1
|
He M, Chen G, Li KJ, Tang XX, Liu XX, Ren CB, Liu HH, Luo H, Debnath SC, Wang PM, Chen HX, Zheng DQ. Characterization and Genomic Analysis of Affinirhizobium gouqiense sp. nov. Isolated from Seawater of Gouqi Island Located in the East China Sea and Reclassification of Rhizobium lemnae to the Genus Affinirhizobium as Affinirhizobium lemnae comb. nov. Curr Microbiol 2024; 81:283. [PMID: 39066927 DOI: 10.1007/s00284-024-03807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
A novel bacterium designated as SSA5.23T was isolated from seawater. Cells of SSA5.23T are Gram-stain-negative, short, rod-shaped, and exhibit motility via numerous peritrichous flagella. The strain could grow at temperatures ranging from 15 to 35 °C (optimum at 25 °C), in a salinity range of 0-5.0% (w/v) NaCl, and within a pH range of 6.0-9.0 (optimum at pH 7.0). The predominant cellular fatty acid of SSA5.23T was C18:1 ω7c/C18:1 ω6c, and the major respiratory quinones were Q-9 and Q-10. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol were identified as the primary polar lipids. The complete genome (5.47 Mb) of SSA5.23T comprises of a circular chromosome of 3.64 Mb and three plasmids, specifically sized at 59.73 kb, 227.82 kb, and 1.54 Mb, respectively. Certain genes located on the plasmids play roles in denitrification, oxidative stress resistance, and osmotic tolerance, which likely contribute to the adaptability of this strain in marine conditions. Core-proteome average amino acid identity analysis effectively identified the strain's affiliation with the genus Affinirhizobium, showing the highest value (89.9%) with Affinirhizobium pseudoryzae DSM 19479T. This classification was further supported by the phylogenetic analysis of concatenated alignment of 170 single-copy orthologous proteins. When compared to related reference strains, SSA5.23T displayed an average nucleotide identity ranging from 74.9 to 80.3% and digital DNA-DNA hybridization values ranging from 19.9 to 23.9%. Our findings confirmed that strain SSA5.23T represents a novel species of the genus Affinirhizobium, for which the name Affinirhizobium gouqiense sp. nov. (type strain SSA5.23T = LMG 32560T = MCCC 1K07165T) was suggested.
Collapse
Affiliation(s)
- Min He
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Gen Chen
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Ke-Jing Li
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Xing-Xing Tang
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Xiao-Xiao Liu
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Chang-Bin Ren
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Hou-Hong Liu
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Hai Luo
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Sanjit Chandra Debnath
- Ocean College, Zhejiang University, Zhoushan, 316021, China
- Biosciences, University of Exeter, Exeter, Geoffrey Pope Building, Devon, EX4 4HB, UK
| | - Pin-Mei Wang
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | | | - Dao-Qiong Zheng
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
- Ocean College, Zhejiang University, Zhoushan, 316021, China.
| |
Collapse
|
2
|
Martínez JM, García R, Leandro T, Amils R. Draft genome sequence of the deep-subsurface Ciceribacter sp. strain T2.26MG-112.2, a second Rhizobiaceae isolated from the Iberian Pyrite Belt at 492.6 mbs. Microbiol Resour Announc 2024; 13:e0050223. [PMID: 38563744 PMCID: PMC11080525 DOI: 10.1128/mra.00502-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/15/2024] [Indexed: 04/04/2024] Open
Abstract
T2.26MG-112.2 is a Ciceribacter strain that has been isolated from the deep subsurface of the Iberian Pyrite Belt. We report its draft genome consisting of a chromosome of ≈4.9 Mb and a plasmid of 357 kb. The annotation reveals 4,824 coding sequences, 48 tRNA genes, and 1 rRNA operon.
