van den Hoogen J, Geisen S, Routh D. Soil nematode abundance and functional group composition at a global scale. Nature 2019;572:194–98.
Google Scholar
Yeates GW, Bongers T, Degoede RGM, Freckman DW, Georgieva SS. Feeding habits in soil nematode families and genera – an outline for soil ecologists. J Nematol. 1993;25:315–31.
Google Scholar
Nicol JM, Turner SJ, Coyne DL, Nijs Ld, Hockland S, Maafi ZT. Current nematode threats to world agriculture. In: Jones J, Gheysen G, Fenoll C, editors. Genomics and Molecular Genetics of Plant-Nematode Interactions. Dordrecht: Springer; 2011. p. 21–43.
Decraemer W, Hunt D. Structure and Classification. In: R. N. Perry, M. Moens, Eds. Plant Nematology. CABI, Wallingford, Oxfordshire, UK and Boston, USA, 2005, pp. 26–27.
Fleming TR, Maule AG, Fleming CC. Chemosensory responses of plant parasitic nematodes to selected phytochemicals reveal long-term habituation traits. J Nematol. 2017;49:462–71.
Google Scholar
Murungi LK, Kirwa H, Coyne D, Teal PEA, Beck JJ, Torto B. Identification of key root volatiles signaling preference of tomato over spinach by the root knot nematode Meloidogyne incognita. J AgricFood Chem. 2018;66:7328–36.
Google Scholar
Wang CL, Masler EP, Rogers ST. Responses of Heterodera glycines and Meloidogyne incognita infective juveniles to root tissues, root exudates, and root extracts from three plant species. Plant Dis. 2018;102:1733–40.
Google Scholar
Sikder MM, Vestergård M. Impacts of root metabolites on soil nematodes. Front Plant Sci. 2020;10:1792.
Google Scholar
van Dam NM, Tytgat TOG, Kirkegaard JA. Root and shoot glucosinolates: A comparison of their diversity, function and interactions in natural and managed ecosystems. Phytochem Rev. 2009;8:171–86.
Google Scholar
Bressan M, Roncato MA, Bellvert F, et al. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J. 2009;3:1243–57.
Google Scholar
Mucha S, Heinzlmeir S, Kriechbaumer V, Strickland B, Kirchhelle C, Choudhary M, et al. The formation of a camalexin biosynthetic metabolon. Plant Cell. 2019;31:2697–710.
Google Scholar
Kettles GJ, Drurey C, Schoonbeek HJ, Maule AJ, Hogenhout SA. Resistance of Arabidopsis thaliana to the green peach aphid, Myzus persicae, involves camalexin and is regulated by microRNAs. N. Phytol. 2013;198:1178–90.
Google Scholar
Tsuji J, Jackson EP, Gage DA, Hammerschmidt R, Somerville SC. Phytoalexin accumulation in Arabidopsis thaliana during the hypersensitive reaction to Pseudomonas syringae pv. syringae. Plant Physiol. 1992;98:1304–9.
Google Scholar
Thomma BPHJ, Nelissen I, Eggermont K, Broekaert WF. Deficiency in phytoalexin production causes enhanced susceptibility of Arabidopsis thaliana to the fungus Alternaria brassicicola. Plant J 1999;19:163–71.
Google Scholar
Teixeira MA, Wei LH, Kaloshian I. Root-knot nematodes induce pattern-triggered immunity in Arabidopsis thaliana roots. N Phytol. 2016;211:276–87.
Google Scholar
Shah SJ, Anjam MS, Mendy B, Anwer MA, Habash SS, Lozano-Torres JL, et al. Damage-associated responses of the host contribute to defence against cyst nematodes but not root-knot nematodes. J Exp Bot. 2017;68:5949–60.
Google Scholar
Ali MA, Wieczorek K, Kreil DP, Bohlmann H. The beet cyst nematode Heterodera schachtii modulates the expression of WRKY transcription factors in syncytia to favour its development in Arabidopsis roots. PLoS One. 2014;9:e102360.
Google Scholar
Lazzeri L, Curto G, Leoni O, Dallavalle E. Effects of glucosinolates and their enzymatic hydrolysis products via myrosinase on the root-knot nematode Meloidogyne incognita (Kofoid et White) Chitw. J Agric Food Chem. 2004;52:6703–07.
Google Scholar
Avato P, D’Addabbo T, Leonetti P, Argentieri MP. Nematicidal potential of Brassicaceae. Phytochem Rev. 2013;12:791–802.
Google Scholar
Mathesius U. Flavonoid functions in plants and their interactions with other organisms. Plants (Basel) 2018;7:30.
