Molecular diversity and distribution of marine fungi

BMfungi

Published in Proceedings of the Royal Society B

Molecular diversity and distribution of marine fungi across 130 European environmental samples

Thomas A. Richards, Guy Leonard, Frédéric Mahé, Javier del Campo, Sarah Romac, Meredith D. M. Jones, Finlay Maguire, Micah Dunthorn, Colomban De Vargas, Ramon Massana, Aurélie Chambouvet

Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal ‘OTU clusters’ that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments.

The Protist Ribosomal Reference database (PR2)

Published this week at Nucleic Acids Research

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cédric Berney, Lucie Bittner, Christophe Boutte, Gaétan Burgaud, Colomban de Vargas, Johan Decelle, Javier del Campo, John R. Dolan, Micah Dunthorn, Bente Edvardsen, Maria Holzmann, Wiebe H.C.F. Kooistra, Enrique Lara, Noan Le Bescot, Ramiro Logares, Frédéric Mahé, Ramon Massana, Marina Montresor, Raphael Morard, Fabrice Not, Jan Pawlowski, Ian Probert, Anne-Laure Sauvadet, Raffaele Siano, Thorsten Stoeck, Daniel Vaulot, Pascal Zimmermann and Richard Christen

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.