scholarly journals Variability and Community Composition of Marine Unicellular Eukaryote Assemblages in a Eutrophic Mediterranean Urban Coastal Area with Marked Plankton Blooms and Red Tides

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 114
Author(s):  
Savvas Genitsaris ◽  
Natassa Stefanidou ◽  
Maria Moustaka-Gouni ◽  
Ulrich Sommer ◽  
George Tsipas
Keyword(s):  
Coastal Area ◽  
High Throughput Sequencing ◽  
Spatial Separation ◽  
18S Rrna Gene ◽  
Small Scale ◽  
Unicellular Eukaryote ◽  
Rrna Gene ◽  
Red Tides ◽  
Phytoplankton Blooms ◽  
Taxonomic Groups

The Thessaloniki Bay is a eutrophic coastal area which has been characterized in recent years by frequent and intense phytoplankton blooms and red tides. The aim of the study was to investigate the underexplored diversity of marine unicellular eukaryotes in four different sampling sites in Thessaloniki Bay during a year of plankton blooms, red tides, and mucilage aggregates. High-Throughput Sequencing (HTS) was applied in extracted DNA from weekly water samples targeting the 18S rRNA gene. In almost all samples, phytoplankton blooms and/or red tides and mucilage aggregates were observed. The metabarcoding analysis has detected the known unicellular eukaryotic groups frequently observed in the Bay, dominated by Bacillariophyta and Dinoflagellata, and revealed taxonomic groups previously undetected in the study area (MALVs, MAST, and Cercozoa). The dominant OTUs were closely related to species known to participate in red tides, harmful blooms, and mucilage aggregates. Other OTUs, present also during the blooms in low abundance (number of reads), were closely related to known harmful species, suggesting the occurrence of rare taxa with potential negative impacts on human health not detectable with classical microscopy. Overall, the unicellular eukaryote assemblages showed temporal patterns rather than small-scale spatial separation responding to the variability of physical and chemical factors.

scholarly journals Protist community composition during early phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)

2014 ◽  
Vol 11 (7) ◽  
pp. 11179-11215 ◽  
Author(s):  
C. Georges ◽  
S. Monchy ◽  
S. Genitsaris ◽  
U. Christaki
Keyword(s):  
Southern Ocean ◽  
Community Composition ◽  
Reference Site ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Phytoplankton Blooms ◽  
Natural Iron ◽  
High Nutrient ◽  
Taxonomic Groups ◽  
High Level

Abstract. Microbial eukaryotic community composition was examined by 18S rRNA gene tag pyrosequencing, during the early phase of spring phytoplankton blooms induced by natural iron fertilization, off Kerguelen Island in the Southern Ocean (KEOPS2 cruise). A total of 999 operational taxonomical units (OTUs), affiliated to 30 known high-level taxonomic groups, were retrieved from 16 samples collected in the upper 300 m water column. The alveolata group was the most abundant in terms of sequence number and diversity (696 OTUs). The majority of alveolata sequences were affiliated to Dinophyceae and to two major groups of marine alveolates (MALV-I and MALV-II). In the upper 180 m, only 13% of the OTUs were shared between of the fertilized stations and the reference site characterized by high nutrient low chlorophyll (HNLC) waters. Fungi and Cercozoa were present in iron-fertilized waters, but almost absent in the HNLC samples, while Haptophyta and Chlorophyta characterized the HNLC sample. Finally, the 300 m depth samples of all stations were differentiated by the presence of MALV-II and Radiolaria. Multivariate analysis, examining the level of similarity between different samples, showed that protistan assemblages differed significantly between the HNLC and iron-fertilized stations, but also between the diverse iron-fertilized blooms.

scholarly journals Protist community composition during early phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)

2014 ◽  
Vol 11 (20) ◽  
pp. 5847-5863 ◽  
Author(s):  
C. Georges ◽  
S. Monchy ◽  
S. Genitsaris ◽  
U. Christaki
Keyword(s):  
Southern Ocean ◽  
Community Composition ◽  
Reference Site ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Phytoplankton Blooms ◽  
Natural Iron ◽  
High Nutrient ◽  
Taxonomic Groups ◽  
High Level

