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Shi N, He T, Qin H, Wang Z, You S, Wang E, Hu G, Wang F, Yu M, Liu X, Liu Z. Microvirga sesbaniae sp. nov. and Microvirga yunnanensis sp. nov., Pink-Pigmented Bacteria Isolated from Root Nodules of Sesbania cannabina (Retz.) Poir. Microorganisms 2024; 12:1558. [PMID: 39203400 PMCID: PMC11356035 DOI: 10.3390/microorganisms12081558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Four pigment-producing rhizobial strains nodulating Sesbania cannabina (Retz.) Poir. formed a unique group in genus Microvirga in the phylogeny of a 16S rRNA gene and five housekeeping genes (gyrB, recA, dnaK, glnA, and atpD) in a genome analysis, phenotypic characteristics analysis, and chemotaxonomic analysis. These four strains shared as high as 99.3% similarity with Microvirga tunisiensis LmiM8T in the 16S rRNA gene sequence and, in an MLSA, were subdivided into two clusters, ANI (genome average nucleotide) and dDDH (digital DNA-DNA hybridization) which shared sequence similarities lower than the species thresholds with each other and with the reference strains for related Microvirga species. The polar lipids elucidated that phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin were the main components for strain SWF67558T and for strain HBU65207T, with the exception of PC. SWF67558T and HBU65207T strains had similar predominant cellular fatty acids, including C16:0, C18:0, summed feature 2, and summed feature8, but with different contents. In addition, all the four novel strains produced pink-pigment, and the main coloring material extract from strain SWF67558T was identified as zeaxanthin, which presented antioxidant ability and reduction power. With all the phylogenetic and phenotypic divergency, we proposed these pink-pigmented symbiotic bacteria as two novel species, named Microvirga sesbaniae sp. nov. and Microvirga yunnanensis sp. nov., with SWF67558T (=KCTC82331T=GDMCC1.2024T) and HBU65207T (=KCTC92125T=GDMCC1.2023T) as the type strains, respectively.
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Affiliation(s)
- Nan Shi
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Teng He
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Huifang Qin
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Ziye Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Shenghao You
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Entao Wang
- Affiliation Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City 11340, Mexico;
| | - Guoli Hu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming 650224, China;
| | - Miao Yu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Zhenyu Liu
- Institute of Agro-Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
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Gunununu RP, Mohammed M, Jaiswal SK, Dakora FD. Phylogeny and symbiotic effectiveness of indigenous rhizobial microsymbionts of common bean (Phaseolus vulgaris L.) in Malkerns, Eswatini. Sci Rep 2023; 13:17029. [PMID: 37813863 PMCID: PMC10562383 DOI: 10.1038/s41598-023-43634-5] [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: 01/19/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
In most legumes, the rhizobial symbionts exhibit diversity across different environments. Although common bean (Phaseolus vulgaris L.) is one of the important legumes in southern Africa, there is no available information on the genetic diversity and N2-fixing effectiveness of its symbionts in Malkerns, Eswatini. In this study, we assessed the phylogenetic positions of rhizobial microsymbionts of common bean from Malkerns in Eswatini. The isolates obtained showed differences in morpho-physiology and N2-fixing efficiency. A dendrogram constructed from the ERIC-PCR banding patterns, grouped a total of 88 tested isolates into 80 ERIC-PCR types if considered at a 70% similarity cut-off point. Multilocus sequence analysis using 16S rRNA, rpoB, dnaK, gyrB, and glnII and symbiotic (nifH and nodC) gene sequences closely aligned the test isolates to the type strains of Rhizobium muluonense, R. paranaense, R. pusense, R. phaseoli and R. etli. Subjecting the isolates in this study to further description can potentially reveal novel species. Most of the isolates tested were efficient in fixing nitrogen and elicited greater stomatal conductance and photosynthetic rates in the common bean. Relative effectiveness (RE) varied from 18 to 433%, with 75 (85%) out of the 88 tested isolates being more effective than the nitrate fed control plants.
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Affiliation(s)
- Rotondwa P Gunununu
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Mustapha Mohammed
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
- Department of Crop Science, University for Development Studies, P.O. Box TL1882, Tamale, Ghana
| | - Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
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Hnini M, El Attar I, Taha K, Aurag J. Genetic diversity, symbiotic efficiency, stress tolerance, and plant growth promotion traits of rhizobia nodulating Vachellia tortilis subsp. raddiana growing in dryland soils in southern Morocco. Syst Appl Microbiol 2023; 46:126434. [PMID: 37210974 DOI: 10.1016/j.syapm.2023.126434] [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: 01/12/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
In the present study, we analyzed the genetic diversity, phylogenetic relationships, stress tolerance, phytobeneficial traits, and symbiotic characteristics of rhizobial strains isolated from root nodules of Vachellia tortilis subsp. raddiana grown in soils collected in the extreme Southwest of the Anti-Atlas Mountains in Morocco. Subsequent to Rep-PCR fingerprinting, 16S rDNA gene sequencing of 15 representative strains showed that all of them belong to the genus Ensifer. Phylogenetic analysis and concatenation of the housekeeping genes gyrB, rpoB, recA, and dnaK revealed that the entire collection (except strain LMR678) shared 99.08 % to 99.92% similarity with Ensifer sp. USDA 257 and 96.92% to 98.79% with Sinorhizobium BJ1. Phylogenetic analysis of nodC and nodA sequences showed that all strains but one (LMR678) formed a phylogenetic group with the type strain "E. aridi" LMR001T (similarity over 98%). Moreover, it was relevant that most strains belong to the symbiovar vachelliae. In vitro tests revealed that five strains produced IAA, four solubilized inorganic phosphate, and one produced siderophores. All strains showed tolerance to NaCl concentrations ranging from 2 to 12% and grew at up to 10% of PEG6000. A greenhouse plant inoculation test conducted during five months demonstrated that most rhizobial strains were infective and efficient. Strains LMR688, LMR692, and LMR687 exhibited high relative symbiotic efficiency values (respectively 231.6 %, 171.96 %, and 140.84 %). These strains could be considered as the most suitable candidates for inoculation of V. t. subsp. raddiana, to be used as a pioneer plant for restoring arid soils threatened with desertification.
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Affiliation(s)
- Mohamed Hnini
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000 Rabat, Morocco
| | - Imane El Attar
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000 Rabat, Morocco
| | - Kaoutar Taha
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000 Rabat, Morocco
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000 Rabat, Morocco.
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Tang M, Wang H, Qi X, He T, Zhang B, Wang E, Yu M, Wang B, Wang F, Liu Z, Liu X. Diversification of Sinorhizobium populations associated with Medicago polymorpha and Medicago lupulina in purple soil of China. Front Microbiol 2023; 13:1055694. [PMID: 36687603 PMCID: PMC9846747 DOI: 10.3389/fmicb.2022.1055694] [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: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S-23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.
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Affiliation(s)
- Mingxing Tang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Haoyu Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Xin Qi
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Teng He
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Bin Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Miao Yu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Beinan Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming City, China
| | - Zhongkuan Liu
- Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China,*Correspondence: Zhongkuan Liu, ; Xiaoyun Liu,
| | - Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China,*Correspondence: Zhongkuan Liu, ; Xiaoyun Liu,
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Kozieł M, Kalita M, Janczarek M. Genetic diversity of microsymbionts nodulating Trifolium pratense in subpolar and temperate climate regions. Sci Rep 2022; 12:12144. [PMID: 35840628 PMCID: PMC9287440 DOI: 10.1038/s41598-022-16410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.
