메뉴 건너뛰기




Volumn 17, Issue 1, 2015, Pages 239-252

Bacterial networks and co-occurrence relationships in the lettuce root microbiota

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); FLAVOBACTERIUM; LACTUCA; LACTUCA SATIVA; LACTUCA SERRIOLA; OTUS; PROTEOBACTERIA; PSEUDOMONAS; SPHINGOMONADACEAE;

EID: 84921877062     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12686     Document Type: Article
Times cited : (192)

References (49)
  • 1
    • 66749178921 scopus 로고    scopus 로고
    • In vitro antagonists of Rhizoctonia solani tested on lettuce: rhizosphere competence, biocontrol efficiency and rhizosphere microbial community response
    • Adesina, M.F., Grosch, R., Lembke, A., Vatchev, T.D., and Smalla, K. (2009) In vitro antagonists of Rhizoctonia solani tested on lettuce: rhizosphere competence, biocontrol efficiency and rhizosphere microbial community response. FEMS Microbiol Ecol 69: 62-74.
    • (2009) FEMS Microbiol Ecol , vol.69 , pp. 62-74
    • Adesina, M.F.1    Grosch, R.2    Lembke, A.3    Vatchev, T.D.4    Smalla, K.5
  • 2
    • 84874203270 scopus 로고    scopus 로고
    • Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior
    • Badri, D.V., Zolla, G., Bakker, M.G., Manter, D.K., and Vivanco, J.M. (2013) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol 198: 264-273.
    • (2013) New Phytol , vol.198 , pp. 264-273
    • Badri, D.V.1    Zolla, G.2    Bakker, M.G.3    Manter, D.K.4    Vivanco, J.M.5
  • 3
    • 77949282823 scopus 로고    scopus 로고
    • Maize leaf epiphytic bacteria diversity patterns are genetically correlated with resistance to fungal pathogen infection
    • Balint-Kurti, P., Simmons, S.J., Blum, J.E., Ballaré, C.L., and Stapleton, A.E. (2010) Maize leaf epiphytic bacteria diversity patterns are genetically correlated with resistance to fungal pathogen infection. Mol Plant Microbe Interact 23: 473-484.
    • (2010) Mol Plant Microbe Interact , vol.23 , pp. 473-484
    • Balint-Kurti, P.1    Simmons, S.J.2    Blum, J.E.3    Ballaré, C.L.4    Stapleton, A.E.5
  • 4
    • 84855949949 scopus 로고    scopus 로고
    • Using network analysis to explore co-occurrence patterns in soil microbial communities
    • Barberán, A., Bates, S.T., Casamayor, E.O., and Fierer, N. (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6: 343-351.
    • (2012) ISME J , vol.6 , pp. 343-351
    • Barberán, A.1    Bates, S.T.2    Casamayor, E.O.3    Fierer, N.4
  • 5
    • 61649118780 scopus 로고    scopus 로고
    • Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere
    • Berg, G., and Smalla, K. (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1-13.
    • (2009) FEMS Microbiol Ecol , vol.68 , pp. 1-13
    • Berg, G.1    Smalla, K.2
  • 6
    • 0030052649 scopus 로고    scopus 로고
    • Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis strohl and tait 1978)
    • Bernadet, J.-F., Segers, P., Vancammeyt, M., Berthe, F., Kersters, K., and Vandamme, P. (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis strohl and tait 1978). Int J Syst Evol Microbiol 46: 128-148.
    • (1996) Int J Syst Evol Microbiol , vol.46 , pp. 128-148
    • Bernadet, J.-F.1    Segers, P.2    Vancammeyt, M.3    Berthe, F.4    Kersters, K.5    Vandamme, P.6
  • 8
    • 84858866394 scopus 로고    scopus 로고
    • Sphagnum mosses harbour highly-specific bacterial diversity during their whole lifecycle
    • Bragina, A., Berg, C., Cardinale, M., Shcherbakov, A., Chebotar, W., and Berg, G. (2012) Sphagnum mosses harbour highly-specific bacterial diversity during their whole lifecycle. ISME J 6: 802-813.
