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van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
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Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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2
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Moura FT, Helene LCF, Ribeiro RA, Nogueira MA, Hungria M. The outstanding diversity of rhizobia microsymbionts of common bean (Phaseolus vulgaris L.) in Mato Grosso do Sul, central-western Brazil, revealing new Rhizobium species. Arch Microbiol 2023; 205:325. [PMID: 37659972 DOI: 10.1007/s00203-023-03667-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization. The phylogenetic tree of the 16S rRNA gene split the 13 strains into two large clades, seven in the R. etli and six in the R. tropici clade. The MLSA with four housekeeping genes (glnII, gyrB, recA, and rpoA) confirmed the phylogenetic allocation. Genomic comparisons indicated eight strains in five putative new species and the remaining five as R. phaseoli. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparing the putative new species and the closest neighbors ranged from 81.84 to 92.50% and 24.0 to 50.7%, respectively. Other phenotypic, genotypic, and symbiotic features were evaluated. Interestingly, some strains of both R. etli and R. tropici clades lost their nodulation capacity. The data support the description of the new species Rhizobium cerradonense sp. nov. (CNPSo 3464T), Rhizobium atlanticum sp. nov. (CNPSo 3490T), Rhizobium aureum sp. nov. (CNPSo 3968T), Rhizobium pantanalense sp. nov. (CNPSo 4039T), and Rhizobium centroccidentale sp. nov. (CNPSo 4062T).
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Affiliation(s)
- Fernanda Terezinha Moura
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70.040-020, Brazil
| | - Luisa Caroline Ferraz Helene
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
- Vittia Fertilizantes e Biológicos, São Joaquim da Barra, São Paulo, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Marco Antonio Nogueira
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Mariangela Hungria
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil.
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil.
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3
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Young JPW, Jorrin B, Moeskjær S, James EK. Rhizobium brockwellii sp. nov., Rhizobium johnstonii sp. nov. and Rhizobium beringeri sp. nov., three genospecies within the Rhizobium leguminosarum species complex. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486744 DOI: 10.1099/ijsem.0.005979] [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] [Indexed: 07/25/2023] Open
Abstract
Genomic evidence indicates that the
Rhizobium leguminosarum
species complex comprises multiple distinct species, perhaps 18 or more. Of the five earliest genospecies (gs) to be described, only two have formal names: R. leguminosarum sensu stricto (gsE) and
Rhizobium ruizarguesonis
(gsC). Here, we provide formal descriptions and names for the other three genospecies, based on the publicly available genome sequences for multiple strains of each species: Rhizobium brockwellii sp. nov. (gsA, 37 strains, type strain CC275eT=LMG 6122T = ICMP 2163T=NZP 561T = PDDCC 2163T=HAMBI 13T), Rhizobium johnstonii sp. nov. (gsB, 54 strains, type strain 3841T = LMG 32736T=DSM 114642T) and Rhizobium beringeri sp. nov. (gsD, 8 strains, type strain SM51T = LMG 32895T = DSM 115206T). Each species forms a well-supported clade in a phylogeny based on 120 concatenated core genes. All strains have average nucleotide identity (ANI) above 96 % with the relevant type strain and below 96 % with all other type strains. Each species is characterised by a number of genes that are absent or rare in other species.
