Chitinophaga nivalis sp. nov., isolated from forest soil in Pyeongchang, Republic of Korea

Abstract

Rod-shaped Gram-stain-negative, aerobic bacterial strains, designated PC14 and PC15T, were isolated from a forest soil sample collected in Pyeongchang county, Gangwon-do, Republic of Korea. Strains PC14 and PC15T grew at 15–37 °C (optimum, 28–30 °C in tryptone soya agar and Mueller–Hinton agar), hydrolysed chitin and casein, and tolerated pH 8.5 and 2 % (w/v) NaCl. The strains were most closely related to members of the genus Chitinophaga , namely Chitinophaga arvensicola DSM 3695T (98.4 %), Chitinophaga longshanensis Z29T (98.3 %), Chitinophaga ginsengisegetis Gsoil 040T (97.8 %), Chitinophaga polysaccharea MRP-15T (97.8 %) and Chitinophaga niastensis JS16-4T (97.7 %). The type strain grew well on conventional commercial media in the laboratory, including tryptone soya agar, Mueller–Hinton agar, Reasoner's 2A agar, nutrient agar and Luria–Bertani agar. The major polar lipid profile comprised phosphatidylethanolamine, an unidentified aminolipid and unidentified polar lipids. The major respiratory quinone was menaquinone-7. The main fatty acids were iso-C15:0, C16:1 ω5c, C16:0 3-OH, iso-C15:0 3-OH and iso-C17:0 3-OH. The DNA G+C content of the isolated strain based on the whole genome sequence was 46.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains PC14 and PC15T and the reference type strains ranged from 71.0 to 76.5 %, and from 20.3 to 20.7 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain PC15T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Chitinophaga . Therefore, strain PC15T is considered to represent a novel species, for which the name Chitinophaga nivalis sp. nov. is proposed. The type strain is PC15T (=KACC 22893T=JCM 35788T).

Chitinophaga pollutisoli sp. nov., isolated from contaminated sediment

“…MK-7 was identified as the sole respiratory quinone in strain GPA1 T , aligning well with findings in other Chitinophaga members [3][4][5][6][7][8][9][10][32][33][34]. Analysis of cellular fatty acids revealed iso-C 15 : 0 , C 16 : 1 ω5c, and iso-C 17 : 0 3-OH as the major fatty acids (>10.0 % of total fatty acids) in strain GPA1 T , consistent with three reference strains (Table S2).…”

“…The genomes of strains GPA1 T and KACC 19118 T were predicted to contain 5197 and 5443 total genes, respectively, including 5080 and 5329 protein coding sequences, four rRNA operons (16, 23, and 5S rRNA genes), and 63 and 65 tRNA genes, respectively. The G+C contents calculated from the genomes of strains GPA1 T and KACC 19118 T were 53.8 and 55.0 mol%, respectively, aligning closely with the G+C contents observed in Chitinophaga species [3][4][5][6][7][8][9][10]. A summary and comparison of the genomic features of these strains with those of closely related type strains of the genus Chitinophaga are presented in Table 1, revealing generally similar genomic features among them.…”

“…Subsequently, the genus underwent emendation and was established as the type genus of the family Chitinophagaceae within the phylum Bacteroidota [2]. As of April 2024, this genus comprises 47 species with validly published names and eight species with invalidly published names (https://lpsn.dsmz.de/genus/chitinophaga), isolated from diverse environmental habitats including soil [3][4][5], an air conditioner condensate drain line [6], activated sludge [7], plant root [8], arsenic-contaminated soil [9], and vermicompost [10]. Members of the genus Chitinophaga are Gram-stain-negative, non-spore-forming, aerobic rod-shaped bacteria containing menaquinone-7 (MK-7) as the major respiratory quinone, iso-C 15 : 0 , C 16 : 1 ω5c, and iso-C 17 : 0 3-OH as the major cellular fatty acids, and phosphatidylethanolamine (PE) as a major polar lipid [3][4][5][6][7][8][9][10].…”

“…As of April 2024, this genus comprises 47 species with validly published names and eight species with invalidly published names (https://lpsn.dsmz.de/genus/chitinophaga), isolated from diverse environmental habitats including soil [3][4][5], an air conditioner condensate drain line [6], activated sludge [7], plant root [8], arsenic-contaminated soil [9], and vermicompost [10]. Members of the genus Chitinophaga are Gram-stain-negative, non-spore-forming, aerobic rod-shaped bacteria containing menaquinone-7 (MK-7) as the major respiratory quinone, iso-C 15 : 0 , C 16 : 1 ω5c, and iso-C 17 : 0 3-OH as the major cellular fatty acids, and phosphatidylethanolamine (PE) as a major polar lipid [3][4][5][6][7][8][9][10]. The genus Chitinophaga was initially coined to denote bacteria capable of chitin degradation, but interestingly, it has been observed that most Chitinophaga species, except C. pinensis and Chitinophaga filiformis, lack this ability [1,[3][4][5][6][7][8][9][10][11].…”

“…Members of the genus Chitinophaga are Gram-stain-negative, non-spore-forming, aerobic rod-shaped bacteria containing menaquinone-7 (MK-7) as the major respiratory quinone, iso-C 15 : 0 , C 16 : 1 ω5c, and iso-C 17 : 0 3-OH as the major cellular fatty acids, and phosphatidylethanolamine (PE) as a major polar lipid [3][4][5][6][7][8][9][10]. The genus Chitinophaga was initially coined to denote bacteria capable of chitin degradation, but interestingly, it has been observed that most Chitinophaga species, except C. pinensis and Chitinophaga filiformis, lack this ability [1,[3][4][5][6][7][8][9][10][11]. In this study, we isolated a putative novel strain affiliated with the genus Chitinophaga from an enriched culture using phthalic acid (PA) and soil sediment, and its taxonomic characteristics were assessed using a polyphasic approach.…”