but also for competitiveness for nodulation.
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Affiliation(s)
- Virginie Bourion
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Karine Heulin-Gotty
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Véronique Aubert
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre Tisseyre
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Catherine Delaitre
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Denis Vile
- Laboratoire d'Ecophysiologie des Plantes Sous Stress Environnementaux, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Mathieu Siol
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Gérard Duc
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Brigitte Brunel
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Judith Burstin
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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Quides KW, Stomackin GM, Lee HH, Chang JH, Sachs JL. Lotus japonicus alters in planta fitness of Mesorhizobium loti dependent on symbiotic nitrogen fixation. PLoS One 2017; 12:e0185568. [PMID: 28957401 PMCID: PMC5619806 DOI: 10.1371/journal.pone.0185568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/14/2017] [Indexed: 12/19/2022] Open
Abstract
Rhizobial bacteria are known for their capacity to fix nitrogen for legume hosts. However ineffective rhizobial genotypes exist and can trigger the formation of nodules but fix little if any nitrogen for hosts. Legumes must employ mechanisms to minimize exploitation by the ineffective rhizobial genotypes to limit fitness costs and stabilize the symbiosis. Here we address two key questions about these host mechanisms. What stages of the interaction are controlled by the host, and can hosts detect subtle differences in nitrogen fixation? We provide the first explicit evidence for adaptive host control in the interaction between Lotus japonicus and Mesorhizobium loti. In both single inoculation and co-inoculation experiments, less effective rhizobial strains exhibited reduced in planta fitness relative to the wildtype M. loti. We uncovered evidence of host control during nodule formation and during post-infection proliferation of symbionts within nodules. We found a linear relationship between rhizobial fitness and symbiotic effectiveness. Our results suggest that L. japonicus can adaptively modulate the fitness of symbionts as a continuous response to symbiotic nitrogen fixation.
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Affiliation(s)
- Kenjiro W. Quides
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Glenna M. Stomackin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Joel L. Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, CA, United States of America
- * E-mail:
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Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. mSystems 2017; 2:mSystems00035-17. [PMID: 28905000 PMCID: PMC5596199 DOI: 10.1128/msystems.00035-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/31/2017] [Indexed: 01/25/2023] Open
Abstract
The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms. Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes. IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms. Author Video: An author video summary of this article is available.
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38
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Regus JU, Quides KW, O'Neill MR, Suzuki R, Savory EA, Chang JH, Sachs JL. Cell autonomous sanctions in legumes target ineffective rhizobia in nodules with mixed infections. AMERICAN JOURNAL OF BOTANY 2017; 104:1299-1312. [PMID: 29885243 DOI: 10.3732/ajb.1700165] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/11/2017] [Indexed: 05/22/2023]
Affiliation(s)
- John U. Regus
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Kenjiro W. Quides
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Matthew R. O'Neill
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Rina Suzuki
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Elizabeth A. Savory
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Joel L. Sachs
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
- Department of Botany and Plant Sciences, 2142 Batchelor Hall, University of California, Riverside, California 92521 USA
- Institute for Integrative Genome Biology, 5406 Boyce Hall, University of California, Riverside, California 92521 USA
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Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D. Fixation of CO 2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol 2017; 19:2645-2660. [PMID: 28371065 DOI: 10.1111/1462-2920.13746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/25/2017] [Accepted: 03/25/2017] [Indexed: 01/26/2023]
Abstract
The ability of aerobic anoxygenic photoheterotrophs (AAPs) to gain additional energy from sunlight represents a competitive advantage, especially in conditions where light has easy access or under environmental conditions may change quickly, such as those in the world´s oceans. However, the knowledge about the metabolic consequences of aerobic anoxygenic photosynthesis is very limited. Combining transcriptome and metabolome analyses, isotopic labelling techniques, measurements of growth, oxygen uptake rates, flow cytometry, and a number of other biochemical analytical techniques we obtained a comprehensive overview on the complex adaption of the marine bacterium Dinoroseobacter shibae DFL12T during transition from heterotrophy to photoheterotrophy (growth on succinate). Growth in light was characterized by reduced respiration, a decreased metabolic flux through the tricarboxylic acid (TCA) cycle and the assimilation of CO2 via an enhanced flux through the ethylmalonyl-CoA (EMC) pathway, which was shown to be connected to the serine metabolism. Adaptation to photoheterotrophy is mainly characterized by metabolic reactions caused by a surplus of reducing potential and might depend on genes located in one operon, encoding branching point enzymes of the EMC pathway, serine metabolism and the TCA cycle.
