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Busset N, Gully D, Teulet A, Fardoux J, Camuel A, Cornu D, Severac D, Giraud E, Mergaert P. The Type III Effectome of the Symbiotic Bradyrhizobium vignae Strain ORS3257. Biomolecules 2021; 11:1592. [PMID: 34827590 DOI: 10.3390/biom11111592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Many Bradyrhizobium strains are able to establish a Nod factor-independent symbiosis with the leguminous plant Aeschynomene indica by the use of a type III secretion system (T3SS). Recently, an important advance in the understanding of the molecular factors supporting this symbiosis has been achieved by the in silico identification and functional characterization of 27 putative T3SS effectors (T3Es) of Bradyrhizobium vignae ORS3257. In the present study, we experimentally extend this catalog of T3Es by using a multi-omics approach. Transcriptome analysis under non-inducing and inducing conditions in the ORS3257 wild-type strain and the ttsI mutant revealed that the expression of 18 out of the 27 putative effectors previously identified, is under the control of TtsI, the global transcriptional regulator of T3SS and T3Es. Quantitative shotgun proteome analysis of culture supernatant in the wild type and T3SS mutant strains confirmed that 15 of the previously determined candidate T3Es are secreted by the T3SS. Moreover, the combined approaches identified nine additional putative T3Es and one of them was experimentally validated as a novel effector. Our study underscores the power of combined proteome and transcriptome analyses to complement in silico predictions and produce nearly complete effector catalogs. The establishment of the ORS3257 effectome will form the basis for a full appraisal of the symbiotic properties of this strain during its interaction with various host legumes via different processes.
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Biała-Leonhard W, Zanin L, Gottardi S, de Brito Francisco R, Venuti S, Valentinuzzi F, Mimmo T, Cesco S, Bassin B, Martinoia E, Pinton R, Jasiński M, Tomasi N. Identification of an Isoflavonoid Transporter Required for the Nodule Establishment of the Rhizobium- Fabaceae Symbiotic Interaction. Front Plant Sci 2021; 12:758213. [PMID: 34745190 PMCID: PMC8570342 DOI: 10.3389/fpls.2021.758213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/15/2021] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) as well as Phosphorus (P) are key nutrients determining crop productivity. Legumes have developed strategies to overcome nutrient limitation by, for example, forming a symbiotic relationship with N-fixing rhizobia and the release of P-mobilizing exudates and are thus able to grow without supply of N or P fertilizers. The legume-rhizobial symbiosis starts with root release of isoflavonoids that act as signaling molecules perceived by compatible bacteria. Subsequently, bacteria release nod factors, which induce signaling cascades allowing the formation of functional N-fixing nodules. We report here the identification and functional characterization of a plasma membrane-localized MATE-type transporter (LaMATE2) involved in the release of genistein from white lupin roots. The LaMATE2 expression in the root is upregulated under N deficiency as well as low phosphate availability, two nutritional deficiencies that induce the release of this isoflavonoid. LaMATE2 silencing reduced genistein efflux and even more the formation of symbiotic nodules, supporting the crucial role of LaMATE2 in isoflavonoid release and nodulation. Furthermore, silencing of LaMATE2 limited the P-solubilization activity of lupin root exudates. Transport assays in yeast vesicles demonstrated that LaMATE2 acts as a proton-driven isoflavonoid transporter.
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Affiliation(s)
- Wanda Biała-Leonhard
- Department of Plant Molecular Physiology, Polish Academy of Sciences, Institute of Bioorganic Chemistry, Poznań, Poland
| | - Laura Zanin
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Stefano Gottardi
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | | | - Silvia Venuti
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Fabio Valentinuzzi
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
- Faculty of Science and Technology, Free University of Bozen Bolzano, Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen Bolzano, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bozen Bolzano, Bolzano, Italy
| | - Barbara Bassin
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Enrico Martinoia
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Roberto Pinton
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Polish Academy of Sciences, Institute of Bioorganic Chemistry, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Nicola Tomasi
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali, University of Udine, Udine, Italy
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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. Front Plant Sci 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Gnangui SLE, Fossou RK, Ebou A, Amon CER, Koua DK, Kouadjo CGZ, Cowan DA, Zézé A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire. Microorganisms 2021; 9:microorganisms9091842. [PMID: 34576737 PMCID: PMC8472840 DOI: 10.3390/microorganisms9091842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023] Open
Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
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Affiliation(s)
- Sara Laetitia Elphège Gnangui
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Correspondence:
| | - Anicet Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Dominique Kadio Koua
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Claude Ghislaine Zaka Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, 01 Abidjan 1740, Côte d’Ivoire;
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
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Huang YM, Straub D, Blackwell N, Kappler A, Kleindienst S. Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. Appl Environ Microbiol 2021; 87:e0049621. [PMID: 34020935 PMCID: PMC8276803 DOI: 10.1128/aem.00496-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.
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Affiliation(s)
- Yu-Ming Huang
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Cluster of Excellence, EXC 2124, “Controlling Microbes to Fight Infections,” University of Tübingen, Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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Chalasani D, Basu A, Pullabhotla SVSRN, Jorrin B, Neal AL, Poole PS, Podile AR, Tkacz A. Poor Competitiveness of Bradyrhizobium in Pigeon Pea Root Colonization in Indian Soils. mBio 2021; 12:e0042321. [PMID: 34225488 DOI: 10.1128/mBio.00423-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pigeon pea, a legume crop native to India, is the primary source of protein for more than a billion people in developing countries. The plant can form symbioses with N2-fixing bacteria; however, reports of poor crop nodulation in agricultural soils abound. We report here a study of the bacterial community associated with pigeon pea, with a special focus on the symbiont population in different soils and vegetative and non-vegetative plant growth. Location with respect to the plant roots was determined to be the main factor controlling the bacterial community, followed by developmental stage and soil type. Plant genotype plays only a minor role. Pigeon pea roots have a reduced microbial diversity compared to the surrounding soil and select for Proteobacteria, especially for Rhizobium spp., during vegetative growth. While Bradyrhizobium, a native symbiont of pigeon pea, can be found associating with roots, its presence is dependent on plant variety and soil conditions. A combination of 16S rRNA gene amplicon survey, strain isolation, and co-inoculation with nodule-forming Bradyrhizobium spp. and non-N2-fixing Rhizobium spp. demonstrated that the latter is a much more successful colonizer of pigeon pea roots. Poor nodulation of pigeon pea in Indian soils may be caused by a poor Bradyrhizobium competitiveness against non-nodulating root colonizers such as Rhizobium. Hence, inoculant strain selection of symbionts for pigeon pea should be based not only on their nitrogen fixation potential but, more importantly, on their competitiveness in agricultural soils.
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Banasiewicz J, Lisboa BB, da Costa PB, Schlindwein G, Venter SN, Steenkamp ET, Vargas LK, Passaglia LMP, Stępkowski T. Culture-independent assessment of the diazotrophic Bradyrhizobium communities in the Pampa and Atlantic Forest Biomes localities in southern Brazil. Syst Appl Microbiol 2021; 44:126228. [PMID: 34265499 DOI: 10.1016/j.syapm.2021.126228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communities inhabiting soils in southern Brazil. The majority of nifD sequences were generated from DNA isolated from tropical-lowland pasture soils, although some soil samples originated from the Campos de Cima da Serra volcanic plateau. In the nifD tree, all the bradyrhizobial sequences comprised 38 clades, including 18 new clades. The sequences generated in this study were resolved into 22 clades and 21 singletons. The nifD bradyrhizobial assemblage contained Azorhizobium and α-proteobacterial methylotrophic genera, suggesting that these genera may have acquired their nif loci from Bradyrhizobium donors. The most common in the lowland pasture soils subclade III.3D branch comprises the isolates of mainly an American origin. On the other hand, subclade III.4, which was earlier detected in Brazil among Bradyrhizobium isolates nodulating native lupins, appears more common in the Campos de Cima da Serra soils. The second-largest group, Clade XXXVIII, has not yet been reported in culture-dependent studies, while another common group called Clade I represents a symbiovar predominating in Australia. The identification of the diverse nifD Clade I haplotypes in the tropical-lowland pastures infested by Australian Acacia spp implies that the introduction of these legumes to southern Brazil has resulted in the dissemination of their bradyrhizobial symbionts.
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Salmi A, Boulila F. Heavy metals multi-tolerant Bradyrhizobium isolated from mercury mining region in Algeria. J Environ Manage 2021; 289:112547. [PMID: 33839604 DOI: 10.1016/j.jenvman.2021.112547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Heavy metals accumulation in the environment has led to a decrease in the capacity of ecosystems to sustain life as human, animal and plant health is threatened. To remedy this problem, rhizoremediation has been suggested as a solution. Legumes and rhizobia symbiotic association has captivated attention due to its involvement in the restoration of heavy-metal-contaminated sites. Thus, the aim of this study was to isolate and characterize the strains nodulating Calicotome spinosa plant that naturally occurred in two Algerian mercury mines. Fifty-four bacterial strains were isolated, then grouped into sixteen distinct BOX-PCR patterns and were genetically identified as belonging to the Bradyrhizobium genus. The studied strains were able to induce nodules on Retama monosperma, R. reatam, Lupinus albus, while no nodulation was observed in Glycine max, their symbiotic capacity was confirmed by amplifying the nodC gene. The phylogenetic analysis based on the nodC has grouped this Bradyrhizobium strains to either symbiovar genistearum or retamae. The isolates revealed diversity in terms of NaCl; pH tolerance, and phosphate solubilization. Production of siderophores was negative for these strains. All the isolated Bradyrhizobium were tolerant to both Zn and Pb in contrast they were sensitive to Cu and Cd. Interestingly, 43% of strains were tolerant to high Hg levels. Hence, some strains displayed multiple tolerances to heavy metals. Therefore, this is the first time we identify Bradyrhizobium strains originating from a North African mercury mine. This study could help to select mercury and other heavy metal-tolerant rhizobia showing an interesting potential to be used as inoculants to remediate the heavy metal soil accumulation.
