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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 1

gen. nov., sp. nov., isolated from estuary sediment Free

Abstract

A Gram-negative, aerobic, non-flagellated and ovoid- or rod-shaped bacterium, designated strain SM1902, was isolated from the sediment sampled at the Jia River estuary, Yantai, PR China. The strain grew at 10–37 °C (optimum, 25–30 °C), pH 6.0–10.0 (pH 7.0) and with 0.5–13.0 % (w/v) NaCl (2.5%). It reduced nitrate to nitrite, but did not produce bacteriochlorophyll . The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1902 constituted a separated lineage within the family and was closely related to TG-679 and LMIT002 with 96.1 and 94.3 % 16S rRNA gene sequence similarities, respectively. The predominant cellular fatty acid was summed feature 8 (Cω7 and/or Cω6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid. The sole respiratory quinone was ubiquinone-10. The DNA–DNA hybridization values between strain SM1902 and TG-679 and LMIT002 were 19.6 and 19.5 %, respectively; and the average nucleotide identity values between them were 76.1 and 74.2 %, respectively. The genomic DNA G+C content of strain SM1902 was 58.2 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1902 is considered to represent a novel species in a new genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain is SM1902 (=KCTC 72045=MCCC 1K03596=CCTCC AB 2018346).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): estuary sediment , gen. nov. and Rhodobacteraceae
Funding
This study was supported by the:
  • National Key R&D Program of China (Award 2018YFC0310704)
    • Principle Award Recipient: Xiu-Lan Chen
  • National Key R&D Program of China (Award 2018YFC1406504)
    • Principle Award Recipient: Xiao-Yan Song
  • National Key R&D Program of China (Award 2018YFC1406703)
    • Principle Award Recipient: Yu-Zhong Zhang
  • National Key R&D Program of China (Award 2018YFC1406704)
    • Principle Award Recipient: Xi-Ying Zhang
  • AoShan Talents Cultivation Program (Award 2017ASTCP-OS14)
    • Principle Award Recipient: Yu-Zhong Zhang
  • National Science Foundation of China (Award grants 31670063)
    • Principle Award Recipient: Xi-Ying Zhang
  • National Science Foundation of China (Award grants 31870052)
    • Principle Award Recipient: Xiu-Lan Chen
  • Taishan Scholars Program of Shandong Province (Award 2009TS079)
    • Principle Award Recipient: Yu-Zhong Zhang
  • Science and Technology Basic Resources Investigation Program of China (Award 2017FY100804)
    • Principle Award Recipient: Xi-Ying Zhang
  • funding from key laboratory of global change and marine-atmospheric chemistry of the State Oceanic Administration, P. R. China (Award 2018GCMAC16)
    • Principle Award Recipient: Xi-Ying Zhang
  • Natural Science Foundation of Jiangsu Province (Award BK20170397)
    • Principle Award Recipient: Chun-Yang Li
© 2020 The Authors
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2024-12-14
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References

