Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.)

Research in Microbiology

Volumn 163, Issue 5, 2012, Pages 349-356

  Meng, Xianfa ^a   Wang, Lin ^a   Long, Xiaohua ^a   Liu, Zhaopu ^a   Zhang, Zhenhua ^b   Zed, Rengel ^b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Bacterial community structure; Diazotrophs; Jerusalem artichoke; LH PCR; Rhizosphere; T RFLP

Indexed keywords

NITROGEN;

ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; FERTILIZATION; GENETIC VARIABILITY; JERUSALEM ARTICHOKE; LENGTH HETEROGENEITY POLYMERASE CHAIN REACTION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NITRITE OXIDIZING BACTERIUM; NITROGEN FERTILIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE;

BIOTA; FERTILIZERS; HELIANTHUS; METAGENOME; NITROGEN; NITROGEN FIXATION; OXIDOREDUCTASES; PLANT ROOTS; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOSPHERE;

BACTERIA (MICROORGANISMS); HELIANTHUS TUBEROSUS;

EID: 84863780326     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2012.03.005     Document Type: Article

References (54)

1. Baldani J.I., Caruso L., Baldani V.L.D., Goi S.R., Döbereiner D.J. Recent advances in BNF with non-legume plants. Soil Biol. Biochem. 1997, 29:911-922.
2. Baldini M., Danuso F., Turi M., Vannozzi G. Evaluation of new clones of Jerusalem artichoke (Helianthus tuberosus L.) for inulin and sugar yield from stalks and tubers. Ind. Crop Prod. 2004, 19:25-40.
3. Bowen G. Soil temperature, root growth, and plant function. Plant Roots: The Hidden Half 1991, CRC Press.
4. Bray J., Curtis J. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 1957, 27:325-349.
5. Bürgmann H., Widmer F., Von Sigler W., Zeyer J. New molecular screening tools for analysis of free-living diazotrophs in soil. Appl. Environ. Microbiol. 2004, 70:240-247.
6. Clarke K., Warwick R. Change in Marine Communities: An Approach to Statistical Analysis and Interpretation 2001, Primer-E Ltd., Plymouth Marine Laboratory, Plymouth, UK. second ed.
7. Clement B., Kehl L., DeBord K., Kitts C. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 1998, 31:135-142.
8. 2) fixation in natural ecosystems. Global Biogeochem. Cycles 1999, 13:623-645.
9. Coelho M.R.R., De Vos M., Carneiro N.P., Marriel I.E., Paiva E., Seldin L. Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol. Lett. 2008, 279:15-22.
10. Coelho M.R.R., Marriel I., Jenkins S., Lanyon C., Seldin L., O'Donnell A. Molecular detection and quantification of nifH gene sequences in the rhizosphere of sorghum (Sorghum bicolor) sown with two levels of nitrogen fertilizer. Appl. Soil Ecol. 2009, 42:48-53.
11. Davis D.A., Gamble M.D., Bagwell C.E., Bergholz P.W., Lovell C.R. Responses of salt marsh plant rhizosphere diazotroph assemblages to changes in marsh elevation, edaphic conditions and plant host species. Microb. Ecol. 2011, 61:386-398.
12. 2-fixing bacterial diversity in soil under Acacia tortilis ssp. raddiana and Balanites aegyptiaca in the dryland part of Senegal. Environ. Microbiol. 2004, 6:400-415.
13. Deslippe J., Egger K. Molecular diversity of nifH genes from bacteria associated with high arctic dwarf shrubs. Microb. Ecol. 2006, 51:516-525.
14. 2 fixing bacteria. Cienc. Cult. 1992, 44:310-313.
15. Döbereiner J. History and new perspectives of diazotrophs in association with non-leguminous plants. Symbiosis 1992, 13:1-13.
16. Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 1999, 65:1662-1669.
17. Ferrando L., Tarlera S. Activity and diversity of methanotrophs in the soil-water interface and rhizospheric soil from a flooded temperate rice field. J. Appl. Microbiol. 2009, 106:306-316.
18. Hartmann A., Schmid M., Tuinen D., Berg G. Plant-driven selection of microbes. Plant Soil 2009, 321:235-257.
19. Holmes D.E., O'Neil R.A., Vrionis H.A., N'guessan L.A., Ortiz-Bernad I., Larrahondo M.J., Adams L.A., Ward J.A., Nicoll J.S., Nevin K.P. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe (III)-reducing subsurface environments. ISME J. 2007, 1:663-677.
20. Hsu S., Buckley D. Evidence for the functional significance of diazotroph community structure in soil. ISME J. 2008, 3:124-136.
21. Kanungo P., Ramakrishnan B., Rao V. Placement effects of organic sources on nitrogenase activity and nitrogen-fixing bacteria in flooded rice soils. Biol. Fert. Soils 1997, 25:103-108.
22. Kennedy N., Egger K.N. Impact of wildfire intensity and logging on fungal and nitrogen-cycling bacterial communities in British Columbia forest soils. Forest Ecol. Manag. 2010, 260:787-794.
23. Kirk J., Beaudette L., Hart M., Moutoglis P., Klironomos J., Lee H., Trevors J. Methods of studying soil microbial diversity. J. Microbiol. Methods 2004, 58:169-188.
24. Knauth S., Hurek T., Brar D., Reinhold-Hurek B. Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice. Environ. Microbiol. 2005, 7:1725-1733.
