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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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Munoz Santa I, Nagel S, Taylor JD. Incorporating the pedigree information in multi-environment trial analyses for improving common vetch. FRONTIERS IN PLANT SCIENCE 2023; 14:1166133. [PMID: 37655219 PMCID: PMC10467272 DOI: 10.3389/fpls.2023.1166133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023]
Abstract
Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents.
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Affiliation(s)
- Isabel Munoz Santa
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Stuart Nagel
- South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Julian Daniel Taylor
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
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Zhang J, Wang N, Li S, Brunel B, Wang J, Feng Y, Yang T, Zong X. Genotypic composition and performance of pea-nodulating rhizobia from soils outside the native plant-host range. Front Microbiol 2023; 14:1201140. [PMID: 37469428 PMCID: PMC10353855 DOI: 10.3389/fmicb.2023.1201140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 07/21/2023] Open
Abstract
Cultivated soils need to shelter suitable rhizobia for legume cropping, especially in areas outside of the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with Pisum sativum L. in soils of Hebei Province, a region that has recently experienced an expansion of pea production in China. A total of 43 rhizobial isolates were obtained from root-nodules and characterized genetically and symbiotically. The isolates discriminated into 12 genotypes as defined by PCR-RFLP of IGS DNA. Multiple locus sequence analysis (MLSA) based on the 16S rRNA, recA, atpD and gyrB of representative strains placed them into five clusters of four defined species (R. sophorae, R. indicum, R. changzhiense, and R. anhuiense) and a novel Rhizobium genospecies. R. sophorae was the dominant group (58%) followed by R. indicum (23%). The other groups composed of R. changzhiense (14%), R. anhuiense (1 isolate) and the new genospecies (1 isolate), were minor and site-specific. Based on nodC phylogeny, all representatives were intermingled within the symbiovar viciae with R. sophorae and R. changzhiense being a new record. All the tested strains showed efficient symbiotic fixation on pea plants, with half of them exhibiting better plant biomass performance. This suggests that the pea-nodulating rhizobia in Hebei Province form a specific community of efficient symbiotic rhizobia on pea, distinct from those reported in other countries.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
- Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou, Henan Province, China
| | - Nan Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Brigitte Brunel
- LSTM, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, IRD, Montpellier, France
| | - Jingqi Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Yufeng Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Tao Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuxiao Zong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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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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Hsouna J, Gritli T, Ilahi H, Ellouze W, Mansouri M, Chihaoui SA, Bouhnik O, Missbah El Idrissi M, Abdelmoumen H, Wipf D, Courty PE, Bekki A, Tambong JT, Mnasri B. Genotypic and symbiotic diversity studies of rhizobia nodulating Acacia saligna in Tunisia reveal two novel symbiovars within the Rhizobium leguminosarum complex and Bradyrhizobium. Syst Appl Microbiol 2022; 45:126343. [PMID: 35759954 DOI: 10.1016/j.syapm.2022.126343] [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: 02/21/2022] [Revised: 05/08/2022] [Accepted: 06/12/2022] [Indexed: 11/15/2022]
Abstract
Acacia saligna is an invasive alien species that has the ability to establish symbiotic relationships with rhizobia. In the present study, genotypic and symbiotic diversity of native rhizobia associated with A. saligna in Tunisia were studied. A total of 100 bacterial strains were selected and three different ribotypes were identified based on rrs PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, gyrB and glnII) assigned 30 isolates to four putative new lineages and a single strain to Sinorhizobium meliloti. Thirteen slow-growing isolates representing the most dominant IGS (intergenic spacer) profile clustered distinctly from known rhizobia species within Bradyrhizobium with the closest related species being Bradyrhizobium shewense and Bradyrhizobium niftali, which had 95.17% and 95.1% sequence identity, respectively. Two slow-growing isolates, 1AS28L and 5AS6L, had B. frederekii as their closest species with a sequence identity of 95.2%, an indication that these strains could constitute a new lineage. Strains 1AS14I, 1AS12I and 6AS6 clustered distinctly from known rhizobia species but within the Rhizobium leguminosarum complex (Rlc) with the most closely related species being Rhizobium indicum with 96.3% sequence identity. Similarly, the remaining 11 strains showed 96.9 % and 97.2% similarity values with R. changzhiense and R. indicum, respectively. Based on nodC and nodA phylogenies and cross inoculation tests, these 14 strains of Rlc species clearly diverged from strains of Sinorhizobium and Rlc symbiovars, and formed a new symbiovar for which the name sv. "salignae" is proposed. Bacterial strains isolated in this study that were taxonomically assigned to Bradyrhizobium harbored different symbiotic genes and the data suggested a new symbiovar, for which sv. "cyanophyllae" is proposed. Isolates formed effective nodules on A. saligna.
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Affiliation(s)
- Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, 4902 Victoria Avenue North, Vineland Station, Ontario L0R 2E0, Canada.
| | - Maroua Mansouri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Omar Bouhnik
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Mustapha Missbah El Idrissi
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Daniel Wipf
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Abdelkader Bekki
- Laboratory of Rhizobia Biotechnology and Plant Breeding, University Oran1, Es Senia 31000, Algeria
| | - James T Tambong
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia.
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Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.
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Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
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Kang M, Seo T. Rhizobium setariae sp. nov., an Indole-3-Acetic Acid-Producing Bacterium Isolated from Green Foxtail, Setaria viridis. Curr Microbiol 2022; 79:162. [PMID: 35435479 DOI: 10.1007/s00284-022-02860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
A Gram-negative, indole-3-acetic acid-producing, aerobic, motile strain, designated as KVB221T, was isolated from a green foxtail plant, Setaria viridis, from a park near the coast of Haeundae Beach, Busan, Republic of Korea. The 16S rRNA gene analysis revealed strain KVB221T to be a member of the genus Rhizobium, from which Rhizobium alvei TNR-22T (97.2%), Rhizobium daejeonense L61T (96.9%), and Rhizobium ipomoeae shin9-1T (95.7%) were selected for comparative analysis. Growth of the strain was observed at 10-50 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 7), and in the presence of 0-8% NaCl (optimum 0%). The strain was observed to produce 36.3 ± 0.8 μg/ml of indole following 5 days of incubation. The major fatty acids are comprised of C16:0, C19:0 cyclo ω8c, C18:1 ω7c, and the unresolved group summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), while major polar lipids are identified as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylmonomethylethanolamine (PME). The predominant quinone is Q-10 and the DNA G+C content of the strain is 59.3%. Based on publicly available genome data between strain KVB221T and its closely related strains, the average nucleotide identity and in silico DNA-DNA hybridization values ranged from 72.7 to 73.1 and 19.7 to 20.4%, respectively. Based on the chemotaxonomic, phenotypic, and genomic comparisons reported here, we propose Rhizobium setariae sp. nov. as a novel species belonging to the genus Rhizobium. The type strain is KVB221T (= KACC 21713T = NBRC 114644T).
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Affiliation(s)
- Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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