Login | Register

Microbiomics of Populus


Microbiomics of Populus

Naik, Sachin ORCID: https://orcid.org/0000-0002-3121-1084 (2020) Microbiomics of Populus. PhD thesis, Concordia University.

[thumbnail of Naik_PhD_F2020.pdf]
Text (application/pdf)
Naik_PhD_F2020.pdf - Accepted Version
Available under License Spectrum Terms of Access.
[thumbnail of Appendices.xlsx.cpgz]
Spreadsheet (application/gzip)
Appendices.xlsx.cpgz - Accepted Version
Available under License Spectrum Terms of Access.


Species of the genus Populus, commonly known as poplars, are one of the most widely used groups of forest trees in North America and Europe. Poplars play a significant ecological role as a pioneer species in the boreal forest, and as a dominant species in riparian forests where they serve as rich wildlife habitats. Numerous natural and artificial hybrids of poplars with superior qualities are widely used in commercial plantations. However, many hybrid poplars are susceptible to the leaf spot and stem canker causative pathogenic fungal species, Sphaerulina musiva which limits the utility of hybrid poplars as plantation trees. At present, there is no control measure to combat the disease caused by S. musiva. The plant microbiome—mainly endophytic microbes—are known to interact with pathogenic microbes and play a crucial role in the ecology and evolution of plants. Understanding the endophytic microbial associations in Poplars along with their interactions with S. musiva is invaluable for developing new methods for combating the stem cankers caused by this pathogen. In the present study, we found a number of endophytic microbes in Poplars that inhibit the fungal pathogen S. musiva and may serve as a potential source to develop biocontrol agents against S. musiva.

In the first study (Chapter 2), we characterized the endophytic fungal community in Populus species in the Gault Nature Reserve in Mont-Saint-Hilaire, Quebec. We investigated the dual culture interactions of endophytes against S. musiva. We isolated 367 endophytic fungal isolates grouped into 46 genera. Alternaria was the dominant and most common genus isolated. We found certain genera of endophytic fungi were unique to specific Populus species. Only a few endophytic fungi exhibited antagonistic activity against S. musiva and showed differential competitive ability. The endophytic fungus Fusarium sporotrichioides showed the strongest antagonistic activity against S. musiva and can be used as a potential source to develop a biocontrol microbe against S. musiva.

In the second study (Chapter 3), we investigated interactions between Bacillus velezensis EB14, an endophytic bacterial strain isolated from poplars, and S. musiva. We found significant inhibition of S. musiva by the endophytic bacterium, B. velezensis. We also discovered the production of anti-fungal Iturin compounds (iturin A1, subtulene A, iturin A2, iturin A9 and fengycin) along with four unknown compounds in Bacillus velezensis. In addition, we found that B. velezensis EB14 exhibited varying level of competitive ability against the endophytic fungal microbiome of Populus.

In the third study (Chapter 4), we elucidated the evolutionary relationships of the isolated Bacillus strain EB14, and performed a comparative genome analysis of the Bacillus velezensis EB14 strain with its closest relatives. We report the 4.07Mbp draft genome of Bacillus velezensis EB14. This genome encodes 12 secondary metabolite gene clusters which includes Surfactin, Rhizoactin, Bacillibactin, Fengycin, Bacillaene, Difficidin, Macrolactin, and Bacilysin. The presence of genes involved in plant bacterial interactions further validates the potential of using Bacillus velezensis EB14 strain to develop as a biocontrol microbe in forestry and agriculture. Furthermore, pan and core genome analysis revealed that Bacillus strains associated with plants possessed genes involved in cell wall degradation, polyketide synthesis, and environment sensors. Most of these genes were clade specific and found in B. amyloliquefaciens, B. siamensis, and the conspecific group of B. velezensis.

The last chapter (Chapter 5), examines one of the most perplexing questions in endophyte biology: How and why do endophytes produce metabolites similar to host plant derived secondary metabolites? Here, we review the endophyte literature on secondary metabolite production and show that detailed studies are required for conclusive demonstration of metabolite production, as well as to explain the adaptive significance of production of these metabolites by endophytic fungi.

Divisions:Concordia University > Faculty of Arts and Science > Biology
Item Type:Thesis (PhD)
Authors:Naik, Sachin
Institution:Concordia University
Degree Name:Ph. D.
Date:2 July 2020
Thesis Supervisor(s):Dayanandan, Selvadurai
Keywords:Sphaerulina musiva, Endophtyic Fungi, Populus, Microbiome, Bacillus velezensis, Comparative genome, Tree Health
ID Code:987350
Deposited By: SACHIN NAIK
Deposited On:27 Oct 2022 13:51
Last Modified:28 Oct 2022 00:00


Abarenkov K, Tedersoo L, Nilsson RH, et al (2010) Plutof-a web based workbench for ecological and taxonomic research, with an online implementation for fungal its sequences. Evol Bioinforma 2010:189–196. doi: 10.4137/EBO.S6271
Albrectsen BR, Björkén L, Varad A, et al (2010) Endophytic fungi in European aspen (Populus tremula) leaves - Diversity, detection, and a suggested correlation with herbivory resistance. Fungal Divers 41:17–28. doi: 10.1007/s13225-009-0011-y
Albrectsen BR, Siddique AB, Decker VHG, et al (2018) Both plant genotype and herbivory shape aspen endophyte communities. Oecologia 187:535–545. doi: 10.1007/s00442-018-4097-3
Arau WL, Marcon J, Maccheroni W, et al (2002) Diversity of Endophytic Bacterial Populations and Their Interaction with. Society 68:4906–4914. doi: 10.1128/AEM.68.10.4906
Arias RS, Sagardoy MA, Van Vuurde JWL (1999) Spatio-temporal distribution of naturally occurring Bacillus spp. and other bacteria on the phylloplane of soybean under field conditions. J Basic Microbiol 39:283–292. doi: 10.1002/(SICI)1521-4028(199912)39:5/6<283::AID-JOBM283>3.0.CO;2-G
Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21:51–66. doi: 10.1016/j.fbr.2007.05.003
Arnold AE, Herre EA (2003) Canopy cover and leaf age affect colonization by tropical fungal endophytes: Ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95:388–398. doi: 10.1080/15572536.2004.11833083
Arnold AE, Maynard Z, Gilbert GS, et al (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274. doi: 10.1046/j.1461-0248.2000.00159.x
Arnold AE, Mejía LC, Kyllo D, et al (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci U S A 100:15649–15654. doi: 10.1073/pnas.2533483100
Arnold AE, Miadlikowska J, Higgins KL, et al (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283–97. doi: 10.1093/sysbio/syp001
Bacon CW, Hill NS. 1996. Symptomless grass endophytes: Products of coevolutionary symbioses and their role in the ecological adaptations of infected grasses. In: Endophytic fungi in grasses and woody plants: systematics, ecology, and evolution. (eds. S.C. Redlin and L.M.Carris).APS Press, Minnesota.155-178.
Bálint M, Tiffin P, Hallström B, et al (2013) Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera). PLoS One 8:. doi: 10.1371/journal.pone.0053987
Baltrus DA (2017) Adaptation, specialization, and coevolution within phytobiomes. Curr Opin Plant Biol 38:109–116. doi: 10.1016/j.pbi.2017.04.023
Baltruschat H, Fodor J, Harrach BD, et al (2008) Salt tolerance of barley induced by the root endophyte Piriformospora indica is associated with a strong increase in antioxidants. New Phytol 180:501–510. doi: 10.1111/j.1469-8137.2008.02583.x
Bartholomew, J. W., & Mittwer T (2011) The Gram stain. MLO Med Lab Obs 43:38. doi: 10.1097/00013542-199704000-00006
Baas Becking, L.G.M. 1931. Gaia of leven en aarde. The Hague, the Netherlands: Nijhoff. Ambtsrede R.U. Leiden (in Dutch).

Baas Becking, L.G.M.1934. Geobiologie of inleiding tot de milieukunde. The Hague, the Netherlands: W.P. Van Stoc- kum & Zoon (in Dutch).

