1887

Abstract

Strain ISS155, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of , in the , with 017 as closest relative (94.3 % similarity). Its major cellular fatty acids are C, C and C; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2 mol%. A phylogenomic analysis using UBCG merges strain ISS155 in a clade with , , and type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available type strain genomes show that strain ISS155 is related to them by values lower than 60 %, with a maximum of 58 % to 017 and 57 % to T7902 and 2-40. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155 represents a new genus and species in , for which we propose the name gen. nov., sp. nov., and strain ISS155 (=CECT 9533=LMG 31237) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003906
2019-12-03
2019-12-11
Loading full text...

Full text loading...

References

  1. Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine Gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015;6: 281 [CrossRef]
    [Google Scholar]
  2. Parte AC. LPSN - List of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68: 1825– 1829 [CrossRef]
    [Google Scholar]
  3. Ling S-K, Xia J, Liu Y, Chen G-J, Du Z-J. Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii. Int J Syst Evol Microbiol 2017;67: 3778– 3783 [CrossRef]
    [Google Scholar]
  4. Huang Z, Lai Q, Zhang D, Shao Z. Agaribacterium haliotis gen. nov., sp. nov., isolated from abalone faeces. Int J Syst Evol Microbiol 2017;67: 3819– 3823 [CrossRef]
    [Google Scholar]
  5. Iwaki H, Yamamoto T, Hasegawa Y. Isolation of marine xylene-utilizing bacteria and characterization of Halioxenophilus aromaticivorans gen. nov., sp. nov. and its xylene degradation gene cluster. FEMS Microbiol Lett 2018;365: fny042 [CrossRef]
    [Google Scholar]
  6. Distel DL, Morrill W, MacLaren-Toussaint N, Franks D, Waterbury J. Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic gamma-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae). Int J Syst Evol Microbiol 2002;52: 2261– 2269 [CrossRef]
    [Google Scholar]
  7. Brito TL, Campos AB, Bastiaan von Meijenfeldt FA, Daniel JP, Ribeiro GB et al. The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei. PLoS One 2018;13: e0200437 [CrossRef]
    [Google Scholar]
  8. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K et al. A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol 2014;80: 7659– 7666 [CrossRef]
    [Google Scholar]
  9. Page KA, Connon SA, Giovannoni SJ. Representative freshwater bacterioplankton isolated from crater lake, Oregon. Appl Environ Microbiol 2004;70: 6542– 6550 [CrossRef]
    [Google Scholar]
  10. Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR. Comparative genomics of Thalassobius including the description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Front Microbiol 2017;8: 2645 [CrossRef]
    [Google Scholar]
  11. Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ. Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis. Int J Syst Evol Microbiol 2018;68: 2515– 2522 [CrossRef]
    [Google Scholar]
  12. Heimbrook ME, Wang WL, Campbell G. Staining bacterial flagella easily. J Clin Microbiol 1989;27: 2612– 2615
    [Google Scholar]
  13. Baumann P, Baumann L. The marine gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes In Starr MP, Stolp H, Trueper HG, Balows A. (editors) The Prokaryotes2 Springer; 1981; pp 1302– 1331
    [Google Scholar]
  14. Lee C, Kim JY, Lee WI, Nelson KL, Yoon J et al. Bactericidal effect of zero-valent iron nanoparticles on Escherichia coli. Environ Sci Technol 2008;42: 4927– 4933 [CrossRef]
    [Google Scholar]
  15. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 1997;47: 369– 376 [CrossRef]
    [Google Scholar]
  16. Ekborg NA, Gonzalez JM, Howard MB, Taylor LE, Hutcheson SW et al. Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides. Int J Syst Evol Microbiol 2005;55: 1545– 1549 [CrossRef]
    [Google Scholar]
  17. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: DE: MIDI Inc; 1990
    [Google Scholar]
  18. MIDI Sherlock Microbial Identification System Operating Manual, version 6.1 Newark, DE: MIDI Inc; 2008
    [Google Scholar]
  19. 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]
  20. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66: 199– 202 [CrossRef]
    [Google Scholar]
  21. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37: 911– 917 [CrossRef]
    [Google Scholar]
  22. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics In: Methods for General and Molecular Microbiology, 3rd ed. 2007; pp 330– 393
    [Google Scholar]
  23. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A. Assembling genomes and mini-metagenomes from highly chimeric reads In Deng M, Jiang R, Sun F, Zhang X. (editors) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science7821 Berlin, Heidelberg: Springer; 2013
    [Google Scholar]
  24. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29: 1072– 1075 [CrossRef]
    [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25: 1043– 1055 [CrossRef]
    [Google Scholar]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30: 2068– 2069 [CrossRef]
    [Google Scholar]
  27. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008;9: 75 [CrossRef]
    [Google Scholar]
  28. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014;42: D206– D214 [CrossRef]
    [Google Scholar]
  29. 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]
  30. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints2016: e1900v1
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  32. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32: 929– 931 [CrossRef]
    [Google Scholar]
  33. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer K-H et al. Update of the All-Species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010;33: 291– 299 [CrossRef]
    [Google Scholar]
  34. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32: 1363– 1371 [CrossRef]
    [Google Scholar]
  35. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56: 281– 285 [CrossRef]
    [Google Scholar]
  36. Yoon S-H, Ha S-M, 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 [CrossRef]
    [Google Scholar]
  37. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014;42: e73 [CrossRef]
    [Google Scholar]
  38. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018;68: 2393– 2411 [CrossRef]
    [Google Scholar]
  39. Chen M-H, Sheu S-Y, Arun AB, Young C-C, Chen CA et al. Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera. Int J Syst Evol Microbiol 2011;61: 1887– 1893 [CrossRef]
    [Google Scholar]
  40. González JM, Weiner RM. Phylogenetic characterization of marine bacterium strain 2-40, a degrader of complex polysaccharides. Int J Syst Evol Microbiol 2000;50 Pt 2: 831– 834 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003906
Loading
/content/journal/ijsem/10.1099/ijsem.0.003906
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