Weston LA, Mathesius U. Flavonoids: Their structure, biosynthesis and role in the rhizosphere, including allelopathy. J Chem Ecol. 2013;39:283–97.
Google Scholar
Badri DV, Loyola-Vargas VM, Broeckling CD, De-la-Pena C, Jasinski M, Santelia D, et al. Altered profile of secondary metabolites in the root exudates of Arabidopsis ATP-binding cassette transporter mutants. Plant Physiol. 2008;146:762–71.
Google Scholar
Cesco S, Neumann G, Tomasi N, Pinton R, Weisskopf L. Release of plant-borne flavonoids into the rhizosphere and their role in plant nutrition. Plant Soil. 2010;329:1–25.
Google Scholar
Drewnowski A, Gomez-Carneros C. Bitter taste, phytonutrients, and the consumer: A review. Am J Clin Nutr. 2000;72:1424–35.
Google Scholar
Chin S, Behm CA, Mathesius U. Functions of flavonoids in plant-nematode interactions. Plants (Basel) 2018;7:1–17.
Kaplan DT, Keen NT, Thomason IJ. Association of glyceollin with the incompatible response of soybean roots to Meloidogyne incognita. Physiol Plant Pathol. 1980;16:309–18.
Google Scholar
Aoudia H, Ntalli N, Aissani N, Yahiaoui-Zaidi R, Caboni P. Nematotoxic phenolic compounds from Melia azedarach against Meloidogyne incognita. J AgricFood Chem. 2012;60:11675–80.
Google Scholar
Kennedy MJ, Niblack TL, Krishnan HB. Infection by Heterodera glycines elevates isoflavonoid production and influences soybean nodulation. J Nematol. 1999;31:341–47.
Google Scholar
Collingborn FMB, Gowen SR, Mueller-Harvey I. Investigations into the biochemical basis for nematode resistance in roots of three Musa cultivars in response to Radopholus similis infection. J Agric Food Chem. 2000;48:5297–301.
Google Scholar
Cook R, Tiller SA, Mizen KA, Edwards R. Isoflavonoid metabolism in resistant and susceptible cultivars of white clover infected with the stem nematode Ditylenchus dipsaci. J Plant Physiol. 1995;146:348–54.
Google Scholar
Kirwa HK, Murungi LK, Beck JJ, Torto B. Elicitation of differential responses in the root-knot nematode Meloidogyne incognita to tomato root exudate cytokinin, flavonoids, and alkaloids. J AgricFood Chem. 2018;66:11291–300.
Google Scholar
Wuyts N, Swennen R, De, Waele D. Effects of plant phenylpropanoid pathway products and selected terpenoids and alkaloids on the behaviour of the plant-parasitic nematodes Radopholus similis. Pratylenchus penetrans Meloidogyne Incogn Nematol. 2006;8:89–101.
Google Scholar
Hartwig UA, Joseph CM, Phillips DA. Flavonoids released naturally from alfalfa seeds enhance growth rate of Rhizobium meliloti. Plant Physiol. 1991;95:797–803.
Google Scholar
Hassan S, Mathesius U. The role of flavonoids in root-rhizosphere signalling: Opportunities and challenges for improving plant-microbe interactions. J Exp Bot. 2012;63:3429–44.
Google Scholar
Kudjordjie EN, Sapkota R, Nicolaisen M. Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites. PLoS One. 2021;10:e0259171.
Rønn R, Vestergård M, Ekelund F. Interactions between bacteria, protozoa and nematodes in soil. Acta Protozool. 2012;51:223–35.
Thakur MP, Geisen S. Trophic regulations of the soil microbiome. Trends Microbiol. 2019;27:771–80.
Google Scholar
Elhady A, Gine A, Topalovic O, Jacquiod S, Sorensen SJ, Sorribas FJ, et al. Microbiomes associated with infective stages of root-knot and lesion nematodes in soil. PLoS One. 2017;12:e0177145.
Google Scholar
Toju H, Tanaka Y. Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes. R Soc Open Sci. 2019;6:181693.
Google Scholar
Topalović O, Bredenbruch S, Schleker ASS, Heuer H. Microbes attaching to endoparasitic phytonematodes in soil trigger plant defense upon root penetration by the nematode. Front Plant Sci 2020;11:138.
Google Scholar
Schaad NW, Walker JT. The use of density-gradient centrifugation for the purification of eggs of Meloidogyne spp. J Nematol. 1975;7:203–04.
Google Scholar
Hooper DJ, Hallmann J, Subbotin SA. Methods for extraction, processing and detection of plant and soil nematodes. In: Luc M, Sikora RA, Bridge J, editors. Plant parasitic nematodes in subtropical and tropical agriculture. Second ed. Wallingford, UK: CABI Publishing; 2005. p. 53.
