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.

scholarly journals Plankton Microorganisms Coinciding with Two Consecutive Mass Fish Kills in a Newly Reconstructed Lake

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Andreas Oikonomou ◽  
Matina Katsiapi ◽  
Hera Karayanni ◽  
Maria Moustaka-Gouni ◽  
Konstantinos Ar. Kormas
Keyword(s):  
Gene Diversity ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Prymnesium Parvum ◽  
Fish Kill ◽  
Aquatic Life ◽  
Unicellular Eukaryotes ◽  
Toxic Cyanobacteria ◽  
Causative Agents ◽  
Lake Karla

Lake Karla, Greece, was dried up in 1962 and its refilling started in 2009. We examined the Cyanobacteria and unicellular eukaryotes found during two fish kill incidents, in March and April 2010, in order to detect possible causative agents. Both microscopic and molecular (16S/18S rRNA gene diversity) identification were applied. Potentially toxic Cyanobacteria included representatives of thePlanktothrixandAnabaenagroups. Known toxic eukaryotes or parasites related to fish kill events werePrymnesium parvumandPfiesteriacf.piscicida, the latter being reported in an inland lake for the second time. Other potentially harmful microorganisms, for fish and other aquatic life, included representatives of Fungi, Mesomycetozoa, Alveolata, and Heterokontophyta (stramenopiles). In addition, Euglenophyta, Chlorophyta, and diatoms were represented by species indicative of hypertrophic conditions. The pioneers of L. Karla’s plankton during the first months of its water refilling process included species that could cause the two observed fish kill events.

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 Comparison of invertebrate diversity in lake waters and their resting eggs in sediments, as revealed by high-throughput sequencing (HTS)

2020 ◽  
pp. 19
Author(s):  
Xiaoyan Wang ◽  
Qing Wang ◽  
Yufeng Yang ◽  
Wenbo Yu
Keyword(s):  
High Throughput ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Essential Feature ◽  
Resting Eggs ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Promising Alternative ◽  
Invertebrate Diversity ◽  
Significant Difference

Aquatic invertebrate diversity reflects water quality and the health of aquatic ecosystems and should be monitored as an essential feature of freshwater ecosystems. The resting eggs of aquatic invertebrates in sediments populate the overlying water. The diversity of invertebrates in waters and their resting eggs in sediments in Baiyangdian Lake, Xiongan, North China, were assessed using high-throughput sequencing (HTS) with a pair of 18S rRNA gene adaptor-linked primers. The total of 99 operational taxonomic units (OTUs) derived from 353,755 invertebrate sequences (mostly zooplankton) were revealed by this study. A total of 50 species in the water samples including 20 rotifers, 11 copepods, 1 cladoceran and 18 other species were sorted out. In the sediment 37 species, including 21 rotifers, 3 copepods, 1 cladoceran and 12 other species, were identified. There were 24 species in common between water and corresponding sediments. Invertebrate OTU richness in water samples was higher than that in sediments (p < 0.01), while there was no significant difference in the Shannon-Wiener index. These results suggest that HTS is a promising alternative for efficient biodiversity assessment and monitoring.

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.

scholarly journals Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments

2020 ◽  
Vol 12 (9) ◽  
pp. 3624 ◽  
Author(s):  
Tatyana Tourova ◽  
Diyana Sokolova ◽  
Tamara Nazina ◽  
Denis Grouzdev ◽  
Eugeni Kurshev ◽  
...  
Keyword(s):  
Amino Acids ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Petrochemical Plant ◽  
Industrial Water ◽  
Aqueous Environments ◽  
The 16S Rrna Gene ◽  
Xenobiotic Degradation

The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater. Both communities have a high potential ability to carry out the carbohydrates and amino acids metabolism, but the potential for xenobiotic degradation, including styrene degradation, was relatively higher in the biofilms in industrial water. Bacteria of the genera Erythrobacter, Maribacter, and Mycobacterium were potential styrene-degraders in seawater, and Pseudomonas and Arenimonas in industrial water. Our results suggest that marine and industrial waters contain microbial populations potentially capable of degrading PS, and these populations may be used for the isolation of efficient PS degraders.

scholarly journals Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea

2015 ◽  
Author(s):  
Yue OO Hu ◽  
Bengt Karlson ◽  
Sophie Charvet ◽  
Anders F Andersson
Keyword(s):  
Baltic Sea ◽  
Deep Sequencing ◽  
High Throughput Sequencing ◽  
Salinity Gradient ◽  
Niche Partitioning ◽  
Freshwater Ecosystems ◽  
Marker Genes ◽  
Rrna Gene ◽  
The Baltic Sea ◽  
The Baltic

Microscopic plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but also novel groups to the Baltic were identified, such as relatives to the coccolithophore Emiliana huxleyi in the northern Baltic Sea. The deep sequencing also enabled accurate enumeration of highly resolved (> 99% identity) operational taxonomic units, which revealed contrasting distribution profiles among closely related populations, reflecting niche partitioning into ecotypes. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

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.

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