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Affiliation(s)
- Adouda Salmi
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
| | - Farida Boulila
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria
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Yudistira H, Geddes BA, Geddes CM, Gulden RH, Oresnik IJ. qPCR assay targeting Bradyrhizobium japonicum shows that row spacing and soybean density affects Bradyrhizobium population. Can J Microbiol 2021; 67:529-536. [PMID: 33049159 DOI: 10.1139/cjm-2020-0334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ability for a soybean plant to be efficiently nodulated when grown as a crop is dependent on the number of effective Bradyrhizobium japonicum that can be found in close proximity to the developing seedling shortly after planting. In Manitoba, the growing of soybean as a crop has increased from less than 500 000 acres in 2008 to over 2.3 million acres in 2017. Since the large increase in soybean production is relatively recent, populations of B. japonicum have not yet developed. In response to this, we developed a primer pair that can identify B. japonicum, and be used to determine the titre found in field soil. Their utility was demonstrated by being used to determine whether row spacing of soybean affects B. japonicum populations, as well as to follow B. japonicum populations in a soybean field over the course of a field season. The data show that plant density can affect B. japonicum populations. Moreover, evidence is presented that suggests plant development affects overall B. japonicum populations.
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Affiliation(s)
- Harry Yudistira
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Barney A Geddes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Charles M Geddes
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Robert H Gulden
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Ivan J Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Lamin H, Alami S, Lamrabet M, Bouhnik O, Bennis M, Abdelmoumen H, Bedmar EJ, Missbah-El Idrissi M. Bradyrhizobium sp. sv. retamae nodulates Retama monosperma grown in a lead and zinc mine tailings in Eastern Morocco. Braz J Microbiol 2021; 52:639-649. [PMID: 33447935 PMCID: PMC8105474 DOI: 10.1007/s42770-021-00420-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022] Open
Abstract
The aim of this work was to characterize and identify some bacteria isolated from the root nodules of Retama monosperma grown in Sidi Boubker lead and zinc mine tailings. Very few root nodules were obtained on the root nodules of R. monosperma grown in these soils. The three bacteria isolated from the root nodules were tolerant in vitro to different concentrations of heavy metals, including lead and zinc. The rep-PCR experiments showed that the three isolates have different molecular fingerprints and were considered as three different strains. The analysis of their 16S rRNA gene sequences proved their affiliation to the genus Bradyrhizobium. The analysis and phylogeny of the housekeeping genes atpD, glnII, gyrB, recA, and rpoB confirmed that the closest species was B. valentinum with similarity percentages of 95.61 to 95.82%. The three isolates recovered from the root nodules were slow-growing rhizobia capable to renodulate their original host plant in the presence of Pb-acetate. They were able to nodulate R. sphaerocarpa and Lupinus luteus also but not Glycine max or Phaseolus vulgaris. The phylogeny of the nodA and nodC nodulation genes as well as the nifH gene of the three strains showed that they belong to the symbiovar retamae of the genus Bradyrhizobium. The three strains isolated could be considered for use as inoculum for Retama plants before use in phytoremediation experiments.
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Affiliation(s)
- Hanane Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Soufiane Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080, Granada, Spain
| | - Mustapha Missbah-El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco.
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WONGDEE JENJIRA, YUTTAVANICHAKUL WATCHARIN, LONGTHONGLANG APHAKORN, TEAMTISONG KAMONLUCK, BOONKERD NANTAKORN, TEAUMROONG NEUNG, TITTABUTR PANLADA. Enhancing the Efficiency of Soybean Inoculant for Nodulation under Multi-Environmental Stress Conditions. Pol J Microbiol 2021; 70:257-271. [PMID: 34349815 PMCID: PMC8326982 DOI: 10.33073/pjm-2021-024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/10/2022] Open
Abstract
The development of rhizobial inoculants with increased resistance to abiotic stress is critical to mitigating the challenges related to climate change. This study aims at developing a soybean stress-tolerant Bradyrhizobium inoculant to be used under the mixed stress conditions of acidity, high temperature, and drought. Six isolates of Bradyrhizobium with high symbiotic performance on soybean were tested to determine their growth or survival abilities under in vitro conditions. The representative stress-tolerant Bradyrhizobium isolates 184, 188, and 194 were selected to test their ability to promote soybean growth under stress conditions compared to the type strain Bradyrhizobium diazoefficiens USDA110. The plant experiment indicated that isolate 194 performed better in symbiosis with soybean than other Bradyrhizobium strains under stress conditions. Based on the stress tolerance index, soybeans inoculated with isolate 194 showed a high growth performance and significantly better nodulation competition ability than USDA110 under several stress conditions. Interestingly, supplementation of sucrose in the culture medium significantly enhances the survival of the isolate and leads to improved plant biomass under various stress conditions. Analysis of the intra-cellular sugars of isolate 194 supplemented with sucrose showed the accumulation of compatible solutes, such as trehalose and glycerol, that may act as osmoprotectants. This study indicates that inoculation of stress-tolerant Bradyrhizobium together with sucrose supplementation in a medium could enhance bacterial survival and symbiosis efficiency under stress conditions. Although it can be applied for inoculant production, this strategy requires validation of its performance in field conditions before adopting this technology.
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Affiliation(s)
- JENJIRA WONGDEE
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - WATCHARIN YUTTAVANICHAKUL
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - APHAKORN LONGTHONGLANG
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - KAMONLUCK TEAMTISONG
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - NANTAKORN BOONKERD
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - NEUNG TEAUMROONG
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - PANLADA TITTABUTR
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Liu G, Liu X, Liu W, Gao K, Chen X, Wang ET, Zhao Z, Du W, Li Y. Biodiversity and Geographic Distribution of Rhizobia Nodulating With Vigna minima. Front Microbiol 2021; 12:665839. [PMID: 34017318 PMCID: PMC8129581 DOI: 10.3389/fmicb.2021.665839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Vigna minima is a climbing annual plant widely distributed in barren wilderness, grass land, and shrub bush of China and other countries such as Japan. However, the rhizobia nodulating with this plant has never been systematically studied. In order to reveal the biodiversity of nodulating rhizobia symbiosis with V. minima, a total of 874 rhizobium isolates were obtained from root nodules of the plant spread in 11 sampling sites of Shandong Peninsula, China, and they were designated as 41 haplotypes in the genus Bradyrhizobium based upon recA sequence analyses. By multilocus sequence analysis (MLSA) of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB), the 41 strains representing different recA haplotypes were classified into nine defined species and nine novel genospecies. Bradyrhizobium elkanii, Bradyrhizobium ferriligni, and Bradyrhizobium pachyrhizi were the predominant and universally distributed groups. The phylogeny of symbiotic genes of nodC and nifH showed similar topology and phylogenetic relationships, in which all the representative strains were classified into two clades grouped with strains nodulating with Vigna spp., demonstrating that Vigna spp. shared common nodulating groups in the natural environment. All the representative strains formed nodules with V. minima in a nodulation test performed in green house conditions. The correlation between V. minima nodulating rhizobia and soil characteristics analyzed by CANOCO indicates that available nitrogen, total nitrogen, and organic carbon in the soil samples were the main factors affecting the distribution of rhizobia isolated in this study. This study systematically uncovered the biodiversity and distribution characteristics of V. minima nodulating rhizobia for the first time, which provided novel information for the formation of the corresponding rhizobium community.
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Affiliation(s)
- Guohua Liu
- College of Life Science, Yantai University, Yantai, China
| | - Xiaoling Liu
- College of Life Science, Yantai University, Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Kangning Gao
- College of Resources and Environment, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoli Chen
- The Fruit Trees Work Station of Penglai, Yantai, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenjun Zhao
- College of Life Science, Yantai University, Yantai, China
| | - Wenxiao Du
- College of Life Science, Yantai University, Yantai, China
| | - Yan Li
- College of Life Science, Yantai University, Yantai, China.,Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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Torres-Martínez L, Porter SS, Wendlandt C, Purcell J, Ortiz-Barbosa G, Rothschild J, Lampe M, Warisha F, Le T, Weisberg AJ, Chang JH, Sachs JL. Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation. Evolution 2021; 75:1070-1086. [PMID: 33782951 DOI: 10.1111/evo.14222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/18/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022]
Abstract
Specialization in mutualisms is thought to be a major driver of diversification, but few studies have explored how novel specialization evolves, or its relation to the evolution of other niche axes. A fundamental question is whether generalist interactions evolve to become more specialized (i.e., oscillation hypothesis) or if partner switches evolve without any change in niche breadth (i.e., musical chairs hypothesis). We examined alternative models for the evolution of specialization by estimating the mutualistic, climatic, and edaphic niche breadths of sister plant species, combining phylogenetic, environmental, and experimental data on Acmispon strigosus and Acmispon wrangelianus genotypes across their overlapping ranges in California. We found that specialization along all three niche axes was asymmetric across species, such that the species with broader climatic and edaphic niches, Acmispon strigosus, was also able to gain benefit from and invest in associating with a broader set of microbial mutualists. Our data are consistent with the oscillation model of specialization, and a parallel narrowing of the edaphic, climatic, and mutualistic dimensions of the host species niche. Our findings provide novel evidence that the evolution of specialization in mutualism is accompanied by specialization in other niche dimensions.