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Affiliation(s)
- Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
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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; 72:005243. [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/03/2022] [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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Biocontrol potential and antifungal mechanism of a novel Streptomyces sichuanensis against Fusarium oxysporum f. sp. cubense tropical race 4 in vitro and in vivo. Appl Microbiol Biotechnol 2022; 106:1633-1649. [PMID: 35141868 DOI: 10.1007/s00253-022-11788-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/01/2023]
Abstract
Most commercial banana cultivars are highly susceptible to Fusarium wilt caused by soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4). Biological control using antagonistic microorganism has been considered as an alternative method to fungicide. Our previous study showed that Streptomyces sp. SCA3-4 T had a broad-spectrum antifungal activity from the rhizosphere soil of Opuntia stricta in a dry hot valley. Here, the sequenced genome of strain SCA3-4 T contained 6614 predicted genes with 72.38% of G + C content. A polymorphic tree was constructed using the multilocus sequence analysis (MLSA) of five house-keeping gene alleles (atpD, gyrB, recA, rpoB, and trpB). Strain SCA3-4 T formed a distinct clade with Streptomyces mobaraensis NBRC 13819 T with 71% of bootstrap. Average nucleotide identity (ANI) values between genomes of strain SCA3-4 T and S. mobaraensis NBRC 13819 T was 85.83% below 95-96% of the novel species threshold, and named after Streptomyces sichuanensis sp. nov. The type strain is SCA3-4 T (= GDMCC 4.214 T = JCM 34964 T). Genomic analysis revealed that strain SCA3-4 T contained 36 known biosynthetic gene clusters of secondary metabolites. Antifungal activity of strain SCA3-4 T was closely associated with the production of siderophore and its extracts induced the apoptosis of Foc TR4 cells. A total of 12 potential antifungal metabolites including terpenoids, esters, acid, macrolides etc. were obtained by the gas chromatography-mass spectrometry (GC-MS). Greenhouse experiment indicated that strain SCA3-4 T could significantly inhibit infection of Foc TR4 in the roots and corms of banana seedlings and reduce disease index. Therefore, strain SCA3-4 T is an important microbial resource for exploring novel natural compounds and developing biopesticides to manage Foc TR4. KEY POINTS: • Strain SCA3-4 T was identified as a novel species of Streptomyces. • Siderophore participates in the antifungal regulation. • Secondary metabolites of strain SCA3-4 T improves the plant resistance to Foc TR4.
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Khairnar M, Hagir A, Parmar K, Sayyed RZ, James EK, Rahi P. Phylogenetic diversity and plant growth-promoting activities of rhizobia nodulating fenugreek (Trigonella foenum-graecum Linn.) cultivated in different agroclimatic regions of India. FEMS Microbiol Ecol 2022; 98:6526309. [PMID: 35142840 DOI: 10.1093/femsec/fiac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/15/2021] [Accepted: 02/08/2022] [Indexed: 11/15/2022] Open
Abstract
Fenugreek (Trigonella foenum-graecum Linn.), is an extensively cultivated legume crop used as a herb, spice, and traditional medicine in India. The symbiotic efficiency and plant growth-promoting potential of fenugreek rhizobia depend on the symbiont strain and environmental factors. We isolated 176 root-nodulating bacteria from fenugreek cultivated in different agroclimatic regions of India. MALDI-TOF MS-based identification and phylogenetic analyses based on 16S rRNA and five housekeeping genes classified the fenugreek-rhizobia as Ensifer (Sinorhizobium) meliloti. However, the strains represent separate sub-lineages of E. meliloti, distinct from all reported sub-lineages across the globe. We also observed the spatial distribution of fenugreek rhizobia, as the three sub-lineages of E. meliloti recorded during this study were specific to their respective agroclimatic regions. According to the symbiotic gene (nodC and nifH) phylogenies, all three sub-lineages of E. meliloti harboured symbiotic genes similar to symbiovar meliloti; as with the housekeeping genes, these also revealed a spatial distribution for different clades of sv. meliloti. The strains could nodulate fenugreek plants and they showed plant growth-promoting potential. Significant differences were found in the plant growth parameters in response to inoculation with the various strains, suggesting strain-level differences. This study demonstrates that fenugreek rhizobia in India are diverse and spatially distributed in different agro-climatic regions.
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Affiliation(s)
- Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Ashwini Hagir
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Krupa Parmar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Riyazali Zafarali Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science, and Commerce College, Shahada 425409, India
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
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Maitra S, Brestic M, Bhadra P, Shankar T, Praharaj S, Palai JB, Shah MMR, Barek V, Ondrisik P, Skalický M, Hossain A. Bioinoculants-Natural Biological Resources for Sustainable Plant Production. Microorganisms 2021; 10:51. [PMID: 35056500 PMCID: PMC8780112 DOI: 10.3390/microorganisms10010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.
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Affiliation(s)
- Sagar Maitra
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Preetha Bhadra
- Department of Biotechnology, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India;
| | - Tanmoy Shankar
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Subhashisa Praharaj
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Jnana Bharati Palai
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | | | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Peter Ondrisik
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Milan Skalický
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Akbar Hossain
- Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh;
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11
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Ilahi H, Hsouna J, Ellouze W, Gritli T, Chihaoui SA, Barhoumi F, Najib Elfeddy M, Bachkouel S, Ouahmane L, Tambong JT, Mnasri B. Phylogenetic study of rhizobia nodulating pea (Pisum sativum) isolated from different geographic locations in Tunisia. Syst Appl Microbiol 2021; 44:126221. [PMID: 34119907 DOI: 10.1016/j.syapm.2021.126221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Nodulated Pisum sativum plants showed the presence of native rhizobia in 16 out of 23 soil samples collected especially in northern and central Tunisia. A total of 130 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, dnaK and glnII) assigned 35 isolates to Rhizobium laguerreae, R. ruizarguesonis, Agrobacterium radiobacter, Ensifer meliloti and two putative genospecies. R. laguerreae was the most dominant species nodulating P. sativum with 63%. The isolates 21PS7 and 21PS15 were assigned to R. ruizarguesonis, and this is the first report of this species in Tunisia. Two putative new lineages were identified, since strains 25PS6, 10PS4 and 12PS15 clustered distinctly from known rhizobia species but within the R. leguminosarum complex (Rlc) with the most closely related species being R. indicum with 96.4% sequence identity. Similarly, strains 16PS2, 3PS9 and 3PS18 showed 97.4% and 97.6% similarity with R. sophorae and R. laguerreae, respectively. Based on 16S-23S intergenic spacer (IGS) fingerprinting, there was no clear association between the strains and their geographic locations. According to nodC and nodA phylogenies, strains of Rlc species and, interestingly, strain 8PS18 identified as E. meliloti, harbored the symbiotic genes of symbiovar viciae and clustered in two different clades showing heterogeneity within the symbiovar. All these strains nodulated and fixed nitrogen with pea plants. However, the strains belonging to A. radiobacter and the two remaining strains of E. meliloti were unable to nodulate P. sativum, suggesting that they were non-symbiotic strains. The results of this study further suggest that the Tunisian Rhizobium community is more diverse than previously reported.
