Lin Shih-Yao, Hameed Asif, Tsai Chia-Fang, Young Chiu-Chung
Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan.
Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India.
Antonie Van Leeuwenhoek. 2023 Dec;116(12):1345-1357. doi: 10.1007/s10482-023-01891-4. Epub 2023 Oct 14.
An auxin-producing bacterial strain, CC-SYL302, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302 was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302 belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 (with 93.3% similarity) and F. cucumis R2A45-3 (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302 and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302 exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C, iso-C, iso-C, iso-C 3-OH, iso-C 3-OH, C ω6c/C ω7c and C 10-methyl/iso-C ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302 exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302 (= BCRC 81320 = JCM 34764).
从台湾稻田土壤中分离出一株产生长素的细菌菌株CC-SYL302，并采用多相分类法进行鉴定。观察到该菌细胞为需氧、不运动、不产芽孢的杆菌，过氧化氢酶和氧化酶检测呈阳性。能产生类胡萝卜素，但不存在柔韧杆菌类色素。菌株CC-SYL302在25℃、pH 7.0和2%（w/v）NaCl条件下生长最佳。基于16S rRNA基因序列分析，确定菌株CC-SYL302属于黄杆菌科黄杆菌属。该菌株最接近的已知亲缘种是柑橘黄杆菌YIM 102701-2（相似度为93.3%）和黄瓜黄杆菌R2A45-3（相似度为93.1%）。计算了数字DNA-DNA杂交（dDDH）值以评估菌株CC-SYL302与其最接近亲缘种之间的遗传距离，柑橘黄杆菌的平均值为21.3%，黄瓜黄杆菌的平均值为20.4%。菌株CC-SYL302与黄杆菌属成员的直系同源平均核苷酸同一性（OrthoANI）值最高，范围为67.2%至72.1%（n = 22）。主要的细胞脂肪酸（>5%）包括异-C、异-C、异-C、异-C 3-OH、异-C 3-OH、C ω6c/C ω7c和C 10-甲基/异-C ω9c。极性脂质谱由磷脂酰乙醇胺、一种未鉴定的氨基脂质、一种未鉴定的氨基磷脂和九种未鉴定的极性脂质组成。基因组（2.7 Mb）的GC含量为33.6%，主要的多胺是腐胺和共高亚精胺。菌株CC-SYL302表现出独特的系统发育、表型和化学分类特征，以及在16S rRNA基因序列、OrthoANI、dDDH和系统基因组定位的比较分析中的独特结果。因此，建议将该菌株定为黄杆菌属的一个新物种，命名为农业黄杆菌（Flavobacterium agricola sp. nov.）。模式菌株为CC-SYL302（=BCRC 81320 = JCM 34764）。
