Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns?

New Phytologist

Volumn 202, Issue 4, 2014, Pages 1101-1104

  Lekberg, Ylva ^a,b   Gibbons, Sean M ^a,c,d   Rosendahl, Søren ^e  

^a MPG Ranch   (United States)

^b UNIVERSITY OF MONTANA   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

454 Titanium sequencing; Arbuscular mycorrhizal fungi (AMF); Monophyletic clade; Operational taxonomic unit (OTU) delineation; QIIME; Universal threshold

Indexed keywords

ARBUSCULAR; FUNGI;

ALGORITHM; BIODIVERSITY; CLASSIFICATION; COMPARATIVE STUDY; ECOLOGY; FUNGUS; GENETICS; MOLECULAR EVOLUTION; MYCORRHIZA; PHYLOGENY; PHYSIOLOGY;

ALGORITHMS; BIODIVERSITY; ECOLOGY; EVOLUTION, MOLECULAR; FUNGI; MYCORRHIZAE; PHYLOGENY;

EID: 84899961930     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12758     Document Type: Letter

References (30)

1. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
2. Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H. 2013. ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources 13: 218-224.
3. Breiman L. 2001. Random forests. Machine Learning 45: 5-32.
4. Bunn RA, Lekberg Y, Gallagher C, Rosendahl S, Ramsey PW. 2014. Grassland invaders and their mycorrhizal symbionts: a study across climate and invasion gradients. Ecology and Evolution. doi: 10.1002/ece3.917.
5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.
6. Caporaso JG, Lauber CH, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal 6: 1621-1624.
7. Dickie IA. 2010. Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytologist 188: 916-918.
8. Dumbrell AJ, Ashton PD, Aziz N, Feng G, Nelson M, Dytham C, Fitter AH, Helgason T. 2011. Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytologist 190: 794-804.
9. Knights D, Costello EK, Knight R. 2011b. Supervised classification of human microbiota. FEMS Microbiology Reviews 35: 343-359.
10. Knights D, Parfrey Wegener L, Zaneveld J, Lozupone C, Knight R. 2011a. Human-associated microbial signatures: examining their predictive value. Cell Host & Microbe 10: 292-296.
11. Koch AM, Croll D, Sanders IR. 2006. Genetic variability in populations of arbuscular mycorrhizal fungi causes variation in plant growth. Ecology Letters 9: 103-110.
12. Koeppel AF, Wu M. 2013. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Research 41: 5175-5188.
13. Krüger M, Krüger C, Walker C, Stockinger H, Schüßler A. 2012. Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizaal fungi from phylum to species level. New Phytologist 193: 970-984.
14. Lekberg Y, Gibbons SM, Rosendahl S, Ramsey PW. 2013. Severe plant invasions can increase mycorrhizal fungal abundance and diversity. The ISME Journal 7: 1424-1433.
15. Lekberg Y, Koide RT, Rohr JR, Aldrich-Wolfe L, Morton JB. 2007. Role of niche restrictions and dispersal in the composition of arbuscular mycorrhizal fungal communities. Journal of Ecology 95: 95-105.
16. Lekberg Y, Schnoor T, Kjøller R, Gibbons SM, Hansen LH, Al-Soud WA, Sørensen SJ, Rosendahl S. 2011. 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. Journal of Ecology 100: 151-160.
17. Munkvold L, Kjøller R, Vestberg M, Rosendahl S, Jakobsen I. 2004. High functional diversity within species of arbuscular mycorrhizal fungi. New Phytologist 164: 357-364.
18. Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241.
19. Powell JR, Monaghan MT, Öpik M, Rillig MC. 2011. Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories. Molecular Ecology 20: 655-666.
20. Reeder J, Knight R. 2010. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods 7: 668-669.
21. Rosendahl S. 2008. Communities, populations and individuals of arbuscular mycorrhizal fungi. New Phytologist 178: 253-266.
22. Rosendahl S, Stukenbrock EH. 2004. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rDNA sequences. Molecular Ecology 13: 3179-3186.
23. Schloss PD, Handelsman J. 2006. Toward a census of bacteria in soil. PLoS Computational Biology 2: 786-793.
24. Smith SE, Read DJ. 2008. Mycorrhizal symbiosis. Cambridge, UK: Academic Press.
25. Stackebrandt E, Goebel BM. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rDNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44: 846-849.
26. Stockinger H, Krüger M, Schüßler A. 2010. DNA barcoding of arbuscular mycorrhizal fungi. New Phytologist 187: 461-474.
27. Stockinger H, Walker C, Schüßler A. 2009. 'Glomus intraradices DAOM197198', a model fungus in arbuscular mycorrhiza research, is not Glomus intraradices. New Phytologist 183: 1176-1187.
28. Sykorova Z, Ineichen K, Wiemken A, Redecker D. 2007. The cultivation bias: different communities of arbuscular mycorrhizal fungi detected in roots from the field, from bait plants transplanted to the field, and from a greenhouse trap experiment. Mycorrhiza 18: 1-14.
29. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. 2010. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291-301.
30. Youngblut N, Shae A, Read JS, McMahon KD, Whitaker RJ. 2013. Lineage-specific responses of microbial communities to environmental change. Applied Environmental Microbiology 79: 39-47.