Abstract. Microbial eukaryotic community composition was examined by 18S rRNA gene tag pyrosequencing, during the early phase of spring phytoplankton blooms induced by natural iron fertilization, off Kerguelen Island in the Southern Ocean (KEOPS2 cruise). A total of 999 operational taxonomical units (OTUs), affiliated to 30 known high-level taxonomic groups, were retrieved from 16 samples collected in the upper 300 m water column. The alveolata group was the most abundant in terms of sequence number and diversity (696 OTUs). The majority of alveolata sequences were affiliated to Dinophyceae and to two major groups of marine alveolates (MALV-I and MALV-II). In the upper 180 m, only 13% of the OTUs were shared between of the fertilized stations and the reference site characterized by high-nutrient low-chlorophyll (HNLC) waters. Fungi and Cercozoa were present in iron-fertilized waters, but almost absent in the HNLC samples, while Haptophyta and Chlorophyta characterized the HNLC sample. Finally, the 300 m depth samples of all stations were differentiated by the presence of MALV-II and Radiolaria. Multivariate analysis, examining the level of similarity between different samples, showed that protistan assemblages differed significantly between the HNLC and iron-fertilized stations, but also between the diverse iron-fertilized blooms.

scholarly journals Marked changes in diversity and relative activity of picoeukaryotes with depth in the global ocean

2019 ◽  
Author(s):  
Caterina R. Giner ◽  
Vanessa Balagué ◽  
Massimo C. Pernice ◽  
Carlos M. Duarte ◽  
Josep M. Gasol ◽  
...  
Keyword(s):  
Community Structure ◽  
Water Column ◽  
High Throughput Sequencing ◽  
Hot Spot ◽  
18S Rrna Gene ◽  
Relative Activity ◽  
Global Ocean ◽  
Rrna Gene ◽  
M Cell ◽  
Taxonomic Groups

ABSTRACTMicrobial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for picoeukaryotes (0.2-3µm cell size). Here we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and minimum oxygen zone) and bathypelagic. Communities were analysed by high-throughput sequencing of the 18S rRNA gene, as represented by DNA (community structure) and RNA (metabolic expression), followed by delineation of Operational Taxonomic Units (OTUs). We found a clear stratification of the picoeukaryotic communities along the water column, with two differentiated assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased or decreased their abundances with depth. We used the rRNA:rDNA ratio of each individual OTU as a proxy of its metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Overall, our results characterize the change in community structure and activity of picoeukaryotes in the global-ocean water column, suggesting that the mesopeagic layer is a hot-spot of picoeukaryotic activity.

scholarly journals Taxa–area and distance–decay relationships of unicellular eukaryotes along an elevation gradient of mountainous freshwater ecosystems

2019 ◽  
Vol 41 (6) ◽  
pp. 821-834
Author(s):  
Sofia C Macingo ◽  
Konstantinos A Kormas ◽  
Andreas Oikonomou ◽  
Hera Karayanni
Keyword(s):  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Elevation Gradient ◽  
Environmental Filtering ◽  
18S Rrna Gene ◽  
Freshwater Ecosystems ◽  
Distance Decay ◽  
Unicellular Eukaryote ◽  
Rrna Gene ◽  
Unicellular Eukaryotes

Abstract Unicellular eukaryotes have pivotal ecological roles in aquatic ecosystems by participating in biogeochemical processes and structuring microbial food webs. However, revealing their biogeographical patterns remains challenging, as it is reflected in the rather limited available knowledge. In this study, two central patterns, the taxa–area and the distance–decay relationships, were tested for freshwater unicellular eukaryotes. Sampling was performed in 31 mountainous freshwater ecosystems in Thessaly (Greece). Sampling sites had different geohydromorphological characteristics (altitude, 124–704 m; depth, 0.3–1 m; surface area, 188–123 000 m2; geographical distances, 0.03–48.4 km). Unicellular eukaryote diversity was assessed by 18S rRNA gene diversity with high-throughput sequencing. Five supergroups (Stramenopiles, Alveolata, Rhizaria, Archaeplastida and Opisthokonta) were found with the most abundant taxa being Stramenopiles and Alveolata. Aquatic unicellular eukaryotes showed statistically significant but weak DDR and TAR. This can be attributed to the large proportion of specialists (91.9% of operational taxonomic units according to Levin’s index). These results indicate that although mountainous pools and ponds can host high diversity of unicellular eukaryotes, the shaping of their communities is mainly regulated by niche-specific processes and environmental filtering and to a lesser extent by species dispersion processes.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters

2020 ◽  
Author(s):  
Tatiana A Belevich ◽  
Irina A Milyutina ◽  
Galina A Abyzova ◽  
Aleksey V Troitsky
Keyword(s):  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Global Climate ◽  
Atmospheric Oxygen ◽  
18S Rrna Gene ◽  
Anthropogenic Activity ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Russian Arctic ◽  
Arctic Seas

Abstract Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To get more knowledge about Mamiellophyceae distribution and diversity special study were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July-September 2017 in the Barents, Kara, and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A—uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with M. polaris dominating north of 72°N. The presence of Ostreococcus tauri, O. lucimarinus and O. mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.

