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Frankia Torreyi Sp. Nov., an Actinobacterium Isolated From

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Frankia Torreyi Sp. Nov., an Actinobacterium Isolated From 1 Frankia torreyi sp. nov., an actinobacterium isolated from Comptonia peregrina that 2 effectively nodulates members of Myricaceae and Alnus species 3 4 5 Imen Nouioui1, Faten Ghodhbane-Gtari2, 3, Marlen Jando4, Louis S. Tisa5, Hans-Peter Klenk1, 6 Maher Gtari3* 7 8 1. School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, 9 Newcastle upon Tyne, NE1 7RU, United Kingdom. 10 2. Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST), 11 2092 Tunis, Tunisia. 12 3. Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre 13 Urbain Nord, BP 676-1080 Tunis Cedex, Tunisia. 14 4. Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, 15 Inhoffenstraße 7B, 38124 Braunschweig, Germany. 16 5. Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire. 17 USA. 18 19 Corresponding author: Maher Gtari [email protected] 20 Section: Actinobacteria 21 Keywords: Frankia, symbiosis, chemotaxonomy, phenotyping 22 23 Running title: Description of Frankia torreyi sp. nov. 24 The journal’s contents category (New taxa-Actinobacteria) 25 The GenBank accession numbers of strain CpI1T for 16S rRNA gene and genome sequences 26 are MH423838 and JYFN00000000.1 respectively. 27 28 29 30 1 31 Abstract 32 Strain CpI1T is the first isolate of the genus Frankia that was obtained from Comptonia 33 peregrina root nodules in 1978. In this study, a polyphasic approach was performed to identify 34 the taxonomic position of strain CpI1T among the genus Frankia. It contained meso- 35 Diaminopimelic acid as the diagnostic diamino acid, and had galactose, glucose, mannose, 36 rhamnose, ribose and xylose as cell wall sugars. Polar lipids consisted of phosphatidylinositol 37 (PI), diphosphatidylglycerol (DPG), glycophospholipids (GPL1-3), phosphatidylglycerol (PG), 38 aminophospholipid (APL) and unknown phospholipids (PL1-2) and lipids (L). The predominant 39 menaquinone was MK-9 (H8), while the major fatty acid are iso-C16:0 and C17:1 ω 8c. The 16S 40 rRNA gene sequence identity varied from 97.4 to 99.6 % with the type strains of Frankia 41 species. Phylogenetic analyses based on 16S rRNA gene sequences and multilocus sequence 42 analysis (MLSA) using atp1, ftsZ, dnaK, gyrA and secA gene sequences showed that Frankia 43 alni ACN14aT is the closest phylogenetic relative. The genome size of strain CpI1T is 7.6 Mb 44 with a digital DNA G+C content of 72.4%. Digital DNA:DNA hybridization (dDDH) values 45 between strain CpI1T and its closest phylogenetic relative F. alni ACN14aT was 44.1% well 46 below the threshold of 70 % for distinguishing between bacterial genomic species. Based on 47 the phenotypic, phylogenetic and genomic data, strain CpI1T (= DSM44263T = CECT9035T) 48 warrants its classification as a type strain of a novel species for which the name Frankia torreyi 49 sp. nov. is proposed. 50 51 52 53 54 55 56 57 2 58 Introduction 59 The genus Frankia (Brunchorst 1886) of the family Frankiaceae (Becking 1970) and the order 60 Frankiales (Sen et al. 2014) covers soil-dwelling actinobacteria most of which fix nitrogen in 61 association with diverse dicotyledonous hosts, collectively named actinorhizal plants (Benson 62 and Silvester 1993; Schwencke and Carú 2001; Chaia et al. 2010). Based on single locus marker 63 of either the 16S rRNA (Normand et al. 1996), gyrB (Nouioui et al. 2011) or gln II (Normand 64 et al. 1996; Nouioui et al. 2011), the 16S-23S rRNA internal transcribed spacer (Ghodhbane- 65 Gtari et al. 2010), multilocus sequence analysis (MLSA) [atp1, ftsZ, dnaK, gyrA and secA] 66 (Gtari et al. 2015), or core genome (Tisa et al. 2016) phylogenies, Frankia strains are classified 67 into one of the four groups in line with the host plant specificity (Baker 1987). Cluster 1 68 encompasses strains infective towards Alnus (Betulaceae), Allocasuarina and Casuarina 69 (Casuarinaceae), and Myricaceae, while cluster 2 housed strains that are infective on 70 Coriariaceae, Datiscaceae, Dryadoideae, and Ceanothus (Rhamnaceae). Cluster 3 represents 71 Frankia associated with Elaeagnaceae, Colletieae (Rhamnaceae), Myricaceae, and 72 Gynmmostoma (Casuarinaceae). Additionally, cluster 4 includes atypical Frankia strains, 73 which are devoid from the abilities to fix nitrogen and/or to re-infect their host plants. Recently, 74 two to four species have been validly named within each of the four clusters. Frankia alni 75 (Nouioui et al. 2016), Frankia casuarinae (Nouioui et al. 2016) and Frankia canadensis 76 (Normand et al. 2018) of cluster 1. Frankia coriariae (Nouioui et al. 2017a), “Candidatus 77 Frankia datiscae” (Persson et al. 2011) and Candidatus Frankia californiensis (Normand et al. 78 2017) in cluster 2. Frankia elaeagni (Nouioui et al. 2016), Frankia discariae (Nouioui et al. 79 2017b) and Frankia irregularis (Nouioui et al. 2018a) within cluster 3. Cluster 4 contains 80 Frankia inefficax (Nouioui et al. 2017c), Frankia asymbiotica (Nouioui et al. 2017d) and 81 Frankia saprophytica (Nouioui et al. 2018b). 