Distinctive Bacterial Communities in the Rhizoplane of Four Tropical Tree Species

Microbial Ecology

Volumn 64, Issue 4, 2012, Pages 1018-1027

  Oh, Yoon Myung ^a   Kim, Mincheol ^a   Lee Cruz, Larisa ^a   Lai Hoe, Ang ^b   Go, Rusea ^c   Ainuddin, N ^c   Rahim, Raha Abdul ^c   Shukor, Noraini ^c   Adams, Jonathan M ^a  

^a Seoul National University   (South Korea)

^b FOREST RESEARCH CENTRE   (Malaysia)

^c UNIVERSITY PUTRA MALAYSIA   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIUM; BACTEROIDETES; BETAPROTEOBACTERIA; CLASSIFICATION; CONIFER; DNA SEQUENCE; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MALAYSIA; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; RHIZOSPHERE; RNA GENE; SPECIES DIFFERENCE; STREPTOPHYTA; TREE; TROPIC CLIMATE;

BACTERIA; BACTEROIDETES; BETAPROTEOBACTERIA; CONIFEROPHYTA; DNA, BACTERIAL; ECOSYSTEM; GENES, RRNA; MALAYSIA; MOLECULAR SEQUENCE DATA; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; STREPTOPHYTA; TREES; TROPICAL CLIMATE;

ACIDOBACTERIA; ACIDOBACTERIUM; AGATHIS BORNEENSIS; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; BURKHOLDERIA; DIPTEROCARPUS KERRII; DYELLA; DYERA COSTULATA; FUNGI; GNETUM; GNETUM GNEMON;

EID: 84867672803     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-012-0082-2     Document Type: Article

References (67)

