Molecular diversity of fungal communities in agricultural soils from Lower Austria

Fungal Diversity

Volumn 44, Issue , 2010, Pages 65-75

  Klaubauf, Sylvia ^a,d   Inselsbacher, Erich ^b,c,e   Zechmeister Boltenstern, Sophie ^c   Wanek, Wolfgang ^b   Gottsberger, Richard ^a,f   Strauss, Joseph ^a   Gorfer, Markus ^a  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b UNIVERSITY OF VIENNA   (Austria)

^c FEDERAL RESEARCH AND TRAINING CENTRE FOR FORESTS   (Austria)

^d CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^e Department of Forest Ecology and Management   (Switzerland)

^f NONE   (Austria)

Author keywords

Agricultural soil; Diversity; Fungal communities; SCGI; Soil clone group I

Indexed keywords

ASCOMYCOTA; HELOTIALES; HYPOCREALES; SORDARIALES; TETRACLADIUM;

EID: 79955830682     PISSN: 15602745     EISSN: 18789129     Source Type: Journal    
DOI: 10.1007/s13225-010-0053-1     Document Type: Article

References (51)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Anderson IC, Cairney JW (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6:769-779 (Pubitemid 39017262)
3. Anderson IC, Campbell CD, Prosser JI (2003) Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ Microbiol 5:36-47 (Pubitemid 36345744)
4. Bärlocher F (ed) (1992) The ecology of aquatic hyphomycetes. Springer, Berlin
5. 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
6. Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller JM, Abang MM, Zhang JZ, Yang YL, Phoulivong S, Liu ZY, Prihastuti H, Shivas RG, McKenzie EHC, Johnston PR (2009) A polyphasic approach for studying Colletotrichum. Fungal Divers 39:183-204
7. Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76:999-1007
8. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791
9. Christensen M (1989) A view of fungal ecology. Mycologia 81:1-19 (Pubitemid 20424190)
10. Curlevski N, Xu Z, Anderson I, Cairney J (2010) Diversity of soil and rhizosphere fungi under Araucaria bidwillii (Bunya pine) at an Australian tropical montane rainforest site. Fungal Divers 40:12-22
11. de Castro A, Quirino B, PappasG, Kurokawa A, Neto E, Krüger R (2008) Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields. Arch Microbiol 190:129-139
12. Domsch KH, Gams W (1970) Pilze aus Agrarböden. Gustav Fischer Verlag, Stuttgart
13. Domsch KH, Gams W, Anderson TH (1993) Compendium of soil fungi. IHW, Eching
14. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059-7066 (Pubitemid 350076828)
15. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol 2:113-118
16. Giavelli G, Rossi O, Sartore F (1986) Comparative evaluation of four species diversity indices related to two specific ecological situations. Field Stud 6:429-438
17. Götz M, Nirenberg H, Krause S, Wolters H, Draeger S, Buchner A, Lottmann J, Berg G, Smalla K (2006) Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods. FEMS Microbiol Ecol 58:404-413 (Pubitemid 44748150)
18. Hagn A, Pritsch K, Schloter M, Munch JC (2003) Fungal diversity in agricultural soil under different farming management systems, with special reference to biocontrol strains of Trichoderma spp. Biol Fertil Soils 38:236-244 (Pubitemid 37118175)
19. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319 (Pubitemid 39341624)
20. Hughes KW, Petersen RH, Lickey EB (2009) Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species' delimitation across basidiomycete fungi. New Phytol 182:795-798
21. Inselsbacher E, Hinko-Najera Umana N, Stange FC, Gorfer M, Schüller E, Ripka K, Zechmeister-Boltenstern S, Hood-Novotny R, Strauss J, Wanek W (2010) Short-term competition between crop plants and soil microbes for inorganic N fertilizer. Soil Biol Biochem 42:360-372
22. Inselsbacher E, Ripka K, Klaubauf S, Fedosoyenko D, Hackl E, Gorfer M, Hood-Novotny R, Von Wirén N, Sessitsch A, Zechmeister- Boltenstern S, Wanek W, Strauss J (2009) A cost-effective highthroughputmicrocosmsystemfor studying nitrogen dynamics at the plant-microbe-soil interface. Plant Soil 317:293-307
