Abarenkov K, Nilsson RH, Larsson KH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T. The UNITE database for molecular identification of fungi—recent updates and future perspectives. New Phytol. 2010;186:281–5.
Article
PubMed
Google Scholar
Alabouvette C. Fusarium wilt suppressive soils: an example of disease-suppressive soils. Australasian Plant Pathol. 1999;28:57–64.
Article
Google Scholar
Alabouvette C, Lemanceau P, Steinberg C. Recent advances in the biological control of Fusarium wilts. Pest Sci. 1993;37:365–73.
Article
Google Scholar
Aleandri MP, Chilosi G, Bruni N, Tomassini A, Vettraino AM, Vannini A. Use of nursery potting mixes amended with local Trichoderma strains with multiple complementary mechanisms to control soil-borne diseases. Crop Prot. 2015;67:269–78.
Article
Google Scholar
Angelopoulou DJ, Naska EJ, Paplomatas EJ, Tjamos SE. Biological control agents (BCAs) of V. dahliae wilt: influence of application rates and delivery method on plant protection, triggering of host defense mechanisms and rhizosphere populations of BCAs. Plant Pathol. 2014;63(5):1062–106.
Article
Google Scholar
Antoniou A, Tsolakidou MD, Stringlis IA, Pantelides IS. Rhizosphere microbiome recruited from a suppressive compost improves plant fitness and increases protection against vascular wilt pathogens of tomato. Front Plant Sci. 2017;8:2022. https://doi.org/10.3389/fpls.2017.02022.
Article
PubMed
PubMed Central
Google Scholar
Araujo R, Dunlap C, Barnett S, Franco CMM. Decoding wheat endosphere-rhizosphere microbiomes in Rhizoctonia solani–infested soils challenged by streptomyces biocontrol agents. Front Plant Science. 2019;10:1038. https://doi.org/10.3389/fpls.2019.01038.
Article
Google Scholar
Araujo ASF, Miranda ARL, Oliveira MLJ, Santos VM, Nuñes LAPL, Melo WJ. Soil microbial properties after 5 years of consecutive amendment with composted tannery sludge. Environ Monit. Assess. 2015;187:1–7.
Article
CAS
Google Scholar
Avila Miranda ME, Estrella A, Peña Cabriales JJ. Colonization of the rhizosphere, rhizoplane and endorhiza of garlic (Allium sativum L.) by strains of Trichoderma harzianum and their capacity to control allium white-rot under field conditions. Soil Biol Biochem. 2006;38:1823–30.
Article
CAS
Google Scholar
Avilés M, Borrero C. Identifying characteristics of V. dahliae wilt suppressiveness in olive mill composts. Plant Dis. 2017;101(9):1568–77.
Article
PubMed
Google Scholar
Abdallah RA, Mokni-Tlili S, Nefzi A, Jabnoun-Khiareddine H, Daami-Remadi M. Biocontrol of Fusarium wilt and growth promotion of tomato plants using endophytic bacteria isolated from Nicotiana glauca organs. Biol Control. 2016;97:80–8.
Article
Google Scholar
Bai Y, Wang G, Cheng Y, Shi P, Yang C, Yang H, Xu Z. Soil acidification in continuously cropped tobacco alters bacterial community structure and diversity via the accumulation of phenolic acids. Sci Rep. 2019;9:12499. https://doi.org/10.1038/s41598-019-48611-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baker K, Cook RJ. Biological control of plant pathogens. San Francisco: Freeman WH Publisher; 1974.
Google Scholar
Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. Lineages of acidophilic archaea revealed by community genomic analysis. Science. 2006;314:1933–5. https://doi.org/10.1126/science.1132690.
Article
CAS
PubMed
Google Scholar
Bastida F, Selevsek N, Torres IF, Hernández T, García C. Soil restoration with organic amendments: linking cellular functionality and ecosystem processes. Sci Rep. 2015;5:15550.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berendsen RL, Pieterse CMJ, Bakker PAHM. The rhizosphere microbiome and plant health. Trends Plant Sci. 2012;17(8):478–86.
Article
CAS
PubMed
Google Scholar
Bernard E, Larkin RP, Tavantzis S, Erich MS, Alyokhin A, Sewell G, Lannan A, Gross SD. Compost, rapeseed rotation, and biocontrol agents significantly impact soil microbial communities in organic and conventional potato production systems. Appl Soil Ecol. 2012;52:29–41.
Article
Google Scholar
Berry BM, Sylvester-Bradley R, Philipp L, Hatch DJ, Cuttle SP, Rayns FW, Gosling P. Is the productivity of organic farms restricted by the supply of available nitrogen? Soil Use Manage. 2002;18:248–55.
Article
Google Scholar
Bevivino A, Paganin P, Bacci G, Florio A, Pellicer MS, Papaleo MC, Mengoni A, Ledda L, Fani R, Benedetti A, Dalmastri C. Soil bacterial community response to differences in agricultural management along with seasonal changes in a mediterranean region. PLoS ONE. 2014;9(8):e105515. https://doi.org/10.1371/journal.pone.0105515.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bhadauria BP, Singh Y, Puri S, Singh PK. Ecofriendly management of Fusarium wilt of Brinjal. Ecol Environ Conserv. 2012;18:1049–52.
Google Scholar
Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 2004;9:418–25.
Article
CAS
PubMed
Google Scholar
Blaya J, Frutos C, Marhuenda J, Pascual A, Ros M. Microbiota characterization of compost using omics approaches opens new perspectives for Phytophthora root rot control. PLoS ONE. 2016;11(8):1–19. https://doi.org/10.1371/journal.pone.0158048.
Article
CAS
Google Scholar
Blaya J, López-Mondéjar R, Lloret E, Pascual JA, Ros M. Changes induced by Trichoderma harzianum in suppressive compost controlling Fusarium wilt. Pest Biochem Physiol. 2013;107:112–9.
Article
CAS
Google Scholar
Bonanomi G, Antignani V, Pane C, Scala F. Suppression of soilborne fungal diseases with organic amendments. J Plant Pathol. 2007;89:311–24.
Google Scholar
Bonanomi G, D’Ascoli R, Scotti R, Gaglione SA, Caceres MG, Sultana S, Scelza R, Rao MA, Zoina A. Soil quality recovery and crop yield enhancement by combined application of compost and wood to vegetables grown under plastic tunnels. Agric Ecosyst Environ. 2014;192:1–7. https://doi.org/10.1016/j.agee.2014.03.029.
Article
CAS
Google Scholar
Bonanomi G, De Filippis F, Cesarano G, La Storia A, Ercolini D, Scala F. Organic farming induces changes in soil microbiota that affect agro-ecosystem functions. Soil Biol Biochem. 2016;103:327–36. https://doi.org/10.1016/j.soilbio.2016.09.005.
Article
CAS
Google Scholar
Bonanomi G, Gaglione SA, Cesarano G, Sarker TC, Pascale M, Scala F, Zoina A. Frequent application of organic matter to agricultural soil increases fungistasis. Pedosphere. 2017;27:86–95. https://doi.org/10.1016/S1002-0160%5b15%5d600.
Article
Google Scholar
Borrero C, Castillo S, Segarra G, Trillas MI, Castaño R, Avilés M. Capacity of composts made from agriculture industry residues to suppress different plant diseases. Acta Hortic. 2013;1013:459–63.
Google Scholar
Bouizgarne B. Bacteria for plant growth promotion and disease management. In: Maheshwari DK, editor. Bacteria in agrobiology: disease management. Berlin: Springer; 2013. p. 15–47.