Beijerinck MW. 1888. Cultur des Bacillus radicola aus den Knöllchen. Bot Ztg 46:740–750.
Benhamou N, Chet I (1997) Cellular and molecular mechanisms involved in the interaction between Trichoderma harzianum and Pythium ultimum. Appl Environ Microbiol 63:2095–2099. doi: 10.1128/aem.63.5.2095-2099.1997
Berg G, Grube M, Schloter M, Smalla K (2014) Unraveling the plant microbiome: Looking back and future perspectives. Front Microbiol 5:1–7. doi: 10.3389/fmicb.2014.00148
Berg G, Köberl M, Rybakova D, et al (2017) Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiol Ecol 93:1–9. doi: 10.1093/femsec/fix050
Bertelli C, Laird MR, Williams KP, et al (2017) IslandViewer 4 : expanded prediction of genomic islands for larger-scale datasets. 45:30–35. doi: 10.1093/nar/gkx343
Bier JE (1939) Septoria Canker of Introduced and Native Hybrid Poplars. Can J Res 17c:195–204. doi: 10.1139/cjr39c-019
Blin K, Shaw S, Steinke K, et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. doi: 10.1093/nar/gkz310
Blom J, Rueckert C, Niu B, et al (2012) The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of Iturin A. J Bacteriol 194:1845–1846. doi: 10.1128/JB.06762-11
Bonito G, Hameed K, Ventura R, et al (2016) Isolating a functionally relevant guild of fungi from the root microbiome of Populus. Fungal Ecol 22:35–42. doi: 10.1016/j.funeco.2016.04.007
Bonito G, Reynolds H, Robeson MS, et al (2014) Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol 23:3356–3370. doi: 10.1111/mec.12821
Bown P, Plumb J, Sánchez-Baracaldo P, et al (2003) Sequence heterogeneity of green (Chlorophyta) endophytic algae associated with a population of Chondrus crispus (Gigartinaceae, Rhodophyta). Eur J Phycol 38:153–163. doi: 10.1080/0967026031000095525
Brettin T, Davis JJ, Disz T, et al (2015) RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:. doi: 10.1038/srep08365
Brynildsrud O, Bohlin J, Scheffer L, Eldholm V (2016) Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol 17:1–9. doi: 10.1186/s13059-016-1108-8
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. doi: 10.1016/j.funeco.2015.07.005
Busby PE, Peay KG, Newcombe G (2015) Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity. New Phytol n/a-n/a. doi: 10.1111/nph.13742
Busby PE, Peay KG, Newcombe G (2016a) Common foliar fungi of <em>Populus trichocarpa</em> modify <em>Melampsora</em> rust disease severity. New Phytol 209:1681–1692. doi: 10.1111/nph.13742
Busby PE, Ridout M, Newcombe G (2016b) Fungal endophytes: modifiers of plant disease. Plant Mol Biol 90:645–655. doi: 10.1007/s11103-015-0412-0
Busby PE, Zimmerman N, Weston DJ, et al (2013) Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi. Ecosphere 4:art125. doi: 10.1890/ES13-00127.1
Butcher RA, Schroeder FC, Fischbach MA, et al (2007) The identification of bacillaene , the product of the PksX megacomplex in Bacillus subtilis
Cabanettes F, Klopp C (2018) D-GENIES: Dot plot large genomes in an interactive, efficient and simple way. PeerJ 2018:. doi: 10.7717/peerj.4958
Callan B (2007) Septoria musiva isolated from cankered stems in hybrid poplar stool beds, Fraser Valley, British Columbia. North Am Fungi 1–9. doi: 10.2509/pnwf.2007.002.007
Campanile G, Ruscelli A, Luisi N (2007) Antagonistic activity of endophytic fungi towards Diplodia corticola assessed by in vitro and in planta tests. Eur J Plant Pathol 117:237–246. doi: 10.1007/s10658-006-9089-1
Cao Y, Pi H, Chandrangsu P, et al (2018) Antagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum. Sci Rep 8:4360. doi: 10.1038/s41598-018-22782-z
Carrol G (2012) Fungal Endophytes in Stems and Leaves : From Latent Pathogen to Mutualistic Symbiont Author ( s ): George Carroll Reviewed work ( s ): Published by : Ecological Society of America Stable URL : http://www.jstor.org/stable/1943154 . Ecology 69:2–9. doi: 10.2307/1943154
Carroll GC, Carroll FE (1978) Studies on the incidence of coniferous needle endophytes in the Pacific Northwest. Can J Bot 56:3034–3043. doi: 10.1139/b78-367
Case RJ, Boucher Y, Dahllo I, et al (2007) Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies ᰔ. 73:278–288. doi: 10.1128/AEM.01177-06
Chandra S (2012) APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. Endophytic fungi Nov. sources Anticancer lead Mol. 95:47–59
Chatterjee S, Ghosh R, Mandal NC (2019) Production of bioactive compounds with bactericidal and antioxidant potential by endophytic fungus Alternaria alternata AE1 isolated from Azadirachta indica A. Juss. PLoS One 14:1–18. doi: 10.1371/journal.pone.0214744
Cheffi M, Bouket AC, Alenezi FN, et al (2019) Olea europaea L . Root Endophyte Bacillus velezensis OEE1 Counteracts Oomycete and Fungal Harmful Pathogens and Harbours a Large Repertoire of Secreted and Volatile Metabolites and Beneficial Functional Genes. 1–33. doi: 10.3390/microorganisms7090314
Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41:252–263. doi: 10.1007/s002480000087
Chen L, Gu W, Xu H yan, et al (2018a) Complete genome sequence of Bacillus velezensis 157 isolated from Eucommia ulmoides with pathogenic bacteria inhibiting and lignocellulolytic enzymes production by SSF. 3 Biotech 8:1–10. doi: 10.1007/s13205-018-1125-2
Chen L, Gu W, Xu H yan, et al (2018b) Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass. 3 Biotech 8:1–5. doi: 10.1007/s13205-018-1270-7
Chen X, Zhang Y, Zhang Z, et al (2018c) PGAweb: A web server for bacterial pan-genome analysis. Front Microbiol 9:1–8. doi: 10.3389/fmicb.2018.01910
Chen XH, Koumoutsi A, Scholz R, et al (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014. doi: 10.1038/nbt1325
Choi HK, Kim SI, Song JY, et al (2001) Localization of paclitaxel in suspension culture of Taxus chinensis. J. Microbiol. Biotechnol. 11:458–462
Chow SY, Williams HJ, Pennington JD, et al (2007) Studies on taxadiene synthase: interception of the cyclization cascade at the verticillene stage and rearrangement to phomactatriene. Tetrahedron 63:6204–6209. doi: 10.1016/j.tet.2007.03.029
Christian N, Sullivan C, Visser ND, Clay K (2016) Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation. Microb Ecol 72:621–632. doi: 10.1007/s00248-016-0804-y
Clarridge JE (2004) Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clin Microbiol Rev 17:840–862. doi: 10.1128/CMR.17.4.840
Clay K (1998) Fungal Endophytes of Grasses : A Defensive Mutualism between Plants and Fungi. Ecology 69:10–16
Clay K, Schardl C (2002) Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. Am Nat 160:. doi: 10.1086/342161
Claydon N, Allan M, Hanson JR, Avent AG (1987) Antifungal alkyl pyrones of Trichoderma harzianum. Trans Br Mycol Soc 88:503–513. doi: 10.1016/s0007-1536(87)80034-7
Clevenger KD, Bok JW, Ye R, et al (2017) A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol 13:895–901. doi: 10.1038/nchembio.2408
Coenye T, Vandamme P (2003) Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729. doi: 10.1046/j.1462-2920.2003.00471.x
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 42:669–678. doi: 10.1016/j.soilbio.2009.11.024
Compant S, Mitter B, Colli-Mull JG, et al (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 62:188–197. doi: 10.1007/s00248-011-9883-y
Conesa A, Götz S, García-Gómez JM, et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–6. doi: 10.1093/bioinformatics/bti610
Contreras-Moreira B, Vinuesa P (2013) GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 79:7696–7701. doi: 10.1128/AEM.02411-13
Coutte F, Lecouturier D, Dimitrov K, et al (2017) Microbial lipopeptide production and purification bioprocesses, current progress and future challenges. Biotechnol J 12:1–10. doi: 10.1002/biot.201600566
