1887

Abstract

The actinobacterial strain 15G-AUS-rot was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus . Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rot to the family and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rot were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C, antiso-C and iso-C. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed is proposed for strain 15G-AUS-rot (=DSM 107803=JCM 32974).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004825
2021-05-17
2022-01-24
Loading full text...

Full text loading...

References

  1. Park YH, Suzuki K, Yim DG, Lee KC, Kim E et al. Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. Antonie van Leeuwenhoek 1993; 64:307–313 [View Article][PubMed]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Evol Microbiol 1997; 47:479–491
    [Google Scholar]
  3. Evtushenko LI, Takeuchi M. The family Microbacteriaceae. Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. eds In The Prokaryotes: Volume 3: Archaea Bacteria: Firmicutes, Actinomycetes New York: Springer; 2006 pp 1020–1098
    [Google Scholar]
  4. Trutko SM, Dorofeeva LV, Evtushenko LI, Ostrovskii DN, Hintz M. Isoprenoid pigments in representatives of the family Microbacteriaceae. Microbiology 2005; 74:284–289 [View Article]
    [Google Scholar]
  5. Sharma AK, Zhaxybayeva O, Papke RT, Doolittle WF. Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments. Environ Microbiol 2008; 10:1039–1056 [View Article][PubMed]
    [Google Scholar]
  6. Sharma AK, Sommerfeld K, Bullerjahn GS, Matteson AR, Wilhelm SW. Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME J 2009; 3:726–737 [View Article]
    [Google Scholar]
  7. Dwulit-Smith JR, Hamilton JJ, Stevenson DM, He S, Oyserman BO. acl Actinobacteria assemble a functional actinorhodopsin with natively synthesized retinal. Appl Environ Microbiol 2018; 84:24
    [Google Scholar]
  8. Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:119 [View Article]
    [Google Scholar]
  9. Hahn MW, Lünsdorf H, Wu Q, Schauer M, Höfle MG. Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl Environ Microbiol 2003; 69:1442–1451 [View Article][PubMed]
    [Google Scholar]
  10. Hahn MW. Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. Int J Syst Evol Microbiol 2009; 59:112–117 [View Article][PubMed]
    [Google Scholar]
  11. Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U. Rhodoluna lacicola gen. nov., sp nov., a planktonic freshwater bacterium with stream-lined genome. Int J Syst Evol Microbiol 2014; 64:3254–3263 [View Article][PubMed]
    [Google Scholar]
  12. Pitt A, Schmidt J, Koll U, Hahn MW. Rhodoluna limnophila sp. nov., a bacterium with 1.4 Mbp genome size isolated from freshwater habitats located in Salzburg, Austria. Int J Syst Evol Microbiol 2019; 69:3946–3954 [View Article][PubMed]
    [Google Scholar]
  13. Pitt A, Schmidt J, Koll U, Hahn MW. Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria. Int J Syst Evol Microbiol 2019; 69:2739–2749 [View Article][PubMed]
    [Google Scholar]
  14. Hahn MW, Stadler P, QL W, Pöckl M. The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J Microbiol Methods 2004; 57:379–390
    [Google Scholar]
  15. Roller C, Wagner M, Amann R, Ludwig W, Schleifer KH. In-situ probing of gram-positive bacteria with high DNA G+C content using 23S-ribosomal-rRNA-targeted oligonucleotides. Microbiology 1994; 140:2849–2858 [View Article]
    [Google Scholar]
  16. Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S. Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol 2017; 67:2555–2568 [View Article][PubMed]
    [Google Scholar]
  17. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  18. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  19. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  20. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  21. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T. eds In Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  22. Schumann P. Peptidoglycan Structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
  23. Kim SJ, Tamura T, Hamada M, Ahn JH, Weon HY. Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 2012; 62:2410–2416 [View Article][PubMed]
    [Google Scholar]
  24. Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T. Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air. Int J Syst Evol Microbiol 2013; 63:2436–2441 [View Article][PubMed]
    [Google Scholar]
  25. Hoetzinger M, Schmidt J, Jezberova J, Koll U, Hahn MW. Microdiversification of a pelagic Polynucleobacter species is mainly driven by acquisition of genomic islands from a partially interspecific gene pool. Appl Environ Microbiol 2017; 83:19 [View Article]
    [Google Scholar]
  26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. 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]
  27. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  28. Chen IMA, Chu K, Palaniappan K, Pillay M, Ratner A. IMG/M v.5.0: An integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666
    [Google Scholar]
  29. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article][PubMed]
    [Google Scholar]
  30. Keffer JL, Hahn MW, Maresca JA. Characterization of an unconventional rhodopsin from the freshwater actinobacterium Rhodoluna lacicola. J Bacteriol 2015; 197:2704–2712 [View Article][PubMed]
    [Google Scholar]
  31. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A. 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]
  32. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  33. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
  34. Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005; 33:511–518 [View Article][PubMed]
    [Google Scholar]
  35. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
    [Google Scholar]
  36. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  37. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees. Proceedings of the Gateway Computing Environments Workshop (GCE) New Orleans, LA: IEEE; 2010 pp 1–8
    [Google Scholar]
  38. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article][PubMed]
    [Google Scholar]
  39. Navarro J, Moser D, Flores A, Ross C, Rosen M. Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake. Microb Ecol 2008; 57:307–320 [View Article][PubMed]
    [Google Scholar]
  40. Zhang R, Wu Q, Piceno YM, Desantis TZ, Saunders FM. Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis. FEMS Microbiol Ecol 2013; 86:277–287 [View Article][PubMed]
    [Google Scholar]
  41. Xing P, Hahn MW, QL W. Low taxon richness of bacterioplankton in high-altitude lakes of the eastern Tibetan Plateau, with a predominance of Bacteroidetes and Synechococcus spp. Appl Environ Microbiol 2009; 75:7017–7025 [View Article]
    [Google Scholar]
  42. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR. 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]
  43. Kim M, HS O, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351
    [Google Scholar]
  44. Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philosophical Transactions of the Royal Society B-Biological Sciences 2006; 361:1929–1940 [View Article]
    [Google Scholar]
  45. Rossello-Mora R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article]
    [Google Scholar]
  46. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for Bacteria and Archaea based on a standard genome relatedness index. mBio 2020; 11:02419–e02475 [View Article]
    [Google Scholar]
  47. Rodríguez-R L, Konstantinidis K. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118
    [Google Scholar]
  48. Rodríguez-R L, Konstantinidis K. The Enveomics Collection: A Toolbox for Specialized Analyses of Microbial Genomes and Metagenomes 2016
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004825
Loading
/content/journal/ijsem/10.1099/ijsem.0.004825
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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