1887

Abstract

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41, was isolated from Antarctic intertidal sediment. The isolate grew at 0–37 °C and with 0.5–10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41 constituted a distinct phylogenetic line within the family and was closely related with some species in the genera , , , , and with 98.6–95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C, summed feature 8 (C ω7 and/or C ω6) and C and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41 was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41 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 S4J41 (=MCCC 1K03508=KCTC 62793). Moreover, the transfer of Kim . 2019 to gen. nov. as comb. nov. (type strain 318-1=JCM 30927=KCTC 72105) is also proposed.

Funding
This study was supported by the:
  • Xi-Ying zhang , China Scholarship Council , (Award file No. 201906225012)
  • Xi-Ying zhang , the Science and Technology Basic Resources Investigation Program of China , (Award 2017FY100804)
  • Yu-Zhong Zhang , Taishan Scholars Program of Shandong Province , (Award tspd20181203)
  • Xi-Ying zhang , National Key R&D Program of China , (Award 2018YFC1406704)
  • Yu-Zhong Zhang , National Key R&D Program of China , (Award 2018YFC1406703)
  • Hai-Nan Su , National Key R&D Program of China , (Award 2018YFC1406701)
  • Xi-Ying zhang , National Science Foundation of China , (Award 31670063)
  • Yu-Zhong Zhang , Qingdao National Laboratory for Marine Science and Technology , (Award 2017ASTCP-OS14)
  • Xiao-Yan Song , National Key R&D Program of China , (Award 2018YFC1406504)
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2020-06-04
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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. New York: Springer; 2005 pp 161–229
    [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 [CrossRef]
    [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 pp 439–512
    [Google Scholar]
  4. Yuan X-X, Wang N, Zhang M-Y, Chen X-L, Li C-Y et al. Chachezhania antarctica gen. nov., sp. nov., a novel member of the family 'Rhodobacteraceae' isolated from Antarctic seawater. Antonie Van Leeuwenhoek 2019; 112:1841–1848 [CrossRef]
    [Google Scholar]
  5. Liu C, Zhang X-Y, Su H-N, Zhou M-Y, Chen B et al. Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:1566–1572 [CrossRef]
    [Google Scholar]
  6. Lee YM, Yang JY, Baek K, Han SJ, Shin SC et al. Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter . Int J Syst Evol Microbiol 2016; 66:1068–1073 [CrossRef]
    [Google Scholar]
  7. Youn UJ, Lee JH, Han SJ. Diketopiperazine and alloxazine alkaloids from the antarctic bacteria, Pseudorhodobacter psychrotolerans sp. nov. Biochem Syst Ecol 2019; 85:21–23 [CrossRef]
    [Google Scholar]
  8. 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]
  9. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped blast and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [CrossRef]
    [Google Scholar]
  10. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [CrossRef]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  15. 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]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [Google Scholar]
  17. 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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  19. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef]
    [Google Scholar]
  21. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [CrossRef]
    [Google Scholar]
  22. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [CrossRef]
    [Google Scholar]
  23. Lefort V, Longueville J-E, Gascuel O. SMS: smart model selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [CrossRef]
    [Google Scholar]
  24. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [CrossRef]
    [Google Scholar]
  25. 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]
  26. 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 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [CrossRef]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial Systematics. Method Microbiol 1987; 19:161–207
    [Google Scholar]
  32. 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; 49:R16
    [Google Scholar]
  33. 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]
  34. 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]
  35. Kim J, Kim D-Y, Yang K-H, Kim S, Lee S-S. Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea. Int J Syst Evol Microbiol 2019; 69:2854–2861 [CrossRef]
    [Google Scholar]
  36. Zhang Y-J, Yu N, Zhang X-Y, Chen S. Pseudopuniceibacterium sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sediment. Int J Syst Evol Microbiol 2019; 69:2541–2546 [CrossRef]
    [Google Scholar]
  37. 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 [CrossRef]
    [Google Scholar]
  38. 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 [CrossRef]
    [Google Scholar]
  39. 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 [CrossRef]
    [Google Scholar]
  40. Muramatsu Y, Uchino Y, Kasai H, Suzuki K-ichiro, Nakagawa Y et al. Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int J Syst Evol Microbiol 2007; 57:1304–1309 [CrossRef]
    [Google Scholar]
  41. Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Faimali M et al. Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 2008; 58:2726–2733 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  43. 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]
