Species abundance distributions and richness estimations in fungal metagenomics - Lessons learned from community ecology

Molecular Ecology

Volumn 20, Issue 2, 2011, Pages 275-285

  Unterseher, Martin ^a   Jumpponen, Ari ^b   Öpik, Maarja ^c   Tedersoo, Leho ^c   Moora, Mari ^c   Dormann, Carsten F ^d   Schnittler, Martin ^a  

^a UNIVERSITY OF GREIFSWALD   (Germany)

^b KANSAS STATE UNIVERSITY   (United States)

^c UNIVERSITY OF TARTU   (Estonia)

^d HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

Author keywords

ectomycorhizal fungi; fungal diversity; Glomeromycota; high throughput parallel sequencing; microbial ecology; phyllosphere fungi

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA; RIBOSOME RNA;

ARTICLE; BIODIVERSITY; DNA SEQUENCE; ECOSYSTEM; EPIDEMIOLOGY; FUNGUS; GENETICS; GLOMEROMYCOTA; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; MYCORRHIZA; PHYLOGENY; POLYMERASE CHAIN REACTION; SMALL RIBOSOMAL SUBUNIT; SPECIES DIFFERENCE;

BIODIVERSITY; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; FUNGI; GLOMEROMYCOTA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MYCORRHIZAE; PHYLOGENY; POLYMERASE CHAIN REACTION; RIBOSOME SUBUNITS, SMALL; RNA, RIBOSOMAL; SAMPLING STUDIES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ARBUSCULAR; FUNGI; GLOMEROMYCOTA;

EID: 78651322088     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04948.x     Document Type: Article

References (51)