Chapter
Google Scholar
Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26:1146–53. https://doi.org/10.1038/nbt.1495.
Article
CAS
PubMed
PubMed Central
Google Scholar
Breidenbach B, Blaser MB, Klose M, Conrad R. Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environ Microbiol. 2016;18:2868–85.
Article
CAS
PubMed
Google Scholar
Bronick C, Lal R. Soil structure and management: a review. Geoderma. 2005;124:3–22. https://doi.org/10.1016/j.geoderma.2004.03.005.
Article
CAS
Google Scholar
Bulluck LR, Brosius M, Evanylo GK, Ristaino JB. Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms. Appl Soil Ecol. 2002;19:147–60. https://doi.org/10.1016/S0929-1393(01)00187-1.
Article
Google Scholar
Cao Y, Fanning S, Proos S, Jordan K, Srikumar S. A review on the applications of next generation sequencing technologies as applied to food-related microbiome studies. Front Microbiol. 2017;8:1829. https://doi.org/10.3389/fmicb.2017.01829.
Article
PubMed
PubMed Central
Google Scholar
Cao Y, Zhang Z, Ling N, Yuan Y, Zheng X, Shen B, Shen Q. Bacillus subtilis SQR 9 can control Fusarium wilt in cucumber by colonizing plant roots. Biol Fertil Soils. 2011;47:495–506.
Article
CAS
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.
Article
PubMed
Google Scholar
Caravaca F, Hernández T, García C, Roldán A. Improvement of rhizosphere aggregate stability of afforested semiarid plant species subjected to mycorrhizal inoculation and compost addition. Geoderma. 2002;108:133–44.
Article
CAS
Google Scholar
Castãno R, Borrero C, Avilés M. Organic matter fractions by SP-MAS 13C NMR and microbial communities involved in the suppression of fusarium wilt in organic growth media. Biol Control. 2011;58(3):286–93.
Article
Google Scholar
Castãno R, Borrero C, Trillas MI, Avilés M. Selection of biological control agents against tomato Fusarium wilt and evaluation in greenhouse conditions of two selected agents in three growing media. Biocontrol. 2013;58:105–16.
Article
Google Scholar
Celik I, Ortas I, Kilic S. Effects of compost, mycorrhiza, manure and fertilizer on some physical properties of a Chromoxerert soil. Soil Till Res. 2004;78:59–67.
Article
Google Scholar
Cesarano G, De Filippis F, La Storia A, Scala F, Bonanomi G. Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition. Appl Soil Ecol. 2017;120:254–64.
Article
Google Scholar
Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y. Microbial and biochemical basis of a Fusarium oxysporum f sp melonis wilt-suppressive soil. ISME J. 2016;10:119–29.
Article
CAS
PubMed
Google Scholar
Chen W, Hoitink HAJ, Schmitthenner A. Factors affecting suppression of pythium damping-off in container media amended with composts. Phytopathology. 1987;77(5):755–60.
Article
Google Scholar
Chilosi G, Aleandri MP, Bruni N, Tomassini A, Torresi V, Muganu M, Paolocci M, Vettraino A, Vannini A. Assessment of suitability and suppressiveness of on-farm green compost as a substitute of peat in the production of lavender plants. Biocontrol Sci Technol. 2017;27(4):539–55.
Article
Google Scholar
Claudia C, McLean M, Berjak P. In vitro studies on the potential for biological control of Aspergillus flavus and Fusarium moniliforme by Trichoderma spp. Mycopathologia. 1997;137:115–24.
Article
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, Mcgarrell DM, Sun Y, Brown CT, Porrasalfaro A, Kuske CR, Tiedje JM. Ribosomal database project: data and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633.
Article
CAS
PubMed
Google Scholar
Cordier C, Gianinazzi S, Gianinazzi-Pearson V. Colonisation patterns of root tissues by Phytophthora nicotianae var parasitica related to reduced disease in mycorrhizal tomato. Plant Soil. 1996;185(2):223–32.
Article
CAS
Google Scholar
Cotxarrera L, Trillas MI, Steinberg C, Alabouvette C. Use of sewage sludge compost and Trichoderma asperellum isolates to suppress Fusarium oxysporum f sp melonis wilt of tomato. Soil Biol Biochem. 2002;34:467–76.
Article
CAS
Google Scholar
Cretoiu MS, Korthals GW, Visser JHM, Van Elsas JD. Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field. Appl Environ Microbiol. 2013;79:5291–301.
Article
CAS
PubMed
PubMed Central
Google Scholar
Croteau GA, Zibilske LM. Influence of papermill processing residuals on saprophytic growth and disease caused by Rhizoctonia solani. Appl Soil Ecol. 1998;10:103–15.
Article
Google Scholar
Danon M, Franke-Whittle IH, Insam H, Chen Y, Hadar Y. Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiol Ecol. 2008;65(1):133–44. https://doi.org/10.1111/j.1574-6941.2008.00506.x.
Article
CAS
PubMed
Google Scholar
Da Mota FF, Gomes EA, Seldin L. Auxin production and detection of the gene coding for the auxin efflux carrier (AEC) protein in Paenibacillus polymyxa. J Microbiol. 2008;46(3):257–64.
Article
CAS
PubMed
Google Scholar
De Corato U. Disease-suppressive compost enhances natural soil suppressiveness against soil-borne plant pathogens: a critical review. Rhizosphere. 2020;13:100192. https://doi.org/10.1016/j.rhisph.2020.100192.
Article
Google Scholar
De Corato U, Patruno L, Avella N, Lacolla G, Cucci G. Composts from green sources show an increased suppressiveness to soilborne plant pathogenic fungi: relationships between physicochemical properties, disease suppression, and the microbiome. Crop Prot. 2019;124:104870. https://doi.org/10.1016/j.cropro.2019.104870.
Article
CAS
Google Scholar
De Corato U, Salimbeni R, De Pretis A, Patruno L, Avella N, Lacolla G, Cucci G. Microbiota from ‘next-generation green compost’ improves suppressiveness of composted Municipal-Solid-Waste to soil-borne plant pathogens. Biol Control. 2018;124:1–17. https://doi.org/10.1016/j.biocontrol.2018.05.020.
Article
Google Scholar
De Corato U, Viola E, Arcieri G, Valerio V, Zimbardi F. Use of composted agro-energy co-products and agricultural residues against soil-borne pathogens in horticultural soil-less systems. Sci Hortic. 2016;210:166–79. https://doi.org/10.1016/j.scienta.2016.07.027.
Article
Google Scholar
Deepa C, Dastager SG, Pandey A. Plant growth-promoting activity in newly isolated Bacillus thioparus (NII-0902) from Western ghat forest, India. World J Microbiol. Biotechnol. 2010;26(12):2277–83.
Article
Google Scholar
de la Cruz JMR, Lora JM, Hidalgo-Galiego A, Dominguez F, Pintor-Toro JA, Llobell A, Benitez T. Carbon source control on β-glucanases, chitobiase and chitinase from Trichoderma harzianum. Ann Microbiol. 1993;159:316–22.
Google Scholar
De Meyer G, Bigrimana G, Elad Y, Hofte M. Induced systemic resistance in T. harzianum T396 biocontrol of Botrytis cinerea. Eur J Plant Pathol. 1998;104:279–86.
Article
Google Scholar
Deng X, Zhang N, Shen Z, Zhu C, Li R, Falcao Salles J, Shen Q. Rhizosphere bacteria assembly derived from fumigation and organic amendment triggers the direct and indirect suppression of tomato bacterial wilt disease. Appl Soil Ecol. 2019. https://doi.org/10.1016/j.apsoil.2019.103364(in press).