Collapse
Affiliation(s)
- José M. Martínez
- Scientific Program Interactions with the Environment, Molecular Ecology of Extreme Environments, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - R. García
- Scientific Program Interactions with the Environment, Molecular Ecology of Extreme Environments, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
- Grupo de investigación de alto rendimiento en Ingeniería Química y Ambiental, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos (URJC), Móstoles, Spain
| | - T. Leandro
- Scientific Program Interactions with the Environment, Molecular Ecology of Extreme Environments, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Lisbon, Portugal
| | - R. Amils
- Scientific Program Interactions with the Environment, Molecular Ecology of Extreme Environments, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
- Planetology and Habitability Department, Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, Spain
| |
Collapse
|
3
|
diCenzo GC, Yang Y, Young JPW, Kuzmanović N. Refining the taxonomy of the order Hyphomicrobiales ( Rhizobiales) based on whole genome comparisons of over 130 type strains. Int J Syst Evol Microbiol 2024; 74. [PMID: 38619983 DOI: 10.1099/ijsem.0.006328] [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: 04/17/2024] Open
Abstract
The alphaproteobacterial order Hyphomicrobiales consists of 38 families comprising at least 152 validly published genera as of January 2024. The order Hyphomicrobiales was first described in 1957 and underwent important revisions in 2020. However, we show that several inconsistencies in the taxonomy of this order remain and we argue that there is a need for a consistent framework for defining families within the order. We propose a common genome-based framework for defining families within the order Hyphomicrobiales, suggesting that families represent monophyletic groups in core-genome phylogenies that share pairwise average amino acid identity values above ~75 % when calculated from a core set of 59 proteins. Applying this framework, we propose the formation of four new families and to reassign the genera Salaquimonas, Rhodoblastus, and Rhodoligotrophos into Salaquimonadaceae fam. nov., Rhodoblastaceae fam. nov., and Rhodoligotrophaceae fam. nov., respectively, and the genera Albibacter, Chenggangzhangella, Hansschlegelia, and Methylopila into Methylopilaceae fam. nov. We further propose to unify the families Bartonellaceae, Brucellaceae, Phyllobacteriaceae, and Notoacmeibacteraceae as Bartonellaceae; the families Segnochrobactraceae and Pseudoxanthobacteraceae as Segnochrobactraceae; the families Lichenihabitantaceae and Lichenibacteriaceae as Lichenihabitantaceae; and the families Breoghaniaceae and Stappiaceae as Stappiaceae. Lastly, we propose to reassign several genera to existing families. Specifically, we propose to reassign the genus Pseudohoeflea to the family Rhizobiaceae; the genera Oricola, Roseitalea, and Oceaniradius to the family Ahrensiaceae; the genus Limoniibacter to the emended family Bartonellaceae; the genus Faunimonas to the family Afifellaceae; and the genus Pseudochelatococcus to the family Chelatococcaceae. Our data also support the recent proposal to reassign the genus Prosthecomicrobium to the family Kaistiaceae.
Collapse
Affiliation(s)
- George C diCenzo
- Department of Biology, Queen's University, Kingston, ON, K7P 0S7, Canada
| | - Yuqi Yang
- Department of Biology, Queen's University, Kingston, ON, K7P 0S7, Canada
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Nemanja Kuzmanović
- Institute for Plant Protection in Horticulture and Urban Green, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, 38104, Germany
| |
Collapse
|
4
|
Zhang Y, Chen Y, Penttinen P, Wang X, Quan Y, Wen L, Yang M, Zhang X, Chen Q, Zhang L, Zhang J, Zhang X, Xu K. Ciceribacter sichuanensis sp. nov., a plant growth promoting rhizobacterium isolated from root nodules of soybean in Sichuan, China. Antonie Van Leeuwenhoek 2024; 117:46. [PMID: 38427093 DOI: 10.1007/s10482-024-01941-5] [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: 05/15/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
The fast-growing rhizobia-like strains S101T and S153, isolated from root nodules of soybean (Glycine max) in Sichuan, People's Republic of China, underwent characterization using a polyphasic taxonomy approach. The strains exhibited growth at 20-40 °C (optimum, 28 °C), pH 4.0-10.0 (optimum, pH 7.0) and up to 2.0% (w/v) NaCl (optimum, 0.01%) on Yeast Mannitol Agar plates. The 16S rRNA gene of strain S101T showed 98.4% sequence similarity to the closest type strain, Ciceribacter daejeonense L61T. Major cellular fatty acids in strain S101T included summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant quinone was ubiquinone-10. The polar lipids of strain S101T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethyl ethanolamine, phosphatidyl ethanolamine, amino phospholipid, unidentified phosphoglycolipid and unidentified amino-containing lipids. The DNA G + C contents of S101T and S153 were 61.1 and 61.3 mol%, respectively. Digital DNA-DNA hybridization relatedness and average nucleotide identity values between S101T and C. daejeonense L61T were 46.2% and 91.4-92.2%, respectively. In addition, strain S101T promoted the growth of soybean and carried nitrogen fixation genes in its genome, hinting at potential applications in sustainable agriculture. We propose that strains S101T and S153 represent a novel species, named Ciceribacter sichuanensis sp. nov., with strain S101T as the type strain (= CGMCC 1.61309 T = JCM 35649 T).