1. Bellemain E, Carlsen T, Brochmann C, et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Mircobiology, 10, 189.
2. Bisby FA, Coddington J, Thorpe JP, et al. (1995) Characterization of biodiversity. In: Global Biodiversity Assessment (eds, Heywood VH, Gardener K,). pp. 22-106, Cambridge University Press for UNEP, Cambridge.
3. Buée M, Reich M, Murat C, et al. (2009) 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184, 449-456.
4. Coddington JA, Agnarsson I, Miller JA, Kuntner M, Hormiga G, (2009) Undersampling bias: the null hypothesis for singleton species in tropical arthropod surveys. Journal of Animal Ecology, 78, 573-584.
5. Colwell RK, (2009) Estimates: statistical estimation of species richness and shared species from samples. Version 8.2. User's guide and application published at:. (assessed 27/10/2010)
6. Colwell RK, Coddington JA, (1994) Estimating terrestrial biodiversity through extrapolation. Philosophical Transactions of the Royal Society London B, 345, 101-118.
7. Connolly S, Hughes T, Bellwood D, Karlson R, (2005) Community structure of corals and reef fishes at multiple scales. Science, 309, 1363.
8. Dewdney AK, (1998) A general theory of the sampling process with applications to the "veil line". Theoretical Population Biology, 54, 294-302.
9. Dickie IA, (2010) Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytologist, 188, 916-918.
10. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH, (2010) Idiosyncrasy and overdominance in the structure of natural communities of arbuscular mycorrhizal fungi: is there a role for stochastic processes? Journal of Ecology, 98, 419-428.
11. Fisher RA, Corbet AS, Williams CB, (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology, 12, 42-58.
12. Fonseca A, Inácio J, (2006) Phylloplane yeasts. In: Biodiversity and Ecophysiology of Yeasts (eds, Rosa CA, Péter G,). pp. 263-301, Springer-Verlag, Berlin, Heidelberg.
13. Galand P, Casamayor E, Kirchman D, Lovejoy C, (2009) Ecology of the rare microbial biosphere of the arctic ocean. Proceedings of the National Academy of Sciences of the United States of America, 106, 22427-22432.
14. Golicher D, O'Hara R, Ruíz-Montoya L, Cayuela L, (2006) Lifting a veil on diversity: a Bayesian approach to fitting relative-abundance models. Ecological Applications, 16, 202-212.
15. Gotelli N, Colwell R, (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.
16. Hanski I, (1982) Dynamics of regional distribution: The core and satellite species hypothesis. Oikos, 38, 210-221.
17. Hubbell SP, (2001) The Unified Neutral Theory of Biodiversity and Biogegraphy. Princeton University Press, New Jersey.
18. Jost L, (2007) Partitioning diversity into independent aopha and beta components. Ecology, 88, 2427-2439.
19. Jumpponen A, Jones KL, (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, 184, 438-448.
20. Jumpponen A, Jones KL, (2010) Seasonally dynamic fungal communities in the quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytologist, 186, 496-513.
21. Keijser BJF, Zaura E, Huse SM, et al. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. Journal of Dental Research, 87, 1016-1020.
22. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12, 118-123.
23. MacArthur RH, (1957) On the relative abundance of bird species. Proceedings of the National Academy of Sciences of the United States of America, 43, 293-295.
24. Magurran A, Henderson P, (2003) Explaining the excess of rare species in natural species abundance distributions. Nature, 422, 714-716.
25. May RM, (1975) Patterns of species abundance and diversity. In: Ecology and Evolution of Communities (eds, Cody ML, Diamond JM,). pp. 81-120, Harvard University Press, Cambridge, MA.
26. McGill B, Etienne R, Gray J, et al. (2007) Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters, 10, 995-1015.
27. McPherson J, Jetz W, (2007) Effects of species' ecology on the accuracy of distribution models. Ecography, 30, 135-151.
28. Medinger R, Nolte V, Pandey RV, et al. (2010) Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology, 19, S1, 32-40.
29. O'Hara RB, (2005) Species richness estimators: how many species can dance on the head of a pin? Journal of Animal Ecology, 74, 375-386.
30. Ãpik 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 Phytologist, 184, 424-437.
31. Pedrõs-Aliõ C, (2006) Marine microbial diversity: can it be determined? Trends in Microbiology, 14, 257-263.
32. Preston FW, (1948) The commonness, and rarity, of species. Ecology, 29, 254-283.
33. Quince C, Curtis T, Sloan W, (2008) The rational exploration of microbial diversity. ISME Journal, 2, 997-1006.
34. Quince C, Lanzen A, Curtis TP, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6, 639-641.
35. R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL.
36. Schadt C, Martin A, Lipson D, Schmidt S, (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science, 301, 1359-1361.
37. Schnittler M, Tesmer J, (2008) A habitat colonisation model for spore-dispersed organisms-does it work with eumycetozoans? Mycological Research, 112, 697-707.
38. Sogin M, Morrison H, Huber J, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America, 103, 12115-12120.
39. Stoeck T, Behnke A, Christen R, et al. (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology, 7, 72.
40. Sun Y, Cai Y, Liu L, et al. (2009) ESPRIT: Estimating species richness using large collections of 16s rRNA pyrosequences. Nucleic Acids Research, 37, e76.
41. Taylor JW, Jacobson DJ, Kroken S, et al. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31, 21-32.
42. Tedersoo L, Nilsson RH, Abarenkov K, et al. (2010) 454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist, 188, 291-301.
43. Tokeshi M, (1990) Niche apportionment or random assortment: species abundance patterns revisited. Journal of Animal Ecology, 59, 1129-1146.
44. Ugland KI, Gray JS, Ellingsen KE, (2003) The species-accumulation curve and estimation of species richness. Journal of Animal Ecology, 72, 888-897.
45. Ulrich W, Ollik M, Ugland KI, (2010) A meta-analysis of species-abundance distributions. Oikos, 119, 1149-1155.
46. Unterseher M, Schnittler M, (2010) Species richness analysis and its rDNA phylogeny revealed the majority of cultivable foliar endophytes from beech (Fagus sylvatica). Fungal Ecology, 3, 366-378.
47. Unterseher M, Reiher A, Finstermeier K, Otto P, Morawetz W, (2007) Species richness and distribution patterns of leaf-inhabiting endophytic fungi in a temperate forest canopy. Mycological Progress, 6, 201-212.
48. Unterseher M, Schnittler M, Dormann C, Sickert A, (2008) Application of species richness estimators for the assessment of fungal diversity. FEMS Microbiology Letters, 282, 205-213.
49. Whittaker RH, (1977) Evolution of species diversity in land communities. Evolutionary Biology, 10, 1-67.
50. Williamson M, Gaston K, (2005) The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution. Journal of Animal Ecology, 74, 409-422.
51. von Wintzingerode F, Göbel UB, Stackebrandt E, (1997) Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews, 21, 213-229.