1887

Abstract

Two bacterial strains, 1N and 5N, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N (0.65×1.85 µm) and 5N (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N and 5N occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N and 5N were distinct from one another and their closest related type strains: RP11, LMG 27731 and CF1. The genomes of 1N and 5N had an average nucleotide identity (91.6 and 91.3%) and DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N and 5N from each other and their closest relatives. The only ubiquinone present in strains 1N and 5N was Q-8. The major cellular fatty acids were C, 3OH-C, C cyclo, C cyclo ω8 and summed features 2 (3OH-C / C iso I), 3 (C ω6/ω7) and 8 (C ω7/ω6). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of . Our polyphasic approach demonstrated that strains 1N and 5N represent novel species from the genus for which the names sp. nov. (type strain 1N=DSM 110721=LMG 31704) and sp. nov. (type strain 5N=DSM 110722=LMG 31705) are proposed.

Funding
This study was supported by the:
  • K. Taylor Cyle , Department of Workforce Development, State of Wisconsin (US) , (Award 2019-67011-29513)
  • Daniel H. Buckley , U.S. Department of Energy, Office of Biological & Environmental Research Genomic Science Program , (Award DE-SC0016364)
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/content/journal/ijsem/10.1099/ijsem.0.004387
2020-08-18
2020-10-30
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References

  1. Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: Proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring env. Front Genet 2014; 5:1–22
    [Google Scholar]
  2. Estrada-de Los Santos P, Palmer M, Beukes C, Steenkamp ET, Briscoe L et al. Whole genome analyses suggests that Burkholderia sensu lato contains two additional novel genera implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae . Genes 2018; 9:389
    [Google Scholar]
  3. Lin Q, Lv Y, Gao Z, Qiu LH. Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina . Int J Syst Evol Microbiol 2019
    [Google Scholar]
  4. Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR et al. Genome data provides high support for generic boundaries in Burkholderia sensu lato . Front Microbiol 2017; 8:1–12
    [Google Scholar]
  5. Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia . Int J Syst Evol Microbiol 2016; 66:2836–2846
    [Google Scholar]
  6. Vandamme P, Goris J, Chen WM, De Vos P, Willems A. Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst Appl Microbiol 2002; 25:507–512
    [Google Scholar]
  7. Chen WM, James EK, Coenye T, Chou JH, Barrios E et al. Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 2006; 56:1847–1851
    [Google Scholar]
  8. Bournaud C, Moulin L, Cnockaert M, de Faria S, Prin Y et al. Paraburkholderia piptadeniae sp. nov. and Paraburkholderia ribeironis sp. nov., two root-nodulating symbiotic species of Piptadenia gonoacantha in Brazil. Int J Syst Evol Microbiol 2017; 67:432–440
    [Google Scholar]
  9. Elliott GN, Chen WM, Chou JH, Wang HC, Sheu SY et al. Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta . New Phytol 2007; 173:168–180
    [Google Scholar]
  10. Chen WM, de Faria SM, James EK, Elliott GN, Lin KY et al. Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella . Int J Syst Evol Microbiol 2007; 57:1055–1059
    [Google Scholar]
  11. Cunha C de O, Zuleta LFG, de Almeida LGP, Ciapina LP, Borges WL et al. Complete genome sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a heat-tolerant, nitrogen-fixing symbiont of Mimosa flocculosa . J Bacteriol 2012; 194:6675–6676
    [Google Scholar]
  12. Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E et al. Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil. Int J Syst Evol Microbiol 2012; 62:2272–2278
    [Google Scholar]
  13. Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E et al. Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp. Int J Syst Evol Microbiol 2013; 63:435–441
    [Google Scholar]
  14. Martínez-Aguilar L, Salazar-Salazar C, Méndez RD, Caballero-Mellado J, Hirsch AM et al. Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris . Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 2013; 104:1063–1071
    [Google Scholar]
  15. De MSE, Cnockaert M, Ardley JK, Maker G, Yates R et al. Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2013; 63:3950–3957
    [Google Scholar]
