Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

Abstract

An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27T (98.0 %) and Pedobacter agri PB92T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12T were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12T is proposed to represent a novel species of the genus Pedobacter , for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12T (=KCTC 82363T=NBRC 114901T).

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa , a Himalayan medicinal herb

“…isolated from the rhizospheric soil of the medicinal plant Echinacea purpurea helps in root elongation and morphology ( 89 ); the genera was first isolated from roots of rice grown in soil ( 90 ) and also from rhizosphere of barley ( Hordeum secalinum) ( 91 ). Genus Pedobacter has been isolated as endophyte in many plants like maize, Carex pumila , rice, wheat, potato with varied plant growth promotion properties ( 44 , 92 – 95 ). Luteolibacter abundance in the rhizosphere and rhizoplane of Miscanthus x giganteus and its role in heavy metal-contaminated soil remediation has already been reported ( 96 ).…”

Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum

“…Gram reaction was tested by the Gram Stain Solution kit (Difco) according to the manufacturer's instructions. Motility was determined by diffusion growing on MA supplemented with 0.4 % agar [32]. Anaerobic growth was determined after incubation on MA for 7 days at 25 °C in an anaerobic chamber (Coy Scientific).…”

“…To determine the optimal growth medium composition, strain N5 T was tested on different agar media including Luria-Bertani agar (LBA; Difco), Reasoner's 2A agar (R2A; MB Cells), marine agar 2216 (MA; Difco), nutrient agar (NA; beef extract 3.0 gl -1 , peptone 5.0 g l -1 and agar 15.0 gl -1 ) and potato dextrose agar (PDA; Difco), respectively. The temperature range for growth was determined by incubating the bacteria on MA at different temperatures (4,10,15,20,25,30,32,35,37 and 40 °C) for 3 days. The NaCl concentration for growth was determined by incubating the bacteria in marine broth 2216 in the presence of different NaCl concentrations [0-6 % (w/v) NaCl at an interval of 1.0 %] at 25 °C and 150 r.p.m.…”