    • (2012) ISME J , vol.6 , pp. 802-813
    • Bragina, A.1    Berg, C.2    Cardinale, M.3    Shcherbakov, A.4    Chebotar, W.5    Berg, G.6
  • 9
    • 33748928488 scopus 로고    scopus 로고
    • Fitness of human enteric pathogens on plants and implications for food safety
    • Brandl, M.T. (2006) Fitness of human enteric pathogens on plants and implications for food safety. Annu Rev Phytopathol 44: 367-392.
    • (2006) Annu Rev Phytopathol , vol.44 , pp. 367-392
    • Brandl, M.T.1
  • 10
    • 84886795788 scopus 로고    scopus 로고
    • Microbiota-mediated colonization resistance against intestinal pathogens
    • Buffie, C.G., and Pamer, E.G. (2013) Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 13: 790-801.
    • (2013) Nat Rev Immunol , vol.13 , pp. 790-801
    • Buffie, C.G.1    Pamer, E.G.2
  • 13
    • 79952005915 scopus 로고    scopus 로고
    • Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    • Caporaso, J.G., Lauber, C., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., etal. (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS 108: 4516-4522.
    • (2011) PNAS , vol.108 , pp. 4516-4522
    • Caporaso, J.G.1    Lauber, C.2    Walters, W.A.3    Berg-Lyons, D.4    Lozupone, C.A.5    Turnbaugh, P.J.6
  • 19
    • 78650389722 scopus 로고    scopus 로고
    • Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca species) phyllosphere
    • Hunter, P.J., Hand, P., Pink, D., Whipps, J.M., and Bending, G.D. (2010) Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca species) phyllosphere. Appl Environ Microbiol 76: 8117-8125.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 8117-8125
    • Hunter, P.J.1    Hand, P.2    Pink, D.3    Whipps, J.M.4    Bending, G.D.5
  • 20
    • 84868094960 scopus 로고    scopus 로고
    • Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    • Kembel, S.W., Wu, M., Eisen, J.A., and Green, J.L. (2012) Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol 8: e1002743.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002743
    • Kembel, S.W.1    Wu, M.2    Eisen, J.A.3    Green, J.L.4
  • 22
    • 51149092825 scopus 로고    scopus 로고
    • Description of morphological characters of lettuce (Lactuca sativa L) genetic resources
    • Křístková, E., Doležalová, I., Lebeda, A., Vinter, V., and Novotná, A. (2008) Description of morphological characters of lettuce (Lactuca sativa L) genetic resources. Hort Sci 35: 113-129.
    • (2008) Hort Sci , vol.35 , pp. 113-129
    • Křístková, E.1    Doležalová, I.2    Lebeda, A.3    Vinter, V.4    Novotná, A.5
  • 23
    • 84859726112 scopus 로고    scopus 로고
    • Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities
    • Latz, E., Eisenhauer, N., Rall, B.C., Allan, E., Roscher, C., Scheu, S., etal. (2012) Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities. J Ecol 100: 597-604.
    • (2012) J Ecol , vol.100 , pp. 597-604
    • Latz, E.1    Eisenhauer, N.2    Rall, B.C.3    Allan, E.4    Roscher, C.5    Scheu, S.6
  • 25
    • 0030718540 scopus 로고    scopus 로고
    • Biodiversity regulates ecosystem predictability
    • McGrady-Steed, J., Harris, P., and Morin, P. (1997) Biodiversity regulates ecosystem predictability. Nature 390: 162-165.
    • (1997) Nature , vol.390 , pp. 162-165
    • McGrady-Steed, J.1    Harris, P.2    Morin, P.3
  • 27
    • 0034004745 scopus 로고    scopus 로고
    • Bacterial community structure and colonization patterns of Fagus sylvatica L ectomycorrhizospheres as determined by fluorescence in situ hybridization and confocal laser scanning microscopy
    • Mogge, B., Loferer, C., Agerer, R., Hutzler, P., and Hartmann, A. (2000) Bacterial community structure and colonization patterns of Fagus sylvatica L ectomycorrhizospheres as determined by fluorescence in situ hybridization and confocal laser scanning microscopy. Mycorrhiza 9: 271-278.
