Microbial Diversity in Compost is Critical in Suppressing Plant Fungal Pathogen Survival and Enhancing Cucumber Seedling Growth

References

• Asha, B. B., S. C. Nayaka, A. U. Shankar, C. Srinivas, and S. R. Niranjana. 2011. Biological control of F. oxysporum f. sp. lycopersici causing wilt of tomato by Pseudomonas fluorescens. International Microbiology Research 3:79–84. doi:10.9735/0975-5276.3.2.79-84.
   Google Scholar
• Bechard, J., K. C. Eastwell, P. L. Sholberg, G. Mazza, and B. Skura. 1998. Isolation and partial chemical characterization of an antimicrobial peptide produced by a strain of Bacillus subtilis. Journal of Agricultural and Food Chemistry 46:5355–61. doi:10.1021/jf9803987.
   Web of Science ®Google Scholar
• Berendsen, R. L., C. M. J. Pieterse, and P. A. H. M. Bakker. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science 17:478–86. doi:10.1016/j.tplants.2012.04.001.
   PubMed Web of Science ®Google Scholar
• Blumer, C., and D. Haas. 2000. Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Archives of Microbiology 173:170–77. doi:10.1007/s002039900127.
   PubMed Web of Science ®Google Scholar
• Bodour, A. A., K. P. Drees, and R. M. Maier. 2003. Distribution of biosurfactant-producing bacteria in undisturbed and contaminated arid southwestern soils. Applied and Environmental Microbiology 69:3270–78. doi:10.1128/AEM.69.6.3280-3287.2003.
   Web of Science ®Google Scholar
• Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335–6. doi:10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Chao, A.. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11:265–70.
   Web of Science ®Google Scholar
• Chen, M. H., and E. B. Nelson. 2008. Seed-colonizing microbes from municipal biosolids compost suppress Pythium ultimum damping-off on different plant species. Phytopathology 98:1012–18. doi:10.1094/PHYTO-98-9-1012.
   PubMed Web of Science ®Google Scholar
• Chen, X. P., Y. G. Zhu, Y. Xia, J. P. Shen, and J. Z. He. 2008. Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environmental Microbiology 10:1978–1987. doi:10.1111/j.1462-2920.2008.01613.x.
   PubMed Web of Science ®Google Scholar
• Crane, K. W., and J. P. Grover. 2010. Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities. Journal of Theoretical Biology 262:517–27. doi:10.1016/j.jtbi.2009.10.027.
   PubMed Web of Science ®Google Scholar
• Darrasse, A., A. Darsonval, T. Boureau, M. N. Brisset, K. Durand, and M. A. Jacques. 2010. Transmission of plant-pathogenic bacteria by nonhost seeds without induction of an associated defense reaction at emergence. Applied and Environmental Microbiology 76:6787–96. doi:10.1128/AEM.01098-10.
   PubMed Web of Science ®Google Scholar
• Dean, R., J. A. Van Kan, Z. A. Pretorius, K. E. Hammond-Kosack, A. Di Pietro, P. D. Spanu, et al. 2012. The Top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology 13:414–30. doi:10.1111/j.1364-3703.2011.00783.x.
   PubMed Web of Science ®Google Scholar
• Engelbrektson, A., V. Kunin, K. C. Wrighton, N. Zvenigorodsky, F. Chen, H. Ochman, et al. 2010. Experimental factors affecting PCR based estimates of microbial species richness and evenness. The ISME Journal 4:642–7. doi:10.1038/ismej.2009.153.
   PubMed Web of Science ®Google Scholar
• Finkel, O. M., G. Castrillo, S. H. Paredes, I. S. González, and J. L. Dangl. 2017. Understanding and exploiting plant beneficial microbes. Current Opinion in Plant Biology 38:155–63. doi:10.1016/j.pbi.2017.04.018.
   PubMed Web of Science ®Google Scholar
• Gomez-Gil, L., J. C. Almiron, P. L. R. Carrillo, C. N. O. Medina, G. B. Ruiz, P. R. Rodriguez, et al. 2018. Nitrate assimilation pathway (NAP): role of structural (nit) and transporter (ntr1) genes in Fusarium oxysporum f. sp. lycopersici growth and pathogenicity. Current Genetics 64:493–507. doi:10.1007/s00294-017-0766-8.
   PubMed Web of Science ®Google Scholar
• Hadar, Y.. 2011. Suppressive compost: when plant pathology met microbial ecology. Phytoparasitica 39:311–4. doi:10.1007/s12600-011-0177-1.
