scholarly journals Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250645
Author(s):  
Vinod Kumar ◽  
Sabah Al Momin ◽  
Vanitha V. Kumar ◽  
Jasim Ahmed ◽  
Lamya Al-Musallam ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
18S Rrna ◽  
Biological Diversity ◽  
Marine Ecosystem ◽  
Distribution Patterns ◽  
Arid Environment ◽  
18S Rrna Gene ◽  
Anthropogenic Factors ◽  
Rrna Gene

The microbial communities play a crucial role in ecosystem functioning through interactions among individuals and taxonomic groups in a highly dynamic marine ecosystem. The structure and functioning of the microbial communities are often influenced by the changes in the surrounding environment. Monitoring the microbial diversity of the marine ecosystem helps to understand spatial patterns of microbial community and changes due to season, climate, and various drivers of biological diversity. Kuwait is characterized by an arid environment with a high degree of temperature variation during summer and winter. Our understanding of spatial distribution patterns of microbial communities, their diversity, and the influence of human activities on the degree of changes in the diversity of the microbial community in Kuwait territorial waters remain unclear. In this study, we employed 18S rRNA sequencing to explore marine microalgal community composition and dynamics in seawater samples collected from Kuwait waters over two seasonal cycles across six locations. A total of 448,184 sequences across 36 replicates corresponding to 12 samples from six stations were obtained. The quality-filtered sequences were clustered into 1,293 representative sequences, which were then classified into different eukaryotic taxa. This study reveals that the phytoplankton community in Kuwait waters is diverse and shows significant variations among different taxa during summer and winter. Dinoflagellates and diatoms were the most abundant season-dependent microalgae taxa in Kuwait waters. Alexandrium and Pyrophacus were abundant in summer, whereas Gonyaulax was abundant during the winter. The abundance of Coscinodiscus and Navicula, of the diatom genera, were also dependent upon both seasonal and possible anthropogenic factors. Our results demonstrate the effectiveness of a sequencing-based approach, which could be used to improve the accuracy of quantitative eukaryotic microbial community profiles.

scholarly journals Gastrointestinal Segments Influenced Fermentation End-Products, Microbiota and Microbial Abundances in Goats

2021 ◽  
Author(s):  
Tsegay Gebremariam ◽  
Zhiliang Tan
Keyword(s):  
Fatty Acids ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Copies ◽  
End Products ◽  
The Impact

Abstract Purpose: Carbohydrate diets altered fermentation end-products and microbial community in the gastrointestinal tracts (GIT) of goats. Gastrointestinal contents used to determine the impact of carbohydrate feeds on fermentation end-products and microbial community in goats.Methodology: in the study goats were assigned to one of the two treatments corn meal (CM) or Corn gluten (CG) in a randomized block design (400 g/kg DM each). Goats were slaughtered, GIT liquids were used to determine dissolved gasses, fatty acids and microbial community.Results: Goats fed CG increased molar acetate (P < 0.05), lowered butyrate and propionate in the fore and hindgut comparing to those goats received CM. Goats received CM had higher (P < 0.05) dH2 while lowered dH2S in the fore and hindgut than those goats fed with CG treatment. The fore and hindgut had higher (P < 0.01) 16S rRNA gene copies of bacteria, protozoa, methanogens and 18S rRNA gene copies fungi than in the ileum and cecum. Goats fed CG diet had higher (P < 0.05)16S rRNA gene copies of bacteria, protozoa, methanogens, and 18S rRNA gene copies of fungi than those goats fed with CM diet. Conclusion fore and hindguts improved dissolved gasses, fatty acids and microbial community comparing with in the ileum and cecum. Goats fed CM had improved the Methanobacterials order and Methanobrevibacter genus as compared with those goats fed CG. The study suggested that hindgut segments have a reasonable contribution as foregut to methane emissions from goats.

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 Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽  
2021 ◽  
Vol 6 (5) ◽  
pp. 44
Author(s):  
Jae-Hyun Lim ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Sampling Site ◽  
Community Change ◽  
Rrna Gene ◽  
Water Column Stratification ◽  
Metagenomics Data ◽  
Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

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 Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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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