16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

2018 ◽  
Vol 81 (5) ◽  
pp. 848-859
Author(s):  
MIYO NAKANO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Animal Feed ◽  
Rrna Gene ◽  
Universal Primer ◽  
Food Matrices ◽  
Taxonomic Groups ◽  
The 16S Rrna Gene

ABSTRACT High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.

scholarly journals Marteilia refringens and Marteilia pararefringens sp. nov. are distinct parasites of bivalves and have different European distributions

Parasitology ◽  
2018 ◽  
Vol 145 (11) ◽  
pp. 1483-1492 ◽  
Author(s):  
R. Kerr ◽  
G. M. Ward ◽  
G. D. Stentiford ◽  
A. Alfjorden ◽  
S. Mortensen ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Separate Species ◽  
Target Region ◽  
Genetic Lineages ◽  
Specific Pcr ◽  
Northern European ◽  
The Uk

AbstractMarteilia refringens causes marteiliosis in oysters, mussels and other bivalve molluscs. This parasite previously comprised two species, M. refringens and Marteilia maurini, which were synonymized in 2007 and subsequently referred to as M. refringens ‘O-type’ and ‘M-type’. O-type has caused mass mortalities of the flat oyster Ostrea edulis. We used high throughput sequencing and histology to intensively screen flat oysters and mussels (Mytilus edulis) from the UK, Sweden and Norway for infection by both types and to generate multi-gene datasets to clarify their genetic distinctiveness. Mussels from the UK, Norway and Sweden were more frequently polymerase chain reaction (PCR)-positive for M-type (75/849) than oysters (11/542). We did not detect O-type in any northern European samples, and no histology-confirmed Marteilia-infected oysters were found in the UK, Norway and Sweden, even where co-habiting mussels were infected by the M-type. The two genetic lineages within ‘M. refringens’ are robustly distinguishable at species level. We therefore formally define them as separate species: M. refringens (previously O-type) and Marteilia pararefringens sp. nov. (M-type). We designed and tested new Marteilia-specific PCR primers amplifying from the 3’ end of the 18S rRNA gene through to the 5.8S gene, which specifically amplified the target region from both tissue and environmental samples.

scholarly journals Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies

2020 ◽  
Author(s):  
Stephen J. Taerum ◽  
Blaire Steven ◽  
Daniel J. Gage ◽  
Lindsay R. Triplett
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Universal Primers ◽  
Rrna Gene ◽  
Plant Host ◽  
Eukaryotic Diversity ◽  
Rrna Gene Sequencing

AbstractProtists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes, but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of plant host DNA during 18S rRNA gene library preparation. We designed a PNA clamp, PoacV9_01, specific to the V9 region of the 18S rRNA gene for plants in the family Poaceae. PoacV9_01 suppressed the amplification of five species of grain crops in quantitative PCR reactions. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65% to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.

scholarly journals Validation of a PNA Clamping Method for Reducing Host DNA Amplification and Increasing Eukaryotic Diversity in Rhizosphere Microbiome Studies

2020 ◽  
Vol 4 (4) ◽  
pp. 291-302
Author(s):  
Stephen J. Taerum ◽  
Blaire Steven ◽  
Daniel J. Gage ◽  
Lindsay R. Triplett
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Universal Primers ◽  
Rrna Gene ◽  
Crop Species ◽  
Eukaryotic Diversity

Protists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here, we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of maize host DNA during 18S rRNA gene library preparation. PNA clamps targeting the V4 and V9 hypervariable regions of the 18S rRNA gene of maize were designed and evaluated in silico, and the performance of the V9 targeting clamp PoacV9_01 was evaluated in vitro. PoacV9_01 suppressed the amplification of five crop species in quantitative PCR assays. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65 to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.

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