Diazotrophic endophytes of native black cottonwood and willow

Symbiosis

Volumn 47, Issue 1, 2009, Pages 23-33

  Doty, Sharon L ^a   Oakley, Brian ^b,d   Xin, Gang ^c,e   Kang, Jun Won ^a   Singleton, Glenda ^a   Khan, Zareen ^a   Vajzovic, Azra ^a   Staley, James T ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Department of Microbiology ^*

^c University of Washington   (United States)

^d UNIVERSITY OF WARWICK   (United Kingdom)

^e Hydranautics   (United States)

Author keywords

Endophyte; Nitrogen fixation; Poplar; Salicaceae; Willow

Indexed keywords

BACTERIUM; DICOTYLEDON; ENDOPHYTE; ENZYME ACTIVITY; GENE; NUTRIENT; RIPARIAN VEGETATION;

ACINETOBACTER; BACTERIA (MICROORGANISMS); BURKHOLDERIA; POPULUS TRICHOCARPA; RAHNELLA; SALICACEAE; SALIX; SALIX SITCHENSIS; SPHINGOMONAS;

EID: 62949112081     PISSN: 03345114     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03179967     Document Type: Article

References (70)

1. Adhikari, T.B., Joseph, CM., Yang, G., Phillips, D.A., and Nelson, L.M. 2001. Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice. Canadian Journal of Microbiology 47: 916-924.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. Asis, C.A., Jr. and Adachi, K. 2004. Isolation of endophytic diazotroph Pantoea agglomerans and nondiazotroph Entero-bacter asburiae from sweetpotato stem in Japan. Letters in Applied Microbiology 38 19-23.
4. Barac, T., Taghavi, S., Borremans, B., Provoost, A., Oeyen, L., Colpaert, J.V., Vangronsveld, J., and van der Lelie, D. 2004. Engineered endophytic bacteria improve phyto-remediation of water-soluble, volatile, organic pollutants. Nature Biotechnology 22: 583-588.
5. Behrendt, U., Ulrich, A., Schumann, P., Erler, W., Burghardt, J., and Weyfarth, W. 1999. A taxonomic study of bacteria isolated from grasses: a proposed new species, Pseudomonas graminis sp nov. International Journal of Systematic Bacteriology 49: 297-308.
6. Berge, O., Heulin, T., Achouak, W., Richard, C, Bally, R., and Balandreau, J. 1991. Rahnella aquatilis, a nitrogen-fixing enteric bacterium associated with the rhizosphere of wheat and maize. Canadian Journal of Microbiology 37:195-203.
7. Boerjan, W. 2005. Biotechnology and the domestication of forest trees. Current Opinion in Biotechnology 16: 1-8.
8. Braatne, J.H., Rood, S.B., and Heilman, P.E. 1996. Life history, ecology, and conservation of riparian cottonwoods in North America. In: Biology of Populus and its Implications for Management and Conservation. Stettler, R.F., Bradshaw, H.D., Heilman, P.E., and Hinckley, T.M., eds. NRC Research Press, Ottawa, pp. 57-85.
9. Brighnigna, L., Montaini, P., Favilla, F., and Trejo, A.C. 1992. The role of the nitrogen-fixing bacterial microflora in the epiphytism of Tillandsia (Bromeliaceae). American Journal of Botany 79: 723-727.
10. Burgmann, H., Widmer, F., Sigler, W.V., and Zeyer, J. 2004. New molecular screening tools for the analysis of free-living diazotrophs in soil. Applied and Environmental Microbiology 70: 240-247.
11. 2-fixing rhizospheric and endophytic species. International Journal of Systematic and Evolutionary Microbiology 54: 1165-1172.
12. Calvo, J., Calvente, V., de Orellano, M.E., Benuzzi, D., and Sanz de Tosetti, M.I. 2007. Biological control of postharvest spoilage caused by Penicillium expansum and Botrytis cinerea in apple by using the bacterium Rahnella aquatilis. International Journal of Food Microbiology 113: 251-257.
13. Cankar, K., Kraigher, H., Ravnikar, M., and Rupnik, M. 2005. Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiology Letters 244: 341-345.