Topalovic O, Elhady A, Hallmann J, Richert-Poggeler KR, Heuer H. Bacteria isolated from the cuticle of plant-parasitic nematodes attached to and antagonized the root-knot nematode Meloidogyne hapla. Sci Rep. 2019;9:11477.
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2019.
Porazinska DL, Giblin-Davis RM, Faller L, Farmerie W, Kanzaki N, Morris K, et al. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol Ecol Resour. 2009;9:1439–50.
Google Scholar
Sapkota R, Nicolaisen M. High-throughput sequencing of nematode communities from total soil DNA extractions. BMC Ecol. 2015;15:3.
Google Scholar
Sikder MM, Vestergård M, Sapkota R, Kyndt T, Nicolaisen M. Evaluation of metabarcoding primers for analysis of soil nematode communities. Diversity (Basel) 2020;12:388.
Google Scholar
Ihrmark K, Bodeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, et al. New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol. 2012;82:666–77.
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Google Scholar
Sapkota R, Skantar AM, Nicolaisen M. A TaqMan real-time PCR assay for detection of Meloidogyne hapla in root galls and in soil. Nematol. 2016;18:147–54.
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: A versatile open source tool for metagenomics. Peer J. 2016;4:e2584.
Google Scholar
Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:914–19.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D6.
Google Scholar
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42:D643–D8.
Google Scholar
UNITE. UNITE QIIME release for Fungi [Internet]. UNITE Community. 2020.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–36.
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
Google Scholar
Oksanen J, Blanchet FG, Kindt R, Friendly M, Legendre P, McGlinn D, et al. Vegan: Community Ecology Package. Ordination methods, diversity analysis and other functions for community and vegetation ecologists. R Package Version 2.5-5 ed: The Comprehensive R Archive Network; 2019.
Love MI, Huber W, Anders S. Moderated estimation of fold change anddispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics 2014;30:3123–24.
Google Scholar
Kudjordjie EN, Sapkota R, Steffensen SK, Fomsgaard IS, Nicolaisen M. Maize synthesized benzoxazinoids affect the host associated microbiome. Microbiome 2019;7:59.
Google Scholar
McCarthy DJ, Chen YS, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288–97.
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139–40.
Google Scholar
Frerigmann H, Gigolashvili T. MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana. Mol Plant. 2014;7:814–28.
Google Scholar
Schulz E, Tohge T, Zuther E, Fernie AR, Hincha DK. Flavonoids are determinants of freezing tolerance and cold acclimation in Arabidopsis thaliana. Sci Rep. 2016;6:34027.
Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell. 2000;12:2383–94.
Google Scholar
Du SS, Zhang HM, Bai CQ, Wang CF, Liu QZ, Liu ZL, et al. Nematocidal flavone-C-glycosides against the root-knot nematode (Meloidogyne incognita) from Arisaema erubescens tubers. Molecules 2011;16:5079–86.
Google Scholar
Zhou DM, Feng H, Schuelke T, De Santiago A, Zhang QM, Zhang JF, et al. Rhizosphere microbiomes from root knot nematode non-infested plants suppress nematode Infection. Micro Ecol. 2019;78:470–81.
Google Scholar
Topalović O, Vestergård M. Can microorganisms assist the survival and parasitism of plant-parasitic nematodes? Trends Parasitol. 2021;37:947–58.
Google Scholar
De Mesel I, Derycke S, Moens T, Van der Gucht K, Vincx M, Swings J. Top-down impact of bacterivorous nematodes on the bacterial community structure: a microcosm study. Environ Microbiol. 2004;6:733–44.
Google Scholar
Adam M, Westphal A, Hallmann J, Heuer H. Specific microbial attachment to root knot nematodes in suppressive soil. Appl Environ Microbiol. 2014;80:2679–86.
Google Scholar
Ramyabharathi S, Sankari Meena K, Rajendran L, Karthikeyan G, Jonathan EI, Raguchander T. Biocontrol of wilt-nematode complex infecting gerbera by Bacillus subtilis under protected cultivation. Egypt J Biol Pest Co. 2018;28:21.
Jamal Q, Cho JY, Moon JH, Munir S, Anees M, Kim KY. Identification for the first time of cyclo (D-Pro-L-Leu) produced by Bacillus amyloliquefaciens y1 as a nematocide for control of Meloidogyne incognita. Molecules 2017;22:1839.
Google Scholar
Moosavi MR, Zare R. Fungi as biological control agents of plant-parasitic nematodes. In: Mérillon J-M, Ramawat KG, editors. Plant Defence: Biological Control. Progress in Biological Control 22. 2nd Edition ed. Switzerland: Springer; 2020. p. 333–84.
