Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

Abstract

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

Characteristics and Biological Activity of Exopolysaccharide Produced by Lysobacter sp. MMG2 Isolated from the Roots of Tagetes patula

“…For isolation, the root sample (10 g) was crushed using a sterilized mortar and mixed in 5 mL sterile phosphate-buffered saline (PBS), pH 7.4 (10 mM, Welgene, Gyeongsan, South Korea). Then, the solution was serially diluted up to 10 −5 using a previously described standard method [ 41 , 42 ]. An 800 µL aliquot of this sample was spread onto tryptic soy agar (TSA) plates (Difco) supplemented with 1% glucose ( v / w ; Biopure, Cambridge, MA, USA) and incubated at 30 °C for 7 days.…”

Ideonella oryzae sp. nov., isolated from soil, and Spirosoma liriopis sp. nov., isolated from fruits of Liriope platyphylla

“…Chloroform–methanol–water (65 : 25 : 4, v/v/v) was used to develop the first direction and chloroform–methanol–acetic acid–water (80 : 15 : 12 : 4, v/v/v/v) was used for the second direction. Molybdophosphoric acid (phosphomolybdic acid reagent, 5 % v/v solution in ethanol; Sigma), ninhydrin reagent (0.2 % solution; Sigma), α -naphthol reagent and Zinzadze reagent (molybdenum blue spray reagent, 1.3 %; Sigma) were sprayed on developed plates to identify total polar lipids, aminolipids, glycolipids and phospholipids, respectively [26]. For carotenoid analysis, 10 ml methanol–acetone (1 : 1, v/v) was used to extract the carotenoids and a spectrophotometer (Multiskan GO, Thermo Fisher Scientific) was used to assess the absorption spectrum of the pigments [45].…”

“…ANI and dDDH values were calculated using the ANI calculator from EzBioCloud and Genome-to-Genome Distance Calculator, respectively [30]. Furthermore, phylogenetic trees were reconstructed using an up-to-date bacterial core gene set (UBCG), and genomes of closely related taxa were obtained from the EzBiolcloud Whole Genome database and NCBI Genome Database [26,30,33,34].…”

“…Sequencing of the two novel strains was performed by Macrogen Co., Ltd (Seoul, Republic of Korea) using the Illumina platform sequencer with a pairedend read length of 151 bp, and assembled using the SPAdes analysis version 3.13.0 [22,26]. Genomic contamination and completeness were assessed using the bioinformatics tool CheckM (https://ecogenomics.github.io/CheckM) [26]. The NCBI Prokaryotic Genome Automatic Annotation Pipeline (www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html) and the Rapid Annotation using Subsystems Technology server were used to annotate the estimated genomes [26,31].…”

Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils

“…The optimum pH range for bacterial growth was determined by adjusting the pH of tryptic soy broth (TSB; MBcell) from pH 4 to 10 (at intervals of 1 pH unit) by using citrate/NaH 2 PO 4 (pH 4.0–5.0), phosphate (pH 6.0–8.0) and Tris (pH 9.0–10.0) buffers before sterilizing the growth medium and subsequent cultivation of the bacterial strains at 30 °C for 2 days [44]. Assessment of the hydrolysis of cellulose, starch, chitin, casein, Tween 20, Tween 80 and DNase was conducted as previously described [45]. Other physiological and biochemical properties were tested using the commercial API 20NE, API ZYM and API 50CH systems (all three from bioMérieux) according to the manufacturer’s instructions [46].…”