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Diazotrophic endophytes of native black cottonwood and willow

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Abstract

Poplar and willow are economically-important, fast-growing tree species with the ability to colonize nutrient-poor environments. To initiate a study on the possible contribution of endophytes to this ability, we isolated bacteria from within surface-sterilized stems of native poplar (Populus trichocarpa) and willow (Salix sitchensis) in a riparian system in western Washington state. Several of the isolates grew well in nitrogen-limited medium. The presence ofnifH, a gene encoding one of the subunits of nitrogenase, was confirmed in several of the isolates including species ofBurkholderia, Rahnella, Sphingomonas, andAcinetobacter. Nitrogenase activity (as measured by the acetylene reduction assay) was also confirmed in some of the isolates. The presence of these diazotrophic microorganisms may help explain the ability of these pioneering tree species to grow under nitrogen limitation.

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References

  • Adhikari, T.B., Joseph, C.M., 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Asis, C.A., Jr. and Adachi, K. 2004. Isolation of endophytic diazotrophPantoea agglomerans and nondiazotrophEnterobacter asburiae from sweetpotato stem in Japan.Letters in Applied Microbiology 38: 19–23.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • Boerjan, W. 2005. Biotechnology and the domestication of forest trees.Current Opinion in Biotechnology 16: 1–8.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • Brighnigna, L., Montaini, P., Favilla, F., and Trejo, A.C. 1992. The role of the nitrogen-fixing bacterial microflora in the epiphytism ofTillandsia (Bromeliaceae).American Journal of Botany 79: 723–727.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Caballero-Mellado, J., Martinez-Aguilar, L., Paredes-Valdez, G., and Estrada-de Los Santos, P. 2004.Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species.International Journal of Systematic and Evolutionary Microbiology 54: 1165–1172.

    Article  PubMed  CAS  Google Scholar 

  • Calvo, J., Calvente, V., de Orellano, M.E., Benuzzi, D., and Sanz de Tosetti, M.I. 2007. Biological control of postharvest spoilage caused byPenicillium expansum andBotrytis cinerea in apple by using the bacteriumRahnella aquatilis.International Journal of Food Microbiology 113: 251–257.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Döbereiner, J. 1992. History and new perspectives of diazotrophs in association with non-leguminous plants.Symbiosis 13: 1–13.

    Google Scholar 

  • Döbereiner, J. and Pedrosa, F.O. 1987.Nitrogen Fixing Bacteria In Non-Leguminous Crop Plants. Science Tech Publishers, Madison, WI, USA

    Google Scholar 

  • Döbereiner, J. 1977. N2 fixation associated with non-leguminous plants.Basic Lift Science 9: 451–461.

    Google Scholar 

  • 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.

  • 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 endophyticRhizobium in stems ofPopulus.Symbiosis 39: 27–36.

    CAS  Google Scholar 

  • Ederer, M.M., Crawford, R.L., Herwig, R.P., and Orser, C.S. 1997. PCP degradation is mediated by closely related strains of the genusSphingomonas.Molecular Ecology 6: 39–49.

    Article  PubMed  CAS  Google Scholar 

  • Elbeltagy, A., Nishioka, K., Sato, T., Suzuki, H., Ye, B., Hamada, T., Isawa, T., Mitsui, H., and Minamisawa, K. 2001. Endophytic colonization and in planta nitrogen fixation by aHerbaspirillum sp. isolated from wild rice species.Applied and Environmental Microbiology 67: 5285–5293.

    Article  PubMed  CAS  Google Scholar 

  • Fain, M.G. and Haddock, J.D. 2001. Phenotypic and phylogenetic characterization ofBurkholderia (Pseudomonas) sp. strain LB400Current Microbiology 42: 269–275.

    PubMed  CAS  Google Scholar 

  • Feng,Y., Shen, D., and Song, W. 2006. Rice endophytePantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates.Journal of Applied Microbiology 100: 938–945.

    Article  PubMed  CAS  Google Scholar 

  • 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 ofAcetobacter diazotrophicus PAL5.Journal of Bacteriology 181: 6987–6995.

    PubMed  CAS  Google Scholar 

  • Foster, L.J., Kwan, B.H., and Vancov, T. 2004. Microbial degradation of the organophosphate pesticide, Ethion.FEMS Microbiology Letters 240: 49–53.

    Article  PubMed  CAS  Google Scholar 

  • Gadkari, D., Morsdorf, G., and Meyer, O. 1992. Chemolithoautotrophic assimilation of dinitrogen byStreptomyces thermoautotrophicus UBT1: identification of an unusual N2-fixing system.Journal of Bacteriology 174: 6840–6843.

    PubMed  CAS  Google Scholar 

  • Germaine, K., Keogh, E., Garcia-Cabellos, G., Borremans, B., van der Lelie, D., Barac, T., Oeyen, L., VangronsveId, J., Moore, F.P., Moore, E.R.B., Campbell, C.D., Ryan, D., and Dowling, D.N. 2004. Colinisation of poplar trees bygfp expressing bacterial endophytes.FEMS Microbiology Ecology 48: 109–118.

    Article  PubMed  CAS  Google Scholar 

  • Harms, H., Wilkes, H., Wittich, R., and Fortnagel, P. 1995. Metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans bySphingomonas sp. strain HH69.Applied and Environmental Microbiology 61: 2499–2505.

