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Cao K, Chen J, Li Q, Gu P, Li L, Huang R. Bacteria from nodules of Abrus mollis Hance: genetic diversity and screening of highly efficient growth-promoting strains. Front Microbiol 2024; 15:1345000. [PMID: 38680912 PMCID: PMC11045970 DOI: 10.3389/fmicb.2024.1345000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/21/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Abrus mollis Hance. (AM) is an important species used in southern Chinese medicine. It is mainly found in Guangdong and Guangxi provinces in China, and it is effective in the treatment of hepatitis. Endophytic bacteria are known to affect the growth and quality of medicinal plants. However, there are limited reports describing endophytic bacteria related to AM. Methods In the present study, Illumina-based 16S rRNA gene sequencing was used to investigate the endophytic bacterial communities of root nodules of AM at five sampling sites in Guangxi. In addition, 179 strains of endophytic bacteria were isolated and categorized into 13 haplotypes based on recA sequence analysis. Results The phylogeny of the 16S rRNA gene sequences revealed a predominance of nonrhizobial endophytes. Microbial diversity analysis showed that Proteobacteria was the dominant phylum in all samples, while Bradyrhizobium was the dominant genus in different samples. An efficient strain, Rhizobium tropici FM-19, was screened and obtained through greenhouse experiments. The AM plants inoculated with this strain showed the best growth performance and high nitrogen fixation and nodulation capacity. Notably, total phenols and total flavonoids, important active components in AM, increased by 30.9 and 42.7%, respectively, after inoculation with Rhizobium tropici FM-19. Discussion This study provides insights into the complex microbial diversity of AM nodules and provides strain information for the efficient cultivation of AM.
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Affiliation(s)
- Kexin Cao
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Jianhua Chen
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Qiuling Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Peng Gu
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Liangbo Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Rongshao Huang
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
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2
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Zarrabian M, Montiel J, Sandal N, Ferguson S, Jin H, Lin YY, Klingl V, Marín M, James EK, Parniske M, Stougaard J, Andersen SU. A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1006-1017. [PMID: 35852471 DOI: 10.1094/mpmi-06-22-0124-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mohammad Zarrabian
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico. Cuernavaca, Mexico
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Yen-Yu Lin
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Verena Klingl
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Macarena Marín
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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3
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Klepa MS, Helene LCF, O´Hara G, Hungria M. Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium
is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains – CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T – previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the
Bradyrhizobium elkanii
supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes – atpD, dnaK, glnII, gyrB, recA and rpoB – did not cluster the strains under study as conspecific to any described
Bradyrhizobium
species. Average nucleotide identity and digital DNA–DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed
Bradyrhizobium
species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.
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Affiliation(s)
- 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
| | - 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
| | - Graham O´Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- 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
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4
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Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z. Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica. Syst Appl Microbiol 2022; 45:126337. [DOI: 10.1016/j.syapm.2022.126337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
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5
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Tasiya T, van Zyl E, Coetzee MPA, Stepkowski T, Venter SN, Steenkamp ET. Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns. Mol Phylogenet Evol 2021; 167:107338. [PMID: 34757168 DOI: 10.1016/j.ympev.2021.107338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321T and Bradyrhizobium ivorense CI-1BT, while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BBT (SARCC 730T = LMG 31409T), Bradyrhizobium oropedii sp. nov. Pear76T (SARCC 731T = LMG 31408T), and Bradyrhizobium altum sp. nov. Pear77T (SARCC 754T = LMG 31407T) to accommodate three novel species, all of which are symbionts of legumes in South Africa.