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Affiliation(s)
- Nelli Bill
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
| | - Jürgen Tomasch
- Department of Microbial Communication, Helmholtz-Centre for Infection Research (HZI), Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Alexander Riemer
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
| | - Katrin Müller
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
| | - Sarah Kleist
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
| | - Kerstin Schmidt-Hohagen
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
| | - Irene Wagner-Döbler
- Department of Microbial Communication, Helmholtz-Centre for Infection Research (HZI), Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Dietmar Schomburg
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Rebenring 56, Braunschweig, D-38106, Germany
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Marcos-García M, García-Fraile P, Filipová A, Menéndez E, Mateos PF, Velázquez E, Cajthaml T, Rivas R. Mesorhizobium bacterial strains isolated from the legume Lotus corniculatus are an alternative source for the production of polyhydroxyalkanoates (PHAs) to obtain bioplastics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:17436-17445. [PMID: 28593540 DOI: 10.1007/s11356-017-9319-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
Polyhydroxyalkanoic acids (PHAs) are natural polyesters that can be used to produce bioplastics which are biodegradable. Numerous microorganisms accumulate PHAs as energy reserves. Combinations of different PHAs monomers lead to the production of bioplastics with very different properties. In the present work, we show the capability of strains belonging to various phylogenetic lineages within the genus Mesorhizobium, isolated from Lotus corniculatus nodules, to produce different PHA monomers. Among our strains, we found the production of 3-hydroxybutyrate, 3-hydroxyvalerate, 3-hydroxydodecanoate, and 3-hydroxyhexadecanoate. Most of the PHA-positive strains were phylogenetically related to the species M. jarvisii. However, our findings suggest that the ability to produce different monomers forming PHAs is strain-dependent.
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Affiliation(s)
- Marta Marcos-García
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
| | - Paula García-Fraile
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic.
| | - Alena Filipová
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic
- Přírodovědecká fakulta, Univerzita Karlova, Prague, Czech Republic
| | - Esther Menéndez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Évora, Portugal
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - Tomáš Cajthaml
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic
- Přírodovědecká fakulta, Univerzita Karlova, Prague, Czech Republic
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
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Liu C, Sakimoto KK, Colón BC, Silver PA, Nocera DG. Ambient nitrogen reduction cycle using a hybrid inorganic-biological system. Proc Natl Acad Sci U S A 2017; 114:6450-6455. [PMID: 28588143 PMCID: PMC5488957 DOI: 10.1073/pnas.1706371114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We demonstrate the synthesis of NH3 from N2 and H2O at ambient conditions in a single reactor by coupling hydrogen generation from catalytic water splitting to a H2-oxidizing bacterium Xanthobacter autotrophicus, which performs N2 and CO2 reduction to solid biomass. Living cells of X. autotrophicus may be directly applied as a biofertilizer to improve growth of radishes, a model crop plant, by up to ∼1,440% in terms of storage root mass. The NH3 generated from nitrogenase (N2ase) in X. autotrophicus can be diverted from biomass formation to an extracellular ammonia production with the addition of a glutamate synthetase inhibitor. The N2 reduction reaction proceeds at a low driving force with a turnover number of 9 × 109 cell-1 and turnover frequency of 1.9 × 104 s-1⋅cell-1 without the use of sacrificial chemical reagents or carbon feedstocks other than CO2 This approach can be powered by renewable electricity, enabling the sustainable and selective production of ammonia and biofertilizers in a distributed manner.
