Alkhalaf LM, Ryan KS (2015) Biosynthetic manipulation of tryptophan in bacteria: pathways and mechanisms. Chem Biol 19(3):317–328. https://doi.org/10.1016/j.chembiol.2015.02.005
Article
CAS
Google Scholar
Bai Y, Muller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Munch PC, Spaepen S, Remus-Emsermann M, Huttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528:364–369. https://doi.org/10.1038/nature16192
Article
CAS
PubMed
Google Scholar
Bardwell L (2005) A walk-through of the yeast mating pheromone response pathway. Peptides. 26(2):339–350. https://doi.org/10.1016/j.peptides.2004.10.002
Article
PubMed
PubMed Central
Google Scholar
Berg G, Rybakova D, Grube M, Koberl M (2016) The plant microbiome explored: implications for experimental botany. J Exp Bot 67:995–1002. https://doi.org/10.1093/jxb/erv466
Article
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flflexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 doi: 101093/bioinformatics/btu170
Article
CAS
PubMed
PubMed Central
Google Scholar
Bouffaud ML, Poirier MA, Muller D, Moenne-Loccoz Y (2014) Root microbiome relates to plant host evolution in maize and other Poaceae. Environ Microbiol 16:2804–2814. https://doi.org/10.1111/1462-2920.12442
Article
PubMed
Google Scholar
Bulgarelli D, Rott M, Schlaeppi K, Ver LTE, Ahmadinejad N, Assenza F, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root inhabiting bacterial microbiota. Nature 488:91–95. https://doi.org/10.1038/nature11336
Article
CAS
PubMed
Google Scholar
Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64(1):807–838. https://doi.org/10.1146/annurev-arplant-050312-120106
Article
CAS
PubMed
Google Scholar
Cao J, Yang C, Li L, Jiang L, Wu Y, Wu C, Bu Q, Xia G, Liu X, Luo Y (2016) Rice plasma membrane proteomics reveals Magnaporthe oryzae promotes susceptibility by sequential activation of host hormone signaling pathways. Mol Plant-Microbe Interact 29:902–913. https://doi.org/10.1094/MPMI-08-16-0165-R
Article
CAS
PubMed
Google Scholar
Carrion VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM (2019) Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366(6465):606–612. https://doi.org/10.1126/science.aaw9285
Article
CAS
PubMed
Google Scholar
Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crüsemann M, Bok Lee Y, Kim J, Giaever G, Nislow C, Moore BS, Thomashow LS, Weller DM, Kwak YS (2016) Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J 10:119–129. https://doi.org/10.1038/ismej.2015.95
Article
CAS
PubMed
Google Scholar
Chaibub AA, Carvalho JCB, Silva CS, Collevatti RG, Gonçalves FJ, Côrtes MVCB, Filippi MCC, Faria FP, Lopes DCB, Araújo LG (2016) Defence responses in rice plants in prior and simultaneous applications of Cladosporium sp. during leaf blast suppression. Environ Sci Pollut Res 23(21):21554–21564. https://doi.org/10.1007/s11356-016-7379-5
Article
CAS
Google Scholar
Chapelle E, Mendes R, Bakker PA, Raaijmakers JM (2016) Fungal invasion of the rhizosphere microbiome. ISME J 10(1):265–268. https://doi.org/10.1038/ismej.2015.82
Article
CAS
PubMed
Google Scholar
Chen H, Boutros PC (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12:35. https://doi.org/10.1186/1471-2105-12-35
Edwards J, Johnson C, Santos-Medellı´n C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA 112:E911–E920. https://doi.org/10.1073/pnas.1414592112
Article
CAS
PubMed
PubMed Central
Google Scholar
Eyre AW, Wang M, Oh Y, Dean RA (2019) Identification and characterization of the core rice seed microbiome. Phytobiomes J 3:148–157. https://doi.org/10.1094/PBIOMES-01-19-0009-R
Article
Google Scholar
Foster AJ, Littlejohn GR, Soanes DM, Talbot NJ (2016) Strategies for nutrient acquisition by Magnaporthe oryzae during the infection of rice. In: Host pathogen interaction: microbial metabolism, pathogenicity and Antiinfectives, pp 93–108. https://doi.org/10.1002/9783527682386