23. Izzo A, Agbowo J, Bruns TD (2005) Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. New Phytol 166:619-629 (Pubitemid 40561053)
24. Jackson LE, Burger M, Cavagnaro TR (2008) Roots, nitrogen transformations, and ecosystem services. Annu Rev Plant Biol 59:341-363 (Pubitemid 351813034)
25. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719-1728
26. Joergensen RG, Wichern F (2008) Quantitative assessment of the fungal contribution to microbial tissue in soil. Soil Biol Biochem 40:2977-2991
27. Kennedy N, Clipson N (2003) Fingerprinting the fungal community. Mycologist 17:158-164 (Pubitemid 38377622)
28. Klironomos JN (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417:67-70 (Pubitemid 34498816)
29. Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform 7:371
30. Lynch MD, Thorn RG (2006) Diversity of basidiomycetes in Michigan agricultural soils. Appl Environ Microbiol 72:7050-7056 (Pubitemid 44748418)
31. Magurran AE (2004) Measuring biological diversity. Blackwell, London.
32. Menkis A, Vasiliauskas R, Taylor AF, Stenlid J, Finlay R (2005) Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation. Mycorrhiza 16:33-41 (Pubitemid 41618815)
33. Nemergut DR, Townsend AR, Sattin SR, Freeman KR, Fierer N, Neff JC, Bowman WD, Schadt CW, Weintraub MN, Schmidt SK (2008) The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environ Microbiol 10:3093-3105
34. Porter TM, Schadt CW, Rizvi L, Martin AP, Schmidt SK, Scott-Denton L, Vilgalys R, Moncalvo JM (2008) Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Mol Phylogenet Evol 46:635-644 (Pubitemid 351215923)
35. Rosling A, Landeweert R, Lindahl BD, Larsson KH, Kuyper TW, Taylor AFS, Finlay RD (2003) Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytol 159:775-783 (Pubitemid 37024079)
36. Ryberg M, Kristiansson E, Sjokvist E, Nilsson RH (2009) An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytol 181:471-477 (Pubitemid 352840363)
37. Sambrook J, Russell D (2001) Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory Press, USA
38. Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359-1361 (Pubitemid 37075807)
39. Schwarzenbach K, Enkerli J, Widmer F (2007) Objective criteria to assess representativity of soil fungal community profiles. J Microbiol Methods 68:358-366 (Pubitemid 46157256)
40. Seena S, Wynberg N, Bärlocher F (2008) Fungal diversity during leaf decomposition in a stream assessed through clone libraries. Fungal Divers 30:1-14
41. Selosse MA, Vohnik M, Chauvet E (2008) Out of the rivers: are some aquatic hyphomycetes plant endophytes? New Phytol 178:3-7 (Pubitemid 351341350)
42. Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S,Wernars K (2001) Diversity and seasonal fluctuations of the dominantmembers of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284-2291 (Pubitemid 33641418)
43. Stromberger ME (2005) Fungal communities of agroecosystems. In: Dighton J, White JF, Oudemans P (eds) The fungal community: its organization and role in the ecosystem, 3rd edn. CRC Press, Boca Raton, pp 813-832
44. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
45. Taylor DL, Bruns TD (1999) Community structure of ectomycorrhizal fungi in a Pinus muricata forest: minimal overlap between the mature forest and resistant propagule communities. Mol Ecol 8:1837-1850 (Pubitemid 30036918)
46. Urban A, Puschenreiter M, Strauss J, Gorfer M (2008) Diversity and structure of ectomycorrhizal and co-associated fungal communities in a serpentine soil. Mycorrhiza 18:339-354
47. 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
48. van der Heijden MG, 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 (Pubitemid 351172045)
49. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J,Young JP (2002) Extensive fungal diversity in plant roots. Science 295:2051 (Pubitemid 34229460)
50. Waldrop MP, Zak DR, Blackwood CB, Curtis CD, Tilman D (2006) Resource availability controls fungal diversity across a plant diversity gradient. Ecol Lett 9:1127-1135 (Pubitemid 44401585)
51. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MH, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315-322