Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium

Syst Appl Microbiol. 2014 Oct;37(7):474-9. doi: 10.1016/j.syapm.2014.08.004. Epub 2014 Sep 6.


Fifteen actinobacterial isolates retrieved from the endophytic community of the salt-marsh plant Halimione portulacoides were characterised in this study. ERIC-PCR fingerprinting analysis divided these isolates into two groups represented by strains PA15(T) and PA36(T), respectively. 16S rRNA gene sequence analyses showed the isolates belonged to the genus Microbacterium, with Microbacterium saccharophilum NCIMB 14782(T) as the closest phylogenetic relative to which they have pairwise sequence similarities of 98.7-98.8%. Strains PA15(T) and PA36(T) are closely related having a pairwise sequence similarity of 99.8%. However, DNA-DNA hybridization result between both was well under 70% confirming them as distinct genomic species. Both strains have a B2β peptidoglycan type with ornithine as diaminoacid, MK-10 and MK-11 as major menaquinones, anteiso-C15:0, anteiso-C17:0 and iso-C16:0 as major fatty acids. These features as well as DNA-DNA hybridization results clearly separate them from M. saccharophilum. On the basis of physiological, chemotaxonomic and genetic characteristics we propose that the isolates studied represent two novel species of the genus Microbacterium, Microbacterium endophyticum sp. nov. (type strain PA15(T)=DSM 27099(T)=CECT 8354(T)) and Microbacterium halimionae sp. nov. (type strain PA36(T)=DSM 27576(T)=CECT 8593(T)).

Keywords: Endophytic; Halophytes; Microbacterium; Salt-marsh.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinobacteria / classification*
  • Actinobacteria / genetics
  • Actinobacteria / isolation & purification*
  • Amaranthaceae / microbiology*
  • Bacterial Typing Techniques
  • Cell Wall / chemistry
  • Cluster Analysis
  • Cytosol / chemistry
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Endophytes / classification*
  • Endophytes / genetics
  • Endophytes / isolation & purification*
  • Fatty Acids / analysis
  • Molecular Sequence Data
  • Molecular Typing
  • Nucleic Acid Hybridization
  • Ornithine / analysis
  • Peptidoglycan / analysis
  • Phylogeny
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Vitamin K 2 / analysis


  • DNA, Bacterial
  • DNA, Ribosomal
  • Fatty Acids
  • Peptidoglycan
  • RNA, Ribosomal, 16S
  • Vitamin K 2
  • Ornithine

Associated data

  • GENBANK/KJ920264
  • GENBANK/KJ920265
  • GENBANK/KJ920266
  • GENBANK/KJ920267
  • GENBANK/KJ920268
  • GENBANK/KJ920269
  • GENBANK/KJ920270
  • GENBANK/KJ920271
  • GENBANK/KJ920272
  • GENBANK/KJ920273
  • GENBANK/KJ920274
  • GENBANK/KJ920275
  • GENBANK/KJ920276
  • GENBANK/KJ920277
  • GENBANK/KJ920278