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Affiliation(s)
- Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Jihed Hsouna
- 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, Vineland Station, Ontario L0R 2E0, Canada
| | - Takwa Gritli
- 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
| | - Fathi Barhoumi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Mohamed Najib Elfeddy
- Phytobacteriology Laboratory, Plant Protection Research Unit, CRRA Marrakesh, National Institute for Agronomical Research, Marrakesh 40000, Morocco
| | - Sarra Bachkouel
- Research Support and Technology Transfer Unity, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - James T Tambong
- Agriculture and Agri-Food Canada, 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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12
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Lamin H, Alami S, Lamrabet M, Bouhnik O, Bennis M, Abdelmoumen H, Bedmar EJ, Missbah-El Idrissi M. Bradyrhizobium sp. sv. retamae nodulates Retama monosperma grown in a lead and zinc mine tailings in Eastern Morocco. Braz J Microbiol 2021; 52:639-649. [PMID: 33447935 PMCID: PMC8105474 DOI: 10.1007/s42770-021-00420-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022] Open
Abstract
The aim of this work was to characterize and identify some bacteria isolated from the root nodules of Retama monosperma grown in Sidi Boubker lead and zinc mine tailings. Very few root nodules were obtained on the root nodules of R. monosperma grown in these soils. The three bacteria isolated from the root nodules were tolerant in vitro to different concentrations of heavy metals, including lead and zinc. The rep-PCR experiments showed that the three isolates have different molecular fingerprints and were considered as three different strains. The analysis of their 16S rRNA gene sequences proved their affiliation to the genus Bradyrhizobium. The analysis and phylogeny of the housekeeping genes atpD, glnII, gyrB, recA, and rpoB confirmed that the closest species was B. valentinum with similarity percentages of 95.61 to 95.82%. The three isolates recovered from the root nodules were slow-growing rhizobia capable to renodulate their original host plant in the presence of Pb-acetate. They were able to nodulate R. sphaerocarpa and Lupinus luteus also but not Glycine max or Phaseolus vulgaris. The phylogeny of the nodA and nodC nodulation genes as well as the nifH gene of the three strains showed that they belong to the symbiovar retamae of the genus Bradyrhizobium. The three strains isolated could be considered for use as inoculum for Retama plants before use in phytoremediation experiments.
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Affiliation(s)
- Hanane Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Soufiane Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080, Granada, Spain
| | - Mustapha Missbah-El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco.
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Alami S, Lamin H, Bennis M, Bouhnik O, Lamrabet M, El Hachimi ML, Abdelmoumen H, Bedmar EJ, Missbah El Idrissi M. Characterization of Retama sphaerocarpa microsymbionts in Zaida lead mine tailings in the Moroccan middle Atlas. Syst Appl Microbiol 2021; 44:126207. [PMID: 34015589 DOI: 10.1016/j.syapm.2021.126207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
In the Moroccan Middle Atlas, the tailings rich in lead and other metal residues, in the abandoned Zaida mining district, represent a real threat to environment and the neighboring villages' inhabitants' health. In this semi-arid to arid area, phytostabilisation would be the best choice to limit the transfer of heavy metals to populations and groundwater. The aim of this work was to characterize the bacteria that nodulate Retama sphaerocarpa, spontaneous nitrogen fixing shrubby legume, native to the Zaida mining area, with great potential to develop for phytostabilisation. Forty-three bacteria isolated from root nodules of the plant were characterized. Based on REP-PCR and ARDRA, four strains were selected for further molecular analyzes. The 16S rRNA gene sequences analysis revealed that the isolated strains are members of the genus Bradyrhizobium, and the phylogenetic analysis of the housekeeping genes glnII, atpD, gyrB, rpoB, recA and dnaK individual sequences and their concatenation showed that the strains are close to B. algeriense RST89T and B. valentinum LmjM3T with similarity percentages of 89.07% to 95.66% which suggest that the newly isolated strains from this mining site may belong to a potential novel species. The phylogeny of the nodA and nodC genes showed that the strains belong to the symbiovar retamae of the genus Bradyrhizobium. These strains nodulate also R. monosperma, R. dasycarpa and Lupinus luteus.
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Affiliation(s)
- Soufiane Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Hanane Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | | | - Hanaa Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080 Granada, Spain
| | - Mustapha Missbah El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco.
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Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil. Curr Microbiol 2021; 78:2165-2172. [PMID: 33839887 DOI: 10.1007/s00284-021-02462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
A Gram-negative, facultative anaerobic, non-lagellated and rod-shaped bacterium FML-4T was isolated from a chlorothalonil-contaminated soil in Nanjing, China. Phylogenetic analyses of 16S rRNA genes revealed that the strain FML-4T shared the highest sequence similarity of 97.1% with Ciceribacter thiooxidans KCTC 52231T, followed by Rhizobium rosettiformans CCM 7583T (97.0%) and R. daejeonense KCTC 12121T (96.8%). Although the sequence similarities of the housekeeping genes thrC, rceA, glnII, and atpD between strain FML-4T and C. thiooxidans KCTC 52231T were 83.8%, 88.7%, 86.2%, and 92.0%, respectively, strain FML-4T formed a monophyletic clade in the cluster of Rhizobium species. Importantly, the feature gene of the genus Rhizobium, nifH gene (encoding the dinitrogenase reductase), was detected in strain FML-4T but not in C. thiooxidans KCTC 52231T. In addition, strain FML-4T contained the summed feature 8 (C18:1ω7c and/or C18:1ω6c), C19:0 cyclo ω8c and C16:0 as the major fatty acids. Genome sequencing of strain FML-4T revealed a genome size of 7.3 Mbp and a G+C content of 63.0 mol%. Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization, average nucleotide identity (ANI, similarity 77.3-75.4%), and digital DNA-DNA hybridization (dDDH, similarity 24.5-22.3%), it was concluded that strain FML-4T represented a novel species of the genus Rhizobium, for which the name Rhizobium flavescens sp. nov. was proposed (type strain FML-4T = CCTCC AB 2019354T = KCTC 62839T).
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The leguminous trees Vachellia seyal (Del.) and Prosopis juliflora (Swartz) DC and their association with rhizobial strains from the root-influence zone of the grass Sporobolus robustus Kunth. Symbiosis 2021. [DOI: 10.1007/s13199-021-00763-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil ( Lens culinaris Medik.). PLANTS 2020; 10:plants10010015. [PMID: 33374129 PMCID: PMC7823456 DOI: 10.3390/plants10010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.
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Liu X, You S, Liu H, Yuan B, Wang H, James EK, Wang F, Cao W, Liu ZK. Diversity and Geographic Distribution of Microsymbionts Associated With Invasive Mimosa Species in Southern China. Front Microbiol 2020; 11:563389. [PMID: 33250864 PMCID: PMC7673401 DOI: 10.3389/fmicb.2020.563389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022] Open
Abstract
In order to investigated diversity and geographic distribitution of rhizobia associated with invasive Mimosa species, Mimosa nodules and soils around the plants were sampled from five provinces in southern China. In total, 361 isolates were obtained from Mimosa pudica and Mimosa diplotricha in 25 locations. A multi-locus sequence analysis (MLSA) including 16S rRNA, atpD, dnaK, glnA, gyrB, and recA identified the isolates into eight genospecies corresponding to Paraburkhleria mimosarum, Paraburkholderia phymatum, Paraburkholeria carbensis, Cupriavidus taiwanensis, Cupriavidus sp., Rhizobium altiplani, Rhizobium mesoamericanum, and Rhizobium etli. The majority of the isolates were Cupriavidus (62.6%), followed by Paraburkholderia (33.5%) and Rhizobium (2.9%). Cupriavidus strains were more predominant in nodules of M. diplotricha (76.2) than in M. pudica (59.9%), and the distribution of P. phymatum in those two plant species was reverse (3.4:18.2%). Four symbiotypes were defined among the isolates based upon the phylogeny of nodA-nifH genes, represented by P. mimosarum, P. phymatum–P. caribensis, Cupriavidus spp., and Rhizobium spp. The species affiliation and the symbiotype division among the isolates demonstrated the multiple origins of Mimosa rhizobia in China: most were similar to those found in the original centers of Mimosa plants, but Cupriavidus sp. might have a local origin. The unbalanced distribution of symbionts between the two Mimosa species might be related to the soil pH, organic matter and available nitrogen; Cupriavidus spp. generally dominated most of the soils colonized by Mimosa in this study, but it had a particular preference for neutral-alkaline soils with low fertility whereas. While Paraburkholderia spp. preferred more acidic and fertile soils. The Rhizobium spp. tended to prefer neutral–acidic soils with high fertility soils.
