The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease

  • Jia Zhao
  • Yuguo WangEmail author
  • Hong Liang
  • Jing Huang
  • Zhe Chen
  • Yuanjun Nie
Original Article


We aimed to evaluate the capability of bio-organic fertilizer suppressing watermelon Fusarium wilt disease, compare the variations of the rhizosphere bacterial and fungal community compositions after treatment with different fertilizers, and explore mechanisms causing disease suppression in rhizosphere microbial community. A rhizobacterium (Bacillus amyloliquefaciens JDF35) was identified to control watermelon Fusarium wilt disease. Bio-organic fertilizer JDF35 (BOF) was generated by inoculating JDF35 into the organic fertilizer (OF) composed of cow and chicken manure compost (1:50 v/w). A three successive growing season pot experiment was designed to evaluate the effects of BOF compared with OF and chemical fertilizer (CF). Next-generation sequencing using the Illumina MiSeq platform was used to investigate the variations in rhizosphere microbial community composition. The growth of the watermelon plants, soil pH, and available N, P and K concentrations were the highest in the BOF treatment. The Fusarium wilt incidence in the BOF treatment was lower than that in the CF and OF treatment, and the differences for disease incidence were significant (P < 0.001). The diversity of the rhizosphere bacterial community was higher, and that of the fungal was lower in the BOF treatment. Most importantly, the BOF treatment had lowest abundances of Fusarium. The application of the BOF altered the composition of rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant growth.


Watermelon Bacillus amyloliquefaciens Illumina MiSeq platform Fusarium wilt disease suppression Bio-organic fertilizer 



We thank Institute of agro-products quality safety and testing research for generously providing FON.

Compliance with ethical standards


This work was financially supported in part by grants from the Independent Innovation of Science and Technology Program of Shanxi Province (2015zzcx-22), Shanxi Academy of Agricultural Science Scientific and Technological Research Projects (YGG1414), and the Youth's Foundational Research Project of Shanxi Province (201701D221169).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11738_2017_2581_MOESM1_ESM.tiff (7 mb)
Fig. S1 Phylogenetic tree (Neighbor-Joining Tree), based on 16S rRNA gene sequences, showing the relationship between Bacillus amyloliquefaciens strain JDF35 and other closely related strains. (TIFF 7151 kb)
11738_2017_2581_MOESM2_ESM.tif (2.4 mb)
Fig. S2 Rarefaction curves of bacteria (a) and fungi (b) at 97% similarity levels of the rhizosphere soil of each replicate (treated with bio-organic fertilizer (BOF), or cow and chicken manure compost (OF) or chemical fertilizer (CF)). (TIFF 2478 kb)
11738_2017_2581_MOESM3_ESM.docx (14 kb)
Supplementary material 3 (DOCX 13 kb)
11738_2017_2581_MOESM4_ESM.docx (14 kb)
Supplementary material 4 (DOCX 14 kb)


