Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 8

gen. nov., sp. nov., the first bacteriochlorophyll -containing, psychrophilic and acidophilic bacteriobiont of lichen species Free

Abstract

Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll -containing bacterial strains, KEBCLARHB70R, KAMCLST3051 and KAMCLST3152, were isolated from the thalli of and lichens. Cells from the strains were coccoid and reproduced by binary division. They were motile at the early stages of growth and utilized sugars and alcohols. All strains were psychrophilic and acidophilic, capable of growth between pH 3.5 and 7.5 (optimum, pH 5.5), and at 4–30 °C (optimum, 10–15 °C). The major fatty acids were C ω7 and C; the lipids were phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, phosphatidylglycerol, glycolipids, diphosphatidylglycerol and polar lipids with an unknown structure. The quinone was Q-10. The DNA G+C content was 67.8 mol%. Comparative 16S rRNA gene analysis together with other data, supported that the strains, KEBCLARHB70R, KAMCLST3051 and KAMCLST3152 belonged to the same species. Whole genome analysis of the strain KEBCLARHB70R and average amino acid identity values confirmed its distinctive phylogenetic position within the family . Phenotypic, ecological and genomic characteristics distinguished strains KEBCLARHB70R, KAMCLST3051 and KAMCLST3152 from all genera in the family . Therefore, we propose a novel genus and a novel species, gen. nov., sp. nov., for these novel members. Strain KEBCLARHB70R (=KCTC 72321=VKM B-3305) has been designated as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acetobacteraceae , BChla , Cladonia , endobionts , Lichenicoccus and lichens
Funding
This study was supported by the:
  • Российский Фонд Фундаментальных Исследований (РФФИ) (Award 19-04-00297a)
    • Principle Award Recipient: Timofey A Pankratov
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004318
2020-07-13
2025-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4591.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004318&mimeType=html&fmt=ahah