Cregger MA, Veach AM, Yang ZK, et al (2018) The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6:1–14. doi: 10.1186/s40168-018-0413-8
Croteau R, Ketchum REB, Long RM, et al (2006) Taxol biosynthesis and molecular genetics. Phytochem. Rev. 5:75–97
De Wit R, Bouvier T (2006) “Everything is everywhere, but, the environment selects”; what did Baas Becking and Beijerinck really say? Environ Microbiol 8:755–758. doi: 10.1111/j.1462-2920.2006.01017.x
DeFilippi S, Groulx E, Megalla M, et al (2018) Fungal Competitors Affect Production of Antimicrobial Lipopeptides in Bacillus subtilis Strain B9–5. J Chem Ecol 1–10. doi: 10.1007/s10886-018-0938-0
Deleu M, Paquot M, Nylander T (2008) Effect of Fengycin , a Lipopeptide Produced by Bacillus subtilis , on Model Biomembranes. Biophys J 94:2667–2679. doi: 10.1529/biophysj.107.114090
Derbowka, D.R., Andersen, S., Lee, Andersen, S., Stenberg, C. (2012) Poplar and willow cultivation and utilization in Canada. 2008–2011 Canadian Country Progress Report. Canadian Report to the 24th IPC Session, Dehradun, India—International Poplar Commis.
Di M, Li-xin Z, Qiao-peng T, et al (2019) Complete genome sequence of Bacillus amyloliquefaciens YP6 , a plant growth rhizobacteria efficiently degrading a wide range of organophosphorus pesticides. 18:2–6. doi: 10.1016/S2095-3119(19)62658-4
Dillen SY, Djomo SN, Al Afas N, et al (2013) Biomass yield and energy balance of a short-rotation poplar coppice with multiple clones on degraded land during 16 years. Biomass and Bioenergy 56:157–165. doi: 10.1016/j.biombioe.2013.04.019
Ding W, Baumdicker F, Neher RA (2018) panX: pan-genome analysis and exploration. Nucleic Acids Res 46:e5. doi: 10.1093/nar/gkx977
Ding X, Liu K, Zhang Y (2017) De novo transcriptome assembly and characterization of the 10-hydroxycamptothecin-producing Xylaria sp . M71 following salicylic acid treatment §. 55:871–872. doi: 10.1007/s12275-017-7173-1
Dingle J, McGee P a (2003) Some endophytic fungi reduce the density of pustules of Puccinia recondita f. sp. tritici in wheat. Mycol Res 107:310–316. doi: 10.1017/S0953756203007512
Dissanayake AJ, Purahong W, Wubet T, et al (2018) Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera). Fungal Divers 90:85–107. doi: 10.1007/s13225-018-0399-3
dos Santos ÁF, Machado EB, Stanosz GR, Smith DR (2010) First report of Septoria musiva in poplar in Brazil. Trop Plant Pathol 35:052–053
Doty SL, Dosher MR, Singleton GL, et al (2005) Identification of an endophytic Rhizobium in stems of Populus. Symbiosis 39:27–35. doi: 10.1371/journal.pone.0155979
Du Y, Ma J, Yin Z, et al (2019) Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis. BMC Genomics 20:1–16. doi: 10.1186/s12864-019-5646-9
Dunlap CA (2015) Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis. Int J Syst Evol Microbiol 65:3507–3510. doi: 10.1099/ijsem.0.000444
Dunlap CA, Kim SJ, Kwon SW, Rooney AP (2016) Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. Plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus velezensis based on phylogenom. Int J Syst Evol Microbiol 66:1212–1217. doi: 10.1099/ijsem.0.000858
Durham WF, Tannenbaum MG (1998) Effects of endophyte consumption on food intake, growth, and reproduction in prairie voles. Can J Zool 76:960–969. doi: 10.1139/z98-021
Edgar RC (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:1–19. doi: 10.1186/1471-2105-5-113
Edgar RC, Drive RM, Valley M (2004) MUSCLE : multiple sequence alignment with high accuracy and high throughput. 32:1792–1797. doi: 10.1093/nar/gkh340
Eisenreich W, Menhardt B, Hylandst PJ, et al (1996) Studies on the biosynthesis of taxol: The taxane carbon skeleton is not of mevalonoid origin (NMR spectroscopy/Taxus chinensis/plant cell culture/terpene). Biochemistry 93:6431–6436
Fan B, Blom J, Klenk HP, Borriss R (2017) Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis species complex. Front Microbiol 8:1–15. doi: 10.3389/fmicb.2017.00022
Fan B, Wang C, Ding X, et al (2019) AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. Database (Oxford) 2019:1–7. doi: 10.1093/database/baz071
Fan B, Wang C, Song X, et al (2018) Bacillus velezensis FZB42 in 2018: The gram-positive model strain for plant growth promotion and biocontrol. Front Microbiol 9:1–14. doi: 10.3389/fmicb.2018.02491
Fao. (2012) Improving lives with poplars and willows. Synthesis of Country Progress Reports. 24th Session of the International Poplar Commission, Dehradun, India, 30 Oct–2 Nov. Working Paper IPC/12. Forest Assessment, Management and Conservation Division, FAO. Rome.
Faust K, Raes J (2012) Microbial interactions: From networks to models. Nat Rev Microbiol 10:538–550. doi: 10.1038/nrmicro2832
Feau N, Hamelin RC (2017) Say hello to my little friends: how microbiota can modulate tree health. New Phytol 215:508–510. doi: 10.1111/NPH.14649
Feau N, Mottet MJ, Périnet P, et al (2010a) Recent advances related to poplar leaf spot and canker caused by Septoria musiva. Can J Plant Pathol 32:122–134. doi: 10.1080/07060661003740009
Feau N, Mottet MJ, Périnet P, et al (2010b) Recent advances related to poplar leaf spot and canker caused by Septoria musiva. Can J Plant Pathol 32:122–134. doi: 10.1080/07060661003740009
Felsenstein J (1985) Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution (N Y) 39:783. doi: 10.2307/2408678
Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S (2017) The evolution of the host microbiome as an ecosystem on a leash. Nature 548:43–51. doi: 10.1038/nature23292
Frank AC (2011) The Genomes of Endophytic Bacteria. In: Pirttilä AM, Frank AC (eds) Endophytes of Forest Trees: Biology and Applications. Springer Netherlands, Dordrecht, pp 107–136
Frey-Klett P, Burlinson P, Deveau A, et al (2011) Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists. Microbiol Mol Biol Rev 75:583–609. doi: 10.1128/MMBR.00020-11
Fröhlich J, Hyde KD (1999) Biodiversity of palm fungi in the tropics: Are global fungal diversity estimates realistic? Biodivers Conserv 8:977–1004. doi: 10.1023/A:1008895913857
Ganley RJ, Sniezko RA, Newcombe G (2008a) Endophyte-mediated resistance against white pine blister rust in Pinus monticola. For Ecol Manage 255:2751–2760. doi: 10.1016/j.foreco.2008.01.052
Ganley RJ, Sniezko RA, Newcombe G (2008b) Endophyte-mediated resistance against white pine blister rust in Pinus monticola. For Ecol Manage 255:2751–2760. doi: 10.1016/j.foreco.2008.01.052
Gao F, Dai C, Liu X (2010) Mechanisms of fungal endophytes in plant protection against pathogens. African J Microbiol Res 4:1346–1351
Geer LY, Marchler-Bauer A, Geer RC, et al (2009) The NCBI BioSystems database. Nucleic Acids Res 38:492–496. doi: 10.1093/nar/gkp858
Gontia-Mishra I, Tripathi N, Tiwari S (2014) A simple and rapid DNA extraction protocol for filamentous fungi efficient for molecular studies. Indian J Biotechnol 13:536–539. doi: 10.1371/journal.pone.0159924
Gottel NR, Castro HF, Kerley M, et al (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944. doi: 10.1128/AEM.05255-11
Grosch R, Scherwinski K, Lottmann J, Berg G (2006) Fungal antagonists of the plant pathogen Rhizoctonia solani: selection, control efficacy and influence on the indigenous microbial community. Mycol Res 110:1464–1474. doi: 10.1016/j.mycres.2006.09.014
Gunawardena AHLAN, Greenwood JS, Dengler NG (2004) Programmed Cell Death Remodels Lace Plant Leaf Shape during Development. Plant Cell 16:60–73. doi: 10.1105/tpc.016188
Gurudatt PS, Priti V, Shweta S, et al (2010) Attenuation of camptothecin production and negative relation between hyphal biomass and camptothecin content in endophytic fungal strains isolated from Nothapodytes nimmoniana Grahm (Icacinaceae). Curr Sci 98:1006–1010