  16. De Meyer SE, Cnockaert M, Ardley JK, Van Wyk BE, Vandamme PA et al. Burkholderia dilworthii sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2014; 64:1090–1095
    [Google Scholar]
  17. Caballero-Mellado J, Martínez-Aguilar L, Paredes-Valdez G, Estrada-de los Santos P. Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. Int J Syst Evol Microbiol 2004; 54:1165–1172
    [Google Scholar]
  18. Reis VM, Estrada-de los Santos P, Tenorio-Salgado S, Vogel J, Stoffels M et al. Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int J Syst Evol Microbiol 2004; 54:2155–2162
    [Google Scholar]
  19. Perin L, Martínez-Aguilar L, Paredes-Valdez G, Baldani JI, Estrada-de los Santos P et al. Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. Int J Syst Evol Microbiol 2006; 56:1931–1937
    [Google Scholar]
  20. da Silva PRA, Simões-Araújo JL, Vidal MS, Cruz LM, de SEM et al. Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium. Brazilian J Microbiol 2018; 49:210–211
    [Google Scholar]
  21. Chan YK. Utilization of simple phenolics for dinitrogen fixation by soil diazotrophic bacteria. Plant Soil 1986; 90:141–150
    [Google Scholar]
  22. De Meyer SE, Cnockaert M, Moulin L, Howieson JG, Vandamme P et al. Symbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov. Int J Syst Evol Microbiol 2018; 68:2607–2614 [CrossRef][PubMed]
    [Google Scholar]
  23. Guo JK, Ding YZ, Feng RW, Wang RG, YM X et al. Burkholderia metalliresistens sp. nov., a multiple metal-resistant and phosphate-solubilising species isolated from heavy metal-polluted soil in Southeast China. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 2015; 107:1591–1598
    [Google Scholar]
  24. Gao Z-H, Ruan S-L, Huang Y-X, Lv Y-Y, Qiu L-H. Paraburkholderia phosphatilytica sp. nov., a phosphate-solubilizing bacterium isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:196–202 [CrossRef][PubMed]
    [Google Scholar]
  25. Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J 2019; 13:413–429
    [Google Scholar]
  26. Wilhelm RC, DeRito CM, Shapleigh JP, Buckley DH, Madsen EL. Phenolic acid-degrading Paraburkholderia Prime Decomposition in Forest Soil. MBio
    [Google Scholar]
  27. Zwetsloot MJ, Muñoz Ucros J, Wickings K, Wilhelm RC, Sparks JP et al. Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil. Soil Biol Biochem 2020; 145:
    [Google Scholar]
  28. Cyle KT, Klein AR, Aristilde L, Martinez CE. Ecophysiological study of Paraburkholderia sp. 1N under soil solution conditions: Dynamic substrate preferences and characterization of carbon use efficiency. Appl Environ Microbiol
    [Google Scholar]
  29. Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, Derito CM et al. Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. Int J Syst Evol Microbiol 2020
    [Google Scholar]
  30. Haeckl FPJ, Baldim JL, Iskakova D, Kurita KL, Soares MG et al. A selective genome-guided method for environmental Burkholderia isolation. J Ind Microbiol Biotechnol 2019; 46:345–362
    [Google Scholar]
  31. Fahey TJ, Yavitt JB, Sherman RE, Groffman PM, Fisk MC et al. Transport of carbon and nitrogen between litter and soil organic matter in a northern hardwood forest. Ecosystems 2011; 14:326–340
    [Google Scholar]
  32. Goodale CL, Fredriksen G, Weiss MS, McCalley CK, Sparks JP et al. Soil processes drive seasonal variation in retention of 15N tracers in a deciduous forest catchment. Ecology 2015; 96:2653–2668
    [Google Scholar]
  33. Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 2000; 66:5488–5491
    [Google Scholar]
  34. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120
    [Google Scholar]
  35. Gordon A, G.J. H. Fastx-toolkit. FASTQ/A short-reads preprocessing tools. http://hannonlab.cshl.edu/fastx_toolkit ; 2010; 5
  36. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477
    [Google Scholar]
  37. Kolmogorov M, Raney B, Paten B, Pham S. Ragout - a reference-assisted assembly tool for bacterial genomes. Bioinformatics 2014; 30:302–309
    [Google Scholar]
  38. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States department of energy systems biology Knowledgebase. Nat Biotechnol 2018; 36:566-569 [CrossRef][PubMed]
    [Google Scholar]
  39. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [CrossRef]
    [Google Scholar]
  40. 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
    [Google Scholar]