Ashrafi S, Stadler M, Dababat AA, Richert-Poggeler KR, Finckh MR, Maier W. Monocillium gamsii sp nov and Monocillium bulbillosum: two nematode-associated fungi parasitising the eggs of Heterodera filipjevi. Mycokeys. 2017;27:21–38.
Nuaima RH, Ashrafi S, Maier W, Heuer H. Fungi isolated from cysts of the beet cyst nematode parasitized its eggs and counterbalanced root damages. J Pest Sci. 2021;94:563–72.
Iqbal M, Dubey M, McEwan K, Menzel U, Franko MA, Viketoft M, et al. Evaluation of Clonostachys rosea for control of plant parasitic nematodes in soil and in roots of carrot and wheat. Phytopathology 2018;108:52–59.
Google Scholar
DiLegge MJ, Manter DK, Vivanco JM. A novel approach to determine generalist nematophagous microbes reveals Mortierella globalpina as a new biocontrol agent against Meloidogyne spp. nematodes. Sci Rep. 2019;9:7521.
Google Scholar
Goswami J, Pandey RK, Tewari JP, Goswami BK. Management of root knot nematode on tomato through application of fungal antagonists, Acremonium strictum and Trichoderma harzianum. J Environ Sci Health. 2008;43:237–40.
Google Scholar
Chen Q, Peng D. Nematode chitin and application. In: Yang Q, Fukamizo T, editors. Targeting Chitin-containing Organisms. Advances in Experimental Medicine and Biology. 1142. Singapore: Springer; 2019. pp. 209–219.
Zhou WQ, Verma VC, Wheeler TA, Woodward JE, Starr JL, Sword GA. Tapping into the cotton fungal phytobiome for novel nematode biological control tools. Phytobiomes J 2020;4:19–26.
Alcazar R, von Reth M, Bautor J, Chae E, Weigel D, Koornneef M, et al. Analysis of a plant complex resistance gene locus underlying immune-related hybrid incompatibility and its occurrence in nature. PLoS Genet. 2014;10:e1004848.
Google Scholar
Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid. J Biol Chem. 2000;275:33712–17.
Google Scholar
Hull AK, Vij R, Celenza JL. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc Natl Acad Sci USA. 2000;97:2379–84.
Google Scholar
Zhao YD, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, et al. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. GenesDev. 2002;16:3100–12.
Google Scholar
Schlaeppi K, Bodenhausen N, Buchala A, Mauch F, Reymond P. The glutathione-deficient mutant pad2-1 accumulates lower amounts of glucosinolates and is more susceptible to the insect herbivore Spodoptera littoralis. Plant J. 2008;55:774–86.
Google Scholar
Schuhegger R, Nafisi M, Mansourova M, Petersen BL, et al. CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis. Plant Physiol. 2006;141:1248–54.
Google Scholar
Glawischnig E. The role of cytochrome P450 enzymes in the biosynthesis of camalexin. Biochem Soc Trans. 2006;34:1206–8.
Google Scholar
Haughn GW, Davin L, Giblin M, Underhill EW. Biochemical genetics of plant secondary metabolites in Arabidopsis thaliana: The glucosinolates. Plant Physiol. 1991;97:217–26.
Google Scholar
Kroymann J, Textor S, Tokuhisa JG, Falk KL, Bartram S, Gershenzon J, et al. A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway. Plant Physiol. 2001;127:1077–88.
Google Scholar
Textor S, de Kraker JW, Hause B, Gershenzon J, Tokuhisa JG. MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol. 2007;144:60–71.
Google Scholar
Barth C, Jander G. Arabidopsis myrosinases TGG1 and TGG2 have redundant function in glucosinolate breakdown and insect defense. Plant J. 2006;46:549–62.
Google Scholar
Dong XY, Braun EL, Grotewold E. Functional conservation of plant secondary metabolic enzymes revealed by complementation of Arabidopsis flavonoid mutants with maize genes. Plant Physiol. 2001;127:46–57.
Google Scholar
Peer WA, Brown DE, Tague BW, Muday GK, Taiz L, Murphy AS. Flavonoid accumulation patterns of transparent testa mutants of Arabidopsis. Plant Physiol. 2001;126:536–48.
Google Scholar
Gonzalez A, Brown M, Hatlestad G, Akhavan N, Smith T, Hembd A, et al. TTG2 controls the developmental regulation of seed coat tannins in Arabidopsis by regulating vacuolar transport steps in the proanthocyanidin pathway. Dev Biol. 2016;419:54–63.
Google Scholar
Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, et al. The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell. 1999;11:1337–49.
Google Scholar
Source: Ecology - nature.com
