Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

Abstract

Protist parasites are ecologically important, as they can have great impact on host population dynamics and functioning of entire ecosystems. Nevertheless, little is known about their prevalence in aquatic habitats. Here, we investigate the diversity and distributional patterns of the protist parasites Perkinsus and Parvilucifera (Perkinsea). Our approach included 454 pyrosequencing of the 18S rDNA gene obtained from a high-altitude lake (Lake Finsevatn, Norway) and phylogenetic analyses of all publicly available sequences related to Perkinsea. The applied PCR primers target a 450 bp region that encompass the variable V4 region of the 18S rDNA gene and have been optimized for the Titanium upgrade of the 454 technology. Nearly 5000 sequences longer than 150 bp were recovered from nearly all eukaryotic supergroups, and of those, 13 unique sequences were affiliated to Perkinsea. Thus, our new strategy for 454 amplicon sequencing was able to recover a large diversity of distantly related eukaryotes and previously unknown species of Perkinsea. In addition, we identified 40 Perkinsea sequences in GenBank generated by other recent diversity surveys. Importantly, phylogenetic analyses of these sequences identified 17 habitat-specific marine and freshwater clades . Hence, only a few successful transitions between these habitats have taken place over the entire history of Perkinsea, suggesting that the boundary between marine and fresh waters may constitute a barrier to cross-colonizations for intracellular parasites.

Recent radiation in a marine and freshwater dinoflagellate species flock

“…Thus at least five freshwater species are interspersed among the marine/brackish species. This is atypical, as most groups of freshwater dinoflagellates are phylogenetically distinct from the marine groups (Logares et al, 2007b), a pattern which is also true for many other protists (for example, Alverson et al, 2007;Bråte et al 2010). Based on the current phylogenetic trees, it is not possible to determine whether S. hangoei was originally a marine species or whether it had a freshwater ancestor that recolonized the marine environment.…”

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system

“…The 18S rRNA genes of eukaryotes were amplified using primers 3NDf (5 ′ -GGC AAG TCT GGT GCC AG-3 ′ ) and V4 euk R2 (5 ′ -ACG GTA TCT (AG)AT C(AG)T CTT CG-3 ′ ) (Brate et al, 2010). Barcodes that allow sample multiplexing during pyrosequencing were incorporated in the 5' end of primer 533R and 3NDf.…”

Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

“…Although this approach is appropriate for many studies, screening a wide range of potential hosts is not generally feasible and is therefore not a good way to estimate the diversity or size of the group. We hypothesised that there are many undetected haplosporidian lineages, as has been demonstrated in free-living protists (Bass and Cavalier-Smith, 2004;Bråte et al, 2010;Howe et al, 2011;Jones et al, 2011). Because haplosporidians are important pathogens with global impacts on aquaculture, it is important to appreciate their diversity, particularly as changing climates and intensifying farming activities may provoke previously non-problematic parasites to emerge, causing outbreaks, high mortalities and threats to aquaculture (Okamura and Feist, 2011).…”