References

  1. Komagata K, Iino T, Yamada Y. The family Acetobacteraceae.. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Germany: Springer; 2014 pp 3–78
     [Google Scholar]
  2. Bates ST, Cropsey GWG, Caporaso JG, Knight R, Fierer N. Bacterial communities associated with the lichen symbiosis. Appl Environ Microbiol 2011; 77:1309–1314 [View Article][PubMed]
     [Google Scholar]
  3. Cardinale M, Vieira de Castro J, Müller H, Berg G, Grube M. In situ analysis of the bacterial community associated with the reindeer lichen Cladonia arbuscula reveals predominance of Alphaproteobacteria . FEMS Microbiol Ecol 2008; 66:63–71 [View Article][PubMed]
     [Google Scholar]
  4. Noh H-J, Lee YM, Park CH, Lee HK, Cho J-C et al. Microbiome in Cladonia squamosa is vertically stratified according to microclimatic conditions. Front Microbiol 2020; 11:268 [View Article][PubMed]
     [Google Scholar]
  5. Muthukumarasamy R, Revathi G, Seshadri S, Lakshminarasimhan C. Gluconacetobacter diazotrophicus (syn. Acetobacter diazotrophicus), a promising diazotrophic endophyte in tropics. Curr. Sci 2002; 83:137–145
     [Google Scholar]
  6. Ramírez-Bahena MH, Tejedor C, Martín I, Velázquez E, Peix A. Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil. Int J Syst Evol Microbiol 2013; 63:1760–1765 [View Article][PubMed]
     [Google Scholar]
  7. Pankratov TA. Bacterial complexes of Khibiny Mountains lichens revealed in Cladonia uncialis, C. portentosa, Alectoria ochroleuca, and Nephroma arcticum . Microbiology 2018; 87:79–88 [View Article]
     [Google Scholar]
  8. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematic New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  9. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  10. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587589 [View Article][PubMed]
     [Google Scholar]
  11. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
     [Google Scholar]
  12. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article]
     [Google Scholar]
  13. Yukphan P, Malimas T, Muramatsu Y, Takahashi M, Kaneyasu M et al. Ameyamaea chiangmaiensis gen. nov., sp. nov., an acetic acid bacterium in the alpha-proteobacteria. Biosci Biotechnol Biochem 2009; 73:2156–2162 [View Article][PubMed]
     [Google Scholar]
  14. Yukphan P, Malimas T, Potacharoen W, Tanasupawat S, Tanticharoen M et al. Neoasaia chiangmaiensis gen. nov., sp. nov., a novel osmotolerant acetic acid bacterium in the alpha-proteobacteria. J Gen Appl Microbiol 2005; 51:301–311 [View Article][PubMed]
     [Google Scholar]
  15. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  16. Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001; 56:2.4.1–2.4.2 [View Article][PubMed]
     [Google Scholar]
  17. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
     [Google Scholar]
  18. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A et al. Prokaryotic Genome Annotation Pipeline. The NCBI Handbook [Internet], 2nd ed. Bethesda, MD: NCBI; 2013
     [Google Scholar]
  20. Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biol Evol 2018; 10:928–938 [View Article][PubMed]
     [Google Scholar]
  21. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
     [Google Scholar]
  22. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article][PubMed]
     [Google Scholar]
  23. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. Isme J 2017; 11:2399–2406 [View Article][PubMed]
     [Google Scholar]
  24. Pankratov TA, Kirsanova LA, Kaparullina EN, Kevbrin VV, Dedysh SN. Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 2012; 62:430–437 [View Article][PubMed]
     [Google Scholar]
  25. Gerhardt P. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981
     [Google Scholar]
  26. Ashikhmin A, Makhneva Z, Bolshakov M, Moskalenko A. Distribution of colored carotenoids between light-harvesting complexes in the process of recovering carotenoid biosynthesis in Ectothiorhodospira haloalkaliphila cells. J Photochem Photobiol B 2014; 141:59–66 [View Article][PubMed]
     [Google Scholar]
  27. Pankratov TA, Grouzdev DS, Patutina EO, Kolganova TV, Suzina NE et al. 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 . Antonie van Leeuwenhoek 2020; 113:477–489 [View Article][PubMed]
     [Google Scholar]
  28. Pankratov TA, Tindall BJ, Liesack W, Dedysh SN. Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. Int J Syst Evol Microbiol 2007; 57:2349–2354 [View Article][PubMed]
     [Google Scholar]
  29. Siebers M, Brands M, Wewer V et al. Lipids in plant–microbe interactions. BBA-Mol Cell Biol L 2016; 1861:1379–1395
     [Google Scholar]
  30. Rintala H, Pitkäranta M, Toivola M, Paulin L, Nevalainen A et al. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 2008; 8:56 [View Article][PubMed]
     [Google Scholar]
  31. Täubel M, Rintala H, Pitkäranta M, Paulin L, Laitinen S et al. The occupant as a source of house dust bacteria. J Allergy Clin Immunol 2009; 124:834–840 [View Article][PubMed]
     [Google Scholar]
  32. Kavroulakis N, Ntougias S. Bacterial and β-proteobacterial diversity in Olea europaea var. mastoidis- and O. europaea var. koroneiki-generated olive mill wastewaters: influence of cultivation and harvesting practice on bacterial community structure. World J Microbiol Biotechnol 2011; 27:57–66 [View Article]
     [Google Scholar]
  33. Yergeau E, Bokhorst S, Kang S, Zhou J, Greer CW et al. Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. Isme J 2012; 6:692–702 [View Article][PubMed]
     [Google Scholar]
  34. Murakami T, Segawa T, Bodington D, Dial R, Takeuchi N et al. Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus . FEMS Microbiol Ecol 2015; 91:fiv003 [View Article][PubMed]
     [Google Scholar]
  35. Gonella E, Crotti E, Mandrioli M, Daffonchio D, Alma A et al. Asaia symbionts interfere with infection by Flavescence dorée phytoplasma in leafhoppers. J Pest Sci 2018; 91:1033–1046 [View Article]
     [Google Scholar]
  36. Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R et al. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 2001; 67:1874–1884 [View Article][PubMed]
     [Google Scholar]
  37. Greenberg DE, Porcella SF, Stock F, Wong A, Conville PS et al. Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae . Int J Syst Evol Microbiol 2006; 56:2609–2616 [View Article][PubMed]
     [Google Scholar]
  38. Sievers M, Swings J. Gluconacetobacter Yamada, Hoshino, and Ishikawa 1998b, 32VP. In Brenner DJ, Krieg NR, Stanley JT. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2015 pp 1–11
     [Google Scholar]
  39. Sievers M, Swings J. Acetobacter Beijerinck 1898, 215AL. In Brenner DJ, Krieg NR, Stanley JT. (editors) Bergey’s Manual of Systematic Bacteriology 2015 New York: Springer; pp 1–7
     [Google Scholar]
  40. Yamashita S-I, Uchimura T, Komagata K. Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989. Int J Syst Evol Microbiol 2004; 54:865–870 [View Article][PubMed]
     [Google Scholar]
  41. Sievers M, Swings J. Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989, 54VP. In Brenner DJ, Krieg NR, Stanley JT. (editors) Bergey’s Manual of Systematic Bacteriology 2015 New York: Springer; pp 1–5
     [Google Scholar]
  42. Yamada Y, Katsura K, Kawasaki H, Widyastuti Y, Saono S et al. Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the alpha-proteobacteria. Int J Syst Evol Microbiol 2000; 50 Pt 2:823–829 [View Article][PubMed]
     [Google Scholar]
  43. Pfennig N. Rhodopseudomonas globiformis, sp. n., a new species of the Rhodospirillaceae . Arch Microbiol 1974; 100:197–206 [View Article]
     [Google Scholar]
  44. Imhoff JF, Truper HG, Pfennig N. Rearrangement of the Species and Genera of the Phototrophic "Purple Nonsulfur Bacteria". Int J Syst Bacteriol 1984; 34:340–343 [View Article]
     [Google Scholar]
  45. Hiraishi A, Matsuzawa Y, Kanbe T, Wakao N. Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments. Int J Syst Evol Microbiol 2000; 50 Pt 4:1539–1546 [View Article][PubMed]
     [Google Scholar]
  46. Owen RJ, Hill LR, Lapage SP. Determination of DNA base compositions from melting profiles in dilute buffers. Biopolymers 1969; 7:503–516 [View Article][PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004318
Loading
Lichenicoccus roseus gen. nov., sp. nov., the first bacteriochlorophyll a-containing, psychrophilic and acidophilic Acetobacteraceae bacteriobiont of lichen Cladonia species
Int J Syst Evol Microbiol 70, 4591 (2020); https://doi.org/10.1099/ijsem.0.004318
/content/journal/ijsem/10.1099/ijsem.0.004318
/content/journal/ijsem/10.1099/ijsem.0.004318
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error