  1. Garrity GM, Bell JA, Lilburn T, Family I. Rhodobacteraceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology 2, 2nd ed. Springer: New York; 2005 p 161
     [Google Scholar]
  2. Garrity GM, Bell JA, Lilburn T. Rhodobacteraceae fam. nov. In List of new names and new combinations previously effectively, but not validly, published, Validation List no. 107. Int J Syst Evol Microbiol 2006; 56:1–6
     [Google Scholar]
  3. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The Family Rhodobacteraceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes-Alphaproteobacteria and Betaproteobacteria 8, 4th ed. Berlin: Springer; 2014 p 439
     [Google Scholar]
  4. Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. Isme J 2017; 11:1483–1499 [View Article]
     [Google Scholar]
  5. 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]
     [Google Scholar]
  6. Ren Y, Chen C, Ye Y, Wang R, Han S et al. Meridianimarinicoccus roseus gen. nov., sp. nov., a novel genus of the family Rhodobacteraceae isolated from seawater. Int J Syst Evol Microbiol 2019; 69:504–510 [View Article]
     [Google Scholar]
  7. Zhu J, Hong P, Wang S, Hu Z, Wang H. Phycocomes zhengii gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae isolated from the phycosphere of Chlorella vulgaris . Int J Syst Evol Microbiol 2019; 69:535–541 [View Article]
     [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
     [Google Scholar]
  9. 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]
     [Google Scholar]
  10. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  15. Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S et al. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 2017; 27:768–777 [View Article]
     [Google Scholar]
  16. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
     [Google Scholar]
  17. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article]
     [Google Scholar]
  18. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article]
     [Google Scholar]
  19. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
     [Google Scholar]
  20. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8:275–282 [View Article]
     [Google Scholar]
  21. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [View Article]
     [Google Scholar]
  22. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  23. 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]
     [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  25. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  26. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article]
     [Google Scholar]
  27. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  28. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  29. Yi H, Lim YW, Chun J. Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int J Syst Evol Microbiol 2007; 57:815–819 [View Article]
     [Google Scholar]
  30. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 21–41
     [Google Scholar]
  31. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  32. Ruiz-Ponte C, Cilia V, Lambert C, Nicolas JL. Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus . Int J Syst Bacteriol 1998; 48 Pt 2:537–542 [View Article]
     [Google Scholar]
  33. Suyama T, Shigematsu T, Takaichi S, Nodasaka Y, Fujikawa S et al. Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the Proteobacteria. Int J Syst Bacteriol 1999; 49:449–457 [View Article]
     [Google Scholar]
  34. Biebl H, Allgaier M, Lünsdorf H, Pukall R, Tindall BJ et al. Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a . Int J Syst Evol Microbiol 2005; 55:2377–2383 [View Article]
     [Google Scholar]
  35. Muramatsu Y, Uchino Y, Kasai H, Suzuki K-i, Nakagawa Y. Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int J Syst Evol Microbiol 2007; 57:1304–1309 [View Article]
     [Google Scholar]
  36. Petursdottir SK, Kristjansson JK. Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the blue lagoon geothermal lake in Iceland. Extremophiles 1997; 1:94–99 [View Article]
     [Google Scholar]
  37. Uchino Y, Hirata A, Yokota A, Sugiyama J. Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 1998; 44:201–210 [View Article]
     [Google Scholar]
  38. González JM, Covert JS, Whitman WB, Henriksen JR, Mayer F et al. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 2003; 53:1261–1269 [View Article]
     [Google Scholar]
  39. Oh KH, Jung YT, Oh TK, Yoon JH. Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2011; 61:1182–1188 [View Article]
     [Google Scholar]
  40. Huo Y-Y, Xu X-W, Li X, Liu C, Cui H-L et al. Ruegeria marina sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:347–350 [View Article]
     [Google Scholar]
  41. Park S, Yoon J-H. Ruegeria arenilitoris sp. nov., isolated from the seashore sand around a seaweed farm. Antonie Van Leeuwenhoek 2012; 102:581–589 [View Article]
     [Google Scholar]
  42. Lee J, Whon TW, Shin N-R, Roh SW, Kim J et al. Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii . Int J Syst Evol Microbiol 2012; 62:2851–2857 [View Article]
     [Google Scholar]
  43. Kim YO, Park S, Nam BH, Kang SJ, Hur YB et al. Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi . Int J Syst Evol Microbiol 2012; 62:925–930 [View Article]
     [Google Scholar]
  44. Kampfer P, Arun AB, Rekha PD, Busse H-J, Young C-C et al. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int J Syst Evol Microbiol 2013; 63:2538–2544 [View Article]
     [Google Scholar]
  45. Lucena T, Ruvira MA, Macián MC, Pujalte MJ, Arahal DR. Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov. Syst Appl Microbiol 2013; 36:325–329 [View Article]
     [Google Scholar]
  46. Kim Y-O, Park S, Nam B-H, Jung Y-T, Kim D-G et al. Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi. Antonie Van Leeuwenhoek 2014; 105:551–558 [View Article]
     [Google Scholar]
  47. Zhang G, Haroon MF, Zhang R, Dong X, Wang D et al. Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine–seawater interface at Erba deep in the red sea. Int J Syst Evol Microbiol 2017; 67:4624–4631 [View Article]
     [Google Scholar]
  48. 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 [View Article]
     [Google Scholar]
  49. Zhang L, Wang KL, Yin Q, Liang JY, Xu Y. Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel . Int J Syst Evol Microbiol 2018; 68:2653–2658 [View Article]
     [Google Scholar]
  50. 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 [View Article]
     [Google Scholar]
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Fluviibacterium aquatile gen. nov., sp. nov., isolated from estuary sediment
Int J Syst Evol Microbiol 70, 105 (2020); https://doi.org/10.1099/ijsem.0.003722
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