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Affiliation(s)
- Lorena Torres-Martínez
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, Washington, 98686, United States of America
| | - Camille Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, Washington, 98686, United States of America
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, California, 92521, United States of America
| | - Gabriel Ortiz-Barbosa
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, 92521, United States of America
| | - Jacob Rothschild
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Mathew Lampe
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Farsamin Warisha
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Tram Le
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, United States of America
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, United States of America
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, 92521.,Department of Microbiology and Plant Pathology, University of California, Riverside, California, 92521, United States of America.,Institute of Integrative Genome Biology, University of California, Riverside, California, 92521, United States of America
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Banasiewicz J, Granada CE, Lisboa BB, Grzesiuk M, Matuśkiewicz W, Bałka M, Schlindwein G, Vargas LK, Passaglia LMP, Stępkowski T. Diversity and phylogenetic affinities of Bradyrhizobium isolates from Pampa and Atlantic Forest Biomes. Syst Appl Microbiol 2021; 44:126203. [PMID: 33857759 DOI: 10.1016/j.syapm.2021.126203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
In this work, we investigated Bradyrhizobium strains isolated from soils collected from the rhizosphere of native and exotic legumes species inhabiting two ecoclimatic zones - asubtropical-lowland pasture (Pampa Biome) and a volcanic plateau covered by Araucaria Moist Forests (Atlantic Forest Biome). The rhizobial strains were isolated from the nodules of seven native and one exotic legume species used as rhizobium traps. Single-gene (recA, glnII, dnaK) and combined-gene MLSA analyses (dnaK-glnII-gyrB-recA-rpoB) revealed that nearly 85% of the isolates clustered in B. elkanii supergroup, while the remaining (except for two isolates) in B. japonicum supergroup, albeit, in most cases, separately from the type strains of Bradyrhizobium species. As a symbiotic gene marker, a portion of nifD gene was sequenced for 194 strains. In the nifD-tree, an American branch III.3D (104 isolates), was the most numerous among the isolates. A significant portion of the isolates clustered in American groups; subclade III.4 (40 strains), Clade VII (3 strains), and a new Clade XX (4 strains). Most of the remaining strains belonged to a pantropical III.3C branch (39 isolates). On the other hand, identification of isolates belonging, respectively, to Clade I and Clade II may result of spreading of the Australian (Clade I) and European (Clade II) bradyrhizobia following the introduction of their legume hosts. Our study indicated that the American groups predominated in the symbiotic Bradyrhizobium communities in southern Brazil. However, there is a significant component of exotic lineages, resulting from the dispersal of pantropical Fabaceae taxa and the introduction of exotic legumes.
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Affiliation(s)
- Joanna Banasiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Camille E Granada
- Universidade do Vale do Taquari - UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil
| | - Bruno B Lisboa
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Małgorzata Grzesiuk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Weronika Matuśkiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Mateusz Bałka
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Gilson Schlindwein
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciano K Vargas
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul., Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
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Dardis C, Quelas JI, Mengucci F, Althabegoiti MJ, Lodeiro AR, Mongiardini EJ. Dual Control of Flagellar Synthesis and Exopolysaccharide Production by FlbD-FliX Class II Regulatory Proteins in Bradyrhizobium diazoefficiens. J Bacteriol 2021; 203:e00403-20. [PMID: 33468586 DOI: 10.1128/JB.00403-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Bradyrhizobium diazoefficiens, the N2-fixing symbiont of soybean, has two independent flagellar systems: a single subpolar flagellum and several lateral flagella. Each flagellum is a very complex organelle composed of 30 to 40 different proteins located inside and outside the cell whereby flagellar gene expression must be tightly controlled. Such control is achieved by a hierarchy of regulators that ensure the timing of synthesis and the allocation of the different flagellar substructures. Previously, we analyzed the gene organization, expression, and function of the lateral flagellar system. Here, we studied the role of the response regulator FlbD and its trans-acting regulator FliX in the regulation of subpolar flagellar genes. We found that the LP-ring, distal rod, and hook of the subpolar flagellum were tightly controlled by FlbD and FliX. Furthermore, we obtained evidence for the existence of cross-regulation between these gene products and the expression of LafR, the master regulator of lateral flagella. In addition, we observed that extracellular polysaccharide production and biofilm formation also responded to these flagellar regulators. In this regard, FlbD might contribute to the switch between the planktonic and sessile states.IMPORTANCE Most environmental bacteria switch between two free-living states: planktonic, in which individual cells swim propelled by flagella, and sessile, in which bacteria form biofilms. Apart from being essential for locomotion, the flagellum has accessory functions during biofilm formation. The synthesis of flagella is a highly regulated process, and coordination with accessory functions requires the interconnection of various regulatory networks. Here, we show the role of class II regulators involved in the synthesis of the B. diazoefficiens subpolar flagellum and their possible participation in cross-regulation with the lateral flagellar system and exopolysaccharide production. These findings highlight the coordination of the synthetic processes of external structures, such as subpolar and lateral flagella, with exopolysaccharides, which are the main component of the biofilm matrix.
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Bünger W, Sarkar A, Grönemeyer JL, Zielinski J, Revermann R, Hurek T, Reinhold-Hurek B. Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber. Front Microbiol 2021; 12:611704. [PMID: 33584615 PMCID: PMC7876412 DOI: 10.3389/fmicb.2021.611704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Pterocarpus angolensis, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of P. angolensis to form nodules with a diverse range of rhizobia. In drought-prone areas under climate change with higher temperatures, inoculants that are heat-tolerant and adapted to these conditions are likely to be of advantage. Sources of bacterial isolates were roots of P. angolensis from nurseries in the Kavango region, other shrubs from this area growing near Pterocarpus such as Indigofera rautanenii, Desmodium barbatum, Chamaecrista sp., or shrubs from drought-prone areas in Namaqualand (Wiborgia monoptera, Leobordea digitata) or Kalahari (Indigofera alternans). Only slight protrusions were observed on P. angolensis roots, from which a non-nodulating Microbacterium sp. was isolated. Rhizobia that were isolated from nodules of other shrubs were affiliated to Bradyrhizobium ripae WR4T, Bradyrhizobium spp. (WR23/WR74/WR93/WR96), or Ensifer/Mesorhizobium (WR41/WR52). As many plant growth-promoting rhizobacteria (PGPR), nodule isolates produced siderophores and solubilized phosphate. Among them, only the Bradyrhizobium strains nodulated P. angolensis under controlled conditions in the laboratory. Isolates were further characterized by multilocus sequence analysis and were found to be distant from known Bradyrhizobium species. Among additional reference species tested for nodulation on P. angolensis, Bradyrhizobium vignae 7-2T and Bradyrhizobium namibiense 5-10T from the Kavango region of Namibia as well as Bradyrhizobium elkanii LMG6234T and Bradyrhizobium yuanmingense LMG21728T induced nitrogen-fixing nodules, while Bradyrhizobium diazoefficiens USDA110T and Bradyrhizobium tropiciagri SEMIA6148T did not. This suggests a broad microsymbiont range from Bradyrhizobium japonicum and B. elkanii lineages. Phylogenetic analysis of nodC genes indicated that nodulating bradyrhizobia did not belong to a specific symbiovar. Also, for I. rautanenii and Wiborgia, nodule isolates B. ripae WR4T or Mesorhizobium sp. WR52, respectively, were authenticated. Characterization of symbionts inducing effective root nodules in P. angolensis and other shrubs from Subsahara Africa (SSA) give insights in their symbiotic partners for the first time and might help in future to develop bioinoculants for young seedlings in nurseries, and for reforestation efforts in Southern Africa.
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Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Abhijit Sarkar
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Janina Zielinski
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rasmus Revermann
- Department of Biodiversity, Ecology and Evolution of Plants, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
- Faculty of Natural Resources and Spatial Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
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Ramírez MDA, España M, Sekimoto H, Okazaki S, Yokoyama T, Ohkama-Ohtsu N. Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela. Microbes Environ 2021; 36:ME20157. [PMID: 34092740 PMCID: PMC8209454 DOI: 10.1264/jsme2.me20157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/26/2021] [Indexed: 11/12/2022] Open
Abstract
Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and β-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.
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Affiliation(s)
- María Daniela Artigas Ramírez
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, 870 Uehara, Yaeyama, Taketomi, Okinawa, 907–1541, Japan
- Institute of Global Innovation Research and Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
| | | | - Hitoshi Sekimoto
- Faculty of Agriculture, Utsunomiya University, Utsunomiya 321–8505, Japan
| | - Shin Okazaki
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
- Faculty of Food and Agricultural Science, Fukushima University, Kanayagawa 1, Fukushima city, Fukushima, 960–1296, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
- Institute of Global Innovation Research and Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
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Rodrigues TF, Bender FR, Sanzovo AWS, Ferreira E, Nogueira MA, Hungria M. Impact of pesticides in properties of Bradyrhizobium spp. and in the symbiotic performance with soybean. World J Microbiol Biotechnol 2020; 36:172. [PMID: 33068168 DOI: 10.1007/s11274-020-02949-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/10/2020] [Indexed: 12/26/2022]
Abstract
Soybean [Glycine max (L.) Merr.] has great economic and nutritional importance mainly due to its high protein content. All plant's N needs can be met by the symbiosis with elite Bradyrhizobium strains applied as inoculants to the seeds at sowing time; however, the increasing use of pesticides in seed treatments can impair the contribution of the biological nitrogen fixation. In this study, we report decreases in cell survival of two strains, B. japonicum SEMIA 5079 and B. elkanii SEMIA 587 in seeds inoculated and treated with StandakTop™, composed of the fungicides pyraclostrobin and thiophanate-methyl and the insecticide fipronil, the pesticides most used in soybean seed treatment in several countries. Cell death was enhanced with the time of exposure to the pesticides, and B. elkanii was less tolerant, with almost no detectable viable cells after 15 days. Change in colony morphology with smaller colonies was observed in the presence of the pesticides, being more drastic with the time of exposure, and attributed to an adaptive response towards survival in the presence of the abiotic stress. However, morphological changes were reversible after elimination of the stressing agent and symbiotic performance under controlled greenhouse conditions was similar between strains that had been or not exposed to the pesticides. In addition, no changes in DNA profiles (BOX-PCR) of both strains were observed after the contact with the pesticides. In two field experiments, impacting effects of the pesticides were observed mainly on the total N accumulated in grains of plants relying on both N2-fixation and N-fertilizer. Our data indicate that StandakTop® affects parameters never reported before, including colony morphology of Bradyrhizobium spp. and N metabolism and/or N remobilization to soybean grains.
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Affiliation(s)
- Thiago Fernandes Rodrigues
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86.057-970, Brazil
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil
| | - Flavia Raquel Bender
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86.057-970, Brazil
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil
| | - Alisson Wilson Santos Sanzovo
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil
- Department of Agronomy, Universidade Estadual de Londrina, C.P. 6001, Londrina, Paraná, 86.057-970, Brazil
| | - Eduara Ferreira
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil
| | - Marco Antonio Nogueira
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil
- Department of Agronomy, Universidade Estadual de Londrina, C.P. 6001, Londrina, Paraná, 86.057-970, Brazil
| | - Mariangela Hungria
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86.057-970, Brazil.
- Embrapa Soja, Caixa Postal 231, Londrina, Paraná, CEP 86001-970, Brazil.