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Affiliation(s)
- Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa
| | - Taponeswa Tasiya
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stepkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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6
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Rhem MFK, Silva VC, Dos Santos JMF, Zilli JÉ, James EK, Fragomeni Simon M, Gross E. The large mimosoid genus Inga Mill. (tribe Ingeae, Caesalpinioideae) is nodulated by diverse Bradyrhizobium strains in its main centers of diversity in Brazil. Syst Appl Microbiol 2021; 44:126268. [PMID: 34649028 DOI: 10.1016/j.syapm.2021.126268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/11/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Inga (Caesalpinioideae) is the type genus of the Ingeae tribe in the mimosoid clade. It comprises about 300 species, all trees or treelets, and has an exclusively neotropical distribution, with Brazil as its main center of diversity. In this study, we analyzed the diversity of 40 strains of rhizobia isolated from root nodules collected from ten species of Inga belonging to different types of vegetation in Brazil. Sequences of their housekeeping genes (dnaK, recA, rpoB, gyrB and glnII), 16S rRNA genes, internal transcribed spacer (ITS) regions, as well as their symbiosis-essential genes (nodC and nifH) were used to characterize them genetically. The ability of the rhizobia to form nodules on Inga spp., and on the promiscuous legume siratro (Macroptilium atropurpureum) was also evaluated. A multilocus sequence analysis (MLSA) combined with an analysis of the ITS region showed that the isolates were distributed into four main groups (A-D) within the large genus Bradyrhizobium. Analysis of the nodC and nifH genes showed that the isolates formed a separate branch from all described species of Bradyrhizobium, except for B. ingae. Most of the tested isolates formed nodules on siratro and all isolates tested nodulated Inga spp. Our results suggest a unique co-evolutionary history of Bradyrhizobium and Inga and demonstrate the existence of potential new species of microsymbionts nodulating this important and representative genus of leguminous tree from the Caesalpinioideae mimosoid clade.
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Affiliation(s)
| | - Verônica Cordeiro Silva
- Programa de Pós-Graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | | | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - Eduardo Gross
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.
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7
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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] [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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8
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Dabo M, Jaiswal SK, Dakora FD. Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils. FEMS Microbiol Ecol 2020; 95:5490326. [PMID: 31095296 PMCID: PMC6531793 DOI: 10.1093/femsec/fiz067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/14/2019] [Indexed: 01/19/2023] Open
Abstract
The legume host and soil environment play a major role in establishing effective symbiosis with diverse rhizobia for plant growth promotion and nodule formation. The aim of this study was to assess the morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that the isolates were highly diverse in their appearance on yeast mannitol agar plates. The isolates tested also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml−1 and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis showed that soil pH and mineral nutrients significantly influenced bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient which resulted in 45 unique BOX-types. Phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic gene phylogenies suggested that the isolates’ sym loci probably relates to the isolates’ geographical origin. The results indicated that geographical origin did affect the isolates’ phylogenetic placement and could be the basis for allopatric speciation
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Affiliation(s)
- Mamadou Dabo
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
| | - Sanjay K Jaiswal
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
| | - Felix D Dakora
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
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9
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Identification of Bradyrhizobium elkanii USDA61 Type III Effectors Determining Symbiosis with Vigna mungo. Genes (Basel) 2020; 11:genes11050474. [PMID: 32349348 PMCID: PMC7291247 DOI: 10.3390/genes11050474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Bradyrhizobium elkanii USDA61 possesses a functional type III secretion system (T3SS) that controls host-specific symbioses with legumes. Here, we demonstrated that B. elkanii T3SS is essential for the nodulation of several southern Asiatic Vigna mungo cultivars. Strikingly, inactivation of either Nod factor synthesis or T3SS in B. elkanii abolished nodulation of the V. mungo plants. Among the effectors, NopL was identified as a key determinant for T3SS-dependent symbiosis. Mutations of other effector genes, such as innB, nopP2, and bel2-5, also impacted symbiotic effectiveness, depending on host genotypes. The nopL deletion mutant formed no nodules on V. mungo, but infection thread formation was still maintained, thereby suggesting its pivotal role in nodule organogenesis. Phylogenetic analyses revealed that NopL was exclusively conserved among Bradyrhizobium and Sinorhizobium (Ensifer) species and showed a different phylogenetic lineage from T3SS. These findings suggest that V. mungo evolved a unique symbiotic signaling cascade that requires both NFs and T3Es (NopL).
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10
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol 2020; 70:2937-2948. [PMID: 32242793 DOI: 10.1099/ijsem.0.004124] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95-96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria. As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.
