Abstract
Plant-parasitic nematodes are a serious threat to global agriculture. Although the control of plant-parasitic nematodes mainly depends on chemical methods, the need for environmentally friendly alternative approaches for the control of nematodes has been realized in the recent past. In order to find alternative methods to control plant-parasitic nematodes, endophytic microorganisms have been extensively studied in various plant species. These studies have used an array of molecular techniques from simple PCR to next-generation sequencing approaches. Metagenomic studies of endophytes are believed to be the most advanced and effective techniques to disentangle and understand interactions between endophytes and plant-parasitic nematodes.
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Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud M-C, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso M-N, Schiex T, Smant G, Weissenbach J, Wincker P (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26:909–915
Abdelfattah A, Wisniewski M, Nicosia MGLD, Cacciola SO, Schena L (2016) Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs. PLoS One 11(8):e0160470
Agbenin NO, Emechebe AM, Marley PS, Akpa AD (2005) Evaluation of nematicidal action of some botanicals on Meloidogyne incognita in vivo and in vitro. J Agric Rural Dev Trop Subtrop 106(1):29–39
Ahrén D, Tunlid A (2003) Evolution of parasitism in nematode-trapping fungi. J Nematol 35(2):194–197
Akinsanya MA, Goh JK, Lim SP, Ting ASY (2015) Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genom Data 6:159–163
Albrectsen BR, Siddique AB, Decker VHG, Unterseher M, Robinson KM (2018) Both plant genotype and herbivory shape aspen endophyte communities. Oecologia 187(2):535–545
Al-Hazmi AS, TariqJaveed M (2016) Effects of different inoculum densities of Trichoderma harzianum and Trichoderma viride against Meloidogyne javanica on tomato. Saudi J Biol Sci 23(2):288–292
Aly AH, Debbab A, Kjer J, Proksch P (2010) Fungal endophytes from higher plants: a prolific source of phytochemicals and other bioactive natural products. Fungal Divers 41(1):1–16
Aly AH, Debbab A, Proksch P (2011) Fungal endophytes: unique plant inhabitants with great promises. Appl Microbiol Biotechnol 90(6):1829–1845
Anke H, Stadler M, Mayer A, Sterner O (1995) Secondary metabolites with nematicidal and antimicrobial activity from nematophagous fungi and Ascomycetes. Can J Bot 73(S1):932–939
Anon (2012) National food security—the wheat initiative—an international research initiative for wheat improvement. In: Second global conference on agricultural research for development, Punta del Este, Uruguay
Ansari RA, Khan TA (2012a) Parasitic association of root-knot nematode, Meloidogyne incognita on guava. e-J Sci Technol 5:65–67
Ansari RA, Khan TA (2012b) Diversity and community structure of phytonematodes associated with guava in and around Aligarh, Uttar Pradesh, India. Trends Biosci 5(3):202–204
Ansari RA, Mahmood I (2017a) Optimization of organic and bio-organic fertilizers on soil properties and growth of pigeon pea. Sci Hortic 226:1–9
Ansari RA, Mahmood I (2017b) Determination of disease incidence caused by Meloidogyne spp. and or Fusarium udum on pigeonpea in Aligarh district: a survey. Trends Biosci 10(24):5239–5243
Ansari RA, Mahmood I (2019a) Plant health under biotic stress: volume 2: microbial interactions. Springer, Singapore. https://doi.org/10.1007/978-981-13-6040-4. Accessed 20 May 2019
Ansari RA, Mahmood I (2019b) Plant health under biotic stress: volume 1: organic strategies. Springer, Singapore. https://doi.org/10.1007/978-981-13-6043-5. Accessed 20 May 2019
Ansari RA, Mahmood I, Rizvi R, Sumbul A (2017a) Siderophores: augmentation of soil health and crop productivity. In: Kumar V, Kumar M, Sharma S, Prasad R (eds) Probiotics in agroecosystem. Springer, Singapore, pp 291–312
Ansari RA, Rizvi R, Sumbul A, Mahmood I (2017b) PGPR: current vogue in sustainable crop production. In: Kumar V, Kumar M, Sharma S, Prasad R (eds) Probiotics and plant health. Springer, Singapore, pp 455–472
Ansari RA, Sumbul A, Rizvi R, Mahmood I (2019) Organic soil amendments: potential tool for soil and plant health management. In: Ansari RA, Mahmood I (eds) Plant health under biotic stress. Springer, Singapore, pp 1–35
Arnold AE, Mejía LC, Kyllo D, Rojas EI, Maynard Z, Robbins N, Herre EA (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci 100(26):15649
Arnold AE, Henk DA, Eells RL, Lutzoni F, Vilgalys R (2007) Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99(2):185–206
Aschehoug ET, Metlen KL, Callaway RM, Newcombe G (2012) Fungal endophytes directly increase the competitive effects of an invasive forb. Ecology 93(1):3–8
Bacon CW, Glenn AE, Yates IE (2008) Fusarium verticillioides: managing the endophytic association with maize for reduced fumonisins accumulation. Toxin Rev 27(3–4):411–446
Bae H, Roberts DP, Lim H-S, Strem MD, Park S-C, Ryu C-M, Melnick RL, Bailey BA (2011) Endophytic Trichoderma isolates from tropical environments delay disease onset and induce resistance against Phytophthora capsici in hot pepper using multiple mechanisms. Mol Plant-Microbe Interact 24(3):336–351
