A decade's perspective on the impact of DNA sequencing on aquatic hyphomycete research
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Anderson, 2007, Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules, J. Microbiol. Method, 68, 248, 10.1016/j.mimet.2006.08.005
Anderson, 2011, Population genetics of the aquatic fungus Tetracladium marchalianum over space and time, PLoS One, 6, e15908, 10.1371/journal.pone.0015908
Baldrian, 2012, Active and total microbial communities in forest soil are largely different and highly stratified during decomposition, ISME J., 6, 248, 10.1038/ismej.2011.95
Bärlocher, 2010, Molecular approaches promise a deeper and broader understanding of the evolutionary ecology of aquatic hyphomycetes, J. N. Am. Benthol. Soc., 29, 1037, 10.1899/09-081.1
Bärlocher, 1974, Dynamics of the fungal population on leaves in a stream, J. Ecol., 63, 761, 10.2307/2258954
Bärlocher, 2008, Raised water temperature lowers diversity of hyporheic aquatic hyphomycetes, Freshwater Biol., 53, 368
Bärlocher, 2012, Processing of Eucalyptus viminalis leaves in Australian streams – importance of aquatic hyphomycetes and zoosporic fungi, Fund. Appl. Limnol., 179/4, 305, 10.1127/1863-9135/2012/0229
Baschien, 2006, Phylogeny of selected aquatic hyphomycetes based on morphological and molecular data, Nova Hedwigia, 83, 311, 10.1127/0029-5035/2006/0083-0311
Bauer, 2003, Classicula: the teleomorph of Naiadella fluitans, Mycologia, 95, 756, 10.2307/3761949
Belliveau, 2005, Molecular evidence confirms multiple origin of aquatic hyphomycetes, Mycol. Res., 109, 1407, 10.1017/S0953756205004119
Berbee, 2001, Fungal molecular evolution: gene trees and geologic time, 67
Buée, 2009, 454 pyrosequencing analyses of forest soils reveal and unexpected high fungal diversity, New Phytol., 184, 449, 10.1111/j.1469-8137.2009.03003.x
Campbell, 2009, Evolutionary relationships between aquatic anamorphs and teleomorphs: Tricladium and Varicosporium, Mycol. Res., 113, 1322, 10.1016/j.mycres.2009.09.003
Campbell, 2006, Evolutionary relationships among aquatic anamorphs and telemomorphs: Lemonniera, Margaritispora, and Goniopila, Mycol. Res., 110, 1025, 10.1016/j.mycres.2006.04.012
DeLong, 2009, The microbial ocean from genomes to biomes, Nature, 459, 200, 10.1038/nature08059
Duarte, 2008, Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams, Freshwater Biol., 53, 91
Duarte, 2010, Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques, Microbiol. Res., 165, 351, 10.1016/j.micres.2009.06.002
Duarte, 2009, Microbial decomposer communities are mainly structured by the trophic status in circumneutral and alkaline streams, Appl. Environ. Microbiol., 75, 6211, 10.1128/AEM.00971-09
Duarte, 2012, Preliminary insights into the phylogeography of six aquatic hyphomycete species, PLoS One, 7, e45289, 10.1371/journal.pone.0045289
Dupuis, 2012, Multi-locus species delimitation in closely related animals and fungi: one marker is not enough, Mol. Ecol, 21, 4422, 10.1111/j.1365-294X.2012.05642.x
Edwards, 2006, Using pyrosequencing to shed light on deep mine microbial ecology, BMC Genomics, 7, 57, 10.1186/1471-2164-7-57
Ghannoum, 2010, Characterization of the oral fungal microbiome (mycobiome) in healthy individuals, PLoS Pathog., 6, e1000713, 10.1371/journal.ppat.1000713
Gygi, 1999, Correlation between protein and mRNA abundance in yeast, Mol. Cell. Biol., 19, 1720, 10.1128/MCB.19.3.1720
Head, 1998, Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivable microorganisms, Microb. Ecol., 35, 1, 10.1007/s002489900056
