1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 7

sp. nov., isolated from oceans during the oceans expedition, with a preference for mesopelagic waters Free

Abstract

Strain ISS653, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C, iso-C 2-OH, and iso-C 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family with the type strains of (93.2 %), (93.1 %) and (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with (81 % AAI; 78.9 % ANI), (76 % AAI; 76.3 % ANI), (72 % AAI, 74.9 % ANI), (64 % AAI, 70.8 % ANI) and (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653 in a clade with species of the genus . We conclude that strain ISS653 represents a novel species of the genus for which we propose the name sp. nov., and strain ISS653 (=CECT 9532=LMG 31236) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Flavobacteriaceae , marine bacteria , Mesonia , Mesonia oceanica , mesopelagic zone and taxogenomics
Funding
This study was supported by the:
  • Ministerio de Economía y Competitividad (Award CTM2017-87736-R)
    • Principle Award Recipient: Silvia G. Acinas
  • Ministerio de Economía y Competitividad. (Award CTM2016-80095-C2-1-R)
    • Principle Award Recipient: Carlos Pedrós-Alió
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004296
2020-06-26
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4329.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004296&mimeType=html&fmt=ahah

References

  1. Bernardet JF. Flavobacteriaceae. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc; 2015
     [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 [View Article][PubMed]
     [Google Scholar]
  3. Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG et al. Ecology of marine Bacteroidetes: a comparative genomics approach. Isme J 2013; 7:1026–1037 [View Article][PubMed]
     [Google Scholar]
  4. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M et al. Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm. Int J Syst Evol Microbiol 2003; 53:1967–1971 [View Article][PubMed]
     [Google Scholar]
  5. Nedashkovskaya OI, Kim SB, Zhukova NV, Kwak J, Mikhailov VV et al. Mesonia mobilis sp. nov., isolated from seawater, and emended description of the genus Mesonia . Int J Syst Evol Microbiol 2006; 56:2433–2436 [View Article][PubMed]
     [Google Scholar]
  6. Kang HS, Lee SD. Mesonia phycicola sp. nov., isolated from seaweed, and emended description of the genus Mesonia . Int J Syst Evol Microbiol 2010; 60:591–594 [View Article][PubMed]
     [Google Scholar]
  7. Lee S-Y, Lee M-H, Yoon J-H. Mesonia ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Mesonia . Int J Syst Evol Microbiol 2012; 62:1804–1808 [View Article][PubMed]
     [Google Scholar]
  8. Choi A, Baek K, Lee H, Cho J-C. Mesonia aquimarina sp. nov., a marine bacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2015; 65:135–140 [View Article][PubMed]
     [Google Scholar]
  9. Kolberg J, Busse H-J, Wilke T, Schubert P, Kämpfer P et al. Mesonia hippocampi sp. nov., isolated from the brood pouch of a diseased Barbour's seahorse (Hippocampus barbouri). Int J Syst Evol Microbiol 2015; 65:2241–2247 [View Article][PubMed]
     [Google Scholar]
  10. Wang F-Q, Xie Z-H, Zhao J-X, Chen G-J, Du Z-J. Mesonia sediminis sp. nov., isolated from a sea cucumber culture pond. Antonie van Leeuwenhoek 2015; 108:1205–1212 [View Article][PubMed]
     [Google Scholar]
  11. Sung H-R, Joh K, Shin K-S. Mesonia maritima sp. nov., isolated from seawater of the South Sea of Korea. Int J Syst Evol Microbiol 2017; 67:2574–2580 [View Article][PubMed]
     [Google Scholar]
  12. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes . Front Microbiol 2019; 10:10 [View Article][PubMed]
     [Google Scholar]
  13. Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N et al. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data 2015; 2:150023 [View Article][PubMed]
     [Google Scholar]
  14. Sanz-Sáez I, Salazar G, Lara E, Royo-Llonch M, Vaqué D et al. Diversity patterns of marine cultivable bacteria along vertical and latitudinal gradients.. bioRxiv 2019
     [Google Scholar]
  15. Lucena T, Arahal DR, Sanz-Sáez I, Acinas SG, Sánchez O et al. Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae . Int J Syst Evol Microbiol 2020; 70:1231–1239 [View Article][PubMed]
     [Google Scholar]
  16. 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 [View Article][PubMed]
     [Google Scholar]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. 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 [View Article][PubMed]
     [Google Scholar]
  19. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. 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 Science 7821 Berlin, Heidelberg: Springer;
     [Google Scholar]
  20. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Bonheyo G, Graham D, Shoemaker NB, Salyers AA. Transfer region of a Bacteroides conjugative transposon, CTnDOT. Plasmid 2001; 45:41–51 [View Article][PubMed]
     [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016:e1900v1
     [Google Scholar]
  27. 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 [View Article][PubMed]
     [Google Scholar]
  28. 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 [View Article][PubMed]
     [Google Scholar]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 2016; 18:1403–1414 [View Article][PubMed]
     [Google Scholar]
  31. Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G et al. Global trends in marine plankton diversity across kingdoms of life. Cell 2019; 179:1084–1097 [View Article][PubMed]
     [Google Scholar]
  32. 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 [View Article][PubMed]
     [Google Scholar]
  33. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  34. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark: DE: MIDI Inc; 1990
     [Google Scholar]
  35. MIDI Sherlock Microbial Identification System Operating Manual, version 6.1 Newark, DE: MIDI Inc; 2008
     [Google Scholar]
  36. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350 [View Article][PubMed]
     [Google Scholar]
  37. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020
     [Google Scholar]
  38. Liang Q-Y, Xu Z-X, Zhang J, Chen G-J, Du Z-J. Salegentibacter sediminis sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal sediment. Int J Syst Evol Microbiol 2018; 68:2375–2380 [View Article][PubMed]
     [Google Scholar]
  39. Li A-Z, Han X-B, Lin L-Z, Zhang M-X, Zhu H-H. Gramella antarctica sp. nov., isolated from marine surface sediment. Int J Syst Evol Microbiol 2018; 68:358–363 [View Article][PubMed]
     [Google Scholar]
  40. Qin Q-L, Zhao D-L, Wang J, Chen X-L, Dang H-Y et al. Wangia profunda gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sediment. FEMS Microbiol Lett 2007; 271:53–58 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004296
Loading
Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters
Int J Syst Evol Microbiol 70, 4329 (2020); https://doi.org/10.1099/ijsem.0.004296
/content/journal/ijsem/10.1099/ijsem.0.004296
/content/journal/ijsem/10.1099/ijsem.0.004296
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