Baldani J, Caruso L, Baldani VLD, Goi SR, Döbereiner J (1997) Recent advances in BNF with non-legume plants. Soil Biol Biochem 29(5–6):911–922
Beijerinck MW (1888) Cultur des Bacillus radicicola aus den Knöllchen. Bot Ztg 46:740–750
Bergna A, Cernava T, Rändler M, Grosch R, Zachow C, Berg G (2019) Tomato seeds preferably transmit plant beneficial endophytes. Phytobiomes 2(4):183–193
Bernard GC, Egnin M, Bonsi C (2017) The impact of plant-parasitic nematodes on agriculture and methods of control. In: Shah MM, Mahamood M (eds) Nematology-concepts, diagnosis and control. Intechopen, Rijeka, Croatia
Bertalan M, Albano R, de Pádua V, Rouws L, Rojas C, Hemerly A, Teixeira K, Schwab S, Araujo J, Oliveira A (2009) Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10(1):450
Blodgett JT, Eyles A, Bonello P (2007) Organ-dependent induction of systemic resistance and systemic susceptibility in Pinus nigra inoculated with Sphaeropsis sapinea and Diplodia scrobiculata. Tree Physiol 27(4):511–517
Bonfil DJ, Dolgin B, Mufradi I, Asido S (2004) Bioassay to forecast cereal cyst nematode damage to wheat in fields. Precis Agric 5(4):329–344
Bonos SA, Wilson MM, Meyer WA, Reed Funk C (2005) Suppression of red thread in fine fescues through endophyte-mediated resistance. Appl Turfgrass Sci 2(1):1
Bordallo JJ, Lopez-Llorca LV, Jansson HB, Salinas J, Persmark L, Asensio L (2002) Colonization of plant roots by egg-parasitic and nematode-trapping fungi. New Phytol 154(2):491–499
Bordiec S, Paquis S, Lacroix H, Dhondt S, Ait Barka E, Kauffmann S, Jeandet P, Mazeyrat-Gourbeyre F, Clément C, Baillieul F (2010) Comparative analysis of defence responses induced by the endophytic plant growth-promoting rhizobacterium Burkholderia phytofirmans strain PsJN and the non-host bacterium Pseudomonas syringae pv. pisi in grapevine cell suspensions. J Exp Bot 62(2):595–603
Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotech 27:30–37
Bridge J, Plowright RA, Peng DL (2005) Nematode parasites of rice. In: Luo M, Sikora RA, Bridge J (eds) Plant parasitic nematodes in subtropical and tropical agriculture. CABI Publishing, Wallingford, pp 87–130
Bulgari D, Casati P, Brusetti L, Quaglino F, Brasca M, Daffonchio D, Bianco PA (2009) Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR. J Microbiol 47(4):393–401
Bullington LS, Larkin BG (2015) Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines. Fungal Ecol 17:170–178
Bush LP, Cornelius PL, Buckner RC, Varney DR, Chapman RA, Burrus PB, Kennedy CW, Jones TA, Saunders MJ (1982) Association of N-acetyl loline and N-formyl loline with Epichloe typhina in tall fescue. Crop Sci 22(5):941–943
Campbell WC (2012) History of avermectin and ivermectin, with notes on the history of other macrocyclic lactone antiparasitic agents. Curr Pharm Biotechnol 13(6):853–865
Carroll G (1988) Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69(1):2–9
Carroll GC (1991) Fungal associates of woody plants as insect antagonists in leaves and stems. In: Barbosa P, Krischik VA, Jones CG (eds) Microbial mediation of plant-herbivore interactions. Wiley, New York, pp 253–271
Castillo UF, Strobel GA, Ford EJ, Hess WM, Porter H, Jensen JB, Albert H, Robison R, Condron MAM, Teplow DB (2002) Munumbicins, wide-spectrum antibiotics produced by Streptomyces NRRL 30562, endophytic on Kennedia nigriscansa. Microbiology 148(9):2675–2685
Castillo U, Harper JK, Strobel GA, Sears J, Alesi K, Ford E, Lin J, Hunter M, Maranta M, Ge H (2003) Kakadumycins, novel antibiotics from Streptomyces sp. NRRL 30566, an endophyte of Grevillea pteridifolia. FEMS Microbiol Lett 224(2):183–190
Chanway CP (1996) Endophytes: they’re not just fungi! Can J Bot 74:321–322
Chanway CP (1998) Bacterial endophytes: ecological and practical implications. In: Endophytism in plant pathology, the 7th international congress of plant pathology, Edinburgh, Scotland, pp 149–170
Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41(3):252–263
Chen SY, Dickson DW, Mitchell DJ (1996) Pathogenicity of fungi to eggs of Heterodera glycines. J Nematol 28(2):148–158
Clarke BB, White JF Jr, Hurley RH, Torres MS, Sun S, Huff DR (2006) Endophyte-mediated suppression of dollar spot disease in fine fescues. Plant Dis 90(8):994–998
Clay K (1988) Fungal endophytes of grasses: a defensive mutualism between plants and fungi. Ecology 69(1):10–16
Cocking EC (2003) Endophytic colonization of plant roots by nitrogen-fixing bacteria. Plant Soil 252(1):169–175
Compant S, Kaplan H, Sessitsch A, Nowak J, Ait Barka E, Clément C (2008) Endophytic colonization of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN: from the rhizosphere to inflorescence tissues. FEMS Microbiol Ecol 63(1):84–93
Compant S, Clément C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo-and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42(5):669–678
Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A (2011) Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb Ecol 62(1):188–197
Compant S, Sessitsch A, Mathieu F (2012) The 125th anniversary of the first postulation of the soil origin of endophytic bacteria—a tribute to M.L.V. Galippe. Plant Soil 356(1):299–301