Hebert, 2003, Barcoding animal life, cytochrome c oxidase subunit I divergences among closely related species, P. R. Soc. B Biol. Sci., 270, S596
Ingold, 1942, Aquatic hyphomycetes of decaying alder leaves, Trans. Br. Mycol. Soc., 25, 339, 10.1016/S0007-1536(42)80001-7
Ingold, 1959, Aquatic spora of Omo forest, Nigeria, Trans. Br. Mycol. Soc., 42, 479, 10.1016/S0007-1536(59)80049-8
Jacobsen, 2005, Culture independent PCR: an alternative enzyme discovery strategy, J. Microbiol. Method, 60, 63, 10.1016/j.mimet.2004.08.013
Jumpponen, 2009, Massively parallel 454-sequencing indicates hyperdiverse fungal communities in temperate Quercus macorcarpa phyllosphere, New Phytol., 184, 438, 10.1111/j.1469-8137.2009.02990.x
Kanokratana, 2011, Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis, Microb. Ecol., 61, 518, 10.1007/s00248-010-9766-7
Kaushik, 1971, The fate of the dead leaves that fall into streams, Arch. Hydrobiol., 68, 465
Letourneau, 2010, Potential use of barcoding to identify aquatic hyphomycetes, Fungal Divers., 40, 51, 10.1007/s13225-009-0006-8
Medinger, 2010, Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms, Mol. Ecol., 19, 32, 10.1111/j.1365-294X.2009.04478.x
Nikolcheva, 2002, Phylogeny of Tetracladium based on 18S rDNA, Czech Mycol., 53, 285, 10.33585/cmy.53404
Nikolcheva, 2003, Determining diversity of freshwater fungi on decomposing leaves: comparison of traditional and molecular approaches, Appl. Environ. Microbiol., 69, 2548, 10.1128/AEM.69.5.2548-2554.2003
Nilsson, 2009, The ITS region as a target for characterization of fungal communities using emerging sequencing technologies, FEMS Microbiol. Lett., 296, 97, 10.1111/j.1574-6968.2009.01618.x
Nilsson, 2011, Rethinking taxon sampling in the light of environmental sequencing, Cladistics, 27, 197, 10.1111/j.1096-0031.2010.00336.x
Purdy, 2010, Systems biology for ecology: from molecules to ecosystems, Adv. Ecol. Res., 43, 87, 10.1016/B978-0-12-385005-8.00003-4
Ranzoni, 1956, The perfect stage of Flagellospora penicillioides, Am. J. Bot., 43, 13, 10.2307/2438408
Roldán, 1989, Pure culture studies on Tetracladium, Mycol. Res., 93, 452, 10.1016/S0953-7562(89)80039-5
Seena, 2012, Intraspecific variation of the aquatic fungus Articulospora tetracladia: an ubiquitous perspective, PLoS One, 7, e35884, 10.1371/journal.pone.0035884
Seena, 2010, DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species, Fungal Divers., 44, 77, 10.1007/s13225-010-0056-y
Seena, 2008, Fungal diversity during leaf decomposition in a stream assessed through clone libraries, Fungal Divers., 30, 1
Selosse, 2008, Out of the rivers: are some aquatic hyphomycetes plant endophytes?, New Phytol., 178, 3, 10.1111/j.1469-8137.2008.02390.x
Shearer, 2007, Fungal biodiversity in aquatic habitats, Biodivers. Conserv., 16, 49, 10.1007/s10531-006-9120-z
Sokolski, 2006, A fungal endophyte of black spruce (Picea mariana) needles is also an aquatic hyphomycete, Mol. Ecol., 15, 1955, 10.1111/j.1365-294X.2006.02909.x
Solé, 2008, 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., 288, 47, 10.1111/j.1574-6968.2008.01333.x
Suberkropp, 1976, Fungi and bacteria associated with leaves during processing in a woodland stream, Ecology, 57, 707, 10.2307/1936184
Taylor, 2012, An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding, Mol. Ecol. Resour., 10.1111/j.1755-0998.2012.03119.x
Taylor, 2006, Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi, Phil. Trans. R. Soc. B, 361, 1947, 10.1098/rstb.2006.1923
Webster, 1992, Anamorph-teleomorph relationships, 99