Intraspecific variation of the aquatic fungus Articulospora tetracladia: An ubiquitous perspective

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Seena, Sahadevan ^a   Duarte, Sofia ^a   Pascoal, Cláudia ^a   Cássio, Fernanda ^a  

^a UNIVERSITY OF MINHO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

INTERNAL TRANSCRIBED SPACER 1; INTERNAL TRANSCRIBED SPACER 2; SPACER DNA;

AQUATIC SPECIES; ARTICLE; ARTICULOSPORA TETRACLADIA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; DNA SEQUENCE; FUNGUS ISOLATION; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); HAPLOTYPE; HYPHOMYCETES; INTRASPECIFIC VARIATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; CANADA; CLASSIFICATION; DEUTEROMYCETES; DNA BARCODING; EUROPE; GENETICS; ISOLATION AND PURIFICATION; JAPAN; MALAYSIA; MICROBIOLOGY; PHYLOGENY; PHYLOGEOGRAPHY; RIVER;

ARTICULOSPORA TETRACLADIA; FUNGI; HYPHOMYCETES; OTUS;

AQUATIC ORGANISMS; CANADA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA BARCODING, TAXONOMIC; DNA FINGERPRINTING; DNA, INTERGENIC; EUROPE; GENETIC VARIATION; JAPAN; MALAYSIA; MITOSPORIC FUNGI; PHYLOGENY; PHYLOGEOGRAPHY; POLYMERASE CHAIN REACTION; RIVERS;

EID: 84860490772     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035884     Document Type: Article

References (61)