Coombs JT, Franco CMM (2003) Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 69(9):5603–5608
D’Addabbo T, Filotico A, Sasanelli N (1996) Effect of calcium cyanamide and other ammonia fertilizers on Meloydogine incognita. Nematol Mediterr 24(2):209–214
Davis EC, Franklin JB, Shaw AJ, Vilgalys R (2003) Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis. Am J Bot 90(11):1661–1667
Decraemer W, Hunt D (2006) Structure and classification. In: Perry R, Moens M (eds) Plant nematology. CAB International, Oxfordshire, pp 3–32. https://doi.org/10.1079/9781845930561.0000. Accessed 14 Mar 2019
Del Sorbo G, Marziano F, D’Errico FP (2003) Diffusion and effectiveness of the nematophagous fungus Hirsutella rhossiliensis in control of the cyst nematode Heterodera daverti under field conditions. J Plant Pathol 85(3):219–221
Diedhiou P, Hallmann J, Oerke EC, Dehne HW (2003) Effects of arbuscular mycorrhizal fungi and a non-pathogenic Fusarium oxysporum on Meloidogyne incognita infestation of tomato. Mycorrhiza 13(4):199–204
Ding L, Maier A, Fiebig H-H, Lin W-H, Hertweck C (2011) A family of multicyclic indolosesquiterpenes from a bacterial endophyte. Org Biomol Chem 9(11):4029–4031
Dong LQ, Zhang KQ (2006) Microbial control of plant-parasitic nematodes: a five-party interaction. Plant Soil 288(1–2):31–45
Dong Z, Canny MJ, McCully ME, Roboredo MR, Cabadilla CF, Ortega E, Rodes R (1994) A nitrogen-fixing endophyte of sugarcane stems (a new role for the apoplast). Plant Physiol 105(4):1139–1147
Dong M, Yang Z, Cheng G, Peng L, Xu Q, Xu J (2018) Diversity of the bacterial microbiome in the roots of four Saccharum species: S. spontaneum, S. robustum, S. barberi, and S. officinarum. Front Microbiol 9:267
dos Santos MA, Ferraz S, Muchovej JJ (1992) Evaluation of 20 species of fungi from Brazil for biocontrol of Meloidogyne incognita race 3. Nematropica 22(2):183–192
Dungan RS, Ibekwe AM, Yates SR (2003) Effect of propargyl bromide and 1, 3-dichloropropene on microbial communities in an organically amended soil. FEMS Microbiol Ecol 43(1):75–87
Duponnois R, Mateille T, Sene V, Sawadogo A, Fargette M (1996) Effect of different west african species and strains of Arthrobotrys nematophagous fungi on Meloidogyne species. Entomophaga 41(3–4):475–483
Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B, Hamada T, Isawa T, Mitsui H, Minamisawa K (2001) Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 67(11):5285–5293
El-Nagdi W, Youssef M (2004) Soaking faba bean seed in some bio-agents as prophylactic treatment for controlling Meloidogyne incognita root-knot nematode infection. J Pest Sci 77(2):75–78
El-Tarabily KA, Nassar AH, Hardy GESJ, Sivasithamparam K (2009) Plant growth promotion and biological control of Pythium aphanidermatum, a pathogen of cucumber, by endophytic actinomycetes. J Appl Microbiol 106(1):13–26
Eskin N, Vessey K, Tian L (2014) Research progress and perspectives of nitrogen fixing bacterium, Gluconacetobacter diazotrophicus, in monocot plants. Int J Agron 2014:208383
Ezra D, Castillo UF, Strobel GA, Hess WM, Porter H, Jensen JB, Condron MAM, Teplow DB, Sears J, Maranta M (2004) Coronamycins, peptide antibiotics produced by a verticillate Streptomyces sp.(MSU-2110) endophytic on Monstera sp. Microbiology 150(4):785–793
Finotello F, Di Camillo B (2015) Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Brief Funct Genomics 14(2):130–142
Frans AAMDE, Davies G, Kerry R (1992) The use of Verticillium chlamydosporium Goddard and Pasteuria penetrans (Thorne) Sayre & Starr alone and in combination to control Meloidogyne incognita on tomato plants. Fundam Appl Nematol 15(3):235–242
Gamboa MA, Bayman P (2001) Communities of endophytic fungi in leaves of a tropical timber tree (Guarea guidonia: Meliaceae) 1. Biotropica 33(2):352–360
Gautam A, Siddiqui ZA, Mahmood I (1995) Integrated management of Meloidogyne incognita on tomato. Nematol Mediterr 23(2):245–247
Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169(1):30–39
Gunatilaka AAL (2006) Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence. J Nat Prod 69(3):509–526
Guo J, Cole JR, Zhang Q, Brown CT, Tiedje JM (2016) Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl Environ Microbiol 82(1):157–166
Hallmann J (2001) Plant interactions with endophytic bacteria. CABI Publishing, New York
Hallmann J, Sikora RA (1996) Toxicity of fungal endophyte secondary metabolites to plant parasitic nematodes and soil-borne plant pathogenic fungi. Eur J Plant Pathol 102(2):155–162
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43(10):895–914
Handelsman J (2007) Metagenomics and microbial communities. In: Maccarrone Evans M (ed) Encyclopedia of life sciences. Wiley, Hoboken, NJ
Hardoim PR, Van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79(3):293–320
Higginbotham SJ, Arnold AE, Ibañez A, Spadafora C, Coley PD, Kursar TA (2013) Bioactivity of fungal endophytes as a function of endophyte taxonomy and the taxonomy and distribution of their host plants. PLoS One 8(9):e73192
