박사

Metagenomic analysis of soil microbial communities on Ulleungdo and Dokdo Islands : 울릉도와 독도의 토양 미생물군집의 Metagenomic 분석

남윤종 2015년
논문상세정보
' Metagenomic analysis of soil microbial communities on Ulleungdo and Dokdo Islands : 울릉도와 독도의 토양 미생물군집의 Metagenomic 분석' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • dokdo
  • metagenomic
  • pyrosequencing
  • ulleungdo
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
275 0

0.0%

' Metagenomic analysis of soil microbial communities on Ulleungdo and Dokdo Islands : 울릉도와 독도의 토양 미생물군집의 Metagenomic 분석' 의 참고문헌

  • de Hoog, G.S., Vicente, V., Caligiorne, R.B., Kantarcioglu, S.,Tintelnot, K. et al. (2003) Species diversity and polymorphism in theExophiala spinifera clade containing opportunistic black yeast-likefungi. J. Clin. Microbiol., 41, 4767?4778.
  • da Costa, G.L., de Moraes, A.M., and de Oliveira, P.C. (1998)Pathogenic action of Penicillium species on mosquito vectors ofhuman tropical diseases. J. Basic Microbiol., 38, 337?341.
  • You, Y.H., Yoon, H., Kim, H., Lim, S.H., Shin, J.H. et al. (2013) Plantgrowth-promoting activity and genetic diversity of endophytic fungiisolated from native plants in Dokdo Islands for restoration of acoastal ecosystem. J. Life Sci., 23, 95?101.
  • You, Y.H., Yoon, H, Lee, GS., Woo, J.R., Shin, J.H. et al. (2011a)Diversity and plant growth-promotion of endophytic fungi isolatedfrom the roots of plants in Dokdo Islands. J. Life Sci., 21, 992?996.
  • You, Y.H, Yoon, H., Woo, J.R., Seo, Y., Kim, M. et al. (2011b) Plantgrowth-promoting activity of endophytic fungi isolated from the rootsof native plants in Dokdo Islands. J. Life Sci., 21, 1619?1624.
  • Yoon, J. H., Schumann, P., Kang, S. J., Jung, S. Y., and Oh, T. K. (2006f) Isoptericola dokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 56, 2893? 2897.
  • Yoon, J. H., Lee, S. Y., Kang, S. J., and Oh, T. K. (2008b)Phycicoccus dokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 58, 597? 600.
  • Yoon, J. H., Lee, M. H., Kang, S. J., Lee, S. Y., and Oh, T. K. (2006e)Sphingomonas dokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 56, 2165? 2169.
  • Yoon, J. H., Kang, S. J., and Oh, T. K. (2006b) Variovoraxdokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol.,56, 811?814.
  • Yoon, J. H., Kang, S. J., and Oh, T. K. (2006a) Polaribacterdokdonensis sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol., 56, 1251? 1255.
  • Yoon, J. H., Kang, S. J., Oh, H. W., and Oh, T. K. (2006d)Stenotrophomonas dokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 56, 1363? 1367.
  • Yoon, J. H., Kang, S. J., Lee, S. Y., Lee, C. H., and Oh, T. K. (2005a)Maribacter dokdonensis sp. nov., isolated from sea water off aKorean island, Dokdo. Int. J. Syst. Evol. Microbiol., 55, 2051?2055.
  • Yoon, J. H., Kang, S. J., Lee, M. H., and Oh, T. K. (2008a)Nocardioides hankookensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 58, 434? 437.
  • Yoon, J. H., Kang, S. J., Lee, M. H., Oh, H. W., and Oh, T. K. (2006c)Porphyrobacter dokdonensis sp. nov., isolated from sea water. Int. J. Syst. Evol. Microbiol., 56, 1079? 1083.
  • Yoon, J. H., Kang, S. J., Lee S. Y., Lee, M. H., and Oh, T. K. (2005b)Virgibacillus dokdonensis sp. nov., isolated from a Korean island,Dokdo, located at the edge of the East Sea in Korea. Int. J. Syst. Evol. Microbiol., 55, 1833? 1837.
  • Wubet, T., Trogisch, S., Both, S., Scholten, T. et al. (2013)Forest age and plant species composition determine the soil fungalcommunity composition in a Chinese subtropical forest. PLoS One, 8,e66829.