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Affiliation(s)
- Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Brian P Hedlund
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Fossou RK, Pothier JF, Zézé A, Perret X. Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d'Ivoire. Int J Syst Evol Microbiol 2020; 70:1421-1430. [PMID: 32122457 PMCID: PMC7397250 DOI: 10.1099/ijsem.0.003931] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d’Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1BT, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) genes placed these nodule isolates in a separate lineage from current species of the B. elkanii super clade. In phylogenetic analyses of single and concatenated partial dnaK, glnII, gyrB, recA and rpoB sequences, the C. cajan isolates again formed a separate lineage, with strain CI-1BT sharing the highest sequence similarity (95.2 %) with B. tropiciagri SEMIA 6148T. Comparative genomic analyses corroborated the novel species status, with 86 % ANIb and 89 % ANIm as the highest average nucleotide identity (ANI) values with B. elkanii USDA 76T. Although CI-1BT, CI-14A, CI-19D and CI-41S shared similar phenotypic and metabolic properties, growth of CI-41S was slower in/on various media. Symbiotic efficacy varied significantly between isolates, with CI-1BT and CI-41S scoring on the C. cajan ‘Light-Brown’ landrace as the most and least proficient bacteria, respectively. Also proficient on Vigna radiata (mung bean), Vigna unguiculata (cowpea, niébé) and additional C. cajan cultivars, CI-1BT represents a potential bioinoculant adapted to local soil conditions and capable of fostering the growth of diverse legume crops in Côte d'Ivoire. Given the data presented here, we propose the 19 C. cajan isolates to belong to a novel species called Bradyrhizobium ivorense sp. nov., with CI-1BT (=CCOS 1862T=CCMM B1296T) as a type strain.
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Affiliation(s)
- Romain K Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire.,Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Xavier Perret
- Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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Bradyrhizobium uaiense sp. nov., a new highly efficient cowpea symbiont. Arch Microbiol 2020; 202:1135-1141. [DOI: 10.1007/s00203-020-01827-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 12/24/2022]
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14
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Bouznif B, Guefrachi I, Rodríguez de la Vega RC, Hungria M, Mars M, Alunni B, Shykoff JA. Phylogeography of the Bradyrhizobium spp. Associated With Peanut, Arachis hypogaea: Fellow Travelers or New Associations? Front Microbiol 2019; 10:2041. [PMID: 31551977 PMCID: PMC6737463 DOI: 10.3389/fmicb.2019.02041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
Legume plants have colonized almost all terrestrial biotopes. Their ecological success is partly due to the selective advantage provided by their symbiotic association with nitrogen-fixing bacteria called rhizobia, which allow legumes to thrive on marginal lands and nitrogen depleted soils where non-symbiotic plants cannot grow. Additionally, their symbiotic capacities result in a high protein content in their aerial parts and seeds. This interesting nutritional value has led to the domestication and agricultural exploitation of several legumes grown for seeds and/or fodder for human and domestic animal consumption. Several cultivated legume species are thus grown far beyond their natural geographic range. Other legume species have become invasives, spreading into new habitats. The cultivation and establishment of legume species outside of their original range requires either that they are introduced or cultivated along with their original symbiotic partner or that they find an efficient symbiotic partner in their introduced habitat. The peanut, Arachis hypogaea, a native of South America, is now cultivated throughout the world. This species forms root nodules with Bradyrhizobium, but it is unclear whether these came with the seeds from their native range or were acquired locally. Here we propose to investigate the phylogeography of Bradyrhizobium spp. associated with a number of different wild and cultivated legume species from a range of geographical areas, including numerous strains isolated from peanut roots across the areas of peanut cultivation. This will allow us to address the question of whether introduced/cultivated peanuts associate with bacteria from their original geographic range, i.e., were introduced together with their original bacterial symbionts, or whether they acquired their current associations de novo from the bacterial community within the area of introduction. We will base the phylogenetic analysis on sequence data from both housekeeping and core genes and a symbiotic gene (nif). Differences between the phylogenetic signal of symbiotic and non-symbiotic genes could result from horizontal transfer of symbiosis capacity. Thus this study will also allow us to elucidate the processes by which this symbiotic association has evolved within this group of Bradyrhizobium spp.