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Affiliation(s)
- Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Shenghao You
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Huajie Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Baojuan Yuan
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Haoyu Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, China
| | - Weidong Cao
- Institute of Agricultural Resources and Regional Planning of CAAS, Beijing, China
| | - Zhong Kuan Liu
- Institute of Agro-resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC. Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. Genome Biol Evol 2020; 12:2521-2534. [PMID: 33283865 PMCID: PMC7719227 DOI: 10.1093/gbe/evaa221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alexandru Ilie
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Decorosi
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Viti
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, Queen's University, Kingston, Ontario, Canada
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Franklin JB, Hockey K, Maherali H. Population-level variation in host plant response to multiple microbial mutualists. AMERICAN JOURNAL OF BOTANY 2020; 107:1389-1400. [PMID: 33029783 DOI: 10.1002/ajb2.1543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Multipartite mutualisms are widespread in nature, but population-level variation in these interactions is rarely quantified. In the model multipartite mutualism between legumes, arbuscular mycorrhizal (AM) fungi and rhizobia bacteria, host responses to microbial partners are expected to be synergistic because the nutrients provided by each microbe colimit plant growth, but tests of this prediction have not been done in multiple host populations. METHODS To test whether plant response to associations with AM fungi and rhizobia varies among host populations and whether synergistic responses to microbial mutualists are common, we grew 34 Medicago truncatula populations in a factorial experiment that manipulated the presence or absence of each mutualist. RESULTS Plant growth increased in response to each mutualist, but there were no synergistic effects. Instead, plant response to inoculation with AM fungi was an order of magnitude higher than with rhizobia. Plant response to AM fungi varied among populations, whereas responses to rhizobia were relatively uniform. There was a positive correlation between plant host response to each mutualist but no correlation between AM fungal colonization and rhizobia nodulation of plant roots. CONCLUSIONS The greater population divergence in host response to AM fungi relative to rhizobia, weak correlation in host response to each microbial mutualist, and the absence of a correlation between measures of AM fungal and rhizobia performance suggests that each plant-microbe mutualism evolved independently among M. truncatula populations.
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Affiliation(s)
- James B Franklin
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Kendra Hockey
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Lamin H, Alami S, Bouhnik O, Bennis M, Benkritly S, Abdelmoumen H, Bedmar EJ, Missbah-El Idrissi M. Identification of the endosymbionts from Sulla spinosissima growing in a lead mine tailings in Eastern Morocco as Mesorhizobium camelthorni sv. aridi. J Appl Microbiol 2020; 130:948-959. [PMID: 32866324 DOI: 10.1111/jam.14834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023]
Abstract
AIMS To identify the bacteria nodulating Sulla spinosissima growing profusely in a lead and zinc mine tailings in Eastern Morocco. METHODS AND RESULTS In all, 32 rhizobial cultures, isolated from root nodules of S. spinosissima growing in soils of the mining site, were tolerant to different heavy metals. The ERIC-polymerase chain reaction (PCR) fingerprinting analysis clustered the isolates into seven different groups, and the analysis of the 16S rRNA sequences of four selected representative strains, showed they were related to different species of the genus Mesorhizobium. The atpD, glnII and recA housekeeping genes analysis confirmed the affiliation of the four representative strains to Mesorhizobium camelthorni CCNWXJ40-4T , with similarity percentages varying from 96·30 to 98·30%. The sequences of the nifH gene had 97·33-97·78% similarities with that of M. camelthorni CCNWXJ40-4T ; however, the nodC phylogeny of the four strains diverged from the type and other reference strains of M. camelthorni and formed a separated cluster. The four strains nodulate also Astragalus gombiformis and A. armatus but did not nodulate A. boeticus, Vachellia gummifera, Prosopis chilensis, Cicer arietinum, Lens culinaris, Medicago truncatula, Lupinus luteus or Phaseolus vulgaris. CONCLUSIONS Based on similarities of the nodC symbiotic gene and differences in the host range, the strains isolated from S. spinosissima growing in soils of the Sidi Boubker mining site may form a different symbiovar within Mesorhizobium for which the name aridi is proposed. SIGNIFICANCE AND IMPACT OF THE STUDY In this work, we show that strains of M. camelthorni species nodulating S. spinosissima in the arid area of Eastern Morocco constitute a distinct phylogenetic clade of nodulation genes; we named symbiovar aridi, which encompasses also mesorhizobia from other Mediterranean desert legumes.
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Affiliation(s)
- H Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - S Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - O Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - M Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - S Benkritly
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes (LBRAP), Département de Biotechnologie, Faculté des Sciences, Université d'Oran1 Ahmed Ben Bella, Es Senia, Algeria
| | - H Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - E J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - M Missbah-El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
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Deng T, Qian Y, Chen X, Yang X, Guo J, Sun G, Xu M. Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment. J Microbiol 2020; 58:350-356. [PMID: 32342339 DOI: 10.1007/s12275-020-9471-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/21/2019] [Accepted: 01/22/2020] [Indexed: 11/26/2022]
Abstract
A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, non-spore-forming, and rod-shaped with a single flagellum. Phy-logenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA-DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).
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Affiliation(s)
- Tongchu Deng
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P. R. China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Youfen Qian
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
| | - Jun Guo
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P. R. China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, P. R. China.
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Missbah El Idrissi M, Lamin H, Bouhnik O, Lamrabet M, Alami S, Jabrone Y, Bennis M, Bedmar EJ, Abdelmoumen H. Characterization of Pisum sativum and Vicia faba microsymbionts in Morocco and definition of symbiovar viciae in Rhizobium acidisoli. Syst Appl Microbiol 2020; 43:126084. [PMID: 32423773 DOI: 10.1016/j.syapm.2020.126084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
In this work, we analyzed the diversity of seventy-six bacteria isolated from Pea and faba bean nodules in two regions of Morocco. The molecular diversity was realized using the analysis of the sequences of 16S rRNA and six housekeeping genes (recA, glnII, atpD, dnaK, rpoB and gyrB) and two symbiotic genes (nodA and nodC). The phylogeny of the 16S rRNA gene sequences revealed that all strains belong to the genus Rhizobium, being related to the type strains of R. leguminosarum, R. laguerreae, R. indigoferae, R. anhuiense and R. acidisoli. The housekeeping genes phylogenies showed that some strains formed a subclade distinct from the rhizobial species that usually nodulate Vicia faba and Pisum sativum which are closely related to R. acidisoli FH23 with sequence similarity of 98.3%. Analysis of the PGPR activities of the different isolates showed that the strains related to R. laguerreae were able to solubilize phosphates and to produce siderophores and auxin phytohormone. However, R. acidisoli strain F40D2 was unable to solubilize phosphates although they produce siderophores and IAA. The phylogenetic analysis of the nodA and nodC sequences showed that all isolated strains were closely related with the strains of symbiovar viciae. The nodulation tests confirmed the ability to nodulate V. faba and P. sativum but not Cicer arietinum or Phaseolus vulgaris. Hence, in Morocco P. sativum is nodulated by R. laguerreae; whereas V. faba is nodulated by R. laguerreae and the symbiovar viciae of R. acidisoli which has been not previously described in this species.