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Affiliation(s)
- Chong Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371
| | - Kelsey K Sakimoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Brendan C Colón
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;
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Sadykov MR, Ahn JS, Widhelm TJ, Eckrich VM, Endres JL, Driks A, Rutkowski GE, Wingerd KL, Bayles KW. Poly(3-hydroxybutyrate) fuels the tricarboxylic acid cycle andde novolipid biosynthesis duringBacillus anthracissporulation. Mol Microbiol 2017; 104:793-803. [DOI: 10.1111/mmi.13665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Marat R. Sadykov
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Jong-Sam Ahn
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Todd J. Widhelm
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Valerie M. Eckrich
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Jennifer L. Endres
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Adam Driks
- Department of Microbiology and Immunology; Loyola University Chicago, Stritch School of Medicine; Maywood IL 60153 USA
| | | | | | - Kenneth W. Bayles
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
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Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR. J Bacteriol 2017; 199:JB.00776-16. [PMID: 28167519 DOI: 10.1128/jb.00776-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/31/2017] [Indexed: 01/06/2023] Open
Abstract
Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for Makes more granules Regulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR (mmgRΔ33-51). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. melilotiIMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans-encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti, only four out of hundreds of identified sRNA genes have been functionally characterized. Thus, uncovering the biological role of sRNAs currently represents a major issue and one that is particularly challenging because of the usually subtle quantitative regulation contributed by most characterized sRNAs. Here, we have characterized the function of the broadly conserved alphaproteobacterial sRNA gene mmgR in S. meliloti Our results strongly suggest that mmgR encodes a negative regulator of the accumulation of polyhydroxybutyrate, the major carbon and reducing power storage polymer in S. meliloti cells growing under conditions of C/N overbalance.
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Alonso-Pernas P, Arias-Cordero E, Novoselov A, Ebert C, Rybak J, Kaltenpoth M, Westermann M, Neugebauer U, Boland W. Bacterial Community and PHB-Accumulating Bacteria Associated with the Wall and Specialized Niches of the Hindgut of the Forest Cockchafer ( Melolontha hippocastani). Front Microbiol 2017; 8:291. [PMID: 28293223 PMCID: PMC5329036 DOI: 10.3389/fmicb.2017.00291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
A characterization of the bacterial community of the hindgut wall of two larval and the adult stages of the forest cockchafer (Melolontha hippocastani) was carried out using amplicon sequencing of the 16S rRNA gene fragment. We found that, in second-instar larvae, Caulobacteraceae and Pseudomonadaceae showed the highest relative abundances, while in third-instar larvae, the dominant families were Porphyromonadaceae and Bacteroidales-related. In adults, an increase of the relative abundance of Bacteroidetes, Proteobacteria (γ- and δ- classes) and the family Enterococcaceae (Firmicutes) was observed. This suggests that the composition of the hindgut wall community may depend on the insect’s life stage. Additionally, specialized bacterial niches hitherto very poorly described in the literature were spotted at both sides of the distal part of the hindgut chamber. We named these structures “pockets.” Amplicon sequencing of the 16S rRNA gene fragment revealed that the pockets contained a different bacterial community than the surrounding hindgut wall, dominated by Alcaligenaceae and Micrococcaceae-related families. Poly-β-hydroxybutyrate (PHB) accumulation in the pocket was suggested in isolated Achromobacter sp. by Nile Blue staining, and confirmed by gas chromatography–mass spectrometry analysis (GC-MS) on cultured bacterial mass and whole pocket tissue. Raman micro-spectroscopy allowed to visualize the spatial distribution of PHB accumulating bacteria within the pocket tissue. The presence of this polymer might play a role in the colonization of these specialized niches.