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Affiliation(s)
- Besma Bouznif
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Ibtissem Guefrachi
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | | | | | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Benoit Alunni
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Jacqui Anne Shykoff
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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15
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Ibny FYI, Jaiswal SK, Mohammed M, Dakora FD. Symbiotic effectiveness and ecologically adaptive traits of native rhizobial symbionts of Bambara groundnut (Vigna subterranea L. Verdc.) in Africa and their relationship with phylogeny. Sci Rep 2019; 9:12666. [PMID: 31477738 PMCID: PMC6718677 DOI: 10.1038/s41598-019-48944-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/13/2019] [Indexed: 11/09/2022] Open
Abstract
Bambara groundnut (Vigna subterranea L. Verdc.) is an indigenous, drought-tolerant, underutilized African food legume, with the ability to fix atmospheric N2 in symbiosis with soil bacteria called rhizobia. The aim of this study was to assess the morpho-physiological, symbiotic and phylogenetic characteristics of rhizobia nodulating Bambara groundnut in Ghana, Mali and South Africa. The morpho-physiologically diverse isolates tested were also found to exhibit differences in functional efficiency and phylogenetic positions. Based on Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR banding patterns, the isolates were grouped into eight major clusters. The concentrations of Ca, Na and K in soils had a significant (p ≤ 0.01) effect on the distribution of rhizobia. Though many isolates were symbiotically very effective, the effectiveness index varied markedly (p ≤ 0.05) among them. Moreover, the isolates also exhibited tolerance to a wide range of NaCl (0.5–7%), streptomycin (50–500 µg.ml−1), and kanamycin (25–150 µg.ml−1) concentrations. Additionally, these isolates could produce 0.02 to 69.71 µg.ml−1 of indole-3-acetic acid (IAA) in tryptophan-supplemented medium, as well as solubilize tri-calcium phosphate. Phylogenetic analysis of these rhizobial isolates using 16S rRNA, atpD, glnII, gyrB, recA and symbiotic (nifH and nodC) gene sequences revealed distinct and novel evolutionary lineages related to the genus Bradyrhizobium, with some of them being very close to Bradyrhizobium vignae, B. kavangense, B. subterraneum, B. elkanii and B. pachyrhizi.
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Affiliation(s)
- Fadimata Y I Ibny
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Sanjay K Jaiswal
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
| | - Mustapha Mohammed
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Felix D Dakora
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
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16
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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] [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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Ormeño-Orrillo E, Martínez-Romero E. A Genomotaxonomy View of the Bradyrhizobium Genus. Front Microbiol 2019; 10:1334. [PMID: 31263459 PMCID: PMC6585233 DOI: 10.3389/fmicb.2019.01334] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.
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Affiliation(s)
- Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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18
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Ramírez MDA, España M, Aguirre C, Kojima K, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T. Burkholderia and Paraburkholderia are Predominant Soybean Rhizobial Genera in Venezuelan Soils in Different Climatic and Topographical Regions. Microbes Environ 2019; 34:43-58. [PMID: 30773514 PMCID: PMC6440732 DOI: 10.1264/jsme2.me18076] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/25/2018] [Indexed: 11/12/2022] Open
Abstract
The climate, topography, fauna, and flora of Venezuela are highly diverse. However, limited information is currently available on the characterization of soybean rhizobia in Venezuela. To clarify the physiological and genetic diversities of soybean rhizobia in Venezuela, soybean root nodules were collected from 11 soil types located in different topographical regions. A total of 395 root nodules were collected and 120 isolates were obtained. All isolates were classified in terms of stress tolerance under different concentrations of NaCl and Al3+. The tolerance levels of isolates to NaCl and Al3+ varied. Based on sampling origins and stress tolerance levels, 44 isolates were selected for further characterization. An inoculation test indicated that all isolates showed the capacity for root nodulation on soybean. Based on multilocus sequence typing (MLST), 20 isolates were classified into the genera Rhizobium and Bradyrhizobium. The remaining 24 isolates were classified into the genus Burkholderia or Paraburkholderia. There is currently no evidence to demonstrate that the genera Burkholderia and Paraburkholderia are the predominant soybean rhizobia in agricultural fields. Of the 24 isolates classified in (Para) Burkholderia, the nodD-nodB intergenic spacer regions of 10 isolates and the nifH gene sequences of 17 isolates were closely related to the genera Rhizobium and Bradyrhizobium, respectively. The root nodulation numbers of five (Para) Burkholderia isolates were higher than those of the 20 α-rhizobia. Furthermore, among the 44 isolates tested, one Paraburkholderia isolate exhibited the highest nitrogen-fixation activity in root nodules.
