Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Bodenhausen, Natacha ^a,b   Horton, Matthew W ^a   Bergelson, Joy ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACTINOBACTERIA; ARABIDOPSIS; ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; BACTEROIDETES; COMMUNITY STRUCTURE; CONTROLLED STUDY; ENDOPHYTE; EPIPHYTE; FLAVOBACTERIUM; GENE SEQUENCE; HABITAT STRUCTURE; MASSILIA; MICROBIAL COMMUNITY; NONHUMAN; ORGANISMS BY HABITAT; PHYLOGENY; PLANT LEAF; PLANT PATHOGEN INTERACTION; PLANT ROOT; POPULATION ABUNDANCE; PROTEOBACTERIA; PYROSEQUENCING; SPECIES RICHNESS; TISSUE DISTRIBUTION; WILD TYPE;

ARABIDOPSIS; BACTERIA; ECOSYSTEM; ENDOPHYTES; PLANT LEAVES; PLANT ROOTS; SEQUENCE ANALYSIS;

EID: 84874056533     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0056329     Document Type: Article

References (55)

1. Yang CH, Crowley DE, Borneman J, Keen NT, (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci U S A 98: 3889-3894.
2. Marschner P, Yang CH, Lieberei R, Crowley DE, (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33: 1437-1445.
3. Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, et al. (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71: 6784-6792.
4. Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD, (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.
5. Rasche F, Trondl R, Naglreiter C, Reichenauer T, Sessitsch A, (2006) Chilling and cultivar type affect the diversity of bacterial endophytes colonizing sweet pepper (Capsicum anuum L.). Can J Microbiol 52: 1036-1045.
6. van Overbeek L, van Elsas JD, (2008) Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiol Ecol 64: 283-296.
7. Redford AJ, Fierer N, (2009) Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 58: 189-198.
8. Ercolani GL, (1991) Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time. Microb Ecol 21: 35-48.
9. Berg G, 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.
10. Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA (2010) Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J: 719-728.
11. Lindow SE, Brandl MT, (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69: 1875-1883.
12. Badri DV, Weir TL, van der Lelie D, Vivanco JM, (2009) Rhizosphere chemical dialogues: plant-microbe interactions. Curr Opin Biotechnol 20: 642-650.
13. Hutchinson GE, (1961) The paradox of the plankton. American Naturalist 95: 137-145.
14. Chesson PL, Warner RR, (1981) Environmental variability promotes coexistence in lottery competitive-systems. American Naturalist 117: 923-943.
15. Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, et al. (2005) Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51: 215-229.
16. Timms-Wilson TM, Smalla K, Goodall TI, Houlden A, Gallego V,et al. (2006) Microbial diversity in the phyllosphere and rhizosphere of field grown crop plants: Microbial specialisation at the plant surface. In: Bailey MJ, Lilley AK, Timms-Wilson T, M, Spencer-Phililips PTN, editors. Microbial ecology of aerial plant surfaces: CAB International. 21-36.
17. Innerebner G, Knief C, Vorholt JA, (2011) Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microbiol 77: 3202-3210.
18. Micallef SA, Shiaris MP, Colon-Carmona A, (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60: 1729-1742.
19. Reisberg EE, Hildebrandt U, Riederer M, Hentschel U, (2012) Phyllosphere bacterial communities of trichome-bearing and trichomeless Arabidopsis thaliana leaves. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 101: 551-560.
20. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, et al. (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106: 16428-16433.
21. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90.
22. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, et al. (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488: 91-95.
23. Qvit-Raz N, Jurkevitch E, Belkin S, (2008) Drop-size soda lakes: Transient microbial habitats on a salt-secreting desert tree. Genetics 178: 1615-1622.
24. Chelius MK, Triplett EW, (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microbial Ecology. 41: 252-263.
25. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
26. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB,et al. (2011) vegan: Community Ecology Package. R package version 1.17-10.
27. Legendre P, (2005) Species associations: The Kendall coefficient of concordance revisited. J Agric Biol Environ Stat 10: 226-245.
28. Legendre P, Gallagher ED, (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.
29. Jost L, (2007) Partitioning diversity into independent alpha and beta components. Ecology 88: 2427-2439.
30. Sheldon AL (1969) Equitability Indices- Dependence on Species Count. Ecology 50: 466-&.
31. Anderson MJ, (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26: 32-46.
32. Berry KJ, Johnston JE, Mielke PW Jr, (2003) Permutation methods for the analysis of matched-pairs experimental designs. Psychol Rep 92: 1141-1150.
33. Clarke KR, (1993) Nonparametric Multivariate Analyses of Changes in Community Structure. Australian Journal of Ecology 18: 117-143.
34. Schloss PD, Handelsman J, (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 71: 1501-1506.
35. Whittaker RH, (1972) Evolution and measurement of species diversity. Taxon 21: 213-251.
36. Manter DK, Delgado JA, Holm DG, Stong RA, (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60: 157-166.
37. Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA, (2011) Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons. J Appl Microbiol 110: 1203-1214.
38. Becker R, Behrendt U, Hommel B, Kropf S, Ulrich A, (2008) Effects of transgenic fructan-producing potatoes on the community structure of rhizosphere and phyllosphere bacteria. FEMS Microbiol Ecol 66: 411-425.
39. Sun L, Qiu FB, Zhang XX, Dai X, Dong XZ, et al. (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55: 415-424.
40. Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N, (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12: 2885-2893.
41. Uroz S, Buee M, Murat C, Frey-Klett P, Martin F, (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2: 281-288.
42. Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, et al. (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6: 1812-1822.
43. Takeuchi M, Hamana K, Hiraishi A, (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51: 1405-1417.
44. Kniskern JM, Traw MB, Bergelson J, (2007) Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol Plant-Microbe Interact 20: 1512-1522.
45. Lee ZMP, Bussema C, Schmidt TM, (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37: D489-D493.
46. Crosby LD, Criddle CS, (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-802.
47. Garbeva P, van Veen JA, van Elsas JD, (2004) Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42: 243-270.
48. Smalla K, Weinert N, Meincke R, Gottwald C, Heuer H, et al. (2009) Rhizosphere Communities of Genetically Modified Zeaxanthin-Accumulating Potato Plants and Their Parent Cultivar Differ Less than Those of Different Potato Cultivars. Applied and Environmental Microbiology 75: 3859-3865.
49. Rosenblueth M, Martinez-Romero E, (2006) Bacterial endophytes and their interactions with hosts. Molecular Plant-Microbe Interactions 19: 827-837.
50. Lindow SE, Leveau JH, (2002) Phyllosphere microbiology. Current Opinion in Biotechnology 13: 238-243.
51. Hardoim PR, van Overbeek LS, van Elsas JD, (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends in Microbiology 16: 463-471.
52. Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, 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.
53. Beattie GA, Lindow SE, (1999) Bacterial colonization of leaves: a spectrum of strategies. Phytopathology 89: 353-359.
54. Chi F, Shen SH, Cheng HP, Jing YX, Yanni YG, et al. (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.
55. Czajkowski R, de Boer WJ, Velvis H, van der Wolf JM, (2010) Systemic colonization of potato plants by a soilborne, green fluorescent protein-tagged strain of Dickeya sp. biovar 3. Phytopathology 100: 134-142.