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Affiliation(s)
- Mustapha Missbah El Idrissi
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco.
| | - Hanane Lamin
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Soufiane Alami
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Youssef Jabrone
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco; Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080 Granada, Spain
| | - Meryeme Bennis
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080 Granada, Spain
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, Morocco
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Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture. Microorganisms 2020; 8:microorganisms8040608. [PMID: 32331293 PMCID: PMC7232506 DOI: 10.3390/microorganisms8040608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/06/2020] [Accepted: 04/16/2020] [Indexed: 01/31/2023] Open
Abstract
A flagellate, rod–shaped bacterium designated strain M15T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140T (99.64%) and Rhizobium pusense NRCPB10T (99.36%), respectively. The complete genome of the strain M15T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140T (88.11%, 54.80%), R. pusense NRCPB10T (86.00%, 53.00%) and R. nepotum 39/7T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15T (=JCM 32903T = ACCC 60121T), and the strain M15T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.
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The ACC-Deaminase Producing Bacterium Variovorax sp . CT7.15 as a Tool for Improving Calicotome villosa Nodulation and Growth in Arid Regions of Tunisia. Microorganisms 2020; 8:microorganisms8040541. [PMID: 32283666 PMCID: PMC7232455 DOI: 10.3390/microorganisms8040541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Calicotome villosa is a spontaneous Mediterranean legume that can be a good candidate as pioneer plants to limit regression of vegetation cover and loss of biodiversity in Tunisian arid soils. In order to grow legumes in such soils, pairing rhizobia and nodule associated bacteria (NAB) might provide numerous advantages. In this work, cultivable biodiversity of rhizobial symbionts and NAB in nodules of C. villosa plants growing in five arid regions of south Tunisia was characterized. Phylogenetic analysis using 16S rDNA gene, dnak, recA and nodD sequences separated nodule-forming bacteria in six clades associated to genera Ensifer, Neorhizobium, Phyllobacterium and Rhizobium. Among NAB, the strain Variovorax sp. CT7.15 was selected due to its capacity to solubilise phosphate and, more interestingly, its high level of aminocyclopropane-1-carboxylate deaminase (ACC deaminase) activity. C. villosa plants were inoculated with representative rhizobia of each phylogenetic group and co-inoculated with the same rhizobia and strain CT7.15. Compared with single rhizobia inoculation, co-inoculation significantly improved plant growth and nodulation, ameliorated plant physiological state and increased nitrogen content in the plants, independently of the rhizobia used. These results support the benefits of pairing rhizobia and selected NAB to promote legume growth in arid or degraded soils.
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Ruan ZP, Cao WM, Zhang X, Liu JTY, Zhu JC, Hu B, Jiang JD. Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China. Curr Microbiol 2020; 77:1117-1124. [PMID: 31982965 DOI: 10.1007/s00284-020-01889-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
Abstract
A Gram-stain-negative, facultative aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, designated strain NAU-18T was isolated from an oil-contaminated soil in China. Strain NAU-18T could grow at 10-42 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum, 0.5% NaCl in R2A). The predominant fatty acids were C18:1ω7c (71.2%) and Summed feature 2 (5.1%), representing 76.3% of the total fatty acids. The major respiratory quinones were Q9 and Q10. The DNA G + C content of strain NAU-18T was 61.4 mol% based on its draft genome sequence. Genome annotation of strain NAU-18T predicted the presence of 6668 genes, of which 6588 are coding proteins and 80 are RNA genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NAU-18T was a member of the genus Rhizobium and showed 96.93% (with 93.2% coverage) and 96.81% (with 100% coverage) identities with those of Neorhizobium alkalisoli CCBAU 01393T and Rhizobium oryzicola ZYY136T, respectively. In the phylogenetic analysis, strain NAU-18T and R. oryzicola ZYY136T are consistently placed in the same branch. Strain NAU-18T represents a novel species within the genus Rhizobium, for which the name Rhizobium terrae sp. nov. is proposed, with the type strain NAU-18T (=KCTC 62418T = CCTCC AB 2018075T).
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Affiliation(s)
- Zhe-Pu Ruan
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei-Miao Cao
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing-Tian-Yi Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Chun Zhu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Experimental Biology Education Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Hu
- Experimental Biology Education Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae. Genes (Basel) 2019; 10:genes10120991. [PMID: 31805683 PMCID: PMC6947851 DOI: 10.3390/genes10120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.
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Rocha G, Le Queré A, Medina A, Cuéllar A, Contreras JL, Carreño R, Bustillos R, Muñoz-Rojas J, Villegas MDC, Chaintreuil C, Dreyfus B, Munive JA. Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov. Arch Microbiol 2019; 202:309-322. [PMID: 31659382 PMCID: PMC7012998 DOI: 10.1007/s00203-019-01744-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 11/30/2022]
Abstract
In northern Mexico, aridity, salinity and high temperatures limit areas that can be cultivated. To investigate the nature of nitrogen-fixing symbionts of Phaseolus filiformis, an adapted wild bean species native to this region, their phylogenies were inferred by MLSA. Most rhizobia recovered belong to the proposed new species Ensifer aridi. Phylogenetic analyses of nodC and nifH show that Mexican isolates carry symbiotic genes acquired through horizontal gene transfer that are divergent from those previously characterized among bean symbionts. These strains are salt tolerant, able to grow in alkaline conditions, high temperatures, and capable of utilizing a wide range of carbohydrates and organic acids as carbon sources for growth. This study improves the knowledge on diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico and further enlarges the spectrum of microsymbiont with which Phaseolus species can interact with, including cultivated bean varieties, notably under stressed environments. Here, the species Ensifer aridi sp. nov. is proposed as strain type of the Moroccan isolate LMR001T (= LMG 31426T; = HAMBI 3707T) recovered from desert sand dune.
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Affiliation(s)
- Guadalupe Rocha
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Antoine Le Queré
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - Arturo Medina
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Alma Cuéllar
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - José-Luis Contreras
- Facultad de Arquitectura, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Ricardo Carreño
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Rocío Bustillos
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Jesús Muñoz-Rojas
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - María Del Carmen Villegas
- Helyx Affaires SC, Rumania 923-2. Col. Portales-Sur. Alcaldía Benito Juárez, CP-03300, Cd. de México, Mexico
| | - Clémence Chaintreuil
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - Bernard Dreyfus
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - José-Antonio Munive
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico.