Article
Google Scholar
Desantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, Garcia-Cobos S, Kooistra-Smid AM, Raangs EC, Rosema S, Veloo AC, Zhou K, Friedrich AW, Rossen JW. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol. 2017;243:16–24. https://doi.org/10.1016/j.jbiotec.2016.12.022.
Article
CAS
PubMed
Google Scholar
De Weger L, Van Boxtel R, Van der Burg B, Gruters R, Geels F, Schippers B, Lugtenberg B. Siderophores and outer membrane proteins of antagonistic, plant-growth-stimulating, root-colonizing Pseudomonas spp. J Bacteriol. 1986;165(2):585–94.
Article
PubMed
PubMed Central
Google Scholar
Dignam BEA, O’Callaghan M, Condron LM, Raaijmakers JM, Kowalchuk GA, Wakelin SA. Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness. Soil Biol Biochem. 2019;135:396–406. https://doi.org/10.1016/j.soilbio.2019.05.020.
Article
CAS
Google Scholar
Di Lenola M, Grenni P, Proença D, Morais P, Caracciolo A. Comparison of two molecular methods to assess soil microbial diversity. In: Lukac M, Grenni P, Gamboni M, editors. Soil biological communities and ecosystem resilience, sustainability in plant and crop protection series. Switzerland: Springer; 2017. p. 25–42.
Chapter
Google Scholar
Domínguez P, Miranda L, Soria C, de los Santos B, Chamorro M, Romero F, Daugovish O, Lopez-Aranda JM, Medina JJ. Soil biosolarization for sustainable strawberry production. Agron Sustain Dev. 2014;34:821–9.
Article
Google Scholar
Duong TTT, Verma SL, Penfold C, Marschner P. Nutrient release from composts into the surrounding soil. Geoderma. 2013;195(196):42–7.
Article
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Article
CAS
PubMed
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194.
Article
CAS
PubMed
PubMed Central
Google Scholar
El-Masry M, Khalil A, Hassouna M, Ibrahim H. In situ and in vitro suppressive effect of agricultural composts and their water extracts on some phytopathogens. World J Microbiol Biotechnol. 2002;18(6):551–8.
Article
CAS
Google Scholar
Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 2013;4:1111–9. https://doi.org/10.1111/2041-210X.12114.
Article
PubMed Central
Google Scholar
Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GL. Alta-Cyclic: a self-optimizing base caller for next generation sequencing. Nat Methods. 2008;5:679–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Evanylo G, Sherony C, Spargo J, Starner D, Brosius M, Haering K. Soil and water environmental effects of fertilizer- manure-, and compost-based fertility practices in an organic vegetable cropping system. Agr Ecosyst Environ. 2008;127:50–8.
Article
Google Scholar
Fadrosh DW, Bing M, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome. 2014;2:1–7.
Article
Google Scholar
Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: the next culture-independent game changer. Front. Microbiol. 2017;8:1069. https://doi.org/10.3389/fmicb.2017.01069.
Article
PubMed
PubMed Central
Google Scholar
García-Gil JC, Plaza C, Soler-Rovira P, Polo A. Long-term effects of municipal solid waste compost application on soil enzyme activities and microbial biomass. Soil Biol Biochem. 2000;32:1907–13.
Article
Google Scholar
Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2:113–8. https://doi.org/10.1111/j.1365-294X.1993.tb00005.x.
Article
CAS
PubMed
Google Scholar
Ghini R, Patricio FRA, Bettiol W, Almeida IMG, Maia ADHN. Effect of sewage sludge on suppressiveness to soil-borne plant pathogens. Soil Biol Biochem. 2007;39:2797–805.
Article
CAS
Google Scholar
Gil MV, Carballo MT, Calvo LF. Fertilization of maize with compost from cattle manure supplemented with additional mineral nutrients. Waste Manage. 2008;28:1432–40.
Article
CAS
Google Scholar
Griffiths BS, Philippot L. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev. 2013;37:112–29. https://doi.org/10.1111/j.1574-6976.2012.00343.x.
Article
CAS
PubMed
Google Scholar
Haas D, Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 2005;3:307–19.
Article
CAS
PubMed
Google Scholar
Hadar Y, Papadopoulou KK. Suppressive composts: microbial ecology links between abiotic environments and healthy plants. Annu Rev Phytopathol. 2012;50:133–53.
Article
CAS
PubMed
Google Scholar
Haggag WM, Saber MSM. Evaluation of three compost as multi-strain carriers for biofertilizer and biocontrol agents against Fusarium wilt disease of some legume plants. Arab J Biotechnol. 2000;3:133–44.
Google Scholar
Hannan MA, Hasan MM, Hossain I, Rahman SME, Ismail AM, Oh DH. Integrated management of foot rot of lentil using biocontrol agents under field condition. J Microbiol Biotechnol. 2012;22:883–8.
Article
CAS
PubMed
Google Scholar
Hardy GE, Sivasithamparam K. Suppression of Phytophthora nicotianae root rot by a composted eucalyptus bark mix. Aust J Bot. 1991;39:153–9.
Article
Google Scholar
Harman GE, Hayes CK, Lorito M, Broadway RM, Di Pietro A, Peterbauer C, Tronsmo A. Chitinolytic enzymes of Trichoderma harzianum: purification of chitobiosidase and endochitinase. Phytopathology. 1993;83:313–8.
Article
CAS
Google Scholar
Hemmat A, Aghilinategh N, Rezainejad Y, Sadeghi M. Long-term impacts of municipal solid waste compost, sewage sludge and farmyard manure application on organic carbon, bulk density and consistency limits of a calcareous soil in central Iran. Soil Till Res. 2010;108:43–50.
Article
Google Scholar
Himmelstein JC, Maul JE, Everts KL. Impact of five cover crop green manures and actinovate on fusarium wilt of watermelon. Plant Dis. 2014;98:965–72. https://doi.org/10.1094/PDIS-06-13-0585-RE.
Article
CAS
PubMed
Google Scholar
Hoitink HAJ, Boehm MJ. Biocontrol within the contest of soil microbial communities: a substrate-dependent phenomenon. Annu Rev Phytopathol. 1999;37:427–46.
Article
CAS
PubMed
Google Scholar
Hoitink HAJ, Boehm MJ, Hadar Y. Mechanism of suppression of soil borne plant pathogen in compost-amended substrates. In: Hoitink HAJ, Keener HM, editors. Science and engineering of composting: design, environmental, microbiological and utilization aspects. Worthington: Renaissance Publication; 1993. p. 601–21.
Google Scholar
Hoitink HAJ, Fahy PC. Basis for the control of soilborne plant pathogens with composts. Annu Rev Phytopathol. 1986;24:93–114.
Article
Google Scholar
Hoitink HAJ, Krause MS, Han DY. Spectrum and mechanisms of plant disease control with composts. In: Stoffella PJ, Kahn BA, editors. Compost Utilization in Horticultural Cropping Systems. Boca Raton: Lewis Publishers; 2001. p. 263–74.
Google Scholar
Hoitink HAJ, Madden LV, Dorrance AE. Systemic resistance induced by Trichoderma spp.: interaction between the host, the pathogen, the biocontrol agent, and the soil organic matter quality. Phytopathology. 2006;96(2):186–9.
Article
CAS
PubMed
Google Scholar
Hoitink HAJ, Stone AG, Han DY. Suppression of plant diseases by composts. HortScience. 1997;32:184–7.