Huang W-K, Sun J-H, Cui J-K, Wang G-F, Kong L-A, Peng H, Chen S-L, Peng D-L (2014) Efficacy evaluation of fungus Syncephalastrum racemosum and nematicide avermectin against the root-knot nematode Meloidogyne incognita on cucumber. PLoS One 9(2):e89717
Humpherson-Jones FM, Dixon GR, Craig MA, and Ann DM (1992) Control of clubroot using calcium cyanamide: a review. In: Brighton crop protection conference, pests and diseases-1992. British Crop Protection Council, pp 1147–1154
Hurd PJ, Nelson CJ (2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic 8(3):174–183
Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8(7):R143
Ihrmark K, Bödeker I, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, Strid Y, Stenlid J, Brandström-Durling M, Clemmensen KE (2012) New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 82(3):666–677
Inahashi Y, Iwatsuki M, Ishiyama A, Namatame M, Nishihara-Tsukashima A, Matsumoto A, Hirose T, Sunazuka T, Yamada H, Otoguro K, Takahashi Y, Ōmura S, Shiomi K (2011) Spoxazomicins A–C, novel antitrypanosomal alkaloids produced by an endophytic actinomycete, Streptosporangium oxazolinicum K07-0460 T. J Antibiot 64(4):303–307
James EK, Gyaneshwar P, Mathan N, Barraquio WL, Reddy PM, Iannetta PPM, Olivares FL, Ladha JK (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant-Microbe Interact 15(9):894–906
Jansson H-B, Lopez-Llorca LV (2001) Biology of nematophagous fungi. In: Misra JK, Horn BW (eds) Trichomycetes and other fungal groups. Science Publishers, Enfield, pp 145–173
Jansson H-B, Jeyaprakash A, Zuckerman BM (1985) Control of root-knot nematodes on tomato by the endoparasitic fungus Meria coniospora. J Nematol 17(3):327–329
Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jones MGK, Kikuchi T, Manzanilla-López R, Palomares-Rius JE, Wesemael WML, Perry RN (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Mol Plant Pathol 14(9):946–961
Jones LM, Koehler AK, Trnka M, Balek J, Challinor AJ, Atkinson HJ, Urwin PE (2017) Climate change is predicted to alter the current pest status of Globodera pallida and G. rostochiensis in the United Kingdom. Glob Chang Biol 23(11):4497–4507
Kavroulakis N, Ntougias S, Zervakis GI, Ehaliotis C, Haralampidis K, Papadopoulou KK (2007) Role of ethylene in the protection of tomato plants against soil-borne fungal pathogens conferred by an endophytic Fusarium solani strain∗. J Exp Bot 58(14):3853–3864
Kennedy J, Marchesi JR, Dobson AD (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7(1):27
Khan AL, Hamayun M, Kang S-M, Kim Y-H, Jung H-Y, Lee J-H, Lee I-J (2012) Endophytic fungal association via gibberellins and indole acetic acid can improve plant growth under abiotic stress: an example of Paecilomyces formosus LHL10. BMC Microbiol 12(1):3
Khan AL, Waqas M, Kang S-M, Al-Harrasi A, Hussain J, Al-Rawahi A, Al-Khiziri S, Ullah I, Ali L, Jung H-Y (2014) Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth. J Microbiol 52(8):689–695
Kikuchi T, Jones JT, Aikawa T, Kosaka H, Ogura N (2004) A family of glycosyl hydrolase family 45 cellulases from the pine wood nematode Bursaphelenchus xylophilus. FEBS Lett 572(1–3):201–205
Kimmons CA, Gwinn KD, Bernard EC (1990) Nematode reproduction on endophyte-infected and endophyte-free tall fescue. Plant Dis 74(10):757–761
Kloepper JW, Ryu C-M (2006) Bacterial endophytes as elicitors of induced systemic resistance. In: JES B, JCB C, Thomas NS (eds) Microbial root endophytes. Springer Nature, Cham, Switzerland, pp 33–52
Kloepper JW, McInroy JA, Liu K, Hu C-H (2013) Symptoms of Fern distortion syndrome resulting from inoculation with opportunistic endophytic fluorescent Pseudomonas spp. PLoS One 8(3):e58531
Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216
Koch DW (1998) Nematode-resistant oil radish for Heterodera schachtii control. II. Sugarbeet-dry bean-corn rotations. J Sugar Beet Res 35(1–2):63–75
Koskimäki JJ, Hokkanen J, Jaakola L, Suorsa M, Tolonen A, Mattila S, Pirttilä AM, Hohtola A (2009) Flavonoid biosynthesis and degradation play a role in early defence responses of bilberry (Vaccinium myrtillus) against biotic stress. Eur J Plant Pathol 125(4):629–640
Kulkarni SM, Sangit AD (2000) Cultivation of Hohenbuehelia atrocaerulea (Fr.) sing. (Agaricomycetideae): a mushroom with nematicidal potential. Int J Med Mushrooms 2(2):161–163
Kumar V, Maitra S, Shukla RN (2015) Environmental metagenomics: the data assembly and data analysis perspectives. J Inst Eng (India) Ser A 96(1):71–83
Kyndt T, Fernandez D, Gheysen G (2014) Plant-parasitic nematode infections in rice: molecular and cellular insights. Annu Rev Phytopathol 52:135–153
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175
Link HF (1809) Observationes in ordines plantarum naturales. Dissertatio I. Mag Ges Naturf Freunde Berlin 3:3–42
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. BioMed Res Int 2012:251364
Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, Schenk PM (2017) Inner plant values: diversity, colonization and benefits from endophytic bacteria. Front Microbiol 8:2552
Loaces I, Ferrando L, Scavino AF (2011) Dynamics, diversity and function of endophytic siderophore-producing bacteria in rice. Microb Ecol 61(3):606–618