  41. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva E V, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210–3212
    [Google Scholar]
  42. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES et al. Integrative genome Viewer. Nat Biotechnol 2011; 29:24–26
    [Google Scholar]
  43. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356
    [Google Scholar]
  44. 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
    [Google Scholar]
  45. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:206–214
    [Google Scholar]
  46. Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755–763
    [Google Scholar]
  47. Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 2019; 37:420–423
    [Google Scholar]
  48. Sun Y, Cheng Z, Glick BR. The presence of a 1-aminocyclopropane-1-carboxylate (ACC) deaminase deletion mutation alters the physiology of the endophytic plant growth-promoting bacterium Burkholderia phytofirmans PsJN. FEMS Microbiol Lett 2009; 296:131–136
    [Google Scholar]
  49. Checcucci A, Azzarello E, Bazzicalupo M, De Carlo A, Emiliani G et al. Role and regulation of ACC deaminase gene in Sinorhizobium meliloti: Is it a symbiotic, rhizospheric or endophytic gene?. Front Genet 2017; 8:6 [CrossRef][PubMed]
    [Google Scholar]
  50. Nagel R, Bieber JE, Schmidt-Dannert MG, Nett RS, Peters RJ. A third class: functional gibberellin biosynthetic operon in beta-Proteobacteria. Front Microbiol 2018; 9:1–8
    [Google Scholar]
  51. Weilharter A, Mitter B, Shin M V, Chain PSG, Nowak J et al. Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. J Bacteriol 2011; 193:3383–3384
    [Google Scholar]
  52. Zúñiga A, Poupin MJ, Donoso R, Ledger T, Guiliani N et al. Quorum sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN. Mol Plant-Microbe Interact 2013; 26:546–553
    [Google Scholar]
  53. Liu WH, Chen FF, Wang CE, HH F, Fang XQ et al. Indole-3-Acetic acid in Burkholderia pyrrocinia JK-SH007: enzymatic identification of the indole-3-acetamide synthesis pathway. Front Microbiol 2019; 10:1–12
    [Google Scholar]
  54. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91
    [Google Scholar]
  55. Jain C, Rodriguez-r LM, Phillippy A, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114
    [Google Scholar]
  56. Aizawa T, Vijarnsorn P, Nakajima M, Sunairi M. Burkholderia bannensis sp. nov., an acid neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps. Int J Syst Evol Microbiol 2011; 61:1645–1650
    [Google Scholar]
  57. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. technical note 101. Microbial ID, Inc.,Newark, Del 20011–6
    [Google Scholar]
  58. Kaiser P, Geyer R, Surmann P, Fuhrmann H. LC-MS method for screening unknown microbial carotenoids and isoprenoid quinones. J Microbiol Methods 2012; 88:28–34
    [Google Scholar]
  59. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray R, WA W, Krieg N. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  60. Schneider CA, Rasband WS, Eliceiri KW. NIH image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675
    [Google Scholar]
  61. Ducret A, Quardokus EM, Brun Y V. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nat Microbiol 2016; 1:1–7
    [Google Scholar]
  62. Lim JH, Baek SH, Lee ST. Burkholderia sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2008; 58:565–569
    [Google Scholar]
  63. Vandamme P, De Brandt E, Houf K, Salles JF, van Elsas JD et al. Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosph. Int J Syst Evol Microbiol 2013; 63:4707–4718
    [Google Scholar]
  64. Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS et al. Phylogenomic study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 2016; 7:1–19
    [Google Scholar]
  65. Mavengere NR, Ellis AG, Le Roux JJ. Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb. Int J Syst Evol Microbiol 2014; 64:1906–1912
    [Google Scholar]
  66. Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M et al. Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporous . Int J Syst Evol Microbiol 2007; 57:2583–2590
    [Google Scholar]
  67. Zolg W, Ottow J. Pseudomonas glathei sp. nov., a new nitrogen-scavenging rod isolated from acid lateritic relicts in Germany. Zeitschrift fur Allgemaine Mikrobiol 1975; 15:287–299
    [Google Scholar]
  68. Vreeland RH, Litchfield CD, Martin SEL, Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int J Syst Bacteriol 1980; 30:485–495
    [Google Scholar]
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