Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013

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A Gram-stain-negative, tyrosine-metabolizing, non-motile, strictly aerobic, non-spore-forming, rod-shaped marine bacterium, designated strain CC-PW-75T, was isolated from the estuarine water off Pintung, Taiwan. Strain CC-PW-75T formed a distinct phyletic lineage associated with Gemmobacter species, sharing the highest 16S rRNA gene sequence similarity with G. megaterium CF17T and G. straminiformis CAM-8T (96.0% each) followed by G. aquatilis IFAM 1031T and G. nectariphilus AST4T (95.8% each). Analysis of the draft genome (3.76 Mbp) revealed the presence of genes encoding light-harvesting complexes, photosynthetic reaction centers and proteins involved in the metabolism of CO, CO2, HCO3 and H2S. However, bacteriochlorophyll a was not detected. Average nucleotide identity values between the genome sequence of CC-PW-75T and the related Gemmobacter species (n = 6) were estimated to be 72.8–76.3%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid in major amounts, and phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid in minor amounts. C18:1ω7c and/or C18:1ω6c, C18:0 and C18:1ω7c 11-methyl were identified to be major fatty acids. The DNA G + C content was 66.2 mol% (draft genome sequence). Ubiquinone-10 (Q-10) was the sole respiratory quinone. Based on the polyphasic taxonomic evidence, CC-PW-75T is most likely a novel species of the genus Gemmobacter, affiliated to the family Rhodobacteraceae, for which the name Gemmobacter aestuarii sp. nov. is proposed. The type strain is CC-PW-75T (= JCM 19754T = BCRC 80759T). Also, we propose the reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013 using the polyphasic data presented in this study.

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  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

  2. Anil Kumar P, Srinivas TNR, Sasikala C, Ramana CV (2007) Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic, alphaproteobacterium from the Himalayas of India. Int J Syst Evol Microbiol 57:2568–2571

  3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

  4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

  5. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

  6. Chen WM, Cho NT, Huang WC, Young CC, Sheu SY (2013) Description of Gemmobacter fontiphilus sp. nov., isolated from a fresh water spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis. Int J Syst Evol Microbiol 63:470–478

  7. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, Meyer SD, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

  8. Collins MD (1985) Analysis of isoprenoid quinones. Methods Microbiol 18:329–366

  9. GCG (1995) Wisconsin Package Version 8.1 Program Manual. Computer Group, Madison.

  10. Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O'Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161

  11. Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 47:590–592

  12. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

  13. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

  14. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

  15. Hameed A, Lin SY, Lai WA, Shahina M, Liu YC, Hsu YH et al (2016) Idiomarina tyrosinivorans sp. nov., isolated from estuarine surface water. Int J Syst Evol Microbiol 66:5384–5391

  16. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY (1998) Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 8:557–561

  17. Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

  18. Kämpfer P, Jerzak L, Wilharm G, Golke J, Busse HJ, Glaeser SP (2015) Gemmobacter intermedius sp. nov., isolated from a white stork, (Ciconia ciconia). Int J Syst Evol Microbiol 65:778–783

  19. Kang JY, Kim MJ, Chun J, Son KP, Jahng KY (2017) Gemmobacter straminiformis sp. nov., isolated from an artificial fountain. Int J Syst Evol Microbiol 67:5019–5025

  20. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

  21. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

  22. Liu JJ, Zhang XQ, Chi FT, Pan J, Sun C, Wu M (2014) Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds. Int J Syst Evol Microbiol 64:66–71

  23. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

  24. Murray RGE, Doetsch RN, Robinow CF (1994) Determinative and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society of Microbiology, Washington, pp 21–41

  25. Parte AC (2018) LPSN–list of prokaryotic names with standing in nomenclature (, 20 years on. Int J Syst Evol Microbiol 68:1825–1829

  26. Rothe B, Fischer A, Hirsch P, Sittig M, Stackebrandt E (1987) The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov. Arch Microbiol 147:92–99

  27. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

  28. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16

  29. Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Cheng IC, Lee MR, Lai WA, Lee RJ, Young CC (2013) Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium. Int J Syst Evol Microbiol 63:3415–3422

  30. Sheu SY, Sheu DS, Sheu FS, Chen WM (2013a) Gemmobacter tilapiae sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond. Int J Syst Evol Microbiol 63:1550–1556

  31. Sheu SY, Shiau YW, Wei YT, Chen WM (2013b) Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 63:4039–4045

  32. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654

  33. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

  34. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

  35. Suresh G, Sasikala C, Ramana CV (2015) Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov. Int J Syst Evol Microbiol 65:794–798

  36. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

  37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

  38. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266

  39. Watts D, MacBeath JR (2001) Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. Methods Mol Biol 167:153–170

  40. Yoo Y, Lee DW, Lee H, Kwon BO, Khim JS, Yim UH, Park H, Park B, Choi IG, Kim BS, Jeon SW, Kim GH, Kim JJ (2019) Gemmobacter lutimaris sp nov, a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol.

  41. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

  42. Zheng JW, Chen YG, Zhang J, Ni YY, Li WJ, He J, Li SP (2011) Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 61:1921–1926

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This work was financially supported by the “Innovation and Development Center of Sustainable Agriculture” from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) (Grant No. 100S0506) in Taiwan.

The GenBank accession number for the 16S rRNA gene sequence of strain CC-PW-75T is KF732818. The draft genome of CC-PW-75T has been deposited at DDBJ/ENA/GenBank under the Accession No. SSND00000000. The version described in this paper is version SSND01000000.

Author information

MS isolated the strain and carried out physiological tests and literature survey. SYL identified the strain and performed the fatty acid analysis. WAL conducted the biochemical analysis. AH performed polar lipid, quinone, and other chemotaxonomic analysis. YHH dealt with hydrolysis of macromolecules and physiological tests in part. AH together with WMC and CCY analyzed the raw data and drafted the manuscript.

Correspondence to Chiu-Chung Young.

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Communicated by Erko Stackebrandt.

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Hameed, A., Shahina, M., Lin, S. et al. Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013. Arch Microbiol (2020) doi:10.1007/s00203-020-01809-y

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  • Rhodobacteraceae
  • Bacteriochlorophyll
  • RuBisCO
  • Carbon monoxide dehydrogenase
  • Light-harvesting complex