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Affiliation(s)
- J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Beatriz Jorrin
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Sara Moeskjær
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Euan K James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Bouhnik O, Alami S, Lamin H, Lamrabet M, Bennis M, Ouajdi M, Bellaka M, Antri SE, Abbas Y, Abdelmoumen H, Bedmar EJ, Idrissi MME. The Fodder Legume Chamaecytisus albidus Establishes Functional Symbiosis with Different Bradyrhizobial Symbiovars in Morocco. MICROBIAL ECOLOGY 2022; 84:794-807. [PMID: 34625829 DOI: 10.1007/s00248-021-01888-4] [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] [Received: 06/28/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
In this work, we analyzed the symbiotic performance and diversity of rhizobial strains isolated from the endemic shrubby legume Chamaecytisus albidus grown in soils of three different agroforestry ecosystems representing arid and semi-arid forest areas in Morocco. The analysis of the rrs gene sequences from twenty-four representative strains selected after REP-PCR fingerprinting showed that all the strains belong to the genus Bradyrhizobium. Following multi-locus sequence analysis (MLSA) using the rrs, gyrB, recA, glnII, and rpoB housekeeping genes, five representative strains, CA20, CA61, CJ2, CB10, and CB61 were selected for further molecular studies. Phylogenetic analysis of the concatenated glnII, gyrB, recA, and rpoB genes showed that the strain CJ2 isolated from Sahel Doukkala soil is close to Bradyrhizobium canariense BTA-1 T (96.95%); that strains CA20 and CA61 isolated from the Amhach site are more related to Bradyrhizobium valentinum LmjM3T, with 96.40 and 94.57% similarity values; and that the strains CB10 and CB60 isolated from soil in the Bounaga site are more related to Bradyrhizobium murdochi CNPSo 4020 T and Bradyrhizobium. retamae Ro19T, with which they showed 95.45 and 97.34% similarity values, respectively. The phylogenetic analysis of the symbiotic genes showed that the strains belong to symbiovars lupini, genistearum, and retamae. All the five strains are able to nodulate Lupinus luteus, Retama monosperma, and Cytisus monspessilanus, but they do not nodulate Glycine max and Phaseolus vulgaris. The inoculation tests showed that the strains isolated from the 3 regions improve significantly the plant yield as compared to uninoculated plants. However, the strains of Bradyrhizobium sp. sv. retamae isolated from the site of Amhach were the most performing. The phenotypic analysis showed that the strains are able to use a wide range of carbohydrates and amino acids as sole carbon and nitrogen source. The strains isolated from the arid areas of Bounaga and Amhach were more tolerant to salinity and drought stress than strains isolated in the semi-arid area of Sahel Doukkala.
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Affiliation(s)
- Omar Bouhnik
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco.
| | - Soufiane Alami
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
| | - Hanane Lamin
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
| | - Mohammed Ouajdi
- Centre de Recherche Forestière, Département Des Eaux Et Forêts, Avenue Omar Ibn El KhattabAgdal, BP 763, 10050, Rabat, Morocco
| | - Mhammed Bellaka
- Centre de Recherche Forestière, Département Des Eaux Et Forêts, Avenue Omar Ibn El KhattabAgdal, BP 763, 10050, Rabat, Morocco
| | - Salwa El Antri
- Centre de Recherche Forestière, Département Des Eaux Et Forêts, Avenue Omar Ibn El KhattabAgdal, BP 763, 10050, Rabat, Morocco
| | - Younes Abbas
- Faculté Polydiciplinaire, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
| | - Eulogio J Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos Estación Experimental del Zaidín, CSIC Apartado Postal 419, Granada, 18008, Spain
| | - Mustapha Missbah El Idrissi
- Centre de Biotechnologies Végétale Et Microbienne, Biodiversité Et Environnement, Faculté Des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Agdal, BP 1014 RP, Rabat, Morocco
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5
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Mohamad R, Willems A, Le Quéré A, Prevent M, Maynaud G, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium ventifaucium sp. nov. and Mesorhizobium escarrei sp. nov., two novel root-nodulating species isolated from Anthyllis vulneraria. Syst Appl Microbiol 2022; 45:126341. [DOI: 10.1016/j.syapm.2022.126341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 10/18/2022]
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6
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Ferraz Helene LC, Klepa MS, Hungria M. 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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Affiliation(s)
- Luisa Caroline Ferraz Helene
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
| | - Milena Serenato Klepa
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, CP 10011, 86057-970 Londrina, PR, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020 Brasília, DF, Brazil
| | - Mariangela Hungria
- Embrapa Soja, CP 4006, 86085-981 Londrina, PR, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, CP 10011, 86057-970 Londrina, PR, Brazil
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7
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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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8
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Fields B, Moffat EK, Harrison E, Andersen SU, Young JPW, Friman VP. Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex. Environ Microbiol 2021; 24:3463-3485. [PMID: 34398510 DOI: 10.1111/1462-2920.15720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 12/01/2022]
Abstract
Competitive and facilitative interactions influence bacterial community composition, diversity and functioning. However, the role of genetic diversity for determining interactions between coexisting strains of the same, or closely related, species remains poorly understood. Here, we investigated the type (facilitative/inhibitory) and potential underlying mechanisms of pairwise interactions between 24 genetically diverse bacterial strains belonging to three genospecies (gsA,C,E) of the Rhizobium leguminosarum species complex. Interactions were determined indirectly, based on secreted compounds in cell-free supernatants, and directly, as growth inhibition in cocultures. We found supernatants mediated both facilitative and inhibitory interactions that varied greatly between strains and genospecies. Overall, gsE strains indirectly suppressed growth of gsA strains, while their own growth was facilitated by other genospecies' supernatants. Similar genospecies-level patterns were observed in direct competition, where gsA showed the highest susceptibility and gsE the highest inhibition capacity. At the genetic level, increased gsA susceptibility was associated with a non-random distribution of quorum sensing and secondary metabolite genes across genospecies. Together, our results suggest that genetic variation is associated with facilitative and competitive interactions, which could be important ecological mechanisms explaining R. leguminosarum diversity.
