Factors associated with suppression of Fusarium basal rot of onion in New Zealand soils: literature review and greenhouse experiments

References

• Abawi GS, Lorbeer JW. 1972. Several aspects of the ecology and the pathology of Fusarium oxysporum f. sp. cepae. Phytopathology. 62:870–876.
   Web of Science ®Google Scholar
• Acosta-Martínez V, Dowd S, Sun Y, Allen V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem. 40:2762–2770.
   Web of Science ®Google Scholar
• Alabouvette C. 1999. Fusarium wilt suppressive soils: an example of disease-suppressive soils. Australas Plant Pathol. 28:57–64.
   Web of Science ®Google Scholar
• Alabouvette C, Olivain C, Migheli Q, Steinberg C. 2009. Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum. New Phytol. 184:529–544.
   PubMed Web of Science ®Google Scholar
• Bektas I, Kusek M. 2019. Phylogenetic and morphological characterization of Fusarium oxysporium cepae the causal agent of basal rot on onion isolated from Turkey. Fresenius Environ Bull. 28:1733–1742.
   Web of Science ®Google Scholar
• Berendsen RL, Pieterse CMJ, Bakker PAHM. 2012. The second genome and plant health. Trends Plant Sci. 17:478–486.
   PubMed Web of Science ®Google Scholar
• Black L, Conn K, Gabor B, Kao J, Lutton J. 2012. Onion disease guide. A practical guide for seedsmen, growers and Agricultural Advisors. St. Louis, MO, USA. Seminis Plant Health.
   Google Scholar
• Bonilla N, Gutiérrez-Barranquero J, Vicente A, Cazorla F. 2012. Enhancing soil quality and plant health through suppressive organic amendments. Diversity. 4:475–491.
   Google Scholar
• Brewster JL. 2008. Onions and other vegetable alliums, 2nd ed. Wallingford: CABI International.
   Google Scholar
• Callahan B, McMurdie P, Rosen M, Han AW, Johnson AJ, Holmes SP. 2016. DADA2: High-resolution sample inference from illumina amplicon data. Nat Methods. 13:581–583.
   PubMed Web of Science ®Google Scholar
• Campos SB, Lisboa BB, Camargo FAO, Bayer C, Sczyrba A, Dirksen P, Albersmeier A, Kalinowski J, Beneduzi A, Costa PB, et al. 2016. Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems. Soil Biol Biochem. 96:191–197.
   Web of Science ®Google Scholar
• Cawoy H, Bettiol W, Fickers P, Ongena M. 2011. Bacillus-based biological control of plant diseases. In: Stoytcheva M, editor. Pesticides in the modern world – pesticides use and management. Rijeka: InTech; p. 274–302.
   Google Scholar
• Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crusemann M, Bok Lee Y, Kim JF, et al. 2016. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10:119–129.
   PubMed Web of Science ®Google Scholar
• Claydon JJ. 1989. Determination of particle-size distribution in fine-grained soils – pipette method. Lower Hutt, NZ; Department of Scientific and Industrial Research. DSIR Division of Land and Soil Sciences Technical Record LH5.
   Google Scholar
• Cramer C. 2000. Breeding and genetics of fusarium basal rot resistance in onion. Euphytica. 115:159–166.
   Web of Science ®Google Scholar
• Datnoff LE, Elmer WH, Huber DM. 2007. Mineral nutrition and plant disease. St. Paul, MN: American Phytopathological Society.
   Google Scholar
• Day PR. 1965. Particle fractionation and particle size analysis. In: Black CA, editor. Methods of soil analysis, part 1. agronomy, No. 9. Madison, WI: American Society of Agronomy; p. 545–567.
   Google Scholar
• De Cal A, Garcia-Lepe R, Melgarejo P. 2000. Induced resistance by Penicillium oxalicum against Fusarium oxysporum f. sp. lycopersici: histological studies of infected and induced tomato stems. Phytopathology. 90:260–268.
   PubMed Web of Science ®Google Scholar
• Dehne HW, Schonbeck F. 1979. Influence of endotrophic mycorrhiza on plant diseases. II. Phenol metabolism and lignification. J Phytopathol. 95:210–216.
   Web of Science ®Google Scholar
• Entwistle AR. 1990. Root diseases. In: Rabinowitch HD, Brewster JL, editors. Onions and allied crops. Volume II. Boca Raton, FL: CRC Press, Inc; p. 103–154.
   Google Scholar
• Fierer N, Bradford MA, Jackson RB. 2007. Toward an ecological classification of soil bacteria. Ecology. 88:1354–1364.