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Helene LCF, Klepa MS, O'Hara G, Hungria M. Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., isolated from nodules of legumes indigenous to Western Australia. Int J Syst Evol Microbiol 2020; 70:4623-4636. [PMID: 32667875 DOI: 10.1099/ijsem.0.004322] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia, broadly spread in a variety of ecosystems and with remarkable diversity. A polyphasic study was performed to characterize and clarify the taxonomic position of eight bradyrhizobial strains isolated from indigenous legumes to Western Australia. As expected for the genus, the 16S rRNA gene sequences were highly conserved, but the results of multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed three new distinct clades including the following strains: (1) WSM 1744T, WSM 1736 and WSM 1737; (2) WSM 1791T and WSM 1742; and (3) WSM 1741T, WSM 1735 and WSM 1790. The highest ANI values of the three groups in relation to the closest type strains were 92.4, 92.3 and 93.3 %, respectively, below the threshold of species circumscription. The digital DNA-DNA hybridization analysis also confirmed new species descriptions, with less than 52 % relatedness with the closest type strains. The phylogeny of the symbiotic gene nodC clustered the eight strains into the symbiovar retamae, together with seven Bradyrhizobium type strains, sharing from 94.2-98.1 % nucleotide identity (NI), and less than 88.7 % NI with other related strains and symbiovars. Morpho-physiological, phylogenetics, genomic and symbiotic traits were determined for the new groups and our data support the description of three new species, Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., with WSM 1744T (=CNPSo 4013T=LMG 31646T), WSM 1791T (=CNPSo 4014T=LMG 31647T) and WSM 1741T (=CNPSo 4020T=LMG 31651T) designated as type strains, respectively.
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Affiliation(s)
- Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Milena Serenato Klepa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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70
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Rejili M, Off K, Brachmann A, Marín M. Bradyrhizobium hipponense sp. nov., isolated from Lupinus angustifolius growing in the northern region of Tunisia. Int J Syst Evol Microbiol 2020; 70:5539-5550. [PMID: 32897848 DOI: 10.1099/ijsem.0.004445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain aSej3T was isolated from a root nodule of a Lupinus angustifolius plant growing in Bizerte, Tunisia. 16S rRNA gene analysis placed this strain within the genus Bradyrhizobium. Multilocus sequence analysis (MLSA) including three housekeeping genes (glnII, gyrB and recA) grouped aSej3T together with Bradyrhizobium rifense CTAW71T, Bradyrhizobium cytisi CTAW11T, Bradyrhizobium ganzhouense RITF806T, Bradyrhizobium lupini USDA 3051T and Bradyrhizobium canariense BTA-1T. MLSA with five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed that this strain shares less than 93.5 % nucleotide identity with other type strains. Genome sequencing and inspection revealed a genome size of 8.83 Mbp with a G+C content of 62.8 mol%. Genome-wide average nucleotide identity and digital DNA-DNA hybridization values were below 87.5 and 36.2 %, respectively, when compared to described Bradyrhizobium species. Strain aSej3T nodulated L. angustifolius plants under axenic conditions and its nodC gene clustered within the genistearum symbiovar. Altogether, the phylogenetic data and the chemotaxonomic characteristics of this strain support that aSej3T represents a new species for which we propose the name Bradyrhizobium hipponense sp. nov. with the type strain aSej3T (=DSM 108913T=LMG 31020T).
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Affiliation(s)
- Mokhtar Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences, Gabes University, Tunisia
| | - Katja Off
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Andreas Brachmann
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Macarena Marín
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
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71
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Cabral Michel D, Martins da Costa E, Azarias Guimarães A, Soares de Carvalho T, Santos de Castro Caputo P, Willems A, de Souza Moreira FM. Bradyrhizobium campsiandrae sp. nov., a nitrogen-fixing bacterial strain isolated from a native leguminous tree from the Amazon adapted to flooded conditions. Arch Microbiol 2020; 203:233-240. [PMID: 32857180 DOI: 10.1007/s00203-020-02022-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/23/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023]
Abstract
The nitrogen-fixing bacterial strain UFLA 01-1174T was isolated from nodules of Campsiandra laurilifolia Benth. originating from the Amazon region, Brazil. Its taxonomic position was defined using a polyphasic approach. Analysis of the 16S rRNA gene placed the strain in the Bradyrhizobium genus, the closest species being B. guangdongense CCBAU 51649T and B. guangzhouense CCBAU 51670T, both with 99.8% similarity. Multilocus sequence analysis (MLSA) of recA, gyrB, glnII, rpoB, atpD, and dnaK indicated that UFLA 01-1174T is a new species, most closely related to B. stylosanthis BR 446T (94.4%) and B. manausense BR 3351T (93.7%). Average nucleotide identity (ANI) differentiated UFLA 01-1174T from the closest species with values lower than 90%. The G + C content in the DNA of UFLA 01-1174T is 63.6 mol%. Based on this data, we conclude that the strain represents a new species. The name proposed is Bradyrhizobium campsiandrae, with UFLA 01-1174T (= INPA 394BT = LMG 10099T) as type strain.
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Affiliation(s)
- Daniele Cabral Michel
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Elaine Martins da Costa
- Universidade Federal Do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | - Amanda Azarias Guimarães
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Teotonio Soares de Carvalho
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Polyane Santos de Castro Caputo
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fatima Maria de Souza Moreira
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil.
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72
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Cui C, Lin H, Pu W, Guo C, Liu Y, Pei XQ, Wu ZL. Asymmetric Epoxidation and Sulfoxidation Catalyzed by a New Styrene Monooxygenase from Bradyrhizobium. Appl Biochem Biotechnol 2020; 193:65-78. [PMID: 32808246 DOI: 10.1007/s12010-020-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Asymmetric epoxidation catalyzed with styrene monooxygenase (SMO) is a powerful enzymatic process producing enantiopure styrene epoxide derivatives. To establish a more diversified reservoir of SMOs, a new SMO from Bradyrhizobium sp. ORS 375, named BrSMO, was mined from the database and characterized. BrSMO was constituted of an epoxygenase component of 415 amino acid residues and an NADH-dependent flavin reductase component of 175 residues. BrSMO catalyzed the epoxidation of styrene and 7 more styrene derivatives, yielding the corresponding (S)-epoxides with excellent enantiomeric excesses (95- > 99% ee), with the highest activity achieved for styrene. BrSMO also catalyzed the asymmetric sulfoxidation of 7 sulfides, producing the corresponding (R)-sulfoxides (20-90% ee) with good yields.
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Affiliation(s)
- Can Cui
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
| | - Wei Pu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Guo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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73
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Wu Y, Li YH, Shang JY, Wang ET, Chen L, Huo B, Sui XH, Tian CF, Chen WF, Chen WX. Multiple Genes of Symbiotic Plasmid and Chromosome in Type II Peanut Bradyrhizobium Strains Corresponding to the Incompatible Symbiosis With Vigna radiata. Front Microbiol 2020; 11:1175. [PMID: 32655513 PMCID: PMC7324677 DOI: 10.3389/fmicb.2020.01175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/07/2020] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are capable of establishing compatible symbiosis with their hosts of origin and plants in the cross-nodulation group that the hosts of origin belonged to. However, different from the normal peanut Bradyrhizobium (Type I strains), the Type II strains showed incompatible symbiosis with Vigna radiata. Here, we employed transposon mutagenesis to identify the genetic loci related to this incompatibility in Type II strain CCBAU 53363. As results, seven Tn5 transposon insertion mutants resulted in an increase in nodule number on V. radiata. By sequencing analysis of the sequence flanking Tn5 insertion, six mutants were located in the chromosome of CCBAU 53363, respectively encoding acyltransferase (L265) and hypothetical protein (L615)—unique to CCBAU 53363, two hypothetical proteins (L4 and L82), tripartite tricarboxylate transporter substrate binding protein (L373), and sulfur oxidation c-type cytochrome SoxA (L646), while one mutant was in symbiotic plasmid encoding alanine dehydrogenase (L147). Significant differences were observed in L147 gene sequences and the deduced protein 3D structures between the Type II (in symbiotic plasmid) and Type I strains (in chromosome). Conversely, strains in both types shared high homologies in the chromosome genes L373 and L646 and in their protein 3D structures. These data indicated that the symbiotic plasmid gene in Type II strains might have directly affected their symbiosis incompatibility, whereas the chromosome genes might be indirectly involved in this process by regulating the plasmid symbiosis genes. The seven genes may initially explain the complication associated with symbiotic incompatibility.
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Affiliation(s)
- Yue Wu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yong Hua Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiao Ying Shang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - La Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bin Huo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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74
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Hashimoto S, Goto K, Pyromyou P, Songwattana P, Greetatorn T, Tittabutr P, Boonkerd N, Teaumroong N, Uchiumi T. Type III Secretion System of Bradyrhizobium sp. SUTN9-2 Obstructs Symbiosis with Lotus spp. Microbes Environ 2020; 35. [PMID: 32611950 PMCID: PMC7511788 DOI: 10.1264/jsme2.me20041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rhizobial type III secretion system secretes effector proteins into host plant cells, which may either promote or inhibit symbiosis with legumes. We herein demonstrated that the type III secretion system of Bradyrhizobium sp. SUTN9-2 obstructed symbiosis with Lotus japonicus Miyakojima, L. japonicus Gifu, and Lotus burttii. A mutant of SUTN9-2 that is unable to secrete effector proteins showed better nodulation and plant growth promotion than wild-type SUTN9-2 when paired with these Lotus spp. We propose that SUTN9-2 is a useful strain for understanding the mechanisms by which effector proteins obstruct symbiosis between Bradyrhizobium and Lotus spp.
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Affiliation(s)
- Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University
| | - Kohki Goto
- Graduate School of Science and Engineering, Kagoshima University
| | - Pongdet Pyromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University
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75
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Siqueira AF, Sugawara M, Arashida H, Minamisawa K, Sánchez C. Levels of Periplasmic Nitrate Reductase during Denitrification are Lower in Bradyrhizobium japonicum than in Bradyrhizobium diazoefficiens. Microbes Environ 2020; 35. [PMID: 32554940 PMCID: PMC7511789 DOI: 10.1264/jsme2.me19129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Soybean plants host endosymbiotic dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Under oxygen-limiting conditions, Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum perform denitrification by sequentially reducing nitrate (NO3–) to nitrous oxide (N2O) or N2. The anaerobic reduction of NO3– to N2O was previously shown to be lower in B. japonicum than in B. diazoefficiens due to impaired periplasmic nitrate reductase (Nap) activity in B. japonicum. We herein demonstrated that impaired Nap activity in B. japonicum was due to low Nap protein levels, which may be related to a decline in the production of FixP and FixO proteins by the cbb3-type oxidase.
