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Claassens R, Venter SN, Beukes CW, Stępkowski T, Chan WY, Steenkamp ET. Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa. Syst Appl Microbiol 2023; 46:126452. [PMID: 37634485 DOI: 10.1016/j.syapm.2023.126452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.
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Affiliation(s)
- Ricu Claassens
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | | | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa; Right to Care, Centurion, Gauteng, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa.
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New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia. Int J Microbiol 2022; 2022:4623713. [PMID: 35637770 PMCID: PMC9148247 DOI: 10.1155/2022/4623713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes' taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.
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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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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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Culture-independent assessment of the diazotrophic Bradyrhizobium communities in the Pampa and Atlantic Forest Biomes localities in southern Brazil. Syst Appl Microbiol 2021; 44:126228. [PMID: 34265499 DOI: 10.1016/j.syapm.2021.126228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communities inhabiting soils in southern Brazil. The majority of nifD sequences were generated from DNA isolated from tropical-lowland pasture soils, although some soil samples originated from the Campos de Cima da Serra volcanic plateau. In the nifD tree, all the bradyrhizobial sequences comprised 38 clades, including 18 new clades. The sequences generated in this study were resolved into 22 clades and 21 singletons. The nifD bradyrhizobial assemblage contained Azorhizobium and α-proteobacterial methylotrophic genera, suggesting that these genera may have acquired their nif loci from Bradyrhizobium donors. The most common in the lowland pasture soils subclade III.3D branch comprises the isolates of mainly an American origin. On the other hand, subclade III.4, which was earlier detected in Brazil among Bradyrhizobium isolates nodulating native lupins, appears more common in the Campos de Cima da Serra soils. The second-largest group, Clade XXXVIII, has not yet been reported in culture-dependent studies, while another common group called Clade I represents a symbiovar predominating in Australia. The identification of the diverse nifD Clade I haplotypes in the tropical-lowland pastures infested by Australian Acacia spp implies that the introduction of these legumes to southern Brazil has resulted in the dissemination of their bradyrhizobial symbionts.
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Lamin H, Alami S, Lamrabet M, Bouhnik O, Bennis M, Abdelmoumen H, Bedmar EJ, Missbah-El Idrissi M. Bradyrhizobium sp. sv. retamae nodulates Retama monosperma grown in a lead and zinc mine tailings in Eastern Morocco. Braz J Microbiol 2021; 52:639-649. [PMID: 33447935 PMCID: PMC8105474 DOI: 10.1007/s42770-021-00420-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022] Open
Abstract
The aim of this work was to characterize and identify some bacteria isolated from the root nodules of Retama monosperma grown in Sidi Boubker lead and zinc mine tailings. Very few root nodules were obtained on the root nodules of R. monosperma grown in these soils. The three bacteria isolated from the root nodules were tolerant in vitro to different concentrations of heavy metals, including lead and zinc. The rep-PCR experiments showed that the three isolates have different molecular fingerprints and were considered as three different strains. The analysis of their 16S rRNA gene sequences proved their affiliation to the genus Bradyrhizobium. The analysis and phylogeny of the housekeeping genes atpD, glnII, gyrB, recA, and rpoB confirmed that the closest species was B. valentinum with similarity percentages of 95.61 to 95.82%. The three isolates recovered from the root nodules were slow-growing rhizobia capable to renodulate their original host plant in the presence of Pb-acetate. They were able to nodulate R. sphaerocarpa and Lupinus luteus also but not Glycine max or Phaseolus vulgaris. The phylogeny of the nodA and nodC nodulation genes as well as the nifH gene of the three strains showed that they belong to the symbiovar retamae of the genus Bradyrhizobium. The three strains isolated could be considered for use as inoculum for Retama plants before use in phytoremediation experiments.
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Affiliation(s)
- Hanane Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Soufiane Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080, Granada, Spain
| | - Mustapha Missbah-El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco.
