Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root

Abstract

A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 ^T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the JJ-42 ^T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 ^T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C_15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 ^T from the most closely related species. Thus, JJ-42 ^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 ^T (= LMG 32089 ^T = CCM 9085 ^T = DSM 111786 ^T = CIP 111891 ^T) as the type strain.

Keywords: Endophyte; Genome sequence; Paenibacillus allorhizoplanae; Plant associated; Taxonomy; Zea mays.

Fig. 1

Maximum-likelihood tree showing the phylogenetic position of strain JJ-42 ^T among the closest related Paenibacillus species. The tree was generated in ARB using RAxML (GTR-GAMMA, rapid bootstrap analysis) and based on the 16S rRNA gene sequences between positions 95–1475 according to E. coli numbering (Brosius et al. 1978). GenBank/EMBL/DDBJ accession numbers are given in parentheses. Numbers at branch nodes refer to bootstrap values > 70% (100 replicates). Circle marks nodes that were also present in the maximum-parsimony tree. Larger circles were supported by high bootstrap values in the maximum-parsimony tree. Type strains of Cohnella species were used as outgroup. Bar, 0.1 substitutions per nucleotide position

Fig. 2

Whole-genome-based tree showing the phylogenetic placement of strain JJ-42 ^T among type strains of closely related Paenibacillus species. This minimum evolution tree was inferred using JolyTree (https://gitlab.pasteur.fr/GIPhy/JolyTree). Two publicly available Cohnella type strain genomes were used as an outgroup. The genome sequence accession is specified between parentheses next after each taxon name. Branch supports were assessed by the rate of elementary quartets, as estimated by JolyTree (only supports > 0.5 were specified). Bar, 0.025 nucleotide substitutions per site