Short‐term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

Abstract

The short-term variation in the community structure of freshwater small eukaryotes (0.2-5 μm) was investigated in a mesotrophic lake every 2-3 days over one summer by coupling three molecular methods: 454 amplicon pyrosequencing, qPCR and TSA-FISH. The pyrosequencing approach unveiled a much more extensive small-eukaryotic diversity (991 OTUs) than has been described previously. The vast majority of the diversity described was represented by rare OTUs (≤ 0.01% of reads) belonging primarily to Cryptomycota, Dikarya and photosynthetic organisms, which were never detected as abundant in any of the samples. The small eukaryote community was characterized by a continual and important reassembly. These rearrangements involved the 20 'core taxa' (≥ 1% of reads), and, were essentially due to a handful of OTUs that were detected in intermediate abundance (0.01-1% of reads) and sporadically in dominant taxa. Putative bacterivorous (Ciliophora and Cercozoa) as well as parasitic and saprotrophic taxa (Perkinsozoa and Cryptomycota) were involved in these changes of diversity. A putative infection of microalgae by a lacustrine perkinsozoan was also reported for the first time in this study. Open questions regarding both the patterns that govern the rapid small eukaryote reassemblies and the possible biogeography of these organisms arise from this study.

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation

“…Besides, the "rare” or “intermediate” population has recently become an emerging concept in ecology, which has been particularly studied in sea-water samples [27,28,48,49]. Despite different cutoffs used to differentiate the minority taxa (“rare” to “intermediate” taxa), all these studies have shown that minority populations vary more than majority ones and that minority taxa play a crucial role in the ecosystem stability [27,28,48,49].…”

Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California

“…Communities perturbed by nutrient enrichments differed dramatically (< 50% community similarity values) from the original community after only 24 h of incubation (Kim et al 2011). A recent study investigating the small-scale temporal variability of the protistan community using pyrosequencing at a lake in France found overall low similarity (average of 34%) between communities of small eukaryotes collected 2 to 3 d apart (Mangot et al 2013). However, the average similarity among the abundant OTUs (>1% of reads) in their study was 70%, greater than our average BC similarity of 58% for communities separated by 2 or 3 d. High smallscale temporal variability was also reported by Vigil et al (2009), who sampled along the east coast of the USA.…”

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

“…Molecular surveys have shown that Perkinsea-like sequences can be diverse and abundant in freshwater lakes, suggesting this group plays an important role in freshwater food webs [5,9-11]. However, most freshwater Perkinsea have still not been characterised ecologically or morphologically, with one exception, a recently identified Perkinsea-like protist linked to local mortality events of the Southern Leopard frog Rana sphenocephala in the USA in 2003 [12].…”