  • Wang, Z. (2007) Leotiomycetes. Version 26 September 2007. http://tolweb.org/Leotiomycetes/29048/2007.09.26 in The Tree of LifeWeb Project, http://tolweb.org/Wu, Y.T.,
  • Wang, Y. and Qian, P. Y. (2009) Conservative fragments in bacterial16S rRNA genes and primer design for 16S ribosomal DNAamplicons in metagenomic studies. PLoS One, 4, e7401.
  • Wang, Q., Garrity, G.M., Tiedje, J.M., and Cole, J.R. (2007) NaiveBayesian classifier for rapid assignment of rRNA sequences into thenew bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261?5267.
  • Wang, B. and Qiu, Y.L. (2006) Phylogenetic distribution and evolutionof mycorrhizas in land plants. Mycorrhiza, 16 , 299?363.
  • Vilgalys, R. and Hester, M. (1990) Rapid genetic identification andmapping of enzymatically amplified ribosomal DNA from severalCryptococcus species. J. Bacteriol., 172, 4238?4246.
  • Valdez, J.G., Makuch, M.A., Ordovini, A.F., Masuelli, R.W., Overy, D.P. et al. (2006) First report of Penicillium allii as a field pathogen ofgarlic (Allium sativum). Plant Pathol., 55, 583.
  • Tsuge, T., Harimoto, Y., Akimitsu, K., Ohtani, K., Kodama, M. et al. (2013) Host-selective toxins produced by the plant pathogenic fungusAlternaria alternata. FEMS Microbiol. Rev., 37, 44?66.
  • Tripathi, B. M., Kim, M., Singh, D., Lee-Cruz, L., Lai-Hoe, A. et al. (2012) Tropical soil bacterial communities in Malaysia: pH dominatesin the equatorial tropics too. Microb. Ecol., 64, 474?484.
  • Sung, H. R., Yoon, J. H., and Ghim, S. Y. (2012) Shewanelladokdonensis sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol., 62, 1636? 1643.
  • Streit, W.R. and Schmitz, R.A. (2004) Metagenomics--the key to theuncultured microbes. Curr. Opin. Microbiol., 7, 492?498.
  • Steffen, K.T., Cajthaml, T., Snajdr, J., and Baldrian, P. (2007)Differential degradation of oak (Quercus petraea) leaf litter bylitter-decomposing basidiomycetes. Res. Microbiol., 158, 447?455.
  • Spatafora, J.W., Sung, G.H., Sung, J.M., Hywel-Jones, N.L., and White,J.F., Jr. (2007) Phylogenetic evidence for an animal pathogen origin ofergot and the grass endophytes. Mol. Ecol., 16, 1701?1711.
  • Somboonna, N., Assawamakin, A., Wilantho, A., Tangphatsornruang,S., and Tongsima, S. (2012) Metagenomic profiles of free-livingarchaea, bacteria and small eukaryotes in coastal areas of Sichangisland, Thailand. BMC Genomics, 13, S29.
  • Sohn, Y. K. (1995) Geology of Tok Island, Korea: eruptive anddepositional processes of a shoaling to emergent island volcano. Bull. volcanol., 56, 660?674.
  • Slippers, B and Wingfield, M.J. (2007) The Botryosphaeriaceae asendophytes and latent pathogens of woody plants: diversity, ecologyand impact. Fung. Biol. Rev., 21, 90?106.
  • Singh, D., Takahashi, K., Kim, M., Chun, J., and Adams, J. M. (2012)A hump-backed trend in bacterial diversity with elevation of MountFuji, Japan. Microb. Ecol., 63, 429? 437.
  • Singh, D., Shi, L., and Adams, J. M. (2013) Bacterial diversity in themountains of South-West China: Climate dominates over soilparameters. J. Microbiol., 51, 439? 447.
  • Shokralla, S., Spall, J.L., Gibson, J.F., and Hajibabaei, M. (2012)Next-generation sequencing technologies for environmental DNAresearch. Mol. Ecol., 21, 1794?1805.
  • Shin, H.T., Park, S.J., Kang, K.H., and Yoo, J.H. (2004) Theestablishment of conservation area and conservation strategy inUlnung island(III)-flora and management in Dokdo island, SouthKorea. Kor. J. Env. Eco., 18, 221?230.