Long HH, Schmidt DD, Baldwin IT (2008) Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses. PLoS One 3(7):e2702
van Loon LC, Bakker PAHM, van der Heijdt WHW, Wendehenne D, Pugin A (2008) Early responses of tobacco suspension cells to rhizobacterial elicitors of induced systemic resistance. Mol Plant-Microbe Interact 21(12):1609–1621
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL (2013) Practical innovations for high-throughput amplicon sequencing. Nat Methods 10(10):999–1002
Luo H, Mo M, Huang X, Li X, Zhang K (2004) Coprinus comatus: a basidiomycete fungus forms novel spiny structures and infects nematode. Mycologia 96(6):1218–1224
Maier TR, Hewezi T, Peng J, Baum TJ (2013) Isolation of whole esophageal gland cells from plant-parasitic nematodes for transcriptome analyses and effector identification. Mol Plant-Microbe Interact 26(1):31–35
Malinowski DP, Belesky DP (2000) Adaptations of endophyte-infected cool-season grasses to environmental stresses: mechanisms of drought and mineral stress tolerance. Crop Sci 40:923–940
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24(3):133–141
Mareque C, da Silva TF, Vollú RE, Beracochea M, Seldin L, Battistoni F (2018) The endophytic bacterial microbiota associated with sweet sorghum (Sorghum bicolor) is modulated by the application of chemical N fertilizer to the field. Int J Genomics 2018:7403670
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380
Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7(11):1072–1084
Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, Cattonaro F, Morgante M (2011) Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling. Plant J 67(4):736–745
Meaburn E, Schulz R (2012) Next generation sequencing in epigenetics: insights and challenges. Semin Cell Dev Biol 23(2):192–199
Mercado-Blanco J, Lugtenberg BJJ (2014) Biotechnological applications of bacterial endophytes. Curr Biotechnol 3(1):60–75
Mian IH, Godoy G, Shelby RA, Rodriguez-Kabana R, Morgan-Jones G (1982) Chitin amendments for control of Meloidogyne arenaria in infested soil. Nematropica 12(1):71–84
Moens M, Perry RN (2009) Migratory plant endoparasitic nematodes: a group rich in contrasts and divergence. Ann Rev Phytopathol 47:313–332
Mojtahedi H, Santo GS, Hang AN, Wilson JH (1991) Suppression of root-knot nematode populations with selected rapeseed cultivars as green manure. J Nematol 23(2):170–174
Monfil VO, Casas-Flores S (2014) Molecular mechanisms of biocontrol in Trichoderma spp. and their applications in agriculture. In: Gupta VK, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, Tuohy MG (eds) Biotechnology and Biology of Trichoderma. Elsevier, Amsterdam, pp 429–453
Monfort E, Lopez-Llorca LV, Jansson HB, Salinas J, Park JO, Sivasithamparam K (2005) Colonisation of seminal roots of wheat and barley by egg-parasitic nematophagous fungi and their effects on Gaeumannomyces graminis var. tritici and development of root-rot. Soil Biol Biochem 37(7):1229–1235
Mousa WK, Raizada MN (2013) The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective. Front Microbiol 4:65
Müller P, Döring M (2009) Isothermal DNA amplification facilitates the identification of a broad spectrum of bacteria, fungi and protozoa in Eleutherococcus sp. plant tissue cultures. Plant Cell Tiss Org Culture 98(1):35–45
Murali TS, Suryanarayanan TS, Venkatesan G (2007) Fungal endophyte communities in two tropical forests of southern India: diversity and host affiliation. Mycol Prog 6(3):191–199
Nasopoulou C, Pohjanen J, Koskimäki JJ, Zabetakis I, Pirttilä AM (2014) Localization of strawberry (Fragaria x ananassa) and Methylobacterium extorquens genes of strawberry flavor biosynthesis in strawberry tissue by in situ hybridization. J Plant Physiol 171(13):1099–1105
Nassar AH, El-Tarabily KA, Sivasithamparam K (2005) Promotion of plant growth by an auxin-producing isolate of the yeast Williopsis saturnus endophytic in maize (Zea mays L.) roots. Biol Fertil Soils 42(2):97–108
Nicol JM, Elekçioğlu IH, Bolat N, Rivoal R (2007) The global importance of the cereal cyst nematode (Heterodera spp.) on wheat and international approaches to its control. Commun Agric Appl Biol Sci 72(3):677–686
Nicol JM, Turner SJ, Coyne DL, Den Nijs L, Hockland S, Maafi ZT (2011) Current nematode threats to world agriculture. In: Genomics and molecular genetics of plant-nematode interactions. Springer, Dordrecht, Heidelberg, pp 21–43
Noling JW (2009) Nematode management in tomatoes, peppers and eggplant. University of Florida, IFAS Extension, ENY-032 (December). https://edis.ifas.ufl.edu/ng032. Accessed 14 Apr 2019
Ntalli NG, Caboni P (2012) Botanical nematicides in the mediterranean basin. Phytochem Rev 11(4):351–359
Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178(19):5636–5643
O’Dell TE, Massicotte HB, Trappe JM (1993) Root colonization of Lupinus latifolius Agardh. And Pinus contorta Dougl. By Phialocephala fortinii Wang & Wilcox. New Phytol 124(1):93–100
Oka Y, Koltai H, Bar-Eyal M, Mor M, Sharon E, Chet I, Spiegel Y (2000) New strategies for the control of plant-parasitic nematodes. Pest Manage Sci: Formerly Pestic Sci 56(11):983–988
