Ruixingdingia sedimenti gen. nov., sp. nov., a novel taxon within the family Paracoccaceae isolated from sediment of Qiantang River

Lu Xu; Kexin Wang; Luyao Ruan; E Chen; Songqi Yang; Jiguo Qiu; Jiandong Jiang; Jian He; Qirong Shen

doi:10.1099/ijsem.0.006350

Ruixingdingia sedimenti gen. nov., sp. nov., a novel taxon within the family Paracoccaceae isolated from sediment of Qiantang River

Int J Syst Evol Microbiol. 2024 Apr;74(4). doi: 10.1099/ijsem.0.006350.

Authors

Lu Xu¹, Kexin Wang¹, Luyao Ruan¹, E Chen², Songqi Yang³, Jiguo Qiu¹, Jiandong Jiang¹, Jian He^{1

4}, Qirong Shen^{4

5}

Affiliations

¹ College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
² The Environmental Monitoring Center of Gansu Province, Lanzhou 73002, PR China.
³ Gansu Microalgae Technology Innovation Center, Hexi University, Zhangye 7340002, PR China.
⁴ Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China.
⁵ College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.

PMID: 38668744
DOI: 10.1099/ijsem.0.006350

Abstract

A Gram-stain-negative bacterium, designated LG-4^T, was isolated from sediment of Qiantang River in Zhejiang Province, PR China. Cells were strictly aerobic, non-spore-forming, non-motile and short-rod-shaped (1.0-1.2 µm long and 0.7-0.8 µm wide). Growth occurred at 15-42 °C (optimum, 30 °C), at pH 5.0-9.0 (pH 7.0) and at 0-2.0 % (w/v) NaCl (optimum, 0.5 % NaCl). Strain LG-4^T showed 95.75-96.90 % 16S rRNA gene sequence similarity to various type strains of the genera Tabrizicola, Pseudotabrizicola, Phaeovulum, Rhodobacter and Wagnerdoeblera of the family Paracoccaceae, and the most closely related strain was Tabrizicola soli ZQBW^T (96.90 % similarity). The phylogenomic tree showed that strain LG-4^T clustered in the family Paracoccaceae and was positioned outside of the clade composed of the genera Wagnerdoeblera and Falsigemmobacter. The average nucleotide identity and digital DNA-DNA hybridization values between strain LG-4^T and the related type strains were in the range of 74.19-77.56 % and 16.70-25.80 %, respectively. The average amino acid identity (AAI) values between strain LG-4^T and related type strains of the family Paracoccaceae were 60.94-69.73 %, which are below the genus boundary (70 %). The evolutionary distance (ED) values between LG-4^T and the related genera of the family Paracoccaceae were 0.21-0.34, which are within the recommended standard (≥0.21-0.23) for defining a novel genus in the family Paracoccaceae. The predominant cellular fatty acids were C_{18 : 1} ω7c, C_{19 : 0} cyclo ω8c, C_{18 : 0} and C_{16 : 0}, the isoprenoid quinone was Q-10, and the major polar lipids were phospholipid, phosphatidylglycerol, phosphatidylcholine, aminolipid and two unknown polar lipids. The genome size was 4.7 Mb with 68.6 mol% G+C content. On the basis of distinct phylogenetic relationships, low AAI values and high ED values, and differential phenotypic, physiological and biochemical characteristics, strain LG-4^T represents a novel species of a new genus in the family Paracoccaceae, for which the name Ruixingdingia sedimenti gen. nov., sp. nov. is proposed. The type strain is LG-4^T (=MCCC 1K08849^T=KCTC 8136^T).

Keywords: 16S rRNA gene; AAI; ANI; Ruixingdingia sedimenti gen. nov., sp. nov.; dDDH; polyphasic taxonomy.

MeSH terms

Bacterial Typing Techniques*
Base Composition*
China
DNA, Bacterial* / genetics
Fatty Acids* / analysis
Fatty Acids* / chemistry
Geologic Sediments* / microbiology
Nucleic Acid Hybridization*
Phospholipids / analysis
Phylogeny*
RNA, Ribosomal, 16S* / genetics
Rivers* / microbiology
Sequence Analysis, DNA*
Ubiquinone / analogs & derivatives

Substances

RNA, Ribosomal, 16S
Fatty Acids
DNA, Bacterial
Phospholipids
Ubiquinone