Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

FEMS Microbiology Ecology

Volumn 86, Issue 3, 2013, Pages 557-566

  Brown, Shawn P ^a   Callaham, Mac A ^b   Oliver, Alena K ^a   Jumpponen, Ari ^a  

^a KANSAS STATE UNIVERSITY   (United States)

^b USDA FOREST SERVICE   (United States)

Author keywords

Fungi; Ion Torrent Personal Genome Machine; Lightless sequencing; Prescribed fire; Soil

Indexed keywords

FOREST ECOSYSTEM; FOREST FIRE; FOREST MANAGEMENT; FUNGUS; GENOME; ION; MICROBIAL COMMUNITY; PIEDMONT; PRESCRIBED BURNING; RESETTING; TORRENT; VEGETATION;

GEORGIA; UNITED STATES;

FUNGI; PINUS TAEDA;

FUNGAL DNA; RIBOSOMAL SPACER DNA;

ARTICLE; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; EQUIPMENT; FIRE; FUNGUS; GENETICS; HIGH THROUGHPUT SEQUENCING; ION TORRENT PERSONAL GENOME MACHINE; ISOLATION AND PURIFICATION; LIGHTLESS SEQUENCING; METHODOLOGY; MICROBIOLOGY; MYCORRHIZA; PHYSIOLOGY; PRESCRIBED FIRE; SOIL; TREE; UNITED STATES;

FUNGI; ION TORRENT PERSONAL GENOME MACHINE; LIGHTLESS SEQUENCING; PRESCRIBED FIRE; SOIL;

DNA, FUNGAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; FIRES; FUNGI; GEORGIA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MYCORRHIZAE; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; TREES;

EID: 84887613161     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12181     Document Type: Article

References (48)

1. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.
2. Anderson IC, Bastias BA, Genney DR, Parkin PI & Cairney JWG (2007) Basidiomycete fungal communities in Australian sclerophyll forest soil are altered by repeated prescribed burning. Mycol Res 111: 482-486.
3. Artz RRE, Reid E, Anderson IC, Campbell CD & Cairney WG (2009) Long term repeated prescribed burning increases evenness in the basidiomycete laccase gene pool in forest soils. FEMS Microbiol Ecol 67: 397-410.
4. Baar J, Horton TR, Kretzer AM & Bruns TD (1999) Mycorrhizal colonization of Pinus muricata from resistant propagules after a stand-replacing wildfire. New Phytol 143: 409-418.
5. Bastias BA, Huang ZQ, Blumfields T, Xu Z & Cairney JWG (2006a) Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest. Soil Biol Biochem 38: 3492-3501.
6. Bastias BA, Xu ZH & Cairney JWG (2006b) Influence of long-term repeated prescribed burning on mycelial communities of ectomycorrhizal fungi. New Phytol 172: 149-158.
7. Berry D, Mahfoudh KB, Wagner M & Loy A (2011) Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol 77: 7846-7849.
8. Borg G (1997) Non-metric multidimensional scaling function using the majorization algorithm. Modern Multidimensional Scaling (Cox TF, & Cox MAA, eds). Chapman and Hall, London.
9. Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S & Martin F (2009) 454 Pyrosequencing analyses of of forest soils reveal an unexpectedly high fungal diversity. New Phytologist 184: 449-456.
10. Buscardo E, Rodríguez-Echeverría S, Martic MP, Angelis PD, Pereira JS & Freitas H (2010) Impact of wildfire return interval on the ectomycorrhizal resistant propagules communities of a Mediterranean open forest. Fungal Biol 114: 628-636.
11. Caporaso JG, Lauber CL, Walters WA et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6: 1621-1624.
12. Carpenter SE & Trappe JM (1985) Phoenicoid fungi - a proposed term for fungi that fruit after heat-treatment of substrates. Mycotaxon 23: 203-206.
13. Chen DM & Cairney WGJ (2002) Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites. Mycol Res 106: 532-540.
14. Dahlberg A, Schimmel J, Taylor AFS & Johannesson H (2001) Post-fire legacy of ectomycorrhizal fungal communities in the Swedish boreal forest in relation to fire severity and logging intensity. Biol Conserv 100: 151-161.
15. Dooley SR & Treseder KK (2011) The effect of fire on microbial biomass: a meta-analysis of field studies. Biogeochemistry 109: 49-61.
16. Edgar RC, Haas BJ, Clemente JC, Quince C & Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
17. Erlich Y, Mitra PP, de la Bastide M, McCombie WR & Hannon GJ (2008) Alta-cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods 5: 679-682.
18. Fujimura KF, Smith JE, Horton TR, Weber NS & Spatafora JW (2005) Pezizalean mycorrhizas and sporocarps in ponderosa pine (Pinus ponderosa) after prescribed fires in eastern Oregon, USA. Mycorrhiza 15: 79-86.
19. Gardes M & Bruns TD (1993) ITS primers with enhanced specificity for Basidiomycetes - Application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113-118.
20. Gihring TM, Green SJ & Schadt CW (2011) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14: 285-290.
21. Gilbert JA, Meyer F, Antonoploulos D et al. (2010) Meeting report. The terabase metagenomics workshop and the vision of an earth microbiome project. Stand Genomic Sci 3: 243-248.
22. Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11: 759-769.
23. Ihrmark K, Bödeker ITM, Cruz-Martinez K et al. (2012) New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 82: 666-677.
24. Jumpponen A & Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184: 438-448.
25. Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J & Harmsen D (2012) Bacterial community shift in treated periodontitis patients revealed by Ion Torrent 16S rRNA gene amplicon sequencing. PLoS ONE 7: e41606.
26. Lozupone C & Knight C (2007) Global patterns in bacterial diversity. P Natl Acad Sci USA 104: 11436-11440.
27. Lucarotti CJ, Kelsey CT & Auclair AND (1978) Microfungal variations relative to post-fire changes in soil environment. Oecologia 37: 1-12.
28. Luo C, Tsementzi D, Kyrpides N, Read T & Konstantinidis KT (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7: e30087.
29. Magurran AE (1988) Ecological Diversity and its Measurement. Princeton University, Princeton.
30. Margulies M, Egholm M, Altman WE et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
31. Needleman SB & Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
32. Öpik M, Metsis M, Daniell TJ, Zobel M & Morra 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.
33. Phillips RJ & Waldrop TA (2008) Changes in vegetation structure and composition in response to fuel reduction treatments in the South Carolina Piedmont. For Ecol Manage 255: 3107-3116.
34. Quince C, Lanzen A, Davenport RJ & Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
35. Rothberg JM, Hinz W, Rearick TM et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.
36. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mother: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
37. Schloss PD, Gevers D & Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310.
38. Schoenberger MM & Perry DA (1982) The effect of soil disturbance on growth and ectomycorrhizae of Douglas-fir and western hemlock seedlings: a greenhouse bioassay. Can J For Res 12: 343-353.
39. Smith JE, McKay D, Brenner G, McIver J & Spatafora JW (2005) Early impacts of forest restoration treatments on the ectomycorrhizal fungal community and fine root biomass in a mixed conifer forest. J Appl Ecol 42: 526-535.
40. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM & Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. P Natl Acad Sci USA 103: 12115-12120.
41. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, 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 Phytol 188: 291-301.
42. Turnau K (1983) Scanning ultrastructural ontogeny of apothecia in the operculate discomycete Trichophaea abundans. Can J Bot 61: 476-481.
43. Waldrop TA, White DL & Jones SM (1992) Fire regimes for pine-grassland communities in the southeastern United States. For Ecol Manage 47: 195-210.
44. White TJ, Bruns T, Lee S & Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications (Innis MA, Gelfand DH, Sininsky JJ, & White Tj, eds). Acedemic Press, Inc., New York.
45. Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R & O'Donnell A (2012) Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91: 80-88.
46. Wicklow DT & Whittingham WF (1978) Comparison of soil microfungal populations in disturbed and undisturbed forests in northern Wisconsin. Can J Bot 56: 1702-1709.
47. Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR & Greer CW (2012) Next- sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl Environ Microbiol 78: 7626-7637.
48. Yue JC & Clayton MK (2005) A similarity measure based on species proportions. Communications in Statistics - Theory and. Methods 34: 2123-2131.