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Affiliation(s)
- María Daniela Artigas Ramírez
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT)Saiwai-cho 3–5–8, Fuchu, Tokyo 183–8509Japan
| | | | | | - Katsuhiro Kojima
- Faculty of Agriculture, Tokyo University of Agriculture and Technology183–8509Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT)Saiwai-cho 3–5–8, Fuchu, Tokyo 183–8509Japan
| | - Hitoshi Sekimoto
- Faculty of Agriculture, Utsunomiya UniversityUtsunomiya 321–8505Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT)Saiwai-cho 3–5–8, Fuchu, Tokyo 183–8509Japan
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Jaiswal SK, Dakora FD. Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa. Front Microbiol 2019; 10:310. [PMID: 30853952 PMCID: PMC6395442 DOI: 10.3389/fmicb.2019.00310] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/05/2019] [Indexed: 11/17/2022] Open
Abstract
Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
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20
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Mohammed M, Jaiswal SK, Dakora FD. Distribution and correlation between phylogeny and functional traits of cowpea (Vigna unguiculata L. Walp.)-nodulating microsymbionts from Ghana and South Africa. Sci Rep 2018; 8:18006. [PMID: 30573737 PMCID: PMC6302100 DOI: 10.1038/s41598-018-36324-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/18/2018] [Indexed: 12/03/2022] Open
Abstract
Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species' ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A-F). Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, rpoB, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p < 0.05) correlation, which suggests that local environmental factors played a major role in the cowpea-Bradyrhizobium symbiosis.
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Affiliation(s)
- Mustapha Mohammed
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Sanjay K Jaiswal
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
| | - Felix D Dakora
- Chemistry Department, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
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21
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Ahnia H, Bourebaba Y, Durán D, Boulila F, Palacios JM, Rey L, Ruiz-Argüeso T, Boulila A, Imperial J. Bradyrhizobium algeriense sp. nov., a novel species isolated from effective nodules of Retama sphaerocarpa from Northeastern Algeria. Syst Appl Microbiol 2018; 41:333-339. [DOI: 10.1016/j.syapm.2018.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
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22
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and 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.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - 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.
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Bradyrhizobium forestalis sp. nov., an efficient nitrogen-fixing bacterium isolated from nodules of forest legume species in the Amazon. Arch Microbiol 2018; 200:743-752. [DOI: 10.1007/s00203-018-1486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 01/01/2023]
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Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique. Appl Environ Microbiol 2018; 84:AEM.01712-17. [PMID: 29101189 PMCID: PMC5752868 DOI: 10.1128/aem.01712-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/19/2017] [Indexed: 11/22/2022] Open
Abstract
Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes. IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.
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Molecular characterization of novel Bradyrhizobium strains nodulating Eriosema chinense and Flemingia vestita , important unexplored native legumes of the sub-Himalayan region (Meghalaya) of India. Syst Appl Microbiol 2017; 40:334-344. [DOI: 10.1016/j.syapm.2017.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022]
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26
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Araújo J, Flores-Félix JD, Igual JM, Peix A, González-Andrés F, Díaz-Alcántara CA, Velázquez E. Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan. Int J Syst Evol Microbiol 2017; 67:2236-2241. [PMID: 28671523 DOI: 10.1099/ijsem.0.001932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium, being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, 'Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA-DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense, 'Bradyrhizobium americanum' and Bradyrhizobium daqingense, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium. Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.
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Affiliation(s)
- Juan Araújo
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - César Antonio Díaz-Alcántara
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
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27
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Degefu T, Wolde-meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40:205-214. [DOI: 10.1016/j.syapm.2017.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
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Bradyrhizobium brasilense sp. nov., a symbiotic nitrogen-fixing bacterium isolated from Brazilian tropical soils. Arch Microbiol 2017; 199:1211-1221. [DOI: 10.1007/s00203-017-1390-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 12/22/2022]
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Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. Phylogenetic multilocus sequence analysis of indigenous slow-growing rhizobia nodulating cowpea ( Vigna unguiculata L.) in Greece. Syst Appl Microbiol 2017; 40:179-189. [DOI: 10.1016/j.syapm.2017.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/01/2022]
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Leite J, Passos SR, Simões-Araújo JL, Rumjanek NG, Xavier GR, Zilli JÉ. Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil. Braz J Microbiol 2017; 49:703-713. [PMID: 28410799 PMCID: PMC6175698 DOI: 10.1016/j.bjm.2017.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022] Open
Abstract
The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an “eco-friendly agricultural practice”. Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA–DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.