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76
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Banerjee G, Basak S, Roy T, Chattopadhyay P. Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp. FEMS Microbiol Ecol 2020; 95:5586991. [PMID: 31609448 DOI: 10.1093/femsec/fiz165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/13/2019] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
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Affiliation(s)
- Goutam Banerjee
- Department of Biochemistry, University of Calcutta, West Bengal 700019, India
| | - Swarnendu Basak
- Department of Medical Zoology, Kyung Hee University, School of Medicine, Seoul 02447, Republic of Korea
| | - Tathagato Roy
- Member of Jeevak Herb Welfare Society (registration number S/1L/78148 OF 2010-2011), Santiniketan, 731235, India.,Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, U.S
| | - Pritam Chattopadhyay
- Department of Biotechnology, Gauhati University, Guwahati, Assam 781014, India.,Department of Botany, M.U.C. Women's College, University of Bardhaman, Bardhaman, West Bengal 713104, India
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77
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Tewari S, Sharma S. Rhizobial-metabolite based biocontrol of fusarium wilt in pigeon pea. Microb Pathog 2020; 147:104278. [PMID: 32473389 DOI: 10.1016/j.micpath.2020.104278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/15/2020] [Accepted: 05/25/2020] [Indexed: 11/24/2022]
Abstract
The application of rhizobial cells for improving pigeon pea fitness has been practiced for ages. As cell-based approaches have limitations, the focus is on the usage of cell-free formulations. In the present study exopolysaccharide (EPS) producing, plant health promoting Bradyrhizobium sp. IC-4059 was monitored for its biocontrol potential against Fusarium udum. Strain IC-4059, its EPS, and supernatant antagonized F.udum by 52.6%, 20.5%, and 48.1%, respectively in comparison to control. Diverse formulations prepared using EPS, supernatant, and cells of strain IC-4059 were: EPS based, supernatant based, IC-4059 liquid culture (rhizobia based), dual combination (IC-4059 cells + supernatant; IC-4059 cells + EPS; EPS + supernatant), and triple combination (IC-4059 cells + supernatant + EPS). The potency of these bioformulations was observed under in planta tubes followed by in vivo pot study, both in F.udum infested and non-infested sets taking pigeon pea cultivar UPAS-120 as a model crop. The study highlighted that seeds receiving triple combination exhibited significantly higher plant growth attributes, nodule enhancing, and disease suppressing activity in comparison to individual application of Bradyrhizobium. Antifungal compounds were analyzed by a metabolomic approach using UPLC-MS. Thus, the study disseminates the tripartite role of triple formulation as a plant growth stimulator, nodule enhancer, and disease suppressor, both under in vitro and in vivo conditions in the presence of phytopathogen F. udum.
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Affiliation(s)
- Sakshi Tewari
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Sibponkrung S, Kondo T, Tanaka K, Tittabutr P, Boonkerd N, Yoshida KI, Teaumroong N. Co-Inoculation of Bacillus velezensis Strain S141 and Bradyrhizobium Strains Promotes Nodule Growth and Nitrogen Fixation. Microorganisms 2020; 8:E678. [PMID: 32392716 DOI: 10.3390/microorganisms8050678] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 11/29/2022] Open
Abstract
The objective of this research was to evaluate the PGPR effect on nodulation and nitrogen-fixing efficiency of soybean (Glycine max (L.) Merr.) by co-inoculation with Bradyrhizobiumdiazoefficiens USDA110. Co-inoculation of Bacillusvelezensis S141 with USDA110 into soybean resulted in enhanced nodulation and N2-fixing efficiency by producing larger nodules. To understand the role of S141 on soybean and USDA110 symbiosis, putative genes related to IAA biosynthesis were disrupted, suggesting that co-inoculation of USDA110 with S141ΔyhcX reduces the number of large size nodules. It was revealed that yhcX may play a major role in IAA biosynthesis in S141 as well as provide a major impact on soybean growth promotion. The disruption of genes related to cytokinin biosynthesis and co-inoculation of USDA110 with S141ΔIPI reduced the number of very large size nodules, and it appears that IPI might play an important role in nodule size of soybean–Bradyrhizobium symbiosis. However, it was possible that not only IAA and cytokinin but also some other substances secreted from S141 facilitate Bradyrhizobium to trigger bigger nodule formation, resulting in enhanced N2-fixation. Therefore, the ability of S141 with Bradyrhizobium co-inoculation to enhance soybean N2-fixation strategy could be further developed for supreme soybean inoculants.
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Iturralde ET, Stocco MC, Faura A, Mónaco CI, Cordo C, Pérez-Giménez J, Lodeiro AR. Coinoculation of soybean plants with Bradyrhizobium japonicum and Trichoderma harzianum: Coexistence of both microbes and relief of nitrate inhibition of nodulation. ACTA ACUST UNITED AC 2020; 26:e00461. [PMID: 32420051 PMCID: PMC7218258 DOI: 10.1016/j.btre.2020.e00461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
Bradyrhizobium japonicum and Trichoderma harzianum coexisted in soybean rhizosphere. Soybean inoculated with both microbes nodulated with high nitrate concentrations. T. harzianum produced auxins in culture medium. Auxins applied with B. japonicum alone relieved nitrate inhibition of nodulation.
Coinoculation of plants with mixtures of beneficial microbes sometimes produces synergistic effects. In this study, the effect of soybean coinoculation with the N2-fixing Bradyrhizobium japonicum E109 and the biocontrol fungus Trichoderma harzianum Th5cc was analyzed. Nodulation by E109 was not hampered by Th5cc, which antagonized five out of seven soybean pathogens tested. Furthermore, Th5cc relieved nitrate-inhibition of nodulation, enabling the formation of nodules containing infected cells with bacteroids in the presence of the otherwise inhibitory 10 mM KNO3. Th5cc released micromolar amounts of auxin, and addition of 11 μM indoleacetic acid to soybean plants inoculated with E109 in the absence of Th5cc also induced nodulation in the presence of 10 mM KNO3. Thus, Th5cc may release auxins into the soybean rhizosphere, which hormones might participate in overcoming the nitrate-inhibition of nodulation. Our results suggest that soybean plants coinoculated with these microorganisms might benefit from biocontrol while contributing to soil-nitrogen preservation.
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Key Words
- AG, arabinose-gluconate medium
- Bradyrhizobium
- CFU, colony-forming units
- CR, Congo Red
- Coinoculation
- DAI, days after inoculation
- IAA, indoleacetic acid
- LPCB, lactophenol cotton blue
- MFS, modified Fåhræus solution
- Nitrate
- PDA, potato-dextrose agar
- PGPM, plant-growth promoting microbe
- Soybean
- Trichoderma
- YM, yeast-extract mannitol medium
- YMA, YM with 1.5 % (w/v) agar
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Affiliation(s)
- Esteban Tomás Iturralde
- Laboratorio de Interacciones entre Rizobios y Soja (Lirys), IBBM CCT-La Plata CONICET and Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Marina Celeste Stocco
- CIDEFI, CIC-PBA and Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calles 60 y 119 (1900), La Plata, Argentina
| | - Andrés Faura
- Rizobacter Argentina SA, Avda. Dr. Arturo Frondizi 1150, Parque Industrial (2700), Pergamino, Argentina
| | - Cecilia Inés Mónaco
- CIDEFI, CIC-PBA and Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calles 60 y 119 (1900), La Plata, Argentina
| | - Cristina Cordo
- CIDEFI, CIC-PBA and Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calles 60 y 119 (1900), La Plata, Argentina
| | - Julieta Pérez-Giménez
- Laboratorio de Interacciones entre Rizobios y Soja (Lirys), IBBM CCT-La Plata CONICET and Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Aníbal Roberto Lodeiro
- Laboratorio de Interacciones entre Rizobios y Soja (Lirys), IBBM CCT-La Plata CONICET and Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina.,Laboratorio de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calles 60 y 119 (1900), La Plata, Argentina
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80
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Lopez NV, Farsar CJ, Harmon DE, Ruiz C. Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria. Microbiologyopen 2020; 9:1247-1263. [PMID: 32246583 PMCID: PMC7294306 DOI: 10.1002/mbo3.1034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/01/2023] Open
Abstract
Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 104 cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.
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Affiliation(s)
- Nicolas V. Lopez
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Cameron J. Farsar
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Dana E. Harmon
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Cristian Ruiz
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
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81
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Soares R, Trejo J, Lorite MJ, Figueira E, Sanjuán J, Videira e Castro I. Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus. Microorganisms 2020; 8:microorganisms8040499. [PMID: 32244524 PMCID: PMC7232477 DOI: 10.3390/microorganisms8040499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 11/18/2022] Open
Abstract
Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty highly diverse bacterial strains were isolated from root nodules of wild Lotus parviflorus plants growing in two field locations in Portugal. However, only 10% of these isolates could nodulate one or more legume hosts tested, whereas 90% were thought to be opportunistic nodule associated bacteria. Phylogenetic studies place the nodulating isolates within the Bradyrhizobium genus, which is closely related to B. canariense and other Bradyrhizobium sp. strains isolated from genistoid legumes and Ornithopus spp. Symbiotic nodC and nifH gene phylogenies were fully consistent with the taxonomic assignment and host range. The non-nodulating bacteria isolated were alpha- (Rhizobium/Agrobacterium), beta- (Massilia) and gamma-proteobacteria (Pseudomonas, Lysobacter, Luteibacter, Stenotrophomonas and Rahnella), as well as some bacteroidetes from genera Sphingobacterium and Mucilaginibacter. Some of these nodule-associated bacteria expressed plant growth promotion (PGP) traits, such as production of lytic enzymes, antagonistic activity against phytopathogens, phosphate solubilization, or siderophore production. This argues for a potential beneficial role of these L. parviflorus nodule-associated bacteria.