Gyenis L, Ostry ME (2003) Biological Control of Septoria Leaf Spot Disease of Hybrid Poplar in the Field
Hadfield J, Croucher NJ, Goater RJ, et al (2018) Phandango: An interactive viewer for bacterial population genomics. Bioinformatics 34:292–293. doi: 10.1093/bioinformatics/btx610
Haft DH (2015) Using comparative genomics to drive new discoveries in microbiology. Curr Opin Microbiol 23:189–196. doi: 10.1016/j.mib.2014.11.017
Hale IL, Broders K, Iriarte G (2014) A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity. Front Plant Sci 5:1–7. doi: 10.3389/fpls.2014.00492
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914. doi: 10.1139/m97-131
Hamzah TNT, Lee SY, Hidayat A, et al (2018) Diversity and characterization of endophytic fungi isolated from the tropical mangrove species, Rhizophora mucronata, and identification of potential antagonists against the soil-borne fungus, Fusarium solani. Front Microbiol 9:1–17. doi: 10.3389/fmicb.2018.01707
Hardoim PR, van Overbeek LS, Berg G, et al (2015a) The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 79:293–320. doi: 10.1128/mmbr.00050-14
Hardoim PR, van Overbeek LS, Berg G, et al (2015b) The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 79:293–320. doi: 10.1128/MMBR.00050-14
Hardoim PR, van Overbeek LS, Elsas JD van (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471. doi: 10.1016/j.tim.2008.07.008
Hassani MA, Durán P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6:58. doi: 10.1186/s40168-018-0445-0
Hawkes C V., Connor EW (2017) Translating Phytobiomes from Theory to Practice: Ecological and Evolutionary Considerations. Phytobiomes 1:57–69. doi: 10.1094/PBIOMES-05-17-0019-RVW
Heinig U, Scholz S, Jennewein S (2013) Getting to the bottom of Taxol biosynthesis by fungi. Fungal Divers 60:161–170. doi: 10.1007/s13225-013-0228-7
Herath P, Beauseigle S, Dhillon B, et al (2016) Anthropogenic signature in the incidence and distribution of an emerging pathogen of poplars. Biol Invasions 18:1147–1161. doi: 10.1007/s10530-015-1051-8
Higgins KL, Arnold AE, Coley PD, Kursar TA (2014) Communities of fungal endophytes in tropical forest grasses: Highly diverse host- and habitat generalists characterized by strong spatial structure. Fungal Ecol 8:1–11. doi: 10.1016/j.funeco.2013.12.005
Higgins KL, Arnold AE, Miadlikowska J, et al (2007) Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol Phylogenet Evol 42:543–555. doi: 10.1016/j.ympev.2006.07.012
Hoffman MT, Arnold AE (2008) Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycol Res 112:331–344. doi: 10.1016/j.mycres.2007.10.014
Huang XQ, Röder MS (2004) Molecular mapping of powdery mildew resistance genes in wheat: A review. Euphytica 137:203–223. doi: 10.1023/B:EUPH.0000041576.74566.d7
Hubbard M, Germida JJ, Vujanovic V (2014) Fungal endophyte colonization coincides with altered DNA methylation in drought-stressed wheat seedlings. Can J Plant Sci 94:223–234. doi: 10.4141/CJPS2012-111
Hutchinson LJ (1999) Wood-inhabiting microfungi isolated from Populus tremouloides from Alberta and northeastern British Columbia. Can J Bot 77:898–905. doi: 10.1139/cjb-77-6-898
Idriss EE, Makarewicz O, Farouk A, et al (2002) Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148:2097–2109. doi: 10.1099/00221287-148-7-2097
Iniguez AL, Dong Y, Carter HD, et al (2005) Regulation of enteric endophytic bacterial colonization by plant defenses. Mol Plant-Microbe Interact 18:169–178. doi: 10.1094/MPMI-18-0169
Izuno A, Tanabe AS, Toju H, et al (2016) Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: A massively parallel next-generation sequencing analysis. Mycoscience 57:171–180. doi: 10.1016/j.myc.2015.12.005
James EK, Gyaneshwar P, Mathan N, et al (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant-Microbe Interact 15:894–906. doi: 10.1094/MPMI.2002.15.9.894
Johnson JS, Spakowicz DJ, Hong BY, et al (2019) Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 10:1–11. doi: 10.1038/s41467-019-13036-1
Joubert PM, Doty SL (2018) Endophytic Yeasts: Biology, Ecology and Applications. 3–14. doi: 10.1007/978-3-319-89833-9_1
Kačík F, Ďurkovič J, Kačíková D (2012) Chemical profiles of wood components of poplar clones for their energy utilization. Energies 5:5243–5256. doi: 10.3390/en5125243
Kelemu S, White J, Muñoz F, Takayama Y (2001) An endophyte of the tropical forage grass Brachiaria brizantha: Isolating, identifying, and characterizing the fungus, and determining its antimycotic properties. Can J Microbiol 47:55–62. doi: 10.1139/cjm-47-1-55
Kembel SW, Mueller RC (2014) Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities 1. Botany 92:303–311. doi: 10.1139/cjb-2013-0194
Kemen E (2014) Microbe-microbe interactions determine oomycete and fungal host colonization. Curr Opin Plant Biol 20:75–81. doi: 10.1016/j.pbi.2014.04.005
Khoyratty S, Dupont J, Lacoste S, et al (2015) Fungal endophytes of Vanilla planifolia across Réunion Island: Isolation, distribution and biotransformation. BMC Plant Biol 15:1–19. doi: 10.1186/s12870-015-0522-5
Kõljalg U, Abarenkov K, Nilsson RH, et al (2019) The UNITE Database for Molecular Identification and for Communicating Fungal Species. Biodivers Inf Sci Stand 3:4–6. doi: 10.3897/biss.3.37402
Kong WJ, Yan YC, Li XY, Liu ZY (2018) Draft genome sequence of Bacillus velezensis PEBA20, a strain with a plant growthpromoting effect and biocontrol potential. Genome Announc 6:20–21. doi: 10.1128/genomeA.00286-18
Koumoutsi A, Henne A, Liesegang H, et al (2004) Structural and Functional Characterization of Gene Clusters Directing Nonribosomal Synthesis of Bioactive Cyclic Lipopeptides in. Society 186:1084–1096. doi: 10.1128/JB.186.4.1084
Krebs B, Höding B, Kübart S, et al (1998) Verlag Eugen Ulmer KG Use of Bacillus subtilis as biocontrol agent . I . Activities and characterization of Bacillus subtilis strains / Anwendung von Bacillus subtilis als Mittel für den biologischen Pflanzenschutz . I . Aktivitäten und Charakterisierung
Krings M, Taylor TN, Hass H, et al (2007) Fungal endophytes in a 400-million-yr-old land plant: Infection pathways, spatial distribution, and host responses. New Phytol 174:648–657. doi: 10.1111/j.1469-8137.2007.02008.x
Kumar DSS, Hyde KD (2004) Biodiversity and tissue-recurrence of endophytic fungi in Tripterygium wilfordii. Fungal Divers 17:69–90
Kumar S, Stecher G, Li M, et al (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. doi: 10.1093/molbev/msy096
Kumara PM, Shweta S, Vasanthakumari MM, et al (2014) Endophytes and plant secondary metabolite synthesis: Molecular and evolutionary perspective. In: Advances in Endophytic Research. pp 177–190
Kumaran RS, Kim HJ, Hur BK (2010) Taxol promising fungal endophyte, Pestalotiopsis species isolated from Taxus cuspidata. J Biosci Bioeng 110:541–546. doi: 10.1016/j.jbiosc.2010.06.007
Kusari P, Kusari S, Eckelmann D, et al (2016) Cross-species biosynthesis of maytansine in Maytenus serrata. RSC Adv 6:10011–10016. doi: 10.1039/C5RA25042K
Kusari P, Kusari S, Spiteller M, Kayser O (2015) Implications of endophyte-plant crosstalk in light of quorum responses for plant biotechnology. Appl. Microbiol. Biotechnol. 99:5383–5390
Kusari S, Hertweck C, Spiteller M (2012) Chemistry &amp; Biology Chemical Ecology of Endophytic Fungi: Origins of Secondary Metabolites. doi: 10.1016/j.chembiol.2012.06.004
Kusari S, Zühlke S, Spiteller M (2011) Effect of artificial reconstitution of the interaction between the plant camptotheca acuminata and the fungal endophyte fusarium solani on camptothecin biosynthesis. J Nat Prod 74:764–775. doi: 10.1021/np1008398