1. Fernandes I, Pascoal C, Cássio F, (2011) Intraspecific traits change biodiversity effects on ecosystem functioning under metal stress. Oecologia 166: 1019-1028.
2. Wilkinson A, Solan M, Taylor AFS, Alexander IJ, Johnson D, (2010) Intraspecific diversity regulates fungal productivity and respiration. PLoS ONE 5: e12604.
3. Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellen M, (2008) Ecological consequences of genetic diversity. Ecol Lett 11: 609-623.
4. Bärlocher F, (2005) Freshwater fungal communities. In: Dighton J, White JF, Oudemans P, editors. The fungal community: its organization and role in the ecosystem Boca Raton CRC pp. 39-59.
5. Peláez F, Platas G, Colldo J, Diez MT, (1996) Infraspecific variation in two species of aquatic hyphomycetes assessed by RAPD analysis. Mycol Res 100: 831-837.
6. Charcosset J-Y, Gardes M, (1999) Infraspecific genetic diversity and substrate preference in the aquatic hyphomycete Tetrachaetum elegans. Mycol Res 103: 736-742.
7. Laitung B, Chauvet E, Feau N, Feve K, Chikhi L, et al. (2004) Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus. Mol Ecol 13: 1679-1692.
8. Anderson JL, Shearer CA, (2011) Population genetics of the aquatic fungus Tetracladium marchalianum over space and time. PLoS ONE 6: e15908.
9. Ingold CT, (1942) Aquatic hyphomycetes of decaying alder leaves. Trans Br Mycol Soc 25: 339-417.
10. Duarte S, Pascoal C, Cássio F, (2008) High diversity of fungi may mitigate the impact of pollution on plant litter decomposition in streams. Microb Ecol 56: 688-695.
11. Duarte S, Pascoal C, Garabétian F, Cássio F, Charcosset J-Y, (2009) Microbial decomposer communities are mainly structured by trophic status in circumneutral and alkaline streams. Appl Environ Microb 75: 6211-6221.
12. Pascoal C, Cássio F, (2004) Contribution of fungi and bacteria to leaf litter decomposition in a polluted river. Appl Environ Microbiol 70: 5266-5273.
13. Pascoal C, Cássio F, Marvanová L, (2005) Anthropogenic stress may affect aquatic hyphomycete diversity more than leaf decomposition in a low order stream. Arch Hydrobiol 162: 481-496.
14. Sridhar KR, Duarte S, Cássio F, Pascoal C, (2009) The role of early fungal colonizers in leaf-litter decomposition in Portuguese streams impacted by agricultural runoff. Intern Rev Hydrobiol 94: 399-409.
15. Baudoin JM, Guérold F, Felten V, Chauvet E, Wagner P, et al. (2008) Elevated aluminium concentration in acidified headwater streams lowers aquatic hyphomycete diversity and impairs leaf-litter breakdown. Microb Ecol 56: 260-269.
16. Fabre E, (1998) Aquatic hyphomycetes in three rivers of southwestern France. II. Spatial and temporal differences between species. Can J Bot 76: 107-114.
17. Harrington TJ, (1997) Aquatic hyphomycetes of 21 rivers in southern Ireland. Proc R Ir Acad 97B: 139-148.
18. Gönczöl J, (1976) Ecological observations on the aquatic hyphomycetes of Hungary II. Acta Bot Acad Sci Hung 22: 51-60.
19. Del Frate G, Caretta G, (1983) Aquatic hyphomycetes of a mountain stream in Valsesia (Piemonte). Hydrobiologia 102: 69-71.
20. Ingold CT, (1949) Aquatic hyphomycetes from Switzerland. Trans Br Mycol Soc 32: 341-345.
21. Iqbal SH, (1994) Species diversity of freshwater hyphomycetes in some streams of Pakistan. Comparison of sampling techniques. Mycoscience 35: 331-343.
22. Chan SY, Goh TK, Hyde KD, (2000) Ingoldian fungi in Lam Tsuen river and Tai Po Kau forest stream. Fungal Divers 5: 109-118.
23. Rajashekhar M, Kaveriappa KM, (2003) Diversity of aquatic hyphomycetes in the aquatic ecosystems of the Western Ghats of India. Hydrobiologia 501: 167-177.
24. Suberkropp K, (2001) Fungal growth, production, and sporulation during leaf decomposition in two streams. Appl Environ Microbiol 67: 5063-5068.
25. Schoenlein-Crusius IH, Grandi RAP, (2003) The diversity of aquatic hyphomycetes in South America. Braz J Microbiol 34: 183-193.
26. Smits G, Fernández R, Cressa C, (2007) Preliminary study of aquatic hyphomycetes from Venezuelan streams. Acta Bot Venezuelica 30: 345-355.
27. Aimer RD, Segedin BP, (1985) Some aquatic hyphomycetes from New Zealand streams. N Z J Bot 23: 273-299.
28. Duarte S, Pascoal C, Cássio F, Bärlocher F, (2006) Aquatic hyphomycete diversity and identity affect leaf litter decomposition in microcosms. Oecologia 147: 658-666.
29. Pascoal C, Cássio F, Nikolcheva L, Bärlocher F, (2010) Realized fungal diversity increases functional stability of leaf litter decomposition under zinc stress. Microb Ecol 59: 84-93.
30. Bärlocher F, Corkum M, (2003) Nutrient enrichment overwhelms diversity effects in leaf decomposition by stream fungi. Oikos 101: 247-252.
31. Seena S, Pascoal C, Marvanová L, Cássio F, (2010) DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species. Fungal Divers 44: 77-87.
32. Myers RM, Fischer SG, Lerman LS, Maniatis T, (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13: 3131-3145.
33. White TJ, Bruns T, Lee S, Taylor JW, (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications New York Academic Press Inc pp. 315-322.
34. Duarte S, Pascoal C, Alves A, Correia A, Cássio F, (2010) Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques. Microbiol Res 165: 351-362.
35. Muyzer G, de Waal EC, Uitterlinden AG, (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16 S rRNA. Appl Environ Microbiol 59: 695-700.
36. 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.
37. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
38. Kimura M, (1980) A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
39. Ramirez-Flandes S, Ulloa O, (2008) Bosque: integrated phylogenetic analysis software. Bioinformatics 24: 2539-2541.
40. Excoffier L, Lischer HEL, (2010) Arlequin suite ver 3.5: a new series of programs to perform genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
41. Tajima F, (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
42. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
43. Nei M, Li WH, (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS USA 76: 5269-5273.
44. Hudson RR, Slatkin M, Maddison WP, (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
45. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
46. Muyzer G, Smalla K, (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73: 127-141.
47. Nikolcheva LG, Bourque T, Bärlocher F, (2005) Fungal diversity during initial stages of leaf decomposition in a stream. Mycol Res 109: 246-253.
48. Nikolcheva LG, Cockshutt AM, Bärlocher F, (2003) Determining diversity of freshwater fungi on decomposing leaves: comparison of traditional and molecular approaches. Appl Environ Microbiol 69: 2548-2554.
49. Tacão M, Moura A, Alves A, Henriques I, Saavedra MJ, et al. (2005) Evaluation of 16 S rDNA- and gyrB-DGGE for typing members of the genus Aeromonas. FEMS Microbiol Lett 246: 11-18.
50. Muyzer G, Brinkoff T, Nübel U, Santegoeds C, Schäfer H, et al. (2004) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD, editors. Molecular Microbial Ecology Manual Netherlands Kluwer academic publishers pp. 743-770.
51. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH, (2008) Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinforma 4: 193-201.
52. Weir BS, Hill WG, (2002) Estimating F-statistics. Annu Rev Genet 36: 721-750.
53. Hartl DL, Clark AG, (2007) Principles of population genetics. Sunderland Sinauer Associates.
54. Bärlocher F, (2009) Reproduction and dispersal in aquatic hyphomycetes. Mycoscience 50: 3-8.
55. Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D, (2006) Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philos Trans R Soc B 361: 1947-1963.
56. Halling RE, Osmundson TW, Neves MA, (2008) Pacific boletes: implications for biogeographic relationships. Mycol Res 112: 437-447.
57. Hosaka K, Castellano MA, Spatafora JW, (2008) Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota). Mycol Res 112: 448-462.
58. Lumbsch HT, Buchanan PK, May TW, Mueller GM, (2008) Phylogeography and biogeography of fungi. Mycol Res 112: 423-424.
59. Moncalvo JM, Buchanan PK, (2008) Molecular evidence for long distance dispersal across the Southern Hemisphere in the Ganoderma applanatum-australe species complex (Basidiomycota). Mycol Res 112: 425-436.
60. Wirtz N, Printzen C, Thorsten Lumbsch H, (2008) The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycol Res 112: 472-484.
61. Seymour FA, Cresswell JE, Fisher PJ, Lappin-Scott HM, Haag H, et al. (2004) The influence of genotypic variation on metabolite diversity in populations of two endophytic fungal species. Fungal Genet Biol 41: 721-734.