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Affiliation(s)
- Jakson Leite
- Departamento de Solos, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Samuel Ribeiro Passos
- Departamento de Ciências Ambientais, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Jean Luiz Simões-Araújo
- Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Norma Gouvêa Rumjanek
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Gustavo Ribeiro Xavier
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Jerri Édson Zilli
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil.
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil. Arch Microbiol 2017; 199:657-664. [DOI: 10.1007/s00203-017-1340-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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33
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Yu X, Li Y, Li Y, Xu C, Cui Y, Xiang Q, Gu Y, Zhao K, Zhang X, Penttinen P, Chen Q. Pongamia pinnata inoculated with Bradyrhizobium liaoningense PZHK1 shows potential for phytoremediation of mine tailings. Appl Microbiol Biotechnol 2016; 101:1739-1751. [DOI: 10.1007/s00253-016-7996-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/28/2016] [Accepted: 11/05/2016] [Indexed: 10/20/2022]
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35
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Beukes CW, Stępkowski T, Venter SN, Cłapa T, Phalane FL, le Roux MM, Steenkamp ET. Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci. Mol Phylogenet Evol 2016; 100:206-218. [DOI: 10.1016/j.ympev.2016.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
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36
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Naamala J, Jaiswal SK, Dakora FD. Antibiotics Resistance in Rhizobium: Type, Process, Mechanism and Benefit for Agriculture. Curr Microbiol 2016; 72:804-16. [DOI: 10.1007/s00284-016-1005-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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37
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Yang L, Poles MA, Fisch GS, Ma Y, Nossa C, Phelan JA, Pei Z. HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. AIDS 2016; 30:19-29. [PMID: 26731752 DOI: 10.1097/qad.0000000000000935] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To evaluate the impact of HIV infection on colonization resistance in the proximal gut. DESIGN It was a case-control study. METHODS We contrasted microbiota composition between eight HIV-1-infected patients and eight HIV-negative controls to characterize community alteration and detect exogenous bacteria in the esophagus, stomach, and duodenum, as well as the mouth using a universal 16s ribosomal RNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts. RESULTS HIV infection was associated with an enrichment of Proteobacteria (P=0.020) and depletion of Firmicutes (P = 0.005) in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4 T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 cell counts were normal. The two species coexisted and exhibited a decreasing trend proximally toward the stomach and esophagus and were virtually absent in the mouth. B. fungorum always outnumbered B. pachyrhizi in a ratio of approximately 15 to 1 regardless of the body sites (P < 0.0001, r = 0.965). Their abundance was inversely correlated with CD4 cell counts (P = 0.004) but not viral load. Overgrowth of potential opportunistic pathogens for example, Prevotella, Fusobacterium, and Ralstonia and depletion of beneficial bacteria, for example, Lactobacillus was also observed in HIV patients. CONCLUSIONS The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 cell counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes.
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Li YH, Wang R, Zhang XX, Young JPW, Wang ET, Sui XH, Chen WX. Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut. Int J Syst Evol Microbiol 2015; 65:4655-4661. [DOI: 10.1099/ijsem.0.000629] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.
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Affiliation(s)
- Yong Hua Li
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Rui Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | | | - En Tao Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Xin Hua Sui
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Wen Xin Chen
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
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Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Parma MM, Melo IS, Martínez-Romero E, Hungria M. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes. Int J Syst Evol Microbiol 2015; 65:4424-4433. [PMID: 26362866 DOI: 10.1099/ijsem.0.000592] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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40
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Tiwari R, Howieson J, Yates R, Tian R, Held B, Tapia R, Han C, Seshadri R, Reddy TBK, Huntemann M, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. Stand Genomic Sci 2015; 10:113. [PMID: 26629308 PMCID: PMC4665870 DOI: 10.1186/s40793-015-0115-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 11/25/2015] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L. princei, L. atlanticus, L. pilosus). In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71 contigs arranged into two scaffolds. The assembled genome contains 8,432 protein-coding genes, 66 RNA genes and a single rRNA operon. This improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE Joint Genome Institute 2010 Community Sequencing Project.