Kusari S, Zühlke S, Spiteller M (2009) An Endophytic Fungus from Camptotheca acuminata That Produces Camptothecin and Analogues. J Nat Prod 72:2–7. doi: 10.1021/np800455b
Lamit LJ, Holeski LM, Flores-Rentería L, et al (2016) Tree genotype influences ectomycorrhizal fungal community structure: Ecological and evolutionary implications. Fungal Ecol 1–11. doi: 10.1016/j.funeco.2016.05.013
Lamit LJ, Lau MK, Sthultz CM, et al (2014) Tree genotype and genetically based growth traits structure twig endophyte communities. Am J Bot 101:467–478. doi: 10.3732/ajb.1400034
Lang C, Seven J, Polle A (2011) Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed Central European forest. Mycorrhiza 21:297–308. doi: 10.1007/s00572-010-0338-y
Lankau RA, Keymer DP (2016) Ectomycorrhizal fungal richness declines towards the host species’ range edge. Mol Ecol 25:3224–3241. doi: 10.1111/mec.13628
LeBoldus JM, Blenis P, Thomas BR, et al (2009) Susceptibility of Populus balsamifera to Septoria musiva : A Field Study and Greenhouse Experiment. Plant Dis 93:1146–1150. doi: 10.1094/PDIS-93-11-1146
Letunic I, Bork P (2019) Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:W256–W259. doi: 10.1093/nar/gkz239
Li H (2017) Minimap2 : pairwise alignment for nucleotide sequences. 1–6
Li JY, Sidhu RS, Ford EJ, et al (1998) The induction of taxol production in the endophytic fungus — Periconia sp from Torreya grandifolia. 259–264
Li L, Ma M, Huang R, et al (2012) Induction of chlamydospore formation in fusarium by cyclic lipopeptide antibiotics from bacillus subtilis C2. J Chem Ecol 38:966–974. doi: 10.1007/s10886-012-0171-1
Li S-W, Liu M-Y, Yang R-Q (2019) Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2 . Int J Genomics 2019:1–16. doi: 10.1155/2019/7410823
Li S, Zhang Z, Cain A, et al (2005) Antifungal activity of camptothecin, trifolin, and hyperoside isolated from Camptotheca acuminata. J Agric Food Chem 53:32–37. doi: 10.1021/jf0484780
Liang H, Maynard CA, Allen RD, Powell WA (2001) Increased Septoria musiva resistance in transgenic hybrid poplar leaves expressing a wheat oxalate oxidase gene. Plant Mol Biol 45:619–629. doi: 10.1023/A:1010631318831
Lim SBY, Junqueira CM, Uchida A, et al (2018) crossm Genome Sequence of Bacillus velezensis SGAir0473 , Isolated from Tropical Air Collected in Singapore. 4–5
Lin X, Hezari M, Koepp AE, et al (1996) Mechanism of taxadiene synthase, a diterpene cyclase that catalyzes the first step of taxol biosynthesis in Pacific yew. Biochemistry 35:2968–2977. doi: 10.1021/bi9526239
Link HF. 1809. Observationes in ordines plantarum naturales, dissertatio prima, complectens anandrarum ordines Epiphytas, Mucedines, Gastromycos et Fungos. Der Gesellschaft Naturforschender Freunde zu Berlin, Berlin, Germany.
Liu, J., Liu, G. 2018. Analysis of Secondary Metabolites from Plant Endophytic Fungi. In: Ma W., Wolpert T. (eds) Plant Pathogenic Fungi and Oomycetes. Methods in Molecular Biology, vol 1848. Humana Press, New York, NY.
Liu and Reinscheid (2004) Camptothecin-resistant fungal endophytes of. Mycol Prog 3:189–192
Liu K, Ding X, Deng B (2009) Isolation and characterization of endophytic taxol-producing fungi from Taxus chinensis. 1171–1177. doi: 10.1007/s10295-009-0598-8
Loaces I, Ferrando L, Scavino AF (2011) Dynamics, Diversity and Function of Endophytic Siderophore-Producing Bacteria in Rice. Microb Ecol 61:606–618. doi: 10.1007/s00248-010-9780-9
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:. doi: 10.1371/journal.pone.0002702
Lopes R, Tsui S, Gonçalves PJRO, de Queiroz MV (2018) A look into a multifunctional toolbox: endophytic Bacillus species provide broad and underexploited benefits for plants. World J Microbiol Biotechnol 34:1–10. doi: 10.1007/s11274-018-2479-7
Madej CW, Clay K (1991) Avian seed preference and weight loss experiments: the effect of fungal endophyte-infected tall fescue seeds. Oecologia 88:296–302. doi: 10.1007/BF00320825
Martin-Garcia J, Espiga E, Pando V, Diez J (2011) Factors influencing endophytic communities in poplar plantations. Silva Fenn 45:169–180. doi: 10.14214/sf.40
Martín-García J, Müller MM, Diez JJ (2012) ITS-based comparison of endophytic mycota in twigs of native Populus nigra and cultivated P. X euramericana (cv. I-214) stands in Northern Spain. Ann For Sci 69:49–57. doi: 10.1007/s13595-011-0129-4
Martin R, Gazis R, Skaltsas D, et al (2015) Unexpected diversity of basidiomycetous endophytes in sapwood and leaves of Hevea. Mycologia 107:284–297. doi: 10.3852/14-206
Martínez-Álvarez P, Fernández-González RA, Vicente Sanz-Ros A, et al (2016) Two fungal endophytes reduce the severity of pitch canker disease in Pinus radiata seedlings. Biol Control 94:1–10. doi: 10.1016/j.biocontrol.2015.11.011
Martiny JBH, Bohannan BJM, Brown JH, et al (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112. doi: 10.1038/nrmicro1341
Maxwell DL, Kruger EL, Stanosz GR (1997) Effects of water stress on colonization of poplar stems and excised leaf disks by Septoria musiva. Phytopathology 87:381–388. doi: 10.1094/PHYTO.1997.87.4.381
Medema MH, Blin K, Cimermancic P, et al (2011) AntiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:339–346. doi: 10.1093/nar/gkr466
Mejía LC, Rojas EI, Maynard Z, et al (2008) Endophytic fungi as biocontrol agents of Theobroma cacao pathogens. Biol Control 46:4–14. doi: 10.1016/j.biocontrol.2008.01.012
Melin E (1922) On the Mycorrhizas of Pinus Silvestris L . and Picea Abies Karst. J Ecol 9:254–257
Melnick RL, Zidack NK, Bailey BA, et al (2008) Bacterial endophytes: Bacillus spp. from annual crops as potential biological control agents of black pod rot of cacao. Biol Control 46:46–56. doi: 10.1016/j.biocontrol.2008.01.022
Melo FMP de, Fiore MF, Moraes LAB de, et al (2009) Antifungal compound produced by the cassava endophyte Bacillus pumilus MAIIIM4a. Sci Agric 66:583–592. doi: 10.1590/S0103-90162009000500002
Mercado-Blanco J, Prieto P (2012) Bacterial endophytes and root hairs. Plant Soil 361:301–306. doi: 10.1007/s11104-012-1212-9
Merrikh CN, Merrikh H (2018) Gene inversion potentiates bacterial evolvability and virulence. Nat Commun 9:1–10. doi: 10.1038/s41467-018-07110-3
Miller MA, Pfeiffer W, Schwartz T (2011) The CIPRES science gateway: a community resource for phylogenetic analyses. Proc 2011 TeraGrid Conf Extrem Digit Discov 41. doi: 10.1145/2016741.2016785
Moissl-Eichinger C, Pausan M, Taffner J, et al (2018) Archaea Are Interactive Components of Complex Microbiomes. Trends Microbiol 26:70–85. doi: 10.1016/j.tim.2017.07.004
Mousa WK, Shearer C, Limay-rios V, et al (2016) fungal pathogen Fusarium graminearum. Nat Microbiol. doi: 10.1038/nmicrobiol.2016.167
Moy M, Belanger F, Duncan R, et al (2000) Identification of epiphyllous mycelial nets on leaves of grasses infected by clavicipitaceous endophytes. Symbiosis 28:291–302
Mu JH, Bollon AP, Sidhu RS (1999) Analysis of β-tubulin cDNAs from taxol-resistant Pestalotiopsis microspora and taxol-sensitive Pythium ultimum and comparison of the taxol-binding properties of their products. Mol Gen Genet 262:857–868. doi: 10.1007/s004380051151
Mukherjee AK, Das K (2005) Correlation between diverse cyclic lipopeptides production and regulation of growth and substrate utilization by Bacillus subtilis strains in a particular habitat. FEMS Microbiol Ecol 54:479–489. doi: 10.1016/j.femsec.2005.06.003
Müller H, Berg C, Landa BB, et al (2015) Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front Microbiol 6:1–9. doi: 10.3389/fmicb.2015.00138