Onofre-Lemus J, Hernández-Lucas I, Girard L, Caballero-Mellado J (2009) ACC (1-aminocyclopropane-1-carboxylate) deaminase activity, a widespread trait in Burkholderia species, and its growth-promoting effect on tomato plants. Appl Environ Microbiol 75(20):6581–6590
Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, Dowling DN (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microb 6:745
Ownley BH, Griffin MR, Klingeman WE, Gwinn KD, Moulton JK, Pereira RM (2008) Beauveria bassiana: endophytic colonization and plant disease control. J Invertebr Pathol 98(3):267–270
Ownley BH, Gwinn KD, Vega FE (2010) Endophytic fungal entomopathogens with activity against plant pathogens: ecology and evolution. BioControl 55(1):113–128
Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A, Kanzaki N, Jones JT, Kikuchi T (2014) Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi. BMC Evol Biol 14(1):69
Pavlo A, Leonid O, Iryna Z, Natalia K, Maria PA (2011) Endophytic bacteria enhancing growth and disease resistance of potato (Solanum tuberosum L.). Biol Control 56(1):43–49
Pérez MP, Navas-Cortés JA, Pascual-Villalobos MJ, Castillo P (2003) Nematicidal activity of essential oils and organic amendments from Asteraceae against root-knot nematodes. Plant Pathol 52(3):395–401
Persmark L, Marban-Mendoza N, Jansson H-B (1995) Nematophagous fungi from agricultural soils of Central America. Nematropica 25(2):117–124
Petrini O (1986) Taxonomy of endophytic fungi of aerial plant tissues. In: Fokkema N, van den Heuvel J (eds) Microbiology of the phyllosphere. Cambridge University Press, Cambridge, pp 175–187
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11(11):789–799
Ploeg A (2008) Biofumigation to manage plant-parasitic nematodes. In: Ciancio A, Mukerji KG (eds) Integrated management and biocontrol of vegetable and grain crops nematodes. Springer, Dordrecht, the Netherlands, pp 239–248
Ploeg AT, Stapleton JJ (2001) The effects of temperature, time, and amendment of soil with broccoli residues on the infestation of melon by two root-knot nematode species. Plant Prot Q 11:1–3
Proença DN, Francisco R, Santos CV, Lopes A, Fonseca L, Abrantes IMO, Morais PV (2010) Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease. PLoS One 5(12):e15191
van der Putten WH, Cook R, Costa S, Davies KG, Fargette M, Freitas H, Hol WHG, Kerry BR, Maher N, Mateille T (2006) Nematode interactions in nature: models for sustainable control of nematode pests of crop plants. Adv Agron 89:227–260
Qiao K, Liu X, Wang H, Xia X, Ji X, Wang K (2012) Effect of abamectin on root-knot nematodes and tomato yield. Pest Manag Sci 68(6):853–857
Quentin M, Abad P, Favery B (2013) Plant parasitic nematode effectors target host defense and nuclear functions to establish feeding cells. Front Plant Sci 4:53
Redman RS, Sheehan KB, Stout RG, Rodriguez RJ, Henson JM (2002) Thermotolerance generated by plant/fungal symbiosis. Science 298(5598):1581–1581
Reinhold-Hurek B, Hurek T (1998) Life in grasses: diazotrophic endophytes. Trends Microbiol 6(4):139–144
Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14(4):435–443
Reiter B, Pfeifer U, Schwab H, Sessitsch A (2002) Response of endophytic bacterial communities in potato plants to infection with Erwinia carotovora subsp. atroseptica. Appl Environ Microbiol 68(5):2261–2268
Rizvi R, Mahmood I, Tiyagi SA, Khan Z (2012) Effect of some botanicals for the management of plant-parasitic nematodes and soil-inhabiting fungi infesting chickpea. Turk J Agric For 36(6):710–719
Robert-Seilaniantz A, Grant M, Jones JDG (2011) Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu Rev Phytopathol 49:317–343
Rodriguez RJ, White JF Jr, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182(2):314–330
Rosskopf EN, Chellemi DO, Kokalis-Burelle N, Church GT (2005) Alternatives to methyl bromide: a Florida perspective. Plant Health Prog 6(1):19–48
Rungin S, Indananda C, Suttiviriya P, Kruasuwan W, Jaemsaeng R, Thamchaipenet A (2012) Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant (Oryza sativa L. cv. KDML105). Antonie Van Leeuwenhoek 102(3):463–472
Safeena MIS, Zakeel MCM (2019) Strategies for the management of soil-borne pathogens and crop production under saline environment. In: Ansari RA, Mahmood I (eds) Plant health under biotic stress. Springer, Singapore, pp 213–229
Saikkonen K, Ion D, Gyllenberg M (2002) The persistence of vertically transmitted fungi in grass metapopulations. Proc R Soc Lond B Biol Sci 269(1498):1397–1403
Samac D, Kinkel L (2001) Suppression of the root-lesion nematode (Pratylenchus penetrans) in alfalfa (Medicago sativa) by Streptomyces spp. Plant Soil 235(1):35–44
Santo GS, O’bannon JH, Finley AM, Golden AM (1980) Occurrence and host range of a new root-knot nematode (Meloidogyne chitwoodi) in the Pacific northwest. Plant Dis 64(10):951–952
Sasser JN, Freckman DW (1987) A world perspective on nematology: the role of the society. In: Veeck J, Dickson D, Hyattsville M (eds) Vistas on nematology. Society of Nematologists, Hyattsville, MD, pp 7–14
