scholarly journals Rapid Changes in Microbial Community Structures along a Meandering River

2020 ◽  
Vol 8 (11) ◽  
pp. 1631
Author(s):  
Perrine Cruaud ◽  
Adrien Vigneron ◽  
Caetano C. Dorea ◽  
Manuel J. Rodriguez ◽  
Steve J. Charette
Keyword(s):  
River System ◽  
18S Rrna Gene ◽  
Lake Ecosystem ◽  
Rrna Gene ◽  
Strong Impact ◽  
River Channels ◽  
Community Structures ◽  
Meandering River ◽  
Lake Outlet ◽  
Organic Particles

Streams and rivers convey freshwater from lands to the oceans, transporting various organic particles, minerals, and living organisms. Microbial communities are key components of freshwater food webs and take up, utilize, and transform this material. However, there are still important gaps in our understanding of the dynamic of these organisms along the river channels. Using high-throughput 16S and 18S rRNA gene sequencing and quantitative PCR on a 11-km long transect of the Saint-Charles River (Quebec, CA), starting from its main source, the Saint-Charles Lake, we show that bacterial and protist community structures in the river drifted quickly but progressively downstream of its source. The dominant Operational Taxonomic Units (OTUs) of the lake, notably related to Cyanobacteria, decreased in proportions, whereas relative proportions of other OTUs, such as a Pseudarcicella OTU, increased along the river course, becoming quickly predominant in the river system. Both prokaryotic and protist communities changed along the river transect, suggesting a strong impact of the shift from a stratified lake ecosystem to a continuously mixed river environment. This might reflect the cumulative effects of the increasing water turbulence, fluctuations of physicochemical conditions, differential predation pressure in the river, especially in the lake outlet by benthic filter feeders, or the relocation of microorganisms, through flocculation, sedimentation, resuspension, or inoculation from the watershed. Our study reveals that the transit of water in a river system can greatly impact both bacterial and micro-eukaryotic community composition, even over a short distance, and, potentially, the transformation of materials in the water column.

scholarly journals Long-chain diols in rivers: distribution and potential biological sources

2018 ◽  
Vol 15 (13) ◽  
pp. 4147-4161 ◽  
Author(s):  
Julie Lattaud ◽  
Frédérique Kirkels ◽  
Francien Peterse ◽  
Chantal V. Freymond ◽  
Timothy I. Eglinton ◽  
...  
Keyword(s):  
River Flow ◽  
River System ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
River Systems ◽  
Eukaryotic Diversity ◽  
Fractional Abundance ◽  
Biological Sources ◽  
Rrna Gene Sequencing ◽  
Long Chain

Abstract. Long-chain diols (LCDs) occur widespread in marine environments and also in lakes and rivers. Transport of LCDs from rivers may impact the distribution of LCDs in coastal environments, however relatively little is known about the distribution and biological sources of LCDs in river systems. In this study, we investigated the distribution of LCDs in suspended particulate matter (SPM) of three river systems (Godavari, Danube, and Rhine) in relation with precipitation, temperature, and source catchments. The dominant long-chain diol is the C32 1,15-diol followed by the C30 1,15-diol in all studied river systems. In regions influenced by marine waters, such as delta systems, the fractional abundance of the C30 1,15-diol is substantially higher than in the river itself, suggesting different LCD producers in marine and freshwater environments. A change in the LCD distribution along the downstream transects of the rivers studied was not observed. However, an effect of river flow is observed; i.e., the concentration of the C32 1,15-diol is higher in stagnant waters such as reservoirs and during seasons with river low stands. A seasonal change in the LCD distribution was observed in the Rhine, likely due to a change in the producers. Eukaryotic diversity analysis by 18S rRNA gene sequencing of SPM from the Rhine showed extremely low abundances of sequences (i.e., < 0.32 % of total reads) related to known algal LCD producers. Furthermore, incubation of the river water with 13C-labeled bicarbonate did not result in 13C incorporation into LCDs. This indicates that the LCDs present are mainly of fossil origin in the fast-flowing part of the Rhine. Overall, our results suggest that the LCD producers in rivers predominantly reside in lakes or side ponds that are part of the river system.

Impacts of urbanization on river system structure: a case study on Qinhuai River Basin, Yangtze River Delta

2014 ◽  
Vol 70 (4) ◽  
pp. 671-677 ◽  
Author(s):  
Xiaomin Ji ◽  
Youpeng Xu ◽  
Longfei Han ◽  
Liu Yang
Keyword(s):  
River Basin ◽  
River System ◽  
Yangtze River Delta ◽  
System Structure ◽  
River Channels ◽  
Stream Structure ◽  
Impervious Area ◽  
The Status ◽  
Urbanized Areas ◽  
Qinhuai River

Stream structure is usually dominated by various human activities over a short term. An analysis of variation in stream structure from 1979 to 2009 in the Qinhuai River Basin, China, was performed based on remote sensing images and topographic maps by using ArcGIS. A series of river parameters derived from river geomorphology are listed to describe the status of river structure in the past and present. Results showed that urbanization caused a huge increase in the impervious area. The number of rivers in the study area has decreased and length of rivers has shortened. Over the 30 years, there was a 41.03% decrease in river length. Complexity and stability of streams have also changed and consequently the storage capacities of river channels in intensively urbanized areas are much lower than in moderately urbanized areas, indicating a greater risk of floods. Therefore, more attention should be paid to the urban disturbance to rivers.

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.

scholarly journals Crassicauda boopis in a fin whale (Balaenoptera physalus) ship-struck in the eastern North Atlantic Ocean

2017 ◽  
Vol 3 ◽  
Author(s):  
LAETITIA LEMPEREUR ◽  
MORGAN DELOBELLE ◽  
MARJAN DOOM ◽  
JAN HAELTERS ◽  
ETIENNE LEVY ◽  
...  
Keyword(s):  
North Atlantic ◽  
18S Rrna ◽  
North Atlantic Ocean ◽  
18S Rrna Gene ◽  
The Body ◽  
Rrna Gene ◽  
Balaenoptera Physalus ◽  
Fin Whale ◽  
Eastern North Atlantic ◽  
The Right

SUMMARY On 9 November 2015, a juvenile male fin whale of 11·60 m length was observed on the bulb of a merchant vessel in the Channel Terneuzen – Ghent (The Netherlands – Belgium). A severe parasitosis was present in the right heart ventricle and caudal caval vein. Parasites were identified as Crassicauda boopis based on macroscopic and microscopic observations. The sequence of the 18S rRNA gene obtained from the parasite samples was 100% similar to the sequence of the 18S rRNA gene from Crassicauda magna available on GenBank. While adults of C. boopis and C. magna are morphologically distinct and found at different locations in the body, the molecular analysis of the 18S rRNA gene seems insufficient for reliable species identification. Although numerous C. boopis were found, the cause of death was identified as due to the collision with the ship, as suggested by the presence of a large haematoma, and the absence of evidence of renal failure. The young age of this whale and the absence of severe chronic reaction may suggest that the infestation was not yet at an advanced chronic stage.

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