Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf

FEMS Microbiology Ecology

Volumn 84, Issue 3, 2013, Pages 519-531

  Kuramae, Eiko E ^a,b   Hillekens, Remy H E ^a   de Hollander, Mattias ^a,b   van der Heijden, Marcel G A ^c,d   van den Berg, Marlies ^a   van Straalen, Nico M ^b   Kowalchuk, George A ^a,b,d  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c Research Station ART   (Switzerland)

^d UTRECHT UNIVERSITY   (Netherlands)

Author keywords

18S rRNA gene; Amino acid permeases; Basidiomycota; Metatranscriptome; Next generation sequencing; Transporters

Indexed keywords

TRANSCRIPTOME;

AMINO ACID; CELLULOSE; COMMUNITY COMPOSITION; DECOMPOSITION; DEGRADATION; FUNGUS; GENE EXPRESSION; LEAF LITTER; MAIZE; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; SOIL ECOSYSTEM; SOIL MICROORGANISM;

ARTICLE; ASCOMYCETES; BASIDIOMYCETES; CLASSIFICATION; ECOSYSTEM; FUNGAL GENE; FUNGUS; GENETICS; HIGH THROUGHPUT SEQUENCING; MAIZE; METABOLISM; METAGENOME; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PLANT LEAF; RNA GENE; SOIL;

ASCOMYCOTA; BASE SEQUENCE; BASIDIOMYCOTA; ECOSYSTEM; FUNGI; GENES, FUNGAL; GENES, RRNA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; PLANT LEAVES; SOIL; SOIL MICROBIOLOGY; TRANSCRIPTOME; ZEA MAYS;

ASCOMYCOTA; BASIDIOMYCOTA; CHAETOMIACEAE; FUNGI; MUCORACEAE; PSATHYRELLACEAE; SCHIZOPHYLLACEAE; SEBACINACEAE; SORDARIACEAE; TREMELLACEAE; TREMELLALES; ZEA MAYS;

EID: 84877690780     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12080     Document Type: Article

References (60)

1. Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Bol 215: 403-410.
2. Anderson IC & Cairney JWG II (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6: 769-779.
3. Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, Wesolowski-Louvel M & Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1: 632-642.
4. Baldrian P (2006) Fungal laccases - occurrence and properties. FEMS Microbiol Rev 30: 215-242.
5. Baldrian P, Kolarik M, Stursova M et al. (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6: 248-258.
6. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R & Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908-917.
7. Bourbonnais R & Paice MG (1990) Oxidation of nonphenolic substrates. An expanded role for laccase in lignin biodegradation. FEBS Lett 267: 99-102.
8. 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.
9. Buee M, Maurice JP, Zeller B et al. (2011) Influence of tree species on richness and diversity of epigeous fungal communities in a French temperate forest stand. Fungal Ecol 4: 22-31.
10. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V & Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37: 233-238.
11. Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
12. Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L & Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7: e28967.
13. DeLong EF (2009) The microbial ocean from genomes to biomes. Nature 459: 200-206.
14. Dumbrell AJ, Ashton PD, Aziz N et al. (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190: 794-804.
15. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
16. Edgar RC, Haas BJ, Clemente JC, Quince C & Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 1-7.
17. Edwards IP, Zak DR, Kellner H, Eisenlord SD & Pregitzer KS (2011) Simulated atmospheric N deposition alters fungal community composition and suppresses lignolytic gene expression in a northern hardwood forest. PLoS ONE 6: e20421.
18. Falkowski PG, Fenchel T & Delong EF (2008) The microbial engines that drive Earth's biogeochemical cycles. Science 320: 1034-1039.
19. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
20. Hagn A, Pritsch K, Ludwig W & Schloter M (2003) Theoretical and practical approaches to evaluate suitable primer sets for the analysis of soil fungal communities. Acta Biotechnol 23: 373-381.
21. Hannula SE, de Boer W & van Veen JA (2010) In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar. Soil Biol Biochem 42: 2211-2223.
22. van der Heijden MGA, Bardgett RD & van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310.
23. Huson DH, Auch AF, Qi J & Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
24. Jumpponen A (2011) Analysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots. Mycorrhiza 21: 453-464.
25. Kellner H & Vandenbol M (2010) Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS ONE 5: e10971.
26. Kellner H, Luis P, Schlitt B & Buscot F (2009) Temporal changes in diversity and expression patterns of fungal laccase genes within the organic horizon of a brown forest soil. Soil Biol Biochem 41: 1380-1389.
27. Kuramae EE, Yergeau E, Wong LC, Pijl AS, van Veen JA & Kowalchuk GA (2012) Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol 79: 12-24.
28. Lauber CL, Hamady M, Knight R & Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
29. Levasseur A, Plumi F, Coutinho PM et al. (2008) FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genet Biol 45: 638-645.
30. Lim YW, Kim BK, Kim C et al. (2010) Assessment of soil fungal communities using pyrosequencing. J Microbiol 48: 284-289.
31. Lozupone CA & Klein DA (1999) Chytridiomycota of little importance in soils? ASM News 65: 662-663.
32. Lozupone CA & Klein DA (2002) Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils. Mycologia 94: 411-420.
33. Lundell TK, Makela MR & Hilden K (2010) Lignin-modifying enzymes in filamentous basidiomycetes - ecological, functional and phylogenetic review. J Basic Microbiol 50: 5-20.
34. Mahajan S & Master ER (2010) Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose. Appl Microbiol Biot 86: 1903-1914.
35. Manici LM & Caputo F (2009) Fungal community diversity and soil health in intensive potato cropping systems of the east Po valley, northern Italy. Ann Appl Biol 155: 245-258.
36. Manning G, Plowman GD, Hunter T & Sudarsanam S (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 27: 514-520.
37. McGrath KC, Thomas-Hall SR, Cheng CT, Leo L, Alexa A, Schmidt S & Schenk PM (2008) Isolation and analysis of mRNA from environmental microbial communities. J Microbiol Methods 75: 172-176.
38. Nacke H, Thurmer A, Wollherr A et al. (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE 6: e17000.
39. Ngo TT & Lenhoff HM (1980) A sensitive and versatile chromogenic assay for peroxidase and peroxidase-coupled reactions. Anal Biochem 105: 389-397.
40. Osono T (2007) Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecol Res 22: 955-974.
41. Parks DH & Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
42. Pelaez F, Martinez MJ & Martinez AT (1995) Screening of 68 apecies of basidiomycetes for enzymes involved in lignin degradation. Mycol Res 99: 37-42.
43. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J & Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
44. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF & Sloan WT (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
45. Richardson M (2009) The ecology of the Zygomycetes and its impact on environmental exposure. Clin Microbiol Infect 5: 2-9.
46. Roesch LF, Fulthorpe RR, Riva A et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
47. Rusch DB, Halpern AL, Sutton G et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical pacific. PLoS Biol 5: 398-431.
48. Sinsabaugh RL (2010) Phenol oxidase, peroxidase and organic matter dynamics of soil. Soil Biol Biochem 42: 391-404.
49. Smit E, Leeflang P, Glandorf B, van Elsas JD & Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65: 2614-2621.
50. Snajdr J, Valaskova V, Merhautova V, Cajthaml T & Baldrian P (2008) Activity and spatial distribution of lignocellulose-degrading enzymes during forest soil colonization by saprotrophic basidiomycetes. Enzyme Microb Technol 43: 186-192.
51. Steffen KT, Hofrichter M & Hatakka A (2000) Mineralisation of C-14-labelled synthetic lignin and ligninolytic enzyme activities of litter-decomposing basidiomycetous fungi. Appl Microbiol Biot 54: 819-825.
52. Swanson AR, Vadell EM & Cavender JC (1999) Global distribution of forest soil dictyostelids. J Biogeogr 26: 133-148.
53. Thorn RG & Lynch MDJ (2007) Fungi and eukaryotic algae. Soil Microbiology, Ecology and Biochemistry, 3rd edn. (Paul EA, ed), p. 154. Ft. Collins, Colorado State University.
54. Tian BY, Huang QG, Xu Y, Wang CX, Lv RR & Huang JZ (2010) Microbial community structure and diversity in a native forest wood-decomposed hollow-stump ecosystem. World J Microbiol Biotechnol 26: 233-240.
55. Urich T, Lanzen A, Qi J, Huson DH, Schleper C & Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
56. Valaskova V, Snajdr J, Bittner B, Cajthaml T, Merhautova V, Hoffichter M & Baldrian P (2007) Production of lignocellulose-degrading enzymes and degradation of leaf litter by saprotrophic basidiomycetes isolated from a Quercus petraea forest. Soil Biol Biochem 39: 2651-2660.
57. Verbruggen E, Roling WFM, Gamper HA, Kowalchuk GA, Verhoef HA & van der Heijden MGA (2010) Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils. New Phytol 186: 968-979.
58. Verbruggen E, Kuramae EE, Hillekens R, de Hollander M, Kiers ET, Röling WFM, Kowalchuk GA & van der Heijden MGA (2012) Testing potential effects of Bt maize on mycorrhizal fungal communities via DNA- and RNA- based pyrosequencing and molecular fingerprinting. Appl Environ Microbiol 78: 7384-7392.
59. Warnecke F, Luginbuhl P, Ivanova N et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565.
60. Zugmaier W, Bauer R & Oberwinkler F (1994) Studies in heterobasidiomycetes. 104. Mycoparasitism of some Tremella species. Mycologia 86: 49-56.