  • Schoch, C.L., Crous, P.W., Groenewald, J.Z., Boehm, E.W., Burgess,T.I. et al. (2009) A class-wide phylogenetic assessment ofDothideomycetes. Stud. Mycol., 64, 1?15.
  • Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M. etal. (2009) Introducing mothur: open-source, platform-independent,community-supported software for describing and comparingmicrobial communities. Appl. Environ. Microbiol., 75, 7537?7541.
  • Samson, R.A., Seifert, K.A., Kuijpers, A.F., Houbraken, J.A., andFrisvad, J.C. (2004) Phylogenetic analysis of Penicillium subgenusPencillium using partial beta-tubulin sequences. Stud. Mycol., 49, 175?200.
  • Rosling, A., Cox, F., Cruz-Martinez, K., Ihrmark, K., Grelet, G.A. etal. (2011) Archaeorhizomycetes: Unearthing an ancient class ofubiquitous soil fungi. Science, 333, 876?879.
  • Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. etal. (2007) Pyrosequencing enumerates and contrasts soil microbialdiversity. ISME J., 1, 283? 290.
  • Porter, T.M. and Golding, G.B. (2012) Factors that affect large subunitribosomal DNA amplicon sequencing studies of fungal communities:classification method, primer choice, and error. PLoS One., 7,e35749.
  • Peterson, R.L., Massicotte, H.B., and Melville, L.H. (2004) Mycorrhizas:anatomy and cell biology. National Research Council Research Press.
  • Peay, K.G., Baraloto, C., and Fine, P.V. (2013) Strong coupling ofplant and fungal community structure across western Amazonianrainforests. ISME J., 7, 1852?1861.
  • Park, S.J., Song, I.G., Park, S.J., and Lim, D.O. (2010) The flora andvegetation of Dokdo island in Ulleung-gun, Gyeongsanbuk-do. Kor. J. Env. Eco., 24, 264?278.
  • Park, S. C., Baik, K. S., Kim, M. S., Chun, J., and Seong, C. N. (2008)Nocardioides dokdonensis sp. nov., an actinomycete isolatedfrom sand sediment. Int. J. Syst. Evol. Microbiol., 58, 2619? 2623.
  • Park, E. J., Chun, J., Cha, C.J., Park, W. S., Jeon, C.O. et al. (2012)Bacterial community analysis during fermentation of tenrepresentative kinds of kimchi with barcoded pyrosequencing. FoodMicrobiol., 30,197? 204.
  • Panaro, N.J., Yuen, P.K., Sakazume, T., Fortina, P., Kricka, L.J. et al. (2000) Evaluation of DNA fragment sizing and quantification by theagilent 2100 bioanalyzer. Clin. Chem., 46, 1851?1853.
  • Oh, K. H., Kang, S. J., Jung, Y. T., Oh, T. K., and Yoon, J. H. (2011)Lysobacter dokdonensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol., 61, 1089? 1093.
  • Miyashita, N. T., Iwanaga, H., Charles, S., Diway, B., Sabang, J. et al. (2013) Soil bacterial community structure in five tropical forests inMalaysia and one temperate forest in Japan revealed bypyrosequencing analyses of 16S rRNA gene sequence variation. GenesGenet. Syst., 88, 93? 103.
  • McGuire, K.L., Fierer, N., Bateman, C., Treseder, K.K., and Turner,B.L. (2012) Fungal community composition in neotropical rain forests:the influence of tree diversity and precipitation. Microb. Ecol., 63,804?812.
  • Liu, K.L., Porras-Alfaro, A., Kuske, C.R., Eichorst, S.A., and Xie, G. (2012) Accurate, rapid taxonomic classification of fungallarge-subunit rRNA genes. Appl. Environ. Microbiol., 78, 1523?1533.
  • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clusteringand comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658?1659.
  • Li, A., Chu, Y., Wang, X., Ren, L., Yu, J. et al. (2013) Apyrosequencing based metagenomic study of methane-producingmicrobial community in solid-state biogas reactor. Biotechnol. Biofuels, 6, 3.