82 Strain CpI1T is the first isolate of the genus Frankia cultivated from the root nodules of 83 Comptonia peregrina (Callaham et al.1978). It is able to fulfil Koch’s postulates by inducing 84 effective root nodules on its original host plant and other members of Myricaceae and Alnus 85 species (Callaham et al. 1978; Lalonde 1979; Baker 1987; Torrey 1990). Strain CpI1T was 86 subjected to polyphasic taxonomic analysis, which underlined the phenotypic and phylogenetic 87 divergence of this strain from all other Frankia species which warrant its classification as the 88 type strain for a new species Frankia torreyi sp. nov. 89 Materials and methods 3 90 Strain CpI1T was maintained in basic propionate (BAP) medium (Murry et al. 1984) 91 supplemented with NH4Cl together with the type strains of all of the Frankia species (Table 1). 92 Four-week-old cultures were phenotypically characterized using GENIII microplates in an 93 Omnilog device (Biolog Inc., Haywood, USA). The ability of the strain to grow on a wide 94 range of carbon and nitrogen sources, under different pH and salinity conditions, and in the 95 presence of antibiotic or toxic compounds was tested as described previously (Nouioui et al. 96 2016). All of the tests were performed in duplicate. Cell wall sugars, diaminopimelic acids 97 (meso-A2pm; meso-diaminopimelate), fatty acids, menaquinone, and polar lipid patterns were 98 determined as described previously (Nouioui et al. 2016). 99 The 16S rRNA gene sequence obtained from a PCR-product was deposited in the GenBank 100 under accession number MH423838. Similarity matrices of the 16S rRNA gene sequences for 101 strain CpI1Tand the type strains of the Frankia species were performed using the genome to 102 genome distance calculator (GGDC) web server (Meier-Kolthoff et al. 2013a, b). Maximum- 103 likelihood (ML) and Maximum-parsimony (MP) trees were inferred using the same pipeline of 104 GGDC server as described previously (Nouioui et al. 2018a). Multilocus sequence analysis 105 (MLSA) based phylogeny was performed using 5 housekeeping genes (membrane-bound ATP 106 synthase, F1 sector, atpI; DNA gyrase subunit A, gyrA; tubulin-like GTP-binding protein, ftsZ; 107 ATPase secretory preprotein translocase, secA and chaperone Hsp70 in DNA biosynthesis, 108 dnaK). Gene sequences were retrieved from GenBank and concatenated to generate Maximum- 109 likelihood (ML) and Maximum-parsimony (MP) trees with the Mega 6.0 software (Tamura et 110 al. 2013) with 1000 bootstrap replicates. Digital DNA:DNA hybridization (dDDH) between 111 strains CpI1T and the rest of the Frankia species was calculated according to the pipeline of 112 GGDC (formula 2) (http://ggdc.dsmz.de/distcalc2.php). 113 114 Results and discussion 115 After 3-4 weeks incubation in BAP broth medium at 28ºC, strain CpI1T produced nonpigmented 116 cells with branched vegetative hyphae, vesicles and multilocular sporangia (Fig 1). Several 117 studies have confirmed the ability to fix nitrogen and to re-infect its host plant (Callaham et al. 118 1978; Lalonde 1979; Baker 1987; Torrey 1990). Based on several biochemical features, strain 119 CpI1T was easily distinguishable from its nearest relative F. alni ACN14aT. Comparatively, 120 strain CpI1T metabolised α-keto-butyric acid, d-gluconic acid, p-hydroxy-phenylacetic acid, 121 citric acid, bromo-succinic acid, α-keto-glutaricacid, D malic acid and acetic acid, while strain 122 ACN14aT oxidised methyl pyruvate and was found to metabolise D-glucose-6-phosphate, D- 123 fructose-6-phosphatea and guanidine hydrochloride better than strain CpI1T (Table 1). 4 T 124 Whole cell hydrolysates for strain CpI1 contained meso-A2pm, and had galactose, glucose, 125 mannose, xylose, ribose and rhamnose as cell wall sugars in concordance with previous reports 126 (Lechevalier and Ruan, 1984). The polar lipid pattern of strain CpI1T is as previously reported 127 (Lopez et al. 1983) and consisted of phosphatidylinositol (PI), diphosphatidylglycerol (DPG), 128 glycophospholipids (GPL1-3), phosphatidylglycerol (PG), aminophospholipid (APL) and 129 unknown phospholipids (PL1-2) and lipids (L) (Fig. S1). Apart from APL and PL, the polar lipid 130 composition of strain CpI1T is similar to F. alni type strain ACN14aT (Nouioui et al. 2016). The 131 predominant isoprenologue was MK-9(H8) (>20%), while its closest neighbour, strain T T 132 ACN14a , had MK-9(H8) and MK-9(H4). The major fatty acids (>15%) of strain CpI1 were 133 iso-C16:0 and C17:1 ω 8c in agreement with previous study (Tunfid et al. 1989) and which is a 134 similar profile as strain ACN14aT. 135 136 Pairwise 16S rRNA gene sequence similarities of strain CpI1T varied from 97.4-99.6 % with 137 the type strains of Frankia species (Table 2) and showed the highest value with F. alni ACN14aT 138 (99.6%). In Figure 2a, these two strains form together a subclade whithin cluster 2 (Alnus, 139 Allocasuarina, Casuarina and Myricaceae infective strain).
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