Abstract
Purpose
Many biotic and abiotic factors influence the structural and functional diversity of microbial communities in the rhizosphere. This study aimed to understand the dynamics of fungal community in the soybean rhizosphere during soybean growth and directly compare the influence of abiotic and biotic factors in shaping the fungal communities across different growth periods.
Materials and methods
High-throughput sequencing based on internal transcribed spacer (ITS) region, quantitative PCR, and statistical analysis approaches were used to measure the fungal community structure, abundance, and dynamic changes of 63 rhizosphere soil samples which were taken from different fertilization regimes and rhizobium inoculation treatments during three soybean growth stages.
Results and discussion
Among the taxa examined, more than 16 fungal classes were detected from the 21 soil samples. Sordariomycetes was the most abundant class, followed by Dothideomycetes, Agaricomycetes, and Eurotiomycetes. Soybean growth stage was the most important factor determining the diversity patterns of the fungal communities. Fungal community diversity was closely related to the base-fertilizer application, and fungal community richness was associated with rhizobium inoculation. Beta diversity of the fungal community based on the Bray-Curtis distance was significantly related to plant growth stage. Network analysis showed that mutual cooperation among fungal taxa became more intimate during the plant growth.
Conclusions
Compared with edaphic properties, plant growth stage was the dominant factor in determining soil fungal community dynamics. Base-fertilizer and rhizobium inoculation affected the alpha diversity of the soil fungi.
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References
Anderson IC, Cairney JW (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6:769–779
Averill C, Turner BL, Finzi AC (2014) Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505:543–545
Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S (2013) Meeting report: fungal ITS workshop (October 2012). Stand Genomic Sci 8:118
Becklin KM, Hertweck KL, Jumpponen A (2012) Host identity impacts rhizosphere fungal communities associated with three alpine plant species. Microbial Ecol 63:682–693
Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13
Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74:738–744
Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456
Cheng W, Johnson DW, Fu S (2003) Rhizosphere effects on decomposition. Soil Sci Soc Am J 67:1418–1427
Christensen M (1989) A view of fungal ecology. Mycologia 81:1–19
Drenovsky R, Vo D, Graham K, Scow K (2004) Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microbial. Ecol 48:424–430
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 103:626–631
Fu S, Cheng W (2002) Rhizosphere priming effects on the decomposition of soil organic matter in C4 and C3 grassland soils. Plant Soil 238:289–294
Holland E, Coleman DC (1987) Litter placement effects on microbial and organic matter dynamics in an agroecosystem. Ecology 2:425–433
Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS (2014) The elemental composition of virus particles: implications for marine biogeochemical cycles. Nature. Rev Microbiol 12:519–528
Liu J, Sui Y, Yu Z, Shi Y, Chu H, Jin J, Liu X, Wang G (2015) Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of Northeast China. Soil Biol Biochem 83:29–39
Lorito M, Woo SL, Fernandez IG, Colucci G, Harman GE, Pintor-Toro JA, Filippone E, Muccifora S, Lawrence CB, Zoina A (1998) Genes from mycoparasitic fungi as a source for improving plant resistance to fungal pathogens. Proc Natl Acad Sci 95:7860–7865
Meiser A, Bálint M, Schmitt I (2014) Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. New Phytol 201:623–635
Newman ME (2006) Modularity and community structure in networks. Proc Natl Acad Sci 103:8577–8582
Olsen SR (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. Circular 939. United States Department Of Agriculture, Washington
Prigent M, Leroy M, Confalonieri F, Dutertre M, DuBow MS (2005) A diversity of bacteriophage forms and genomes can be isolated from the surface sands of the Sahara Desert. Extremophiles 9:289–296
Raes J, Bork P (2008) Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6:693–699
Singh BK, Dawson LA, Macdonald CA, Buckland SM (2009) Impact of biotic and abiotic interaction on soil microbial communities and functions: a field study. Appl Soil Ecol 41:239–248
Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621
Sparks DL, Page A, Helmke P, Loeppert R, Soltanpour P, Tabatabai M, Johnston C, Sumner M (1996) Methods of soil analysis. Part 3-chemical methods. Soil Science Society of America. American Society of Agronomy, Madison
Sugiyama A, Ueda Y, Takase H, Yazaki K (2014) Pyrosequencing assessment of rhizosphere fungal communities from a soybean field. Can J Microbiol 60:687–690
Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Extensive fungal diversity in plant roots. Science 295:2051–2051
Wardle DA, Lindahl BD (2014) Disentangling global soil fungal diversity. Science 346:1052–1053
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications 18:315–322
Zhu B, Cheng W (2012) Nodulated soybean enhances rhizosphere priming effects on soil organic matter decomposition more than non-nodulated soybean. Soil Biol Biochem 51:56–65
Acknowledgments
This work was supported by the National Science Foundation of China (Grant No. 41301265) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15020200).
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Han, LL., Wang, JT., Yang, SH. et al. Temporal dynamics of fungal communities in soybean rhizosphere. J Soils Sediments 17, 491–498 (2017). https://doi.org/10.1007/s11368-016-1534-y
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DOI: https://doi.org/10.1007/s11368-016-1534-y