Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil

Autoři: Lucas Dantas Lopes aff001;  Alexandra J. Weisberg aff002;  Edward W. Davis, II aff002;  Camila de S. Varize aff001;  Michele de C. Pereira e Silva aff001;  Jeff H. Chang aff002;  Joyce E. Loper aff002;  Fernando D. Andreote aff001
Působiště autorů: Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil aff001;  Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to assess genomic and metabolic differences between populations from these habitats. Phylogenomics placed rhizosphere versus bulk soil strains in separate clades clustering with different type strains of the P. putida group. Multivariate analyses indicated that the rhizosphere and bulk soil isolates form distinct populations. Comparative genomics identified several genetic functions (GO-terms) significantly different between populations, including some exclusively present in the rhizosphere or bulk soil strains, such as D-galactonic acid catabolism and cellulose biosynthesis, respectively. The metabolic profiles of rhizosphere and bulk soil populations analyzed by Biolog Ecoplates also differ significantly, most notably by the higher oxidation of D-galactonic/D-galacturonic acid by the rhizosphere population. Accordingly, D-galactonate catabolism operon (dgo) was present in all rhizosphere isolates and absent in the bulk soil population. This study showed that sugarcane rhizosphere and bulk soil harbor different populations of P. putida and identified genes and functions potentially associated with their soil niches.

Klíčová slova:

Agricultural soil science – Comparative genomics – Genome analysis – Genomics – Phylogenetic analysis – Phylogenetics – Rhizosphere – Pseudomonas putida


1. Dennis PG, Miller AJ, Hirsch PR. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol. 2010, 72:313–327. doi: 10.1111/j.1574-6941.2010.00860.x 20370828

2. Cotrufo MF, Soong JL, Horton AJ, Campbell EE, Haddix ML, Wall DH, et al. Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nat Geoscience. 2015, 8: 776–779.

3. Uroz S, Dessaux Y, Oger P. Pyrosequencing reveals a contrasted bacterial diversity betwee oak rhizosphere and surrounding soil. Environ Microbiol Rep. 2010, 2: 281–288. doi: 10.1111/j.1758-2229.2009.00117.x 23766079

4. Blagodatskaya E, Blagodatsky S, Anderson T-H, Kuzyakov Y. Microbial growth and carbon use efficiency in the rhizosphere and root-free soil. PLoS One. 2014, 9(4): e93282. doi: 10.1371/journal.pone.0093282 24722409

5. Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome, significance of plant beneficial, plant pathogenic and human pathogenic microorganisms. FEMS Microbiol Rev. 2014, 37:634–663.

6. Mendes LW, Kuramae EE, Navarrete AA, van Even JA, Tsai SM. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 2014, 8:1577–1587. doi: 10.1038/ismej.2014.17 24553468

7. Lopes LD, Pereira e Silva MC, Andreote FD. Bacterial abilities and adaptation toward the rhizosphere colonization. Front Microbiol. 2016, 7: 134. doi: 10.3389/fmicb.2016.00134

8. Mendes R, Kruijt M, Bruijn I, Dekkers E, Voort M, Schneider JHM, et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science. 2011, 332(6033): 1097–100. doi: 10.1126/science.1203980 21551032

9. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013, 11:789–799. doi: 10.1038/nrmicro3109 24056930

10. Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytol. 2015, 206(4): 1196–1206. doi: 10.1111/nph.13312 25655016

11. Mercado-Blanco J, Bakker PA. Interactions between plants and beneficial Pseudomonas spp.: exploiting bacterial traits for crop protection. Antonie Van Leeuwenhoek. 2007, 92(4):367–389. doi: 10.1007/s10482-007-9167-1 17588129

12. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. 2011, Rev 35: 652–680.

13. Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T. Disease suppressive soils: new insights from the soil microbiome. Phytopathology. 2017, 107(11): 1284–1297. doi: 10.1094/PHYTO-03-17-0111-RVW 28650266

14. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q, Shapiro N, et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol. 2018, 20(6): 2142–2159. doi: 10.1111/1462-2920.14130 29633519

15. Wu X, Monchy S, Taghavi S, Zhu W, Ramos JL, van der Lelie D. Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida. FEMS Microbiol Rev. 2011, 35: 299–323. doi: 10.1111/j.1574-6976.2010.00249.x 20796030

16. Udaondo Z, Molina L, Segura A, Duque E, Ramos JL. Analysis of the core genome and pangenome of Pseudomonas putida. Environ Microbiol. 2016, 18: 3268–3283. doi: 10.1111/1462-2920.13015 26261031

17. Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A, Kasai D, et al. Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group. J Gen Appl Microbiol. 2017, 63(1): 1–10. doi: 10.2323/jgam.2016.06.003 27989998

18. Roca A, Pizarro-Tobías P, Udaondo Z, Fernández M, Matilla MA, Molina-Henares MA, et al. Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol. 2013, 15(3): 780–794 doi: 10.1111/1462-2920.12037 23206161

19. Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A. Multifunctional Pseudomonas putida strain FBKV2 from arid rhizosphere soil and its growth promotional effects on maize under drought stress. Rhizosphere. 2016, 1: 4–13.

20. Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, et al. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Applied and Environ Microbiol. 2009, 75(3): 748–757.

21. Meziane H, van der Sluis I, van Loon LC, Höfte M, Bakker PA. Determinants of Pseudomonas putida WCS358 involved in inducing systemic resistance in plants. Mol Plant Pathol. 2005, 6(2): 177–185. doi: 10.1111/j.1364-3703.2005.00276.x 20565648

22. Cánovas D, Cases I, de Lorenzo V. Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environ Microbiol. 2003, 5(12): 1242–1256. 14641571

23. Hu X, Wang J, Wang F, Chen Q, Huang Y, Cui Z. Complete genome sequence of the p-nitrophenol-degrading bacterium Pseudomonas putida DLL-E4. Genome Announc. 2014, 2(3): e00596–14. doi: 10.1128/genomeA.00596-14 24948765

24. Tay M, Roizman D, Cohen Y, Tolker-Nielsen T, Givskov M, Yang L. Draft genome sequence of the model naphthalene-utilizing organism Pseudomonas putida OUS82. Genome Announc. 2014, 2(1): e01161–13. doi: 10.1128/genomeA.01161-13 24435866

25. Cordero OX, Polz MF. Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol. 2014, 12(4): 263–273. doi: 10.1038/nrmicro3218 24590245

26. Cohan FM. What are bacterial species? Annu Rev Microbiol. 2002, 56: 457–487. doi: 10.1146/annurev.micro.56.012302.160634 12142474

27. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, et al. The role of ecological theory in microbial ecology. Nat Rev Microbiol. 2007, 5(5): 384–392. doi: 10.1038/nrmicro1643 17435792

28. Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, et al. Population genomics of early events in the ecological differentiation of bacteria. Science. 2012, 336:48–51. doi: 10.1126/science.1218198 22491847

29. Lopes LD, Pereira e Silva MC, Weisberg AJ, Davis EW, Yan Q, Varize CS, et al. Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population. Env Microbiol. 2018, 20(12): 4401–4414.

30. Lopes LD, Davis EW, Pereira e Silva MC, Weisberg AJ, Bresciani L, Chang JH, et al. Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity. Environ Microbiol. 2018, 20(1): 62–74. doi: 10.1111/1462-2920.13957 29027341

31. Davis EW II, Weisberg AJ, Tabima JF, Grunwald NJ, Chang JH. Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ. 2016, 4: e2222. doi: 10.7717/peerj.2222 27547538

32. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7, improvements in performance and usability. Mol Biol Evol. 2013, 30:772–780. doi: 10.1093/molbev/mst010 23329690

33. Stamatakis A. RAxMLversion 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014, 30:1312–1313. doi: 10.1093/bioinformatics/btu033 24451623

34. Rogers JS. Maximum likelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Syst Biol. 2001, 50(5):713–1722. doi: 10.1080/106351501753328839 12116941

35. Hodcroft E. TreeCollapserCL4. 2018,

36. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016, 44(W1): W242–5. doi: 10.1093/nar/gkw290 27095192

37. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics. 2004, 21(10): 2319–2335.

38. 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. doi: 10.1186/1471-2105-14-60 23432962

39. Sokal RR, Michener CD. A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull. 1958, 38:1409–1438.

40. Clarke KR, Gorley RN, editors. PRIMER v6: User Manual/Tutorial. Plymouth, PRIMER-E; 2006.

41. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13, 2178–2189. doi: 10.1101/gr.1224503 12952885

42. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013, 79(24): 7696–7701. doi: 10.1128/AEM.02411-13 24096415

43. Jombart T, Devilled S, Bollox F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010, 11: 94. doi: 10.1186/1471-2156-11-94 20950446

44. Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008, 24(11): 1403–1405. doi: 10.1093/bioinformatics/btn129 18397895

45. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5, genome-scale protein function classification. Bioinformatics. 2014, 30(9): 1236–1240. doi: 10.1093/bioinformatics/btu031 24451626

46. Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014, 30:3123–3124. doi: 10.1093/bioinformatics/btu494 25061070

47. Garland JL. Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiol Ecol. 1997, 24(4): 289–300.

48. Atlas RM. Handbook of microbiological media. CRC Press, Inc.: Boca Raton, FL, USA; 1993.

49. ter Braak CJF, Smilauer P, editors. CANOCO reference manual and CanoDraw for windows user’s guide: software for canonical community ordination (version 4.5). Microcomputer Power: Ithaca; 2002.

50. Hammer Ø, Harper DAT, Ryan PD. PAST: paleontological statistics software package for education and data analysis. Paleontol Electron. 2001, 4: 1–9.