Article
Google Scholar
Huang Y, Sun L, Zhao J, Huang R, Li R, Shen Q. Utilization of different waste proteins to create a novel PGPR-containing bio-organic fertilizer. Scientific Reports. 2015;5:7766. https://doi.org/10.1038/srep07766.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang X, Zhang N, Yong X, Yang X, Shen Q. Biocontrol of Rhizoctonia solani damping-off disease in cucumber with Bacillus pumilus SQR-N43. Microbiol Res. 2012;167:135–43.
Article
CAS
PubMed
Google Scholar
Hussain I, Alam SS, Khan I, Shah B, Naeem A, Khan N, Ullah W, Iqbal B, Adnan M, Junaid K, Shah SRA, Ahmed N, Iqbal M. Study on the biological control of fusarium wilt of tomato. J Entomol Zool Studies. 2016;4(2):525–8.
Google Scholar
Hwang BK, Ahn SJ, Moon SS. Production, purification, and antifungal activity of the antibiotic nucleoside, tubercidin, produced by Streptomyces violaceus-niger. Can J Bot. 1994;72:480–5.
Article
CAS
Google Scholar
Insam H, Riddech N, Klammer S, editors. Microbiology of composting. Heidelberg: Springer; 2002. p. 435–44.
Book
Google Scholar
Islam MdR, Jeong YT, Lee YS, Song CH. Isolation and identification of antifungal compounds from Bacillus subtilis C9 inhibiting the growth of plant pathogenic fungi. Mycobiology. 2012;40(1):59–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jagadeesan B, Gerner-Smid P, Allard MW, Leuillet S, Winkler A, et al. The use of next generation sequencing for improving food safety: translation into practice. Food Microbiol. 2019;79:96–115. https://doi.org/10.1016/j.fm.2018.11.005.
Article
CAS
PubMed
Google Scholar
Jaiswal AK, Elad Y, Cytryn E, Graber ER, Frenkel O. Activating biochar by manipulating the bacterial and fungal microbiome through pre-conditioning. New Phytol. 2018. https://doi.org/10.1111/nph.15042.
Article
PubMed
Google Scholar
Jambhulkar PP, Sharma M, Lakshman D, Sharma P. Natural mechanisms of soil suppressiveness against diseases caused by Fusarium, Rhizoctonia, Pythium, and Phytophthora. In: Meghvansi MK, Varma A, editors. Organic amendments and soil suppressiveness in plant disease management. Springer: New York; 2015. p. 95–124.
Chapter
Google Scholar
Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol. 2006;72:1719–28. https://doi.org/10.1128/AEM.72.3.1719-1728.2006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jayaraj J, Parthasarathi P, Adhakrishnan NV. Characterization of a Pseudomonas fluorescens strain from tomato rhizosphere and its use for integrated management of tomato damping-off. Biocontrol. 2007;52:683–702.
Article
Google Scholar
Jiang YJ, Liang YT, Li CM, Wang F, Sui YY, Suvannang N, Zhou JZ, Sun B. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol Biochem. 2016;95:250–61.
Article
CAS
Google Scholar
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10(1):5029. https://doi.org/10.1038/s41467-019-13036-1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones DL, Rousk J, Edwards-Jones G, DeLuca TH, Murphy DV. Biochar mediated changes in soil quality and plant growth in a three year field trial. Soil BiolBiochem. 2012;45:113–24. https://doi.org/10.1016/j.soilbio.2011.10.012.
Article
CAS
Google Scholar
Joshi D, Hooda KS, Bhatt JC. Integration of soil solarization with bio-fumigation and Trichoderma spp for management of damping-off in tomato (Lycopersicon esculentum) in the mid altitude region of north-western Himalayas. Indian J Agric Sci. 2009;79:754–7.
Google Scholar
Kanaan H, Hadar Y, Medina S, Krasnovsky A, Mordechai-Lebiush S, Tsror L, Katan J, Raviv M. Effect of compost properties on progress rate of Verticillium dahliae attack on eggplant (Solanum melongena L.). Compost Sci Utiliz. 2017. https://doi.org/10.1080/1065657X.2017.1366375.
Article
Google Scholar
Kariuki GM, Muriuki LK, Kibiro EM. The impact of suppressive soils on plant pathogens and agricultural productivity. In: Meghvansi MK, Varma A, editors. Organic amendments and soil suppressiveness in plant disease management. Springer: New York; 2015. p. 3–24. https://doi.org/10.1007/978-3-319-23075-7.
Chapter
Google Scholar
Kefalogianni I, Gkizi D, Pappa E, Dulaj L, Tjamos SE, Chatzipavlidis I. Combined use of biocontrol agents and zeolite as a management strategy against F. oxysporum f. sp. melonis and V. dahliae wilt. Biocontrol. 2017;62(2):139–50.
Article
CAS
Google Scholar
Kibblewhite MG, Ritz K, Swift MJ. Soil health in agricultural systems. Trans R Soc Biol Sci. 2008;363:685–701.
Article
CAS
Google Scholar
Kilany M, Ibrahim EH, AlAmry S, Al Roman S, Siddiqui S. Microbial suppressiveness of Pythium damping-Off diseases. In: Meghvansi MK, Varma A, editors. Organic amendments and soil suppressiveness in plant disease management. Springer: New York; 2015. p. 187–206. https://doi.org/10.1007/978-3-319-23075-7.
Chapter
Google Scholar
Kim YC, Leveau J, McSpadden Gardener BB, Pierson EA, Pierson LS, Ryu CM. The multifactorial basis for plant health promotion by plant-associated bacteria. Appl Environ Microbiol. 2011;77:1548–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klammer S, Knapp B, Insam H, Dell’Abate MT, Ros M. Bacterial community patterns and thermal analyses of composts of various origins. Waste Manag Res. 2008;26(2):173–87.
Article
PubMed
Google Scholar
Kloepper JW, Rodriguez-Ubana R, Zehnder GW, Murphy JF, Sikora E, Fernandez C. Plant root–bacterial interactions in biological control of soilborne diseases and potential extension to systemic and foliar diseases. Aust Plant Pathol. 1999;28:21–6.
Article
Google Scholar
Krause SM, Madden LV, Hoitink HAJ. Effect of potting mix microbial carrying capacity on biological control of Rhizoctonia solani damping off of radish and R. solani crown and root rot of poinsettia. Phytopathology. 2001;91:1116–23.
Article
CAS
PubMed
Google Scholar
Kullnig-Gradinger CM, Szakacs G, Kubicek CP. Phylogeny and evolution of the fungal genus Trichoderma: a multigene approach. Mycol Res. 2002;106:757–67.
Article
CAS
Google Scholar
Kwok OCH, Fahy PC, Hoitink HAJ, Kuter GA. Interactions between bacteria and Trichoderma hamatum in suppression of Rhizoctonia solani damping-off in bark compost media. Phytopathology. 1987;77(8):1206–12.
Article
Google Scholar
Lang J, Hu J, Ran W, Xu Y, Shen Q. Control of cotton Verticillium wilt and fungal diversity of rhizosphere soils by bio-organic fertilizer. Biol Fertil Soils. 2012;48:191–203.
Article
Google Scholar
Larkin RP, Fravel DR. Efficacy of various fungal and bacterial biocontrol organisms for control of fusarium wilt of tomato. Plant Dis. 1998;82(9):1022–8.