  44. Oh K-H, Jung Y-T, Oh T-K, Yoon J-H. Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2011; 61:1182–1188 [CrossRef]
    [Google Scholar]
  45. Kim Y-O, Park S, Nam B-H, Kang S-J, Hur YB et al. Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi . Int J Syst Evol Microbiol 2012; 62:925–930 [CrossRef]
    [Google Scholar]
  46. Kämpfer 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 [CrossRef]
    [Google Scholar]
  47. Zhang L, Wang K-L, Yin Q, Liang J-Y, 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 [CrossRef]
    [Google Scholar]
  48. Lucena T, Ruvira MA, Macián MC, Pujalte MJ, Arahal DR et al. Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov. Syst Appl Microbiol 2013; 36:325–329 [CrossRef]
    [Google Scholar]
  49. 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 [CrossRef]
    [Google Scholar]
  50. 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 [CrossRef]
    [Google Scholar]
  51. 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 [CrossRef]
    [Google Scholar]
  52. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera . Int J Syst Evol Microbiol 2006; 56:1293–1304 [CrossRef]
    [Google Scholar]
  53. 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; 48:537–542 [CrossRef]
    [Google Scholar]
  54. Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Mollica A et al. Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 2009; 59:811–817 [CrossRef]
    [Google Scholar]
  55. Sonnenschein EC, Phippen CBW, Nielsen KF, Mateiu RV, Melchiorsen J et al. Phaeobacter piscinae sp. nov., a species of the Roseobacter group and potential aquaculture probiont. Int J Syst Evol Microbiol 2017; 67:4559–4564 [CrossRef]
    [Google Scholar]
  56. Breider S, Freese HM, Spröer C, Simon M, Overmann J et al. Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour. Int J Syst Evol Microbiol 2017; 67:2153–2159 [CrossRef]
    [Google Scholar]
  57. Zhang C, Neuner K, Wu J, Yao J et al. Puniceibacterium sediminis sp. nov. isolated from Sakhalin Island, Russia. Int. J. Syst. Evol. Microbiol 2015; 65:1462–1466
    [Google Scholar]
  58. Park A-Y, Teeravet S, Pheng S, Lee JR, Kim S-G et al. Sulfitobacter aestuarii sp. nov., a marine bacterium isolated from a tidal flat of the Yellow Sea. Int J Syst Evol Microbiol 2018; 68:1771–1775 [CrossRef]
    [Google Scholar]
  59. Labrenz M, Tindall BJ, Lawson PA, Collins MD, Schumann P et al. Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., alpha-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake. Int J Syst Evol Microbiol 2000; 50:303–313 [CrossRef]
    [Google Scholar]
  60. Ivanova EP, Gorshkova NM, Sawabe T, Zhukova NV, Hayashi K et al. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int J Syst Evol Microbiol 2004; 54:475–480 [CrossRef]
    [Google Scholar]
  61. Yoon J-H, Kang S-J, Lee M-H, Oh T-K. Description of Sulfitobacter Donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter . Int J Syst Evol Microbiol 2007; 57:1788–1792 [CrossRef]
    [Google Scholar]
  62. Kumari P, Bhattacharjee S, Poddar A, Das SK. Sulfitobacter faviae sp. nov., isolated from the coral Faviaveroni . Int J Syst Evol Microbiol 2016; 66:3786–3792 [CrossRef]
    [Google Scholar]
  63. Kwak M-J, Lee J-S, Lee KC, Kim KK, Eom MK et al. Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2014; 64:3760–3767 [CrossRef]
    [Google Scholar]
  64. Wagner-Döbler I, Rheims H, Felske A, El-Ghezal A, Flade-Schröder D et al. Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites. Int J Syst Evol Microbiol 2004; 54:1177–1184 [CrossRef]
    [Google Scholar]
  65. Liu Y, Lai Q, Shao Z. Proposal for transfer of Oceanibulbus indolifex Wagner-Döbler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov. Int J Syst Evol Microbiol 2017; 67:2328–2331 [CrossRef]
    [Google Scholar]
  66. Park JR, Bae J-W, Nam Y-D, Chang H-W, Kwon H-Y et al. Sulfitobacter litoralis sp. nov., a marine bacterium isolated from the East Sea, Korea. Int J Syst Evol Microbiol 2007; 57:692–695 [CrossRef]
    [Google Scholar]
  67. Yoon J-H, Kang S-J, Oh T-K. . Sulfitobacter marinus sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 2007; 57:302–305 [CrossRef]
    [Google Scholar]
  68. Pukall R, Buntefuss D, Frühling A, Rohde M, Kroppenstedt RM et al. Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria . Int J Syst Bacteriol 1999; 49:513–519 [CrossRef]
    [Google Scholar]
  69. Fukui Y, Abe M, Kobayashi M, Satomi M. Sulfitobacter pacificus sp. nov., isolated from the red alga Pyropia yezoensis . Antonie Van Leeuwenhoek 2015; 107:1155–1163 [CrossRef]
    [Google Scholar]
  70. Sorokin DY. Sulfitobacter pontiacus gen. nov., sp. nov. — a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Mikrobiologiya 1995; 64:354–365
    [Google Scholar]
  71. Fukui Y, Abe M, Kobayashi M, Shimada Y, Saito H et al. Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis . Int J Syst Evol Microbiol 2014; 64:438–443 [CrossRef]
    [Google Scholar]
  72. Hong Z, Lai Q, Luo Q, Jiang S, Zhu R et al. Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries . Int J Syst Evol Microbiol 2015; 65:95–100 [CrossRef]
    [Google Scholar]
  73. Park S, Jung Y-T, Won S-M, Park J-M, Yoon J-H et al. Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir. Int J Syst Evol Microbiol 2015; 65:1672–1678 [CrossRef]
    [Google Scholar]
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