Chapter
Google Scholar
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes application to the identification of mycorrhizae and rusts. Mol Ecol 2(2):113–118. https://doi.org/10.1111/j.1365-294X.1993.tb00005.x
Article
CAS
PubMed
Google Scholar
Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944. https://doi.org/10.1128/AEM.05255-11
Article
CAS
PubMed
PubMed Central
Google Scholar
He R, Zeng J, Zhao D, Huang R, Yu Z, Wu QL (2020) Contrasting patterns in diversity and community assembly of Phragmites australis root-associated bacterial communities from different seasons. Appl Environ Microbiol 86(14):e00379–e00320. https://doi.org/10.1128/AEM.00379-20
Article
CAS
PubMed
PubMed Central
Google Scholar
Hol WHG, DeBoer W, Termorshuizen AJ, Meyer KM, Schneider JHM, Van Der Putten WH, Van Dam NM (2013) Heterodera schachtii nematodes interfere with aphid-plant relations on Brassica oleracea. J Chem Ecol 39:1193–1203. https://doi.org/10.1007/s10886-013-0338-4
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu L, Robert CAM, Cadot S, Zhang X, Ye M, BB BL, Manzo D, Chervet N, Steinger T, MGA H, Schlaeppi K, Erb M (2018) Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat Commun 9:2738. https://doi.org/10.1038/s41467-018-05122-7
Article
CAS
PubMed
PubMed Central
Google Scholar
Hussain Q, Liu Y, Zhang A, Pan G, Li L, Zhang X, Song X, Cui L, Jin L (2011) Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux. FEMS Microbiol Ecol 78:116–128. https://doi.org/10.1111/j.1574-6941.2011.01128.x
Article
CAS
PubMed
Google Scholar
Inceoğlu O, Salles JF, van Overbeek L, van Elsas JD (2010) Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Appl Environ Microbiol 76(11):3675–3684. https://doi.org/10.1128/AEM.00040-10
Article
CAS
PubMed
PubMed Central
Google Scholar
Innerebner G, Knief C, Vorholt JA (2011) Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microb 77(10):3202–3210. https://doi.org/10.1128/AEM.00133-11
Article
CAS
Google Scholar
Ishihara A, Hashimoto Y, Tanaka C, Dubouzet JG, Nakao T, Matsuda F, Nishioka T, Miyagawa H, Wakasa K (2008) The tryptophan pathway is involved in the defense responses of rice against pathogenic infection via serotonin production. Plant J 54(3):481–495. https://doi.org/10.1111/j.1365-313X.2008.03441.x
Article
CAS
PubMed
Google Scholar
Jain P, Pundir RK (2017) Potential role of endophytes in sustainable agriculture-recent developments and future prospects. In: Maheshwari DK (ed) Endophytes: biology and biotechnology: volume 1. Springer International Publishing, Cham, pp 145–169 https://link.springer.com/chapter/10.1007/978-3-319-66541-2_7
Chapter
Google Scholar
Jiang YJ, Liang YT, Li CM, Wang F, Sui YY, Suvannang N, Zhou JZ, Sun B (2016) Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol Biochem 95:250–261. https://doi.org/10.1016/j.soilbio.2016.01.007
Article
CAS
Google Scholar
Kang S, Chumley FG, Valent B (1994) Isolation of the mating-type genes of the phytopathogenic fungus Magnaporthe grisea using genomic subtraction. Genetics. 138(2):289–296. https://doi.org/10.1093/genetics/138.2.289
Article
CAS
PubMed
PubMed Central
Google Scholar
Khaitov B, Patiño-Ruiz JD, Pina Schausberger TP (2015) Interrelated effects of mycorrhiza and free-living nitrogen fixers cascade up to aboveground herbivores. Ecol Evol 5:3756–3768. https://doi.org/10.1002/ece3.1654
Article
PubMed
PubMed Central
Google Scholar
Koga H, Dohi K, Nakayachi O, Mori M (2004) A novel inoculation method of Magnaporthe grisea for cytological observation of the infection process using intact leaf sheaths of rice plants. Physiol Mol Plant Pathol 64:67–72. https://doi.org/10.1016/j.pmpp.2004.07.002
Article
Google Scholar
Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee P. A, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, Rubin EM, Lee SW, Kim JF (2018) Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat Biotechnol, 36:1100–1109. doi: https://doi.org/10.1038/nbt.4232
Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, J.L. Dangl JL (2015) Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science, 349:860–864. doi: https://doi.org/10.1126/science.aaa8764, 6250
Lumibao CY, Kimbrough ER, Day RH, Conner WH, Krauss KW, Van Bael SA (2020) Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients. FEMS Microbiol Ecol 96(7):fiaa124. https://doi.org/10.1093/femsec/fiaa124
Article
CAS
PubMed
Google Scholar
Mallon CA, Poly F, Le Roux X, Marring I, van Elsas JD, Salles JF (2015) Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 96:915–926. https://doi.org/10.1890/14-1001.1
Article
PubMed
Google Scholar
Marcel S, Sawers R, Oakeley E, Angliker H, Paszkowski U (2010) Tissue-adapted invasion strategies of the rice blast fungus Magnaporthe oryzae. Plant Cell 22:3177–3187. https://doi.org/10.1105/tpc.110.078048
Article
CAS
PubMed
PubMed Central
Google Scholar
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, De Santis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332(6033):1097–1100. https://doi.org/10.1126/science.1203980
Article
CAS
PubMed
Google Scholar
Nasir F, Tian L, Chang C, Li X, Gao Y, Tran PL, Tian C (2017) Current understanding of pattern-triggered immunity and hormone-mediated defense in rice (Oryza sativa) in response to Magnaporthe oryzae infection. Semin Cell Dev Biol 83:95–105. https://doi.org/10.1016/j.semcdb.2017.10.020
Article
CAS
PubMed
Google Scholar
Ou SH (1980) Pathogen variability and host resistance in rice blast disease. Annu Rev Phytopathol 18:167–187. https://doi.org/10.1146/annurev.py.18.090180.001123
Article
Google Scholar
Prakash PY, Irinyi L, Halliday C, Chen S, Robert V, Meyer W (2017) Online databases for taxonomy and identification of pathogenic Fungi and proposal for a cloud-based dynamic data network platform. J Clin Microbiol 55(4):1011–1024. https://doi.org/10.1128/JCM.02084-16
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin Z, Liao D, Chen Y, Zhang C, An R, Zeng Q, Li X (2019) A widely Metabolomic analysis revealed metabolic alterations of Epimedium Pubescens leaves at different growth stages. Molecules (Basel, Switzerland) 25(1):137. https://doi.org/10.3390/molecules25010137
Article
CAS
Google Scholar
Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901–1914. https://doi.org/10.1534/genetics.105.044891
Article
CAS
PubMed
PubMed Central
Google Scholar
Rojas X, Guo JQ, Leff JW, McNear Jr DH, Fierer N, McCulley RL (2016) Infection with a shoot-specific fungal endophyte (Epichloë) alters tall fescue soil microbial communities. Microb Ecol, 72 :197–206. doi: https://doi.org/10.1007/s00248-016-0750-8, 1
Sesma A, Osbourn AE (2004) The rice leaf blast pathogen undergoes developmental processes typical of root-infecting fungi. Nature 431:582–586. https://doi.org/10.1038/nature02880
Article
CAS
PubMed
Google Scholar
Seybold H, Demetrowitsch TJ, Hassani MA et al (2020) A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition. Nat Commun 11:1910. https://doi.org/10.1038/s41467-020-15633-x
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303
Article
CAS
PubMed
PubMed Central
Google Scholar
Taj A, Jamil N (2018) Bioconversion of tyrosine and tryptophan derived biogenic amines by neuropathogenic bacteria. Biomolecules 8(1):1–9. https://doi.org/10.3390/biom8010010
Article
CAS
Google Scholar
Tedersoo L, Tooming-Klunderud A, Anslan S (2018) PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. New Phytol 217(3):1370–1385. https://doi.org/10.1111/nph.14776
Article
CAS
PubMed
Google Scholar
Tian DG, Chen ZJ, Chen ZQ, Zhou YC, Wang ZH, Wang F, Chen SB (2016) Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars. Rice 9(1):1–11. https://doi.org/10.1186/s12284-016-0091-8
