scholarly journals Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany

2021 ◽  
Vol 9 (4) ◽  
pp. 714
Author(s):  
Ekaterina Pushkareva ◽  
Veronika Sommer ◽  
Israel Barrantes ◽  
Ulf Karsten
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Cyanobacterial Community ◽  
Specific Primers ◽  
Ecological Functions ◽  
Detailed Assessment ◽  
The 16S Rrna Gene

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.

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 Phylogenetic information of freshwater copepod (Diaptomus sicilis) with special reference to 18S rRNA

2016 ◽  
Vol 4 (1) ◽  
pp. 25 ◽  
Author(s):  
Gomathi Jeyam Mookkaiah ◽  
Ramanibai Ravichandran
Keyword(s):  
Tamil Nadu ◽  
18S Rrna ◽  
Molecular Data ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Calanoid Copepods ◽  
Universal Primer ◽  
Pcr Products ◽  
The Individual

<p>In the present investigation to isolate freshwater calanoid copepods (<em>Diaptomus sicilis</em>) was characterized and identify the organisms by 18S rRNA sequencing. Plankton samples containing <em>D. sicilis</em> were collected during January 2014 (Post-monsoon) from Madippakkam Lake (12°57'41"N80°11'27"E) Chennai, Tamil Nadu. Immediately after sampling, specimens for genetic analyses were fixed in 95% ethyl alcohol. The total DNA was extracted from the individual copepod <em>D. sicilis</em> using Qiagen Blood tissue kit. The nuclear small subunit 18S rRNA gene was amplified using the Universal primer LCO —1490 (5’-GGTCAACAAATCATAAAGATATTGG-3’) and HCO-2198 (5’-TAAACTTCAGGGTGACCAAAAAATCA-3’). PCR products were loaded onto a 1% TAE agarose gel. Sequences were carried out an automated sequencer. The nucleotide sequence of 1282 base pair region of 18S rRNA was determined for D. sicilis. The similarity of sequences of <em>D. sicilis</em> was retrieved by BLASTn pro­gram and maximum identity and E-value was 76% and 0.00, respectively. The PCR products of <em>D. sicilis</em> individuals showed 80% similarity with the partial nuclear small subunit 18S rRNA gene region of other calanoid copepods. Based on molecular data the freshwater Calanoid copepods showed different algorithms and similar types of topologies useful for designing molecular analyses using phylogeny tree construction.Present molecular stud­ies on the relationship of D. sicilis with other freshwater calanoid copepods indicate that this species is close to <em>D. castor</em> followed by <em>D. keniraensis</em><em>.</em></p>

scholarly journals Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities

2008 ◽  
Vol 74 (9) ◽  
pp. 2814-2821 ◽  
Author(s):  
Katja Metfies ◽  
Linda K. Medlin
Keyword(s):  
In Situ Hybridization ◽  
Secondary Structure ◽  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rrna Molecule ◽  
The 16S Rrna Gene

ABSTRACT DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.

scholarly journals Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e87624 ◽  
Author(s):  
Kenan Hadziavdic ◽  
Katrine Lekang ◽  
Anders Lanzen ◽  
Inge Jonassen ◽  
Eric M. Thompson ◽  
...  
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Specific Primers

scholarly journals Molecular Identification and Phylogenetic Analysis of Heterakis dispar Isolated from Geese

2019 ◽  
Vol 64 (4) ◽  
pp. 753-760
Author(s):  
Kamila Bobrek ◽  
Joanna Hildebrand ◽  
Joanna Urbanowicz ◽  
Andrzej Gaweł
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Parasitic Infection ◽  
Its Region ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ascaridia Galli ◽  
Heterakis Gallinarum ◽  
Pcr Product

Abstract Purpose Heterakidosis is a common parasitic infection caused in domestic birds by Heterakis species: Heterakis gallinarum, H. isolonche, and H. dispar. Among them, the best described species is H. gallinarum, noted mainly in gallinaceous birds. In waterfowl, H. dispar is the predominant species. The variations in morphology and host specificity qualify H. dispar as a different species, but the phylogenetic relationships between heterakids were unclear for a long time, because of a lack of H. dispar sequences. Methods The authors provided the molecular data for H. dispar and analyzed the obtained sequences of the partial 18S rRNA gene and region ITS1-5.8SrRNA-ITS2 with the homological sequences. Results The 18S rRNA PCR product of H. dispar was about 800 bp, and the ITS-5.8S-ITS2 PCR product was about 920 bp, noticeably smaller size compared to H. gallinarum product. The BLAST analysis of H. dispar 18S sequence showed a 99% similarity with the sequences of Heterakis gallinarum and Ascaridia galli, 98% with A. nymphii, but only 94% with the sequence of Heterakis sp. Our ITS sequence of H. dispar was almost identical to the H. isolonche isolate, there is only one nucleotide of difference among the 943 sites analyzed. It also showed a lower similarity to the ITS sequences of H. gallinarum (88%), H. spumosa (87%), and H. dahomensis (87%). Conclusions In our phylogenetic analysis, it is the first attempt at the reconstruction of relationships within this superfamily Heterakoidea based on 18S rDNA and ITS region.

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.

Morphological and molecular characterisation of Xiphinema ifacolum Luc, 1961 (Nematoda: Longidoridae) from Sri Lanka

Nematology ◽  
2018 ◽  
Vol 20 (10) ◽  
pp. 925-937 ◽  
Author(s):  
Solomia Susulovska ◽  
Carolina Cantalapiedra-Navarrete ◽  
Andrij Susulovsky ◽  
Pablo Castillo ◽  
Antonio Archidona-Yuste
Keyword(s):  
Sri Lanka ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Group 4 ◽  
Sao Tome And Principe

Summary Females and juveniles from a population of Xiphinema ifacolum from Sri Lanka are described based on morphology, morphometrics and molecular analyses. Morphologically, females and juveniles from Sri Lanka are similar to original descriptions and other reports from Brazil, Cameroon, Liberia, and São Tomé and Príncipe. The identity of the species was also confirmed by 18S rRNA gene sequences deposited in NCBI from Brazil (AY297826). Integrative diagnosis was completed with molecular data using D2-D3 expansion segments of 28S rRNA, ITS1 region, partial 18S-rRNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). This is the third molecular characterisation for a species of the X. non-americanum Group 4, after X. oleae and X. tica. The use of different ribosomal and mitochondrial markers in this study, particularly, D2-D3, ITS1 and partial coxI, provided a precise and unequivocal tool for the identification of X. ifacolum and contributes to a better knowledge of the diversity within Xiphinema. Morphospecies Group 4 appears to be a paraphyletic group within the X. non-americanum assemblage.

scholarly journals Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Qiu-Fang Zhang ◽  
Hendrikus J Laanbroek
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Condensed Tannins ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Marsh Soil ◽  
Salt Marsh Soil ◽  
The 16S Rrna Gene

ABSTRACT Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.

Sign in / Sign up

Export Citation Format

Share Document