scholarly journals The protistan microplankton community along the Kuroshio Current revealed by 18S rRNA gene clone analysis: a case study of the differences in distribution interplay with ecological variability

2014 ◽  
Vol 9 (2) ◽  
pp. 71-82 ◽  
Author(s):  
Sau Pin Kok ◽  
Kenji Tsuchiya ◽  
Kosei Komatsu ◽  
Tatsuki Toda ◽  
Norio Kurosawa
Keyword(s):  
18S Rrna ◽  
Kuroshio Current ◽  
18S Rrna Gene ◽  
Gene Clone ◽  
Rrna Gene ◽  
Ecological Variability ◽  
Clone Analysis ◽  
The Kuroshio

scholarly journals Diversity and community dynamics of protistan microplankton in Sagami Bay revealed by 18S rRNA gene clone analysis

2012 ◽  
Vol 7 (2) ◽  
pp. 75-86 ◽  
Author(s):  
Sau Pin Kok ◽  
Tomohiko Kikuchi ◽  
Tatsuki Toda ◽  
Norio Kurosawa
Keyword(s):  
18S Rrna ◽  
Community Dynamics ◽  
18S Rrna Gene ◽  
Gene Clone ◽  
Rrna Gene ◽  
Sagami Bay ◽  
Clone Analysis

Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

Polar Biology ◽  
2008 ◽  
Vol 32 (1) ◽  
pp. 93-103 ◽  
Author(s):  
Fei Tian ◽  
Yong Yu ◽  
Bo Chen ◽  
Huirong Li ◽  
Yu-Feng Yao ◽  
...  
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Clone ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Eukaryotic Diversity ◽  
Arctic Sediment

scholarly journals Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

2020 ◽  
Author(s):  
Lukáš Pecina ◽  
Peter Vďačný
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Molecular Analyses ◽  
Ciliate Species ◽  
The Family ◽  
Geometrical Data ◽  
Geometrical Information

The endozoic ciliates of the family Clevelandellidae Kidder, 1938 typically inhabit the hindgut of wood-feeding panesthiine cockroaches. To assess the consistency of species delimitation in clevelandellids, we tested the utility of three sources of taxonomic data: morphometric measurements, cell geometrical information, and 18S rRNA gene sequences. The morphometric and geometrical data delimited the clevelandellid morphospecies consistently and unambiguously. However, only Paraclevelandia brevis Kidder, 1937 represented a homogenous taxon in both morphological and molecular analyses; the morphospecies Clevelandella constricta (Kidder, 1937) and C. hastula (Kidder, 1937) contained two or three distinct, more or less closely related genotypes each; and the genetic homogeneity of the morphospecies C. panesthiae (Kidder, 1937) and C. parapanesthiae (Kidder, 1937) was not corroborated by the 18S rRNA gene sequences at all. Moreover, the 18S rRNA gene phylogenies suggested the C. panesthiae-like morphotype to be the ancestral phenotype from which all other clevelandellid morphotypes arose. The only exception was the C. constricta-like morphotype, which very likely branched off before the diversification of the C. panesthiae-like progenitor. The present molecular analyses also suggested that a huge proportion of the clevelandellid diversity still waits to be discovered, since examination of only four panesthiine populations revealed 10 distinct clevelandellid genotypes/molecular species.

scholarly journals Eukaryotic communities in wastewater treatment processes as revealed by 18S rRNA gene clone library

2012 ◽  
Vol 68 (7) ◽  
pp. III_13-III_19
Author(s):  
Kengo MATSUNAGA ◽  
Kengo KUBOTA ◽  
Erica VONASEK ◽  
Yasuyuki TAKEMURA ◽  
Hideki HARADA
Keyword(s):  
Wastewater Treatment ◽  
Clone Library ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Clone ◽  
Rrna Gene ◽  
Treatment Processes

scholarly journals Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claire Y. T. Wang ◽  
Emma L. Ballard ◽  
Zuleima Pava ◽  
Louise Marquart ◽  
Jane Gaydon ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Plasmodium Falciparum ◽  
18S Rrna ◽  
Drug Efficacy ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Qpcr Assay ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Blood Samples

Abstract Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.

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 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

scholarly journals Molecular Characterization of Ciliate Diversity in Stream Biofilms

2008 ◽  
Vol 74 (6) ◽  
pp. 1740-1747 ◽  
Author(s):  
Andrew Dopheide ◽  
Gavin Lear ◽  
Rebecca Stott ◽  
Gillian Lewis
Keyword(s):  
18S Rrna ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Sequence Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Specific Pcr ◽  
Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

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