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Affiliation(s)
- Ravi Tiwari
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - John Howieson
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Ron Yates
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
- />Department of Agriculture and Food, South Perth, Australia
| | - Rui Tian
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Britanny Held
- />Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | - Roxanne Tapia
- />Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | - Cliff Han
- />Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | | | | | | | - Amrita Pati
- />DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- />DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Nikos Kyrpides
- />DOE Joint Genome Institute, Walnut Creek, CA USA
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
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Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01074-15. [PMID: 26383651 PMCID: PMC4574380 DOI: 10.1128/genomea.01074-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bradyrhizobium pachyrhizi PAC48T has been isolated from a jicama nodule in Costa Rica. The draft genome indicates high similarity with that of Bradyrhizobium elkanii. Several coding sequences (CDSs) of the stress response might help in survival in the tropics. PAC48T carries nodD1 and nodK, similar to Bradyrhizobium (Parasponia) ANU 289 and a particular nodD2 gene.
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42
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Azarias Guimarães A, Florentino LA, Alves Almeida K, Lebbe L, Barroso Silva K, Willems A, de Souza Moreira FM. High diversity of Bradyrhizobium strains isolated from several legume species and land uses in Brazilian tropical ecosystems. Syst Appl Microbiol 2015; 38:433-41. [DOI: 10.1016/j.syapm.2015.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
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43
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Peix A, Ramírez-Bahena MH, Flores-Félix JD, Alonso de la Vega P, Rivas R, Mateos PF, Igual JM, Martínez-Molina E, Trujillo ME, Velázquez E. Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov. Int J Syst Evol Microbiol 2015; 65:1213-1219. [DOI: 10.1099/ijs.0.000082] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species
Rhizobium lupini
was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140T, whose 16S rRNA gene was identical to that of the type strain of
Bradyrhizobium japonicum
,
R. lupini
was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140T belongs to the species
B. japonicum
, but also that it cannot be the original strain of
R. lupini
because this species effectively nodulated Lupinus whereas strain DSM 30140T was able to nodulate soybean but not Lupinus. Since the original type strain of
R. lupini
was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051T we analysed the taxonomic status of this strain showing that although it belongs to the genus
Bradyrhizobium
instead of genus
Rhizobium
, it is phylogenetically distant from
B. japonicum
and closely related to
Bradyrhizobium canariense
. The type strains
R. lupini
USDA 3051T and
B. canariense
BTA-1T share 16S rRNA, recA and glnII gene sequences with similarities of 99.8 %, 96.5 % and 97.1 %, respectively. They presented a DNA–DNA hybridization value of 36 % and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species
Rhizobium lupini
as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051T ( = CECT 8630T = LMG 28514T).
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Affiliation(s)
- Alvaro Peix
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Martha Helena Ramírez-Bahena
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - José David Flores-Félix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | | | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Pedro F. Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - José M. Igual
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
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Rodríguez-Navarro DN, Rodríguez-Carvajal MA, Acosta-Jurado S, Soto MJ, Margaret I, Crespo-Rivas JC, Sanjuan J, Temprano F, Gil-Serrano A, Ruiz-Sainz JE, Vinardell JM. Structure and biological roles of Sinorhizobium fredii HH103 exopolysaccharide. PLoS One 2014; 9:e115391. [PMID: 25521500 PMCID: PMC4270759 DOI: 10.1371/journal.pone.0115391] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/21/2014] [Indexed: 11/25/2022] Open
Abstract
Here we report that the structure of the Sinorhizobium fredii HH103 exopolysaccharide (EPS) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. A S. fredii HH103 exoA mutant (SVQ530), unable to produce EPS, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. Mutant SVQ530 is, however, less competitive to nodulate Vigna unguiculata. Biofilm formation was reduced in mutant SVQ530 but increased in an EPS overproducing mutant. Mutant SVQ530 was impaired in surface motility and showed higher osmosensitivity compared to its wild type strain in media containing 50 mM NaCl or 5% (w/v) sucrose. Neither S. fredii HH103 nor 41 other S. fredii strains were recognized by soybean lectin (SBL). S. fredii HH103 mutants affected in exopolysaccharides (EPS), lipopolysaccharides (LPS), cyclic glucans (CG) or capsular polysaccharides (KPS) were not significantly impaired in their soybean-root attachment capacity, suggesting that these surface polysaccharides might not be relevant in early attachment to soybean roots. These results also indicate that the molecular mechanisms involved in S. fredii attachment to soybean roots might be different to those operating in Bradyrhizobium japonicum.
