Plant and Soil

, 317:135 | Cite as

Effect of soil type and soybean genotype on fungal community in soybean rhizosphere during reproductive growth stages

  • Guanghua Wang
  • Yanxia Xu
  • Jian Jin
  • Judong Liu
  • Qiuying Zhang
  • Xiaobing Liu
Regular Article

Abstract

Fungal communities in soybean rhizosphere from reproductive growth stages R1 (beginning bloom) to R8 (full maturity) were studied based on the polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) banding patterns of partial rDNA internal transcribed spacer regions (ITS1) and sequencing methods. Pot experiment subjecting three soybean genotypes grown in two soils (Mollisol and Alfisol) indicated that the soil type was the major factor in shaping the fungal communities in the soybean rhizosphere. Field experiment was conducted in an Alfisol field with three soybean genotypes, and both pot and field experiments showed that rhizosphere fungal communities shifted with growth stages, and more diversity of communities was found in early reproductive growth stages than later stages. No major difference among fungal communities of three soybean genotypes was detected at individual growth stage. BLAST search of ITS sequence data generated from excised DGGE bands showed that fungi belonging to Ascomycetes and Basidiomycetes predominantly inhabited in the soybean rhizosphere. In addition, a few bands had low similarity with database sequences inferred that unknown fungal groups existed in soybean rhizosphere.

Keywords

DGGE Fungal community ITS region Rhizosphere Soil type Soybean genotype 

Notes

Acknowledgment

The authors are grateful to Professor Makoto Kimura, Nagoya University Japan, for his comments and critical review of this manuscript. This research was supported by grants from Science and Technology Bureau of Heilongjiang Province (GA06B101-3-1) and National Natural Science Foundation of China (40671099).