Collapse
Affiliation(s)
- Yanqin Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Yuanxue Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Ying Quan
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Licheng Wen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Miao Yang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, People's Republic of China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Kaiwei Xu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
| |
Collapse
|
5
|
Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria: Minutes of the closed annual meeting, videoconference on 2 October 2023, followed by online discussion until 31 December 2023. Int J Syst Evol Microbiol 2024; 74. [PMID: 38416034 DOI: 10.1099/ijsem.0.006276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
6
|
Romanenko L, Otstavnykh N, Tanaka N, Kurilenko V, Svetashev V, Tekutyeva L, Mikhailov V, Isaeva M. Characterization and Genomic Analysis of Fererhizobium litorale gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore. Microorganisms 2023; 11:2385. [PMID: 37894043 PMCID: PMC10609224 DOI: 10.3390/microorganisms11102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576T and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576T and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692T, 96.9% to Ensifer adhaerens NBRC 100388T, and 96.8% to Pararhizobium giardinii NBRC 107135T. The ANI values between strain KMM 9576T and Ensifer adhaerens NBRC 100388T, Sinorhizobium fredii USDA 205T, Pararhizobium giardinii NBRC 107135T, and Rhizobium leguminosarum NBRC 14778T were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576T and Rhizobium leguminosarum NBRC 14778T and 'Rhizobium album' NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576T) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C18:1ω7c as the dominant fatty acid followed by 11-methyl C18:1ω7c and C19:0 cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576T and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576T (=NRIC 0957T).
Collapse
Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan;
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Vasily Svetashev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Liudmila Tekutyeva
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnaya St. 42, Volno-Nadezhdinskoye, Primorsky krai, Vladivostok 692481, Russia;
| | - Valery Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| |
Collapse
|
7
|
Ma T, Xue H, Piao C, Jiang N, Li Y. Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov. Front Microbiol 2023; 14:1207256. [PMID: 37601364 PMCID: PMC10434624 DOI: 10.3389/fmicb.2023.1207256] [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: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).
Collapse
Affiliation(s)
| | | | | | | | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
8
|
Christophe G, Hou X, Petit E, Traikia M, Le Cerf D, Rihouey C, Gardarin C, Delattre C, Michaud P, Pierre G, Dubessay P. Description of the Wild Strain Rhizobium rosettiformans DSM26376, Reclassified under Peteryoungia rosettiformans comb.nov., for Producing Glucuronan. Polymers (Basel) 2023; 15:polym15092177. [PMID: 37177323 PMCID: PMC10180729 DOI: 10.3390/polym15092177] [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: 02/10/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Glucuronan is a polysaccharide composed of β-(1,4)-linked d-glucuronic acids having intrinsic properties and biological activities recoverable in many fields of application. Currently, the description of Sinorhyzobium meliloti M5N1CS mutant bacterial strain as the sole source of glucuronan makes it relevant to the exploration of new microorganisms producing glucuronan. In this study, the Peteryoungia rosettifformans strain (Rhizobia), was identified as a wild producer of an exopolysaccharide (RhrBR46) related to glucuronan. Structural and biochemical features, using colorimetric assays, Fourier infrared spectroscopy, nuclear magnetic resonance, high pressure size exclusion chromatography coupled to multi-angle light laser scattering, and enzymatic assays allowed the characterization of a polyglucuronic acid, having a molecular mass (Mw¯) of 1.85 × 105 Da, and being partially O-acetylated at C-2 and/or C-3 positions. The concentration of Mg2+ ions in the cultivation medium has been shown to impact the structure of RhrBR46, by reducing drastically its Mw¯ (73%) and increasing its DA (10%). Comparative structural analyses between RhrBR46 and the glucuronan from Sinorhyzobium meliloti M5N1CS strain revealed differences in terms of molecular weight, degree of acetylation (DA), and the distribution of acetylation pattern. These structural divergences of RhrBR46 might contribute to singular properties or biological activities of RhrBR46, offering new perspectives of application.