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Affiliation(s)
| | - Emma K Moffat
- Department of Biology, University of York, York, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Martins da Costa E, Almeida Ribeiro PR, Soares de Carvalho T, Pereira Vicentin R, Balsanelli E, Maltempi de Souza E, Lebbe L, Willems A, de Souza Moreira FM. Efficient Nitrogen-Fixing Bacteria Isolated from Soybean Nodules in the Semi-arid Region of Northeast Brazil are Classified as Bradyrhizobium brasilense (Symbiovar Sojae). Curr Microbiol 2020; 77:1746-1755. [PMID: 32322907 DOI: 10.1007/s00284-020-01993-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
Soybean (Glycine max L.) is an important legume that greatly benefits from inoculation with nitrogen-fixing bacteria. In a previous study, five efficient nitrogen-fixing bacterial strains, isolated from nodules of soybean inoculated with soil from semi-arid region, Northeast Brazil, were identified as a new group within the genus Bradyrhizobium. The taxonomic status of these strains was evaluated in this study. The phylogenetic analysis of the 16S rRNA gene showed the high similarity of the five strains to Bradyrhizobium brasilense UFLA03-321T (100%), B. pachyrhizi PAC48T (100%), B. ripae WR4T (100%), B. elkanii USDA 76T (99.91%), and B. macuxiense BR 10303T (99.91%). However, multilocus sequence analysis of the housekeeping genes atpD, dnaK, gyrB, recA, and rpoB, average nucleotide identity, and digital DNA-DNA hybridization analyses supported the classification of the group as B. brasilense. Some phenotypic characteristics allowed differentiating the five strains and the type strain of B. brasilense from the two neighboring species (B. pachyrhizi PAC48T and B. elkanii USDA 76T). The nodC and nifH genes' analyses showed that these strains belong to symbiovar sojae, together with B. elkanii (USDA 76T) and B. ferriligni (CCBAU 51502T). The present results support the classification of these five strains as Bradyrhizobium brasilense (symbiovar sojae).
