Sequencing DNA extracted from single conidia of aquatic hyphomycetes

Fungal Ecology

Volumn 3, Issue 3, 2010, Pages 115-121

  Bärlocher, Felix ^a   Charette, Nicholle ^a   Letourneau, Allan ^b   Nikolcheva, Liliya G ^a   Sridhar, Kandikere R ^c  

^a MOUNT ALLISON UNIVERSITY   (Canada)

^b CARLETON UNIVERSITY   (Canada)

^c MANGALORE UNIVERSITY   (India)

Author keywords

Aquatic hyphomycetes; Barcode; DNA extraction; DNA sequence; FTA card; Magnetic beads; PCR; Single spore

Indexed keywords

BACTERIA (MICROORGANISMS); GOSSYPIUM HIRSUTUM; HYPHOMYCETES;

EID: 77954869339     PISSN: 17545048     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funeco.2009.08.003     Document Type: Article

References (41)

1. Altshul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
2. Baas Becking L.G.M. Geobiologie of inleiding tot de milieukunde 1934, WP Van Stockum & Zoon, The Hague.
3. Bärlocher F. Freshwater fungal communities. The Fungal Community 2005, 39-59. CRC Press, Boca Raton. 3rd edn. J. Dighton, P. Oudemans, J. White (Eds.).
4. Bärlocher F. Molecular approaches applied to aquatic hyphomycetes. Fungal Biology Reviews 2007, 1:19-24.
5. Bärlocher F., Seena S., Wilson K.P., Williams D.D. Raised water temperature lowers diversity of hyporheic aquatic hyphomycetes. Freshwater Biology 2008, 53:368-379.
6. Barber P., Boyce S.L. Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proceedings of the Royal Society Series B 2006, 273:2053-2061.
7. Baschien C., Manz W., Neu T.R., Marvanová L., Szewzyk U. In situ detection of freshwater fungi in an alpine Stream by new taxon-specific Fluorescence In Situ Hybridization probes. Applied and Environmental Microbiology 2008, 74:6427-6436.
8. Bermingham S., Maltby L., Dewey F.M. Monoclonal antibodies as tools to quantify mycelium of aquatic hyphomycetes. New Phytologist 1996, 132:593-601.
9. Borman A.M., Linton C.J., Miles S.-J., Campbell C.K., Johnson E.M. Ultra-rapid preparation of total genomic DNA from isolates of yeast and mould using Whatman FTA filter paper technology - a reusable DNA archiving system. Medical Mycology 2006, 44:389-398.
10. Covich A.P., Austin M.C., Bärlocher F., Chauvet E., Cardinale B.J., Biles C.L., Inchausti P., Dangles O., Solan M., Gessner M.O., Statzner B., Moss B. The role of biodiversity in the functioning of freshwater and marine benthic ecosystems. BioScience 2004, 54:767-775.
11. Dang K.D., Gessner M.O., Chauvet E. Influence of conidial traits and leaf structure on attachment success of aquatic hyphomycetes on leaf litter. Mycologia 2007, 99:24-32.
12. De Wit R., Bouvier T. 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?. Environmental Microbiology 2006, 8:755-758.
13. Descals E. Techniques for handling Ingoldian fungi. Methods to Study Litter Decomposition. A Practical Guide 2005, 129-142. Springer, Dordrecht. M.A.S. Graça, F. Bärlocher, M.O. Gessner (Eds.).
14. Dettman J.R., Jacobson D.J., Taylor J.W. Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex. Mycologia 2006, 98:436-446.
15. Edvardsen B., Shalchian-Tabrizi K., Medlin L.K., Dahl E., Brubak S., Paasche E. Genetic variability and molecular phylogeny of Dinophysis species (Dinophyceae) from Norwegian water inferred from single cell analyses of rDNA. Journal of Phycology 2003, 39:395-408.
16. Faggi A., Pini G., Campisi E. Use of magnetic beads to extract fungal DNA. Mycoses 2005, 48:3-7.
17. Fenchel T., Finlay B.J. The ubiquity of small species: patterns of local and global diversity. Bioscience 2004, 54:777-784.
18. Gadkar V., Rillig R.C. Application of Phi29 DNA mediated whole genome application on single spores of arbuscular mycorrhizal (AM) fungi. FEMS Microbiology Letters 2005, 242:65-71.
