A decade's perspective on the impact of DNA sequencing on aquatic hyphomycete research

Fungal Biology Reviews

Volumn 27, Issue 1, 2013, Pages 19-24

  Duarte, Sofia ^a   Seena, Sahadevan ^a   Bärlocher, Felix ^b   Pascoal, Cláudia ^a   Cássio, Fernanda ^a  

^a UNIVERSITY OF MINHO   (Portugal)

^b MOUNT ALLISON UNIVERSITY   (Canada)

Author keywords

Aquatic hyphomycetes; Barcoding; Community level techniques; DNA sequences; Evolution; Phylogeny

Indexed keywords

FUNGI; HYPHOMYCETES;

EID: 84877587617     PISSN: 17494613     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fbr.2013.02.003     Document Type: Review

References (51)

1. Anderson I.C., Parkin P.I. Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. J. Microbiol. Method 2007, 68:248-253.
2. Anderson J.L., Shearer C.A. Population genetics of the aquatic fungus Tetracladium marchalianum over space and time. PLoS One 2011, 6(1):e15908.
3. Baldrian P., Kolarik K., Stursova M., Kopecky J., Valaskova V., Vetrovsky T., Zifcakova L., Snajdr J., Ridl J., Vlcek C., Voriskova J. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J. 2012, 6:248-258.
4. Bärlocher F. Molecular approaches promise a deeper and broader understanding of the evolutionary ecology of aquatic hyphomycetes. J. N. Am. Benthol. Soc. 2010, 29:1037-1041.
5. Bärlocher F., Kendrick B. Dynamics of the fungal population on leaves in a stream. J. Ecol. 1974, 63:761-791.
6. Bärlocher F., Seena S., Wilson K.P., Williams D.D. Raised water temperature lowers diversity of hyporheic aquatic hyphomycetes. Freshwater Biol. 2008, 53:368-379.
7. Bärlocher F., Stewart M., Ryder D.S. Processing of Eucalyptus viminalis leaves in Australian streams - importance of aquatic hyphomycetes and zoosporic fungi. Fund. Appl. Limnol. 2012, 179/4:305-319.
8. Baschien C., Marvanová L., Szewzyk U. Phylogeny of selected aquatic hyphomycetes based on morphological and molecular data. Nova Hedwigia 2006, 83:311-352.
9. Bauer R.D., Begerow D., Oberwinkler F., Marvanová L. Classicula: the teleomorph of Naiadella fluitans. Mycologia 2003, 95:756-764.
10. Belliveau M., Bärlocher F. Molecular evidence confirms multiple origin of aquatic hyphomycetes. Mycol. Res. 2005, 109:1407-1417.
11. Berbee M.L., Taylor J.W. Fungal molecular evolution: gene trees and geologic time. The Fungal Holomorph. Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics 2001, 67-78. CAB International, Wallingford. D.R. Reynolds, J.W. Taylor (Eds.).
12. Buée M., Reich M., Murat C., Morin E., Nilsson R.H., Uroz S., Martin F. 454 pyrosequencing analyses of forest soils reveal and unexpected high fungal diversity. New Phytol. 2009, 184:449-456.
13. Campbell J., Marvanová L., Gulis V. Evolutionary relationships between aquatic anamorphs and teleomorphs: Tricladium and Varicosporium. Mycol. Res. 2009, 113:1322-1334.
14. Campbell J., Shearer C., Marvanová L. Evolutionary relationships among aquatic anamorphs and telemomorphs: Lemonniera, Margaritispora, and Goniopila. Mycol. Res. 2006, 110:1025-1033.
15. DeLong E.F. The microbial ocean from genomes to biomes. Nature 2009, 459:200-206.
16. Duarte S., Pascoal C., Alves A., Correia A., Cássio F. Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams. Freshwater Biol. 2008, 53:91-101.
17. Duarte S., Pascoal C., Alves A., Correia A., Cássio F. Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques. Microbiol. Res. 2010, 165:351-362.
18. Duarte S., Pascoal C., Garabetian F., Cássio F., Charcosset J.-Y. Microbial decomposer communities are mainly structured by the trophic status in circumneutral and alkaline streams. Appl. Environ. Microbiol. 2009, 75:6211-6221.
19. Duarte S., Seena S., Bärlocher F., Cássio F., Pascoal C. Preliminary insights into the phylogeography of six aquatic hyphomycete species. PLoS One 2012, 7(9):e45289.
20. Dupuis J.R., Roe A.D., Sperling F.A.H. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol. Ecol 2012, 21:4422-4436.
21. Edwards R.A., Rodriguez-Brito B., Wegley L., Haynes M., Breitbart M., Peterson D.M., Saar M.O., Alexander S., Alexander E.C., Rohwer F. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 2006, 7:57.
22. Ghannoum M.A., Jurevic J., Mukherjee P.K., Cui F., Sikaroodi M., Naqvi A., Gillevet P.M. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010, 6:e1000713.
23. Gygi S.P., Rochon Y., Franz B.R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19:1720-1730.
