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Characterization of Tropical Tree Rhizobia and Description of Mesorhizobium Plurifarium Sp

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Characterization of Tropical Tree Rhizobia and Description of Mesorhizobium Plurifarium Sp < Printed in Great Britain > International Journal of Systematic Bacteriology (1998), 48, 369-382 Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Philippe de/Lajudie,’t3 Anne WiIlem~,~~~Giselle Nick,’ Fatima Moreiraf5 Flore Molouba,’ Bart Hostef3Urbain Torckf3Marc Neyra,’ MattR ew D. Collinsf4Kristina LindstrÖm,‘/Bernard Dreyfuslt and Monique Gillis3 Author for correspondence: Monique Gillis. Tel: $32 9 264 5117. Fax: +32 9 264 5092. e-mail: [email protected] 1 Laboratoire de A collection of strains isolated from root nodules of Acacia species in Senegal Microbiologie des Sols, was analysed previously by electrophoresis of total cell protein, ORSTOM BP 1386, Dakar, Senegal, West Africa auxanographic tests, rRNA-DNA hybridization, 165 rRNA gene sequencing, DNA base composition and DNA-DNA hybridization [de Lajudie, P., Willems, A., 2 Department of Applied Chemistry & Microbiology, Pot, B. & 7 other authors (1994). Intl Syst Bacterio/ 44,715-7331. Strains from University of Helsinki, PO Acacia were shown to belong to two groups, Sinorhizobium terangae, and a Box 56, Biocentre 1, so-called gel electrophoretic cluster U, which also included some reference Viikinkaari 9, FIN-O0014 Helsinki, Finland strains from Brazil. Further taxonomic characterization of this group using the same techniques plus repetitive extragenic palindromic-PCR and nodulation 3 Laboratoriumvoor - Microbiologie, Universiteit tests is presented in this paper. Reference strains from Sudan and a number of Gent, K.-L. new rhizobia isolated from nodules of Acacia senegal, Acacia tortilis subsp. Ledeganckstraat 35, B- raddiana and Prosopis ju/Íf/ora in Senegal were included. As a result of this 9000 Ghent, Belgium polyphasic approach, the creation of a new species, Mesorhizobium 4 Microbiology Department, p/urifarÍum, is proposed for a genotypically and phenotypically distinct group Reading Laboratory, Institute of Food Research, corresponding to the former cluster U and containing strains isolated from Whiteknights Road, Acacia, Leucaena, Prosopis and Chamaecrista in West Africa (Senegal), East Reading RG6 6BZ, UK Africa (Sudan) and South America (Brazil). The type strain of Mesorhizobium LMG 5 Escola Superior de plurifarium ORS 1032 has been deposited in the LMG collection as 11892. Agricultura de Lavras, Caixa postal 37, CEP 37200- 970, Lavras MG, Brazil Keywords: tropical tree rhizobia, Acacia, Mesorhizobiuin plurifarium sp. nov., polyphasic taxonomy INTRODUCTION Proteobacteria (for reviews see 25, 48, 49). Although the close relationship between Agrobacterium and I\ In recent years numerous changes have occurred in the Rhizobium has been known for a long time, the classification of the Rhizobium-Agrobacteriunz group complex intertwined relationship of the different ‘1 which, together with the genera Ochrobactrum, Phyllo- species of the group is only gradually being elucidated ;$ bacteriunt, Brucella and Bartonella, constitute a sep- by polyphasic taxonomic studies and 16s rRNA gene arate rRNA cluster in the alpha subclass of the comparisons (6, 13, 14, 36, 39, 46, 47). Within the Agrobacteriunz-Rhizobium rRNA group, several sub- groups can be distinguished: a first sub-group contains Rhizobium leguininosaruin, Rhizobium tropici types A ?Present address: LSTM ORSTOMKIRAD-Foret, Baillarguet, BP 5035, and ByRhizobium etli and Agrobacteriunz biovar 2; a 34032 MontpellierCedex 1, France. second one consists of Rhizobium galegae, Agro- Abbreviations: ARDRA, amplified rDNA restriction analysis; REP-PCR, bacterium biovar 1, Agrobacteriunz vitis and Agro- repetitive extragenic palindromic-PCR; UPGMA, unweighted- pair-group\ bacterium rubi; a third sub-group contains Sino- method with averages. _- _- - - - ‘i rhizobium, including Sinorhizobium Ji-edii, Sino- The EMBLaccessionnumbersfgrthe new sequencedata areY14158for M. plurifariumLMG 11892T,Y14161 forM,p/urifariumLMG10056.Y14159for \ rhizobium terangae, Sinorhizobium saheli, Sinorhizo- bium medicae and Sinorhizobium rneliloti (6, 35); the P. de Laiudie and others fourth sub-group is the most divergent branch from Zhang et al. (50) and genospecies 3 and 4 found among Cicer the other three sublineages and corresponds to the isolates by Nour et al. (30). recently proposed genus Mesorhizobium (16, 20) Growth and culture conditions. All Rhizobium and Brady- including Mesorhizobium loti (15), Mesorhizobizim rhizobium strains were maintained on yeast mannitol agar huakuii (4), Mesorhizobium ciceri (30), cluster U (6), (YMA), containing (g 1-l): mannitol, 10; sodium glutamate, 0.5; K,HPO,, 0.5; MgSO,.7H,O, 0.2; NaC1, 0.05; CaCl,, Rh izobìum t iaiishanense (5), Rhizobium