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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
| | - Paula R Almeida Ribeiro
- Departamento de Ciência Do Solo, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil
| | | | - Rayssa Pereira Vicentin
- Departamento de Ciência Do Solo, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica E Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica E Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, 81531990, Brazil
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium
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10
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Delamuta JRM, Scherer AJ, Ribeiro RA, Hungria M. Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. Int J Syst Evol Microbiol 2020; 70:4233-4244. [PMID: 32568030 DOI: 10.1099/ijsem.0.004278] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Anderson José Scherer
- 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
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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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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12
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de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, Lassalle F, Lindström K, Mhamdi R, Martínez-Romero E, Moulin L, Mousavi SA, Nesme X, Peix A, Puławska J, Steenkamp E, Stępkowski T, Tian CF, Vinuesa P, Wei G, Willems A, Zilli J, Young P. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852-1863. [PMID: 31140963 DOI: 10.1099/ijsem.0.003426] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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Affiliation(s)
| | - Mitchell Andrews
- 2Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Julie Ardley
- 3School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | | | - Estelle Jumas-Bilak
- 5UMR 5569, Department of Microbiology, Faculty of Pharmacy, University of Montpellier, France
| | - Nemanja Kuzmanović
- 6Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Florent Lassalle
- 7Department of Infectious Disease Epidemiology - MRC Centre for Outbreak Analysis and Modelling, St Mary's Hospital, Praed Street, London W2 1NY, UK
| | - Kristina Lindström
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Ridha Mhamdi
- 9Centre of Biotechnology of Borj-Cedria, BP 901 Hammam-lif 2050, Tunisia
| | - Esperanza Martínez-Romero
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Lionel Moulin
- 11IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Seyed Abdollah Mousavi
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Xavier Nesme
- 12LEM, UCBL, CNRS, INRA, Univ Lyon, Villeurbanne, France
| | - Alvaro Peix
- 13Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Joanna Puławska
- 14Department of Phytopathology, Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Emma Steenkamp
- 15Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Tomasz Stępkowski
- 16Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Chang-Fu Tian
- 17State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China
| | - Pablo Vinuesa
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Gehong Wei
- 18Northwest A&F University, Yangling, Shaanxi, PR China
| | - Anne Willems
- 19Department Biochemistry and Microbiology, Lab. Microbiology, Ghent University, Belgium
| | - Jerri Zilli
- 20Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, Brazil, 23891-000, Brazil
| | - Peter Young
- 21Department of Biology, University of York, York YO10 5DD, UK
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13
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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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14
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Ramírez-Puebla ST, Hernández MAR, Guerrero Ruiz G, Ormeño-Orrillo E, Martinez-Romero JC, Servín-Garcidueñas LE, Núñez-de la Mora A, Amescua-Villela G, Negrete-Yankelevich S, Martínez-Romero E. Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid. Syst Appl Microbiol 2018; 42:373-382. [PMID: 30612723 DOI: 10.1016/j.syapm.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
Abstract
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.
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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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15
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Kuzmanović N, Smalla K, Gronow S, Puławska J. Rhizobium tumorigenes sp. nov., a novel plant tumorigenic bacterium isolated from cane gall tumors on thornless blackberry. Sci Rep 2018; 8:9051. [PMID: 29899540 PMCID: PMC5998023 DOI: 10.1038/s41598-018-27485-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/04/2018] [Indexed: 12/02/2022] Open
Abstract
Four plant tumorigenic strains 932, 1019, 1078T and 1081 isolated from cane gall tumors on thornless blackberry (Rubus sp.) were characterized. They shared low sequence identity with related Rhizobium spp. based on comparisons of 16S rRNA gene (≤98%) and housekeeping genes atpD, recA and rpoB (<90%). Phylogenetic analysis indicated that the strains studied represent a novel species within the genus Rhizobium, with Rhizobium tubonense CCBAU 85046T as their closest relative. Furthermore, obtained average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) values calculated for whole-genome sequences of strain 1078T and related Rhizobium spp. confirmed the authenticity of the novel species. The ANI-Blast (ANIb), ANI-MUMmer (ANIm) and in silico DDH values between strain 1078T and most closely related R. tubonense CCBAU 85046T were 76.17%, 84.11% and 21.3%, respectively. The novel species can be distinguished from R. tubonense based on phenotypic and chemotaxonomic properties. Here, we demonstrated that four strains studied represent a novel species of the genus Rhizobium, for which the name Rhizobium tumorigenes sp. nov. is proposed (type strain 1078T = DSM 104880T = CFBP 8567T). R. tumorigenes is a new plant tumorigenic species carrying the tumor-inducing (Ti) plasmid.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
| | - Joanna Puławska
- Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
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16
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Máthé I, Tóth E, Mentes A, Szabó A, Márialigeti K, Schumann P, Felföldi T. A new Rhizobium species isolated from the water of a crater lake, description of Rhizobium aquaticum sp. nov. Antonie van Leeuwenhoek 2018; 111:2175-2183. [DOI: 10.1007/s10482-018-1110-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/01/2018] [Indexed: 11/28/2022]
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17
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Stefan A, Van Cauwenberghe J, Rosu CM, Stedel C, Labrou NE, Flemetakis E, Efrose RC. Genetic diversity and structure of Rhizobium leguminosarum populations associated with clover plants are influenced by local environmental variables. Syst Appl Microbiol 2018; 41:251-259. [PMID: 29452714 DOI: 10.1016/j.syapm.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/15/2022]
Abstract
The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA). Multilocus sequence typing (MLST) analysis revealed that red clover plants are nodulated by a wide genetic diversity of R. leguminosarum symbiovar trifolii sequence types (STs), highly similar to the ones previously found in white clover. Rhizobial genetic variation was found mainly within the two clover populations for both chromosomal and plasmid types. Many STs appear to be unique for this region and the genetic composition of rhizobia differs significantly among the clover populations. Furthermore, our results showed that both soil pH and altitude contributed to plasmid sequence type composition while differences in chromosomal composition were affected by the altitude and were strongly correlated with distance.