24. Head I.M., Saunders J.R., Pickup R.W. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivable microorganisms. Microb. Ecol. 1998, 35:1-21.
25. Hebert P.D.N., Ratnasingham S., DeWaard J.R. Barcoding animal life, cytochrome c oxidase subunit I divergences among closely related species. P. R. Soc. B Biol. Sci. 2003, 270:S596-S599.
26. Ingold C.T. Aquatic hyphomycetes of decaying alder leaves. Trans. Br. Mycol. Soc. 1942, 25:339-417.
27. Ingold C.T. Aquatic spora of Omo forest, Nigeria. Trans. Br. Mycol. Soc. 1959, 42:479-485.
28. Jacobsen J., Lydolph M., Lange L. Culture independent PCR: an alternative enzyme discovery strategy. J. Microbiol. Method 2005, 60:63-71.
29. Jumpponen A., Jones K.L. Massively parallel 454-sequencing indicates hyperdiverse fungal communities in temperate Quercus macorcarpa phyllosphere. New Phytol. 2009, 184:438-448.
30. Kanokratana P., Uengwetwanit T., Rattanachomsri U., Bunterngsook B., Nimchua T., Tangphatsornruang S., Plengvidhya V., Champreda V., Eurwilaichitr L. Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microb. Ecol. 2011, 61:518-528.
31. Kaushik N.K., Hynes H.B.N. The fate of the dead leaves that fall into streams. Arch. Hydrobiol. 1971, 68:465-515.
32. Letourneau A., Seena S., Marvanová L., Bärlocher F. Potential use of barcoding to identify aquatic hyphomycetes. Fungal Divers. 2010, 40:51-64.
33. Medinger R., Nolte V., Pandey R.V., Jost S., Ottenwa B., Schlötterer C., Boenigk J. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol. Ecol. 2010, 19:32-40.
34. Nikolcheva L.G., Bärlocher F. Phylogeny of Tetracladium based on 18S rDNA. Czech Mycol. 2002, 53:285-295.
35. Nikolcheva L.G., Cockshutt A.M., Bärlocher F. Determining diversity of freshwater fungi on decomposing leaves: comparison of traditional and molecular approaches. Appl. Environ. Microbiol. 2003, 69:2548-2554.
36. Nilsson R.H., Ryberg M., Abarenkov K., Sjökvist E., Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol. Lett. 2009, 296:97-101.
37. Nilsson R.H., Ryberg M., Sjökvist E., Abarenkov K. Rethinking taxon sampling in the light of environmental sequencing. Cladistics 2011, 27:197-203.
38. Purdy K.J., Hurd P.J., Moya-Laraño J., Trimmer M., Oakley B.B., Woodward G. Systems biology for ecology: from molecules to ecosystems. Adv. Ecol. Res. 2010, 43:87-149.
39. Ranzoni F.V. The perfect stage of Flagellospora penicillioides. Am. J. Bot. 1956, 43:13-17.
40. Roldán A., Descals E., Honrubia M. Pure culture studies on Tetracladium. Mycol. Res. 1989, 93:452-465.
41. Seena S., Duarte S., Pascoal C., Cássio F. Intraspecific variation of the aquatic fungus Articulospora tetracladia: an ubiquitous perspective. PLoS One 2012, 7(4):e35884.
42. Seena S., Pascoal C., Marvanová L., Cássio F. DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species. Fungal Divers. 2010, 44:77-87.
43. Seena S., Wynberg N., Bärlocher F. Fungal diversity during leaf decomposition in a stream assessed through clone libraries. Fungal Divers. 2008, 30:1-14.
44. Selosse M.-A., Vohník M., Chauvet E. Out of the rivers: are some aquatic hyphomycetes plant endophytes?. New Phytol. 2008, 178:3-7.
45. Shearer C.A., Descals E., Volkmann-Kohlmeyer B., Kohlmeyer J., Marvanová L., et al. Fungal biodiversity in aquatic habitats. Biodivers. Conserv. 2007, 16:49-67.
46. Sokolski S., Piché Y., Chauvet E., Bérubé J.A. A fungal endophyte of black spruce (Picea mariana) needles is also an aquatic hyphomycete. Mol. Ecol. 2006, 15:1955-1962.
47. Solé M., Kellner H., Brock S., Buscot F., Schlosser D. Extracellular laccase activity and transcript levels of putative laccase genes during removal of the xenoestrogen technical nonylphenol by the aquatic hyphomycete Clavariopsis aquatica. FEMS Microbiol. Lett. 2008, 288:47-54.
48. Suberkropp K., Klug M.J. Fungi and bacteria associated with leaves during processing in a woodland stream. Ecology 1976, 57:707-719.
49. Taylor H.R., Harris W.E. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol. Ecol. Resour. 2012, 10.1111/j.1755-0998.2012.03119.x.
50. Taylor J.W., Turner E., Townsend J.P., Dettman J.R., Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Phil. Trans. R. Soc. B 2006, 361:1947-1963.
51. Webster J. Anamorph-teleomorph relationships. The Ecology of Aquatic Hyphomycetes 1992, 99-117. Springer, Berlin and New York. F. Bärlocher (Ed.).