  1. Alguacil MM, Torrecillas E, Caravaca F, Fernández DA, Azcón R, Roldán A (2011) The application of an organic amendment modifies the arbuscular mycorrhizal fungal communities colonizing native seedlings grown in a heavy-metal-polluted soil. Soil Biol Biochem 43:1498–1508Google Scholar
  2. An M, Zhou X, Wu F, Ma Y, Yang P (2011) Rhizosphere soil microorganism populations and community structures of different watermelon cultivars with differing resistance to Fusarium oxysporum f. sp. niveum. Can J Microbiol 57:355–365PubMedGoogle Scholar
  3. Bais HP, Fall R, Vivanco JM (2004) Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol 134:307–319PubMedPubMedCentralGoogle Scholar
  4. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266PubMedGoogle Scholar
  5. Bargabus RL, Zidack NK, Sherwood JE, Jacobsen BJ (2003) Oxidative burst elicited by Bacillus mycoides isolate Bac J, a biological control agent, occurs independently of hypersensitive cell death in sugar beet. Mol. Plant-Microbe Interact. 16:1145–1153PubMedGoogle Scholar
  6. Berg G (2009) Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18PubMedGoogle Scholar
  7. Bever JD, Platt TG, Morton ER (2012) Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol 66:265PubMedPubMedCentralGoogle Scholar
  8. Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2:e197PubMedPubMedCentralGoogle Scholar
  9. Cao Y, Zhang Z, Ling N, Yuan Y, Zheng X, Shen B, Shen Q (2011) Bacillus subtilis SQR 9 can control Fusarium wilt in cucumber by colonizing plant roots. Biol Fertil Soils 47:495–506Google Scholar
  10. Caporaso JG, Lauber CL, Walters WA et al (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci 108:4516–4522PubMedGoogle Scholar
  11. Chen LH, Huang XQ, Zhang FG, Zhao DK, Yang XM, Shen QR (2012) Application of Trichoderma harzianum SQR-T037 bio-organic fertiliser significantly controls Fusarium wilt and affects the microbial communities of continuously cropped soil of cucumber. J Sci Food Agric 92:2465–2470PubMedGoogle Scholar
  12. Chen X-H, Zhang B-W, Li H, Peng X-X (2015) Myo-inositol improves the host’s ability to eliminate balofloxacin-resistant Escherichia coli. Sci Rep 5:10720PubMedPubMedCentralGoogle Scholar
  13. Chen X-H, Liu S-R, Peng B et al (2017) Exogenous l-Valine promotes phagocytosis to kill multidrug-resistant bacterial pathogens. Front Immunol 8:207PubMedPubMedCentralGoogle Scholar
  14. Ding C, Shen Q, Zhang R, Chen W (2013) Evaluation of rhizosphere bacteria and derived bio-organic fertilizers as potential biocontrol agents against bacterial wilt (Ralstonia solanacearum) of potato. Plant Soil 366:453–466Google Scholar
  15. Edwards J, Johnson C, Santos-Medellin C et al (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA 112:E911–E911920PubMedGoogle Scholar
  16. El-Hassan SA, Gowen SR (2006) Formulation and delivery of the bacterial antagonist Bacillus subtilis for management of lentil vascular wilt caused by Fusarium oxysporum f. sp. lentis. J Phytopathol 154:148–155Google Scholar
  17. Faheem M, Raza W, Zhong W, Nan Z, Shen Q, Xu Y (2015) Evaluation of the biocontrol potential of Streptomyces goshikiensis YCXU against Fusarium oxysporum f. sp. niveum. Biol Control 81:101–110Google Scholar
  18. Fang S, Liu D, Tian Y, Deng S, Shang X (2013) Tree species composition influences enzyme activities and microbial biomass in the rhizosphere: a rhizobox approach. PLoS One 8:e61461PubMedPubMedCentralGoogle Scholar
  19. Fuchs J-G, Moënne-Loccoz Y, Défago G (1997) Nonpathogenic Fusarium oxysporum strain Fo47 induces resistance to Fusarium wilt in tomato. Plant Dis 81:492–496PubMedGoogle Scholar
  20. Garbeva P, Van Veen JA, Van Elsas JD (2004a) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270PubMedGoogle Scholar
  21. Garbeva P, Van Veen JA, Van Elsas JD (2004b) Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS Microbiol Ecol 47:51–64PubMedGoogle Scholar
  22. Garbeva P, Postma J, Van Veen JA, Van Elsas JD (2006) Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3. Environ Microbiol 8:233–246PubMedGoogle Scholar
  23. Goldberg SMD, Johnson J, Busam D et al (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci 103:11240–11245PubMedGoogle Scholar
