1887

Abstract

Two Gram-negative, aerobic, rod-shaped bacterial strains, 7MK25 and 6Y81, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain 7MK25 showed the highest similarity (93.6 %) to AR4, followed by DSM 9653 (93.3 %). Strain 6Y81 had the highest similarity of 97.9 % to RmlP026, followed by RmlP001 (97.2 %). Phylogenomic analysis using the UBCG and PhyloPhlAn methods consistently showed that strain 7MK25 formed a sister clade to , while strain 6Y81 formed an independent clade within the genus , both in the order . The digital DNA–DNA hybridization and average nucleotide identity values between strains 7MK25, 6Y81 and their close relatives were in the ranges of 19.1–29.9 % and 72.5–85.5 %, respectively. The major fatty acids of 7MK25 were summed feature 8 (C ω7/C ω6), C cyclo ω8, C and C cyclo, while those of 6Y81 were summed feature 8 (C ω7/C ω6), C and C 3-OH. Strains 7MK25 and 6Y81 took diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as their dominant polar lipids, and Q-10 as their major respiratory quinone. On the basis of phenotypic and phylogenetic data, strain 7MK25 is proposed to represent a novel species of a novel genus with name gen. nov., sp. nov., within a novel family fam. nov., with 7MK25 (=KCTC 62738=GDMCC 1.1452) as its type strain. Strain 6Y81 represents a novel species in the genus , for which the name sp. nov. (type strain 6Y81=KACC 21 727=GDMCC 1.2176) is proposed. fam. nov. with as the type genus is also proposed to solve the non-monophylectic problem of the family .

Keyword(s): novel species , phylogeny and taxonomy
Funding
This study was supported by the:
  • Special Fund Project for Science and Technology Innovation Strategy of Guangdong Province (Award 2018B020205003)
    • Principle Award Recipient: NotApplicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006348
2024-04-23
2024-05-03
Loading full text...

Full text loading...