14. Chen, W.M., Moulin, L., Bontemps, C, Vandamme, P., Bena, G., and Boivin-Masson, C. 2003. Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. Journal of Bacteriology 185: 7266-7272.
15. Cocking, E.C. 2005. Intracellular colonization of cereals and other crop plants by nitrogen-fixing bacteria for reduced inputs of synthetic nitrogen fertilizers. In vitro Cellular and Developmental Biology-Plant 41: 369-373.
16. Cook, R.J., Thomashow, L.S., Weller, D.M., Fujimoto, D., Mazzola, M., Bangera, G., and Kim, D.-S. 1995. Molecular mechanisms of defense by rhizobacteria against root disease. Proceedings of the National Academy of Sciences USA 92: 4197-4201.
17. DeSantis, T.Z., Hugenholtz, P., Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M., Phan, R., and Andersen, G.L. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34: 394-399.
18. Döbereiner, J. 1992. History and new perspectives of diazotrophs in association with non-leguminous plants. Symbiosis 13: 1-13.
19. Döbereiner, J. and Pedrosa, F.O. 1987. Nitrogen Fixing Bacteria In Non-Leguminous Crop Plants. Science Tech Publishers, Madison, WI, USA.
20. 2 fixation associated with non-leguminous plants. Basic Life Science 9:451-461.
21. Doty, S.L. 2008. Tansley Review: Enhancing phytoremediation through the use of transgenics and endophytes. New Phytologist doi: 10.1111/j.1469-8137.2008.02446.X.
22. Doty, S.L., Dosher, M.R., Singleton, G.L., Moore, A.L., van Aken, B., Stettler, R.F., Strand, S.E., and Gordon, M.P. 2005. Identification of an endophytic Rhizobium in stems of Populus. Symbiosis 39: 27-36.
23. Ederer, M.M., Crawford, R.L., Herwig, R.P., and Orser, C.S. 1997. PCP degradation is mediated by closely related strains of the genus Sphingomonas. Molecular Ecology 6: 39-49.
24. Elbeltagy, A., Nishioka, K., Sato, T., Suzuki, H., Ye, B., Hamada, T., Isawa, T., Mitsui, H., and Minamisawa, K. 2001. Endophytic colonization and in plant a nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Applied and Environmental Microbiology 67: 5285-5293.
25. Fain, M.G. and Haddock, J.D. 2001. Phenotypic and phylogenetic characterization of Burkholderia (Pseudomonas) sp. strain LB400. Current Microbiology 42: 269-275.
26. Feng.Y., Shen, D., and Song, W. 2006. Rice endophyte Pantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates. Journal of Applied Microbiology 100: 938-945.
27. Flores-Encarnacion, M., Contreras-Zentella, M., Soto-Urzua, L., Aguilar, G.R., Baca, B.E., and Escamilla, J.E. 1999. The respiratory system and diazotropic activity of Acetobacter diazotrophicus PAL5. Journal of Bacteriology 181: 6987-6995.
28. Foster, L.J., Kwan, B.H., and Vancov, T. 2004. Microbial degradation of the organophosphate pesticide, Ethion. FEMS Microbiology Letters 240: 49-53.
29. 2-fixing system. Journal of Bacteriology 174: 6840-6843.
30. Germaine, K., Keogh, E., Garcia-Cabellos, G., Borremans, B., van der Lelie, D., Barac, T., Oeyen, L., Vangronsveld, J., Moore, F.P., Moore, E.R.B., Campbell, CD., Ryan, D., and Dowling, D.N. 2004. Colinisation of poplar trees by gfp expressing bacterial endophytes. FEMS Microbiology Ecology 48: 109-118.
31. Harms, H., Wilkes, H., Wittich, R., and Fortnagel, P. 1995. Metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans by Sphingomonas sp. strain HH69. Applied and Environmental Microbiology 61: 2499-2505.
32. Hashidoko, Y., Hayashi, H., Hasegawa, T., Purnomo, E., Osaki, M., and Tahara, S. 2006. Frequent isolation of sphingomonads from local rice varieties and other weeds grown on acid sulphate soil in South Kalimantan, Indonesia. Tropics 154: 395.
33. Hirsch, A.M. 2004. Plant-microbe symbioses: A continuum from commensalism to parasitism. Symbiosis 37: 345-363.