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Zhao T, Cheng K, Cao YH, Ouwehand AC, Jiao CF, Yao S. Identification and Antibiotic Resistance Assessment of Ensifer adhaerens YX1, a Vitamin B 12 -Producing Strain Used as a Food and Feed Additive. J Food Sci 2019; 84:2925-2931. [PMID: 31546283 DOI: 10.1111/1750-3841.14804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022]
Abstract
This study provides phenotypic and molecular analyses of the antibiotic resistance of Ensifer adhaerens strain YX1 (CICC 11008s), a strain that was identified using a polyphasic taxonomy approach. The antibiotic resistance profile of E. adhaerens YX1 was assessed using the Clinical & Laboratory Standards Inst. (CLSI) method. The strain was susceptible to ciprofloxacin, levofloxacin, norfloxacin, ofloxacin, gentamicin, tobramycin, chloramphenicol, tetracycline, imipenem, and ceftazidime, and resistant to kanamycin, streptomycin, fosfomycin, and nitrofurantoin. The antibiotic resistance genes nsfA, nsfB, fosA, aph, and aadA1 were not detected in E. adhaerens YX1 via PCR using gene-specific primers. Subsequently, the genome sequence of E. adhaerens was screened for antibiotic genes. Although no antibiotic resistance genes were identified using the ResFinder database, five genes copies of one resistance gene, adeF, were detected using the Comprehensive Antibiotic Resistance Database (CARD). The results of this study will be useful for understanding the phenotypic and genotypic aspects of E. adhaerens antibiotic resistance. No safety issues were identified for E. adhaerens YX1 in terms of antibiotic resistance. Performing similar studies will be conducive to the safety assessment and control of the use of E. adhaerens in the food and feed industry. PRACTICAL APPLICATION: Few relevant reports are currently available regarding antibiotic resistance assessments or other safety evaluations for Ensifer adhaerens. Because of a lack of relevant information on the safety of this bacterium, including the genetic basis of antibiotic resistance in the production strain, it has not been recommended for use in the "qualified presumption of safety" (QPS) list and subsequent updated lists. The current study shows no safety issue of E. adhaerens YX1 in terms of its antibiotic resistance. These results are important as they provide an initial basis for an understanding of the antibiotic resistance/susceptibility of E. adhaerens YX1 (CICC 11008s), which produces vitamin B12 and is widely used in the food and feed industry.
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Affiliation(s)
- Ting Zhao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Kun Cheng
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Yan-Hua Cao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Arthur C Ouwehand
- DuPont Nutrition & Health, Sokeritehtaantie 20, 02460, Kantvik, Finland
| | - Cui-Feng Jiao
- Hebei Yuxing Bio-engineering Co., Ltd., Xicheng District, Ningjin, Xingtai, Heibei, 055550, China
| | - Su Yao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
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Bouhnik O, ElFaik S, Alami S, Talbi C, Lamin H, Abdelmoumen H, Tortosa Muñoz G, J. Bedmar E, Missbah El Idrissi M. Ensifer fredii symbiovar vachelliae nodulates endemic Vachellia gummifera in semiarid Moroccan areas. Syst Appl Microbiol 2019; 42:125999. [DOI: 10.1016/j.syapm.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
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Lamin H, Alami S, Bouhnik O, ElFaik S, Abdelmoumen H, Bedmar EJ, Missbah-El Idrissi M. Nodulation of Retama monosperma by Ensifer aridi in an Abandonned Lead Mine Soils in Eastern Morocco. Front Microbiol 2019; 10:1456. [PMID: 31396163 PMCID: PMC6663986 DOI: 10.3389/fmicb.2019.01456] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/11/2019] [Indexed: 12/02/2022] Open
Abstract
Millions tons of lead and zinc wastes from the abandoned Touissit mine are stored in the open air as dikes in the vicinity of the villages in Eastern Morocco and pose a real danger to both the environment and local populations. To prevent the movement of minerals to the nearby villages and limit the damages to the environment and health, we proposed the nitrogen-fixing leguminous shrub Retama monosperma, as a model plant to use for phytostabilization experimentations. This plant species is known by its ability to grow in hard climatic conditions and in heavy metals contaminated soils. The isolation of bacterial strains nodulating R. monosperma in the abandoned mine soils will permit the selection of rhizobia to inoculate young plant seedlings before their use for the phytostabilization of the mine tailings. In this work, 44 bacteria were isolated from the root nodules of R. Monosperma grown in the Touissit abandoned mine. Twenty-four isolates were considered as true rhizobia as they possess a copy of the nodC symbiotic gene and were able to renodulate their original host. The phenotypic characterization showed that all the strains are tolerant in vitro to different concentrations of heavy metals. The analysis of the 16S rRNA sequences of two selected representative strains showed they were related to different strains of Ensifer aridi isolated from different legumes in three continents deserts. The glnII, recA, and gyrB housekeeping genes analysis confirmed the affiliation of the strains to E. aridi. Moreover, the phylogenic analysis of nodA, nodC, and nifH symbiotic genes showed that the strains are more related to E. aridi JNVUTP6 species isolated from Tephrosia purpurea root nodules in the Thar Desert in India. To our knowledge, this is the first report about the isolation of E. aridi from R. monosperma root nodules.
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Affiliation(s)
- Hanane Lamin
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Soufiane Alami
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Omar Bouhnik
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Salma ElFaik
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mustapha Missbah-El Idrissi
- Center for Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Alami S, Lamin H, Bouhnik O, El Faik S, Filali-Maltouf A, Abdelmoumen H, Bedmar EJ, Missbah El Idrissi M. Astragalus algarbiensis is nodulated by the genistearum symbiovar of Bradyrhizobium spp. in Morocco. Syst Appl Microbiol 2019; 42:440-447. [DOI: 10.1016/j.syapm.2019.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/07/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
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de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, Lassalle F, Lindström K, Mhamdi R, Martínez-Romero E, Moulin L, Mousavi SA, Nesme X, Peix A, Puławska J, Steenkamp E, Stępkowski T, Tian CF, Vinuesa P, Wei G, Willems A, Zilli J, Young P. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852-1863. [PMID: 31140963 DOI: 10.1099/ijsem.0.003426] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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Affiliation(s)
| | - Mitchell Andrews
- 2Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Julie Ardley
- 3School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | | | - Estelle Jumas-Bilak
- 5UMR 5569, Department of Microbiology, Faculty of Pharmacy, University of Montpellier, France
| | - Nemanja Kuzmanović
- 6Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Florent Lassalle
- 7Department of Infectious Disease Epidemiology - MRC Centre for Outbreak Analysis and Modelling, St Mary's Hospital, Praed Street, London W2 1NY, UK
| | - Kristina Lindström
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Ridha Mhamdi
- 9Centre of Biotechnology of Borj-Cedria, BP 901 Hammam-lif 2050, Tunisia
| | - Esperanza Martínez-Romero
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Lionel Moulin
- 11IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Seyed Abdollah Mousavi
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Xavier Nesme
- 12LEM, UCBL, CNRS, INRA, Univ Lyon, Villeurbanne, France
| | - Alvaro Peix
- 13Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Joanna Puławska
- 14Department of Phytopathology, Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Emma Steenkamp
- 15Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Tomasz Stępkowski
- 16Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Chang-Fu Tian
- 17State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China
| | - Pablo Vinuesa
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Gehong Wei
- 18Northwest A&F University, Yangling, Shaanxi, PR China
| | - Anne Willems
- 19Department Biochemistry and Microbiology, Lab. Microbiology, Ghent University, Belgium
| | - Jerri Zilli
- 20Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, Brazil, 23891-000, Brazil
| | - Peter Young
- 21Department of Biology, University of York, York YO10 5DD, UK
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Bünger W, Grönemeyer JL, Sarkar A, Reinhold-Hurek B. Bradyrhizobium ripae sp. nov., a nitrogen-fixing symbiont isolated from nodules of wild legumes in Namibia. Int J Syst Evol Microbiol 2018; 68:3688-3695. [DOI: 10.1099/ijsem.0.002955] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, Center of Bioolecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, Center of Bioolecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
| | - Abhijit Sarkar
- Department of Microbe-Plant Interactions, Center of Bioolecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Center of Bioolecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
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De Meyer SE, Ruthrof KX, Edwards T, Hopkins AJ, Hardy G, O’Hara G, Howieson J. Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining. Syst Appl Microbiol 2018; 41:641-649. [DOI: 10.1016/j.syapm.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
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Hang P, Zhang L, Zhou XY, Hu Q, Jiang JD. Rhizobium album sp. nov., isolated from a propanil-contaminated soil. Antonie van Leeuwenhoek 2018; 112:319-327. [PMID: 30178161 DOI: 10.1007/s10482-018-1160-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/30/2018] [Indexed: 10/28/2022]
Abstract
A novel Gram-stain negative, facultatively anaerobic, non-spore-forming, motile and rod-shaped bacterium (NS-104T) was isolated from a propanil-contaminated soil in Nanjing, China. Growth occurred at pH 5.0-9.0 (optimum 6.0), 16-37 °C (optimum 30 °C) and in the presence of 0-2.0% (w/v) NaCl (optimum, without NaCl). Strain NS-104T showed high 16S rRNA gene sequence identity to Rhizobium azooxidifex DSM 100211T (96.7%). The phylogenetic analysis of the 16S rRNA gene as well as the housekeeping genes recA, atpD and glnA demonstrated that strain NS-104T belongs to the genus Rhizobium. Strain NS-104T did not form nodules on six different legumes, and the nodD, nodC and nifH genes were neither amplified by PCR nor found in the draft genome of strain NS-104T. The sole respiratory quinone was ubiquinone Q-10. The polar lipid profile included the major amounts phosphatidylmonomethylethanolamine, phosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and unidentified aminolipids. The major cellular fatty acids were C18:1ω7c (39.6%), C19:0 cyclo ω8c (29.8%) and C16:0 (11.5%). The G + C content of strain NS-104T was 61.9 mol%. Strain NS-104T therefore represents a new species, for which the name Rhizobium album sp. nov. is proposed, with the type strain NS-104T (= KCTC 62327T = CCTCC AB 2017250T).