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Affiliation(s)
- Ricardo Soares
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Laboratório de Bioquímica Inorgânica e RMN, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Jesús Trejo
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
| | - Maria J. Lorite
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Etelvina Figueira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal;
| | - Juan Sanjuán
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Isabel Videira e Castro
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Correspondence:
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82
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Boudehouche W, Parker MA, Boulila F. Relationships of Bradyrhizobium strains nodulating three Algerian Genista species. Syst Appl Microbiol 2020; 43:126074. [PMID: 32169316 DOI: 10.1016/j.syapm.2020.126074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
The Mediterranean world is the cradle for the diversification of a large number of plant species, including legumes belonging to the Tribe Genisteae. Nodule bacteria from three species of Genista legumes indigenous to northwestern Africa (G. ferox, G. numidica, G. tricuspidata) were sampled across a 150km region of Algeria in order to investigate symbiotic relationships. Partial 23S rRNA sequences from 107 isolates indicated that Bradyrhizobium was the predominant symbiont genus (96% of isolates), with the remainder belonging to Rhizobium or Mesorhizobium. A multilocus sequence analysis on 46 Bradyrhizobium strains using seven housekeeping (HK) genes showed that strains were differentiated into multiple clades with affinities to seven species: B. canariense (17 isolates), B. japonicum (2), B. ottawaense (2), B. cytisi/B. rifense (9), 'B. valentinum' (5), and B. algeriense (11). Extensive discordance between the HK gene phylogeny and a tree for four loci in the symbiosis island (SI) region implied that horizontal transfer of SI loci has been common. Cases of close symbiont relationship across pairs of legumes hosts were evident, with 33% of isolates having as their closest relative a strain sampled from a different Genista species. Nevertheless, tree permutation tests also showed that there was substantial host-related phylogenetic clustering. Thus, each of the three Genista hosts utilized a measurably different array of bacterial lineages.
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Affiliation(s)
- Wafa Boudehouche
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
| | - Matthew A Parker
- Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Farida Boulila
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
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83
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Mengucci F, Dardis C, Mongiardini EJ, Althabegoiti MJ, Partridge JD, Kojima S, Homma M, Quelas JI, Lodeiro AR. Characterization of FliL Proteins in Bradyrhizobium diazoefficiens: Lateral FliL Supports Swimming Motility, and Subpolar FliL Modulates the Lateral Flagellar System. J Bacteriol 2020; 202:e00708-19. [PMID: 31843800 DOI: 10.1128/JB.00708-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023] Open
Abstract
Bradyrhizobium diazoefficiens is a soil alphaproteobacterium that possesses two evolutionarily distinct flagellar systems, a constitutive subpolar flagellum and inducible lateral flagella that, depending on the carbon source, may be expressed simultaneously in liquid medium and used interactively for swimming. In each system, more than 30 genes encode the flagellar proteins, most of which are well characterized. Among the exceptions is FliL, which has been scarcely studied in alphaproteobacteria and whose function in other bacterial classes is somewhat controversial. Because each B. diazoefficiens flagellar system contains its own fliL paralog, we obtained the respective deletions ΔfliLS (subpolar) and ΔfliLL (lateral) to study their functions in swimming. We determined that FliLL was essential for lateral flagellum-driven motility. FliLS was dispensable for swimming in either liquid or semisolid medium; however, it was found to play a crucial role in upregulation of the lateral flagellum regulon under conditions of increased viscosity/flagellar load. Therefore, although FliLS seems to be not essential for swimming, it may participate in a mechanosensor complex that controls lateral flagellum induction.IMPORTANCE Bacterial motility propelled by flagella is an important trait in most environments, where microorganisms must explore the habitat toward beneficial resources and evade toxins. Most bacterial species have a unique flagellar system, but a few species possess two different flagellar systems in the same cell. An example is Bradyrhizobium diazoefficiens, the N2-fixing symbiont of soybean, which uses both systems for swimming. Among the less-characterized flagellar proteins is FliL, a protein typically associated with a flagellum-driven surface-based collective motion called swarming. By using deletion mutants in each flagellar system's fliL, we observed that one of them (lateral) was required for swimming, while the other (subpolar) took part in the control of lateral flagellum synthesis. Hence, this protein seems to participate in the coordination of activity and production of both flagellar systems.
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84
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Hozawa M, Nawata E. The Interaction between Leaf Allelopathy and Symbiosis with Rhizobium of Ulex europaeus on Hawaii Island. Plants (Basel) 2020; 9:plants9020226. [PMID: 32050602 PMCID: PMC7076416 DOI: 10.3390/plants9020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/06/2020] [Indexed: 11/19/2022]
Abstract
The objective of this study was to assess the magnitudes of the leaf allelopathy of Ulex europaeus in two different habitats, and discuss the driver of the differences, including rhizobia. The magnitudes of leaf allelopathy of the samples collected in two different habitats were assessed by comparing the hypocotyl and radicle lengths of the lettuce seeds tested on the samples. One habitat was in and adjacent to an Acasia koa forest, while the other was more than 50 m away. A. koa is indigenous to Hawaii and known to have a close symbiotic relationship with Bradyrhizobium for nitrogen-fixing. Within the past three years, U. europaeus has newly invaded both sampling sites, whereas the A. koa forest has been there for several decades. The combined result of both hypocotyl and radicle lengths of the lettuce seeds tested on both sites by linear model and multicomparison analyses showed no significant difference. But the radicle lengths of the lettuce seeds tested on U. europaeus sampled in and adjacent to the A. koa forest were significantly longer than those of the samples more than 50 m away, as measured by t-test (p = 0.05). This result suggested that the magnitude of the leaf allelopathy of U. europaeus depended on the distance of the habitat from the A. koa forest.
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Affiliation(s)
- Mika Hozawa
- Correspondence: ; Tel.: +81-757-536-353; Fax: +81-757-536-352
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85
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Paudel D, Liu F, Wang L, Crook M, Maya S, Peng Z, Kelley K, Ané JM, Wang J. Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection. Front Microbiol 2020; 11:93. [PMID: 32117123 PMCID: PMC7020250 DOI: 10.3389/fmicb.2020.00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
In many legumes, the colonization of roots by rhizobia is via "root hair entry" and its molecular mechanisms have been extensively studied. However, the nodulation of peanuts (Arachis hypogaea L.) by Bradyrhizobium strains requires an intercellular colonization process called "crack entry," which is understudied. To understand the intercellular crack entry process, it is critical to develop the tools and resources related to the rhizobium in addition to focus on investigating the mechanisms of the plant host. In this study, we isolated a Bradyrhizobium sp. strain, Lb8 from peanut root nodules and sequenced it using PacBio long reads. The complete genome sequence was a circular chromosome of 8,718,147 base-pair (bp) with an average GC content of 63.14%. No plasmid sequence was detected in the sequenced DNA sample. A total of 8,433 potential protein-encoding genes, one rRNA cluster, and 51 tRNA genes were annotated. Fifty-eight percent of the predicted genes showed similarity to genes of known functions and were classified into 27 subsystems representing various biological processes. The genome shared 92% of the gene families with B. diazoefficens USDA 110T. A presumptive symbiosis island of 778 Kb was detected, which included two clusters of nif and nod genes. A total of 711 putative protein-encoding genes were in this region, among which 455 genes have potential functions related to symbiotic nitrogen fixation and DNA transmission. Of 21 genes annotated as transposase, 16 were located in the symbiosis island. Lb8 possessed both Type III and Type IV protein secretion systems, and our work elucidated the association of flagellar Type III secretion systems in bradyrhizobia. These observations suggested that complex rearrangement, such as horizontal transfer and insertion of different DNA elements, might be responsible for the plasticity of the Bradyrhizobium genome.
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Affiliation(s)
- Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Fengxia Liu
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Matthew Crook
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Stephanie Maya
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Karen Kelley
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Jean-Michel Ané
- Departments of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States.,Plant Molecular and Cellular Biology Program, Genetic Institute, University of Florida, Gainesville, FL, United States
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86
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Wasai-Hara S, Hara S, Morikawa T, Sugawara M, Takami H, Yoneda J, Tokunaga T, Minamisawa K. Diversity of Bradyrhizobium in Non-Leguminous Sorghum Plants: B. ottawaense Isolates Unique in Genes for N 2O Reductase and Lack of the Type VI Secretion System. Microbes Environ 2020; 35. [PMID: 31932539 PMCID: PMC7104290 DOI: 10.1264/jsme2.me19102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Diverse members of Bradyrhizobium diazoefficiens, B. japonicum, and B. ottawaense were isolated from the roots of field-grown sorghum plants in Fukushima, and classified into “Rhizobia” with nodulated soybeans, “Free-living diazotrophs”, and “Non-diazotrophs” by nitrogen fixation and nodulation assays. Genome analyses revealed that B. ottawaense members possessed genes for N2O reduction, but lacked those for the Type VI secretion system (T6SS). T6SS is a new bacterial weapon against microbial competitors. Since T6SS-possessing B. diazoefficiens and B. japonicum have mainly been isolated from soybean nodules in Japan, T6SS-lacking B. ottawaense members may be a cryptic lineage of soybean bradyrhizobia in Japan.
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Affiliation(s)
| | | | | | | | - Hideto Takami
- Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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87
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Kalita M, Małek W, Coutinho TA. Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus. Syst Appl Microbiol 2020; 43:126056. [PMID: 31987702 DOI: 10.1016/j.syapm.2020.126056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.
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Affiliation(s)
- Michał Kalita
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland.
| | - Wanda Małek
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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88
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Greetatorn T, Hashimoto S, Maeda T, Fukudome M, Piromyou P, Teamtisong K, Tittabutr P, Boonkerd N, Kawaguchi M, Uchiumi T, Teaumroong N. Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation. Microbes Environ 2020; 35:ME20049. [PMID: 32727975 PMCID: PMC7511792 DOI: 10.1264/jsme2.me20049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.
