Chitinophaga fulva sp. nov., isolated from forest soil

Chitinophaga defluvii sp. nov., a Cyhalofop-Butyl-Degrading Bacterium Isolated from Municipal Sludge

A yellow-colored, Gram-stain-negative, non-motile, and rod-shaped bacterium, designated strain H8T, was isolated from municipal sludge in Huaibei, China. Strain H8T was able to grow at 15-37 °C (optimum at 30 °C), pH 6.0-8.0 (optimum at pH 7.0), and 0-2.5% (w/v) NaCl concentration (optimum at 0%). This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain H8T represented to the genus Chitinophaga and shared highest sequence similarities with C. arvensicola DSM 3695T (97.5%), C. niastensis JS16-4T (97.3%), C. hostae 2R12T (97.1%), and C. ginsengisegetis Gsoil 040T (96.8%). The 16S rRNA gene similarities with other members of the genus Chitinophaga are less than 96.3%. The only respiratory quinone was a menaquinone with seven isoprene units (MK-7); the major polar lipid was phosphatidylethanolamine; and the predominant fatty acids were iso-C15:0 and C16:1 ω5c. The genome size of strain H8T was 7.6 Mb, with 44.3% G + C content. The DNA-DNA relatedness and the average nucleotide identity values among strain H8T and other relatives were all less than 19.7% and 72.6%, respectively, which fall below the threshold value of 70% and 95% for the strain to be considered as novel. The morphological, physiological, chemotaxonomic, and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbors. Thus, strain H8T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga defluvii sp. nov. is proposed. The type strain is H8T (= CCTCC AB 2023228T = KCTC 102174T).

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

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 hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea

A Gram-negative, rod-shaped aerobic bacterium designated as strain 2R12T was isolated from the rhizosphere soil of Hosta plantaginea. Phylogenetic analyses based on the 16S rRNA gene revealed that strain 2R12T should be assigned to the genus Chitinophaga with the highest sequence similarity to Chitinophaga arvensicola DSM 3695T (99.1 %) and Chitinophaga ginsengisegetis DSM 18108T (98.6 %). The major fatty acids of strain 2R12T (>10 %) were iso-C15 : 0, C16 :1 ω5c and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant respiratory quinone was MK-7. The genomic DNA G+C content was 46.1 mol%. The average nucleotide identity values of strain 2R12T with C. arvensicola DSM 3695T and C. ginsengisegetis DSM 18108T were 77.9 and 78.8 %, respectively, while in silico DNA–DNA hybridization values for strain 2R12T with these strains were 22.8 and 23.3 %, respectively. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain 2R12T represents a novel species in the genus Chitinophaga , for which the name Chitinophaga hostae sp. nov. is proposed. The type strain is 2R12T (=ACCC 61757T=JCM 34719T).

Cellulomonas fulva sp. nov., isolated from oil-contaminated soil

A yellow-coloured, Gram-stain-positive, motile, aerobic and rod-shaped bacteria, designated DKR-3T, was isolated from oil-contaminated experimental soil. Strain DKR-3T could grow at pH 5.0–10.5 (optimum, pH 7.0–8.5), at 10–40 °C (optimum, 25–32 °C) and tolerated 3.5 % of NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence indicated that strain DKR-3T formed a lineage within the family Cellulomonadaceae and was clustered with members of the genus Cellulomonas . Strain DKR-3T had highest 16S rRNA gene sequence similarities to Cellulomonas gelida DSM 20111T (98.3 %), Cellulomonas persica JCM 18111T (98.2 %) and Cellulomonas uda DSM 20107T (97.8 %). The predominant respiratory quinone was tetrahydrogenated menaquinone with nine isoprene units [MK-9(H4)]. The principal cellular fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall diamino acid was l-ornithine whereas rhamnose and glucose were the cell-wall sugars. The DNA G+C content was 74.2mol %. The genome of strain DKR-3T was 3.74 Mb and contained three putative biosynthetic gene clusters. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain DKR-3T and its phylogenetically related members were below the species threshold values. Based on a polyphasic study, strain DKR-3T represents a novel species belonging to the genus Cellulomonas , for which the name Cellulomonas fulva sp. nov. is proposed. The type strain is DKR-3T (=KACC 22071T=NBRC 114730T).

Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as strain B61^T, was isolated from rhizosphere soil of banana collected from Dongguan, Guangdong Province, PR China. Growth occurred at 15-40 °C, within a pH range of pH 6.0-9.0. Results of 16S rRNA gene sequence similarity and phylogenetic analyses showed that strain B61^T was most closely related to 'Chitinophaga agri' KACC 21303 (98.9 %) and Chitinophaga pinensis DSM 2588^T (98.8 %). The genome size was 7.6 Mb with a G+C content of 45.2 mol%. The genome-inferred average nucleotide identity values between strain B61^T and two closely related strains were 79.2 and 79.3 %, respectively, with corresponding digital DNA-DNA hybridization values of 22.3 and 22.6 %. The major fatty acids of the novel strain were iso-C_15:0, C_16:1 ω5c and iso-C_17:0 3-OH and the sole respiratory quinone was menaquinone 7 (MK-7). The polar lipids consisted of phosphatidylethanolamine, five unidentified aminolipids, four unidentified glycolipids and six unidentified lipids. The phenotypic and phylogenetic results clearly supported that strain B61^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga rhizophila, sp. nov. is proposed, with the type strain B61^T (=GDMCC 1.2608^T=KCTC 82856^T).

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303^T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16-37 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 7.0) and 0-2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga. Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729^T, Chitinophaga qingshengii JN246^T, Chitinophaga varians 10-7 W-9003^T and Chitinophaga fulva G-6-1-13^T. When the genomic sequences of strains 1303^T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA-DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C_15 : 0, C_16 : 1  ω5c, iso-C_17 : 0 3-OH and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303^T and 1310 represent members of a novel species of the genus Chitinophaga, for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303^T (=KACC 22075^T=TBRC 12926^T).

Chitinophaga silvatica sp. nov., isolated from forest soil, and reclassification of Chitinophaga extrema as a later heterotypic synonym of Chitinophaga solisilvae

A novel bacterial strain, designated K2CV101002-2^T, was isolated from forest soil collected at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that it belonged to the genus Chitinophaga and was most closely related to Chitinophaga terrae KP01^T (99.0 %), followed by Chitinophaga extrema Mgbs1^T (98.3 %) and Chitinophaga solisilvae O9^T (98.1 %). The draft genome sequence was 6.8 Mb long with a relative low G+C content of 39.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the novel strain and closely related type strains were 71.4‒76.2 % and 18.4‒19.6 %, respectively. Meanwhile the corresponding values between C. extrema Mgbs1^T and C. solisilvae O9^T were 98.6 and 88.1 %, respectively. The novel strain contained iso-C_15:0, C_16:1 ω5c and iso-C_17:0 3-OH as the major fatty acids and MK-7 as the predominant respiratory quinone. The polyphasic study clearly supported that strain K2CV101002-2^T represents a new species of the genus Chitinophaga, for which the name Chtinophaga silvatica sp. nov. (type strain K2CV101002-2^T=GDMCC 1.1288^T=JCM 32696^T) is proposed. In addition, Chitinophaga extrema Goh et al. 2020 should be taken as a later heterotypic synonym of Chitinophaga solisilvae Ping et al. 2020.