   PubMed Web of Science ®Google Scholar
• Fiers M, Edel-Hermann V, Chatot C, Le Hingrat Y, Alabouvette C, Steinberg C. 2012. Potato soil-borne diseases. A review. Agron Sustain Dev. 32:93–132.
   Web of Science ®Google Scholar
• Finney DM, Buyer JS, Kaye JP. 2017. Living cover crops have immediate impacts on soil microbial community structure and function. J Soil Water Conserv. 72:361–373.
   Web of Science ®Google Scholar
• Garbeva P, Van Veen JA, Van Elsas JD. 2004. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol. 42:243–270.
   PubMed Web of Science ®Google Scholar
• Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS. 2003. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol. 69:1800–1809.
   PubMed Web of Science ®Google Scholar
• Gomez Exposito R, de Bruijn I, Postma J, Raaijmakers JM. 2017. Current insights into the role of rhizosphere bacteria in disease suppressive soils. Front Microbiol. 8:2529.
   PubMed Web of Science ®Google Scholar
• Griffin DE. 2012. Managing abiotic factors of compost to increase soilborne disease suppression. J Nat Resour Life Sci Educ. 41:31–34.
   Google Scholar
• Haas D, Defago G. 2005. Biological control of soilborne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 3:307–319.
   PubMed Web of Science ®Google Scholar
• Hamasaki R, Valenzuela H, Shimabuku R. 1999. Bulb onion growing in Hawaii. Manoa, HI: College of Tropical Agriculture and Human Resources, University of Hawaii.
   Google Scholar
• Havey MJ. 1995. Fusarium basal plate rot. In: Schwartz HF, Mohan SK, editors. Compendium of onion and garlic diseases. St. Paul, MN: APS Press; p. 10–11.
   Google Scholar
• Hoitink HAJ, Boehm MJ. 1999. Biocontrol within the context of soil microbial communities: a substrate-dependent phenomenon. Annu Rev Phytopathol. 37:427–446.
   PubMed Web of Science ®Google Scholar
• Hoper H, Alabouvette C. 1996. Importance of physical and chemical soil properties in the suppressiveness of soils to plant diseases. Eur J Soil Biol. 32:41–58.
   Web of Science ®Google Scholar
• Imperiali N, Dennert F, Schneider J, Laessle T, Velatta C, Fesselet M, Wyler M, Mascher F, Mavrodi O, Mavrodi D, et al. 2017. Relationships between root pathogen resistance, abundance and expression of Pseudomonas antimicrobial genes, and soil properties in representative Swiss agricultural soils. Front Plant Sci. 8:427.
   PubMed Web of Science ®Google Scholar
• Jangid K, Williams MA, Franzluebbers AJ, Sanderlin JS, Reeves JH, Jenkins MB, Endale DM, Coleman DC, Whitman WB. 2008. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biol Biochem. 40:2843–2853.
   Web of Science ®Google Scholar
• Janvier C, Villeneuve F, Alabouvette C, Edel-Hermann V, Mateille T, Steinberg C. 2007. Soil health through soil disease suppression: which strategy from descriptors to indicators? Soil Biol Biochem. 39:1–23.
   Web of Science ®Google Scholar
• Killham K. 1994. Soil ecology. Cambridge, UK: Cambridge University Press.
   Google Scholar
• Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41:e1–e1.
   PubMed Web of Science ®Google Scholar
• Koljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 22:5271–5277.
   PubMed Web of Science ®Google Scholar
• Lauber CL, Strickland MS, Bradford MA, Fierer N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem. 40:2407–2415.
   Web of Science ®Google Scholar
• Lemanceau P. 1989. Role of competition for carbon and iron in mechanisms of soil suppressiveness to Fusarium wilts. In: Tjamos EC, Beckman CH, editors. Vascular wilt diseases of plants: basic studies and control. Berlin, Heidelberg: Springer; p. 385–396.
   Google Scholar
• Lobmann MT, Vetukuri RR, de Zinger L, Alsanius BW, Grenville-Briggs LJ, Walter AJ. 2016. The occurrence of pathogen suppressive soils in Sweden in relation to soil biota, soil properties, and farming practices. Appl Soil Ecol. 107:57–65.
   Web of Science ®Google Scholar
• Mahatma MK, Mahatma L. 2015. Soil suppressive microorganisms and their impact on fungal wilt pathogens. In: Meghvansi MK, Varma A, editors. Organic amendments and soil suppressiveness in plant disease management. soil biology 46. Cham: Springer International; p. 249–274.