  • Lee, Y.G., Kim, B.J., Park, G.U., and Ahn, B.Y. (2010) Characteristicsof Precipitation and Temperature at Ulleung-do and Dok-do, Koreafor Recent Four Years (2005~2008). J. Environ. Sci. Int., 19, 1109?1118.
  • Lee, J.H., Cho, H.J., Lee, B.C., Oh, S.H., and Bae, K.H. (2007) Forestvegetation types and growth characteristics of Seongin-bong inUlleung Island, Korea. Korean J. Agric. For. Meteorol., 9, 37?48.
  • Lee, H. S., Kwon, K. K., Yang, S. H., Bae, S. S., Park, C. H. et al. (2008) Description of Croceitalea gen. nov. in the familyFlavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphereof the marine alga Ecklonia kurome. Int. J. Syst. Evol. Microbiol.,58, 2505? 2510.
  • Kodsueb, R., Dhanasekaran, V., Aptroot, A., Lumyong, S., McKenzie,E.H. et al. (2006) The family Pleosporaceae: intergeneric relationshipsand phylogenetic perspectives based on sequence analyses of partial28S rDNA. Mycologia, 98, 571?583.
  • Kirk, P.M., Cannon, P.F., David, J.C., and Stalpers, J. (2001)Ainsworth and Bisby’s Dictionary of the Fungi (9th ed.). Wallingford,UK: CAB International.
  • Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M. et al. (2012)Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequencedatabase with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol., 62, 716? 721.
  • Kim, M.H., Oh, Y.J., Kim, C.S., Han, M.S., Lee, J.T. et al. (2007) Theflora and vegetation distribution in Dokdo. Kor. J. Environ. Agric.,26, 85?93.
  • Kim, M., You, Y.H., Yoon, H., Kim, H., Seo, Y. et al. (2012) Geneticdiversity of endophytic fungal strains isolated from the roots ofcoastal plants in Ulleung Island for restoration of coastal ecosystem. J. Life Sci., 22, 1384?1391.
  • Kim, H. M., Hwang, C. Y., and Cho, B. C. (2010) Arcobacter marinussp. nov. Int. J. Syst. Evol. Microbiol., 60, 531? 536.
  • Kim, C.H., Park, J.W., Lee, M.H., and Park, C.H. (2013) Detailedbathymetry and submarine terraces in the coastal area of the Dokdovolcano in the Ulleung basin, the East Sea (Sea of Japan). J. coastalres., 65, 523?528.
  • Khan, S.A., Hamayun, M., Yoon, H., Kim, H.Y., Suh, S.J. et al. (2008)Plant growth promotion and Penicillium citrinum. BMC Microbiol., 8,231.
  • Kernaghan, G. (2005) Mycorrhizal diversity: Cause and effect?Pedobiologia, 49, 511?520.
  • Janssen, P. H. (2006) Identifying the dominant soil bacterial taxa inlibraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol., 72, 1719? 1728.
  • Islam, E. and Sar, P. (2011) Culture-dependent and -independentmolecular analysis of the bacterial community within uranium ore. J. Basic Microbiol., 51, 372? 384.
  • Horton, T.R. and Bruns, T.D. (2001) The molecular revolution inectomycorrhizal ecology: peeking into the black-box. Mol. Ecol., 10,1855?1871.
  • Hong, S. W., Lee, J. S., and Chung, K. S. (2011) Polymerase chainreaction-denaturing gradient gel electrophoresis analysis ofbacterial community structure in the food, intestines, and feces ofearthworms. J. Microbiol., 49, 544? 550.
  • Hollister, E.B., Schadt, C.W., Palumbo, A.V., Ansley, R.J., andBoutton, T.W. (2010) Structural and functional diversity of soilbacterial and fungal communities following woody plantencroachment in the southern Great Plains. Soil Biol. Biochem., 42,1816?1824.
  • Hedeler, C., Wong, H.M., Cornell, M.J., Alam, I., Soanes, D.M. et al. (2007) e-Fungi: a data resource for comparative analysis of fungalgenomes. BMC Genomics, 8, 426.
  • Heck, K.L., Van Belle, G., and Simberloff, D. (1975) Explicitcalculation of the rarefaction diversity measurement and thedetermination of sufficient sample size. Ecology, 56, 1459?1461.