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Affiliation(s)
- Andrei Stefan
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n Col. Chamilpa, Cuernavaca, Morelos CP 62210, Mexico; Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Craita M Rosu
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Catalina Stedel
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Rodica C Efrose
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania.
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Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P. Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia. Syst Appl Microbiol 2018; 41:184-190. [PMID: 29402492 DOI: 10.1016/j.syapm.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 10/18/2022]
Abstract
Two non-pathogenic strains R89-1 and R90T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261T and Agrobacterium skierniewicense Ch11T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G+C content is 56mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90T (=CCM 8736T=DSM 104667T).
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Affiliation(s)
- Jiří Zahradník
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic; Faculty of Science, Charles University Prague, Viničná 5, CZ-128 44 Prague 2, Czech Republic.
| | - Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Hana Pařízková
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Michal Grulich
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Kyslíková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Pavel Kyslík
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic.
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Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
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20
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Young JPW. Bacteria Are Smartphones and Mobile Genes Are Apps. Trends Microbiol 2016; 24:931-932. [DOI: 10.1016/j.tim.2016.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022]
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21
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Gordon BR, Klinger CR, Weese DJ, Lau JA, Burke PV, Dentinger BTM, Heath KD. Decoupled genomic elements and the evolution of partner quality in nitrogen-fixing rhizobia. Ecol Evol 2016; 6:1317-27. [PMID: 27087920 PMCID: PMC4775534 DOI: 10.1002/ece3.1953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 01/24/2023] Open
Abstract
Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long-term impacts of global changes, such as increased N (nitrogen) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or HGT (horizontal gene transfer). In a previous work using the legume/rhizobia mutualism, we demonstrated that long-term nitrogen fertilization caused the evolution of less-mutualistic rhizobia. Here, we use our 63 previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N fertilization. We find evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and suggest MoFe subunit interaction sites in the evolution of less-mutualistic rhizobia. These results provide insight into the mechanisms behind the evolutionary response of rhizobia to long-term N fertilization, and we discuss the implications of our results for the evolution of the mutualism.