    PubMed  CAS  Google Scholar 

  • Hashidoko, Y., Hayashi, H., Hasegawa, T., Pumomo, 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.

    Google Scholar 

  • Hirsch, A.M. 2004. Plant-microbe symbioses: A continuum from commensalism to parasitism.Symbiosis 37: 345–363.

    CAS  Google Scholar 

  • Hutner, S.H. 1972. Inorganic nutrition.Annual Review of Microbiology 26: 313–346.

    Article  PubMed  CAS  Google Scholar 

  • Kessler, P.S. and Leigh, J.A. 1999. Genetics of nitrogen regulation inMethanococcus maripaludis.Genetics 152: 1343–1351.

    PubMed  CAS  Google Scholar 

  • Khan, A.A., Wang, R.F., Coo, W.W., Franklin, W., and Cerniglia, C.E. 1996. Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium,Beijerinckia sp. strain B1, asSphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing.International Journal of Systematic Bacteriology 46: 466–469.

    Article  PubMed  CAS  Google Scholar 

  • Kim, H., Nishiyama, M., Kunito, T., Senoo, K., Kawahara, K., Murakami, K., and Oyaizu, H. 1998. High population ofSphingomonas species on plant surface.Journal of Applied Microbiology 85: 731–736.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Liu, Z., Yang, C., and Qiao, C.L., 2007. Biodegradation of p-nitrophenol and 4-chlorophenol byStenotrophomonas sp.FEMS Microbiology Letters 277: 150–156.

    Article  PubMed  CAS  Google Scholar 

  • Ludwig, W., Strunk, O., Westram, R., and et al. 2004. ARB: A software environment for sequence data.Nucleic Acids Research 14: 358–366.

    Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Minerdi, D., Fani, R., Gallo, R., Boarino, A., and Bonfante, P. 2001. Nitrogen fixation genes in an endosymbioticBurkholderia strain.Applied and Environmental Microbiology 67: 725–732.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Reinhold-Hurek, B. and Hurek, T. 1998. Life in grasses: diazotrophic endophytes.Trends in Microbiology 6: 139–144.

    Article  PubMed  CAS  Google Scholar 

  • Reis, V.M., Baldani, J.I., Baldani, V.L.D., and Dobereiner, J. 2000. Biological dinitrogen fixation in gramineae and palm trees.Critical Reviews in Plant Sciences 10: 227–247.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Ribbe, M., Gadkari, D., and Meyer, O. 1997. N2 fixation byStreptomyces thermoautotrophicus involves a molybdenumdinitrogenase and a manganese-superoxide oxidoreductase that couple N2 reduction to the oxidation of superoxide produced from O2 by a molybdenum-CO dehydrogenase.Journal of Biological Chemistry 272: 26627–26633.

    Article  PubMed  CAS  Google Scholar 

  • 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.

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Sevilla, M., Burris, R.H., Gunapala, N., and Kennedy, C. 2001. Comparison of benefit to sugarcane plant growth and15N2 incorporation following inoculation of sterile plants withAcetobacter diazotrophicus wild-type andNif-mutant strains.Molecular Plant Microbe Interactions 14: 358–366.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Staley, J.T. 1968.Prosthecomicrobium andAncalomicrobium: new prosthecate freshwater bacteria.Journal of Bacteriology 95: 1921–1942.

    PubMed  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Takeuchi, M., Hamana., K., and Hiraishi, A. 2001. Proposal of the genusSphingomonas sensu stricto and three new genera,Sphingobium, Novosphingobium andSphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.International Journal of Systematic Evolutionary Microbiology 51: 1405–1417.

    CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • van Aken, B., Peres, C.M., 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 × nigra DN34).International Journal of Systematic and Evolutionary Microbiology 54: 1191–1196.

    Article  PubMed  CAS  Google Scholar 

  • van Aken, B., 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 phytosymbioticMethylobacterium sp. associated with poplar tissues (Populus deltoides × nigra DN34).Applied and Environmental Microbiology 70: 508–517.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Yrjala, K., Suomalainen, S., Suhonen, E.L., Kilpi, S., Paulin, L., and Romantschuk, M. 1998. Characterization and reclassification of an aromatic- and chloroaromatic-degradingPseudomonas sp., strain HV3, asSphingomonas sp. HV3.International Journal of Systematic Bacteriology 48: 1057–1062.

    Article  PubMed  CAS  Google Scholar 

  • Zhuang, X., Chen, J., Shim, H., and Bai, Z. 2007. New advances in plant growth-promoting rhizobacteria for bioremediation.Environmental International 33: 406–413.

    Article  Google Scholar 

  • 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 bySphingomonas herbicidovorans sp. nov.Applied and Environmental Microbiology 62: 4318–4322.

    PubMed  CAS  Google Scholar 

  • Zylstra, G.J. and Kim, E. 1997. Aromatic hydrocarbon degradation bySphingomonas yanoikuyae B1.Journal of Industrial Microbiology and Biotechnology 19: 408–414.

    Article  CAS  Google Scholar 

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Doty, S.L., Oakley, B., Xin, G. et al. Diazotrophic endophytes of native black cottonwood and willow. Symbiosis 47, 23–33 (2009). https://doi.org/10.1007/BF03179967

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