Abstract
The diversity of planktonic eukaryotic microbes was studied at a coastal station of the eastern English Channel (EEC) from March 2011 to July 2015 (77 samples) using high throughput sequencing (454-pyrosequencing and Illumina) of the V2-V3 hypervariable region of the 18S SSU rDNA gene. Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing >1% of the total number of OTUs) were observed with the two methods (Kolmogorov-Smirnov p-value = 0.22). Eight super-groups were identified throughout all samples: Alveolata, Stramenopiles, Opisthokonta, Hacrobia, Archeaplastida, Apusozoa, Rhizaria, and Amoebozoa (ordered by decreasing OTU richness). To gain further insight into microbial activity in the EEC, ribosomal RNA was extracted for samples from 2013–2015 (30 samples). Analysis of 18S rDNA and rRNA sequences led to the detection of 696 and 700 OTUs, respectively. Cluster analysis based on OTUs’ abundance indicated three major seasonal groups that were associated to spring, winter/autumn, and summer conditions. The clusters inferred from rRNA data showed a clearer seasonal representation of the community succession than the one based on rDNA. The rRNA/rDNA ratio was used as a proxy for relative cell activity. When all OTUs were considered, the average rRNA:rDNA ratio showed a linear trend around the 1:1 line, suggesting a linear relation between OTU abundance (rDNA) and activity (rRNA). However, this ratio was highly variable over time when considering individual OTUs. Interestingly, the OTU affiliated with P. globosa displayed rRNA:rDNA ratio that allowed to delimit high vs low abundance and high vs low activity periods. It unveiled quite well the Phaeocystis bloom dynamic regarding cell proliferation and activity, and could even be used as early indicator of an upcoming bloom.
Highlights
Planktonic eukaryote microbes are abundant, ubiquitous in aquatic environments and extremely diverse in terms of taxonomy and metabolism [1]
Our main objectives were to establish an overview of diversity in the mesoeutrophic coastal area of eastern English Channel (EEC) and to study relationships between diversity and potential activity in microbial eukaryote communities by establishing rRNA:rDNA ratios
Microbial eukaryote community structure and seasonal succession were similar between surveys and years for the most abundant taxonomic groups, representing the majority of reads (>90)
Summary
Planktonic eukaryote microbes are abundant, ubiquitous in aquatic environments and extremely diverse in terms of taxonomy and metabolism [1]. High-throughput sequencing targeting the 16S/18S rDNA genes coupled with analysis using efficient bioinformatics tools, made it possible to reveal the vast diversity of marine microbes. They accumulate rRNA during unfavorable conditions, in period of low activity, shortly before favorable conditions return [33,34] To our knowledge, such “anticipatory life strategy” has not been reported for eukaryote microbes in marine environments. Our main objectives were to establish an overview of diversity in the mesoeutrophic coastal area of EEC and to study relationships between diversity and potential activity in microbial eukaryote communities by establishing rRNA:rDNA ratios. The main questions were as follows: (i) what are the composition and succession of planktonic eukaryote communities in relation to environmental parameters in the EEC? (ii) What are the main differences/similarities between the rDNA and rRNA datasets? (iii) What is the ecological relevance of the rDNA:rRNA ratio values?
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