These authors contributed equally to the work.
1462-2920/asset/olbannerleft.jpg?v=1&s=5f82e8ee67d9627dd0834a0e122ea6814218421f)
1462-2920/asset/olbannerright.jpg?v=1&s=54f2b0280cb9fa7eecc1a1eca2cb11cc173e435a)
You have free access to this content
Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach
Article first published online: 17 NOV 2009
DOI: 10.1111/j.1462-2920.2009.02099.x
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd
Issue
Environmental Microbiology
Special Issue: Symbiosis. Editors: Professors Paola Bonfante, Karen Visick, and Moriya Ohkuma
Volume 12, Issue 8, pages 2165–2179, August 2010
Additional Information
How to Cite
Lumini, E., Orgiazzi, A., Borriello, R., Bonfante, P. and Bianciotto, V. (2010), Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Environmental Microbiology, 12: 2165–2179. doi: 10.1111/j.1462-2920.2009.02099.x
- †
These authors contributed equally to the work.
Publication History
- Issue published online: 4 AUG 2010
- Article first published online: 17 NOV 2009
- Received 19 May, 2009; accepted 29 September, 2009.
References
- , , , , , and (2008) The impact of tillage practices on arbuscular mycorrhizal fungal diversity in subtropical crops. Ecol Appl 18: 527–536.
- , , , , and (2008) Molecular community analysis of arbuscular mycorrhizal fungi in roots of geothermal soils in Yellowstone National Park (USA). Microb Ecol 56: 649–559.
- , , and (2006) Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ Microbiol 8: 1–10.
- , , , , , and (2004) A contribution to the knowledge of the order Quercetalia ilicis Br.-Bl. ex Molinier 1934 of Sardinia. Fitosociologia 41: 29–51.
- , , , , , and (2008) Glomus irregulare, a new arbuscular mycorrhizal fungus in the Glomeromycota. Mycotaxon 106: 247–267.
- , , , , and (2008) Genetic diversity of the arbuscular mycorrhizal fungus Glomus intraradices as determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected. New Phytol 180: 452–465.
- , and (2002) Arbuscular mycorrhizal fungi respond to increasing plant diversity. Can J Bot 80: 120–130.
- , , , , , , and (2009) Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus Glomus intraradices. New Phytol 181: 924–937.
- , , , and (2005) Contrasting root associated fungi of three common oak-woodland plant species based on molecular identification: host specificity or non-specific amplification? Mycorrhiza 15: 365–372.
- , , , and (2001) The mycorrhizal soil infectivity and arbuscular mycorrhizal fungal spore communities in soils of different aged fallows in Senegal. Appl Soil Ecol 17: 239–251.
- (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797.
- , , , , , , et al. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7: 57.
- , , , , , , et al. (2008) The metagenomics of disease-suppressive soils – experiences from the METACONTROL project. Trends Biotechnol 26: 591–601.
- , , , , , , et al. (2008) Novelty, uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 74: 5422–5428.
- (2005) phylip (Phylogeny Inference Package), Version 3.6. Distributed by the Author. Seattle, WA, USA: Department of Genome Sciences, University of Washington.
- , , , and (2008) Distantly sampled soils carry few species in common. ISME J 2: 901–910.
- , , and (2007) Mycorrhizal Fungi: their habitats and nutritional strategies. In The Mycota IV Environmental and Microbial Relationships, 2nd edn. Berlin-Heidelberg, Germany: Springer-Verlag, pp. 229–256.
- , , , , , and (2006) Organic and mineral fertilization, respectively, increase and decrease the development of external mycelium of arbuscular mycorrhizal fungi in a long-term field experiment. Mycorrhiza 16: 159–166.
- , , and (2006) Sequences, sequence clusters and bacterial species. Philos T R Soc B 361: 1917–1927.
- , and (2002) Host plant benefit from association with arbuscular mycorrhizal fungi: variation due to differences in size of mycelium. Biol Fert Soils 36: 357–366.
- , and (2007) Functional traits in mycorrhizal ecology: their use for predicting the impact of arbuscular mycorrhizal fungal communities on plant growth and ecosystem functioning. New Phytol 174: 244–250.
- , , , , , , et al. (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396: 69–72.
- , , and (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296–310.
- , , , , and (1998) Ploughing up the wood-wide web? Nature 394: 431.
- , , , , , and (2002) Selectivity and functional diversity in arbuscular mycorrhizas of co-occurring fungi and plants from a temperate deciduous woodland. J Ecol 90: 371–384.
- , , , and (2007) Specificity and resilience in the arbuscular mycorrhizal fungi of a natural woodland community. J Ecol 94: 623–630.
- , , and (2007) Differences in the species composition of arbuscular mycorrhizal fungi in spore, root and soil communities in a grassland ecosystem. Environ Microbiol 9: 1930–1938.
