Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)

Rachik, Sara; Christaki, Urania; Li, Luen Luen; Genitsaris, Savvas; Breton, Elsa; Monchy, Sébastien

doi:10.1371/journal.pone.0196987

Cited by 16 publications

(11 citation statements)

References 73 publications

(98 reference statements)

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“…This novel study characterized the eukaryotic communities in drinking water utilizing also RNA as a template. Activity recovery (RNA–DNA) [20] was considered a more appropriate way to handle this data instead of the RNA/DNA ratio [19, 51, 52] in order to keep also zero values in the analysis. In the relative activity recovery, the scale was limited to lower variation (− 100 to 100), and thus, the distribution of the results was even more extensive than in the RNA/DNA ratio calculation (scale in this data was − 3400- to 14,600-fold).…”

Section: Discussionmentioning

confidence: 99%

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

et al. 2019

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Background Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect their activity and survival. Methods Eukaryotes were characterized by Illumina high-throughput sequencing targeting 18S rRNA gene (DNA) that estimates the total community and the 18S rRNA gene transcript (RNA) that is more representative of the active part of the community. DWDS cold water ( N = 124), hot water ( N = 40), and biofilm ( N = 16) samples were collected from four cities in Finland. The sampled DWDSs were from two waterworks A–B with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks C–D and one of ground waterworks E). In each DWDS, samples were collected from three locations during four seasons of 1 year. Results A beta-diversity analysis revealed that the main driver shaping the eukaryotic communities was the DWDS (A–E) ( R = 0.73, P < 0.001, ANOSIM). The kingdoms Chloroplastida (green plants and algae), Metazoa (animals: rotifers, nematodes), Fungi (e.g., Cryptomycota ), Alveolata (ciliates, dinoflagellates), and Stramenopiles (algae Ochrophyta ) were well represented and active—judging based on the rRNA gene transcripts—depending on the surrounding conditions. The unchlorinated cold water of systems (A–B) contained a higher estimated total number of taxa (Chao1, average 380–480) than chlorinated cold water in systems C–E (Chao1 ≤ 210). Within each DWDS, unique eukaryotic communities were identified at different locations as was the case also for cold water, hot water, and biofilms. A season did not have a consistent impact on the eukaryotic community among DWDSs. Conclusions This study comprehensively characterized the eukaryotic community members within the DWDS of well-maintained ground and surface waterworks providing good quality water. The study gives an indication that each DWDS houses a unique eukaryotic community, mainly dependent on the raw water source and water treatment processes in place at the corresponding waterworks. In particular, disinfection as well as hot water temperature seemed to represent a strong selection pressure that controlled the number of active eukaryotic species. Electronic supplementary material The online version of this article (10.1186/s40168-019-0715-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

et al. 2019

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“…Significant changes of the RNA: DNA ratio may indicate ecological season events. A recent study have found that the changes of RNA: DNA ratio of Phaeocystis globose , collected at a coastal station of the eastern English Channel, unveiled well to the Phaeocystis bloom dynamic (Rachik et al, 2018).…”

Section: Introductionmentioning

confidence: 92%

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Wang

Xie

et al. 2019

Front. Microbiol.

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Picoeukaryotes play an important role in the biogenic element cycle and energy flow in oligotrophic ecosystems. However, their biodiversity and activity are poorly studied in open ocean systems, such as the northwestern Pacific Ocean, which is characterized by a complex hydrological setting. Here, we investigated the diversity and activity of picoeukaryotes in the northwestern Pacific Ocean using high-throughput sequencing targeting the V9 region of 18S rDNA and rRNA. Our results showed that the DNA picoeukaryotic communities were mainly represented by Mamiellophyceae, MAST, MALV-II, Spirotrichea, Prymnesiophyceae, and MALV-I (69.33% of the total DNA reads), and the RNA communities were dominated by Spirotrichea, Mamiellophyceae, MAST, Pelagophyceae, and MALV-II (67.46% of the total RNA reads). The number of operational taxonomic units (OTUs) was significantly affected by temperature and salinity, and was decreased with the increasing nutrient concentration both in the DNA and RNA surveys. Significant differences were observed in the community composition between DNA-based and RNA-based molecular approaches, and these differences were mainly attributed to Mamiellophyceae, Spirotrichea, and Pelagophyceae. The RNA: DNA ratio was used as a proxy for relative metabolic activity of the individual OTUs. We found that the relative metabolic activities of Mamiellophyceae, Spirotrichea, and Pelagophyceae species in the northwestern Pacific Ocean were highly affected by the nutrient concentration, i.e., the NO3 + NO2 and SiO3 concentration. Overall, our study shed light on picoeukaryotic diversity and distribution in the northwestern Pacific Ocean and revealed the correlation between the diversity, relative metabolic activities of marine picoeukaryotes, and the environmental factors.

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“…Comparison of RNA: DNA ratios usually used in the same species or group among different samples, but not for the comparison between different species or groups (Hu et al, 2016). A previous study showed that the RNA: DNA ratio could be a potential indicator of the upcoming Phaeocystis globosa bloom in the eastern English Chanel (Rachik et al, 2018). Xu et al (2017) observed the varied metabolic activities of protist community at different sampling depths in the South China Sea.…”

Section: Introductionmentioning

confidence: 99%

Diversity, Composition, and Activities of Nano- and Pico-Eukaryotes in the Northern South China Sea With Influences of Kuroshio Intrusion

et al. 2021

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Nano- and pico-eukaryotes play important roles in the diversity and functions of marine ecosystems. Warm, saline, and nutrient-depleted water that originates in the Kuroshio Current seasonally intrudes into the northern South China Sea (NSCS) from autumn to spring. To clarify the mechanisms in shaping the community structure of nano- and pico-eukaryotes as well as impacts of the Kuroshio intrusion on the NSCS ecosystem, genomic DNA and RNA were co-extracted from samples collected at two depths from nine stations, and then the V9 region of 18S rDNA and rRNA was sequenced with high-throughput sequencing. Our results showed that Dinophyceae was the most diverse and abundant nanoeukaryotic group during the study period revealed by both DNA and RNA surveys. In contrast, the relative read abundance of MAST, Pelagophyceae, and Dinophyceae in the size fraction of picoeukaryotes might be largely underestimated by the DNA survey. The RNA survey was the more reliable method to investigate the eukaryotic community structure. Environmental filtering played an important role in shaping the community structure, and the sampling depth became the governing factor of the beta diversity under the environmental setting of stratification during the study period. The spatial variations in the diversity of nanoeukaryotes were subject to the dispersal limitation under the size rule. The effects of the Kuroshio intrusion on the nanoeukaryotic community structure might also be explained by the dispersal limitation. Overall, neutral processes are critical in shaping the community structure of nanoeukaryotes. The relative metabolic activities of nanoeukaryotes were relatively stable in accordance with the high similarity of community structure between sampling sites. The responses of the relative metabolic activities of picoeukaryotes to environmental factors displayed two distinct patterns: positive correlations with salinity and nutrients and negative with temperature for Dinophyceae, MAST, and Pelagophyceae, while reversed patterns for Mamiellophyceae and Radiolaria. Our findings improve the understanding of the nano- and pico-eukaryotic communities in the NSCS and the mechanisms of their assembly.

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Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)

Cited by 16 publications

References 73 publications

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Diversity, Composition, and Activities of Nano- and Pico-Eukaryotes in the Northern South China Sea With Influences of Kuroshio Intrusion

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