Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species

Arch Microbiol. 2020 May;202(4):815-824. doi: 10.1007/s00203-019-01791-0. Epub 2019 Dec 16.

Abstract

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81T (= DSM 19542T) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81T not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81T and the animal-associated species Kiloniella majae M56.1T from a spider crab, Kiloniella spongiae MEBiC09566T from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81T contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.

Keywords: Alphaproteobacteria; Chemoorganotrophic marine bacterium; Genome description; Kiloniella laminariae; PKS/NRPS biosynthetic gene clusters.

MeSH terms

  • Alphaproteobacteria / classification
  • Alphaproteobacteria / genetics*
  • Animals
  • Aquatic Organisms / classification
  • Aquatic Organisms / genetics*
  • Aquatic Organisms / microbiology
  • Bacterial Proteins / genetics
  • Base Composition
  • Genomics*
  • Phaeophyta / microbiology
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Species Specificity

Substances

  • Bacterial Proteins
  • RNA, Ribosomal, 16S
  • syringomycin

Supplementary concepts

  • Kiloniella laminariae