51. Thevenot M, Dignac M-F, Rumpel C. Fate of lignins in soils: a review. Soil Biol Biochem. 2010, 42(8): 1200–1211.

52. Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M. Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One. 2016, 11(2): e0150183. doi: 10.1371/journal.pone.0150183 26915094

53. Berg G, Opelt K, Zachow C, Lottman J, Götz M, Costa R, et al. The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs on plant species and site. FEMS Microbiol Ecol. 2006, 56(2): 250–261. doi: 10.1111/j.1574-6941.2005.00025.x 16629754

54. Berg G, Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol. 2009, 68(1):1–13. doi: 10.1111/j.1574-6941.2009.00654.x 19243436

55. Zschiedrich CP, Keidel V, Szurmant H. Molecular mechanisms of two-component signal transduction. J Mol Biol. 2016, 428(19): 3752–3775. doi: 10.1016/j.jmb.2016.08.003 27519796

56. Venturi V, Keel C. Signaling in the rhizosphere. Trends Plant Sci. 2016, 21(3): 187–198. doi: 10.1016/j.tplants.2016.01.005 26832945

57. White AP, Gibson DL, Kim W, Kay WW, Surette MG. Thin aggregative fimbriae and cellulose enhance long-term survival and persistence of Salmonella. J Bacteriol. 2006, 188(9): 3219–3227. doi: 10.1128/JB.188.9.3219-3227.2006 16621814

58. Carminati A, Moradi AB, Vetterlein D, Vontobel P, Lehmann E, Weller U. Dynamics of soil water content in the rhizosphere. Plant and Soil. 2010, 332(1–2): 163–176.

59. Cherubin MR, Franco ALC, Cerri CEP, Karlen DL, Pavinatto PS, Rodrigues M, et al. Phosphorus pools responses to land-use change for sugarcane expansion in weathered Brazilian soils. Geoderma. 2016, 265: 27–38

60. Bogino PC, Oliva Mde L, Sorroche FG, Giordano W. The role of bacterial biofilms and surface components in plant-bacterial associations. Int J Mol Sci. 2013, 14(8): 15838–59. doi: 10.3390/ijms140815838 23903045

61. Alshalchi SA, Anderson GG. Expression of the lipopolysaccharide biosynthesis gene lpxD affects biofilm formation of Pseudomonas aeruginosa. Archives of Microbiology. 2015, 197(2): 135–145. doi: 10.1007/s00203-014-1030-y 25173672

62. Russo DM, Abdian PL, Posadas DM, Williams A, Vozza N, Giordano W, et al. Lipopolysaccharide O-chain core region required for cellular cohesion and compaction of in vitro and root biofilms developed by Rhizobium leguminosarum. Appl Environ Microbiol. 2015, 81(3): 1013–1023. doi: 10.1128/AEM.03175-14 25416773

63. Steinberg N, Kolodkin-Gal I. The matrix reloaded: how sensing the extracellular matrix synchronizes bacterial communities. J Bacteriol. 2015, 197(13): 2092–2103. doi: 10.1128/JB.02516-14 25825428

64. Morgan JLW, McNamara JT, Fischer M, Rich J, Chen H-M, Withers SG, et al. Observing cellulose biosynthesis and membrance translocation in crystallo. Nature. 2016, 531(7594): 329–334. doi: 10.1038/nature16966 26958837

65. Bringhurst RM, Cardon ZG, Gage DJ. Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor. Proc Natl Acad Sci U S A. 2001, 98(8): 4540–4545. doi: 10.1073/pnas.071375898 11274355

66. Knee EM, Gong F-C, Gao M, Teplltskl M, Jones AR, Foxworthy A, et al. Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source. Mol Plant Microb Interact. 2001, 14(6): 775–784.

67. Wang S-J, Loh K-C. Biotransformation kinetics of Pseudomonas putida for cometabolism of phenol and 4-chlorophenol in the presence of sodium-glutamate. Biodegradation. 2001, 12:189–199. 11826900

68. McNeil M, Darvill AG, Fry SC, Albersheim P. Structure and function of the primary cell walls of plants. Ann Rev Biochem. 1984, 53: 625–663. doi: 10.1146/ 6383202

69. Tawaraya K, Horie R, Saito A, Shinano T, Wagatsuma T, Saito K, et al. Metabolite profiling of shoot extracts, root extracts, and root exudates of rice plant under phosphorus deficiency. J Plant Nutr. 2015, 36: 1138–1159.

70. Ljunggren H, Fahraeus G. The role of polygalacturonase in root-hair invasion by nodule bacteria. J Gen Microbiol. 1961, 26: 521–528. doi: 10.1099/00221287-26-3-521 14466017

71. Lescat M, Launay A, Ghalayini M, Magnan M, Glodt J, Pintard C, et al. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol Ecol. 2017, 26(7): 1802–1817. doi: 10.1111/mec.13851 27661780

72. Boer H, Maaheimo H, Koivula A, Pentillä M, Richard P. Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene. Appl Microbiol Biotechnol. 2010, 86: 901–909. doi: 10.1007/s00253-009-2333-9 19921179

Článek vyšel v časopise


2019 Číslo 10
Nejčtenější tento týden