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Affiliation(s)
- Pol Alonso-Pernas
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology Jena, Germany
| | - Erika Arias-Cordero
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology Jena, Germany
| | - Alexey Novoselov
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology Jena, Germany
| | - Christina Ebert
- Center for Sepsis Control and Care, Jena University HospitalJena, Germany; Leibniz Institute of Photonic TechnologyJena, Germany
| | - Jürgen Rybak
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Zoology, Johannes Gutenberg University Mainz Mainz, Germany
| | | | - Ute Neugebauer
- Center for Sepsis Control and Care, Jena University HospitalJena, Germany; Leibniz Institute of Photonic TechnologyJena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology Jena, Germany
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Zamani M, diCenzo GC, Milunovic B, Finan TM. A putative 3-hydroxyisobutyryl-CoA hydrolase is required for efficient symbiotic nitrogen fixation in Sinorhizobium meliloti and Sinorhizobium fredii NGR234. Environ Microbiol 2016; 19:218-236. [PMID: 27727485 DOI: 10.1111/1462-2920.13570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/06/2016] [Indexed: 12/12/2022]
Abstract
We report that the smb20752 gene of the alfalfa symbiont Sinorhizobium meliloti is a novel symbiotic gene required for full N2 -fixation. Deletion of smb20752 resulted in lower nitrogenase activity and smaller nodules without impacting overall nodule morphology. Orthologs of smb20752 were present in all alpha and beta rhizobia, including the ngr_b20860 gene of Sinorhizobium fredii NGR234. A ngr_b20860 mutant formed Fix- determinate nodules that developed normally to a late stage of the symbiosis on the host plants Macroptilium atropurpureum and Vigna unguiculata. However an early symbiotic defect was evident during symbiosis with Leucaena leucocephala, producing Fix- indeterminate nodules. The smb20752 and ngr_b20860 genes encode putative 3-hydroxyisobutyryl-CoA (HIB-CoA) hydrolases. HIB-CoA hydrolases are required for l-valine catabolism and appear to prevent the accumulation of toxic metabolic intermediates, particularly methacrylyl-CoA. Evidence presented here and elsewhere (Curson et al., , PLoS ONE 9:e97660) demonstrated that Smb20752 and NGR_b20860 can also prevent metabolic toxicity, are required for l-valine metabolism, and play an undefined role in 3-hydroxybutyrate catabolism. We present evidence that the symbiotic defect of the HIB-CoA hydrolase mutants is independent of the inability to catabolize l-valine and suggest it relates to the toxicity resulting from metabolism of other compounds possibly related to 3-hydroxybutyric acid.
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Affiliation(s)
- Maryam Zamani
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario, Canada, L8S 4K1
| | - George C diCenzo
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario, Canada, L8S 4K1
| | - Branislava Milunovic
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario, Canada, L8S 4K1
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario, Canada, L8S 4K1
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Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Sci Rep 2016; 6:37389. [PMID: 27869215 PMCID: PMC5116747 DOI: 10.1038/srep37389] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/27/2016] [Indexed: 12/03/2022] Open
Abstract
Bacterial species in the plant-beneficial-environmental clade of Burkholderia represent a substantial component of rhizosphere microbes in many plant species. To better understand the molecular mechanisms of the interaction, we combined functional studies with high-resolution dual transcriptome analysis of sugarcane and root-associated diazotrophic Burkholderia strain Q208. We show that Burkholderia Q208 forms a biofilm at the root surface and suppresses the virulence factors that typically trigger immune response in plants. Up-regulation of bd-type cytochromes in Burkholderia Q208 suggests an increased energy production and creates the microaerobic conditions suitable for BNF. In this environment, a series of metabolic pathways are activated in Burkholderia Q208 implicated in oxalotrophy, microaerobic respiration, and formation of PHB granules, enabling energy production under microaerobic conditions. In the plant, genes involved in hypoxia survival are up-regulated and through increased ethylene production, larger aerenchyma is produced in roots which in turn facilitates diffusion of oxygen within the cortex. The detected changes in gene expression, physiology and morphology in the partnership are evidence of a sophisticated interplay between sugarcane and a plant-growth promoting Burkholderia species that advance our understanding of the mutually beneficial processes occurring in the rhizosphere.