Article
PubMed
Google Scholar
Latha P, Anand T, Prakasam V, Jonathan EI, Paramathma M, Samiyappan R. Combining Pseudomonas, Bacillus and Trichoderma strains with organic amendments and micronutrient to enhance suppression of collar and root rot disease in physic nut. Appl Soil Ecol. 2011;49:215–23.
Article
Google Scholar
Lazarovits G. Managing soilborne disease of potatoes using ecologically based approaches. Am J Potato Res. 2010;87:401–11.
Article
Google Scholar
Lazarovits G, Abbasi PA, Conn KL, Hill JE, Hemmingsen JE. Fish emulsion and liquid swine manure: model systems for development of organic amendments as fertilizers with disease suppressive properties. In: Bettiol W, Morandi M, editors. Biocontrole de Doenças de Plantas: Uso e Perspectivas. Jaguariúna-SP: Embrapa Meio Ambiente; 2009. p. 49–67.
Google Scholar
Lazarovits G, Conn KL, Abbasi PA, Tenuta M. Understanding the mode of action of organic soil amendments provides the way for improved management of soilborne plant pathogens. Acta Hortic. 2005;698:215–24.
Article
Google Scholar
Lehmann J, Rillig MC, Thies J, Masiello CA, Hockaday WC, Crowley D. Biochar effects on soil biota—a review. Soil Biol Biochem. 2011;43:1812–36.
Article
CAS
Google Scholar
Lemanceau P, Alabouvette C. Suppression of fusarium wilts by fluorescent pseudomonads: mechanisms and applications. Biocontrol Sci Technol. 2008;3:219–34. https://doi.org/10.1080/09583159309355278.
Article
Google Scholar
Lemos LN, et al. Bioinformatics for microbiome research: concepts, strategies, and advances. The Brazilian Microbiome. Cham: Springer; 2017. p. 111–23.
Chapter
Google Scholar
Leonard SR, Mammel MK, Lacher DW, Elkins CA. Strain-level discrimination of shiga toxin-producing Escherichia coli in spinach using metagenomic sequencing. PLoS ONE. 2016;11(12):e0167870. https://doi.org/10.1371/journal.pone.0167870.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Cai X, Gong J, Xu T, Ding G, Li J. Long-term organic farming manipulated rhizospheric microbiome and bacillus antagonism against pepper blight (Phytophthora capsici). Front Microbiol. 2019;10:342. https://doi.org/10.3389/fmicb.2019.00342.
Article
PubMed
PubMed Central
Google Scholar
Li X, de Boer W, Zhang Y, Ding C, Zhang T, Wang X. Suppression of soil-borne Fusarium pathogens of peanut by intercropping with the medicinal herb Atractylodes lancea. Soil Biol Biochem. 2018;116:120–30. https://doi.org/10.1016/j.soilbio.2017.09.029.
Article
CAS
Google Scholar
Li XG, Ding CF, Zhang TL, Wang XX. Fungal pathogen accumulation at the expense of plant-beneficial fungi as a consequence of consecutive peanut monoculturing. Soil Biol Biochem. 2014;72:11–8.
Article
CAS
Google Scholar
Liu L, Kloepper JW, Tuzun S. Induction of systemic resistance in cucumber against Fusarium wilting plant growth-promoting rhizobacteria. Phytopathology. 1995;85:695–8.
Article
Google Scholar
Liu M, Wang X, Sun L, Zhao J, Ling Z, Li Z, Zhao X. High-efficiency cultivation model of cherry tomato and rice rotation in south of China. Hum Agric Sci. 2018;26:21–3.
Google Scholar
Liu H, Xiong W, Zhang R, Hang X, Wang D, Li R, Shen Q. Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora. Plant Soil. 2018;423:229–40. https://doi.org/10.1007/s11104-017-3504-6.
Article
CAS
Google Scholar
Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol. 2015;13(12):787–94. https://doi.org/10.1038/nrmicro3565.
Article
CAS
PubMed
Google Scholar
Lopes AR, Manaia CM, Nuñes OC. Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing. FEMS Microbiol Ecol. 2014;87:650–63.
Article
CAS
PubMed
Google Scholar
Lozupone C, Hamady M, Knight R. UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006;7:371.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu L, Yin S, Liu X, Zhang W, Gu T, Shen Q, Qiu H. Fungal networks in yield-invigorating and -debilitating soils induced by prolonged potato monoculture. Soil Biol Biochem. 2013;65:186–94.
Article
CAS
Google Scholar
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. Direct comparisons of illumina vs roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE. 2012;7(2):e30087. https://doi.org/10.1371/journal.pone.0030087.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mago T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
Article
CAS
Google Scholar
Mahatma MK, Mahatma L. 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. Springer: New York; 2015. p. 249–75. https://doi.org/10.1007/978-3-319-23075-7.
Chapter
Google Scholar
Manici LM, Caputo F. Soil fungal communities as indicators for replanting new peach orchards in intensively cultivated areas. Eur J Agronomy. 2010;33:188–96.
Article
Google Scholar
Manici LM, Caputo F, Babini V. Effect of green manure on Pythium spp. population and microbial communities in intensive cropping systems. Plant Soil. 2004;263:133–42.
Article
CAS
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–80.
Article
PubMed
PubMed Central
Google Scholar
Martin St. CCG. 2015 Enhancing soil suppressiveness using compost. In: Meghvansi MK, Varma A, eds. Organic amendments and soil suppressiveness in plant disease management 2015, pp. 25–50. Springer Series Soil biology, Vol. 46, ISSN 1613-3382, ISSN 2196-4831 (electronic), ISBN 978-3-319-23074-0, ISBN 978-3-319-23075-7 (eBook). Springer International Publishing Switzerland. https://doi.org/10.1007/978-3-319-23075-7.
Martínez-Blanco J, Lazcano C, Christensen TH, Muñoz P, Rieradevall J, Møller J, Antón A, Boldrin A. Compost benefits for agriculture evaluated by life cycle assessment. A review. Agron Sustain Dev. 2013;33:721–32.
Article
Google Scholar
Maurhfiofer M, Flace C, Meuwly P, Defagu G. Induction of systemic resistance in cucumber by Pseudomonas syringae pv. syringae. Physiol Mol Plant Pathol. 1994;38:223–35.
Google Scholar
McGee CF, Doyle O, Gaffney MT. Bio-prospecting for potential microbial biocontrol agents from composted waste materials. Acta Hortic. 2016;1112:335–42.
Article
Google Scholar
McQuilken MP, Whipps JM, Lynch JM. Effects of water extract of a composted manure straw mixture on the plant pathogen Botrytis cinerea. World J Microbiol Biotechnol. 1994;10:20–6.
Article
CAS
PubMed
Google Scholar
Mehta C, Palni U, Franke-Whittle I, Sharma A. Compost: its role, mechanism and impact on reducing soil-borne plant diseases. Waste Manag. 2014;34(3):607–22.
Article
CAS
PubMed
Google Scholar
Melero S, Porras JCR, Herencia JF, Madejon E. Chemical and biochemical properties in a silty loam soil under conventional and organic management. Soil Tillage Res. 2006;90:162–70. https://doi.org/10.1016/j.still.2005.08.016.
Article
Google Scholar
Melero-Vara JM, López-Herrera CJ, Prados-Ligero AM, Vela-Delgado MD, Navas-Becerra JA, Basallote-Ureba MJ. Effects of soil amendment with poultry manure on carnation Fusarium wilt in greenhouses in southwest Spain. Crop Prot. 2011;30:970–6.
Article
Google Scholar
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, De Santis TZ, Andersen GL, Bakker PA, Raaijmakers JM. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science. 2011;332:1097–100.