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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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Oren A. Prokaryotic names: the bold and the beautiful. FEMS Microbiol Lett 2020; 367:5854537. [PMID: 32510563 DOI: 10.1093/femsle/fnaa096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/05/2020] [Indexed: 11/14/2022] Open
Abstract
In recent years, names of ∼170 new genera and ∼1020 new species were added annually to the list of prokaryotic names with standing in the nomenclature. These names were formed in accordance with the Rules of the International Code of Nomenclature of Prokaryotes. Most of these names are not very interesting as specific epithets and word elements from existing names are repeatedly recycled. The rules of the Code provide many opportunities to create names in far more original ways. A survey of the lists of names of genera and species of prokaryotes shows that there is no lack of interesting names. The annotated selection presented here proves that at least some authors have exploited the possibilities allowed by the rules of the Code to name novel organisms in ways that are more attractive. I here call upon all colleagues who describe new taxa to devote more thought to the naming of new genera and species. It takes some effort, and it requires proper use of the lexicon of Classical Greek and Latin as well as an understanding of the Code and the guidelines of its orthography appendix. Creation of attractive names will boost the general interest in prokaryotic nomenclature.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
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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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Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species. Syst Appl Microbiol 2020; 43:126053. [PMID: 31937424 DOI: 10.1016/j.syapm.2020.126053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 01/01/2023]
Abstract
Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.
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Klepa MS, Urquiaga MCDO, Somasegaran P, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium niftali sp. nov., an effective nitrogen-fixing symbiont of partridge pea [Chamaecrista fasciculata (Michx.) Greene], a native caesalpinioid legume broadly distributed in the USA. Int J Syst Evol Microbiol 2019; 69:3448-3459. [DOI: 10.1099/ijsem.0.003640] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
| | - Maria Clara de Oliveira Urquiaga
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, 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
| | | | - Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
| | - Mariangela Hungria
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, 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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Draft Genome Sequence of Bradyrhizobium elkanii Strain SEMIA 938, Used in Commercial Inoculants for Lupinus spp. in Brazil. Microbiol Resour Announc 2019; 8:8/28/e00546-19. [PMID: 31296682 PMCID: PMC6624765 DOI: 10.1128/mra.00546-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Due to its high capacity for nitrogen fixation, strain SEMIA 938 is used in commercial inoculants for lupins in Brazil. Its genome was estimated at 8,780,064 bp and indicates that it belongs to the Bradyrhizobium elkanii species, while the analysis of nodulation genes classifies the strain in the symbiovar sojae. Due to its high capacity for nitrogen fixation, strain SEMIA 938 is used in commercial inoculants for lupins in Brazil. Its genome was estimated at 8,780,064 bp and indicates that it belongs to the Bradyrhizobium elkanii species, while the analysis of nodulation genes classifies the strain in the symbiovar sojae.
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Klepa MS, Ferraz Helene LC, O’Hara G, Hungria M. Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia. Int J Syst Evol Microbiol 2019; 71:004742. [PMID: 33709900 PMCID: PMC8375429 DOI: 10.1099/ijsem.0.004742] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 01/16/2023] Open
Abstract
Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean (Glycine max) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains-CNPSo 4010T, CNPSo 4016T, and CNPSo 4019T-trapped from Western Australian soils with Glycine clandestina, Glycine tabacina and Glycine max, respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010T and CNPSo 4016T had Bradyrhizobium yuanmingense CCBAU 10071T as the closest species, whereas strain CNPSo 4019T was closer to Bradyrhizobium liaoningense LMG 18230T. The multilocus sequence analysis (MLSA) with five housekeeping genes-dnaK, glnII, gyrB, recA and rpoB-confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA-DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010T and CNPSo 4019T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense, respectively, while strain CNPSo 4016T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium. We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010T (=WSM 4802T=LMG 31645T) isolated from Glycine clandestina, Bradyrhizobium glycinis sp. nov. for CNPSo 4016T (=WSM 4801T=LMG 31649T) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019T (=WSM 4799T=LMG 31650T) isolated from G. max.