1. Brodie E, Edwards S, Clipson N (2002) Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem. Microbial Ecol 44: 260-270.
2. Fang CW, Radosevich M, Fuhrmann JJ (2001) Characterization of rhizosphere microbial community structure in five similar grass species using FAME and BIOLOG analyses. Soil Biol Biochem 33: 679-682.
3. Broughton LC, Gross KL (2000) Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field. Oecologia 125: 420-427.
4. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PG, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie van Leeuwenhoek 81: 509-520.
5. McCaig AE, Glover LA, Prosser JI (2001) Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol 67: 4554-4559.
6. Grayston SJ, Wang SQ, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30: 369-378.
7. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microb 67: 4742-4751.
8. Wieland G, Neumann R, Backhaus H (2001) Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 67: 5849-5854.
9. Dunfield KE, Germida JJ (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl Environ Microbiol 69: 7310-7318.
10. van Elsas JD, Speksnijder AJ, van Overbeek LS (2008) A procedure for the metagenomics exploration of disease-suppressive soils. J Microbiol Methods 75: 515-522.
11. 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.
12. Buckley DH, Schmidt TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5: 441-452.
13. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800-1809.
14. Johnson MJ, Lee KY, Scow KM (2003) DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114: 279-303.
15. DiCello F, Bevivino A, Chiarini L, Fani R, Paffetti D, Tabacchioni S, Dalmastri C (1997) Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl Environ Microbiol 63: 4485-4493.
16. Uroz S, Calvaruso C, Turpaul MP, Pierrat JC, Mustin C, Frey-Klett P (2007) Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. Appl Environ Microbiol 73: 3019-3027.
17. Cocking EC (2003) Endophytic colonization of plant roots by nitrogen-fixing bacteria. Plant Soil 252: 169-175.
18. Nieto KF, Frankenberger WT (1989) Biosynthesis of cytokinins in soil. Soil Sci Soc Am J 53: 735-740.
19. Hamdan H, Weller DM, Thomashow LS (1991) Relative importance of fluorescent siderophores and other factors in biological-control of Gaeumannomyces graminis var tritici by Pseudomonas fluorescens 2-79 and M4-80r. Appl Environ Microbiol 57: 3270-3277.
20. Berg G, Zachow C, Lottmann J, Gotz M, Costa R, Smalla K (2005) Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae Kleb. Appl Environ Microbiol 71: 4203-4213.
21. Marilley L, Aragno M (1999) Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl Soil Ecol 13: 127-136.
22. Marilley L, Vogt G, Blanc M, Aragno M (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA. Plant Soil 198: 219-224.
23. Acosta-Martinez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: 2762-2770.
24. Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221-1230.
25. 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.
26. StreitwolfEngel R, Boller T, Wiemken A, Sanders IR (1997) Clonal growth traits of two Prunella species are determined by co-occurring arbuscular mycorrhizal fungi from a calcareous grassland. J Ecol 85: 181-191.
27. Newsham KK, Fitter AH, Watkinson AR (1995) Arbuscular mycorrhiza protect an annual grass from root pathogenic fungi in the field. J Ecol 83: 991-1000.
28. Brundrett M (1991) Mycorrhizas in Natural Ecosystems. Adv Ecol Res 21: 171-313.
29. Miethling R, Wieland G, Backhaus H, Tebbe CC (2000) Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecol 40: 43-56.
30. McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65: 1721-1730.
31. Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71: 6784-6792.
32. Teixeira LCRS, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4: 989-1001.
33. Buyer JS, Roberts DP, Russek-Cohen E (1999) Microbial community structure and function in the spermosphere as affected by soil and seed type. Can J Microbiol 45: 138-144.
34. Dalmastri C, Chiarini L, Cantale C, Bevivino A, Tabacchioni S (1999) Soil type and maize cultivar affect the genetic diversity of maize root-associated Burkholderia cepacia populations. Microbial Ecol 38: 273-284.
35. Day JM, Neves MCP, Döbereiner J (1974) Nitrogenase activity on the roots of tropical forage grasses. Soil Biol Biochem 7: 107-112.
36. Döbereiner J, Day JM, Dart PJ (1972) Nitrogenase activity in the rhizosphere of sugar cane and some other tropical grasses. Plant Soil 37: 191-196.
37. Gomes NCM, Heuer H, Schonfeld J, Costa R, Mendonca-Hagler L, Smalla K (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232: 167-180.
38. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55: 856-866.
39. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106: 16428-16433.
40. Chun J, Kim KY, Lee JH, Choi Y (2010) The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol 10: 101.
41. Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44: 7777-7782.
42. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716-721.
43. Clarke KR, Gorley RN (2006) Primer v6: user manual/tutorials. Primer-E Ltd, Plymouth.
44. White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Compute Biol 5: e1000352.
45. Suarez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonca-Previato L, James EK, Venturi V (2012) Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 63: 249-266.
46. Caballero-Mellado J, Martinez-Aguilar L, Paredes-Valdez G, Santos PE (2004) Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. Int J Syst Evol Microbiol 54: 1165-1172.
47. Reis VM, Estrada-de los Santos P, Tenorio-Salgado S, Vogel J, Stoffels M, Guyon S, Mavingui P, Baldani VL, Schmid M, Baldani JI, Balandreau J, Hartmann A, Caballero-Mellado J (2004) Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int J Syst Evol Microbiol 54: 2155-2162.
48. Chen WM, de Faria SM, Chou JH, James EK, Elliott GN, Sprent JI, Bontemps C, Young JP, Vandamme P (2008) Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 58: 2174-2179.
49. Caballero-Mellado J, Onofre-Lemus J, Estrada-de Los Santos P, Martinez-Aguilar L (2007) The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation. Appl Environ Microbiol 73: 5308-5319.
50. Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, NA A, Chun J, Adams JM (2012) Distinctive phyllosphere bacterial communities in tropical trees. Microb Ecol 63: 674-681.
51. Reynolds HL, Packer A, Bever JD, Clay K (2003) Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84: 2281-2291.
52. Singh BK, Nunan N, Ridgway KP, McNicol J, Young JPW, Daniell TJ, Prosser JI, Millard P (2008) Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots. Environ Microbiol 10: 534-541.
53. Wamberg C, Christensen S, Jakobsen I, Muller AK, Sorensen SJ (2003) The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum). Soil Biol Biochem 35: 1349-1357.
54. Olsson PA, Wallander H (1998) Interactions between ectomycorrhizal fungi and the bacterial community in soils amended with various primary minerals. FEMS Microbiol Ecol 27: 195-205.
55. de Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29: 795-811.
56. Dixona RK, Gargb VK, Raoc MV (1993) Inoculation of Leucaena and Prosopis seedlings with Glomus and Rhizobium species in saline soil: rhizosphere relations and seedling growth. Arid Soil Res Rehabil 7: 133-144.
57. Mangan SA, Schnitzer SA, Herre EA, Mack KM, Valencia MC, Sanchez EI, Bever JD (2010) Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466: 752-755.
58. Timonen S, Hurek T (2006) Characterization of culturable bacterial populations associating with Pinus sylvestris-Suillus bovinus mycorrhizospheres. Can J Microbiol 52: 769-778.
59. Kielak A, Pijl AS, van Veen JA, Kowalchuk GA (2008) Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol Ecol 63: 372-382.
60. Gyaneshwar P, Hirsch AM, Moulin L, Chen WM, Elliott GN, Bontemps C, Estrada-de los Santos P, Gross E, DosReis FB, Sprent JI, Young JPW, James EK (2011) Legume-nodulating Betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe In 24: 1276-1288.
61. Pagan JD, Child JJ, Scowcroft WR, Gibson AH (1975) Nitrogen-fixation by Rhizobium cultured on a defined medium. Nature 256: 406-407.
62. Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, A NA, Chun J, Adams JM (2011) Distinctive phyllosphere bacterial communities in tropical trees. Microb Ecol.
63. Chiu CH, Waddingdon M, Hsieh WS, Greenberg D, Schreckenberger PC, Carnahan AM (2000) Atypical Chryseobacterium meningosepticum and meningitis and sepsis in newborns and the immunocompromised, Taiwan. Emerg Infect Dis 6: 481-486.
64. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
65. Yergeau E, Kang S, He Z, Zhou J, Kowalchuk GA (2007) Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1: 163-179.
66. Brejda JJ, Moser LE, Vogel KP (1998) Evaluation of switchgrass rhizosphere microflora for enhancing seedling yield and nutrient uptake. Agron J 90: 753-758.
67. Edwards DP, Fisher B, Boyd E (2010) Protecting degraded rainforests: enhancement of forest carbon stocks under REDD. Conserv Lett 3: 313-316.