Article
CAS
PubMed
Google Scholar
Meng T, Wang Q, Abbasi P, Ma Y. Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils. Appl Microbiol Biotechnol. 2019;103:1497–509. https://doi.org/10.1007/s00253-018-9564-6.
Article
CAS
PubMed
Google Scholar
Mercado-Blanco J, Abrantes I, Barra Caracciolo A, Bevivino A, Ciancio A, Grenni P, Hrynkiewicz K, Kredics L, Proença DN. Belowground microbiota and the health of tree crops. Front Microbiol. 2018;9:1006. https://doi.org/10.3389/fmicb.2018.01006.
Article
PubMed
PubMed Central
Google Scholar
Mercado-Blanco J, Rodriguez-Jurado D, Hervàs A, Jimènez-Dìaz JM. Suppression of Verticillium dahliae wilt in olive planting stocks by root associated fluorescent Pseudomonas spp. Biol Control. 2004;30:474–86.
Article
Google Scholar
Meyer JR, Linderman R. Selective influence on populations of rhizosphere or rhizoplane bacteria and actinomycetes by mycorrhizas formed by Glomus fasciculatum. Soil Biol Biochem. 1986;18(2):191–6.
Article
Google Scholar
Morra L, Pagano L, Iovieno P, Baldantoni D, Alfani A. Soil and vegetable crop response to addition of different levels of municipal waste compost under Mediterranean greenhouse conditions. Agron Sustain Dev. 2010;30:701–9.
Article
Google Scholar
Murugan R, Kumar S. Influence of long-term fertilisation and crop rotation on changes in fungal and bacterial residues in a tropical rice-field soil. Biol Fertil Soils. 2013;49:847–56.
Article
Google Scholar
Nair A, Ngouajio M. Soil microbial biomass, functional microbial diversity, and nematode community structure as affected by cover crops and compost in an organic vegetable production system. Appl Soil Ecol. 2012;58:45–55.
Article
Google Scholar
Nannipieri P, Penton CR, Purahong W, Schloter M, et al. Recommendations for soil microbiome analyses. Biol Fertil Soils. 2019;55:765–6.
Article
CAS
Google Scholar
Nayyar A, Hamel C, Lafond G, Gossen BD, Hanson K, Germida J. Soil microbial quality associated with yield reduction in continuous-pea. Appl Soil Ecol. 2009;43:115–21. https://doi.org/10.1016/j.apsoil.2009.06.008.
Article
Google Scholar
Neeraj Singh K. Organic amendments to soil inoculated arbuscular mycorrhizal fungi and Pseudomonas fluorescens treatments reduce the development of root-rot disease and enhance the yield of Phaseolus vulgaris L. Eur J Soil Biol. 2011;47:288–95.
Article
Google Scholar
Ng EL, Bandow C, Proença DN, Santos S, Guilherme R, Morais PV, et al. Does altered rainfall regime change pesticide effects in soil? A terrestrial model ecosystem study from Mediterranean Portugal on the effects of pyrimethanil to soil microbial communities under extremes in rainfall. Appl Soil Ecol. 2014;84:245–53. https://doi.org/10.1016/j.apsoil.2014.08.006.
Article
Google Scholar
Nguyen NV, Kim YY, Oh KT, Jung WJ, Park RD. Antifungal activity of chitinases from Trichoderma aureoviride DY-59 and Rhizopus microsporus VS-9. Curr Microbiol. 2008;56:28–32.
Article
CAS
PubMed
Google Scholar
Noble R, Coventry E. Suppression of soil-borne plant diseases with composts: a review. Biocontrol Sci Technol. 2005;15:3–20. https://doi.org/10.1080/09583150400015904.
Article
Google Scholar
O’Donnell AG, Colvan SR, Malosso E. Twenty years of molecular analysis of bacterial communities in soils and what have we learned about function? In: Bardgett RD, Usher MB, Hopkins DW, editors. Biological diversity and function in soils. New York: Cambridge University Press; 2005. p. 44–73.
Chapter
Google Scholar
Ou Y, Penton CR, Geisen S, Shen Z, Sun Y, Lv N, Wang B, Ruan Y, Xiong W, Li R, Shen Q. Deciphering underlying drivers of disease suppressiveness against pathogenic Fusarium oxysporum. Front Microbiol. 2019;10:2535. https://doi.org/10.3389/fmicb.2019.02535.
Article
PubMed
PubMed Central
Google Scholar
Palaniyandi SA, Yang SH, Zhang L, Suh JW. Effects of actinobacteria on plant disease suppression and growth promotion. Appl Microbiol Biotechnol. 2013;97:9621–36.
Article
CAS
PubMed
Google Scholar
Pane C, Celano G, Piccolo A, Villecco D, Spaccini R, Palese AM, Zaccardelli M. Effects of on-farm composted tomato residues on soil biological activity and yields in a tomato cropping system. Chem Biol Technol Agric. 2015. https://doi.org/10.1186/s40538-014-0026-9.
Article
Google Scholar
Pane C, Piccolo A, Spaccini R, Celano G, Villecco D, Zaccardelli M. Agricultural waste-based composts exhibiting suppressivity to diseases caused by the phytopathogenic soil-borne fungi Rhizoctonia solani and Sclerotinia minor. Appl Soil Ecol. 2013;65:43–51.
Article
Google Scholar
Pérez-Piqueres A, Edel-Hermann W, Alabouvette C, Steinberg C. Response of soil microbial communities to compost amendments. Soil Biol Biochem. 2006;38:460–70.
Article
CAS
Google Scholar
Pharand B, Carisse O, Benhamou N. Cytological aspects of compost-mediated induced resistance against fusarium crown and root rot in tomato. Phytopathology. 2002;92(4):424–38.
Article
PubMed
Google Scholar
Porras-Alfaro A, Liu K-L, Kuske CR, Xie G. From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition. Appl Environ Microbiol. 2014;80:829–40. https://doi.org/10.1128/AEM.02894-13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Postma J, Schilder MT, Bloem J, van Leeumen-Haagsma WK. Soil suppressiveness and functional diversity of the soil microflora in organic farming systems. Soil Biol Biochem. 2008;40:2394–406.
Article
CAS
Google Scholar
Proença DN, Francisco R, Kublik S, Schöler A, Vestergaard G, Schloter M, et al. The microbiome of endophytic, wood colonizing bacteria from pine trees as affected by pine wilt disease. Sci. Rep. 2017;7:4205. https://doi.org/10.1038/s41598-017-04141-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pugliese M, Liu BP, Gullino ML, Garibaldi A. Selection of antagonists from compost to control soil-borne pathogens. J Plant Dis Prot. 2008;115:220–8.
Article
Google Scholar
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. Accurate determination of microbial diversity from 454-pyrosequencing data. Nat Methods. 2009;6:639–41.
Article
CAS
PubMed
Google Scholar
Raaijmakers JM, Leeman M, Van Oorschot MMP, Van der Sluis I, Schippers B, Bakker PAHM. Dose–response relationships in biological control of Fusarium wilt of radish by Pseudomonas spp. Phytopathology. 1995;85:1075–81.
Article
Google Scholar
Ruano-Rosa D, Mercado-Blanco J. Combining biocontrol agents and organics amendments to manage soil-borne phytopathogens. In: Meghvansi MK, Varma A (Eds.) Organic amendments and soil suppressiveness in plant disease management. 2015, pp. 457–478. ISSN 1613-3382, ISSN 2196-4831 (electronic), ISBN 978-3-319-23074-0, ISBN 978-3-319-23075-7 (eBook). Springer International Publishing Switzerland. http://doi.org/10.1007/978-3-319-23075-7.
