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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 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
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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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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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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.
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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
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Shen L, Liu JJ, Liu PX, An MM, He XW, Zhao GZ. A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis. Arch Microbiol 2021; 204:50. [PMID: 34935074 DOI: 10.1007/s00203-021-02706-8] [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: 08/25/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Strain XQZ8T, isolated from the rhizosphere soil of a Populus popularis plant in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XQZ8T was related to members of the genus Rhizobium and had the highest 16S rRNA gene sequence similarity to Rhizobium smilacinae PTYR-5T (96.6%). The average nucleotide identity and digital DNA-DNA hybridization value between strain XQZ8T and R. smilacinae PTYR-5T were 77.5% and 21.4%, respectively. TYGS whole-genome-based taxonomic and multi-locus sequence analyses of three concatenated housekeeping genes (atpD-recA-glnII) further indicated that strain XQZ8T was a new member of the genus Rhizobium. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 2 (C12:0 aldehyde/unknown 10.928), C16:0, and C19:0 cyclo ω8c. The major respiratory quinones were Q-9 and Q-10. The polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid, and three unidentified lipids. The genomic DNA G + C content of the strain was 60.1 mol%. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XQZ8T represents a novel species of the genus Rhizobium, for which the name Rhizobium populisoli sp. nov. is proposed. The type strain is XQZ8T (= JCM 34442T = GDMCC 1.2201T).
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Affiliation(s)
- Lei Shen
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.,College of Life Sciences, Langfang Normal University, Langfang, 065000, People's Republic of China
| | - Jing-Ju Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Peng-Xiao Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Miao-Miao An
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Xiang-Wei He
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Guo-Zhu Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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