Analysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots

Abstract

Use of the reverse-transcribed small subunit of the ribosomal RNA (rRNA) was tested for exploring seasonal dynamics of fungal communities associated with the roots of the dominant tallgrass prairie grass, Andropogon gerardii. Ribosomal RNA was extracted, reverse-transcribed, and PCR-amplified in four sampling events in May, July, September, and November. Analyses of cloned PCR amplicons indicated that the A. gerardii rhizospheres host phylogenetically diverse fungal communities and that these communities are seasonally dynamic. Operational taxonomic units with Basic Local Alignment Search Tool affinities within the order Helotiales were dominant in the rhizosphere in May. These putative saprobes were largely replaced by arbuscular mycorrhizal fungi with likely affinities within Glomerales suggesting that the fungal communities are not only compositionally but also functionally dynamic. These data suggest replacement of functional guilds comprised of saprobic fungi by mutualistic fungi in the course of a growing season.

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References

  1. Agnelli A, Ascher J, Corti G, Ceccherini MT, Pietramellara G, Nannipieri P (2007) Purification and isotopic signatures (delta C-13, delta N-15, Delta C-14) of soil extracellular DNA. Biol Fertility Soils 44:353–361. doi:10.1007/s00374-007-0213-y

    Article  CAS  Google Scholar 

  2. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    PubMed  Article  CAS  Google Scholar 

  3. Anderson IC, Parkin PI (2007) Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. J Microbiol Methods 68:248–253. doi:10.1016/j.mimet.2006.08.005

    PubMed  Article  CAS  Google Scholar 

  4. Anderson IC, Parkin PI, Campbell CD (2008) DNA- and RNA-derived assessments of fungal community composition in soil amended with sewage sludge rich in cadmium, copper and zinc. Soil Biol Biochem 40:2358–2365. doi:10.1016/j.soilbio.2008.05.015

    Article  CAS  Google Scholar 

  5. Bastias BA, Anderson IC, Xu Z, Cairney JWG (2007) RNA- and DNA-based profiling of soil fungal communities in a native Australian eucalypt forest and adjacent Pinus elliotti plantation. Soil Biol Biochem 39:3108–3114. doi:10.1016/j.soilbio.2007.06.022

    Article  CAS  Google Scholar 

  6. Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360

    PubMed  Article  CAS  Google Scholar 

  7. 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. doi:10.1111/j.1469-8137.2009.03003.x

    PubMed  Article  CAS  Google Scholar 

  8. Ceccherini MT, Ascher J, Pietramellara G, Vogel TM, Nannipieri P (2007) Vertical advection of extracellular DNA by water capillarity in soil columns. Soil Biol Biochem 39:158–163. doi:10.1016/j.soilbio.2006.07.006

    Article  CAS  Google Scholar 

  9. Colwell RK (2006) EstimateS: statistical estimation of species richness and shared species from samples, version 8

  10. Egerton-Warburton LM, Johnson NC, Allen EB (2007) Mycorrhizal community dynamics following nitrogen fertilization: a cross-site test in five grasslands. Ecol Monogr 77:527–544

    Article  Google Scholar 

  11. Eom AH, Wilson GWT, Hartnett DC (2001) Effects of ungulate grazers on arbuscular mycorrhizal symbiosis and fungal community structure in tallgrass prairie. Mycologia 93:233–242

    Article  Google Scholar 

  12. Eom AH, Hartnett DC, Wilson GWT (2000) Host plant species effects on arbuscular mycorrhizal fungal communities in tallgrass prairie. Oecologia 122:435–444

    Article  Google Scholar 

  13. Eom AH, Hartnett DC, Wilson GWT, Figge DAH (1999) The effect of fire, mowing and fertilizer amendment on arbuscular mycorrhizas in tallgrass prairie. Am Midl Nat 142:55–70

    Article  Google Scholar 

  14. Gemma JN, Koske RE (1988) Seasonal variation in spore abundance and dormancy of Gigaspora gigantea and in mycorrhizal inoculum potential of a dune soil. Mycologia 80:211–216