mediterraneum (29) and Rhizobium sp. (Cicer)genomic groups 3 and 4 0.04; FeCl,, 0.004; yeast extract (Difco), 1 ;pH 6.8; agar, 20. Azorhizobium and Agrobacteritim strains were maintained (29). Several emerging rhizobial groups already be can on yeast extract peptone medium (YEB) containing (in g per identified as belonging to Mesorhizobium (18, 28, 31, litre 0.01 M phosphate buffer, pH 7.2): peptone (Oxoid), 5; 43). yeast extract (Oxoid), 1; beef extract (Oxoid), 5; sucrose, 5 In a previous polyphasic study of tropical rhizobia (6) and MgSO, .7H,O, 0.592. All strains were stored at - 80 "C on the same medium plus 15 % (v/v) glycerol. For protein we described a new group belonging to the Meso- and DNA preparations we used tryptone yeast extract rhizobium branch, the so-called cluster U, comprising medium (TY) containing (in g l-l, pH 6.8-7): tryptone strains isolated from different leguminous species in (Oxoid), 5; yeast extract (Oxoid), 0.75; KH,PO,, 0.454; Africa, Brazil and New Zealand. Our results showed Na,HPO,. 12H,O, 2.388; CaCl,, 1; agar, 20 (LabM was that cluster U constituted a separate protein gel used for protein preparation agar). Incubation was at 30 "C electrophoretic cluster. Two representative strains for 48 h for Rhizobium, Sinorhizobium, Mesorhizobium, (ORS 1001 and ORS 1002) had identical 16s rRNA Azorhizobium and Agrobacterium strains, and for 3 d for gene sequences, and showed 98 and 99.6% sequence Bradyrhizobium strains. similarity with M. loti and M. huakzrii, respectively. Morphological tests. Cell dimensions and morphology were The recently proposed species M. mediterraneum has determined on living and Gram-stained cells by phase- 98.7% 16s rRNA gene similarity with cluster U contrast microscopy. representative strain ORS 1001 (29). PAGE of total bacterial proteins. This was performed using small modifications of the procedure of Laemmli (17), as Considerable internal heterogeneity demonstrated in described previously (6). The normalized densitometric cluster U by protein gel electrophoretic and auxano- traces of the protein electrophoretic patterns were grouped graphic results was confirmed by DNA-DNA hybrid- by numerical analysis, using the GelCompar 2.2 software ization which revealed at least two different geno- package (40). The similarity between each pair of traces was species (6). expressed by the Pearson product-moment correlation coefficient (r)converted for convenience to a percentage (32, Here we report more taxonomic data on cluster U, 33). including nodulation tests on diverse legume plants REP-PCR. Cells for DNA isolation were grown at 28 "C in and further genotypic characterization by repetitive 5 ml yeast extract-mannitol broth (19) to saturation. Total extragenic palindromic-PCR (REP-PCR), 16s rRNA DNA was isolated from 1.5 ml cultures using hexadecyl- gene sequencing and DNA-DNA hybridization. We trimethyl ammonium bromide (2). The concentration was found additional members of cluster U by screening verified by comparing the DNA samples with the known more isolates from Senegal. We also included repres- concentrations of LDNA in agarose gel electrophoresis. entatives of the phenotypic clusters previously formed The oligonucleotide primers (41) were synthesized by the , by 60 rhizobial strains from Acacia senega1 and Institute of Biotechnology, University of Helsinki. PCR Prosopis chilensis in the Sudan (50) and representative amplifications were carried out in 25 pl reaction volume strains of genospecies 3 and 4 reported by Nour et al. containing about 50 ng chromosomal DNA, 35 pmol primer (30) within a group of Cicer isolates. As a result of this (BOXAlR or GTG5) or primers (REPlR-1 and REP2-1 or polyphasic approach, we propose the creation of new ERIClR and ERIC2), 1 mM dNTPs, 2 U Dynazyme DNA a polymerase (Finnzymes) and PCR buffer (10 mM Tris/HCl, species, Mesorhizobium plurifarium, for this group pH 8.8 at 20 OC, 7 mM MgCl,, 50 mM KCl,O.l% Triton X- which is clearly separate from the other Mesorhizobium 100, 10 % DMSO, 170 mg BSA ml-l). The amplifications species. were performed with a DNA thermal cycler (Minicycler; MJ Research). For the REP primers the following tem- perature profile was used: initial denaturation at 95 "C for METHODS 6 min, 30 cycles at 94 "C for 1 min, at 40 "C for 1 min and at Bacterial strains. Rhizobium strains were isolated from root 65 "C for 8 min; final extension at 65 "C for 16 min. For nodules harvested on young seedlings of species of Acacia or ERIC, BOX and GTG primers, the first 7 min at 95 "C was Prosopis grown in tubes in the presence of soil suspension as followed by 30 cycles at 94 "C for 1 min, at 52 "C for 1 min, previously described (6). at 65 "C for 8 min; final extension at 65 "C for 16 min. After the reaction, 8 pl of the.products were separated on 1.5 % All strains used are listed in Table 1. They were checked
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