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Affiliation(s)
- Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Taro Maeda
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Mitsutaka Fukudome
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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89
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Shobudani M, Htwe AZ, Yamakawa T, Ishibashi M, Tsurumaru H. Mutants Disrupted in the Type III Secretion System of Bradyrhizobium elkanii BLY3-8 Overcame Nodulation Restriction by Rj 3-genotype Soybean. Microbes Environ 2020; 35:ME19151. [PMID: 32213755 PMCID: PMC7308571 DOI: 10.1264/jsme2.me19151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Bradyrhizobium elkanii BLY3-8 does not form nodules on the roots of Rj3-genotype soybean (cultivar D-51). This is a cultivar-specific nodulation restriction. The genes A6X20_40975 and A6X20_41030 in strain BLY3-8 were predicted to encode the transcriptional activator and apparatus of the type III secretion system (T3SS) (the proteins TtsI and RhcJ), respectively. Mutants disrupted in these genes overcame the nodulation restriction. These results suggest that an effector injected via T3SS into Rj3-genotype soybean is involved in nodulation restriction by Rj3-genotype soybean.
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Affiliation(s)
- Miku Shobudani
- Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
| | - Aung Zaw Htwe
- Department of Agronomy, Yezin Agricultural University, Yezin, Myanmar
| | - Takeo Yamakawa
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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90
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Favero VO, Carvalho RH, Motta VM, Leite ABC, Coelho MRR, Xavier GR, Rumjanek NG, Urquiaga S. Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean ( Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products. Front Plant Sci 2020; 11:602645. [PMID: 33510747 PMCID: PMC7835340 DOI: 10.3389/fpls.2020.602645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.
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Affiliation(s)
| | | | | | | | | | | | - Norma Gouvêa Rumjanek
- Embrapa Agrobiology, Seropédica, Rio de Janeiro, Brazil
- *Correspondence: Norma Gouvêa Rumjanek,
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91
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Artigas Ramírez MD, España M, Lewandowska S, Yuan K, Okazaki S, Ohkama-Ohtsu N, Yokoyama T. Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela. Microbes Environ 2020; 35:ME19120. [PMID: 31932537 PMCID: PMC7104274 DOI: 10.1264/jsme2.me19120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/10/2019] [Indexed: 12/26/2022] Open
Abstract
Vigna is a genus of legumes cultivated in specific areas of tropical countries. Species in this genus are important crops worldwide. Vigna species are of great agronomic interest in Venezuela because Vigna beans are an excellent alternative to other legumes. However, this type of crop has some cultivation issues due to sensitivity to acidic soils, high temperatures, and salinity stress, which are common in Venezuela. Vigna species establish symbioses mainly with Bradyrhizobium and Ensifer, and Vigna-rhizobia interactions have been examined in Asia, Africa, and America. However, the identities of the rhizobia associated with V. radiata and V. unguiculata in Venezuela remain unknown. In the present study, we isolated Venezuelan symbiotic rhizobia associated with Vigna species from soils with contrasting agroecosystems or from fields in Venezuela. Several types of soils were used for bacterial isolation and nodules were sampled from environments characterized by abiotic stressors, such as high temperatures, high concentrations of NaCl, and acidic or alkaline pH. Venezuelan Vigna-rhizobia were mainly fast-growing. Sequencing of several housekeeping genes showed that in contrast to other continents, Venezuelan Vigna species were nodulated by rhizobia genus including Burkholderia, containing bacteria from several new phylogenetic lineages within the genus Bradyrhizobium. Some Rhizobium and Bradyrhizobium isolates were tolerant of high salinity and Al toxicity. The stress tolerance of strains was dependent on the type of rhizobia, soil origin, and cultivation history. An isolate classified as R. phaseoli showed the highest plant biomass, nitrogen fixation, and excellent abiotic stress response, suggesting a novel promising inoculant for Vigna cultivation in Venezuela.
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Affiliation(s)
- María Daniela Artigas Ramírez
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | | | - Sylwia Lewandowska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, 50–363 Wrocław, 24A, Grunwaldzki—Poland
| | - Kun Yuan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Shin Okazaki
- United Graduated School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
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92
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Speck JJ, James EK, Sugawara M, Sadowsky MJ, Gyaneshwar P. An Alkane Sulfonate Monooxygenase Is Required for Symbiotic Nitrogen Fixation by Bradyrhizobium diazoefficiens (syn. Bradyrhizobium japonicum) USDA110 T. Appl Environ Microbiol 2019; 85:e01552-19. [PMID: 31562172 PMCID: PMC6881790 DOI: 10.1128/aem.01552-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023] Open
Abstract
Sulfur (S)-containing molecules play an important role in symbiotic nitrogen fixation and are critical components of nitrogenase and other iron-S proteins. S deficiency inhibits symbiotic nitrogen fixation by rhizobia. However, despite its importance, little is known about the sources of S that rhizobia utilize during symbiosis. We previously showed that Bradyrhizobium diazoefficiens USDA110T can assimilate both inorganic and organic S and that genes involved in organic S utilization are expressed during symbiosis. Here, we show that a B. diazoefficiens USDA110T mutant with a sulfonate monooxygenase (ssuD) insertion is defective in nitrogen fixation. Microscopy analyses revealed that the ΔssuD mutant was defective in root hair infection and that ΔssuD mutant bacteroids showed degradation compared to the wild-type strain. Moreover, the ΔssuD mutant was significantly more sensitive to hydrogen peroxide-mediated oxidative stress than the wild-type strain. Taken together, these results show that the ability of rhizobia to utilize organic S plays an important role in symbiotic nitrogen fixation. Since nodules have been reported to be an important source of reduced S used during symbiosis and nitrogen fixation, further research will be needed to determine the mechanisms involved in the regulation of S assimilation by rhizobia.IMPORTANCE Rhizobia form symbiotic associations with legumes that lead to the formation of nitrogen-fixing nodules. Sulfur-containing molecules play a crucial role in nitrogen fixation; thus, the rhizobia inside nodules require large amounts of sulfur. Rhizobia can assimilate both inorganic (sulfate) and organic (sulfonates) sources of sulfur. However, very little is known about rhizobial sulfur metabolism during symbiosis. In this report, we show that sulfonate utilization by Bradyrhizobium diazoefficiens is important for symbiotic nitrogen fixation in both soybean and cowpea. The symbiotic defect is probably due to increased sensitivity to oxidative stress from sulfur deficiency in the mutant strain defective for sulfonate utilization. The results of this study can be extended to other rhizobium-legume symbioses, as sulfonate utilization genes are widespread in these bacteria.
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Affiliation(s)
- Justin J Speck
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | | | - Masayuki Sugawara
- Biotechnology Institute, Department of Soil, Water & Climate, University of Minnesota, Saint Paul, Minnesota, USA
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Biotechnology Institute, Department of Plant & Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Michael J Sadowsky
- Biotechnology Institute, Department of Soil, Water & Climate, University of Minnesota, Saint Paul, Minnesota, USA
- Biotechnology Institute, Department of Plant & Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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93
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Woliy K, Degefu T, Frostegård Å. Host Range and Symbiotic Effectiveness of N 2O Reducing Bradyrhizobium Strains. Front Microbiol 2019; 10:2746. [PMID: 31849890 PMCID: PMC6896821 DOI: 10.3389/fmicb.2019.02746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Emissions of the potent greenhouse gas N2O is one of the environmental problems associated with intensive use of synthetic N fertilizers, and novel N2O mitigation strategies are needed to minimize fertilizer applications and N2O release without affecting agricultural efficiencies. Increased incorporation of legume crops in agricultural practices offers a sustainable alternative. Legumes, in their symbiosis with nitrogen fixing bacteria, rhizobia, reduce the need for fertilizers and also respond to the need for increased production of plant-based proteins. Not all combinations of rhizobia and legumes result in efficient nitrogen fixation, and legume crops therefore often need to be inoculated with compatible rhizobial strains. Recent research has demonstrated that some rhizobia are also very efficient N2O reducers. Several nutritionally and economically important legumes form root nodules in symbiosis with bacteria belonging to Bradyrhizobium. Here, the host-ranges of fourteen N2O reducing Bradyrhizobium strains were tested on six legume hosts; cowpea, groundnut, mung bean, haricot bean, soybean, and alfalfa. The plants were grown for 35 days in pots in sterile sand supplemented with N-free nutrient solution. Cowpea was the most promiscuous host nodulated by all test strains, followed by groundnut (11 strains) and mungbean (4 strains). Three test strains were able to nodulate all these three legumes, while none nodulated the other three hosts. For cowpea, five strains increased the shoot dry weight and ten strains the shoot nitrogen content (pairwise comparison; p < 0.05). For groundnut the corresponding results were three and nine strains. The symbiotic effectiveness for the different strains ranged from 45 to 98% in cowpea and 34 to 95% in groundnut, relative to fertilized controls. The N2O reduction capacity of detached nodules from cowpea plants inoculated with one of these strains confirmed active N2O reduction inside the nodules. When released from senescent nodules such strains are expected to also act as sinks for N2O produced by denitrifying organisms in the soil microbial community. Our strategy to search among known N2O-reducing Bradyrhizobium strains for their N2-fixation effectiveness successfully identified several strains which can potentially be used for the production of legume inoculants with the dual capacities of efficacious N2-fixation and N2O reduction.
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Affiliation(s)
- Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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94
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Hakim S, Mirza BS, Imran A, Zaheer A, Yasmin S, Mubeen F, Mclean JE, Mirza MS. Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan. Microbiol Res 2019; 231:126356. [PMID: 31722286 DOI: 10.1016/j.micres.2019.126356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.