   Web of Science ®Google Scholar
• Harrison, K. A., R. Bol, and R. D. Bardgett. 2007. Preferences for different nitrogen forms by coexisting plant species and soil microbes. Ecology 88:989–99. doi:10.1890/06-1018.
   PubMed Web of Science ®Google Scholar
• Huang, S., R. Li, Z. Zhang, L. Li, X. Gu, W. Fan, et al. 2009. The genome of the cucumber, Cucumis sativus L. Nature Genetics 41:1275–81. doi:10.1038/ng.475.
   PubMed Web of Science ®Google Scholar
• Hunt, D. E., L. A. David, D. Gevers, S. P. Preheim, E. J. Alm, and M. F. Polz. 2008. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science (Washington, DC, United States) 320:1081–5. doi:10.1126/science.1157890.
   PubMed Web of Science ®Google Scholar
• Ismail, M. R., H. M. Saud, S. H. Habib, H. Kausar, M. A. Maleque, and M. A. Hakim. 2017. Efficacy evaluation of empty palm oil fruit bunch compost in improving soil characteristics, plant growth and disease suppression of tomata plants under tropical acid soil. Journal of Environmental Biology 38:123. doi:10.22438/jeb/38/1/PRN-126.
   Web of Science ®Google Scholar
• Komada, H.. 1975. Development of a selective medium for quantitative isolation of Fusarium oxysporum from natural soil. Review of Plant Proteome Research 8:114–24.
   Google Scholar
• Kuczynski, J., C. L. Lauber, W. A. Walters, L. W. Parfrey, J. C. Clemente, D. Gevers, et al. 2011. Experimental and analytical tools for studying the human microbiome. Nature Reviews Genetics 13:47–58. doi:10.1038/nrg3129.
   PubMed Web of Science ®Google Scholar
• Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology 12:118–23. doi:10.1111/j.1462-2920.2009.02051.x.
   PubMed Web of Science ®Google Scholar
• Lamprecht, S. C., and Y. T. Tewoldemedhin. 2017. Fusarium species associated with damping-off of rooibos seedlings and the potential of compost as soil amendment for disease suppression. South African Journal of Botany 110:110–7. doi:10.1016/j.sajb.2016.07.009.
   Web of Science ®Google Scholar
• Li, Q. F., C. Y. Wu, X. Deng, and X. W. Hou. 2013. Soil microbial functional diversity from different infection grades of banana fusarium wilt (Fusarium oxysporum f. sp. Cubense). Applied Mechanics and Materials 295:2274–80.
   Google Scholar
• Manici, L. M., F. Caputo, and M. L. Saccà. 2017. Secondary metabolites released into the rhizosphere by Fusarium oxysporum and Fusarium spp. as underestimated component of nonspecific replant disease. Plant and Soil 415:85–98. doi:10.1007/s11104-016-3152-2.
   Web of Science ®Google Scholar
• Michielse, C. B. and Rep M. 2003. Pathogen profile update: Fusarium oxysporum. Molecular Plant Pathology 10:311–24. doi:10.1111/j.1364-3703.2009.00538.x.
   Google Scholar
• Noble, R.. 2011. Risks and benefits of soil amendment with composts in relation to plant pathogens. Australasian Plant Pathology 40:157–67. doi:10.1007/s13313-010-0025-7.
   Web of Science ®Google Scholar
• Ofek, M., Y. Hadar, and D. Minz. 2009. Comparison of effects of compost amendment and of single-strain inoculation on root bacterial communities of young cucumber seedlings. Applied and Environmental Microbiology 75:6441–50. doi:10.1128/AEM.00736-09.
   PubMed Web of Science ®Google Scholar
• Ofek, M., Y. Hadar, and D. Minz. 2011. Colonization of cucumber seeds by bacteria during germination. Environmental Microbiology 13:2794–807. doi:10.1111/j.1462-2920.2011.02551.x.
   PubMed Web of Science ®Google Scholar
• Peiffer, J. A., A. Spor, O. Koren, Z. Jin, S. G. Tringe, J. L. Dangl, et al. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences of the United States 110:6548–53. doi:10.1073/pnas.1302837110.
   PubMed Web of Science ®Google Scholar
• Philippot, L., A. Spor, C. Hénault, D. Bru, F. Bizouard, C. M. Jones, et al. 2013. Loss in microbial diversity affects nitrogen cycling in soil. The ISME Journal 7:1609–19. doi:10.1038/ismej.2013.34.