References

  1. Guo X, Zhang Q, Fu J, Qiu L. Terrirubrum flagellatum gen. nov., sp. nov. of Terrirubraceae fam.nov. and Lichenibacterium dinghuense sp. nov. from forest soiland proposal of Rhodoblastaceae fam. nov Figshare 2024 https://doi.org/10.6084/m9.figshare.24427231
    [Google Scholar]
  2. Pankratov TA, Grouzdev DS, Patutina EO, Kolganova TV, Suzina NE et al. Lichenibacterium ramalinae gen. nov, sp. nov., Lichenibacterium minor sp. nov., the first endophytic, beta-carotene producing bacterial representatives from lichen thalli and the proposal of the new family Lichenibacteriaceae within the order Rhizobiales. Antonie van Leeuwenhoek 2020; 113:477–489 [View Article] [PubMed]
    [Google Scholar]
  3. Ming Y-Z, Liu L, Xian W-D, Jiao J-Y, Liu Z-T et al. Rhabdaerophilum calidifontis gen. nov., sp. nov., a novel bacterium isolated from a hot spring, and proposal of Rhabdaerophilaceae fam. nov. Int J Syst Evol Microbiol 2020; 70:2298–2304 [View Article] [PubMed]
    [Google Scholar]
  4. Das SK, Mishra AK, Tindall BJ, Rainey FA, Stackebrandt E. Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int J Syst Evol Microbiol 1996; 46:981–987 [View Article] [PubMed]
    [Google Scholar]
  5. Im W-T, Yokota A, Kim M-K, Lee S-T. Kaistia adipata gen. nov., sp. nov., a novel alpha-proteobacterium. J Gen Appl Microbiol 2004; 50:249–254 [View Article] [PubMed]
    [Google Scholar]
  6. Tóth EM, Vengring A, Homonnay ZG, Kéki Z, Spröer C et al. Phreatobacter oligotrophus gen. nov., sp. nov., an alphaproteobacterium isolated from ultrapure water of the water purification system of a power plant. Int J Syst Evol Microbiol 2014; 64:839–845 [View Article] [PubMed]
    [Google Scholar]
  7. Martínez-Romero E. Coevolution in rhizobium-legume symbiosis?. DNA Cell Biol 2009; 28:361–370 [View Article] [PubMed]
    [Google Scholar]
  8. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
    [Google Scholar]
  9. Degefu T, Wolde-meskel E, Frostegård Å. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia. Syst Appl Microbiol 2013; 36:272–280 [View Article] [PubMed]
    [Google Scholar]
  10. Pulido-Suárez L, Flores-Félix JD, Socas-Pérez N, Igual JM, Velázquez E et al. Endophytic Bosea spartocytisi sp. nov. coexists with rhizobia in root nodules of spartocytisus supranubius growing in soils of Teide National Park (Canary Islands). Syst Appl Microbiol 2022; 45:126374 [View Article] [PubMed]
    [Google Scholar]
  11. La Scola B, Mallet MN, Grimont PAD, Raoult D. Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al. 1996). Int J Syst Evol Microbiol 2003; 53:15–20 [View Article] [PubMed]
    [Google Scholar]
  12. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article] [PubMed]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. 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] [PubMed]
    [Google Scholar]
  17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  20. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  21. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  22. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–7 [View Article] [PubMed]
    [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  24. 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; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  25. Segata N, Börnigen D, Morgan XC, Huttenhower C. Phylophlan is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:2304 [View Article] [PubMed]
    [Google Scholar]
  26. Eddy SR. Accelerated profile hmm searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
    [Google Scholar]
  27. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  28. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
    [Google Scholar]
  29. Edgar RC. Search and clustering orders of magnitude faster than blast. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
    [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  32. 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 [View Article] [PubMed]
    [Google Scholar]
  33. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  34. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  35. Gerhardt P. Methods for General and Molecular Bacteriology American Society for Microbiology; 1994
    [Google Scholar]
  36. Noh H-J, Baek K, Hwang CY, Shin SC, Hong SG et al. Lichenihabitans psoromatis gen. nov., sp. nov., a member of a novel lineage (Lichenihabitantaceae fam. nov.) within the order of Rhizobiales isolated from Antarctic lichen. Int J Syst Evol Microbiol 2019; 69:3837–3842 [View Article] [PubMed]
    [Google Scholar]
  37. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [PubMed]
    [Google Scholar]
  38. Xia F, Chen M-H, Lv Y-Y, Zhang H-Y, Qiu L-H. Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:3237–3245 [View Article] [PubMed]
    [Google Scholar]
  39. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
    [Google Scholar]
  40. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  41. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  42. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  43. Kroppenstedt RM. Separation of bacterial menaquinones by hplc using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  44. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
    [Google Scholar]
  45. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article] [PubMed]
    [Google Scholar]
  46. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. Phaster: a better, faster version of the phast phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  47. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  48. Willey JM, van der Donk WA. Lantibiotics: peptides of diverse structure and function. Annu Rev Microbiol 2007; 61:477–501 [View Article] [PubMed]
