1887

Abstract

The bacterial strain 53C-WASEF was isolated from a small freshwater ditch located in Eugendorf, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and genome based, with amino acid sequences obtained from 105 single copy genes, suggested that the strain represents a new genus and a new species within the family , which belongs to the class of the phylum . Comparisons of the 16S rRNA gene sequence of strain 53C-WASEF with those of related type strains revealed a highest sequence similarity of 93.5 % to and of 92.9 % to . Interestingly, phylogentic trees indicated the latter as being the closest known relative of the new strain. Phenotypic, chemotaxonomic and genomic traits were investigated. Cells were observed to be small, spherical, motile and unpigmented, and grew chemoorganotrophically and aerobically. The respiratory quinone was MK-7, the predominant fatty acids were anteiso-C, Cω5 and C. The identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genome sequencing revealed genes putatively encoding for flagella synthesis and cellulose degradation. The genome size was 4.1 Mbp and the G+C content 60.6 mol%. For the new genus and the new species, we propose the name gen. nov., sp. nov. (=CIP 111665=DSM 109123).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003980
2020-01-20
2020-02-28
Loading full text...

Full text loading...

References

  1. Hedlund BP, Gosink JJ, Staley JT. Verrucomicrobia div. nov., a new division of the Bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 1997;72:29–38 [CrossRef]
    [Google Scholar]
  2. Euzéby J. List of new names and new combinationspreviously effectively, but not validly, published. Int J Syst Evol Microbiol 2012;62:1–4
    [Google Scholar]
  3. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998;180:4765–4774
    [Google Scholar]
  4. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry 2011;43:1450–1455 [CrossRef]
    [Google Scholar]
  5. Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A et al. Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. Plos One 2018;13:20
    [Google Scholar]
  6. Parte AC. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42:D613–D616 [CrossRef]
    [Google Scholar]
  7. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Prokaryotic nomenclature up-to-date. August 2019..
  8. Rochman FF, Kim J-J, Rijpstra WIC, Sinninghe Damsté JS, Schumann P et al. Oleiharenicola alkalitolerans gen. nov., sp. nov., a new member of the phylum Verrucomicrobia isolated from an oilsands tailings pond. Int J Syst Evol Microbiol 2018;68:1078–1084 [CrossRef]
    [Google Scholar]
  9. Chin KJ, Liesack W, Janssen PH. Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil. Int J Syst Evol Microbiol 2001;51:1965–1968 [CrossRef]
    [Google Scholar]
  10. Rast P, Glöckner I, Boedeker C, Jeske O, Wiegand S et al. Three novel species with peptidoglycan cell walls form the new genus Lacunisphaera gen. nov. in the family Opitutaceae of the Verrucomicrobial subdivision 4. Front Microbiol 2017;8:18 [CrossRef]
    [Google Scholar]
  11. Baek K, Song J, Cho J-C, Chung EJ, Choi A. Nibricoccus aquaticus gen. nov., sp. nov., a new genus of the family Opitutaceae isolated from hyporheic freshwater. Int J Syst Evol Microbiol 2019;69:552–557 [CrossRef]
    [Google Scholar]
  12. Shieh WY, Jean WD. Alterococcus agarolyticus, gen.nov., sp.nov., a halophilic thermophilic bacterium capable of agar degradation. Can J Microbiol 1998;44:637–645 [CrossRef]
    [Google Scholar]
  13. Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JLM. Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals Microaerophily and nitrogen fixation genes. Appl Environ Microbiol 2012;78:1544–1555 [CrossRef]
    [Google Scholar]
  14. Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JLM. Correction for Wertz et al., “Genomic and physiological characterization of the Verrucomicrobia isolate Didymococcus colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes”. Appl Environ Microbiol 2017;83:e00987–17 [CrossRef]
    [Google Scholar]
  15. Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JLM. Second correction for Wertz et al., “Genomic and physiological characterization of the Verrucomicrobia isolate Geminisphaera colitermitum gen. nov., sp. nov., reveals icroaerophily and nitrogen fixation genes”. Appl Environ Microbiol 2018;84:e00952–18 [CrossRef]
    [Google Scholar]
  16. Lin JY, Russell JA, Sanders JG, Wertz JT. Cephaloticoccus gen. nov., a new genus of ‘Verrucomicrobia’ containing two novel species isolated from Cephalotes ant guts. Int J Syst Evol Microbiol 2016;66:3034–3040 [CrossRef]
    [Google Scholar]
  17. Tegtmeier D, Belitz A, Radek R, Heimerl T, Brune A. Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae). Syst Appl Microbiol 2018;41:101–112 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng X-Y et al. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 2011;61:1442–1447 [CrossRef]
    [Google Scholar]
  20. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49:1–7
    [Google Scholar]
  21. Hahn MW, Stadler P, Wu QL, 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 [CrossRef]
    [Google Scholar]
  22. Gupta P, Samant K, Sahu A. Isolation of cellulose-degrading bacteria and determination of their cellulolytic potential. Int J Microbiol 2012;2012:55 [CrossRef]
    [Google Scholar]
  23. Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S et al. 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 [CrossRef]
    [Google Scholar]
  24. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20:16
    [Google Scholar]
  25. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  26. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  27. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37:911–917 [CrossRef]
    [Google Scholar]
  28. Hoetzinger M, Schmidt J, Jezberová 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 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef]
    [Google Scholar]
  30. Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019;47:D666–D677 [CrossRef]
    [Google Scholar]
  31. 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 [CrossRef]
    [Google Scholar]
  32. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef]
    [Google Scholar]
  33. 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 [CrossRef]
    [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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  36. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef]
    [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; pp1–8
    [Google Scholar]
  38. 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 [CrossRef]
    [Google Scholar]
  39. Pitcher RS, Watmough NJ. The bacterial cytochrome cbb3 oxidases. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2004;1655:388–399 [CrossRef]
    [Google Scholar]
  40. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014;12:635–645 [CrossRef]
    [Google Scholar]
  41. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003980
Loading
/content/journal/ijsem/10.1099/ijsem.0.003980
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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