Detection and identification of bacteria intimately associated with fungi of the order Sebacinales

Cellular Microbiology

Volumn 10, Issue 11, 2008, Pages 2235-2246

  Sharma, Monica ^a   Schmid, Michael ^b   Rothballer, Michael ^b   Hause, Gerd ^c   Zuccaro, Alga ^a   Imani, Jafargholi ^a   Kämpfer, Peter ^a   Domann, Eugen ^d   Schäfer, Patrick ^a   Hartmann, Anton ^b   Kogel, Karl Heinz ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^d UNIVERSITY HOSPITAL GIESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT;

ACINETOBACTER; ALPHAPROTEOBACTERIA; ARTICLE; ASEXUAL REPRODUCTION; BACTERIAL TRANSMISSION; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BARLEY; BASIDIOMYCETES; BLUMERIA GRAMINIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA ISOLATION; ECTOMYCORRHIZA; ENDOMYCORRHIZA; FLUORESCENCE IN SITU HYBRIDIZATION; FUNGAL COLONIZATION; MYCELIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PAENIBACILLUS; PHYLOGENY; PIRIFORMOSPORA INDICA; POLYMERASE CHAIN REACTION; POWDERY MILDEW; PRIORITY JOURNAL; PROTOPLAST; RHIZOBIUM RADIOBACTER; RHODOCOCCUS; SEBACINA VERMIFERA; SEBACINALES; SEEDLING;

BASIDIOMYCOTA; HORDEUM; HOST-PARASITE INTERACTIONS; IN SITU HYBRIDIZATION, FLUORESCENCE; PHYLOGENY; RHIZOBIUM; RNA, RIBOSOMAL, 16S; SYMBIOSIS;

ACINETOBACTER; AGROBACTERIUM TUMEFACIENS; BLUMERIA GRAMINIS; ERYSIPHALES; FUNGI; HORDEUM; PAENIBACILLUS; PIRIFORMOSPORA INDICA; PROTEOBACTERIA; RADIOBACTER; RHODOCOCCUS; SEBACINA VERMIFERA; SEBACINALES;

EID: 54049140006     PISSN: 14625814     EISSN: 14625822     Source Type: Journal    
DOI: 10.1111/j.1462-5822.2008.01202.x     Document Type: Article

References (59)

1. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S-rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. App Environ Microbiol 56: 1919-1925.
2. Artursson, V., Finlay, R.D., and Jansson, J.K. (2006) Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ Microbiol 8: 1-10.
3. Aspray, T.J., Frey-Klett, P., Jones, J.E., Whipps, J.M., Garbaye, J., and Bending, G.D. (2006) Mycorrhization helper bacteria: A case of specificity for altering ectomycorrhiza architecture but not ectomycorrhiza formation. Mycorrhiza 16: 533-541.
4. Bertaux, J., Schmid, M., Chemidlin Prévost-Bourre, N., Churin, J.L., Hartmann, A., et al. (2003) In situ identification of intracellular bacteria related to Paenibacillus spp. in the mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N. App Environ Microbiol 69: 4243-4248.
5. Bertaux, J., Schmid, M., Hutzler, P., Hartmann, A., Garbaye, J., and Frey-Klett, P. (2005) Occurrence and distribution of endobacteria in the plant-associated mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N. Environ Microbiol 7: 1786-1795.
6. Bianciotto, V., Minerdi, D., Perotto, S., and Bonfante, P. (1996) Cellular interactions between arbuscular mycorrhizal fungi and rhizosphere bacteria. Protoplasma 193: 123-131.
7. Bianciotto, V., Genre, A., Jargeat, P., Lumini, E., Bécard, G., and Bonfante, P. (2004) Vertical transmission of endobacteria in the arbuscular mycorrhizal fungus Gigaspora margarita through generation of vegetative spores. Appl Environ Microbiol 70: 3600-3608.
8. Brosius, J., Dull, T.J., Sleeter, D.D., and Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148: 107-127.
9. Cardinale, M., Brusetti, L., Quatrini, P., Borin, S., Puglia, A.M., Rizzi, A., et al. (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. App Environ Microbiol 70: 6147-6156.
10. Chun, J., Lee, J.-H., Jung, Y., Kim, M., Kim, S., Kim, B.K., and Lim, Y.W. (2007) EzTaxon: A web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57: 2259-2261.
11. Daims, H., Breuhl, A., Amann, R., Schleifer, K.H., and Wagner, M. (1999) Probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 438-448.
12. Deshmukh, S., Hückelhoven, R., Schäfer, P., Imani, J., Sharma, M., Weiss, M., et al. (2006) The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley. Proc Natl Acad Sci USA 103: 18450-18457.
13. Deshmukh, S.D., and Kogel, K.H. (2007) Piriformospora indica protects barley from root rot caused by Fusarium graminearum. J Plant Dis Prot 114: 263-268.
14. Duponnois, R., and Plenchette, C. (2003) A mycorrhiza helper bacterium enhances ectomycorrhizal and endomycorrhizal symbiosis of Australian Acacia species. Mycorrhiza 13: 85-91.
15. Frey-Klett, P., and Garbaye, J. (2005) Mycorrhiza helper bacteria: A promising model for the genomic analysis of fungal-bacterial interactions. New Phytol 168: 4-8.
16. Frey-Klett, P., Garbaye, J., and Tarkka, M. (2007) Tansley review: The mycorrhiza helper bacteria revisited. New Phytol 176: 22-36.
17. Garbaye, J. (1994) Helper bacteria: A new dimension to the mycorrhizal symbiosis (Tansley Review, 76). New Phytol 128: 197-210.
18. Glickmann, E., and Dessaux, Y. (1995) A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61: 793-796.
19. Haas, J.H., Moore, L.W., Ream, W., and Manulis, S. (1995) Universal PCR Primers for Detection of Phytopathogenic Agrobacterium Strains. Appl Environ Microbiol 61: 2879-2884.
20. Humphry, D.R., Andrews, M., Santos, S.R., James, E.K., Vinogradova, L.V., Perin, L., et al. (2007) Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia. Antonie Van Leeuwenhoek 91: 105-113.
21. Kämpfer, P., and Kroppenstedt, R.M. (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42: 989-1005.
22. Kämpfer, P., Steiof, M., and Dott, W. (1991) Microbiological characterisation of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21: 227-251.
23. Leveau, J.H.J., and Preston, G.M. (2008) Tansley review: Bacterial mycophagy: Definition and diagnosis of a unique bacterial-fungal interaction. New Phytol 177: 859-876.
24. Loy, A., Horn, M., and Wagner, M. (2003) ProbeBase: An online resource for rRNA-targeted oligonucleotide probes. Nucleic Ac Res 31: 514-516.
25. Loy, A., Maixner, F., Wagner, M., and Horn, M. (2007) ProbeBase - an online resource for rRNA-targeted oligonucleotide probes: New features 2007. Nucleic Acids Res 35: 800-804.
26. Ludwig, W., Amann, R., Martinez-Romero, E., Schönhuber, W., Bauer, S., Neef, A., and Schleifer, K.H. (1998) rRNA based identification systems for rhizobia and other bacteria. Pl Soil 204: 1-9.
27. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) arb: A software environment for sequence data. Nucleic Ac Res 32: 1363-1371.
28. Lumini, E., Ghignone, S., Bianciotto, V., and Bonfante, P. (2006) Endobacteria or bacterial endosymbionts? To be or not to be. New Phytol 170: 199-201.
29. Lumini, E., Bianciotto, V., Jargeat, P., Novero, M., Salvioli, A., Faccio, A., et al. (2007) Presymbiotic growth and sporal morphology are affected in the arbuscular mycorrhizal fungus Gigaspora margarita cured of its endobacteria. Cellu Microbiol 9: 1716-1729.
30. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M., and Schleifer, K.H. (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiol 142: 1097-1106.