    • (2000) Mycorrhiza , vol.9 , pp. 271-278
    • Mogge, B.1    Loferer, C.2    Agerer, R.3    Hutzler, P.4    Hartmann, A.5
  • 28
    • 84945912853 scopus 로고    scopus 로고
    • Ongeng, D., Geeraerd, A.H., Springael, D., Ryckeboer, J., Muyanja, C., and Mauriello, G. (2013) Fate of Escherichia coli O157:H7 and Salmonella enterica in the manure-amended soil-plant ecosystem of fresh vegetable crops: A review. Crit Rev Microbiol doi:10.3109/1040841X.2013.829415; epub ahead of print.
  • 29
    • 34948814596 scopus 로고    scopus 로고
    • High specificity but contrasting biodiversity of Sphagnum-associated bacterial and plant communities in bog ecosystems independent of the geographical region
    • Opelt, K., Berg, C., Schönmann, S., Eberl, L., and Berg, G. (2007) High specificity but contrasting biodiversity of Sphagnum-associated bacterial and plant communities in bog ecosystems independent of the geographical region. ISME J 1: 502-516.
    • (2007) ISME J , vol.1 , pp. 502-516
    • Opelt, K.1    Berg, C.2    Schönmann, S.3    Eberl, L.4    Berg, G.5
  • 30
    • 84876117081 scopus 로고    scopus 로고
    • Effects of OTU clustering and PCR artifacts on microbial diversity estimates
    • Patin, N.V., Kunin, V., Lidström, U., and Ashby, M.N. (2013) Effects of OTU clustering and PCR artifacts on microbial diversity estimates. Microb Ecol 65: 709-719.
    • (2013) Microb Ecol , vol.65 , pp. 709-719
    • Patin, N.V.1    Kunin, V.2    Lidström, U.3    Ashby, M.N.4
  • 31
    • 84876259793 scopus 로고    scopus 로고
    • Diversity and heritability of the maize rhizosphere microbiome under field conditions
    • Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S.G., Dangl, J.L., etal. (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110: 6548-6553.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 6548-6553
    • Peiffer, J.A.1    Spor, A.2    Koren, O.3    Jin, Z.4    Tringe, S.G.5    Dangl, J.L.6
  • 34
    • 84867745648 scopus 로고    scopus 로고
    • Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce
    • Rastogi, G., Sbodio, A., Tech, J.J., Suslow, T.V., Coaker, G.L., and Leveau, J.H. (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6: 1812-1822.
    • (2012) ISME J , vol.6 , pp. 1812-1822
    • Rastogi, G.1    Sbodio, A.2    Tech, J.J.3    Suslow, T.V.4    Coaker, G.L.5    Leveau, J.H.6
  • 35
    • 40549140483 scopus 로고    scopus 로고
    • Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms
    • Scherwinski, K., Grosch, R., and Berg, G. (2008) Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms. FEMS Microbiol Ecol 64: 106-116.
    • (2008) FEMS Microbiol Ecol , vol.64 , pp. 106-116
    • Scherwinski, K.1    Grosch, R.2    Berg, G.3
  • 36
    • 42249090569 scopus 로고    scopus 로고
    • Plant-soil-microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms
    • Schweitzer, J.A., Bailey, J.K., Fischer, D.G., LeRoy, C.J., Lonsdorf, E.V., Whitham, T.G., etal. (2008) Plant-soil-microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology 89: 773-781.
    • (2008) Ecology , vol.89 , pp. 773-781
    • Schweitzer, J.A.1    Bailey, J.K.2    Fischer, D.G.3    LeRoy, C.J.4    Lonsdorf, E.V.5    Whitham, T.G.6
  • 37
    • 84880069357 scopus 로고    scopus 로고
    • Unexpected diversity during community succession in the apple flower microbiome
    • Shade, A., McManus, P.S., and Handelsman, J. (2013) Unexpected diversity during community succession in the apple flower microbiome. MBio 4: e602-e612.
    • (2013) MBio , vol.4 , pp. e602-e612
    • Shade, A.1    McManus, P.S.2    Handelsman, J.3
  • 38
    • 63849343340 scopus 로고    scopus 로고
    • Transcriptional activity of paddy soil bacterial communities
    • Shrestha, P.M., Kube, M., Reinhardt, R., and Liesack, W. (2009) Transcriptional activity of paddy soil bacterial communities. Environ Microbiol 11: 960-970.