34. Hutner, S.H. 1972. Inorganic nutrition. Annual Review of Microbiology 26: 313-346.
35. Kessler, P.S. and Leigh, J.A. 1999. Genetics of nitrogen regulation in Methanococcus maripaludis. Genetics 152: 1343-1351.
36. Khan, A.A., Wang, R.F., Cao, W.W., Franklin, W., and Cerniglia, C.E. 1996. Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain Bl, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. International Journal of Systematic Bacteriology 46: 466-469.
37. Kim, H., Nishiyama, M., Kunito, T., Senoo, K., Kawahara, K., Murakami, K., and Oyaizu, H. 1998. High population of Sphingomonas species on plant surface. Journal of Applied Microbiology 85: 731-736.
38. Kuklinsky-Sobral, J., Welington, L.A., Mendes, R., Pizzirani-Kleiner, A.A., and Azevedo, J.L. 2005. Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant and Soil 273: 91-99.
39. Liu, Z., Yang, C, and Qiao, C.L. 2007. Biodegradation of p-nitrophenol and 4-chlorophenol by Stenotrophomonas sp. FEMS Microbiology Letters 277: 150-156.
40. Ludwig, W., Strunk, O., Westram, R., and et al. 2004. ARB: A software environment for sequence data. Nucleic Acids Research 14: 358-366.
41. Mastretta, C., Barac, T., Vangronsveld, J., Newman, L., Taghavi, S., and van der Lelie, D. 2006. Endophytic bacteria and their potential application to improve the phytoremediation of contaminated environments. Biotechnology and Genetic Engineering 23: 175-207.
42. Minerdi, D., Fani, R., Gallo, R., Boarino, A., and Bonfante, P. 2001. Nitrogen fixation genes in an endosymbiotic Burkholderia strain. Applied and Environmental Microbiology 67: 725-732.
43. Moran, N.A., Munson, M.A., Baumann, P., and Ishikawa, H. 1993. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proceedings of the Royal Society of London B253: 167-171.
44. Moulin, L., Munive, A., Dreyfus, B., and Boivin-Masson, C. 2001. Nodulation of legumes by members of the b-subclass of Proteobacteria. Nature 411: 948-950.
45. Murashige, T. and Skoog, F. 1962. A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiology of the Plant 15: 473-497.
46. Muthukumarasamy, R., Kang, U.G., Park, K.D., Jeon, W.T., Park, C.Y., Cho, Y.S., Kwon, S.W., Song, J., Roh, D.H., and Revathi, G. 2007. Enumeration, isolation and identification of diazotrophs from Korean wetland rice varieties grown with long-term application of N and compost and their short-term inoculation effect on rice plants. Journal of Applied Microbiology 102: 981-991.
47. Nejad, P. and Johnson, P.A. 2000. Endophytic bacteria induce growth promotion and wilt disease suppression in oilseed rape and tomato. Biological Control 18: 208-215.
48. Ozawa, T., Ohwaki, A., and Okumura, K. 2003. Isolation and characterization of diazotrophic bacteria from the surface-sterilized roots of some legumes. Scientific Report of the Graduate School of Agriculture and Biological Sciences, Osaka Prefecture University 55: 29-36.
49. Reinhold-Hurek, B. and Hurek, T. 1998. Life in grasses: diazotrophic endophytes. Trends in Microbiology 6: 139-144.
50. Reis, V.M., Baldani, J.I., Baldani, V.L.D., and Döbereiner, J. 2000. Biological dinitrogen fixation in gramineae and palm trees. Critical Reviews in Plant Sciences 10: 227-247.
51. Rentz, J.A., Alvarez, P.J.J., and Schnoor, J.L. 2005. Benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: Implications for phytoremediation. Environmental Pollution 136: 477-484.
52. 2 by a molybdenum-CO dehydrogenase. Journal of Biological Chemistry 112: 26627-26633.