    Article  Google Scholar 

  15. Girvan MS, Bullimore J, Ball AS, Pretty JN, Osborn AM (2004) Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens. Appl Environ Microbiol 70:2692–2701. doi:10.1128/AEM.70.5.2692-2701.2004

    PubMed  Article  CAS  Google Scholar 

  16. Goos RD (1987) Fungi with a twist—the helicosporous hyphomycetes. Mycologia 79:1–22

    Article  Google Scholar 

  17. Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4:17–27. doi:10.1038/ismej.2009.97

    PubMed  Article  CAS  Google Scholar 

  18. Helgason T, Daniell TJ, Husband R, Fitter AH, Young JPW (1998) Ploughing up the wood-wide web? Nature 394:431–431

    PubMed  Article  CAS  Google Scholar 

  19. Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42:878–887. doi:10.1016/j.soilbio.2010.02.019

    Article  CAS  Google Scholar 

  20. Hoshino YT, Matsumoto N (2007) DNA- versus RNA-based denaturing gradient gel electrophoresis profiles of a bacterial community during replenishment after soil fumigation. Soil Biol Biochem 39:434–444. doi:10.1016/j.soilbio.2006.08.013

    Article  CAS  Google Scholar 

  21. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schuessler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Buedel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822. doi:10.1038/nature05110

    PubMed  Article  CAS  Google Scholar 

  22. Jumpponen A, Trowbridge J, Mandyam K, Johnson L (2005) Nitrogen enrichment causes minimal changes in arbuscular mycorrhizal colonization but shifts community composition-evidence from rDNA data. Biol Fertility Soils 41:217–224. doi:10.1007/s00374-005-0845-8

    Article  CAS  Google Scholar 

  23. Jumpponen A (2007) Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affected by primer selection and chimeric data. Microb Ecol 53:233–246. doi:10.1007/s00248-006-0006-x

    PubMed  Article  CAS  Google Scholar 

  24. Jumpponen A, Jones KL, Mattox D, Yaege C (2010) Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 19:41–53. doi: 10.1111/j.1365-294X.2009.04483.x

    Google Scholar 

  25. Koide RT, Shumway DL, Xu B, Sharda JN (2007) On temporal partitioning of a community of ectomycorrhizal fungi. New Phytol 174:420–429. doi:10.1111/j.1469-8137.2007.02000.x

    PubMed  Article  Google Scholar 

  26. Lee PJ, Koske RE (1994) Gigaspora gigantea—seasonal abundance and aging of spores in a sand dune. Mycol Res 98:453–457

    Article  Google Scholar 

  27. Mahmood S, Paton GI, Prosser JI (2005) Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 7:1349–1360. doi:10.1111/j.1462-2920.2005.00822.x

    PubMed  Article  CAS  Google Scholar 

  28. Merryweather J, Fitter A (1998) The arbuscular mycorrhizal fungi of Hyacinthoides non-scripta—II. Seasonal and spatial patterns of fungal populations. New Phytol 138:131–142

    Article  Google Scholar 

  29. Mummey DL, Rillig MC (2008) Spatial characterization of arbuscular mycorrhizal fungal molecular diversity at the submetre scale in a temperate grassland. FEMS Microbiol Ecol 64:260–270. doi:10.1111/j.1574-6941.2008.00475.x

    PubMed  Article  CAS  Google Scholar 

  30. Oehl F, Sieverding E, Ineichen K, Ris EA, Boller T, Wiemken A (2005) Community structure of arbuscular mycorrhizal fungi at different soil depths in extensively and intensively managed agroecosystems. New Phytol 165:273–283. doi:10.1111/j.1469-8137.2004.01235.x

    PubMed  Article  Google Scholar 

  31. Oehl F, Sieverding E, Ineichen K, Maeder P, Wiemken A, Boller T (2009) Distinct sporulation dynamics of arbuscular mycorrhizal fungal communities from different agroecosystems in long-term microcosms. Agric Ecosyst Environ 134:257–268. doi:10.1016/j.agee.2009.07.008