   Google Scholar
• Malathi S. 2015. Biological control of onion basal rot caused by Fusarium oxysporum f. sp. cepae. Asian J Biol Sci. 10:21–26.
   Google Scholar
• Martin KJ, Rygiewicz PT. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol. 5:28.
   PubMed Web of Science ®Google Scholar
• Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal. 17:10–12.
   Google Scholar
• Mazurier S, Corberand T, Lemanceau P, Raaijmakers JM. 2009. Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt. ISME J. 3:977–991.
   PubMed Web of Science ®Google Scholar
• Mazzola M. 2002. Mechanisms of natural soil suppressiveness to soilborne diseases. Antonie Van Leeuwenhoek. 81:557–564.
   PubMed Web of Science ®Google Scholar
• McDaniel MD, Grandy AS. 2016. Soil microbial biomass and function are altered by 12 years of crop rotation. Soil. 2:583–599.
   Web of Science ®Google Scholar
• McDonald MR. 1994. Basal rot. In: Howard RJ, Garland JA, Seaman WL, editors. Diseases and pests of vegetable crops in Canada: an illustrated compendium. Ottawa: The Canadian Phytopathological Society and the Entomological Society of Canada; p. 180–181.
   Google Scholar
• McMurdie PJ, Holmes S. 2013. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 8:e61217–e61217.
   PubMed Web of Science ®Google Scholar
• McMurdie PJ, Holmes S. 2014. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 10:e1003531.
   PubMed Web of Science ®Google Scholar
• Mishra RK, Jaiswal DK, Kumar PR, Saabale SA. 2014. Management of major diseases and insect pests of onion and garlic; a comprehensive review. J Plant Breed Crop Sci. 6:160–170.
   Google Scholar
• Nelson DW, Sommers LE. 1996. Total carbon, organic carbon and organic matter. In: Bartels JM, editor. Methods of soil analysis: Part 3. Chemical methods, 3rd ed. Madison, WI: ASA and SSSA Book Series 5; p. 961–1010.
   Google Scholar
• Nguyen NL, Kim YJ, Hoang VA, Subramaniyam S, Kang JP, Kang CH, Yang DC. 2016. Bacterial diversity and community structure in Korean ginseng field soil are shifted by cultivation time. PLoS One. 11:e0155055.
   PubMed Web of Science ®Google Scholar
• Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu M. 2019. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci Rep. 9:1–9.
   PubMed Web of Science ®Google Scholar
• Omay AB, Rice CW, Maddux LD, Gordon WB. 1997. Changes in soil microbial and chemical properties under long-term crop rotation and fertilization. Soil Sci Soc Am J. 61:1672–1678.
   Web of Science ®Google Scholar
• Orr CH, Stewart CJ, Leifert C, Cooper JM, Cummings SP. 2015. Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems. J Appl Microbiol. 119:1364–5072.
   Web of Science ®Google Scholar
• Orr R, Nelson PN. 2018. Impacts of soil abiotic attributes on Fusarium wilt, focusing on bananas. Appl Soil Ecol. 132:20–33.
   Web of Science ®Google Scholar
• Ozer N, Koycu N, Chilosi G, Magro P. 2004. Resistance to fusarium basal rot of onion in greenhouse and field and associated expression of antifungal compounds. Phytoparasitica. 32:388–394.
   Web of Science ®Google Scholar
• Postma J, Schilder MT, Bloem J, Van Leeuwen-Haagsma WK. 2008. Soil suppressiveness and functional diversity of the soil microflora in organic farming systems. Soil Biol Biochem. 40:2394–2406.
   Web of Science ®Google Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:590–596.
   PubMed Web of Science ®Google Scholar
• Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moenne-Loccoz Y. 2009. The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil. 321:341–361.
   Web of Science ®Google Scholar
• Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T. 2017. Disease suppressive soils: new insights from the soil microbiome. Phytopathology. 107:1284–1297.
   PubMed Web of Science ®Google Scholar
• Schwartz H. 2012. Pest Management strategic plan for dry bulb storage onions in the United States. Western IPM Center Davis, CA. [Accessed 2019 May 19]. https://ipmdata.ipmcenters.org/documents/pmsps/USonionPMSP.pdf.
   Google Scholar
• Schwartz HF. 2004. Soil-borne diseases of onion. Colorado State University Cooperative Extension. [Accessed 2018 Nov 12]. http://extension.colostate.edu/topic-areas/agriculture/ soil-borne-diseases-of-onion-2-940/.