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Choma A, Komaniecka I, Zebracki K. Structure, biosynthesis and function of unusual lipids A from nodule-inducing and N 2-fixing bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:196-209. [PMID: 27836696 DOI: 10.1016/j.bbalip.2016.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/31/2016] [Accepted: 11/04/2016] [Indexed: 10/20/2022]
Abstract
This review focuses on the chemistry and structures of (Brady)rhizobium lipids A, indispensable parts of lipopolysaccharides. These lipids contain unusual (ω-1) hydroxylated very long chain fatty acids, which are synthesized by a very limited group of bacteria, besides rhizobia. The significance and requirement of the very long chain fatty acids for outer membrane stability as well as the genetics of the synthesis pathway are discussed. The biological role of these fatty acids for bacterial life in extremely different environments (soil and intracellular space within nodules) is also considered.
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Affiliation(s)
- Adam Choma
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Iwona Komaniecka
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Kamil Zebracki
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
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Sathiyanarayanan G, Saibaba G, Kiran GS, Yang YH, Selvin J. Marine sponge-associated bacteria as a potential source for polyhydroxyalkanoates. Crit Rev Microbiol 2016; 43:294-312. [DOI: 10.1080/1040841x.2016.1206060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ganesan Sathiyanarayanan
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Ganesan Saibaba
- Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, India
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
- Microbial Carbohydrate Resource Bank, Konkuk University, Seoul, South Korea
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, India
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Muñoz N, Qi X, Li MW, Xie M, Gao Y, Cheung MY, Wong FL, Lam HM. Improvement in nitrogen fixation capacity could be part of the domestication process in soybean. Heredity (Edinb) 2016; 117:84-93. [PMID: 27118154 PMCID: PMC4949726 DOI: 10.1038/hdy.2016.27] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/14/2016] [Accepted: 03/16/2016] [Indexed: 01/21/2023] Open
Abstract
Biological nitrogen fixation (BNF) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. As nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. To test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans after inoculation with the slow-growing Bradyrhizobium diazoefficiens sp. nov. USDA110 and the fast-growing Sinorhizobium (Ensifer) fredii CCBAU45436. Our results showed that, in general, cultivated soybeans gave better performance in BNF. Electron microscopic studies indicated that there was an exceptionally high accumulation of poly-β-hydroxybutyrate bodies in bacteroids in the nodules of all wild soybeans tested, suggesting that the C/N balance in wild soybeans may not be optimized for nitrogen fixation. Furthermore, we identified new quantitative trait loci (QTLs) for total ureides and total nodule fresh weight by employing a recombinant inbred population composed of descendants from a cross between a cultivated and a wild parent. Using nucleotide diversity (θπ), divergence index (Fst) and distribution of fixed single-nucleotide polymorphisms as parameters, we found that some regions in the total ureides QTL on chromosome 17 and the total nodule fresh weight QTL on chromosome 12 exhibited very low diversity among cultivated soybeans, suggesting that these were traits specially selected during the domestication and breeding process.
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Affiliation(s)
- N Muñoz
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
- Centro de Investigaciones
Agropecuarias-INTA, Instituto de Fisiología y Recursos
Genéticos Vegetales, Córdoba,
Argentina
- Cátedra de Fisiología
Vegetal, Facultad de Ciencias Exactas Físicas y Naturales,
Universidad Nacional de Córdoba, Córdoba,
Argentina
| | - X Qi
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M-W Li
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M Xie
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - Y Gao
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - M-Y Cheung
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - F-L Wong
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
| | - H-M Lam
- Centre for Soybean Research of the
Partner State Key Laboratory of Agrobiotechnology and School of Life
Sciences, The Chinese University of Hong Kong, Shatin,
Hong Kong SAR
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Ramírez-Trujillo JA, Dunn MF, Suárez-Rodríguez R, Hernández-Lucas I. The Sinorhizobium meliloti glyoxylate cycle enzyme isocitrate lyase (AceA) is required for the utilization of poly-β-hydroxybutyrate during carbon starvation. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-015-1131-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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