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 Tissue Organ Cult 98:35–45. doi: 10.1007/s11240-009-9536-8
Newcombe G (1998) A review of exapted resistance to diseases of Populus. Eur J For Pathol 28:209–216. doi: 10.1111/j.1439-0329.1998.tb01175.x
Newcombe G, Ostry M (2001) Recessive resistance to Septoria stem canker of hybrid poplar. Phytopathology 91:1081–1084. doi: 10.1094/PHYTO.2001.91.11.1081
Newcombe. G., Ostry, M.E., Hubbes, M., Perinet, P., & Mottet, M.J. 2001. Poplar diseases. In: Dickmann DI, Isebrands JG, Eckenwalder JE, Richardson J (eds) Poplar culture North America. National Research Council of Canada Press, Ottawa: 249–276.
Nilsson RH, Larsson KH, Taylor AFS, et al (2019) The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47:D259–D264. doi: 10.1093/nar/gky1022
Nissinen RM, Männistö MK, van Elsas JD (2012) Endophytic bacterial communities in three arctic plants from low arctic fell tundra are cold-adapted and host-plant specific. FEMS Microbiol Ecol 82:510–522. doi: 10.1111/j.1574-6941.2012.01464.x
Oliveira MNV, Santos TMA, Vale HMM, et al (2013) Endophytic microbial diversity in coffee cherries of coffea arabica from southeastern Brazil. Can J Microbiol 59:221–230. doi: 10.1139/cjm-2012-0674
Ondov BD, Treangen TJ, Melsted P, et al (2016) Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biol 17:1–14. doi: 10.1186/s13059-016-0997-x
Ongena M, Jacques P (2008) Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol 16:115–125. doi: 10.1016/j.tim.2007.12.009
Ostry, M., & McNabb, H. 1983. Diseases of intensively cultured hybrid poplars: a summary of recent research in the north central region. In: Hansen, Edward A (eds) Intensive planting culture 12 years research general technologies. U.S. Department of Agriculture, Forest Service, North Central Forest Experiment Station, St. Paul, MN:102–109.
Ostry, M.E. 1987. Biology of Septoria musiva and Marssonina brunnea in hybrid Populus plantations and control of Septoria canker in nurseries. For Pathol. 17:158–165.
Ostry M, Harlod M (1985) Susceptibility of Populus Species and Hybrids to Disease in the North Central United States. Plant Dis 69:755. doi: 10.1094/pd-69-755
Page AJ, Cummins CA, Hunt M, et al (2015) Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. doi: 10.1093/bioinformatics/btv421
Park YH, Kim Y, Mishra RC, Bae H (2017) Fungal endophytes inhabiting mountain-cultivated ginseng (Panax ginseng Meyer): Diversity and biocontrol activity against ginseng pathogens. Sci Rep 7:1–10. doi: 10.1038/s41598-017-16181-z
Parks DH, Imelfort M, Skennerton CT, et al (2015) CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114
Pathak K V., Keharia H (2014) Identification of surfactins and iturins produced by potent fungal antagonist, Bacillus subtilis K1 isolated from aerial roots of banyan (Ficus benghalensis) tree using mass spectrometry. 3 Biotech 4:283–295. doi: 10.1007/s13205-013-0151-3
Pathak K V., Keharia H, Gupta K, et al (2012) Lipopeptides from the banyan endophyte, Bacillus subtilis K1: Mass spectrometric characterization of a library of fengycins. J Am Soc Mass Spectrom 23:1716–1728. doi: 10.1007/s13361-012-0437-4
Pavlo A, Leonid O, Iryna Z, et al (2011) Endophytic bacteria enhancing growth and disease resistance of potato (Solanum tuberosum L.). Biol Control 56:43–49. doi: 10.1016/j.biocontrol.2010.09.014
Petrini, O. 1991. Fungal endophytes of tree leaves. In Andrews JH, Hirano SS. (ed), Microbial ecology of leaves. Springer-Verlag, New York, NY. , p 179–197. doi:10.1007/978-1-4612-3168-4_9.
Peyronel B. 1924. Prime ricerche sulla micorizae endotrofiche e sulla microflora radicola normalle della fanerograme. Revista Biologia 6: 17– 53.
Pinon, J., Frey, P., Husson, C., & Schipfer, A. 1998. Poplar rust (Melampsora larici- populina): the development of E4 pathotypes in France since 1994. In Proceedings of the First IUFRP Rust Forest Trees WP Conference, 2–7 August 1998, Saariselkä, Finland Finnish Research Institute. Research Papers, 712, 57–64.
Pirozynski K, Malloch D (1975) The Origin of land plants: A matter of mycopartosim. 6:153–164
Piotrowski, J.S. 2007. Succession of Arbuscular Mycorrhizal Fungi: Causes, Consequences, and Considerations. Graduate student Theses, Dissertations & Professional Papers. University of Montana.932.
Pleban S, Chernin L, Chet I (1997) Chitinolytic activity of an endophytic strain of Bacillus cereus. Lett Appl Microbiol 25:284–288. doi: 10.1046/j.1472-765X.1997.00224.x
Porras-Alfaro A, Bayman P (2011) Hidden Fungi, Emergent Properties: Endophytes and Microbiomes. Annu Rev Phytopathol 49:291–315. doi: 10.1146/annurev-phyto-080508-081831
Porter JK. 1994. Chemical constituents of grass endophytes. C.W. Bacon, J.F. White Jr. (Eds.), Biotechnology of Endophytic Fungi of Grasses, CRC Press, Boca Raton, FL (1994), pp. 103-123
Priti V, Ramesha BT, Singh S, et al (2009) How promising are endophytic fungi as alternative sources of plant secondary metabolites. Curr Sci 97:477–478
Raaijmakers JM, Mazzola M (2012) Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria. Annu Rev Phytopathol 50:403–424. doi: 10.1146/annurev-phyto-081211-172908
Raghavendra AKH, Newcombe G (2013) The contribution of foliar endophytes to quantitative resistance to Melampsora rust. New Phytol 197:909–918. doi: 10.1111/nph.12066
Ravel C, Courty C, Coudret A, Charmet G (1997) Beneficial effects of Neotyphodium lolii on the growth and the water status in perennial ryegrass cultivated under nitrogen deficiency or drought stress. Agronomie 17:173–181. doi: 10.1051/agro:19970304
Razafindralambo H, Paquot M, Hbid C, et al (1993) Purification of antifungal lipopeptides by reversed-phase high-performance liquid chromatography. J Chromatogr A 639:81–85. doi: 10.1016/0021-9673(93)83091-6
Reinhold-Hurek B, Hurek T (2011) Living inside plants: Bacterial endophytes. Curr Opin Plant Biol 14:435–443. doi: 10.1016/j.pbi.2011.04.004
Ren J-H, Li H, Wang Y-F, et al (2013) Biocontrol potential of an endophytic Bacillus pumilus JK-SX001 against poplar canker. Biol Control 67:421–430. doi: 10.1016/j.biocontrol.2013.09.012
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2015) JSpeciesWS: A web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. doi: 10.1093/bioinformatics/btv681
Richter M, Rossello R (2009) Shifting the genomic gold standard for the prokaryotic species definition. 1–6
Rodriguez RJ, White JF, Arnold AE, Redman RS (2009) Fungal endophytes: Diversity and functional roles: Tansley review. New Phytol 182:314–330. doi: 10.1111/j.1469-8137.2009.02773.x
Romero-tabarez M, Jansen R, Sylla M, et al (2006) 7- O -Malonyl Macrolactin A , a New Macrolactin Antibiotic from Bacillus subtilis Active against Methicillin-Resistant Staphylococcus aureus , Vancomycin-Resistant Enterococci , and a Small-Colony Variant of Burkholderia cepacia. 50:1701–1709. doi: 10.1128/AAC.50.5.1701
Roongsawang N, Washio K, Morikawa M (2011) Diversity of nonribosomal peptide synthetases involved in the biosynthesis of lipopeptide biosurfactants. Int J Mol Sci 12:141–172. doi: 10.3390/ijms12010141
Rosenblueth M, Martínez-Romero E (2006) Bacterial Endophytes and Their Interactions with Hosts. Mol Plant-Microbe Interact 19:827–837. doi: 10.1094/MPMI-19-0827
Rubini MR, Silva-Ribeiro RT, Pomella AWV, et al (2005) Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches’ Broom Disease. Int J Biol Sci 1:24–33. doi: 10.7150/ijbs.1.24
Rückert C, Blom J, Chen XH, et al (2011) Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. J Biotechnol 155:78–85. doi: 10.1016/j.jbiotec.2011.01.006