Collapse
Affiliation(s)
- Gwendoline Christophe
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Xiaoyang Hou
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Emmanuel Petit
- UMRT INRAe 1158 BioEcoAgro, Laboratoire BIOPI, Institut Universitaire et Technologique, Université de Picardie Jules Verne, F-80025 Amiens, France
| | - Mounir Traikia
- CNRS, ICCF, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Didier Le Cerf
- Polymères Biopolymères Surfaces, Normandie Université, UNIROUEN, INSA Rouen, CNRS, UMR6270, F-76821 Mont Saint-Aignan, France
| | - Christophe Rihouey
- Polymères Biopolymères Surfaces, Normandie Université, UNIROUEN, INSA Rouen, CNRS, UMR6270, F-76821 Mont Saint-Aignan, France
| | - Christine Gardarin
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Cédric Delattre
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- Institut Universitaire de France (IUF), 1 rue Descartes, F-75005 Paris, France
| | - Philippe Michaud
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Guillaume Pierre
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pascal Dubessay
- Clermont Auvergne INP, CNRS, Institut Pascal, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| |
Collapse
|
9
|
Roca-Couso R, Flores-Felix JD, Igual JM, García-Fraile P, Velázquez E, Rivas R. Ferranicluibacter rubi gen. nov., sp. nov., a new member of family Rhizobiaceae isolated from stems of elmleaf blackberry ( Rubus ulmifolius Schott) in Northwest Spain. Int J Syst Evol Microbiol 2023; 73. [PMID: 37093735 DOI: 10.1099/ijsem.0.005789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Strain CRRU44T was isolated from the stems of Rubus ulmifolius plants growing in Salamanca (Spain). The phylogenetic analysis of the 16S rRNA gene sequence places this strain within the family Rhizobiaceae showing that it is equidistant to the type species of several genera from this family with similarity values ranging from 91.0 to 96.3 %. Strain CRRU44T formed a divergent lineage which clustered with Endobacterium cereale RZME27T, Neorhizobium galegae HAMBI540T and Pseudorhizobium pelagicum R1-200B4T. The phylogenomic analysis showed that strain CRRU44T was equal to or more distant from the remaining genera of the family Rhizobiaceae than other genera among them. The calculated average nucleotide identity based on blast and average amino acid identity values with respect to the type species of all genera from the family Rhizobiaceae were lower than 78.5 and 76.5 %, respectively, which are the currently cut-off values proposed to differentiate genera within this family. All these results together with those from phenotypic and chemotaxonomic analyses support that strain CRRU44T represents a novel species of a novel genus within the family Rhizobiaceae, for which the name Ferranicluibacter rubi gen. nov., sp. nov. is proposed (type strain CRRU44T=CECT 30117T=LMG 31822T).
Collapse
Affiliation(s)
- Rocio Roca-Couso
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
| | - Jose David Flores-Felix
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
| | - Jose M Igual
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Raúl Rivas
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| |
Collapse
|
10
|
Gupta RK, Singh AK, Bajaj A, Khardenavis AA, Purohit HJ. Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior. J Basic Microbiol 2023; 63:359-376. [PMID: 36453555 DOI: 10.1002/jobm.202200323] [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: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022]
Abstract
Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4 + -N, and NO3 - -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4 )2 SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.
Collapse
Affiliation(s)
- Rakesh K Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish K Singh
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| |
Collapse
|
11
|
Rajkumari J, Katiyar P, Dheeman S, Pandey P, Maheshwari DK. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 2022; 38:206. [PMID: 36008736 DOI: 10.1007/s11274-022-03370-w] [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: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.
Collapse
Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Prashant Katiyar
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India
| | - Shrivardhan Dheeman
- Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India.
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
| | | |
Collapse
|
13
|
Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F, diCenzo GC. Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation. Int J Syst Evol Microbiol 2022; 72. [PMID: 35238735 PMCID: PMC9558580 DOI: 10.1099/ijsem.0.005243] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The alphaproteobacterial family
Rhizobiaceae
is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. The most problematic is
Rhizobium
, which is notorious for being highly paraphyletic, as most newly described species in the family are assigned to this genus without consideration of their proximity to existing genera, or the need to create novel genera. Moreover, many
Rhizobiaceae
genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family
Rhizobiaceae
, wherein genera are defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86 %. We further propose that additional genomic or phenotypic evidence can justify division of species into separate genera even if they share greater than 86 % cpAAI. Applying this framework, we propose to reclassify
Rhizobium rhizosphaerae
and
Rhizobium oryzae
into Xaviernesmea gen. nov. Data is also provided to support the formation of Peteryoungia aggregata comb. nov., Endobacterium yantingense comb. nov., Neorhizobium petrolearium comb. nov., Pararhizobium arenae comb. nov., Pseudorhizobium tarimense comb. nov. and Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera
Ensifer
and
Sinorhizobium
in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. Despite pairwise cpAAI values for all
Ensifer
species and all
Sinorhizobium
species being >86 %, additional genomic and phenotypic data suggest that they significantly differ in their biology and ecology. We therefore propose emended descriptions of
Ensifer
and
Sinorhizobium
, which we argue should be considered as separate genera.
Collapse
Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute for Plant Protection in Horticulture and Forests, Braunschweig, Germany
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Florent Lassalle
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
14
|
Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of changes in taxonomic opinion no. 35. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
15
|
Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71. [PMID: 34850678 DOI: 10.1099/ijsem.0.005096] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|