    [Google Scholar]
  49. Maffioli S, Monciardini P, Sosio M, Donadio S. New Lantibiotics from Natural and Engineered Strains The Royal Society of Chemistry; 2012 pp 116–139 [View Article]
    [Google Scholar]
  50. Iorio M, Sasso O, Maffioli SI, Bertorelli R, Monciardini P et al. A glycosylated, labionin-containing lanthipeptide with marked antinociceptive activity. ACS Chem Biol 2014; 9:398–404 [View Article] [PubMed]
    [Google Scholar]
  51. 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]
  52. Kanehisa M. Enzyme annotation and metabolic reconstruction using KEGG. Methods Mol Biol 2017; 1611:135–145 [View Article] [PubMed]
    [Google Scholar]
  53. Zhang Z, Wang Y, Hou Q, Zhao H, Li W et al. Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium. Int J Syst Evol Microbiol 2020; 70:2580–2587 [View Article] [PubMed]
    [Google Scholar]
  54. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for’omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
    [Google Scholar]
  55. Kulichevskaya IS, Danilova OV, Tereshina VM, Kevbrin VV, Dedysh SN. Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:2558–2565 [View Article] [PubMed]
    [Google Scholar]
  56. Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W, Dedysh SN. Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from sphagnum peat bog. Int J Syst Evol Microbiol 2006; 56:1397–1402 [View Article] [PubMed]
    [Google Scholar]
  57. Imhoff JF. Transfer of Rhodopseudomonas acidophila to the new genus Rhodoblastus as Rhodoblastus acidophilus gen. nov., comb. nov. Int J Syst Evol Microbiol 2001; 51:1863–1866 [View Article] [PubMed]
    [Google Scholar]
  58. Bao Z, Sato Y, Fujimura R, Ohta H. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales. Int J Syst Evol Microbiol 2014; 64:775–780 [View Article] [PubMed]
    [Google Scholar]
  59. Sun L, Liu H, Chen W, Huang K, Lyu W et al. Alsobacter soli sp. nov., a novel bacterium isolated from paddy soil, emended description of the genus Alsobacter and description of the family Alsobacteraceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3902–3907 [View Article] [PubMed]
    [Google Scholar]
  60. Sazanova AL, Safronova VI, Kuznetsova IG, Karlov DS, Belimov AA et al. Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia. Int J Syst Evol Microbiol 2019; 69:2687–2695 [View Article] [PubMed]
    [Google Scholar]
  61. Albert RA, McGuine M, Pavlons SC, Roecker J, Bruess J et al. Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2019; 69:1376–1383 [View Article] [PubMed]
    [Google Scholar]
  62. Ouattara AS, Assih EA, Thierry S, Cayol J-L, Labat M et al. Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester. Int J Syst Evol Microbiol 2003; 53:1247–1251 [View Article] [PubMed]
    [Google Scholar]
  63. Dedysh SN, Haupt ES, Dunfield PF. Emended description of the family Beijerinckiaceae and transfer of the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:3177–3182 [View Article] [PubMed]
    [Google Scholar]
  64. Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC et al. Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol 2018; 68:2116–2123 [View Article] [PubMed]
    [Google Scholar]
  65. Liu J-H, Wang Y-X, Zhang X-X, Wang Z-G, Chen Y-G et al. Salinarimonas rosea gen. nov., sp. nov., a new member of the alpha-2 subgroup of the proteobacteria. Int J Syst Evol Microbiol 2010; 60:55–60 [View Article] [PubMed]
    [Google Scholar]
  66. Cai M, Wang L, Cai H, Li Y, Wang Y-N et al. Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int J Syst Evol Microbiol 2011; 61:1767–1775 [View Article] [PubMed]
    [Google Scholar]
  67. Zhang X-J, Zhang J, Yao Q, Feng G, Zhu H-H. Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga. Int J Syst Evol Microbiol 2019; 69:667–671 [View Article] [PubMed]
    [Google Scholar]
  68. Zhang J, Song F, Xin YH, Zhang J, Fang C. Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga. Int J Syst Evol Microbiol 2009; 59:1997–2001 [View Article] [PubMed]
    [Google Scholar]
  69. Weon H-Y, Kwon S-W, Son J-A, Jo E-H, Kim S-J et al. Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga. Int J Syst Evol Microbiol 2010; 60:2596–2600 [View Article]
    [Google Scholar]
  70. Kanso S, Patel BKC. Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 2003; 53:401–406 [View Article] [PubMed]
    [Google Scholar]
  71. Madhaiyan M, Poonguzhali S. Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int J Syst Evol Microbiol 2014; 64:2376–2384 [View Article] [PubMed]
    [Google Scholar]
  72. Kato Y, Asahara M, Goto K, Kasai H, Yokota A. Methylobacterium persicinum sp. nov., Methylobacterium komagatae sp. nov., Methylobacterium brachiatum sp. nov., Methylobacterium tardum sp. nov. and Methylobacterium gregans sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2008; 58:1134–1141 [View Article] [PubMed]
    [Google Scholar]
  73. Urakami T, Araki H, Suzuki K-I, Komagata K. Further studies of the genus Methylobacterium and description of Methylobacterium aminovorans sp. nov. Int J Syst Evol Microbiol 1993; 43:504–513 [View Article]
    [Google Scholar]
  74. Green PN, Bousfield IJ. Emendation of Methylobacterium Patt, Cole, and Hanson 1976; Methylobacterium rhodinum (Heumann 1962) comb. nov. corrig.; Methylobacterium radiotolerans (Ito and Iizuka 1971) comb. nov. corrig.; and Methylobacterium mesophilicum (Austin and Goodfellow 1979) comb. nov. Int J Syst Evol Microbiol 1983; 33:875–877 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006348
Loading
/content/journal/ijsem/10.1099/ijsem.0.006348
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare
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