Comparative genomic analysis of the genus Novosphingobium and the description of two novel species Novosphingobium aerophilum sp. nov. and Novosphingobium jiangmenense sp. nov

Syst Appl Microbiol. 2021 May;44(3):126202. doi: 10.1016/j.syapm.2021.126202. Epub 2021 Mar 30.

Abstract

Members of the genus Novosphingobium are well known for their metabolically versatile and great application potential in pollution elimination. The three novel bacterial strains, designated 4Y4T, 4Y9, and 1Y9AT, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequences phylogenetic analysis revealed that the three strains belonged to the genus Novosphingobium. The phylogenomic analysis indicated that the three strains formed two independent and robust branches distinct from all reference strains. The analyses of dDDH values and ANIs between the three strains and their relatives further demonstrated that the three strains represented two different novel genospecies. Comparative genomic analysis of the three isolates and 32 type strains of the genus Novosphingobium showed that the most important central metabolic pathways of these strains appeared to be similar, while specific and specialized metabolic pathways were flexible and variable among these strains. Chemotaxonomic characterization exhibited that the predominant cellular fatty acids were summed feature 8, summed feature 3, and C14:0 2OH; the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the major respiratory quinone and polyamine were Q-10 and spermidine. The DNA G + C contents were 67.6 and 64.7 %. Based on the genotypic and phenotypic characteristics, strains 4Y4T and 1Y9AT are concluded to represent two novel species of the genus Novosphingobium, for which the names Novosphingobium aerophilum sp. nov. (type strain 4Y4T = GDMCC 1.1828 T = KACC 21946 T) and Novosphingobium jiangmenense sp. nov. (type strain 1Y9AT = GDMCC 1.1936 T = KACC 22085 T) are proposed.

Keywords: Comparative genomic analysis; Genotypes and phenotypes; Novosphingobium; Polyphasic taxonomy.

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • DNA, Bacterial / genetics
  • Fatty Acids / chemistry
  • Genomics
  • Nucleic Acid Hybridization
  • Phospholipids / chemistry
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Spermidine / chemistry
  • Sphingomonadaceae / classification*
  • Sphingomonadaceae / isolation & purification
  • Ubiquinone / analogs & derivatives
  • Ubiquinone / chemistry

Substances

  • DNA, Bacterial
  • Fatty Acids
  • Phospholipids
  • RNA, Ribosomal, 16S
  • Ubiquinone
  • coenzyme Q10
  • Spermidine