References

  1. Anderson IC, Campbell CD, Prosser JI (2003) Diversity of fungi in organic soils under a moorland-Scots pine (Pinus sylvestris L.) gradient. Environ Microbiol 5:1121–1132 doi:10.1046/j.1462-2920.2003.00522.x PubMedCrossRefGoogle Scholar
  2. Atkinson D, Watson CA (2000) The beneficial rhizosphere: a dynamic entity. Appl Soil Ecol 15:99–104 doi:10.1016/S0929-1393(00)00084-6 CrossRefGoogle Scholar
  3. Bastias BA, Huang ZQ, Blumfield T, Xu Z, Cairney JWG (2006) Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest. Soil Biol Biochem 38:3492–3501 doi:10.1016/j.soilbio.2006.06.007 CrossRefGoogle Scholar
  4. Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annu Rev Ecol Syst 22:4356–4360 doi:10.1146/annurev.es.22.110191.002521 CrossRefGoogle Scholar
  5. Buchenauer H (1998) Biological control of soil-borne diseases by rhizobacteria. J Plant Dis Prot 105:329–348Google Scholar
  6. 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 doi:10.1139/cjm-45-2-138 CrossRefGoogle Scholar
  7. Buyer JS, Roberts DP, Russek-Cohen E (2002) Soil and plant effects on microbial community structure. Can J Microbiol 48:955–964 doi:10.1139/w02-095 PubMedCrossRefGoogle Scholar
  8. Cahyani VR, Matsuya K, Asakawa S, Kimura M (2004) Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE analysis. Soil Sci Plant Nutr 50:555–563Google Scholar
  9. Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56:236–249 doi:10.1111/j.1574-6941.2005.00026.x PubMedCrossRefGoogle Scholar
  10. 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. Microb Ecol 38:273–284 doi:10.1007/s002489900177 PubMedCrossRefGoogle Scholar
  11. De Ridder-Duine AS, Kowalchuk GA, Gunnewiek PJAK, Smant W, van Veen JA, de Boer W (2005) Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition. Soil Biol Biochem 37:349–357 doi:10.1016/j.soilbio.2004.08.005 CrossRefGoogle Scholar
  12. Duineveld B, Kowalchuck GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178 doi:10.1128/AEM.67.1.172-178.2001 PubMedCrossRefGoogle Scholar
  13. Ebersberger D, Wermbter N, Niklaus PA, Kandeler E (2004) Effect of long term CO2 enrichment on microbial community structure in calcareous grass land. Plant Soil 264:313–323 doi:10.1023/B:PLSO.0000047768.89268.8c CrossRefGoogle Scholar
  14. Garbeva P, Veen JAV, Elsas JDV (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270 doi:10.1146/annurev.phyto.42.012604.135455 PubMedCrossRefGoogle Scholar
  15. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhiza and rusts. Mol Ecol 2:113–118 doi:10.1111/j.1365-294X.1993.tb00005.x PubMedCrossRefGoogle Scholar
  16. Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359PubMedGoogle Scholar
  17. 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 doi:10.1128/AEM.69.3.1800-1809.2003 PubMedCrossRefGoogle Scholar
  18. Gomes NCM, Heuer H, Schönfeld J, Costa R, Hagler-Mendonca 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 doi:10.1023/A:1010350406708 CrossRefGoogle Scholar
  19. Gomes NCM, Fagbola O, Costa R, Rumjanek NG, Buchner A, Hagler-Mendonca L, Smalla K (2003) Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl Environ Microbiol 69:3758–3766 doi:10.1128/AEM.69.7.3758-3766.2003 PubMedCrossRefGoogle Scholar
  20. Graham MH, Haynes RJ (2005) Catabolic diversity of soil microbial communities under sugarcane and other land uses estimated by Biolog and substrate-induced respiration methods. Appl Soil Ecol 29:155–164 doi:10.1016/j.apsoil.2004.11.002 CrossRefGoogle Scholar
  21. 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 doi:10.1016/S0038-0717(97)00124-7 CrossRefGoogle Scholar
  22. Hawksworth DL, Rossman AY (1997) Where are all the undescribed fungi? Phytopthology 87:888–891 doi:10.1094/PHYTO.1997.87.9.888 CrossRefGoogle Scholar
  23. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432 doi:10.1017/S0953756201004725 CrossRefGoogle Scholar
  24. Hiltner L (1904) Uber neuere erfarungen und problem auf dem gebiet der bodenbakteriologie und unter besonderer berucksichtigung der grundung und brache. Arbeitent Dtsch Landwirtschafts-Gesellschaft 98:59–78Google Scholar
  25. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, 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 doi:10.1023/A:1020565523615 PubMedCrossRefGoogle Scholar
  26. Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ Microbiol 2:99–110 doi:10.1046/j.1462-2920.2000.00080.x PubMedCrossRefGoogle Scholar
  27. Liu XB, Herbert SJ (2002) Fifteen years of research examining cultivation of continuous soybean in Northeast China. Field Crops Res 79:1–7 doi:10.1016/S0378-4290(02)00042-4 CrossRefGoogle Scholar
  28. Liu XB, Jin J, Wang GH, Herbert SJ (2008) soybean yield physiology and development of high-yielding practices in Northeat China. Field Crops Res 105:157–171 doi:10.1016/j.fcr.2007.09.003 CrossRefGoogle Scholar
  29. Marschner P, Crowley D, Yang CH (2004) Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant Soil 261:199–208 doi:10.1023/B:PLSO.0000035569.80747.c5 CrossRefGoogle Scholar
  30. Marschner P, Neumann G, Kania A, Weiskopf L, Liebere R (2002) Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.). Plant Soil 246:167–174 doi:10.1023/A:1020663909890 CrossRefGoogle Scholar
  31. 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 doi:10.1016/S0038-0717(01)00052-9 CrossRefGoogle Scholar
  32. Matsuyama T, Nakajima Y, Matsuya K, Ikenaga M, Asakawa S, Kimura M (2007) Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol Biochem 39:463–472 doi:10.1016/j.soilbio.2006.08.016 CrossRefGoogle Scholar
  33. Nazih N, Finlay-Moore O, Hartel PG, Fuhrmann JJ (2001) Whole soil fatty acid methyl ester (FAME) profiles of early soybean rhizosphere as affected by temperature and matric water potential. Soil Biol Biochem 33:693–696 doi:10.1016/S0038-0717(00)00197-8 CrossRefGoogle Scholar
  34. Nelson EB (1990) Exudate molecules initiating fungal responses to seeds and roots. Plant Soil 129:61–73 doi:10.1007/BF00011692 CrossRefGoogle Scholar
  35. Rengel Z (2002) Genetic control of root exudation. Plant Soil 245:59–70 doi:10.1023/A:1020646011229 CrossRefGoogle Scholar
  36. Rovira AD (1959) Root excretions in relation to the rhizosphere effect. IV. Influence of plant species, age of plant, light, temperature, and calcium nutrition on exudation. Plant Soil 11:53–64 doi:10.1007/BF01394753 CrossRefGoogle Scholar
  37. Singh BK, Munro S, Potts JM, Millard P (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36:147–155 doi:10.1016/j.apsoil.2007.01.004 CrossRefGoogle Scholar
  38. 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 Microbiol 67:4742–4751 doi:10.1128/AEM.67.10.4742-4751.2001 PubMedCrossRefGoogle Scholar
  39. Sylvia DM, Chellemi DO (2001) Interactions among root-inhabiting fungi and their implications for biological control of root pathogens. Adv Agron 73:1–33 doi:10.1016/S0065-2113(01)73003-9 CrossRefGoogle Scholar
  40. Watanabe T, Asakawa S, Nakamura A, Nagaoka K, Kimura M (2004) DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol Lett 232:153–163 doi:10.1016/S0378-1097(04)00045-X PubMedCrossRefGoogle Scholar
  41. Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511PubMedGoogle Scholar
  42. White TJ, Buns TD, Lee S, Taylor J (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In: Innis MA, Gefland DH, Sninsky JJ, White TJ (eds) PCR protocols: A guide to methods and applications. Academic, New York, pp 315–322Google Scholar
  43. 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 doi:10.1128/AEM.67.12.5849-5854.2001 PubMedCrossRefGoogle Scholar
  44. Xin H, Ma H (1987) Occurrence and control for soybean root rot. Soybean Sci 6:189–196 in ChineseGoogle Scholar
  45. Yang CH, Crowley DE (2000) Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol 66:345–351PubMedCrossRefGoogle Scholar
  46. Yao H, Jiao X, Wu F (2006) Effect of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity. Plant Soil 284:195–203 doi:10.1007/s11104-006-0023-2 CrossRefGoogle Scholar
  47. Zhou J, Bruns MA, Tieduje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Guanghua Wang
    • 1
  • Yanxia Xu
    • 1
  • Jian Jin
    • 1
  • Judong Liu
    • 1
  • Qiuying Zhang
    • 1
  • Xiaobing Liu
    • 1
  1. 1.Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina

Personalised recommendations