Scavino AF, Pedraza RO (2013) The role of siderophores in plant growth-promoting bacteria. In: Maheshwari D, Saraf M, Aeron A (eds) Bacteria in agrobiology: crop productivity. Springer, Berlin, Heidelberg, pp 265–285
Scholte K (2000) Effect of potato used as a trap crop on potato cyst nematodes and other soil pathogens and on the growth of a subsequent main potato crop. Ann Appl Biol 136(3):229–238
Schulz B, Boyle C (2005) The endophytic continuum. Mycol Res 109(6):661–686
Schwarz M, Köpcke B, Weber RWS, Sterner O, Anke H (2004) 3-Hydroxypropionic acid as a nematicidal principle in endophytic fungi. Phytochemistry 65(15):2239–2245
Scortichini M, Loreti S (2007) Occurrence of an endophytic, potentially pathogenic strain of Pseudomonas syringae in symptomless wild trees of Corylus avellana L. J Plant Pathol 89(3):431–434
Sharon E, Bar-Eyal M, Chet I, Herrera-Estrella A, Kleifeld O, Spiegel Y (2001) Biological control of the root-knot nematode Meloidogyne javanica by Trichoderma harzianum. Phytopathology 91(7):687–693
Shi Y, Lou K, Li C (2009) Promotion of plant growth by phytohormone-producing endophytic microbes of sugar beet. Biol Fertil Soils 45(6):645–653
Siegel MR, Latch GCM, Bush LP, Fannin FF, Rowan DD, Tapper BA, Bacon CW, Johnson MC (1990) Fungal endophyte-infected grasses: alkaloid accumulation and aphid response. J Chem Ecol 16(12):3301–3315
Sikora RA, Pocasangre L, zum Felde A, Niere B, Vu TT, Dababat AA (2008) Mutualistic endophytic fungi and in-planta suppressiveness to plant parasitic nematodes. Biol Control 46(1):15–23
Singh RK, Mishra RP, Jaiswal HK, Kumar V, Pandey SP, Rao SB, Annapurna K (2006) Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis. Curr Microbiol 52(5):345–349
Singh LP, Gill SS, Tuteja N (2011) Unraveling the role of fungal symbionts in plant abiotic stress tolerance. Plant Signal Behav 6(2):175–191
Smant G, Stokkermans JPWG, Yan Y, De Boer JM, Baum TJ, Wang X, Hussey RS, Gommers FJ, Henrissat B, Davis EL (1998) Endogenous cellulases in animals: isolation of β-1, 4-endoglucanase genes from two species of plant-parasitic cyst nematodes. Proc Natl Acad Sci 95(9):4906–4911
Spiegel Y, Chet I (1998) Evaluation of Trichoderma spp. as a biocontrol agent against soilborne fungi and plant-parasitic nematodes in Israel. Integr Pest Manag Rev 3(3):169–175
Stirling GR (2017) Biological control of plant-parasitic nematodes. In: Tjamos EC, Papavizas GC, Cook RJ (eds) Diseases of nematodes. Springer, Boston, MA, pp 103–150
Stone JK, Polishook JD, White JF (2004) Endophytic fungi. In: Foster MS, Bills GF, Mueller GM (eds) Biodiversity of fungi: inventory and monitoring methods. Elsevier Science, Burlington, MA, pp 241–270
Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67(4):491–502
Strobel NE, Hussey RS, Roncadori RW (1982) Interactions of vesicular-arbuscular mycorrhizal fungi, Meloidogyne incognita, and soil fertility on peach. Phytopathology 72(6):690–694
Stutzman-Engwall K, Conlon S, Fedechko R, McArthur H, Pekrun K, Chen Y, Jenne S, La C, Trinh N, Kim S, Zhang Y-X, Fox R, Gustafsson C, Krebber A (2005) Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis. Metab Eng 7(1):27–37
Su L, Shen Z, Ruan Y, Tao C, Chao Y, Li R, Shen Q (2017) Isolation of antagonistic endophytes from banana roots against Meloidogyne javanica and their effects on soil nematode community. Front Microbiol 8:2070
Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55(3):415–424
Tadych M, Bergen M, Dugan FM, White JF Jr (2007) Evaluation of the potential role of water in spread of conidia of the Neotyphodium endophyte of Poa ampla. Mycol Res 111(4):466–472
Taghavi S, van der Lelie D, Hoffman A, Zhang Y-B, Walla MD, Vangronsveld J, Newman L, Monchy S (2010) Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS Genet 6(5):e1000943
Tan RX, Zou WX (2001) Endophytes: a rich source of functional metabolites. Nat Prod Rep 18(4):448–459
Tejesvi MV, Kajula M, Mattila S, Pirttilä AM (2011) Bioactivity and genetic diversity of endophytic fungi in Rhododendron tomentosum Harmaja. Fungal Divers 47(1):97–107
Tejesvi MV, Segura DR, Schnorr KM, Sandvang D, Mattila S, Olsen PB, Neve S, Kruse T, Kristensen HH, Pirttilä AM (2013) An antimicrobial peptide from endophytic Fusarium tricinctum of Rhododendron tomentosum Harmaja. Fungal Divers 60(1):153–159
Thomas T, Gilbert J, Meyer F (2012) Metagenomics-a guide from sampling to data analysis. Microb Inform Exp 2(1):3
Tian B-Y, Cao Y, Zhang K-Q (2015) Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots. Sci Rep 5:17,087
Toju H, Tanabe AS, Yamamoto S, Sato H (2012) High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One 7(7):e40863
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc 7(3):562–578
Trémouillaux-Guiller J, Rohr T, Rohr R, Huss VAR (2002) Discovery of an endophytic alga in Ginkgo biloba. Am J Bot 89(5):727–733
Türktaş M, Kurtoglu KY, Dorado G, Zhang B, Hernandez P, Ünver T (2015) Sequencing of plant genomes: a review. Turk J Agric For 39(3):361–376
Turner SJ, Evans K (1998) The origins, global distribution and biology of potato cyst nematode (Globodera rostochiensis (Woll.) and G. pallida Stone). In: Marks RJ, Brodie BB (eds) Potato cyst nematodes-biology, distribution and control. CAB International, Wallingford, pp 20–21