    • (2009) Environ Microbiol , vol.11 , pp. 960-970
    • Shrestha, P.M.1    Kube, M.2    Reinhardt, R.3    Liesack, W.4
  • 39
    • 0035487320 scopus 로고    scopus 로고
    • Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed
    • Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., etal. (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742-4751.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 4742-4751
    • Smalla, K.1    Wieland, G.2    Buchner, A.3    Zock, A.4    Parzy, J.5    Kaiser, S.6
  • 40
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 28: new features for data integration and network visualization
    • Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L., and Ideker, T. (2011) Cytoscape 28: new features for data integration and network visualization. Bioinformatics 27: 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 41
    • 33947302827 scopus 로고    scopus 로고
    • Taxonomic parameters revisited: tarnished gold standards
    • Stackebrandt, E., and Ebers, J. (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152-155.
    • (2006) Microbiol Today , vol.33 , pp. 152-155
    • Stackebrandt, E.1    Ebers, J.2
  • 42
    • 79952102090 scopus 로고    scopus 로고
    • Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety
    • Teplitski, M., Warriner, K., Bartz, J., and Schneider, K.R. (2011) Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety. Trends Microbiol 19: 121-127.
    • (2011) Trends Microbiol , vol.19 , pp. 121-127
    • Teplitski, M.1    Warriner, K.2    Bartz, J.3    Schneider, K.R.4
  • 44
    • 0030989692 scopus 로고    scopus 로고
    • Origin and domestication of Lactuca sativa L.
    • de Vries, I.M. (1997) Origin and domestication of Lactuca sativa L. Gen Res Crop Evol 44: 165-174.
    • (1997) Gen Res Crop Evol , vol.44 , pp. 165-174
    • de Vries, I.M.1
  • 45
    • 78751687217 scopus 로고    scopus 로고
    • PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa
    • Weinert, N., Piceno, Y., Ding, G.C., Meincke, R., Heuer, H., Berg, G., etal. (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75: 497-506.
    • (2011) FEMS Microbiol Ecol , vol.75 , pp. 497-506
    • Weinert, N.1    Piceno, Y.2    Ding, G.C.3    Meincke, R.4    Heuer, H.5    Berg, G.6
  • 46
    • 70349904401 scopus 로고    scopus 로고
    • Cultivation of uncultured chloroflexi subphyla: significance and ecophysiology of formerly uncultured chloroflexi 'subphylum i' with natural and biotechnological relevance
    • Yamada, T., and Sekiguchi, Y. (2009) Cultivation of uncultured chloroflexi subphyla: significance and ecophysiology of formerly uncultured chloroflexi 'subphylum i' with natural and biotechnological relevance. Microbes Environ 24: 205-216.
    • (2009) Microbes Environ , vol.24 , pp. 205-216
    • Yamada, T.1    Sekiguchi, Y.2
  • 47
    • 33745320006 scopus 로고    scopus 로고
    • Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi
    • Yamada, T., Sekiguchi, Y., Hanada, S., Imachi, H., Ohashi, A., Harada, H., etal. (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56: 1331-1340.
    • (2006) Int J Syst Evol Microbiol , vol.56 , pp. 1331-1340
    • Yamada, T.1    Sekiguchi, Y.2    Hanada, S.3    Imachi, H.4    Ohashi, A.5    Harada, H.6
  • 48
    • 52149085893 scopus 로고    scopus 로고
    • The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains
    • Yarza, P., Richter, M., Peplies, J., Euzeby, J., Amann, R., Schleifer, K.H., etal. (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31: 241-250.
    • (2008) Syst Appl Microbiol , vol.31 , pp. 241-250
    • Yarza, P.1    Richter, M.2    Peplies, J.3    Euzeby, J.4    Amann, R.5    Schleifer, K.H.6
  • 49
    • 84938819834 scopus 로고    scopus 로고
    • Zohary, D., Hopf, M., and Weiss, E. (2012) Domestication of Plants in the Old World: The Origin and Spread of Cultivated Plants in West Asia, Europe and the Nile Valley, 4th edn. Oxford, UK: Oxford University Press.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.