Article
Google Scholar
Tian DG, Yang L, Chen ZZ, Chen ZQ, Wang F, Zhou YC, Chen SB (2018) Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t. Rice 11:47. https://doi.org/10.1186/s12284-018-0240-3
Article
PubMed
PubMed Central
Google Scholar
Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N (2012) Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J, 6:363–383. doi: https://doi.org/10.1038/ismej.2011.100
Usyk M, Zolnik CP, Patel H, Levi MH, Burk RD (2017) Novel ITS1 fungal primers for characterization of the Mycobiome. mSphere 2(6):e00488–e00417. https://doi.org/10.1128/mSphere.00488-17
Article
PubMed
PubMed Central
Google Scholar
Venturi V, Fuqua C (2013) Chemical signaling between plants and plant-pathogenic bacteria. Annu Rev Phytopathol 51:17–37 https://www.annualreviews.org/doi/abs/10.1146/annurev- phyto-082712-102239
Article
CAS
PubMed
Google Scholar
Vu T, Hauschild R, Sikora RA (2006) Fusarium oxysporum endophytes induced systemic resistance against Radopholus similis on banana. Nematology 8:847–852. https://doi.org/10.1163/156854106779799259
Article
Google Scholar
Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R (2015) Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1(1):e00009–e00015. https://doi.org/10.1128/mSystems.00009-15
Article
PubMed
PubMed Central
Google Scholar
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications, vol 18 academic press, London, United Kingdom, pp 315–322
Google Scholar
Xu H, Yang Y, Tian Y, Xu R, Zhong Y, Liong H (2020) Rhizobium inoculation drives the shifting of rhizosphere fungal community in a host genotype dependent manner. Front Microbiol 10:1–14. https://doi.org/10.3389/fmicb.2019.03135
Article
Google Scholar
Yang JW, Yi HS, Kim H, Lee B, Lee S, Ghim SY, Ryu CM (2011) Whitefly infestation of pepper plants elicits defence responses against bacterial pathogens in leaves and roots and changes the below-ground microflora. J Ecol 99:46–56. https://doi.org/10.1111/j.1365-2745.2010.01756.X
Article
CAS
Google Scholar
Yang DL, Yang YN, He ZH (2013) Roles of plant hormones and their interplay in rice immunity. Mol Plant 6:675–685. https://doi.org/10.1093/mp/sst056
Article
CAS
PubMed
Google Scholar
Yuan C, Zhang L, Hu H, Wang J, Shen J, He J (2018) The biogeography of fungal communities in paddy soils is mainly driven by geographic distance. J Soils Sediments 18:1795–1805. https://doi.org/10.1007/s11368-018-1924-4
Article
CAS
Google Scholar
Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA (2015) The soil microbiome inflfluences grapevine-associated microbiota. mBio 6:e02527–e02514. https://doi.org/10.1128/mBio.02527-14
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Brodie EL (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 3(4):470–480. https://doi.org/10.1038/s41564-018-0129-3
Article
CAS
PubMed
Google Scholar
Zhang J, Liu YX, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y (2021) High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat Protoc 16(2):988–1012. https://doi.org/10.1038/s41596-020-00444-7
Article
CAS
PubMed
Google Scholar
Zhong Y, Yang Y, Liu P, Xu R, Rensing C, Fu X, Liao H (2019) Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities. Plant Cell Environ 42:2028–2044. https://doi.org/10.1111/pce.13519
Article
CAS
PubMed
Google Scholar
Zhou JM (2016) Plant pathology: a life and death struggle in rice blast disease. Curr Biol 26(18):843–845. https://doi.org/10.1016/j.cub.2016.08.038
Article
CAS
Google Scholar
Zhou B, Qu S, Liu G, Dolan M, Sakai H, Lu G et al (2006) The eight amino-acid differences within three leucine rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Mol Plant-Microbe Interact 19:1216–1228. https://doi.org/10.1094/MPMI-19-1216
Article
CAS
PubMed
Google Scholar