   Google Scholar
• Siddiqui S, Alamri SA, Alrumman SA, Meghvansi MK, Chaudhary KK, Kilany M, Prasad K. 2015. Role of soil amendment with micronutrients. In: Meghvansi MK, Varma A, editors. Suppression of certain soilborne plant fungal diseases: a review: organic amendments and soil suppressiveness in plant disease management. Cham: Springer International; p. 363–380.
   Google Scholar
• Siegel-Hertz K, Edel-Hermann V, Chapelle E, Terrat S, Raaijmakers JM, Steinberg C. 2018. Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Chateaurenard region. Front. Microbiol. 9:1–16.
   PubMed Web of Science ®Google Scholar
• Snowdon AL. 1991. A colour atlas of post-harvest diseases and disorders of fruits and vegetables. Volume 2. vegetables. London: Wolfe Scientific.
   Google Scholar
• Stirling GR, Smith MK, Smith JP, Stirling AM, Hamill SD. 2012. Organic inputs, tillage and rotation practices influence soil health and suppressiveness to soilborne pests and pathogens of ginger. Australas Plant Pathol. 41:99–112.
   Web of Science ®Google Scholar
• Stover RH. 1962. Fusarium wilt (Panama disease) of bananas and other Musa species. Kew: Commonwealth Mycological Institute.
   Google Scholar
• Torma S, Vilcek J, Losak T, Kuzel S, Martensson A. 2017. Residual plant nutrients in crop residues – an important resource. Acta Agriculturae Scandinavica. Section B. Soil and Plant Science. Acta Agric Scand B. 68:358–366.
   Web of Science ®Google Scholar
• Van Agtmaal M. 2015. Suppression of soil-borne plant pathogens [dissertation]. Wageningen: Wageningen University.
   Google Scholar
• Van Os GJ, Van Ginkel JH. 2001. Suppression of pythium root rot in bulbous iris in relation to biomass and activity of the soil microflora. Soil Biol Biochem. 33:1447–1454.
   Web of Science ®Google Scholar
• Vance ED, Brookes PC, Jenkinson DS. 1987. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem. 19:703–707.
   Web of Science ®Google Scholar
• Veeken AHM, Blok WJ, Curci F, Coenen GCM, Termorshuizen AJ, Hamelers HVM. 2005. Improving quality of composted biowaste to enhance disease suppressiveness of compost-amended, peat-based potting mixes. Soil Biol Biochem. 37:2131–2140.
   Web of Science ®Google Scholar
• Venter ZS, Jacobs K, Hawkins HJ. 2016. The impact of crop rotation on soil microbial diversity: a meta-analysis. Pedobiologia. 59:215–223.
   Web of Science ®Google Scholar
• Wall M, Shannon E, Corgan J. 1993. Onion diseases in New Mexico. New Mexico State University Cooperative Extension Service Circular 538. [Accessed 2019 March 10]. https://aces.nmsu.edu/ces/plantclinic/documents/cr538.pdf.
   Google Scholar
• Weller DM, Raaijmakers JM, McSpadden BB, Thomashow LS. 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol. 40:309–348.
   PubMed Web of Science ®Google Scholar
• Wright PJ, Falloon RE, Hedderley D. 2015. Different vegetable crop rotations affect soil microbial communities and soilborne diseases of potato and onion: literature review and a long-term field evaluation. NZ J Crop Hortic Sci. 43:85–110.
   Web of Science ®Google Scholar
• Xiong W, Jousset A, Guo S, Karlsson I, Zhao Q, Wu H, Kowalchuk GA, Shen Q, Li R, Geisen S. 2018. Soil protist communities form a dynamic hub in the soil microbiome. ISME J. 12:634–638.
   PubMed Web of Science ®Google Scholar
• Yadav RS, Panwar J, Meena HN, Thirumalaisamy PP, Meena RL. 2015. Developing disease-suppressive soil through agronomic management. In: Meghvansi M, Varma A, editors. Organic amendments and soil suppressiveness in plant disease management. Soil Biology, vol. 46. Cham: Springer; p. 61–94.
   Google Scholar
• Zhou D, Jing T, Chen Y, Wang F, Qi D, Feng R, Xie J, Li H. 2019. Deciphering microbial diversity associated with Fusarium wilt-diseased and disease-free banana rhizosphere soil. BMC Microbiology. 19:161.
   PubMed Web of Science ®Google Scholar