25. Lamarche J., Hamelin R.C. No evidence of an impact on the rhizosphere diazotroph community by the expression of Bacillus thuringiensis Cry1Ab toxin by Bt white spruce. Appl. Environ. Microbiol. 2007, 73:6577-6583.
26. Liu W., Marsh T., Cheng H., Forney L. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 1997, 63:4516-4522.
27. Lovell C., Piceno Y., Quattro J., Bagwell C. Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl. Environ. Microbiol. 2000, 66:3814-3822.
28. Mergel A., Schmitz O., Mallmann T., Bothe H. Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil. FEMS Microbiol. Ecol. 2001, 36:33-42.
29. Mills D.E.K., Fitzgerald K., Litchfield C.D., Gillevet P.M. A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. J. Microbiol. Methods 2003, 54:57-74.
30. Newton W. Nitrogen fixation in perspective. Nitrogen Fixation: From Molecules to Crop Productivity 2002, Kluwer Academic Publishers.
31. Piceno Y., Lovell C. Stability in natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb. Ecol. 2000, 39:32-40.
32. Park S.J., Cheng Z., Yang H., Morris E.E., Sutherland M., McSpadden G.B.B., Grewal P.S. Differences in soil chemical properties with distance to roads and age of development in urban areas. Urban Ecosyst 2010, 13:483-497.
33. Pereira e.S.M.C., Semenov A.V., Van Elsas J.D., Salles J.F. Seasonal variations in the diversity and abundance of diazotrophic communities across soils. FEMS Microbiol. Ecol. 2011, 77:57-68.
34. Poly F., Monrozier L., Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res. Microbiol. 2001, 152:95-103.
35. Poly F., Ranjard L., Nazaret S., Gourbiere F., Monrozier L. Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl. Environ. Microbiol. 2001, 67:2255-2262.
36. Rappé M., Kemp P., Giovannoni S. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 1997, 42:811-826.
37. Raymond J., Siefert J., Staples C., Blankenship R. The natural history of nitrogen fixation. Mol. Biol. Evol. 2004, 21:541-554.
38. Roesch L.F., Olivares F., Pereira P.L., Selbach P., Sa D.E., Camargo D.F. Characterization of diazotrophic bacteria associated with maize: effect of plant genotype, ontogeny and nitrogen-supply. World J. Microbiol. Biotechnol. 2006, 22:967-974.
39. Roesch L.F.W., Camargo F.A.O., Bento F.M., Triplett E.W. Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 2008, 302:91-104.
40. 2-fixation in different agroecological zones of southern Australia. Aust. J. Soil Res. 2006, 44:343-354.
41. Saengthongpinit W., Sajjaanantakul T. Influence of harvest time and storage temperature on characteristics of inulin from Jerusalem artichoke (Helianthus tuberosus L.) tubers. Postharvest Biol. Technol. 2005, 37:93-100.
42. Suzuki M., Rappe M., Haimberger Z., Winfield H., Adair N., Strobel J., Giovannoni S. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 1997, 63:983-989.
43. Tamura K., Dudley J., Nei M., Kumar S. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
44. Tan Z., Hurek T., Reinhold-Hurek B. Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ. Microbiol. 2003, 5:1009-1015.
45. Thies J. Soil microbial community analysis using terminal restriction fragment length polymorphisms. Soil Sci. Soc. Am. J. 2007, 71:579-591.
46. Turk K.A., Rees A.P., Zehr J.P., Pereira N., Swift P., Shelley R., Lohan M., Woodward E.M.S., Gilbert J. Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME J. 2011, 5:1201-1212.
47. Van Orsouw N.J., Dhanda R.K., Rines R.D., Smith W.M., Sigalas I., Eng C., Vijg J. Rapid design of denaturing gradient-based two-dimensional electrophoretic gene mutational scanning tests. Nucleic Acids Res. 1998, 26:2398-2406.
48. Wartiainen I., Eriksson T., Zheng W., Rasmussen U. Variation in the active diazotrophic community in rice paddy-nifH PCR-DGGE analysis of rhizosphere and bulk soil. Appl. Soil Ecol. 2008, 39:65-75.
49. Widmer F., Shaffer B., Porteous L., Seidler R. Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade Mountain Range. Appl. Environ. Microbiol. 1999, 65:374-380.
50. Wu T., Chellemi D., Graham J., Martin K., Rosskopf E. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microb. Ecol. 2008, 55:293-310.
51. Young J. Phylogeny and taxonomy of rhizobia. Plant Soil 1996, 186:45-52.
52. Zehr J., Jenkins B., Short S., Steward G. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 2003, 5:539-554.
53. Zhang Y., Li D., Wang H., Xiao Q., Liu X. Molecular diversity of nitrogen-fixing bacteria from the Tibetan Plateau, China. FEMS Microbiol. Lett. 2006, 260:134-142.
54. Zhao G., Liu Z., Chen M., Guo S. Soil properties and yield of Jerusalem artichoke (Helianthus tuberosus L.) with seawater irrigation in North China Plain. Pedosphere 2008, 18:195-202.