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Affiliation(s)
- Ping Hang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xi-Yi Zhou
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Liu LX, Liu SX, Wang YM, Bi JC, Chen HM, Deng J, Zhang C, Hu QS, Li CF. Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk. Int J Syst Evol Microbiol 2018; 68:3125-3131. [PMID: 30132753 DOI: 10.1099/ijsem.0.002947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7T (=CGMCC 1.15338T=JCM 31140T).
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Affiliation(s)
- Long-Xiang Liu
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Si-Xin Liu
- 2College of Materials and Chemical Engineering, Hainan University, Haikou 570228, PR China.,1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Yan-Mei Wang
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Ji-Cai Bi
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Hua-Mei Chen
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Jian Deng
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Cui Zhang
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Qi-Song Hu
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Cong-Fa Li
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
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Msaddak A, Rejili M, Durán D, Rey L, Palacios JM, Imperial J, Ruiz-Argüeso T, Mars M. Definition of two new symbiovars, sv. lupini and sv. mediterranense, within the genera Bradyrhizobium and Phyllobacterium efficiently nodulating Lupinus micranthus in Tunisia. Syst Appl Microbiol 2018; 41:487-493. [PMID: 29803609 DOI: 10.1016/j.syapm.2018.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/21/2018] [Accepted: 04/14/2018] [Indexed: 10/17/2022]
Abstract
In this study, a polyphasic approach was used to analyze three representative strains (LmiH4, LmiM2 and LmiT21) from a collection of six previously described strains isolated in Tunisia from root nodules of Lupinus micranthus. The phylogenetic analysis of the concatenated rrs, recA and glnII genes showed that strain LmiH4 had 100% concatenated gene sequence identity with the type strain Bradyrhizobium retamae Ro19T. Similarly, strain LmiM2 shared 100% concatenated gene sequence identity with the species Bradyrhizobium valentinum LmjM3T. However, strain LmiT21 showed an identical concatenated gene sequence with reference strain Phyllobacterium sophorae CCBAU03422T. The recA-glnII concatenated protein-coding genes used produced incongruent phylogenies compared with 16S rDNA phylogeny. The nodC gene analysis showed that the strains were phylogenetically divergent to the Bradyrhizobium symbiovars defined to date, and represented two new symbiovars. Plant infection analysis revealed that the three strains showed moderate host range and symbiotic specificities. Based on their symbiotic characteristics, we propose that the three strains isolated from Lupinus micranthus nodules belong to two new symbiovars, with the first denominated lupini within the two species Bradyrhizobium valentinum (type strain LmiM2) and B. retamae (type strain LmiH4), and the second denominated mediterranense within the species P. sophorae (type strain LmiT21).
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Affiliation(s)
- Abdelhakim Msaddak
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia.
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | | | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
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Siddiqi MZ, Choi GM, Im WT. Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:482-486. [DOI: 10.1099/ijsem.0.002438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Gyu-Min Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
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Coba de la Peña T, Fedorova E, Pueyo JJ, Lucas MM. The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle? FRONTIERS IN PLANT SCIENCE 2018; 8:2229. [PMID: 29403508 PMCID: PMC5786577 DOI: 10.3389/fpls.2017.02229] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/19/2017] [Indexed: 05/21/2023]
Abstract
In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.
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Affiliation(s)
- Teodoro Coba de la Peña
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Elena Fedorova
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- K. A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia
| | - José J Pueyo
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
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Grönemeyer JL, Bünger W, Reinhold-Hurek B. Bradyrhizobium namibiense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of Lablab purpureus, hyacinth bean, in Namibia. Int J Syst Evol Microbiol 2017; 67:4884-4891. [DOI: 10.1099/ijsem.0.002039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, Center of Molecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
| | - Wiebke Bünger
- Department of Microbe-Plant Interactions, Center of Molecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Center of Molecular Interactions Bremen (CBIB), Faculty of Biology and Chemistry, University of Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
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42
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Degefu T, Wolde-Meskel E, Rasche F. Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia. Int J Syst Evol Microbiol 2017; 68:449-460. [PMID: 29143730 DOI: 10.1099/ijsem.0.002486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δ15N analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I-IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δ15N-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ15N=0.73) and GN102 (δ15N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.
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Affiliation(s)
- Tulu Degefu
- School of Applied Natural Sciences, Applied Biology Program, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593 Stuttgart, Germany
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43
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Msaddak A, Rejili M, Durán D, Rey L, Imperial J, Palacios JM, Ruiz-Argüeso T, Mars M. Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils. FEMS Microbiol Ecol 2017; 93:3828104. [PMID: 28505340 DOI: 10.1093/femsec/fix068] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/12/2017] [Indexed: 11/14/2022] Open
Abstract
The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga.