Ryu C-M, Hu C-H, Locy RD, Kloepper JW. Study of mechanisms for plant growth promotion elicited by rhizobacteria in Arabidopsis thaliana. Plant Soil. 2005;268(1):285–92.
Article
CAS
Google Scholar
Santos I, Bettiol W. Effect of sewage sludge on the rot and seedling damping-off of bean plants caused by Sclerotium rolfsii. Crop Prot. 2003;22:1093–7.
Article
Google Scholar
Santos JA, Nuñes LAPL, Melo WJ, Araujo ASF. Tannery sludge compost amendment rates on soil microbial biomass of two different soils. Eur J Soil Biol. 2011;47:146–51.
Article
Google Scholar
Scheuerell SJ, Sullivan DM, Mahaffee WF. Suppression of seedling damping-off caused by Pythium ultimum, P irregulare and Rhizoctonia solani in container media amended with a diverse range of Pacific Northwest compost sources. Phytopathology. 2005;95:306–15.
Article
PubMed
Google Scholar
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA. 2012;109(16):6241–6.
Article
PubMed
PubMed Central
Google Scholar
Scotti R, Pane C, Spaccini R, Palese AM, Piccolo A, Celano G, Zaccardelli M. On-farm compost: a useful tool to improve soil quality under intensive farming systems. Appl Soil Ecol. 2016;107:13–23.
Article
Google Scholar
Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High throughput sequencing for detection of foodborne pathogens. Front. Microbiol. 2017;8:2029. https://doi.org/10.3389/fmicb.2017.02029.
Article
PubMed
PubMed Central
Google Scholar
Shekhar N, Bhattacharya D, Kumar D, Gupta RK. Biocontrol of wood-rotting fungi with Streptomyces violaceus-Niger XL-2. Can J Microbiol. 2006;52:805–8.
Article
CAS
PubMed
Google Scholar
Shen Z, Xue C, Penton CR, Thomashow LS, Zhang N, Wang B, Ruan Y, Li R, Shen Q. Suppression of banana Panama disease induced by soil microbiome reconstruction through an integrated agricultural strategy. Soil Biol Biochem. 2019;128:164–74. https://doi.org/10.1016/J.SOILBIO.2018.10.016.
Article
CAS
Google Scholar
Shen Z, Xue C, Taylor PWJ, Ou Y, Wang B, Zhao Y, Ruan Y, Li R, Shen Q. Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome. Biol Fert Soils. 2018;54:793–806. https://doi.org/10.1007/s00374-018-1303-8.
Article
CAS
Google Scholar
Shi L, Du N, Shu S, Sun J, Li S, Guo S. Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community. Sci Rep. 2017;7:412–34.
Article
CAS
Google Scholar
Siddiqui Y, Naidu Y, Ali A (2015) Bio-intensive management of fungal diseases of fruits and vegetables utilizating compost and compost teas. In: Meghvansi MK, Varma A (Eds.) Organic amendments and soil suppressiveness in plant disease management 2015, pp. 307–330. Springer Series Soil biology, Vol. 46, ISSN 1613-3382, ISSN 2196-4831 (electronic), ISBN 978-3-319-23074-0, ISBN 978-3-319-23075-7 (eBook). Springer International Publishing Switzerland. http://doi.org/10.1007/978-3-319-23075-7.
Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, et al. High-resolution phylogenetic microbial community profiling. ISME J. 2016;10:2020–32. https://doi.org/10.1038/ismej.2015.249.
Article
PubMed
PubMed Central
Google Scholar
Slatko BE, Garner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol. 2018;122:e59. https://doi.org/10.1002/cpmb.59.
Article
PubMed
PubMed Central
Google Scholar
Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, et al. Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing. PLoS ONE. 2018;13(4):e0195345. https://doi.org/10.1371/journal.pone.0195345.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suàrez-Estrella F, Vargas-Garcìa C, Lopez MJ, Capel C, Moreno J. Antagonistic activity of bacteria and fungi from horticultural compost against Fusarium oxysporum f sp melonis. Crop Prot. 2007;26:46–53.
Article
Google Scholar
Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, et al. Bacterial flora-typing with targeted, chip-based Pyrosequencing. BMC Microbiol. 2007;7(1):108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tejada M, Hernandez MT, Garcia C. Soil restoration using composted plant residues: effects on soil properties. Soil Tillage Res. 2009;102:109–17.
Article
Google Scholar
Termorshuizen AJ, Jeger MJ. Strategies of soil-borne plant pathogenic fungi in relation to disease suppression. Fungal Ecol. 2008;1:108–14.
Article
Google Scholar
Termorshuizen AJ, van Rijn E, van der Gaag DJ, Alabouvette C, Chen Y, Lagerlof J, Malandrakis AA, Paplomatas EJ, Ramert B, Ryckeboer J, Steinberg C, Zmora-Nahum S. Suppressiveness of 18 composts against 7 pathosystems: variability in pathogen response. Soil Biol Biochem. 2006;38:2461–77.
Article
CAS
Google Scholar
Tiemann LK, Grandy AS, Atkinson EE, Marin-Spiotta E, McDaniel MD. Crop rotational diversity enhances belowground communities and functions in an agroecosystem. Ecol Lett. 2015;18:761–71.
Article
CAS
PubMed
Google Scholar
Timmusk S, Nicander B, Granhall U, Tillberg E. Cytokinin production by Paenibacillus polymyxa. Soil Biol Biochem. 1999;31(13):1847–52.
Article
CAS
Google Scholar
Tiquia SM. Microbial community dynamics in manure composts based on 16S and 18S rDNA T-RFLP profiles. Environ Technol. 2005;26(10):1101–13.
Article
CAS
PubMed
Google Scholar
Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, et al. Core microbiomes for sustainable agroecosystems. Nat Plants. 2018;4:247–57. https://doi.org/10.1038/s41477-018-0139-4.
Article
PubMed
Google Scholar
Torres IF, Bastida F, Hernández T, García C. The effects of fresh and stabilized pruning wastes on the biomass, structure and activity of the soil microbial community in a semiarid climate. Appl Soil Ecol. 2015;89:1–9.
Article
Google Scholar
Trillas MI, Casanova E, Cotxarrera L, Ordovàs J, Borrero C, Avilés M. Composts from agricultural waste and the Trichoderma asperellum strain T-34 suppress Rhizoctonia solani in cucumber seedlings. Biol Control. 2006;39:32–8.
Article
Google Scholar
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37–43. https://doi.org/10.1038/nature02340.
Article
CAS
PubMed
Google Scholar
Val-Moraes SP. 2015. Suppressiveness in different soils for Rhizoctonia solani. In: Meghvansi MK, Varma A (Eds.) Organic amendments and soil suppressiveness in plant disease management 2015, pp. 175–186. Springer Series Soil biology, Vol. 46, ISSN 1613-3382, ISSN 2196-4831 (electronic), ISBN 978-3-319-23074-0, ISBN 978-3-319-23075-7 (eBook). Springer International Publishing Switzerland. http://doi.org/10.1007/978-3-319-23075-7.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304(5667):66–74. https://doi.org/10.1126/science.1093857.
Article
PubMed
Google Scholar
Vinale F, Flematti G, Sivasithamparam K, Lorito M, Marra R, Skelton BW, Ghisalberti EL. Harzianic acid, an antifungal and plant growth promoting metabolite from Trichoderma harzianum. J Natl Prod. 2009;72(11):2032–5.