19. Gessner M.O., Gulis V., Kuehn K.A., Chauvet E., Suberkropp K. Fungal decomposers of plant litter in aquatic ecosystems. The Mycota, Vol. IV, Environmental and Microbial Relationships 2007, 301-324. Springer, Berlin. C.P. Kubicek, I.S. Druzhinina (Eds.).
20. Gulis V., Marvanová L., Descals E. An illustrated key to the common temperate species of aquatic hyphomycetes. Methods to Study Litter Decomposition: a Practical Guide 2005, 153-167. Springer, Dordrecht. M.A.S. Graça, F. Bärlocher, M.O. Gessner (Eds.).
21. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
22. Hebert P.D.N., Cywinska A., Ball S.L., deWaard J.R. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B 2003, 270:313-322.
23. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M. Identification of birds through DNA barcodes. PLoS Biology 2004, 2:e312.
24. Ingold C.T. Hooker Lecture 1974. Convergent evolution in aquatic fungi: the tetraradiate spore. Biological Journal of the Linnean Society 1974, 7:1-25.
25. Iqbal S.H., Webster J. Aquatic hyphomycete spora of the River Exe and its tributaries. Transactions of the British Mycological Society 1973, 61:331-346.
26. Kearns S.G., Bärlocher F. Leaf surface roughness influences colonization success of aquatic hyphomycete conidia. Fungal Ecology 2008, 1:13-18.
27. The Functional Consequences of Biodiversity 2001, Princeton University Press, Princeton. A.P. Kinzig, S.W. Pacala, D. Tilman (Eds.).
28. McArthur F.A., Baerlocher M.O., MacLean N.A.B., Hiltz M.D., Bärlocher F. Asking probing questions: can fluorescent in situ hybridization identify and localise aquatic hyphomycetes on leaf litter?. International Review of Hydrobiology 2001, 86:429-438.
29. Nikolcheva L.G., Bärlocher F. Seasonal and substrate preferences of fungi colonizing leaves in streams: traditional versus molecular evidence. Environmental Microbiology 2005, 7:270-280.
30. O'Gorman C.M., Fuller H.T., Dyer P.S. Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature 2008, 457:471-474.
31. Raviraja N.S., Nikolcheva L.G., Bärlocher F. Diversity of aquatic hyphomycete conidia assessed by microscopy and by DGGE. Microbial Ecology 2005, 49:1-7.
32. Richlen M.L., Barber P.H. A technique for the rapid extraction of microalgal DNA from single live and preserved cells. Molecular Ecology Notes 2005, 5:688-691.
33. Rossman A. Report of the planning workshop for All Fungi DNA Barcoding. Inoculum 2007, 58:1-5.
34. Shearer C.A., Lane L. Comparison of three techniques for the study of aquatic hyphomycete communities. Mycologia 1983, 75:498-508.
35. ® databasing paper. BMC Ecology 2004, 4:1-11.
36. Sridhar K.R., Bärlocher F. Viability of aquatic hyphomycete conidia in foam. Canadian Journal of Botany 1994, 72:106-110.
37. Stukenbrock E.H., Rosendahl S. Development and amplification of multiple co-dominant genetic markers from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR. Fungal Genetics and Biology 2005, 42:73-80.
38. Takano Y., Horiguchi T. Acquiring scanning electron microscopical, light microscopical and multiple gene sequence data from a single dinoflagellate cell. Journal of Phycology 2005, 42:251-256.
39. Taylor J.W., Jacobson D.J., Kroken S., Kasuga T. Geiser dM, Hibbett DS, Fisher MC Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 2000, 31:21-32.
40. 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. Philosophical Transactions of the Royal Society Series B 2006, 361:1947-1963.
41. Wood-Eggenschwiler S., Bärlocher F. Geographical distribution of Ingoldian fungi. Verhandlungen der internationalen Vereinigung für Limnologie 1985, 22:2780-2785.