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Affiliation(s)
- Abdelhakim Msaddak
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain.,CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Jose Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Tomas Ruiz-Argüeso
- CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
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44
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Deng T, Chen X, Zhang Q, Zhong Y, Guo J, Sun G, Xu M. Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment. Int J Syst Evol Microbiol 2017; 67:4710-4715. [DOI: 10.1099/ijsem.0.002367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tongchu Deng
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
| | - Qin Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
| | - Yuming Zhong
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, PR China
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45
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de Matos GF, Zilli JE, de Araújo JLS, Parma MM, Melo IS, Radl V, Baldani JI, Rouws LFM. Bradyrhizobium sacchari sp. nov., a legume nodulating bacterium isolated from sugarcane roots. Arch Microbiol 2017; 199:1251-1258. [PMID: 28601967 DOI: 10.1007/s00203-017-1398-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/07/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
Members of the genus Bradyrhizobium are well-known as nitrogen-fixing microsymbionts of a wide variety of leguminous species, but they have also been found in different environments, notably as endophytes in non-legumes such as sugarcane. This study presents a detailed polyphasic characterization of four Bradyrhizobium strains (type strain BR 10280T), previously isolated from roots of sugarcane in Brazil. 16S rRNA sequence analysis, multilocus sequence analysis (MLSA) and analysis of the 16S-23S rRNA internal transcribed spacer showed that these strains form a novel clade close to, but different from B. huanghuaihaiense strain CCBAU 23303T. Average nucleotide identity (ANI) analyses confirmed that BR 10280T represents a novel species. Phylogenetic analysis based on nodC gene sequences also placed the strains close to CCBAU 23303T, but different from this latter strain, the sugarcane strains did not nodulate soybean, although they effectively nodulated Vigna unguiculata, Cajanus cajan and Macroptilium atropurpureum. Physiological traits are in agreement with the placement of the strains in the genus Bradyrhizobium as a novel species for which the name Bradyrhizobium sacchari sp. nov. is proposed.
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Affiliation(s)
- Gustavo Feitosa de Matos
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
- Universidade Federal Rural do Rio de Janeiro, Curso de Pós-graduação em Fitotecnia, Rodovia BR 465 km 07, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | - Jerri Edson Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | | | - Marcia Maria Parma
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Itamar Soares Melo
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Viviane Radl
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landtraße 1, 85764, Oberschleißheim, Germany
| | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
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46
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Tóth E, Szuróczki S, Kéki Z, Bóka K, Szili-Kovács T, Schumann P. Gellertiella hungarica gen. nov., sp. nov., a novel bacterium of the family Rhizobiaceae isolated from a spa in Budapest. Int J Syst Evol Microbiol 2017; 67:4565-4571. [DOI: 10.1099/ijsem.0.002332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Erika Tóth
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Sára Szuróczki
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Tibor Szili-Kovács
- Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Herman O. Str. 15, Hungary
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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47
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Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:4314-4325. [PMID: 28220509 DOI: 10.1002/jsfa.8281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in European soils. The aim of this study was to study the genetic and phenotypic diversity of indigenous cowpea-nodulating rhizobia in Greece. RESULTS The genetic diversity of indigenous rhizobia associated with cowpea was investigated through a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into three groups. Based on the analysis of the 16S rRNA genes, IGS and on the concatenation of six housekeeping genes (recA, glnII, gyrB, truA, thrA and SMc00019), rhizobial isolates were classified within the species Ensifer fredii. However, symbiotic gene phylogenies, based on nodC, nifH and rhcRST genes, showed that the Ensifer isolates are markedly diverged from type and reference strains of E. fredii and formed one clearly separate cluster. The E. fredii strains were able to nodulate and fix nitrogen in cowpea but not in soybean and common bean. CONCLUSION The present study showed that cowpea is nodulated under field conditions by fast-growing rhizobia belonging to the species E. fredii. Based on the phylogenies, similarity levels of symbiotic genes and the host range, the Ensifer isolates may constitute a new symbiovar for which the name 'aegeanense' is proposed. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Christos T Fotiadis
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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48
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Molecular and phenotypic characterization of endophytic bacteria isolated from sulla nodules. Microb Pathog 2017; 111:225-231. [DOI: 10.1016/j.micpath.2017.08.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/18/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022]
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49
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Benedetti VP, Savi DC, Aluizio R, Adamoski D, Kava-Cordeiro V, Galli-Terasawa LV, Glienke C. Analysis of the genetic diversity of Candida isolates obtained from diabetic patients and kidney transplant recipients. Mem Inst Oswaldo Cruz 2017; 0:0. [PMID: 27276363 PMCID: PMC4957493 DOI: 10.1590/0074-02760160042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/16/2016] [Indexed: 11/22/2022] Open
Abstract
Yeasts of the genus Candida have high genetic variability and are the most common opportunistic pathogenic fungi in humans. In this study, we evaluated the genetic diversity among 120 isolates of Candida spp. obtained from diabetic patients, kidney transplant recipients and patients without any immune deficiencies from Paraná state, Brazil. The analysis was performed using the ITS1-5.8S-ITS2 region and a partial sequence of 28S rDNA. In the phylogenetic analysis, we observed a consistent separation of the species C. albicans, C. dubliniensis, C. glabrata, C. tropicalis, C. parapsilosis, C. metapsilosis and C. orthopsilosis, however with low intraspecific variability. In the analysis of the C. albicans species, two clades were formed. Clade A included the largest number of isolates (91.2%) and the majority of isolates from GenBank (71.4%). The phylogenetic analysis showed low intraspecific genetic diversity, and the genetic polymorphisms between C. albicans isolates were similar to genetic divergence found in other studies performed with isolates from Brazil. This low genetic diversity of isolates can be explained by the geographic proximity of the patients evaluated. It was observed that yeast colonisation was highest in renal transplant recipients and diabetic patients and that C. albicans was the species most frequently isolated.
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Affiliation(s)
- Volmir Pitt Benedetti
- Universidade Paranaense, Universidade Paranaense, Departamento de Microbiologia, Francisco Beltrão PR , Brasil, Universidade Paranaense, Departamento de Microbiologia, Francisco Beltrão, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil
| | - Daiani Cristina Savi
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Rodrigo Aluizio
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Douglas Adamoski
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Vanessa Kava-Cordeiro
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Lygia V Galli-Terasawa
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Chirlei Glienke
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
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50
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Kaczmarek M, Mullett MS, McDonald JE, Denman S. Multilocus sequence typing provides insights into the population structure and evolutionary potential of Brenneria goodwinii, associated with acute oak decline. PLoS One 2017; 12:e0178390. [PMID: 28570630 PMCID: PMC5453491 DOI: 10.1371/journal.pone.0178390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/14/2017] [Indexed: 11/18/2022] Open
Abstract
Brenneria goodwinii is one of the most frequently isolated Gram-negative bacteria from native oak species, Quercus robur and Q. petraea, affected by acute oak decline (AOD) in the UK. We investigated the population biology of this bacterial species using a multilocus sequence analysis to determine the population structure and evolutionary potential. Seven partial housekeeping genes were used in the analyses. Amongst 44 bacterial strains from seven different locations, we identified 22 unique sequence types [STs]; only one ST was found at two separate locations. Phylogenetic and cluster-based analyses suggested that B. goodwinii STs form two main distinct groups; however, no geographical pattern of their distribution could be observed. Clonality and recombination tests demonstrated that the studied population is primarily clonal, however both mutation and recombination processes play a role in shaping the genetic structure and evolution of the population. Our study suggests that the B. goodwinii population on oak in the UK has an endemic form, with background recombination appearing to generate new alleles more frequently than mutation, despite the introduction of nucleotide substitutions being approximately twice less likely than mutation. The newly emerged STs subsequently undergo clonal expansion to become dominant genotypes within their specific geographical locations and even within the individual host oak trees.
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Affiliation(s)
- Maciej Kaczmarek
- Bangor University, School of Biological Sciences, Bangor, Gwynedd, United Kingdom
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
- * E-mail: (SD); (MK)
| | - Martin S. Mullett
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - James E. McDonald
- Bangor University, School of Biological Sciences, Bangor, Gwynedd, United Kingdom
| | - Sandra Denman
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
- * E-mail: (SD); (MK)
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