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Affiliation(s)
- Benjamin R. Gordon
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | - Christie R. Klinger
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | - Dylan J. Weese
- Department of BiologySt. Ambrose University518 West Locust StDavenportIowa52803
| | - Jennifer A. Lau
- Kellogg Biological Station and Department of Plant BiologyMichigan State University3700 E. Gull Lake DriveHickory CornersMichigan49060
| | - Patricia V. Burke
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | | | - Katy D. Heath
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
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22
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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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23
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Ribeiro RA, Martins TB, Ormeño-Orrillo E, Marçon Delamuta JR, Rogel MA, Martínez-Romero E, Hungria M. Rhizobium ecuadorense sp. nov., an indigenous N2-fixing symbiont of the Ecuadorian common bean (Phaseolus vulgaris L.) genetic pool. Int J Syst Evol Microbiol 2015; 65:3162-3169. [DOI: 10.1099/ijsem.0.000392] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There are two major centres of genetic diversification of common bean (Phaseolus vilgaris L.), the Mesoamerican and the Andean, and the legume is capable of establishing nitrogen-fixing symbioses with several rhizobia; Rhizobium etli seems to be the dominant species in both centres. Another genetic pool of common bean, in Peru and Ecuador, is receiving increasing attention, and studies of microsymbionts from the region can help to increase our knowledge about coevolution of this symbiosis. We have previously reported several putative new lineages from this region and here present data indicating that strains belonging to one of them, PEL4, represent a novel species. Based on 16S rRNA gene sequence phylogeny, PEL4 strains are positioned in the Rhizobium phaseoli/R. etli/Rhizobium leguminosarum clade, but show unique properties in several morphological, physiological and biochemical analyses, as well as in BOX-PCR profiles ( < 75 % similarity with related species). PEL4 strains also differed from related species based on multilocus sequence analysis of three housekeeping genes (glnII, gyrB and recA). Nucleotide identities of the three concatenated genes between PEL4 strains and related species ranged from 91.8 to 94.2 %, being highest with Rhizobium fabae. DNA–DNA hybridization ( < 47 % DNA relatedness) and average nucleotide identity values of the whole genomes ( < 90.2 %) also supported the novel species status. The PEL4 strains were effective in nodulating and fixing N2 with common beans. The data supported the view that PEL4 strains represent a novel species, Rhizobium ecuadorense sp. nov. The type strain is CNPSo 671T ( = UMR 1450T = PIMAMPIRS I 5T = LMG 27578T).
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Affiliation(s)
- Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | - Talita Busulini Martins
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Biochemistry and Biotechnology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - 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, 86057-9970, Londrina, Paraná, Brazil
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Biochemistry and Biotechnology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-9970, Londrina, Paraná, Brazil
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24
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Kuzmanović N, Puławska J, Prokić A, Ivanović M, Zlatković N, Jones JB, Obradović A. Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Syst Appl Microbiol 2015; 38:373-8. [DOI: 10.1016/j.syapm.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/27/2015] [Accepted: 06/04/2015] [Indexed: 11/28/2022]
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25
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Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 2015; 5:140133. [PMID: 25589577 PMCID: PMC4313370 DOI: 10.1098/rsob.140133] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.
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Affiliation(s)
- Nitin Kumar
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ganesh Lad
- Department of Biology, University of York, York YO10 5DD, UK
| | - Elisa Giuntini
- Department of Biology, University of York, York YO10 5DD, UK
| | - Maria E Kaye
- Department of Biology, University of York, York YO10 5DD, UK
| | | | | | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Xavier Bailly
- Department of Biology, University of York, York YO10 5DD, UK
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26
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Ramírez-Puebla ST, Servín-Garcidueñas LE, Ormeño-Orrillo E, Vera-Ponce de León A, Rosenblueth M, Delaye L, Martínez J, Martínez-Romero E. Species in Wolbachia? Proposal for the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxteri', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylori', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitum' for the different species within Wolbachia supergroups. Syst Appl Microbiol 2015; 38:390-9. [PMID: 26189661 DOI: 10.1016/j.syapm.2015.05.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 05/21/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
Wolbachia are highly extended bacterial endosymbionts that infect arthropods and filarial nematodes and produce contrasting phenotypes on their hosts. Wolbachia taxonomy has been understudied. Currently, Wolbachia strains are classified into phylogenetic supergroups. Here we applied phylogenomic analyses to study Wolbachia evolutionary relationships and examined metrics derived from their genome sequences such as average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, and synteny to shed light on the taxonomy of these bacteria. Draft genome sequences of strains wDacA and wDacB obtained from the carmine cochineal insect Dactylopius coccus were included. Although all analyses indicated that each Wolbachia supergroup represents a distinct evolutionary lineage, we found that some of the analyzed supergroups showed enough internal heterogeneity to be considered as assemblages of more than one species. Thus, supergroups would represent supraspecific groupings. Consequently, Wolbachia pipientis nomen species would apply only to strains of supergroup B and we propose the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxterii', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylorii', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitis' for other supergroups.