   PubMed Web of Science ®Google Scholar
• Postma, J., M. J. E. I. M. Willemsen-de Klein, and A. E. Hoogland. 1996. Biocontrol of Pythium aphanidermatum in closed culture systems. IOBC/WPRS Bulletin 19:42–46.
   Google Scholar
• Postma, J., M. J. E. I.M. Willemsen-de Klein, and J. D. van Elsas. 2000. Effect of the indigenous microflora on the development of root and crown rot caused by Pythium aphanidermatum in cucumber grown on rockwool. Phytopathology 90:125–33. doi:10.1094/PHYTO.2000.90.2.125.
   PubMed Web of Science ®Google Scholar
• Postma, J., B. P. Geraats, R. Pastoor, and J. D. van Elsas. 2005. Characterization of the microbial community involved in the suppression of Pythium aphanidermatum in cucumber grown on rockwool. Phytopathology 95:808–18. doi:10.1094/PHYTO-95-0808.
   PubMed Web of Science ®Google Scholar
• Qiu, M., R. Zhang, C. Xue, S. Zhang, S. Li, N. Zhang, and Q. Shen. 2012. Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biology and Fertility of Soils 48:807–16. doi:10.1007/s00374-012-0675-4.
   Web of Science ®Google Scholar
• Ramette, A., M. Frapolli, G. Défago, and Y. Moënne-Loccoz. 2003. Phylogeny of HCN synthase-encoding hcnBC genes in biocontrol fluorescent pseudomonads and its relationship with host plant species and HCN synthesis ability. Molecular Plant-Microbe Interactions 16:525–35. doi:10.1094/MPMI.2003.16.6.525.
   PubMed Web of Science ®Google Scholar
• Rosenberg, E., and I. Zilber-Rosenberg. 2016. Microbes drive evolution of animals and plants: the hologenome concept. MBio 7:e01395–15. doi:10.1128/mBio.01395-15.
   PubMed Web of Science ®Google Scholar
• Shanon, C. E., and W. Weaver. 1949. The mathematical Theory of Communications. Urbana: University of Illinois Press.
   Google Scholar
• Tautges, N. E., T. S. Sullivan, C. L. Reardon, and I. C. Burke. 2016. Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system. Applied Soil Ecology 108:258–68. doi:10.1016/j.apsoil.2016.09.003.
   Web of Science ®Google Scholar
• Thatcher, L. F., A. H. Williams, G. Garg, S. A. G. Buck, K. B. Singh. 2016. Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors. Bmc Genomics [Electronic Resource] 17:860. doi:10.1186/s12864-016-3192-2.
   Google Scholar
• Thuerig, B., A. Fließbach, N. Berger, J. G. Fuchs, N. Kraus, N. Mahlberg, et al. 2009. Re-establishment of suppressiveness to soil-and air-borne diseases by re-inoculation of soil microbial communities. Soil Biology & Biochemistry 41:2153–61. doi:10.1016/j.soilbio.2009.07.028.
   Web of Science ®Google Scholar
• Vakalounakis, D. J. and G. A. Fragkiadakis. 1999. Genetic diversity of Fusarium oxysporum isolates from cucumber: Differentiation by pathogenicity, vegetative compatibility, and RAPD Fingerprinting. Phytopathol 89:161–8. doi:10.1094/PHYTO.1999.89.2.161.
   PubMed Web of Science ®Google Scholar
• Van der Heijden, M. G. A., J. N. Klironomos, M. Ursic, P. Moutoglis, R. Streitwolf-Engel, T. Boller, et al. 1998. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature (London, United Kingdom) 396:69–72. doi:10.1038/23932.
   Web of Science ®Google Scholar
• Van Elsas, J. D., M. Chiurazzi, C. A. Mallon, D. Elhottovā, V. Krištůfek, and J. F. Salles. 2012. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences of the United States 109:1159–64. doi:10.1073/pnas.1109326109.
   PubMed Web of Science ®Google Scholar
• Vera, J. C., C. W. Wheat, H. W. Fescemyer, M. J. Frilander, D. L. Crawford, I. Hanski, et al. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 17:1636–47. doi:10.1111/j.1365-294X.2008.03666.x.
   PubMed Web of Science ®Google Scholar
• Weller, D. M., J. M. Raaijmakers, B. B. M. Gardener, and L. S. Thomashow. 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annual Review of Phytopathology 40:309–48. doi:10.1146/annurev.phyto.40.030402.110010.
   PubMed Web of Science ®Google Scholar