1887

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Volume 74, Issue 4

gen. nov., sp. nov., a marine lineage in the phylum with genetic potential for carbon and nitrogen fixation No Access

Abstract

A novel bacterial strain, designated WL0086, was isolated from a marine sediment sample collected in Lianyungang city, Jiangsu province, PR China. This strain showed the highest 16S rRNA gene sequence similarity to TAV2 (92.7 %) of the family , and all the unclassified cultured and uncultured isolates with similarities >95 % were from marine environments. Cells were Gram-stain-negative, aerobic, non-motile cocci with a size of 0.6–0.8 µm in diameter. Strain WL0086 was positive for both oxidase and catalase, and grew at 20–37 °C (optimum, 28 °C), with 1.5–11.0 % NaCl (w/v; optimum, 2.5–4.0 %) and at pH 5.0–9.0 (optimum, pH 7.0). The major polar lipid profile of strain WL0086 consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major isoprenoid quinone was menaquinone-7 and the predominant fatty acids were iso-C, anteiso-C, C and C 9. The complete genome consisted of a chromosome with 6 109 182 bp. The G+C content of genomic DNA was 64.0%. Results of phylogenomic analysis based on the 16S rRNA gene sequence and the whole genome suggested that strain WL0086 formed a distinct clade closely neighbouring the members of the family . On the basis of phylogenetic, phenotypic, and chemotaxonomic evidences, strain WL0086 should represent a novel genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is WL0086 (=MCCC 1K05844=JCM 34677=GDMCC 1.2411).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actomonas aquatica gen. nov., sp. nov. , citrate lyase , marine sediment and nitrogen fixation
Funding
This study was supported by the:
  • the Jiangsu Innovation Center of Marine Bioresources (Award 822153216)
    • Principle Award Recipient: AiHua Zhang
  • the Innovation Project for Marine Science and Technology of Jiangsu Province (Award JSZRHYKJ202209)
    • Principle Award Recipient: Dao-FengZhang
© 2024 The Authors
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References