Rudrappa T, Biedrzycki ML, Kunjeti G, et al (2010) The rhizobacterial elicitor acetoin induces systemic resistance in Arabidopsis thaliana. doi: 10.4161/cib.3.2.10584
Ruiz-García C, Béjar V, Martínez-Checa F, et al (2005) Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Int J Syst Evol Microbiol 55:191–195. doi: 10.1099/ijs.0.63310-0
Sachin N, Manjunatha B. L, Mohana Kumara P, Ravikanth G., Shweta Singh, Suryanarayanan T. S, Ganeshaiah K. N., and Uma Shaanker R. 2013. Do endophytic fungi possess pathway genes for plant secondary metabolites? Current Science, 104 (2): 174-182.
Sachman-ruiz B, Lozano L (2015) Draft Genome Sequence of Bacillus amyloliquefaciens JJC33M , Isolated. 3:2015. doi: 10.1128/genomeA.01519-14.Copyright
Sahashi N, Kubono T, Miyasawa Y, Ito S (1999) Temporal variations in isolation frequency of endophytic fungi of Japanese beech. Can J Bot 77:197–202. doi: 10.1139/cjb-77-2-197
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. doi: 10.1093/oxfordjournals.molbev.a040454
Sakalidis ML, Feau N, Dhillon B, Hamelin RC (2016) Genetic patterns reveal historical and contemporary dispersal of a tree pathogen. Biol Invasions 18:1781–1799. doi: 10.1007/s10530-016-1120-7
Santamaría O, Diez JJ (2005) Fungi in leaves, twigs and stem bark of Populus tremula from northern Spain. For Pathol 35:95–104. doi: 10.1111/j.1439-0329.2004.00389.x
Sari E, Etebarian HR, Aminian H (2007) The effects of Bacillus pumilus, isolated from wheat rhizosphere, on resistance in wheat seedling roots against the take-all fungus, Gaeumannomyces graminis var. tritici. J Phytopathol 155:720–727. doi: 10.1111/j.1439-0434.2007.01306.x
Sasirekha B, Srividya S (2016) Siderophore production by Pseudomonas aeruginosa FP6, a biocontrol strain for Rhizoctonia solani and Colletotrichum gloeosporioides causing diseases in chilli. Agric Nat Resour 50:250–256. doi: 10.1016/j.anres.2016.02.003
Sasse J, Martinoia E, Northen T (2018) Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? Trends Plant Sci 23:25–41. doi: 10.1016/j.tplants.2017.09.003
Saucedo-García A, Anaya AL, Espinosa-García FJ, González MC (2014) Diversity and communities of foliar endophytic fungi from different agroecosystems of coffea arabica L. in two regions of Veracruz, Mexico. PLoS One 9:. doi: 10.1371/journal.pone.0098454
Schloss PD, Westcott SL, Ryabin T, et al (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi: 10.1128/AEM.01541-09
Schmidt CS, Lovecká P, Mrnka L, et al (2018) Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro. Microb Ecol 75:955–969. doi: 10.1007/s00248-017-1103-y
Schneider T, Müller A, Miess H, Gross H (2014) Cyclic lipopeptides as antibacterial agents - Potent antibiotic activity mediated by intriguing mode of actions. Int J Med Microbiol 304:37–43. doi: 10.1016/j.ijmm.2013.08.009
Schoch CL, Seifert KA, Huhndorf S, et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109:6241–6246. doi: 10.1073/pnas.1117018109
Seemann T (2014) Prokka : rapid prokaryotic genome annotation. 30:2068–2069. doi: 10.1093/bioinformatics/btu153
Selosse M, Tacon F Le (1998) The land flora: a phototroph–fungus partnership? 13:15–20
Shakya M, Gottel N, Castro H, et al (2013) A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees. PLoS One 8:e76382. doi: 10.1371/journal.pone.0076382
Shehata HR, Lyons EM, Jordan KS, Raizada MN (2016) Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa. J Appl Microbiol 120:756–769. doi: 10.1111/jam.13050
Shi YW, TaPa MS, Li C, et al (2015) Diversity and space–time dynamics of endophytic archaea from sugar beet in the north slope of Tianshan Mountain revealed by 454 pyrosequencing and T-RFLP. World J Microbiol Biotechnol 31:1031–1039. doi: 10.1007/s11274-015-1853-y
Shimizu, K. 1994. Biological control of Septoria leaf spot on hybrid poplars using Streptomyces spp. MS thesis. University of Minnesota, St. Paul.
Shipunov A, Newcombe G, Raghavendra AKH, Anderson CL (2008) Hidden diversity of endophytic fungi in an invasive plant. Am J Bot 95:1096–1108. doi: 10.3732/ajb.0800024
Shweta S, Shivanna MB, Gurumurthy BR, Shaanker RU (2014) Inhibition of fungal endophytes by camptothecine produced by their host plant , Inhibition of fungal endophytes by camptothecine produced by their host plant , Nothapodytes nimmoniana ( Grahm ) Mabb . ( Icacinaceae )
Sieber TN (2007) Endophytic fungi in forest trees: are they mutualists? Fungal Biol Rev 21:75–89. doi: 10.1016/j.fbr.2007.05.004
Simão FA, Waterhouse RM, Ioannidis P, et al (2015) BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. doi: 10.1093/bioinformatics/btv351
Sirikantaramas S, Sudo H, Asano T (2007) Transport of camptothecin in hairy roots of Ophiorrhiza pumila. 68:2881–2886. doi: 10.1016/j.phytochem.2007.08.028
Sirikantaramas S, Yamazaki M, Saito K (2008) Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants. Proc Natl Acad Sci 105:6782–6786. doi: 10.1073/pnas.0801038105
Sirikantaramas S, Yamazaki M, Saito K (2014) How Plants Avoid the Toxicity of Self-Produced Defense Bioactive Compounds. In: Natural Products. John Wiley & Sons, Inc., Hoboken, NJ, USA, pp 67–82
Soares SC, Geyik H, Ramos RTJ, et al (2016) GIPSy: Genomic island prediction software. J Biotechnol. doi: 10.1016/j.jbiotec.2015.09.008
Soliman SSM, Greenwood JS, Bombarely A, et al (2015) An endophyte constructs fungicide-containing extracellular barriers for its host plant. Curr Biol 25:2570–2576. doi: 10.1016/j.cub.2015.08.027
Soliman SSM, Raizada MN (2013) Interactions between Co-Habitating fungi Elicit Synthesis of Taxol from an Endophytic Fungus in Host Taxus Plants. Front Microbiol 4:3. doi: 10.3389/fmicb.2013.00003
Soliman SSM, Trobacher CP, Tsao R, et al (2013) A fungal endophyte induces transcription of genes encoding a redundant fungicide pathway in its host plant. BMC Plant Biol 13:93. doi: 10.1186/1471-2229-13-93
Spielman LJ, Hubbes M, Lin D (1986) Septoria musiva on hybrid poplar in southern Ontario. Plant Dis 70:
Staniek A, Woerdenbag HJ, Kayser O (2009) Taxomyces andreanae: A presumed paclitaxel producer demystified? Planta Med 75:1561–1566. doi: 10.1055/s-0029-1186181
Stierle A, Strobel G, Stierle D (1993) Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science (80- ) 260:214–216. doi: 10.1126/science.8097061
Stone JK, Polishook JOND, White JF (2004) Endophytic fungi. In: Mueller G, Bills GF FM (ed) Biodiversity of fungi: Inventory and monitoring methods. Elsevier B.V., pp 241–270
Strullu-derrien C, Kenrick P, Pressel S, et al (2014) Fungal associations in Horneophyton ligneri from the Rhynie Chert ( c . 407 million year old ) closely resemble those in extant lower land plants : novel insights into ancestral plant – fungus symbioses. 964–979
Sugimoto Y, Tsukahara S, Oh-hara T, et al (1990) Elevated expression of DNA topoisomerase II in camptothecin-resistant human tumor cell lines. Cancer Res 50:7962–5
Sumpavapol P, Tongyonk L, Tanasupawat S, et al (2010) Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand. Int J Syst Evol Microbiol 60:2364–2370. doi: 10.1099/ijs.0.018879-0
Sun L, Qiu F, Zhang X, et al (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55:415–424. doi: 10.1007/s00248-007-9287-1
Suryanarayanan TS (2013) Endophyte research: Going beyond isolation and metabolite documentation. Fungal Ecol. 6:561–568
Suryanarayanan TS, Kumaresan V, Johnson JA (1998) Foliar fungal endophytes from two species of the mangrove Rhizophora. Can J Microbiol 44:1003–1006. doi: 10.1139/w98-087
Suryanarayanan TS, Venkatesan G, Murali TS (2003) Endophytic fungal communities in leaves of tropical forest trees: Diversity and distribution patterns. Curr Sci 85:489–493. doi: 10.2307/24108544
