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Lichenibacterium ramalinae gen. nov, sp. nov., Lichenibacterium minor sp. nov., the first endophytic, beta-carotene producing bacterial representatives from lichen thalli and the proposal of the new family Lichenibacteriaceae within the order Rhizobiales

  • Timofey A. PankratovEmail author
  • Denis S. Grouzdev
  • Ekaterina O. Patutina
  • Tatiana V. Kolganova
  • Nataliya E. Suzina
  • Julia J. Berestovskaya
Original Paper

Abstract

This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56T and 91.76% to Beijerinckia doebereinerae strain LMG 2819T, whilst strain RmlP026T is closely related to B. doebereinerae strain LMG 2819T (91.85%) and Microvirga pakistanensis strain NCCP-1258T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-β-hydroxybutyrate and polyphosphate, to grow at pH 3.5–8.0 and 10–30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C18:1ω7c (68–71%) and their DNA G + C contents determined to be 70.5–70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001T and RmlP026T are distinguishable from related species by the presence of β-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001T (= KCTC 72076T = VKM B-3263T) and the L. minor type strain is RmlP026T (= KCTC 72077T = VKM B-3277T).

Keywords

Lichenibacterium LAR1 Lichen endophytes Rhizobiales Beta-carotene Phylogenetic analysis Symbiotic bacteria 

Notes

Acknowledgements

This work was supported with the Russian Fund of Basic Research (projects 16-04-00966a and 19-04-00297a) and the Ministry of Science and Higher Education of the Russian Federation (cultivation studies by J.J. Berestovskaya).

Authors’ contributions

TP designed the study. TP examined lichen samples, obtained isolates, performed growth experiments; took phase contrast and micro pictures. DG, EP, TK obtained, annotated and analyzed the genome sequences. JB performed growth and physiological experiments. NS prepared ultrathin sections of cells and took pictures. TP and DG wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10482_2019_1357_MOESM1_ESM.doc (7.4 mb)
Supplementary material 1 (DOC 7542 kb)

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.M.V. Lomonosov Moscow State UniversityMoscowRussia
  2. 2.Institute of BioengineeringResearch Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
  3. 3.G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the RASFederal Research Centre “Pushchino Scientific Centre of Biological Investigations RAS”PushchinoRussia
  4. 4.S.N, Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of SciencesMoscowRussia

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