Urwin PE, Lilley CJ, McPherson MJ, Atkinson HJ (1997) Resistance to both cyst and root-knot nematodes conferred by transgenic Arabidopsis expressing a modified plant cystatin. Plant J 12(2):455–461
Vadassery J, Ritter C, Venus Y, Camehl I, Varma A, Shahollari B, Novák O, Strnad M, Ludwig-Müller J, Oelmüller R (2008) The role of auxins and cytokinins in the mutualistic interaction between Arabidopsis and Piriformospora indica. Mol Plant-Microbe Interact 21(10):1371–1383
Van Overbeek L, van Doorn J, Wichers J, van Amerongen A, van Roermund H, Willemsen P (2014) The arable ecosystem as battleground for emergence of new human pathogens. Front Microbiol 5:104
van Wesemael B, Paustian K, Andrén O, Cerri CE, Dodd M, Etchevers J, Goidts E, Grace P, Kätterer T, McConkey BG (2011) How can soil monitoring networks be used to improve predictions of organic carbon pool dynamics and CO2 fluxes in agricultural soils? Plant Soil 338(1–2):247–259
Verma VC, Kharwar RN, Strobel GA (2009) Chemical and functional diversity of natural products from plant associated endophytic fungi. Nat Prod Commun 4(11):1511–1532
Verpoorte R (2000) Secondary metabolism. In: Verpoorte R, Alfermann AW (eds) Metabolic engineering of plant secondary metabolism. Kluwer Academic Publishers, Dordrecht, Boston, pp 1–29
Viaene NM, Abawi GS (1998) Fungi parasitic on juveniles and egg masses of Meloidogyne hapla in organic soils from New York. J Nematol 30(4S):632–638
Villate L, Fievet V, Hanse B, Delemarre F, Plantard O, Esmenjaud D, Van Helden M (2008) Spatial distribution of the dagger nematode Xiphinema index and its associated grapevine fanleaf virus in French vineyard. Phytopathology 98(8):942–948
Vu T, Sikora R, Hauschild R (2006) Fusarium oxysporum endophytes induced systemic resistance against Radopholus similis on banana. Nematology 8(6):847–852
Waceke JW, Waudo SW, Sikora R (2001) Suppression of Meloidogyne hapla by arbuscular mycorrhiza fungi (AMF) on pyrethrum in Kenya. Int J Pest Manage 47(2):135–140
Wang K-H, Mcsorley R, Kokalis-Burelle N (2006) Effects of cover cropping, solarization, and soil fumigation on nematode communities. Plant Soil 286(1–2):229–243
Waqas M, Khan AL, Kamran M, Hamayun M, Kang S-M, Kim Y-H, Lee I-J (2012) Endophytic fungi produce gibberellins and indoleacetic acid and promotes host-plant growth during stress. Molecules 17(9):10,754–10,773
Wemheuer F, Wemheuer B, Kretzschmar D, Pfeiffer B, Herzog S, Daniel R, Vidal S (2016) Impact of grassland management regimes on bacterial endophyte diversity differs with grass species. Lett Appl Microbiol 62(4):323–329
Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B (2017) Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 7:40,914
West CP, Izekor E, Oosterhuis DM, Robbins RT (1988) The effect of Acremonium coenophialum on the growth and nematode infestation of tall fescue. Plant Soil 112(1):3–6
Westerdahl BB (2011) Cultural methods for managing nematodes on vegetables and ornamentals. In: First all African horticultural congress, pp 185–198
Westerdahl BB, Nunez J, and Radewald JD (2008) Trap cropping for managing nematodes on carrots in California. In: Annual international research conference on methyl bromide alternatives and emissions reductions, Orlando, FL
Westphal A (2011) Sustainable approaches to the management of plant-parasitic nematodes and disease complexes. J Nematol 43(2):122–125
Whipps JM, Davies KG (2000) Success in biological control of plant pathogens and nematodes by microorganisms. In: Gurr G, Wratten S (eds) Biological control: measures of success. Springer, Dordrecht, pp 231–269
White TJ, Bruns T, Lee SJWT, Taylor JL (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Academic Press Inc., New York
Williamson VM (1999) Plant nematode resistance genes. Curr Opin Plant Biol 2(4):327–331
Williamson VM, Hussey RS (1996) Nematode pathogenesis and resistance in plants. Plant Cell 8(10):1735–1745
Yan Y, Smant G, Stokkermans J, Qin L, Helder J, Baum T, Schots A, Davis E (1998) Genomic organization of four β-1, 4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications. Gene 220(1–2):61–70
Zabalgogeazcoa I (2008) Review. Fungal endophytes and their interaction with plant pathogens (Revisión. Los hongos endofíticos y sus interacciones con patógenos de plantas). Span J Agric Res 6:138–146
Zakeel MC, Safeena MI (2019) Biofilmed biofertilizer for sustainable agriculture. In: Ansari RA, Mahmood I (eds) Plant health under biotic stress. Springer, Singapore, pp 65–82
Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25(2):139–150
Zhang HW, Song YC, Tan RX (2006) Biology and chemistry of endophytes. Nat Prod Rep 23(5):753–771
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Zakeel, M.C.M., Safeena, M.I.S. (2020). Metagenomic Insights Into Interactions Between Plant Nematodes and Endophytic Microbiome. In: Ansari, R., Rizvi, R., Mahmood, I. (eds) Management of Phytonematodes: Recent Advances and Future Challenges. Springer, Singapore. https://doi.org/10.1007/978-981-15-4087-5_5
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