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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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Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF. Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species. BMC Genomics 2024; 25:419. [PMID: 38684951 PMCID: PMC11057113 DOI: 10.1186/s12864-024-10333-y] [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: 01/31/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUD The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.
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Affiliation(s)
- Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China.
| | - Tingyan Guo
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, México
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Identification of the symbiovar maamori in Mesorhizobium isolated from nodules of Ononis repens in the Maamora forest (Morocco). Symbiosis 2022. [DOI: 10.1007/s13199-022-00890-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Pedron R, Luchi E, Albiac MA, Di Cagno R, Catorci D, Esposito A, Bianconi I, Losa D, Cristofolini M, Guella G, Jousson O. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870580 DOI: 10.1099/ijsem.0.005131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 3P27G6T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6T clustered together with Mesorhizobium australicum WSM2073T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6T (=DSM 110654T=CECT 30067T). Strain 3P27G6T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Elena Luchi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Marta Acin Albiac
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Daniele Catorci
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy.,Department of Physics, University of Trento, 38123 Trento, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Irene Bianconi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Davide Losa
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, 38123 Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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Fall F, Le Roux C, Bâ AM, Fall D, Bakhoum N, Faye MN, Kane A, Ndoye I, Diouf D. The rhizosphere of the halophytic grass Sporobolus robustus Kunth hosts rhizobium genospecies that are efficient on Prosopis juliflora (Sw.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings. Syst Appl Microbiol 2018; 42:232-239. [PMID: 30384991 DOI: 10.1016/j.syapm.2018.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023]
Abstract
The aim of this study was to survey the abundance and genetic diversity of legume-nodulating rhizobia (LNR) in the rhizosphere of a salt-tolerant grass, Sporobolus robustus Kunth, in the dry and rainy seasons along a salinity gradient, and to test their effectiveness on Prosopis juliflora (SW.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings. The results showed a significant decrease in LNR population density and diversity in response to salinity, particularly during the dry season. A phylogenetic analysis of the 16S-23S rRNA ITS region clustered the 232 rhizobium isolates into three genera and 12 distinct representative genotypes: Mesorhizobium (8 genotypes), Ensifer (2 genotypes) and Rhizobium (2 genotypes). Of these genotypes, 2 were only found in the dry season, 4 exclusively in the rainy season and 6 were found in both seasons. Isolates of the Mesorhizobium and Ensifer genera were more abundant than those of Rhizobium, with 55%, 44% and 1% of the total strains, respectively. The abundance of the Mesorhizobium isolates appeared to increase in the dry season, suggesting that they were more adapted to environmental aridity than Ensifer genospecies. Conversely, Ensifer genospecies were more tolerant of high salinity levels than the other genospecies. However, Ensifer genospeciesproved to be the most efficient strains on P. juliflora and V. seyal seedlings. We concluded that S. robustus hosts efficient rhizobium strains in its rhizosphere, suggesting its ability to act as a nurse plant to facilitate seedling recruitment of P. juliflora and V. seyal in saline soils.
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Affiliation(s)
- Fatoumata Fall
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal.
| | | | - Amadou Mustapha Bâ
- CIRAD, UMR LSTM, F-34398 Montpellier, France; Laboratoire de Biologie et Physiologie Végétales, Université des Antilles, Guadeloupe, France
| | - Dioumacor Fall
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Centre National de Recherches Agronomiques (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Niokhor Bakhoum
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Mathieu Ndigue Faye
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Aboubacry Kane
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
| | - Ibrahima Ndoye
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
| | - Diegane Diouf
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485-2494. [PMID: 28771120 DOI: 10.1099/ijsem.0.002144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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Marcos-García M, Menéndez E, Ramírez-Bahena MH, Mateos PF, Peix Á, Velazquez E, Rivas R. Mesorhizobium helmanticense sp. nov., isolated from Lotus corniculatus nodules. Int J Syst Evol Microbiol 2017; 67:2301-2305. [DOI: 10.1099/ijsem.0.001942] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marta Marcos-García
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Esther Menéndez
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro F. Mateos
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacciones Planta-Microorganismo’, Salamanca, Spain
| | - Álvaro Peix
- IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacciones Planta-Microorganismo’, Salamanca, Spain
| | - Encarna Velazquez
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacciones Planta-Microorganismo’, Salamanca, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacciones Planta-Microorganismo’, Salamanca, Spain
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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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Li J, Huang J, Liao S, Wang G. Pseudaminobacter manganicus sp. nov., isolated from sludge of a manganese mine. Int J Syst Evol Microbiol 2016; 67:1589-1594. [PMID: 28036252 DOI: 10.1099/ijsem.0.001765] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, non-motile, capsule-forming and rod-shaped bacterium, designated JH-7T, was isolated from sludge of a manganese mine. The 16S rRNA gene sequence of JH-7T showed highest similarities to those of Pseudaminobacter salicylatoxidans BN12T (97.4 %), Mesorhizobiumthiogangeticum SJTT (97.0 %) and Pseudaminobacter defluvii THI 051T (96.5 %). Phylogenetic trees clustered JH-7T together with P. salicylatoxidans BN12Tand P. defluvii THI 051T. The DNA-DNA hybridization values between JH-7T and P. salicylatoxidans DSM 6986T and between JH-7T and M. thiogangeticum DSM 17097T were 34.8 and 20.1 %, respectively. The major fatty acids of JH-7T (>10 %) were C18 : 1ω7c, C19 : 0cyclo ω8c and C16 : 0. The genomic DNA G+C content was 61.6 mol%. The polyamines of JH-7T were sym-homospermidine (83 %) and putrescine (17 %), and the respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Compared with the members of the genera Pseudaminobacter and Mesorhizobium, JH-7T showed some unique physiological and biochemical characters, such as being negative for H2S production, hydrolysis of Tween 40 and Tween 60, esterase lipase (C8) activity and assimilation of d-ribose and positive for acid production from d-galactose and assimilation of d-fructose. On the basis of the results of the polyphasic taxonomic analysis, JH-7T was considered to represent a novel species of the genus Pseudaminobacter, for which the name Pseudaminobacter manganicus sp. nov. is proposed. The type strain is JH-7T (=KCTC 52258T=CCTCC AB 2016107T).
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Affiliation(s)
- Jiahong Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jing Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shuijiao Liao
- State Key Laboratory of Agricultural Microbiology, College of Basic Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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