참고문헌
- Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A. and Holmes, S. P. 2016. DADA2: highresolution sample inference from Illumina amplicon data. Nat. Methods 13:581-583. https://doi.org/10.1038/nmeth.3869
- Chen, Q., Jiang, J. R., Zhang, G. Z., Cai, L. and Crous, P. W. 2015. Resolving the Phoma enigma. Stud. Mycol. 82:137-217. https://doi.org/10.1016/j.simyco.2015.10.003
- Chi, F., Shen, S.-H., Cheng, H.-P., Jing, Y.-X., Yanni, Y. G. and Dazzo, F. B. 2005. Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl. Environ. Microbiol. 71:7271-7278. https://doi.org/10.1128/AEM.71.11.7271-7278.2005
- Cho, G., Kim, M.-J., Kwon, Y. and Kwak, Y.-S. 2018. Comparison of endophytic microbial community in kiwifruit plant cultivars. Plant Pathol. J. 34:341-346. https://doi.org/10.5423/PPJ.NT.12.2017.0284
- Coleman-Derr, D., Desgarennes, D., Fonseca-Garcia, C., Gross, S., Clingenpeel, S., Woyke, T., North, G., Visel, A., Partida-Martinez, L. P. and Tringe, S. G. 2015. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209:798-811. https://doi.org/10.1111/nph.13697
- Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A. and Schadt, C. W. 2018. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6:31. https://doi.org/10.1186/s40168-018-0413-8
- Daniel, R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3:470-478. https://doi.org/10.1038/nrmicro1160
- Garrido, L. M., Alves, J. M. P., Oliveria, L. S., Gruber, A., Padilla, G. and Araujo, W. L. 2016. Draft genome sequence of Curtobacterium sp. strains ER1/6, and endophytic strain isolated from Citrus sinensis with potential to be used as a biocontrol agent. Genome Announc. 4:e01264-16.
- Hulikere, M. M., Joshi, C. G., Danagoudar, A., Poyya, J., Kudva, A. K. and Dhanajaya, B. L. 2017. Biogenic synthesis of gold nanoparticles by marine endophytic fungus-Cladosporium cladosporioides isolated from seaweed and evaluation of their antioxidant and antimicrobial properties. Process Biochem. 63:137-144. https://doi.org/10.1016/j.procbio.2017.09.008
- Khan, A. L., Waqas, M., Kang, S.-M., Al-Harrasi, A., Hussain, J., Al-Rawahi, A., Al-Khiziri, S., Ullah, I., Ali, L., Jung, H.-Y. and Lee, I.-J. 2014. Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth. J. Microbiol. 52:689-695. https://doi.org/10.1007/s12275-014-4002-7
- Koljalg, U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F. S., Bahram, M., Bates, S. T., Bruns, T. D., Bengtsson-Palme, J., Callaghan, T. M., Douglas, B., Drenkhan, T., Eberhardt, U., Duenas, M., Grebenc, T., Griffith, G. W., Hartmann, M., Kirk, P. M., Kohout, P., Larsson, E., Lindahl, B. D., Lucking, R., Martin, M. P., Matheny, P. B., Nguyen, N. H., Niskanen, T., Oja, J., Peay, K. G., Peintner, U., Peterson, M., Poldmaa, K., Saag, L., Saar, I., Schussler, A., Scott, J. A., Senes, C., Smith, M. E., Suija, A., Taylor, D. L., Telleria, M. T., Weiss, M. and Larsson, K. H. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22:5271-5277. https://doi.org/10.1111/mec.12481
- Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G. and Huttenhower, C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814-821. https://doi.org/10.1038/nbt.2676
- Love, M. I., Huber, W. and Anders, S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550. https://doi.org/10.1186/s13059-014-0550-8
- Lumactud, R., Shen, S. Y., Lau, M. and Fulthorpe, R. 2016. Bacterial endophytes isolated from plants in natural oil seep soils with chronic hydrocarbon contamination. Front. Microbiol. 7:755.
- McMurdie, P. J. and Holmes, S. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217. https://doi.org/10.1371/journal.pone.0061217
- Miao, L.-Y., Mo, X.-C., Xi, X.-Y., Zhou, L., De, G., Ke, Y.-S., Liu, P., Song, F.-J., Jin, W.-W. and Zhang, P. 2018. Transcriptome analysis of a taxol-producing endophytic fungus Cladosporium cladosporioides MD2. AMB Expr. 8:21. https://doi.org/10.1186/s13568-018-0555-x
- Miao, Y.-Y., Shi, S.-L., Zhang, J.-G. and Mohamad, O. A. 2017. Migration, colonization and seedling growth of rhizobia with matrine treatment in alfalfa (Medicago sativa L.). Acta Agric. Scand. B. Soil Plant Sci. 68:26-38.
- Miliute, I., Buzaite, O., Baniulis, D. and Stanys, V. 2015. Bacterial endophytes in agricultural crops and their role in stress tolerance: a review. Zemdirbyste 102:465-478. https://doi.org/10.13080/z-a.2015.102.060
- Montel, E., Bridge, P. D. and Sutton, B. C. 1991. An integrated approach to Phoma systematics. Mycopathologia 115:89-103. https://doi.org/10.1007/BF00436797
- Nguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Schilling J. S. and Kennedy, P. G. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20:241-248. https://doi.org/10.1016/j.funeco.2015.06.006
- Qin, Y., Pan, X. and Yuan, Z. 2016. Seed endophytic microbiota in a coastal plant and phytobeneficial properties of the fungus Cladosporium cladosporioides. Fungal Ecol. 24:53-60. https://doi.org/10.1016/j.funeco.2016.08.011
- Ottesen, A. R., Pena, A. G., White, J. R., Pettengill, J. B., Li, C., Allard, S., Rideout, S., Allard, M., Hill, T., Evans, P., Strain, E., Musser, S., Knight, R. and Brown, E. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 13:114. https://doi.org/10.1186/1471-2180-13-114
- Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glockner, F. O. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596. https://doi.org/10.1093/nar/gks1219
- Quiza, L., St-Arnaud, M. and Yergeau, E. 2015. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. Front. Plant Sci. 6:507.
- Rodriguez, R. J., White, J. F. Jr., Arnold, A. E. and Redman, R. S. 2008. Fungal endophytes: diversity and functional roles. New Phytol. 182:314-330. https://doi.org/10.1111/j.1469-8137.2009.02773.x
- Santoyo, G., Moreno-Hagelsieb, G., del Carmen Orozco-Mosqueda, M. and Glick, B. R. 2016. Plant growth-promoting bacterial endophytes. Microbiol. Res. 183:92-99. https://doi.org/10.1016/j.micres.2015.11.008
- Torres, D. E., Rojas-Martinez, R. I., Zavaleta-Mejia, E., Guevara-Fefer, P., Marquez-Guzman, G. J. and Perez-Martinez, C. 2017. Cladosporium cladosporioides and Cladosporium pseudocladosporioides as potential new fungal antagonists of Puccinia horiana Henn., the causal agent of chrysanthemum white rust. PLoS ONE 12:e0170782. https://doi.org/10.1371/journal.pone.0170782
- Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A. and Dufresne, A. 2015. The importance of the microbiome of the plant holobiont. New Phytol. 206:1196-1206. https://doi.org/10.1111/nph.13312
- Wickham, H. 2016. ggplot2: elegant graphics for data analysis. 2nd ed. Springer International Publishing, Cham, Switzerland. 260 pp.