- , , , , , , and (2006) Communities of arbuscular mycorrhizal fungi in arable soils are not necessarily low in diversity. Mol Ecol 15: 2277–2289.
- , and (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 10: 1855–1871.
- , and (1999) CAP3: a DNA sequence assembly program. Genome Res 9: 868–877.
- , , , , , , and (2007) Microbial population structures in the deep marine biosphere. Science 318: 97–100.
- , and (2008) Microbiology: metagenomics. Nature 455: 481–483.
- , , , and (2004) An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microb Ecol 47: 385–395.
- , , , , , , and (2003) Soil tillage affects the community structure of mycorrhizal fungi in maize roots. Ecol Appl 13: 1164–1176.
- , , , , , , et al. (2003) Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosm. New Phytol 161: 503–515.
- , and (2002) Colonization of roots by arbuscular mycorrhizal fungi using different sources of inoculum. Mycorrhiza 12: 181–184.
- , and (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10: 504–509.
- , , , and (2009) DNA-based species-level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytol 183: 212–223.
- , , , and (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol (in press): doi: 10.1111/j.1462-2920.2009.02051.x.
- , , and (1999) Intrasporal variability of ribosomal sequences in the endomycorrhizal fungus Gigaspora margarita. Mol Ecol 8: 37–45.
- , , and (2008) Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 65: 339–349.
- , , , , and (2007) Role of niche restrictions and dispersal in the composition of arbuscular mycorrhizal fungal communities. J Ecol 95: 95–105.
- , and (2007) Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316: 1746–1748.
- , , , , , , et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
- , , , , and (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71: 5544–5550.
- , , , , , and (2003) Impact of land use intensity on the species diversity of arbuscular mycorrhizal fungi in agroecosystems of central Europe. Appl Environ Microbiol 69: 2816–2824.
- , , , , , and (2005) Community structure of arbuscular mycorrhizal fungi at different soil depths in extensively and intensively managed agroecosystems. New Phytol 165: 273–283.
- , , , and (2006) Composition of root-colonizing arbuscular mycorrhizal fungal communities in different ecosystems around the globe. J Ecol 94: 778–790.
- , , , , , , and (2008) High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest. New Phytol 179: 867–876.
- , and (2007) Unraveling mycorrhiza-induced resistance. Curr Opin Plant Biol 10: 393–398.
- , , , , , , et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639–641.
- , , , and (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 5: 179–181.
- , , , and (2006) Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question. Mycorrhiza 16: 525–531.
- , , , , , , et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283–290.
- , and (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67.
- (2004) Plant and arbuscular mycorrhizal fungal diversity – are we looking at the relevant level of diversity and are we using the right techniques? New Phytol 164: 415–418.
- , , and (2007) Seasonal dynamics of arbuscular mycorrhizal fungal communities in roots in a seminatural grassland. Appl Environ Microbiol 73: 5613–5623.
- , , , and (2005) A new primer for discrimination of arbuscular mycorrhizal fungi with polymerase chain reaction-denature gradient gel electrophoresis. Grassl Sci 51: 179–181. Direct Link:
- , and (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501–1506.
- , , and (2001) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105: 1413–1421.
- , , , , , and (2007) Sebacinales are common mycorrhizal associates of Ericaceae. New Phytol 174: 864–878.
- , , , , and (2009) Cork-oak woodlands as key-habitats for biodiversity conservation in Mediterranean landscapes: a case study using rove and ground beetles (Coleoptera: Staphylinidae, Carabidae). Biodivers Conserv 18: 605–619.
- , , and (1992) Specific amplification of 18S fungal ribosomal genes from vesicular arbuscular endomycorrhizal fungi colonising roots. Appl Environ Microbiol 58: 291–295.
- , and (2008) Mycorrhizal Symbiosis, 3rd edn. New York, USA: Academic Press.
- , , and (2009) ‘Glomus intraradices DAOM197198’, a model fungus in arbuscular mycorrhiza research, is not Glomus intraradices. New Phytol 183: 1176–1187.
- , , , and (2008) Community analysis of arbuscular mycorrhizal fungi and bacteria in the maize mycorrhizosphere in a long-term fertilization trial. FEMS Microbiol Ecol 65: 323–338.
- , , , , , and (2006) Assessment of arbuscular mycorrhizal fungal diversity in roots of Solidago gigantea growing on a polluted soil in northern Italy. Environ Microbiol 8: 971–983.
- , , , , , and (2004) Ecological linkages between aboveground and belowground biota. Science 304: 1629–1633.
- , , , , , , et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560–565.
- , , and (2008) Metagenomics: read length matters. Appl Environ Microbiol 74: 1453–1463.
- (2009) Kissing cousins: mycorrhizal fungi get together. New Phytol 181: 751–753.