  • Hane, J.K., Lowe, R.G., Solomon, P.S., Tan, K.C., Schoch, C.L. et al. (2007) Dothideomycete-plant interactions illuminated by genomesequencing and EST analysis of the wheat pathogen Stagonosporanodorum. Plant Cell, 19, 3347?3368.
  • Handelsman, J. (2004) Metagenomics: application of genomics touncultured microorganisms. Microbiol. Mol. Biol. Rev., 68, 669?685.
  • Haase, G., Sonntag, L., Melzer-Krick, B., and de Hoog, G.S. (1999)Phylogenetic inference by SSU-gene analysis of members of theHerpotrichiellaceae with special reference to human pathogenicspecies. Stud. Mycol., 43, 80?97.
  • Grafenhan, T., Schroers, H.J., Nirenberg, H.I., and Seifert, K.A. (2011)An overview of the taxonomy, phylogeny, and typification ofnectriaceous fungi in Cosmospora, Acremonium, Fusarium, Stilbella,and Volutella. Stud. Mycol., 68, 79?113.
  • Gottel, N.R., Castro, H.F., Kerley, M., Yang, Z., Pelletier, D.A. et al. (2011) Distinct microbial communities within the endosphere andrhizosphere of Populus deltoides roots across contrasting soil types. Appl. Environ. Microbiol., 77, 5934?5944.
  • Gilles, A., Meglecz, E., Pech, N., Ferreira, S., Malausa, T. et al. (2011)Accuracy and quality assessment of 454 GS-FLX Titaniumpyrosequencing. BMC Genomics, 12, 245.
  • Eo, J.K., Choi, M.S., and Eom, A.H. (2014) Diversity of endophyticfungi isolated from korean ginseng leaves. Mycobiology, 42, 147?151.
  • Danielsen, L., Thurmer, A., Meinicke, P., Buee, M., Morin, E. et al. (2012) Fungal soil communities in a young transgenic poplarplantation form a rich reservoir for fungal root communities. Ecol. Evol., 2, 1935?1948.
  • Cong, W.F., Ruijven, J.V., Mommer, L., De Deyn, G.B., Berendse, F. etal. (2014) Plant species richness promotes soil carbon and nitrogenstocks in grasslands without legumes. J. Ecol., 102, 1163?1170.
  • Co-David, D., Langeveld, D., and Noordeloos, M.E. (2009) Molecularphylogeny and spore evolution of Entolomataceae. Persoonia, 23, 147?176.
  • Chung, J.M., Kang, U.C., Park, K.W., Kim, M.S., and Lee, B.C. (2011)A checklist of the native vascular plants of Ulleung Island, Korea. Korea National Arboretum, 99 pp.
  • Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S. et al. (2007) EzTaxon:a web-based tool for the identification of prokaryotes based on16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol.,57, 2259? 2261.
  • Chang, K.I., Kim, Y.B., Suk, M.S., and Byun, S.K. (2002) Hydrographyaround Dokdo. Ocean and Polar Res., 24, 369?389.
  • Carlucci, A., Raimondo, M.L., Santos, J., and Phillips, A.J. (2012)Plectosphaerella species associated with root and collar rots ofhorticultural crops in southern Italy. Persoonia, 28, 34?48.
  • Cannon, P.F. and Kirk, P.M. (2007) Fungal Families of the World. Wallingford, UK: CABI.
  • Buee, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H. et al. (2009)454 Pyrosequencing analyses of forest soils reveal an unexpectedlyhigh fungal diversity. New Phytol., 184, 449?456.
  • Baier, R., Ingenhaag, J., Blaschke, H., Gottlein, A., and Agerer, R. (2006) Vertical distribution of an ectomycorrhizal community in uppersoil horizons of a young Norway spruce (Picea abies [L.] Karst.)stand of the Bavarian Limestone Alps. Mycorrhiza, 16, 197?206.
  • Bai, G. and Shaner, G. (2004) Management and resistance in wheatand barley to fusarium head blight. Annu. Rev. Phytopathol., 42, 135?161.
  • Amann, R. I., Ludwig, W., and Schleifer, K. H. (1995) Phylogeneticidentification and in situ detection of individual microbial cellswithout cultivation. Microbiol. Rev., 59, 143? 169.
  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403?410.