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Affiliation(s)
| | | | | | | | | | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV-Irapuato, Irapuato, Guanajuato, Mexico
| | - Julio Martínez
- Centro de Ciencias Genómicas, UNAM, Cuernavaca, Morelos, Mexico
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27
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Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol 2015; 38:287-91. [DOI: 10.1016/j.syapm.2014.12.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 11/21/2022]
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28
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Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 2015; 38:84-90. [DOI: 10.1016/j.syapm.2014.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 01/26/2023]
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29
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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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30
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Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C, Vial L, Paulin L, de Lajudie P, Lindström K. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Syst Appl Microbiol 2014; 37:208-15. [PMID: 24581678 DOI: 10.1016/j.syapm.2013.12.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/14/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the "R. galegae complex" (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.
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Affiliation(s)
- Seyed Abdollah Mousavi
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland.
| | - Janina Österman
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Niklas Wahlberg
- University of Turku, Laboratory of Genetics, Department of Biology, 20014 Turku, Finland
| | - Xavier Nesme
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Céline Lavire
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Ludovic Vial
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Lars Paulin
- University of Helsinki, Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, Viikinkaari 4, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Philippe de Lajudie
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, Campus de Baillarguet TA A-82/J, 34398 Montpellier Cédex 5, France
| | - Kristina Lindström
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland; University of Helsinki, Department of Environmental Sciences, Viikinkaari 2a, P.O. Box 65, Helsinki FIN-00014, Finland
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López-Guerrero MG, Ormeño-Orrillo E, Rosenblueth M, Martinez-Romero J, Martïnez-Romero E. Buffet hypothesis for microbial nutrition at the rhizosphere. FRONTIERS IN PLANT SCIENCE 2013; 4:188. [PMID: 23785373 PMCID: PMC3682122 DOI: 10.3389/fpls.2013.00188] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/23/2013] [Indexed: 05/31/2023]
Abstract
An emphasis is made on the diversity of nutrients that rhizosphere bacteria may encounter derived from roots, soil, decaying organic matter, seeds, or the microbial community. This nutrient diversity may be considered analogous to a buffet and is contrasting to the hypothesis of oligotrophy at the rhizosphere. Different rhizosphere bacteria may have preferences for some substrates and this would allow a complex community to be established at the rhizosphere. To profit from diverse nutrients, root-associated bacteria should have large degrading capabilities and many transporters (seemingly inducible) that may be encoded in a significant proportion of the large genomes that root-associated bacteria have. Rhizosphere microbes may have a tendency to evolve toward generalists. We propose that many genes with unknown function may encode enzymes that participate in degrading diverse rhizosphere substrates. Knowledge of bacterial genes required for nutrition at the rhizosphere will help to make better use of bacteria as plant-growth promoters in agriculture.
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Affiliation(s)
| | | | | | | | - Esperanza Martïnez-Romero
- *Correspondence: Esperanza Martínez-Romero, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad SN, Cuernavaca, Morelos CP 62210, Mexico e-mail: ,
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32
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Polyphasic characterization of rhizobia isolated from Leucaena leucocephala from Panxi, China. World J Microbiol Biotechnol 2013; 29:2303-15. [PMID: 23749221 DOI: 10.1007/s11274-013-1396-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
Leucaena leucocephala was introduced into Panxi, Sichuan, China, in the 1980s and 1990s for afforestation and preventing water loss and soil erosion in this area. The co-introduction of rhizobial symbionts of introduced plants has drawn attention since they may influence local soil communities. We studied the phylogenetic position of the L. leucocephala isolates and assessed if the rhizobia were introduced together with the host to Panxi, Sichuan, China. The glnII and atpD genes of fifteen representative isolates were sequenced and analyzed, and applied multilocus sequence analyses in which the housekeeping genes recA, glnII and atpD were included. Furthermore, we estimated the within species diversity directly with 23S rDNA and IGS RFLP and indirectly through phenotypic analysis of forty L. leucocephala isolates. The isolates represented seven species and 38 diversified strains in the genera Ensifer, Mesorhizobium, Bradyrhizobium and Rhizobium. The within species diversity of the Ensifer isolates was large, proposing a potential to occupy novel niches. There was not conclusive evidence to show that any of the strains would have been co-introduced with L. leucocephala. On the contrary, we came to a conclusion that the possible introduction should not be inferred from sequence data alone.
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