Article
CAS
Google Scholar
Vitullo D, Altieri R, Esposito A, Nigro F, Ferrara M, Alfano G, Ranalli G, De Cicco V, Lima G. Suppressive biomasses and antagonist bacteria for an eco-compatible control of Verticillium dahliae on nursery-grown olive plants. Int J Environ Sci Technol. 2013;10:209–20.
Article
CAS
Google Scholar
von der Weid I, Duarte GF, van Elsas JD, Seldin L. Paenibacillus brasilensis sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil. Int J Syst Evol Microbiol. 2002;52(6):2147–53.
PubMed
Google Scholar
Wan TT, Zhao HH, Wang W. Effect of biocontrol agent Bacillus amyloliquefaciens SN16-1 and plant pathogen Fusarium oxysporum on tomato rhizosphere bacterial community composition. Biol Control. 2017;112:1–9.
Article
Google Scholar
Wang B, Li R, Ruan Y, Ou Y, Zhao Y, Shen Q. Pineapple–banana rotation reduced the amount of Fusarium oxysporum more than maize–banana rotation mainly through modulating fungal communities. Soil Biol Biochem. 2015;86:77–86.
Article
CAS
Google Scholar
Wang S, Liang Y, Shen T, Yang H, Shen B. Biological characteristics of Streptomyces albospinus CT205 and its biocontrol potential against cucumber Fusarium wilt. Biocontrol Sci. Technol. 2016;26(7):951–63.
Article
Google Scholar
Wang Y, Qian PY. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS ONE. 2009;4:10.
PubMed Central
Google Scholar
Wang B, Yuan J, Zhang J, Shen Z, Zhang M, Li R, Ruan Y, Shen Q. Effects of novel bioorganic fertilizer produced by Bacillus amyloliquefaciens W19 on antagonism of Fusarium wilt of banana. Biol Fertil Soils. 2013;49:435–46.
Article
Google Scholar
Wei G, Kloepper JW, Tuzun S. Induction of systemic resistance of cucumber to Colletotrichum orbiculare by select strains of plant growth-promoting rhizobacteria. Phytopathology. 1991;81(11):1508–12.
Article
Google Scholar
Wei Z, Yang X, Yin S, Shen Q, Ran W, Xu Y. Efficacy of Bacillus-fortified organic fertiliser in controlling bacterial wilt of tomato in the field. Appl Soil Ecol. 2011;48:152–9.
Article
Google Scholar
Weller DM, Raaijmakers JM, Gardener BM, Thomashow LS. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol. 2002;40:309–48.
Article
CAS
PubMed
Google Scholar
White TJ, Bruns TD, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfauld DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. San Diego (USA): Academic Press; 1990. p. 315–22.
Google Scholar
Wu B, Wang X, Yang L, Yang H, Zeng H, Qiu Y, Wang C, Yu J, Li J, Xu D, He Z, Chen S. Effects of Bacillus amyloliquefaciens ZM9 on bacterial wilt and rhizosphere microbial communities of tobacco. Appl Soil Ecol. 2016;103:1–12.
Article
Google Scholar
Wu HS, Yang XN, Fan JQ, Miao WG, Ling N, Xu YC, Huang QW, Shen Q. Suppression of Fusarium wilt of watermelon by a bio-organic fertilizer containing combinations of antagonistic microorganisms. Biocontrol. 2009;54:287–300.
Article
Google Scholar
Xiong W, Li R, Ren Y, Liu C, Zhao Q, Wu H, Jousset A, Shen Q. Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease. Soil Biol Biochem. 2017;107:198–207.
Article
CAS
Google Scholar
Xu LH, Ravnskov S, Larsen J, Nilsson RH, Nicolaisen M. Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing. Soil Biol Biochem. 2012;46:26–32.
Article
CAS
Google Scholar
Xuan DT, Guong VT, Rosling A, Alstrom S, Chai BL, Hogberg N. Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa. Biol Fertil Soils. 2012;48:217–25.
Article
Google Scholar
Yamada KD, Tomii K, Katoh K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics. 2016;32:3246–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yadav RS, Panwar J, Meena HN, Thirumalaisamy PP, Meena RL. Developing disease-suppressive soil through agronomic management. In: Meghvansi MK, Varma A (Eds.) Organic amendments and soil suppressiveness in plant disease management 2015, pp. 61–94. Springer Series Soil biology, Vol. 46, ISSN 1613-3382, ISSN 2196-4831 (electronic), ISBN 978-3-319-23074-0, ISBN 978-3-319-23075-7 (eBook). Springer International Publishing Switzerland. http://doi.org/10.1007/978-3-319-23075-7.
Yang X, Chen L, Yong X, Shen Q. Formulations can affect rhizosphere colonization and biocontrol efficiency of Trichoderma harzianum SQR-T037 against Fusarium wilt of cucumbers. Biol Fertil Soils. 2011;47:239–48.
Article
Google Scholar
Yang W, Jing X, Guan Y, Zhai C, Wang T, Shi D, Sun W, Gu S. Response of fungal communities and co-occurrence network patterns to compost amendment in black soil of Northeast China. Front Microbiol. 2019;10:1562. https://doi.org/10.3389/fmicb.2019.01562.
Article
PubMed
PubMed Central
Google Scholar
Yang X, Noyes NR, Doster E, Martin JN, Linke LM, Magnuson RJ, Yang H, Geornaras I, Woerner DR, Jones KL, Ruiz J, Boucher C, Morley PS, Belk KE. Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain. Appl Environ Microbiol. 2016;82:2433–43. https://doi.org/10.1128/AEM.00078-16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yin C, Jones KL, Peterson DE, Garrett KA, Hulbert SH, Paulitz TC. Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biol Biochem. 2010;42:2111–8.
Article
CAS
Google Scholar
Zaccardelli M, de Nicola F, Villecco D, Scotti R. The development and suppressive activity of soil microbial communities under compost amendment. J Soil Sci Plant Nutr. 2013;13:730–42.
Google Scholar
Zhang M, Li R, Cao L, Shi J, Liu H, Huang Y, Shen Q. Algal sludge from Taihu Lake can be utilized to create novel PGPR-containing bio-organic fertilizers. J Environ Management. 2014;132:230–6. https://doi.org/10.1016/J.JENVMAN.2013.10.031.
Article
Google Scholar
Zhao Q, Dong C, Yang X, Mei X, Ran W, Shen Q, Xu Y. Biocontrol of Fusarium wilt disease for Cucumis melo melon using bio-organic fertilizer. Appl Soil Ecol. 2011;47:67–75.
Article
Google Scholar
Zhao N, Li R, Xin K, Zhao Y, Ruan Y, Fu C. Effects of different solanaceae crop rotations on the soil culturable microbes in an orchard with serious fusarium wilt disease. Chin J Tropical Crops. 2014;35:1469–74.
Google Scholar
Zhao Q, Xiong W, Xing Y, Sun Y, Lin X, Dong Y. Long-term coffee monoculture alters soil chemical properties and microbial communities. Sci Rep. 2018;8:6116. https://doi.org/10.1038/s41598-018-24537-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhen Z, Liu HT, Wang N, Guo LY, Meng J, Ding N, Wu GL, Jiang GM. Effects of manure compost application on soil microbial community diversity and soil microenvironments in a temperate cropland in China. PLoS ONE. 2014;9:e108555.
Article
CAS
PubMed
PubMed Central
Google Scholar