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Affiliation(s)
- Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970, 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
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, 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
| | - Graham O’Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, 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
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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Insights into the Phylogeny, Nodule Function, and Biogeographic Distribution of Microsymbionts Nodulating the Orphan Kersting's Groundnut [ Macrotyloma geocarpum (Harms) Marechal & Baudet] in African Soils. Appl Environ Microbiol 2019; 85:AEM.00342-19. [PMID: 30952658 PMCID: PMC6532025 DOI: 10.1128/aem.00342-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/23/2019] [Indexed: 02/06/2023] Open
Abstract
Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date there is little information on the phylogeny and functional traits of its microsymbionts, aspects that are much needed for its conservation and improvement. This study explored the morphogenetic diversity, phylogenetic relationships, and N2-fixing efficiency of Kersting's groundnut rhizobial isolates from contrasting environments in Ghana, South Africa, and Mozambique. BOX-PCR fingerprinting revealed high diversity among the rhizobial populations, which was influenced by geographic origin. Of the 164 isolates evaluated, 130 BOX-PCR types were identified at a 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA genes and multilocus sequence analysis of protein-coding genes (atpD, glnII, gyrB, and rpoB) and symbiotic genes (nifH and nodC) showed that Kersting's groundnut is primarily nodulated by members of the genus Bradyrhizobium, which are closely related to Bradyrhizobium vignae 7-2T, Bradyrhizobium kavangense 14-3T, Bradyrhizobium subterraneum 58-2-1T, Bradyrhizobium pachyrhizi PAC48T, the type strain of Bradyrhizobium elkanii, and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N2 fixation and induced greater nodulation, leaf chlorophyll concentration, and photosynthetic rates in their homologous host than did the 5 mM KNO3-fed plants and/or the commercial Bradyrhizobium sp. strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing.IMPORTANCE Rhizobia play important roles in agroecosystems, where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the microsymbionts nodulating Kersting's groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N2-fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of microsymbionts nodulating a neglected cultivated legume and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting's groundnut found in this study offers an opportunity for future studies to properly describe, characterize, and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.
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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: 26] [Impact Index Per Article: 5.2] [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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Martins da Costa E, Soares de Carvalho T, Azarias Guimarães A, Ribas Leão AC, Magalhães Cruz L, de Baura VA, Lebbe L, Willems A, de Souza Moreira FM. Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici). Braz J Microbiol 2019; 50:335-345. [PMID: 30759310 DOI: 10.1007/s42770-019-00045-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022] Open
Abstract
Cowpea (Vigna unguiculata L.) is a legume species that considerably benefits from inoculation with nitrogen fixing bacteria of the genus Bradyrhizobium. One of the strains recommended for inoculation in cowpea in Brazil is UFLA03-84 (Bradyrhizobium sp.). The aim of our study was to define the taxonomic position of the UFLA03-84 strain and of two other strains of Bradyrhizobium (UFLA03-144 and INPA237B), all belonging to the same phylogenetic group and isolated from soils of the Brazilian Amazon. Multilocus sequence analysis (MLSA) of the housekeeping genes atpD, gyrB, recA, and rpoB grouped (with similarity higher than 99%) the three strains with Bradyrhizobium viridifuturi SEMIA 690T. The analyses of average nucleotide identity and digital DNA-DNA hybridization supported classification of the group as Bradyrhizobium viridifuturi. The three strains exhibited similar behavior in relation to the most of the phenotypic characteristics evaluated. However, some characteristics exhibited variation, indicating phenotypic diversity within the species. Phylogenetic analysis of the nodC and nifH genes showed that the three strains are members of the same symbiovar (tropici) that contains type strains of Bradyrhizobium species coming from tropical soils (SEMIA 690TB. viridifuturi, CNPSo 1112TB. tropiciagri, CNPSo 2833TB. embrapense, and B. brasilense UFLA03-321T).
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Affiliation(s)
- Elaine Martins da Costa
- Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil.,Universidade Federal do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | | | | | - Aniele Carolina Ribas Leão
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Leonardo Magalhães Cruz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Liesbeth Lebbe
- Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
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Cordeiro AB, Ribeiro RA, Helene LCF, Hungria M. Rhizobium esperanzae sp. nov., a N 2 -fixing root symbiont of Phaseolus vulgaris from Mexican soils. Int J Syst Evol Microbiol 2017; 67:3937-3945. [DOI: 10.1099/ijsem.0.002225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrey Barbosa Cordeiro
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- 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, 70040-020, Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020, Brasília, Distrito Federal, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399 T, Isolated from Nodules of Deguelia costata in Brazil. GENOME ANNOUNCEMENTS 2017; 5:5/36/e00943-17. [PMID: 28883142 PMCID: PMC5589536 DOI: 10.1128/genomea.00943-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SEMIA 6399T is the type strain of Bradyrhizobium mercantei, a nitrogen-fixing symbiont of Deguelia costata. Its draft genome contains 8,842,857 bp with 8,246 predicted coding sequences (CDS), several related to amino acids and derivatives and to stress tolerance, with an emphasis on oxidative stress, in addition to symbiotic genes.