  24. Gopalakrishnan S, Srinivas V, Vidya MS, Rathore A (2013) Plant growth-promoting activities of Streptomyces spp. in sorghum and rice. Springer Plus, vol 2, p 574Google Scholar
  25. Idris EE, Iglesias DJ, Talon M, Borriss R (2007a) Tryptophan-dependent production of indole-3-acetic acid (IAA) affects level of plant growth promotion by Bacillus amyloliquefaciens FZB42. Mol Plant Microbe Interact 20:619–626PubMedPubMedCentralGoogle Scholar
  26. Idris HA, Labuschagne N, Korsten L (2007b) Screening rhizobacteria for biological control of Fusarium root and crown rot of sorghum in Ethiopia. Biol Control 40:97–106Google Scholar
  27. Idriss EE, Makarewicz O, Farouk A et al (2002) Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effecta. Microbiology 148:2097–2109PubMedGoogle Scholar
  28. Jiang C-H, Wu F, Yu Z-Y et al (2015) Study on screening and antagonistic mechanisms of Bacillus amyloliquefaciens 54 against bacterial fruit blotch (BFB) caused by Acidovorax avenae subsp. citrulli. Microbiol Res 170:95–104PubMedGoogle Scholar
  29. Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236PubMedGoogle Scholar
  30. Li J-G, Ren G-D, Jia Z-J, Dong Y-H (2014) Composition and activity of rhizosphere microbial communities associated with healthy and diseased greenhouse tomatoes. Plant Soil 380:337–347Google Scholar
  31. Li X, Zhang YN, Ding C, Jia Z, He Z, Zhang T, Wang X (2015) Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness. Biol Fertil Soils 51:935–946Google Scholar
  32. Ling N, Xue C, Huang Q, Yang X, Xu Y, Shen Q (2010) Development of a mode of application of bioorganic fertilizer for improving the biocontrol efficacy to Fusarium wilt. Biocontrol 55:673–683Google Scholar
  33. Ling N, Zhang W, Tan S, Huang Q, Shen Q (2012) Effect of the nursery application of bioorganic fertilizer on spatial distribution of Fusarium oxysporum f. sp. niveum and its antagonistic bacterium in the rhizosphere of watermelon. Appl Soil Ecol 59:13–19Google Scholar
  34. Ling N, Deng K, Song Y et al (2014) Variation of rhizosphere bacterial community in watermelon continuous mono-cropping soil by long-term application of a novel bioorganic fertilizer. Microbiol Res 169:570–578PubMedGoogle Scholar
  35. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235PubMedPubMedCentralGoogle Scholar
  36. Lozupone C, Hamady M, Knight R (2006) UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinf 7:371Google Scholar
  37. Luo J, Ran W, Hu J, Yang X, Xu Y, Shen Q (2010) Application of bio-organic fertilizer significantly affected fungal diversity of soils. Soil Sci Soc Am J 74:2039–2048Google Scholar
  38. Mazzola M (2004) Assessment and management of soil microbial community structure for disease suppression 1. Annu Rev Phytopathol 42:35–59PubMedGoogle Scholar
  39. Mcmurdie PJ, Holmes S (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217PubMedPubMedCentralGoogle Scholar
  40. Medeiros FHV, Moraes ISF, Da Silva Neto EB, Silveira EB, Rosa De Lima RM (2009) Management of melon bacterial blotch by plant beneficial bacteria. Phytoparasitica 37:453–460Google Scholar
  41. Mendes R, Kruijt M, De Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100PubMedGoogle Scholar
  42. Nannipieri P, Ascher J, Ceccherini M, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655–670Google Scholar
  43. Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799PubMedGoogle Scholar
  44. Poulsen PHB, Al-Soud WA, Bergmark L, Magid J, Hansen LH, Sørensen SJ (2013) Effects of fertilization with urban and agricultural organic wastes in a field trial—Prokaryotic diversity investigated by pyrosequencing. Soil Biol Biochem 57:784–793Google Scholar
  45. Qiu M, Zhang R, Xue C, Zhang S, Li S, Zhang N, Shen Q (2012) Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biol Fertil Soils 48:807–816Google Scholar
  46. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361Google Scholar
  47. Ramamoorthy V, Viswanathan R, Raguchander T, Prakasam V, Samiyappan R (2001) Induction of systemic resistance by plant growth promoting rhizobacteria in crop plants against pests and diseases. Crop Protect. 20:1–11Google Scholar
  48. Rosenzweig N, Tiedje JM, Quensen Iii JF, Meng Q, Hao JJ (2012) Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis 96:718–725PubMedGoogle Scholar
