title: Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing.
abstract: Water samples were collected along transects from the shore to the centre of two French lakes: the deep, volcanic, oligomesotrophic and low allochthonic-impacted Lake Pavin, and the productive and higher allochthonic-impacted Lake Aydat. The biodiversity was analysed using two approaches: the classical approach consisting of cloning/sequencing of the 18S, ITS1, 5.8S, ITS2 and partial 28S region using primers designed for fungus sequences, and the pyrosequencing of 18S rRNA hypervariable V2, V3 and V5 regions using two primer sets (one universal for eukaryotes and one for fungi). The classical approach yielded 146 (Lake Pavin) and 143 (Lake Aydat) sequences, corresponding to 46 and 63 operational taxonomic units (OTUs) respectively. Fungi represented half of the OTUs identified in Lake Pavin and 30% in Lake Aydat, and were dominated by sequences from Chytridiomycota found throughout Lake Pavin but mostly in the central pelagic zone of Lake Aydat. The pyrosequencing approach yielded 42,064 (Pavin) and 61,371 (Aydat) reads, of which 12-15% and 9-19% reads were assigned to fungi in Lakes Pavin and Aydat respectively. Chytridiomycota members were also dominant among these reads, with OTUs displaying up to > 33-fold overrepresentation in the centre compared with the riparian areas of Lake Aydat. Besides fungi, both approaches revealed other major eukaryote groups, with the highest diversity in the central areas of lakes. One of the major findings of our study was that the two lakes displayed contrasting spatial distributions, homogenous for Lake Pavin and heterogeneous for Lake Aydat, which may be related to their peculiarities. This study represents the first unveiling of microbial eukaryote and fungus diversity assessed with two complementary molecular methods, and is considered a major milestone towards understanding the dynamics and ecology of fungi in freshwater lake ecosystems, which are directly link to the abundance and distribution of taxa.
authors.affiliation: LMGE, Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université, Blaise Pascal, BP 80026, 63171 Aubière Cedex, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Monchy
authors.forename: Giovanna
authors.initials: G
authors.lastname: Sanciu
authors.forename: Marlène
authors.initials: M
authors.lastname: Jobard
authors.forename: Serena
authors.initials: S
authors.lastname: Rasconi
authors.forename: Mélanie
authors.initials: M
authors.lastname: Gerphagnon
authors.forename: Magali
authors.initials: M
authors.lastname: Chabé
authors.forename: Amandine
authors.initials: A
authors.lastname: Cian
authors.forename: Dionigia
authors.initials: D
authors.lastname: Meloni
authors.forename: Nathalie
authors.initials: N
authors.lastname: Niquil
authors.forename: Urania
authors.initials: U
authors.lastname: Christaki
authors.forename: Eric
authors.initials: E
authors.lastname: Viscogliosi
authors.forename: Télesphore
authors.initials: T
authors.lastname: Sime-Ngando
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D015169:Colony Count, Microbial; D004275:DNA, Ribosomal / Q000378:metabolism; D004463:Ecology; D017753:Ecosystem; D005618:Fresh Water / Q000382:microbiology*; D005658:Fungi / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D014871:Water Microbiology
chemical_list: D004275:DNA, Ribosomal