  1. Hedlund BP, Gosink JJ, Staley JT. Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 1997; 72:29–38 [View Article] [PubMed]
     [Google Scholar]
  2. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:005056 [View Article] [PubMed]
     [Google Scholar]
  3. 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]
  4. Min L, Wang W, Oren A, Lai Q, Huang Z. Coraliomargarita parva sp. nov., isolated from mangrove sediment and genome-based analysis of the class Opitutae revealed five novel families: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov. Front Microbiol 2023; 14:1202141 [View Article]
     [Google Scholar]
  5. Oren A, Göker M. Validation list no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73:006080 [View Article] [PubMed]
     [Google Scholar]
  6. De Groote D, van Doorn LJ, Ducatelle R, Verschuuren A, Tilmant K et al. Phylogenetic characterization of “Candidatus Helicobacter bovis”, a new gastric helicobacter in cattle. Int J Syst Bacteriol 1999; 49:1707–1715 [View Article] [PubMed]
     [Google Scholar]
  7. Chen WM, Chen TY, Yang CC, Sheu SY. Oleiharenicola lentus sp. nov., isolated from irrigation water. Int J Syst Evol Microbiol 2020; 70:3440–3448 [View Article] [PubMed]
     [Google Scholar]
  8. Rochman FF, Kim J-J, Rijpstra WIC, Sinninghe Damsté JS, Schumann P et al. Oleiharenicola alkalitolerans gen. nov., sp. nov., a new member of the phylum Verrucomicrobia isolated from an oilsands tailings pond. Int J Syst Evol Microbiol 2018; 68:1078–1084 [View Article] [PubMed]
     [Google Scholar]
  9. Shieh WY, Jean WD. Alterococcus agarolyticus, gen.nov., sp.nov., a halophilic thermophilic bacterium capable of agar degradation. Can J Microbiol 1998; 44:637–645 [View Article] [PubMed]
     [Google Scholar]
  10. Kobayashi Y, Kawahara T, Inoue S, Kohda N. Akkermansia biwaensis sp. nov., an anaerobic mucin-degrading bacterium isolated from human faeces. Int J Syst Evol Microbiol 2023; 73:005697 [View Article] [PubMed]
     [Google Scholar]
  11. Pitt A, Schmidt J, Koll U, Hahn MW. Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat. Int J Syst Evol Microbiol 2020; 70:1830–1836 [View Article] [PubMed]
     [Google Scholar]
  12. Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026–1039 [View Article] [PubMed]
     [Google Scholar]
  13. Orellana LH, Francis TB, Ferraro M, Hehemann J-H, Fuchs BM et al. Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME J 2022; 16:630–641 [View Article] [PubMed]
     [Google Scholar]
  14. Freitas S, Hatosy S, Fuhrman JA, Huse SM, Welch DBM et al. Global distribution and diversity of marine Verrucomicrobia. ISME J 2012; 6:1499–1505 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon J, Yasumoto-Hirose M, Matsuo Y, Nozawa M, Matsuda S et al. Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum “Verrucomicrobia”, isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 2007; 57:1377–1385 [View Article] [PubMed]
     [Google Scholar]
  16. Crespo BG, Pommier T, Fernández-Gómez B, Pedrós-Alió C. Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. MicrobiologyOpen 2013; 2:541–552 [View Article] [PubMed]
     [Google Scholar]
  17. Bar-Shalom R, Rozenberg A, Lahyani M, Hassanzadeh B, Sahoo G et al. Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota. ISME J 2023; 17:1063–1073 [View Article] [PubMed]
     [Google Scholar]
  18. Tegtmeier D, Belitz A, Radek R, Heimerl T, Brune A. Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae). Syst Appl Microbiol 2018; 41:101–112 [View Article] [PubMed]
     [Google Scholar]
  19. Baek K, Song J, Cho J-C, Chung EJ, Choi A. Nibricoccus aquaticus gen. nov., sp. nov., a new genus of the family Opitutaceae isolated from hyporheic freshwater. Int J Syst Evol Microbiol 2019; 69:552–557 [View Article] [PubMed]
     [Google Scholar]
  20. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
     [Google Scholar]
  21. Chin KJ, Liesack W, Janssen PH. Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division “Verrucomicrobia” isolated from rice paddy soil. Int J Syst Evol Microbiol 2001; 51:1965–1968 [View Article] [PubMed]
     [Google Scholar]
  22. Chung J-H, Lee J-Y, Choi G-H, Won M, Yeon J et al. Horticoccus luteus gen. nov., sp. nov., a novel member of the phylum Verrucomicrobia isolated from a dichlorodiphenyltrichloroethane (DDT)-contaminated orchard soil. Curr Microbiol 2022; 79:340 [View Article] [PubMed]
     [Google Scholar]
  23. Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JLM. Second correction for Wertz et al., “Genomic and physiological characterization of the Verrucomicrobia isolate Geminisphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes.”. Appl Environ Microbiol 2018; 84:e00952-18 [View Article] [PubMed]
     [Google Scholar]
  24. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  27. 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 [View Article] [PubMed]
     [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  29. Bouali M, Zrafi I, Bakhrouf A, Chaussonnerie S, Sghir A. Bacterial structure and spatiotemporal distribution in a horizontal subsurface flow constructed wetland. Appl Microbiol Biotechnol 2014; 98:3191–3203 [View Article] [PubMed]
     [Google Scholar]
  30. Riesenfeld CS, Murray AE, Baker BJ. Characterization of the microbial community and polyketide biosynthetic potential in the palmerolide-producing tunicate Synoicum adareanum. J Nat Prod 2008; 71:1812–1818 [View Article] [PubMed]
     [Google Scholar]
  31. Pichon D, Gaia V, Norman MD, Boucher-Rodoni R. Phylogenetic diversity of epibiotic bacteria in the accessory nidamental glands of squids (Cephalopoda: Loliginidae and Idiosepiidae). Mar Biol 2005; 147:1323–1332 [View Article]
     [Google Scholar]
  32. Murray AE, Lo C-C, Daligault HE, Avalon NE, Read RW et al. Discovery of an antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential. mSphere 2021; 6:e00759-00721 [View Article] [PubMed]
     [Google Scholar]
  33. Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D’Angelo T et al. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764–770 [View Article] [PubMed]
     [Google Scholar]
  34. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  35. 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] [PubMed]
     [Google Scholar]
  36. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2020; 36:2251–2252 [View Article] [PubMed]
     [Google Scholar]
  37. Zhang D-F, He W, Shao Z, Ahmed I, Zhang Y et al. Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Microbiol 2023; 73:006156 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. Zhang D-F, He W, Shao Z, Ahmed I, Zhang Y et al. EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. BMC Bioinformatics 2023; 24:390 [View Article] [PubMed]
     [Google Scholar]
  40. Muchowska KB, Chevallot-Beroux E, Moran J. Recreating ancient metabolic pathways before enzymes. Bioorg Med Chem 2019; 27:2292–2297 [View Article] [PubMed]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  42. Athayle M, Schaal A, Parlett J. An integrated procedure for the extraction of Isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233241
     [Google Scholar]
  43. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
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Actomonas aquatica gen. nov., sp. nov., a marine lineage in the phylum Verrucomicrobiota with genetic potential for carbon and nitrogen fixation
Int J Syst Evol Microbiol 74, 006314 (2024); https://doi.org/10.1099/ijsem.0.006314
/content/journal/ijsem/10.1099/ijsem.0.006314
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