  49. Sanguin H, Sarniguet A, Gazengel K, Moënne-Loccoz Y, Grundmann GL (2009) Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol 184:694–707PubMedGoogle Scholar
  50. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedPubMedCentralGoogle Scholar
  51. Shen Z, Zhong S, Wang Y et al (2013) Induced soil microbial suppression of banana fusarium wilt disease using compost and biofertilizers to improve yield and quality. Eur J Soil Biol 57:1–8Google Scholar
  52. Shen Z, Ruan Y, Chao X, Zhang J, Li R, Shen Q (2015a) Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol Fertil Soils 51:553–562Google Scholar
  53. Shen Z, Ruan Y, Wang B, Zhong S, Su L, Li R, Shen Q (2015b) Effect of biofertilizer for suppressing Fusarium wilt disease of banana as well as enhancing microbial and chemical properties of soil under greenhouse trial. Appl Soil Ecol 93:111–119Google Scholar
  54. Sturz AV, Christie BR (2003) Beneficial microbial allelopathies in the root zone: the management of soil quality and plant disease with rhizobacteria. Soil Tillage Res 72:107–123Google Scholar
  55. Sun L, Lu Z, Bie X, Lu F, Yang S (2006) Isolation and characterization of a co-producer of fengycins and surfactins, endophytic Bacillus amyloliquefaciens ES-2, from Scutellaria baicalensis Georgi. World J Microbiol Biotechnol 22:1259–1266Google Scholar
  56. Tjamos SE, Flemetakis E, Paplomatas EJ, Katinakis P (2005) Induction of resistance to Verticillium dahliae in Arabidopsis thaliana by the biocontrol agent K-165 and pathogenesis-related proteins gene expression. Mol Plant-Microbe Interact 18:555–561PubMedGoogle Scholar
  57. Wang B, Yuan J, Zhang J et al (2013) Effects of novel bioorganic fertilizer produced by Bacillus amyloliquefaciens W19 on antagonism of Fusarium wilt of banana. Biol Fertil Soils 49:435–446Google Scholar
  58. Wu H-S, Yang X-N, Fan J-Q et al (2009) Suppression of Fusarium wilt of watermelon by a bio-organic fertilizer containing combinations of antagonistic microorganisms. Biocontrol 54:287–300Google Scholar
  59. Xu W, Wang Z, Wu F (2015) The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon. Front Microbiol 6:899PubMedPubMedCentralGoogle Scholar
  60. Yu L, Nicolaisen M, Larsen J, Ravnskov S (2013) Organic fertilization alters the community composition of root associated fungi in Pisum sativum. Soil Biol Biochem 58:36–41Google Scholar
  61. Yu C, Hu XM, Deng W et al (2015) Changes in soil microbial community structure and functional diversity in the rhizosphere surrounding mulberry subjected to long-term fertilization. Appl Soil Ecol 86:30–40Google Scholar
  62. Yuan J, Raza W, Shen Q, Huang Q (2012) Antifungal activity of Bacillus amyloliquefaciens NJN-6 volatile compounds against Fusarium oxysporum f. sp. cubense. Appl Environ Microbiol 78:5942–5944PubMedPubMedCentralGoogle Scholar
  63. Zhang S, Raza W, Yang X et al (2008) Control of Fusarium wilt disease of cucumber plants with the application of a bioorganic fertilizer. Biol Fertil Soils 44:1073–1080Google Scholar
  64. Zhang N, He X, Zhang J et al (2014) Suppression of Fusarium Wilt of banana with application of bio-organic fertilizers. Pedosphere 24:613–624Google Scholar
  65. Zhao Q, Dong C, Yang X, Mei X, Ran W, Shen Q, Xu Y (2011) Biocontrol of Fusarium wilt disease for Cucumis melo melon using bio-organic fertilizer. Appl Soil Ecol 47:67–75Google Scholar
  66. Zhao S, Liu D, Ling N, Chen F, Fang W, Shen Q (2014) Bio-organic fertilizer application significantly reduces the Fusarium oxysporum population and alters the composition of fungi communities of watermelon Fusarium wilt rhizosphere soil. Biol Fertil Soils 50:765–774Google Scholar
  67. Zhi WF, Can CS, Ling C, Hui XW (2015) Rhizosphere microbial communities from resistant and susceptible watermelon cultivars showed different response to Fusarium oxysporum f. sp. niveum inoculationGoogle Scholar

Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2017

Authors and Affiliations

  • Jia Zhao
    • 1
    • 2
  • Yuguo Wang
    • 1
    • 2
    Email author
  • Hong Liang
    • 2
  • Jing Huang
    • 2
  • Zhe Chen
    • 2
  • Yuanjun Nie
    • 2
  1. 1.College of AgricultureShanxi Agriculture UniversityTaiguChina
  2. 2.Biotechnology Research CenterShanxi Academy of Agricultural SciencesTaiyuanChina

Personalised recommendations