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

Flavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing plant growth promoting potential

Members of the genera Flavobacterium, Chryseobacterium and Sphingomonas constitute a group of microorganisms in the rhizosphere associated with plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of five selected strains. Overall genome relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genera Flavobacterium, Chryseobacterium and Sphingomonas were found to be below the established thresholds, respectively. Morphological, physiological, and biochemical characteristics of the strains confirmed their status as five novel species. A large variety of genes involved in plant growth promotion and carbohydrate utilization were found in all strains suggesting a contribution of all strains to PGP. Based on the result of the polyphasic characterization, the following names are proposed: Chryseobacterium terrae sp. nov., with the strain ST-37T as the type strain (= CCM 9260T = LMG 32728T); Flavobacterium plantiphilum sp. nov., with the strain ST-87T as the type strain CIP 112180T = DSM 114790T = LMG 32757T); Flavobacterium rhizophilum sp. nov., with the strain ST-75T as the type strain (= CIP 112185T = DSM 114831T = LMG 32758T); Flavobacterium rhizosphaerae sp. nov., with the strain ST-119T as the type strain (CIP 112181T = DSM 114832T = LMG 32756T); and Sphingomonas plantiphila sp. nov. with the strain ST-64 T as the type strain (= CCM 9261T = CIP 112178T = DSM 114515T = LMG 32729T).

Paenibacillus thermotolerans sp. nov., isolated from a hot spring in Yunnan Province, south-west China

Two Gram-positive, rod-shaped, endospore-forming strains, YIM B05601 and YIM B05602T, were isolated from soil sampled at Hamazui hot spring, Tengchong City, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Paenibacillus, appearing most closely related to Paenibacillus alkalitolerans YIM B00362T (96.9 % sequence similarity). Genome-based phylogenetic analysis confirmed that strains YIM B05601 and YIM B05602T formed a distinct phylogenetic cluster within the genus Paenibacillus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains YIM B05601 and YIM B05602T with the related species P. alkalitolerans YIM B00362T were within the ranges of 74.43-74.57 % and 12.1-18.5 %, respectively, which clearly indicated that strains YIM B05601, YIM B05602T represented a novel species. Strains YIM B05601 and YIM B05602T exhibited 99.6 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 99.8 and 100 %, respectively, suggesting that they belong to the same species. Optimum growth for both strains occurred at pH 7.0 and 45 °C. The diagnostic diamino acid in the cell-wall peptidoglycan of strains YIM B05601 and YIM B05602T was meso-diaminopimelic acid. MK-7 was the predominant menaquinone. The polar lipids of strain YIM B05602T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, four unidentified glycolipids, an unidentified polarlipid and phosphatidylinositol mannoside. The major fatty acids of the two stains were iso-C15 : 0 and anteiso-C15 : 0. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strains YIM B05601 and YIM B05602T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus thermotolerans sp. nov. is proposed. The type strain is YIM B05602T (=CGMCC 1.60051T=KCTC 43460T=NBRC 115924T).

Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil

During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38T and TW40T. Both strains were catalase positive and oxidase negative. Strains TW38T and TW40T demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38T and TW40T affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17T (98.6%) and Paenibacillus arachidis E3T (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38T, TW40T, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38T and TW40T was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38T and TW40T from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38T and TW40T represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38T (= KCTC 43468T = NBRC 116015T) and type strain of Paenibacillus humicola is TW40T (= KCTC 43469T = NBRC 116016T).

Paenibacillus caseinilyticus sp. nov., isolated forest soil

A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78T) was isolated from forest soil. GW78T was catalase-positive and oxidase-negative. The strain was able to grow optimally at 37 °C and at pH 7.0 in Reasoner's 2A media. The phylogenetic and 16S rRNA gene sequence analysis of GW78T showed its affiliation with the genus Paenibacillus. The 16S rRNA gene sequence of GW78T revealed 98.3 % similarity to its nearest neighbour Paenibacillus mucilaginosus VKPM B-7519T. Its chemotaxonomic properties included MK-7 as the sole menaquinone, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine as major polar lipids, and anteiso-C15 : 0, C16 : 1  ω11c and anteiso-C17 : 0 as predominant fatty acids. Digital DNA-DNA hybridization and average nucleotide identity results with its closest relatives were <74.0 % and <14.0 %, respectively. Overall, 16S rRNA gene sequence comparisons, phylogenetic and genomic evidence, and phenotypic and chemotaxonomic data allow the differentiation of GW78T from other members of the genus Paenibacillus. Thus, we propose that strain GW78T represents a novel species of the genus Paenibacillus, with the name Paenibacillus caseinilyticus sp. nov. The type strain is GW78T (=KCTC 43430T=NBRC 116023T).

Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays

A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246^T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4^T (98.4%) and Paenibacillus xanthinolyticus 11N27^T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246^T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246^T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246^T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246^T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246^T (= LMG 32093^T = CCM 9089^T = CIP 111893^T) as the type strain.

Paenibacillus agricola sp. nov., isolated from agricultural soil

A white-coloured, rod-shaped, motile, aerobic, and Gram-stain-positive bacterial strain S3N08^T was isolated from agricultural soil. The strain grew at temperature 10-40 °C, at 0-1.0% (w/v) NaCl concentration, and at pH 6.5-8.0. Catalase was negative and oxidase was positive. The phylogenetic analysis inferred that the strain S3N08^T belonged to the genus Paenibacillus, with the closest relative being Paenibacillus periandrae PM10^T (95.6% 16S rRNA gene sequence similarity). The only menaquinone was MK-7 and the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids were antiso-C_15:0, C_16:0, and iso-C_15:0. The DNA G + C content was 45.1%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain S3N08^T and with closest members were < 72.0% and < 19.0%, respectively. Altogether, the phylogenetic, genomics, phenotypic, and chemotaxonomic evidence illustrated in this study suggested that strain S3N08^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agricola sp. nov. is proposed. The type strain is S3N08^T (= KACC 19666 ^T = NBRC 113430 ^T).