Sy A, Timmers ACJ, Knief C, Vorholt JA (2005) Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol 71:7245–7252. doi: 10.1128/AEM.71.11.7245-7252.2005
Taffner J, Bergna A, Cernava T, Berg G (2020) Tomato-Associated Archaea Show a Cultivar-Specific Rhizosphere Effect but an Unspecific Transmission by Seeds. Phytobiomes J PBIOMES-01-20-0. doi: 10.1094/pbiomes-01-20-0017-r
Tan RX, Zou WX (2001) Endophytes: a rich source of functional metabolites. Nat Prod Rep 18:448–459. doi: 10.1039/b100918o
Tan S, Dong Y, Liao H, et al (2013) Antagonistic bacterium Bacillus amyloliquefaciens induces resistance and controls the bacterial wilt of tomato. Pest Manag Sci 69:1245–52. doi: 10.1002/ps.3491
Tanabe AS, Toju H (2013) Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants. PLoS One 8:. doi: 10.1371/journal.pone.0076910
Tejesvi M V., Mahesh B, Nalini MS, et al (2005) Endophytic fungal assemblages from inner bark and twig of Terminalia arjuna W. & A. (Combretaceae). World J Microbiol Biotechnol 21:1535–1540. doi: 10.1007/s11274-005-7579-5
Tettelin H, Masignani V, Cieslewicz MJ, et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome” (Proceedings of the National Academy of Sciences of the United States of America (September 27, 2005) 102, 39 (13950-13955)). Proc Natl Acad Sci U S A 102:16530. doi: 10.1073/pnas.0508532102
Thasana N, Prapagdee B, Rangkadilok N, et al (2010) Bacillus subtilis SSE4 produces subtulene A, a new lipopeptide antibiotic possessing an unusual C15 unsaturated β-amino acid. FEBS Lett 584:3209–3214. doi: 10.1016/j.febslet.2010.06.005
Trémouillaux-Guiller J, Rohr T, Rohr R, Huss VAR (2002) Discovery of an endophytic alga in Ginkgo biloba. Am J Bot 89:727–733. doi: 10.3732/ajb.89.5.727
Tripathi S, Kamal S, Sheramati I, et al (2008) Mycorrhizal fungi and other root endophytes as biocontrol agents against root pathogens. Mycorrhiza State Art, Genet Mol Biol Eco-Function, Biotechnol Eco-Physiology, Struct Syst (Third Ed 281–306. doi: 10.1007/978-3-540-78826-3_14
Unterseher M, Petzold A, Schnittler M (2012a) Xerotolerant foliar endophytic fungi of Populus euphratica from the Tarim River basin, Central China are conspecific to endophytic ITS phylotypes of Populus tremula from temperate Europe. Fungal Divers 54:133–142. doi: 10.1007/s13225-012-0167-8
Unterseher M, Petzold A, Schnittler M (2012b) Xerotolerant foliar endophytic fungi of Populus euphratica from the Tarim River basin, Central China are conspecific to endophytic ITS phylotypes of Populus tremula from temperate Europe. Fungal Divers 54:133–142. doi: 10.1007/s13225-012-0167-8
Van Overbeek LS, Bergervoet JHW, Jacobs FHH, Van Elsas JD (2004) The low-temperature-induced viable-but-nonculturable state affects the virulence of Ralstonia solanacearum Biovar 2. Phytopathology 94:463–469. doi: 10.1094/PHYTO.2004.94.5.463
Vasanthakumari MM, Jadhav SS, Sachin N, et al (2015) Restoration of camptothecine production in attenuated endophytic fungus on re-inoculation into host plant and treatment with DNA methyltransferase inhibitor. World J Microbiol Biotechnol 31:1629–1639. doi: 10.1007/s11274-015-1916-0
Vincent JB, Weiblen GD, May G (2016) Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Mol Ecol 25:825–841. doi: 10.1111/mec.13510
Vos M, Quince C, Pijl AS, et al (2012) A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity. 7:1–8. doi: 10.1371/journal.pone.0030600
Wagner LJ (1994) Effect of Taxol and Related Compounds on Growth of Plant Pathogenic Fungi. Phytopathology 84:1173
Walter M, Harris-Virgin P, Morgan C, et al (2005) Fungicides for control of flower and berry infections of Botrytis cinerea in boysenberry. Crop Prot 24:625–631. doi: 10.1016/j.cropro.2004.11.005
Waterhouse RM, Seppey M, Simao FA, et al (2018) BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548. doi: 10.1093/molbev/msx319
Waterman, A. M. 1954. Septoria canker of poplars in the United States. U.S. Dep. Agric. Circ. No. 947:1-22.
Wattam AR, Davis JJ, Assaf R, et al (2017) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 45:D535–D542. doi: 10.1093/nar/gkw1017
Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511. doi: 10.1093/jexbot/52.suppl_1.487
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and Direct Sequencing of Fungal Ribosomal Rna Genes for Phylogenetics. PCR Protoc 315–322. doi: 10.1016/b978-0-12-372180-8.50042-1
Wiyakrutta S, Sriubolmas N, Panphut W, et al (2004) Endophytic fungi with anti-microbial, anti-cancer and anti-malarial activities isolated from Thai medicinal plants. World J Microbiol Biotechnol 20:265–272. doi: 10.1023/B:WIBI.0000023832.27679.a8
Xia Y, DeBolt S, Dreyer J, et al (2015) Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices. Front Plant Sci 6:1–10. doi: 10.3389/fpls.2015.00490
Xin G, Glawe D, Doty SL (2009) Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. Mycol Res 113:973–980. doi: 10.1016/j.mycres.2009.06.001
Xiong Z-QQ, Yang Y-YY, Zhao N, Wang Y (2013) Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew, Taxus x media. BMC Microbiol 13:71. doi: 10.1186/1471-2180-13-71
Yamazaki Y, Urano A, Sudo H, et al (2003) Metabolite profiling of alkaloids and strictosidine synthase activity in camptothecin producing plants. Phytochemistry 62:461–470. doi: 10.1016/S0031-9422(02)00543-5
Yang, D., Bernier, L., & Dessureault, M. 1994. Biological control of Septoria leaf spot of poplar by Phaeotheca dimorphospora. Plant Dis. 78:821-825.
Yang Y, Zhao H, Barrero RA, et al (2014) Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics 15:69. doi: 10.1186/1471-2164-15-69
Yazaki K (2005) Transporters of secondary metabolites. Curr Opin Plant Biol 8:301–307. doi: 10.1016/j.pbi.2005.03.011
Yong L, Chun-gen P, GUO., et al (2013) Predominant Species Dynamic and Diversity of Fungal Endophytes in Barks of Two Populus Cultivars. For Res 26:292–298
Young DH, Michelotti EL, Swindell CS, Krauss NE (1992) Antifungal properties of taxol and various analogues Research Articles. Experientia 48:
Yuan J, Zhao M, Li R, et al (2016) Antibacterial Compounds-Macrolactin Alters the Soil Bacterial Community and Abundance of the Gene Encoding PKS. 7:1–10. doi: 10.3389/fmicb.2016.01904
Zeriouh H, Romero D, Garcia-Gutierrez L, et al (2011) The iturin-like lipopeptides are essential components in the biological control arsenal of Bacillus subtilis against bacterial diseases of cucurbits. Mol Plant Microbe Interact 24:1540–52. doi: 10.1094/MPMI-06-11-0162
Zhang N, Yang D, Kendall JRA, et al (2016) Comparative genomic analysis of Bacillus amyloliquefaciens and Bacillus subtilis reveals evolutional traits for adaptation to plant-associated habitats. Front Microbiol 7:. doi: 10.3389/fmicb.2016.02039
Zhang P, Zhou PP, Yu LJ (2009) An endophytic taxol-producing fungus from taxus media, cladosporium cladosporioides MD2. Curr Microbiol 59:227–232. doi: 10.1007/s00284-008-9270-1
Zhao J, Shan T, Mou Y, Zhou L (2011) Plant-Derived Bioactive Compounds Produced by Endophytic Fungi. Mini-Reviews Med Chem 11:159–168. doi: 10.2174/138955711794519492
Zhong L, Zhou Y, Gao S, et al (2011) Endophytic fungi from the hybrid ’ Neva ’ of Populus deltoides Marsh × Populus nigra L . and their antimicrobial activity. 5:3924–3929
All items in Spectrum are protected by copyright, with all rights reserved. The use of items is governed by Spectrum's terms of access.

Repository Staff Only: item control page

Downloads per month over past year

Research related to the current document (at the CORE website)
- Research related to the current document (at the CORE website)
Back to top Back to top