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Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Babur S Mirza
- Missouri State University, Biology Department, Springfield, MO 65897, USA
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Ahmad Zaheer
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan; Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Fathia Mubeen
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Joan E Mclean
- Utah Water Research Laboratory, Utah State University, Logan, Utah, USA
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
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95
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Hashimoto S, Wongdee J, Songwattana P, Greetatorn T, Goto K, Tittabutr P, Boonkerd N, Teaumroong N, Uchiumi T. Homocitrate Synthase Genes of Two Wide-Host-Range Bradyrhizobium Strains are Differently Required for Symbiosis Depending on Host Plants. Microbes Environ 2019; 34:393-401. [PMID: 31597890 PMCID: PMC6934396 DOI: 10.1264/jsme2.me19078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nifV gene encodes homocitrate synthase, the enzyme that catalyzes the formation of homocitrate, which is essential for arranging the FeMo-cofactor in the catalytic center of nitrogenase. Some host plants, such as Lotus japonicus, supply homocitrate to their symbionts, in this case, Mesorhizobium loti, which lacks nifV. In contrast, Bradyrhizobium ORS285, a symbiont of Aeschynomene cross-inoculation (CI) groups 2 and 3, requires nifV for symbiosis with Aeschynomene species that belong to CI group 3, and some species belonging to CI group 2. However, it currently remains unclear whether rhizobial nifV is required for symbiosis with Aeschynomene species belonging to CI group 1 or with other legumes. We generated nifV-disruption (ΔnifV) mutants of two wide-host-range rhizobia, Bradyrhizobium SUTN9-2 and DOA9, to investigate whether they require nifV for symbiosis. Both ΔnifV mutant strains showed significantly less nitrogenase activity in a free-living state than the respective wild-type strains. The symbiotic phenotypes of SUTN9-2, DOA9, and their ΔnifV mutants were examined with four legumes, Aeschynomene americana, Stylosanthes hamata, Indigofera tinctoria, and Desmodium tortuosum. nifV was required for the efficient symbiosis of SUTN9-2 with A. americana (CI group 1), but not for that of DOA9. SUTN9-2 established symbiosis with all three other legumes; nifV was required for symbiosis with I. tinctoria and D. tortuosum. These results suggest that, in addition to Aeschynomene CI groups 2 and 3, CI group 1 and several other legumes require the rhizobial nifV for symbiosis.
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Affiliation(s)
- Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Kohki Goto
- Graduate School of Science and Engineering, Kagoshima University
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University
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96
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Teulet A, Busset N, Fardoux J, Gully D, Chaintreuil C, Cartieaux F, Jauneau A, Comorge V, Okazaki S, Kaneko T, Gressent F, Nouwen N, Arrighi JF, Koebnik R, Mergaert P, Deslandes L, Giraud E. The rhizobial type III effector ErnA confers the ability to form nodules in legumes. Proc Natl Acad Sci U S A 2019; 116:21758-68. [PMID: 31591240 DOI: 10.1073/pnas.1904456116] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Legumes have a tremendous ecological and agronomic importance due to their ability to interact symbiotically with nitrogen-fixing rhizobia. In most of the rhizobial–legume symbioses, the establishment of the interaction requires the plant perception of the bacterial lipochitooligosaccharide Nod factor signal. However, some bradyrhizobia can activate the symbiosis differently, thanks to their type III secretion system, which delivers effector proteins into the host cell. Here, we demonstrate that this symbiotic process relies on a small set of effectors playing distinct and complementary roles. Most remarkably, a nuclear-targeted effector named ErnA conferred the ability to form nodules. The understanding of this alternative pathway toward nitrogen-fixing symbiosis could pave the way for designing new strategies to transfer nodulation into cereals. Several Bradyrhizobium species nodulate the leguminous plant Aeschynomene indica in a type III secretion system-dependent manner, independently of Nod factors. To date, the underlying molecular determinants involved in this symbiotic process remain unknown. To identify the rhizobial effectors involved in nodulation, we mutated 23 out of the 27 effector genes predicted in Bradyrhizobium strain ORS3257. The mutation of nopAO increased nodulation and nitrogenase activity, whereas mutation of 5 other effector genes led to various symbiotic defects. The nopM1 and nopP1 mutants induced a reduced number of nodules, some of which displayed large necrotic zones. The nopT and nopAB mutants induced uninfected nodules, and a mutant in a yet-undescribed effector gene lost the capacity for nodule formation. This effector gene, widely conserved among bradyrhizobia, was named ernA for “effector required for nodulation-A.” Remarkably, expressing ernA in a strain unable to nodulate A. indica conferred nodulation ability. Upon its delivery by Pseudomonas fluorescens into plant cells, ErnA was specifically targeted to the nucleus, and a fluorescence resonance energy transfer–fluorescence lifetime imaging microscopy approach supports the possibility that ErnA binds nucleic acids in the plant nuclei. Ectopic expression of ernA in A. indica roots activated organogenesis of root- and nodule-like structures. Collectively, this study unravels the symbiotic functions of rhizobial type III effectors playing distinct and complementary roles in suppression of host immune functions, infection, and nodule organogenesis, and suggests that ErnA triggers organ development in plants by a mechanism that remains to be elucidated.
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97
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Belin BJ, Tookmanian EM, de Anda J, Wong GCL, Newman DK. Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis. Mol Plant Microbe Interact 2019; 32:1415-1428. [PMID: 31170026 PMCID: PMC7583662 DOI: 10.1094/mpmi-04-19-0111-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here, we demonstrate that the nitrogen-fixation defect conferred by extended hopanoid loss can be fully explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen-fixation levels. Using a single-nodule tracking approach to quantify A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and the presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
| | - Elise M. Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology
| | - Jaime de Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, and California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, U.S.A
| | - Gerard C. L. Wong
- Division of Geological & Planetary Sciences, California Institute of Technology
| | - Dianne K. Newman
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
- Division of Geological & Planetary Sciences, California Institute of Technology
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98
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Bai H, Zhang Y, Yu H, Irfan M, Huang Y, Han M, Yang J, Liu N, Wang H, Han X. Phylogenetic diversity and cross-inoculation of indigenous isolated Bradyrhizobium from nodules of peanut in Liaoning province of China. Mol Biol Res Commun 2019; 8:59-68. [PMID: 31531377 PMCID: PMC6715265 DOI: 10.22099/mbrc.2019.32983.1392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Arachis hypogaea. L is a legume of economic importance, which is nodulated by Bradyrhizobium, a slow-growing bacteria. However there is no well characterization of this rhizobia in many areas of China. In the present study, cross-inoculation experiments were performed in cowpea and soybean. The isolated bacteria strains were characterized physiologyically, biochemically and identified through 16S rDNA sequence analysis showing that it belongs to Bradyrhizobium japonicum. The genetic diversity of the seventeen isolated strains were assessed through PCR-RFLP of 16S rDNA and 16S-23S rDNA IGS region. Cross inoculation test indicated that isolates could nodulate cowpea but not soybean. The cluster analysis based on physiological and biochemical characteristics showed the lower correlation between isolates and sites. The isolates were grouped into four clusters based on 16S rDNA gene sequence analysis. Thirteen polymorphisms were variable across all observations in 16S rDNA RFLP and six different IGS types from isolates. The results implies that there was some association between geographical factor and phylogenetic diversity of indigenous Bradyrhizobium isolates.
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Affiliation(s)
- Hongzhi Bai
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Yanhua Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Haiqiu Yu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Muhammad Irfan
- Department of Biotechnology, University of Sargodha, Sargodha Pakistan
| | - Yuqian Huang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Mei Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Jinfeng Yang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Ning Liu
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Hui Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
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Sánchez C, Minamisawa K. Nitrogen Cycling in Soybean Rhizosphere: Sources and Sinks of Nitrous Oxide (N 2O). Front Microbiol 2019; 10:1943. [PMID: 31497007 PMCID: PMC6712156 DOI: 10.3389/fmicb.2019.01943] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Nitrous oxide (N2O) is the third most important greenhouse gas after carbon dioxide and methane, and a prominent ozone-depleting substance. Agricultural soils are the primary anthropogenic source of N2O because of the constant increase in the use of industrial nitrogen (N) fertilizers. The soybean crop is grown on 6% of the world's arable land, and its production is expected to increase rapidly in the future. In this review, we summarize the current knowledge on N-cycle in the rhizosphere of soybean plants, particularly sources and sinks of N2O. Soybean root nodules are the host of dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Nodule decomposition is the main source of N2O in soybean rhizosphere, where soil organisms mediate the nitrogen transformations that produce N2O. This N2O is either emitted into the atmosphere or further reduced to N2 by the bradyrhizobial N2O reductase (N2OR), encoded by the nos gene cluster. The dominance of nos - indigenous populations of soybean bradyrhizobia results in the emission of N2O into the atmosphere. Hence, inoculation with nos + or nos ++ (mutants with enhanced N2OR activity) bradyrhizobia has proved to be promising strategies to reduce N2O emission in the field. We discussed these strategies, the molecular mechanisms underlying them, and the future perspectives to develop better options for global mitigation of N2O emission from soils.
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Affiliation(s)
- Cristina Sánchez
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Vincent B, Juillot F, Fritsch E, Klonowska A, Gerbert N, Acherar S, Grangeteau C, Hannibal L, Galiana A, Ducousso M, Jourand P. A leguminous species exploiting alpha- and beta-rhizobia for adaptation to ultramafic and volcano-sedimentary soils: an endemic Acacia spirorbis model from New Caledonia. FEMS Microbiol Ecol 2019; 95:5524360. [PMID: 31247638 DOI: 10.1093/femsec/fiz099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
Acacia spirorbis subsp. spirorbis Labill. is a widespread tree legume endemic to New Caledonia that grows in ultramafic (UF) and volcano-sedimentary (VS) soils. The aim of this study was to assess the symbiotic promiscuity of A. spirorbis with nodulating and nitrogen-fixing rhizobia in harsh edaphic conditions. Forty bacterial strains were isolated from root nodules and characterized through (i) multilocus sequence analyses, (ii) symbiotic efficiency and (iii) tolerance to metals. Notably, 32.5% of the rhizobia belonged to the Paraburkholderia genus and were only found in UF soils. The remaining 67.5%, isolated from both UF and VS soils, belonged to the Bradyrhizobium genus. Strains of the Paraburkholderia genus showed significantly higher nitrogen-fixing capacities than those of Bradyrhizobium genus. Strains of the two genera isolated from UF soils showed high metal tolerance and the respective genes occurred in 50% of strains. This is the first report of both alpha- and beta-rhizobia strains associated to an Acacia species adapted to UF and VS soils. Our findings suggest that A. spirorbis is an adaptive plant that establishes symbioses with whatever rhizobia is present in the soil, thus enabling the colonization of contrasted ecosystems.
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Affiliation(s)
- Bryan Vincent
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Farid Juillot
- IRD, IMPMC UMR206, 98848 Nouméa Cedex, New Caledonia
| | | | - Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Noëmie Gerbert
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Sarah Acherar
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Cedric Grangeteau
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Laure Hannibal
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Antoine Galiana
- CIRAD, LSTM UMR082, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Marc Ducousso
- CIRAD, LSTM UMR082, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | - Philippe Jourand
- IRD, LSTM UMR040, TA A-82/J, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
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