    Article  Google Scholar 

  32. Öpik M, Metsis M, Daniell TJ, Zobel M, Moora M (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol 184:424–437. doi:10.1111/j.1469-8137.2009.02920.x

    PubMed  Article  Google Scholar 

  33. Ostle N, Whiteley AS, Bailey MJ, Sleep D, Ineson P, Manefield M (2003) Active microbial RNA turnover in a grassland soil estimated using a (CO2)-C-13 spike. Soil Biol Biochem 35:877–885. doi:10.1016/S0038-0717(03)00117-2

    Article  CAS  Google Scholar 

  34. Pietramellara G, Ascher J, Ceccherini MT, Nannipieri P, Wenderoth D (2007) Adsorption of pure and dirty bacterial DNA on clay minerals and their transformation frequency. Biol Fertility Soils 43:731–739. doi:10.1007/s00374-006-0156-8

    Article  CAS  Google Scholar 

  35. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818

    PubMed  Article  CAS  Google Scholar 

  36. Posada D (2006) ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34:W700–W703. doi:10.1093/nar/gkl042

    PubMed  Article  CAS  Google Scholar 

  37. Poulsen LK, Ballard G, Stahl DA (1993) Use of ribosomal RNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59:1354–1360

    PubMed  CAS  Google Scholar 

  38. Pringle A, Bever JD (2002) Divergent phenologies may facilitate the coexistence of arbuscular mycorrhizal fungi in a North Carolina grassland. Am J Bot 89:1439–1446

    PubMed  Article  Google Scholar 

  39. Prosser JI (2002) Molecular and functional diversity in soil micro-organisms. Plant Soil 244:9–17

    Article  CAS  Google Scholar 

  40. Ros M, Pascual JA, Hernandez MT, Garcia C (2009) Long-term effects of devegetation on composition and activities (including transcription) of fungal communities of a semi-arid soil. Biol Fertility Soils 45:435–441. doi:10.1007/s00374-008-0348-5

    Article  Google Scholar 

  41. Stockinger H, Krüger M, Schüssler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187:461–474

    PubMed  Article  CAS  Google Scholar 

  42. Swofford DL (2001) PAUP*, phylogenetic analysis using parsimony (and other methods). Version 4, Sinauer Associates, Sunderland, MA.

  43. Tsui CKM, Hyde KD, Hodgkiss IJ (2000) Biodiversity of fungi on submerged wood in Hong Kong streams. Aquat Microb Ecol 21:289–298

    Article  Google Scholar 

  44. Tsui CKM, Goh TK, Hyde KD, Hodgkiss IJ (2001) New species or records of Cacumisporium, Helicosporium, Monotosporella and Bahusutrabeeja on submerged wood in Hong Kong streams. Mycologia 93:389–397

    Article  Google Scholar 

  45. Walker JF, Miller OK Jr, Horton JL (2008) Seasonal dynamics of ectomycorrhizal fungus assemblages on oak seedlings in the southeastern Appalachian Mountains. Mycorrhiza 18:123–132. doi:10.1007/s00572-008-0163-8

    PubMed  Article  Google Scholar 

  46. White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, New York, pp 315–322

    Google Scholar 

  47. Wolfe BE, Mummey DL, Rillig MC, Klironomos JN (2007) Small-scale spatial heterogeneity of arbuscular mycorrhizal fungal abundance and community composition in a wetland plant community. Mycorrhiza 17:175–183. doi:10.1007/s00572-006-0089-y

    PubMed  Article  Google Scholar 

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Acknowledgements

This material is based upon work supported by the National Science Foundation under grants 0344838 and 0516456. Konza Prairie Biological Station and its personnel maintain the research site and are funded partly through National Science Foundation Long-Term Ecological Research program. Stacie Kageyama assisted in sampling Andropogon gerardii roots.

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Correspondence to Ari Jumpponen.

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Jumpponen, A. Analysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots. Mycorrhiza 21, 453–464 (2011). https://doi.org/10.1007/s00572-010-0358-7

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Keywords

  • Rhizosphere
  • Ribosomal RNA
  • Seasonal dynamics
  • Tallgrass prairie