1887

Abstract

A novel slow-growing bacterium, designated strain AW1220, was isolated from agricultural floodplain soil sampled at Mashare (Kavango region, Namibia) by using a high-throughput cultivation approach. Strain AW1220 was characterized as a Gram-negative, non-motile, rod-shaped bacterium. Occasionally, some cells attained an unusual length of up to 35 µm. The strain showed positive responses for catalase and cytochrome- oxidase and divided by binary fission and/or budding. The strain had an aerobic chemoorganoheterotrophic metabolism and was also able to grow under micro-oxic conditions. Colonies were small and pink pigmented. Strain AW1220 was found to be a mesophilic, neutrophilic and non-halophilic bacterium. Cells accumulated polyphosphate intracellularly and mainly utilized complex protein substrates for growth. 16S rRNA gene sequence comparisons revealed that strain AW1220 belonged to the class (=group 1). Its closest relatives were found to be T-27 (90.9 % gene sequence similarity), AP64 (90.8 %) and CB-286315 (84.2 %). The genomic G+C content was 73.3 mol%. The major fatty acids were iso-C, Cω7 and/or iso-C 2-OH, iso-Cω9, iso-C 3-OH and C. The predominant respiratory quinone was MK-9, albeit minor amounts of MK-8 and MK-10 are also present. The polar lipids comprised major amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and one unidentified phosphoglycolipid. On the basis of its polyphasic characterization, strain AW1220 represents a novel genus and species of the class for which the name gen. nov., sp. nov. is proposed, with the type strain AW1220 (=DSM 104292=LMG 29977).

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2018-04-01
2024-03-29
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References

  1. Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H et al. Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 2003; 53:1155–1163 [View Article][PubMed]
    [Google Scholar]
  2. DeBruyn JM, Nixon LT, Fawaz MN, Johnson AM, Radosevich M. Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 2011; 77:6295–6300 [View Article][PubMed]
    [Google Scholar]
  3. Hanada S, Sekiguchi Y. The phylum Gemmatimonadetes . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes, 4th ed. vol. 11 Berlin, Heidelberg: Springer; 2014 pp. 677–681
    [Google Scholar]
  4. Kamagata Y. Phylum XXI. Gemmatimonadetes Zhang, Sekiguchi, Hanada, Hugenholtz, Kim, Kamagata and Nakamura 2003, 1161VP. In Krieg N, Staley J, Brown D, Hedlund B, Paster B et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York: Springer; 2010 pp. 781–784 [Crossref]
    [Google Scholar]
  5. Pascual J, García-López M, Bills GF, Genilloud O. Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers. Int J Syst Evol Microbiol 2016; 66:1976–1985 [View Article][PubMed]
    [Google Scholar]
  6. Zeng Y, Baumbach J, Barbosa EG, Azevedo V, Zhang C et al. Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments. Environ Microbiol Rep 2016; 8:139–149 [View Article][PubMed]
    [Google Scholar]
  7. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [View Article][PubMed]
    [Google Scholar]
  8. DeBruyn JM, Radosevich M, Wommack KE, Polson SW, Hauser LJ et al. Genome sequence and methylome of soil bacterium Gemmatirosa kalamazoonensis KBS708T, a member of the rarely cultivated Gemmatimonadetes phylum. Genome Announc 2014; 2:e00226-14 [View Article][PubMed]
    [Google Scholar]
  9. Park D, Kim H, Yoon S. Nitrous oxide reduction by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27. Appl Environ Microbiol 2017; 83:e00502-17 [View Article][PubMed]
    [Google Scholar]
  10. Zeng Y, Feng F, Medová H, Dean J, Koblížek M. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes . Proc Natl Acad Sci USA 2014; 111:7795–7800 [View Article][PubMed]
    [Google Scholar]
  11. Zeng Y, Selyanin V, Lukeš M, Dean J, Kaftan D et al. Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca . Int J Syst Evol Microbiol 2015; 65:2410–2419 [View Article][PubMed]
    [Google Scholar]
  12. DeBruyn JM, Fawaz MN, Peacock AD, Dunlap JR, Nixon LT et al. Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarely-cultivated bacterial phylum Gemmatimonadetes . J Gen Appl Microbiol 2013; 59:305–312 [View Article][PubMed]
    [Google Scholar]
  13. Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 2003; 69:7210–7215 [View Article][PubMed]
    [Google Scholar]
  14. Davis KE, Joseph SJ, Janssen PH. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 2005; 71:826–834 [View Article][PubMed]
    [Google Scholar]
  15. Overmann J. Principles of enrichment, isolation, cultivation, and preservation of prokaryotes. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes, 4th ed. vol. 11 Berlin, Heidelberg: Springer; 2014 pp. 149–207
    [Google Scholar]
  16. Overmann J, Abt B, Sikorski J. The significance and future of cultivation. Annu Rev Microbiol 2017; 71:711–730 [Crossref]
    [Google Scholar]
  17. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ et al. Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015; 38:534–544 [View Article][PubMed]
    [Google Scholar]
  18. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ et al. Terriglobus albidus sp. nov., a member of the family Acidobacteriaceae isolated from Namibian semiarid savannah soil. Int J Syst Evol Microbiol 2015; 65:3297–3304 [View Article][PubMed]
    [Google Scholar]
  19. Pascual J, Foesel BU, Geppert A, Huber KJ, Overmann J. Flaviaesturariibacter luteus sp. nov., isolated from an agricultural floodplain soil, and emended description of the genus Flaviaesturariibacter . Int J Syst Evol Microbiol 2017; 67:1727–1734 [View Article][PubMed]
    [Google Scholar]
  20. Huber KJ, Wüst PK, Rohde M, Overmann J, Foesel BU. Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. Int J Syst Evol Microbiol 2014; 64:1866–1875 [View Article][PubMed]
    [Google Scholar]
  21. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  22. Wanner G, Vogl K, Overmann J. Ultrastructural characterization of the prokaryotic symbiosis in "Chlorochromatium aggregatum". J Bacteriol 2008; 190:3721–3730 [View Article][PubMed]
    [Google Scholar]
  23. Boedeker C, Schüler M, Reintjes G, Jeske O, van Teeseling MC et al. Determining the bacterial cell biology of Planctomycetes. Nat Commun 2017; 8:14853 [View Article][PubMed]
    [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography ofCellular Fatty Acids Newark, DE: MIDI Techn. Inc; 1990
    [Google Scholar]
  25. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  26. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 330–393
    [Google Scholar]
  27. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
    [Google Scholar]
  28. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  29. Munoz R, Yarza P, Ludwig W, Euzéby J, Amann R et al. Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 2011; 34:169–170 [View Article][PubMed]
    [Google Scholar]
  30. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  31. Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.3.99.152.0 Sunderland, MA: Sinauer Associates; 2016
    [Google Scholar]
  32. Pascual J, Macián MC, Arahal DR, Garay E, Pujalte MJ. Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 2010; 60:154–165 [View Article][PubMed]
    [Google Scholar]
  33. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012; 9:772 [View Article][PubMed]
    [Google Scholar]
  34. Tracy CR, Streten-Joyce C, Dalton R, Nussear KE, Gibb KS et al. Microclimate and limits to photosynthesis in a diverse community of hypolithic cyanobacteria in northern Australia. Environ Microbiol 2010; 12:592–607 [View Article][PubMed]
    [Google Scholar]
  35. 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 [View Article][PubMed]
    [Google Scholar]
  36. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  37. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
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