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Affiliation(s)
| | | | | | - María J Soto
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Isabel Margaret
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Juan C Crespo-Rivas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Juan Sanjuan
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Francisco Temprano
- IFAPA, Centro las Torres-Tomejil, Apartado Oficial 41200, Alcalá del Río, (Sevilla), Spain
| | - Antonio Gil-Serrano
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
| | - José E Ruiz-Sainz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - José M Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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45
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Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity. Appl Environ Microbiol 2014; 80:7244-57. [PMID: 25239908 DOI: 10.1128/aem.02417-14] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/10/2014] [Indexed: 02/01/2023] Open
Abstract
The rhizobial community indigenous to the Okavango region has not yet been characterized. The isolation of indigenous rhizobia can provide a basis for the formulation of a rhizobial inoculant. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Isolates were obtained from nodules of local varieties of the pulses cowpea, Bambara groundnut, peanut, hyacinth bean, and common bean. Ninety-one of them were identified by BOX repetitive element PCR (BOX-PCR) and sequence analyses of the 16S-23S rRNA internally transcribed spacer (ITS) and the recA, glnII, rpoB, and nifH genes. A striking geographical distribution was observed. Bradyrhizobium pachyrhizi dominated at sampling sites in Angola which were characterized by acid soils and a semihumid climate. Isolates from the semiarid sampling sites in Namibia were more diverse, with most of them being related to Bradyrhizobium yuanmingense and Bradyrhizobium daqingense. Host plant specificity was observed only for hyacinth bean, which was nodulated by rhizobia presumably representing yet-undescribed species. Furthermore, the isolates were characterized with respect to their adaptation to high temperatures, drought, and local host plants. The adaptation experiments revealed that the Namibian isolates shared an exceptionally high temperature tolerance, but none of the isolates showed considerable adaptation to drought. Moreover, the isolates' performance on different local hosts showed variable results, with most Namibian isolates inducing better nodulation on peanut and hyacinth bean than the Angolan strains. The local predominance of distinct genotypes implies that indigenous strains may exhibit a better performance in inoculant formulations.
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46
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Genetic diversity and evolution of Bradyrhizobium populations nodulating Erythrophleum fordii, an evergreen tree indigenous to the southern subtropical region of China. Appl Environ Microbiol 2014; 80:6184-94. [PMID: 25085491 DOI: 10.1128/aem.01595-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia.
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47
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Durán D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argüeso T. Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. Syst Appl Microbiol 2014; 37:336-41. [DOI: 10.1016/j.syapm.2014.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 11/28/2022]
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48
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Durán D, Rey L, Mayo J, Zúñiga-Dávila D, Imperial J, Ruiz-Argüeso T, Martínez-Romero E, Ormeño-Orrillo E. Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru. Int J Syst Evol Microbiol 2014; 64:2072-2078. [DOI: 10.1099/ijs.0.060426-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of
Bradyrhizobium lablabi
CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus
Bradyrhizobium
. Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus
Bradyrhizobium
(≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus
Bradyrhizobium
were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.
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Affiliation(s)
- David Durán
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Luis Rey
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Juan Mayo
- Laboratorio de Ecología Microbiana y Biotecnología ‘Marino Tabusso’, Universidad Nacional Agraria La Molina, Peru
| | - Doris Zúñiga-Dávila
- Laboratorio de Ecología Microbiana y Biotecnología ‘Marino Tabusso’, Universidad Nacional Agraria La Molina, Peru
| | - Juan Imperial
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
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Cobo-Díaz JF, Martínez-Hidalgo P, Fernández-González AJ, Martínez-Molina E, Toro N, Velázquez E, Fernández-López M. The endemic Genista versicolor from Sierra Nevada National Park in Spain is nodulated by putative new Bradyrhizobium species and a novel symbiovar (sierranevadense). Syst Appl Microbiol 2014; 37:177-85. [DOI: 10.1016/j.syapm.2013.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022]
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50
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Wade TK, Le Quéré A, Laguerre G, N’Zoué A, Ndione JA, doRego F, Sadio O, Ndoye I, Neyra M. Eco-geographical diversity of cowpea bradyrhizobia in Senegal is marked by dominance of two genetic types. Syst Appl Microbiol 2014; 37:129-39. [DOI: 10.1016/j.syapm.2013.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 10/25/2022]
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