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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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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485-2494. [PMID: 28771120 DOI: 10.1099/ijsem.0.002144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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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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Helene LCF, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001870] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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
- 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
| | - Jakeline Renata Marçon Delamuta
- 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
| | - 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
- 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
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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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: 136] [Impact Index Per Article: 19.4] [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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Delamuta JRM, Ribeiro RA, Gomes DF, Souza RC, Chueire LMO, Hungria M. Genome sequence of Bradyrhizobium embrapense strain CNPSo 2833 T, isolated from a root nodule of Desmodium heterocarpon. Braz J Microbiol 2017; 48:9-10. [PMID: 27818093 PMCID: PMC5220625 DOI: 10.1016/j.bjm.2016.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/23/2016] [Indexed: 11/16/2022] Open
Abstract
Bradyrhizobium embrapense CNPSo 2833T is a nitrogen-fixing symbiont of the legume pasture Desmodium. Its draft genome contains 8,267,832 bp and 7876 CDSs. The symbiotic island includes nodulation and nitrogen fixation genes resembling the operon organization of B. japonicum. Several CDSs related to secretion proteins and stress tolerance were also identified.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, Londrina, PR, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Brasília, DF, Brazil
| | | | - Douglas Fabiano Gomes
- Embrapa Soja, Londrina, PR, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Brasília, DF, Brazil
| | - Renata Carolini Souza
- Embrapa Soja, Londrina, PR, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Brasília, DF, Brazil
| | | | - Mariangela Hungria
- Embrapa Soja, Londrina, PR, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Brasília, DF, Brazil.
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Ramírez-Bahena MH, Flores-Félix JD, Chahboune R, Toro M, Velázquez E, Peix A. Bradyrhizobium centrosemae (symbiovar centrosemae) sp. nov., Bradyrhizobium americanum (symbiovar phaseolarum) sp. nov. and a new symbiovar (tropici) of Bradyrhizobium viridifuturi establish symbiosis with Centrosema species native to America. Syst Appl Microbiol 2016; 39:378-83. [DOI: 10.1016/j.syapm.2016.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/30/2016] [Accepted: 06/03/2016] [Indexed: 11/26/2022]
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Delamuta JRM, Ribeiro RA, Araújo JLS, Rouws LFM, Zilli JÉ, Parma MM, Melo IS, Hungria M. Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp. Int J Syst Evol Microbiol 2016; 66:3078-3087. [DOI: 10.1099/ijsem.0.001148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, 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
| | | | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, C.P. 74.505, 23891-000 Seropédica, Rio de Janeiro, Brazil
| | | | | | - Mariangela Hungria
- 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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Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446
T
, a Nitrogen-Fixing Symbiont of the Legume Pasture
Stylosanthes guianensis. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00631-16. [PMID: 27365354 PMCID: PMC4929517 DOI: 10.1128/genomea.00631-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bradyrhizobium stylosanthis BR 446T is a nitrogen-fixing symbiont of the tropical legume pasture Stylosanthes guianensis. Its draft genome contains 8,801,717 bp and 8,239 coding sequences (CDSs). Several putative genes that might confer high competitiveness and saprophytic capacity under the stressful conditions of tropical soils were identified in the genome.
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Genome Sequence of Bradyrhizobium viridifuturi Strain SEMIA 690T, a Nitrogen-Fixing Symbiont of Centrosema pubescens. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01481-15. [PMID: 26679590 PMCID: PMC4683235 DOI: 10.1128/genomea.01481-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SEMIA 690T is a nitrogen-fixing symbiont of Centrosema pubescens, and comprises the recently described species Bradyrhizobium viridifuturi. Its draft genome indicates that it belongs to the Bradyrhizobium elkanii superclade. SEMIA 690T carries two copies of the regulatory nodD gene, and the nod and nif operons resemble those of Bradyrhizobium diazoefficiens.
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