53. Riggs, P.J., Moritz, R.L., Chelius, M.K., Dong, Y., Iniguez, A.L., Kaeppler, S.M., Casler, M.D., and Triplett, E.W. 2002. Isolation and characterization of diazotrophic endophytes from grasses and their effects on plant growth. In: 13th International Congress on Nitrogen Fixation. Hamilton, Ontario, Canada. Nitrogen Fixation: A Global Perspective, pp. 263-267.
54. Ryan, R.P., Germaine, K., Franks, A., Ryan, D.J., and Dowling, D.N. 2008. Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters 278: 1-9.
55. 2 incorporation following inoculation of sterile plants with Acetobacter diazotrophicus wild-type and Nif- mutant strains. Molecular Plant Microbe Interactions 14: 358-366.
56. Siciliano, S.D., Fortin, N., Mihoc, A., Wisse, G., Labelle, S., Beaumier, D., Ouellette, D., Roy, R., Whyte. L.G., Banks, M.K., Schwab, P., Lee, K., and Greer, C.W. 2001. Selection of specific endophytic bacterial genotypes by plants in response to soil contamination. Applied and Environmental Microbiology 6:2469-2475.
57. Staley, J.T. 1968. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. Journal of Bacteriology 95: 1921-1942.
58. Stettler, R.F., Bradshaw, H.D., Heilman, P.E., and Hinckley, T.M. 1996. Biology of Populus and its Implications for Management and Conservation. NRC Research Press, Ottawa.
59. Sturz, A.V., Christie, B.R., and Nowak, S. 2000. Bacterial endophytes: Potential role in developing sustainable systems of crop production. Critical Reviews of Plant Science 19: 1-30.
60. Sun, L., Qiu, F., Zhang, X., Dai, X., Dong, X., and Song, W. 2008. Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microbial Ecology 55: 415-424.
61. Taghavi, S., Barac, T., Greenberg, B., Borremans, B., Vangronsveld, J., and van der Lelie, D. 2005. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Applied and Environmental Microbiology 71: 8500-8505.
62. Takeuchi, M., Hamana, K., and 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. International Journal of Systematic Evolutionary Microbiology 51: 1405-1417.
63. Ulrich, K., Ulrich, A., and Ewald, D. 2008. Diversity of endophytic bacterial communities in poplar grown under field conditions. FEMS Microbiology and Ecology 63: 169-180.
64. van Aken, B., Peres, CM., Doty, S.L., Yoon, J.M., and Schnoor, J.L. 2004a. Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). International Journal of Systematic and Evolutionary Microbiology 54: 1191-1196.
65. van Aken, J3., Yoon, J.M., and Schnoor, J.L. 2004b. Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-l,3,5-trinitro-l, 3,5-triazine, and octahydro-l,3,5,7-tetranitro-l,3,5-tetrazocine by a phyto-symbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoides x nigra DN34). Applied and Environmental Microbiology 70: 508-517.
66. Wang, Y.D., Dong, X.J., Wang, X., Hong, Q., Jiang, X., and Li, S.P. 2007. Isolation of phenol-degrading bacteria from natural soil and their phylogenetic analysis. Huan Jing Ke Xue 28: 623-626.
67. Yrjala, K., Suomalainen, S., Suhonen, E.L., Kilpi, S., Paulin, L., and Romantschuk, M. 1998. Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3. International Journal of Systematic Bacteriology 48: 1057-1062.
68. Zhuang, X., Chen, J., Shim, H., and Bai, Z. 2007. New advances in plant growth-promoting rhizobacteria for bioremediation. Environmental International 33: 406-413.
69. Zipper, C., Nickel, K., Angst, W., and Kohler, H.P. 1996. Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy) propionic acid] in an enantioselective manner by Sphingomonas herbicidovorans sp. nov. Applied and Environmental Microbiology 62: 4318-4322.
70. Zylstra, G.J. and Kim, E. 1997. Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae Bl. Journal of Industrial Microbiology and Biotechnology 19: 408-414.