31. Matheny, P.B., Wang, Z., Binder, M., Curtis, J.M., Lim, Y.W., Nilsson, R.H., et al. (2007) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol 43: 430-451.
32. Meier, H., Amann, R., Ludwig, W., and Schleifer, K.H. (1999) Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G+C content. Syst Appl Microbiol 22: 186-196.
33. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436-439.
34. Nurmiaho-Lassila, E.L., Timonen, S., Haahtela, K., and Sen, R. (1997) Bacterial colonization patterns of intact Pinus sylvestris mycorrhizospheres in dry pine forest soil: An electron microscopy study. Can J Microbiol 43: 1017-1035.
35. Partida-Martinez, L.P., Monajembashi, S., Greulich, K.O., and Hertweck, C. (2007) Endosymbiont-dependent host reproduction maintains bacterial-fungal mutualism. Curr Biol 17: 773-777.
36. Peskan-Berghoefer, T., Shahollaria, B., Giong, P.H., Hehl, S., Markerta, C., Blanke, V., et al. (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol Plant 122: 465-477.
37. Pham, G.H., Kumari, R., Singh, A., Malla, R., Prasad, R., et al. (2004) Axenic culture of symbiotic fungus Piriformospora indica. In Plant Surface Microbiol. Varma, A., Abbott, L., Werner, D., and Hampp, R. (eds). Berlin: Springer-Verlag, pp. 593-611.
38. Prusty, R., Grisafi, P., and Fink, G.R. (2004) The plant hormone indoleacetic acid induces invasive growth in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 101: 4153-4157.
39. Quint, M., and Gray, W.M. (2006) Auxin signaling. Curr Opin Plant Biol 9: 448-453.
40. Rainey, P.B., Cole, A.L.J., Fermor, T.R., and Wood, D.A. (1990) A model system for examining involvement of bacteria in basidiome initiation of Agaricus bisporus. Mycol Res 94: 191-195.
41. Riedlinger, J., Schrey, S.D., Tarkka, M.T., Hampp, R., Kapur, M., and Fiedler, H.P. (2006) Auxofuran, a novel metabolite that stimulates the growth of fly agaric, is produced by the mycorrhiza helper bacterium S treptomyces strain AcH 505. App Environ Microbiol 72: 3550-3557.
42. Robert-Seilaniantz, A., Navarro, L., Bari, R., and Jones, J.D.G. (2007) Pathological hormone imbalances. Curr Opin Plant Biol 10: 372-379.
43. Sbrana, C., Bagnoli, G., Bedini, S., Filippi, C., Giovannetti, M., and Nuti, M.P. (2000) Adhesion to hyphal matrix and antifungal activity of Pseudomonas strains isolated from Tuber borchii ascocarps. Can J Microbiol 46: 259-268.
44. Schäfer, P., Kogel, K.-H. (2008) Plants' fortune with Piriformospora indica et al. -uncovered secrets down under. In The Mycota, Vol. V, 2nd Edition-Plant Relationships. Deising, H. (ed.). Heidelberg: Springer Verlag (in press).
45. Selosse, M.A., Setaro, S., Glatard, F., Richard, F., Urcelay, C., and Weiß, M. (2007) Sebacinales are common mycorrhizal associates of Ericaceae. New Phytol 174: 864-878.
46. Sirrenberg, A., Goebel, C., Grondc, S., Czempinskic, N., Ratzingerb, A., Karlovskyb, P., et al. (2007) Piriformospora indica affects plant growth by auxin production. Physiol Plant 131: 581-589.
47. Smith, S.E., and Read, D. (1997) Mycorrhizal Symbiosis, 2nd edn. London, UK: Academic Press.
48. Straube, A., Hause, G., Fink, G., and Steinberg, G. (2006) Conventional kinesin mediates microtubule-microtubule interactions in vivo. Mol Biol Cell 17: 907-916.
49. Tsavkelova, E.A., Cherdynteseva, T.A., Botina, S.G., and Netrusov, A.I. (2007) Bacteria associated with orchid roots and microbial production of auxin. Microbiol Res 162: 69-76.
50. Vanhoutte, T., Huys, G., Brandt, E.D., Fahey, G.C., Jr, and Swings, J. (2005) Molecular monitoring and characterization of the faecal microbiota of healthy dogs during fructan supplementation. FEMS Microbiol Lett 249: 65-71.
51. Varma, A., Verma, S., Sudha, Sahay, N., Beutehorn, B., and Franken, P. (1999) Piriformospora indica, a cultivable plant-growth promoting root endophyte. Appl Environ Microbiol 65: 2741-2744.
52. Varma, S., Varma, A., Rexer, K.H., Hassel, A., Kost, G., Sarabhoy, A., et al. (1998) Piriformospora indica, gen. et sp. nov., a new root-colonizing fungus. Mycologia 90: 896-903.
53. Velazquez, E., Peix, A., Zurdo-Piñeiro, J.L., Palomo, J.L., Mateos, P.F., Rivas, R., et al. (2005) The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. MPMI 18: 1325-1332.
54. Waller, F., Achatz, B., Baltruschat, H., Fodor, J., Becker, K., Fischer, M., et al. (2005) The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci USA 38: 13386-13391.
55. Walley, F.L., and Germida, J.J. (1997) Response of spring wheat (Triticum aestivum) to interactions between Pseudomonas species and Glomus clarum NT 4. Biol Fertil Soils 24: 365-371.
56. Wang, D., Pei, K., Fu, Y., Sun, Z., Li, S., Liu, H., et al. (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene 394: 13-24.
57. Warcup, J.H. (1988) Mycorrhizal associations of isolates of Sebacina vermifera. New Phytol 110: 227-231.
58. Weiss, M., Selosse, M.A., Rexer, K.H., Urban, A., and Oberwinkler, F. (2004) Sebacinales: A hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol Res 108: 1003-1010.
59. Young, J.M., Kuykendall, L.D., Martinez-Romero, E., Kerr, A., Sawada, H. (2001) A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Evol Microb 51: 89-103.