Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel). Rachik, S., Christaki, U., Li, L. L., Genitsaris, S., Breton, E., & Monchy, S. 13(5):e0196987. Number: 5![Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel) [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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 \textgreater1% 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.
@article{rachik_diversity_2018,
title = {Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)},
volume = {13},
issn = {1932-6203},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196987},
doi = {10.1371/journal.pone.0196987},
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 {\textgreater}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.},
pages = {e0196987},
number = {5},
journaltitle = {{PLOS} {ONE}},
shortjournal = {{PLOS} {ONE}},
author = {Rachik, Sara and Christaki, Urania and Li, Luen Luen and Genitsaris, Savvas and Breton, Elsa and Monchy, Sébastien},
urldate = {2019-12-09},
date = {2018-05-10},
langid = {english},
note = {Number: 5},
keywords = {Community structure, Eukaryota, Fungi, Microbial taxonomy, Principal component analysis, Ribosomal {RNA}, Sequence databases, Taxonomy}
}
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Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing \\textgreater1% 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. 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