scholarly journals DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review

2021 ◽  
Vol 8 ◽  
Author(s):  
Romy Gielings ◽  
Maria Fais ◽  
Diego Fontaneto ◽  
Simon Creer ◽  
Filipe Oliveira Costa ◽  
...  
Keyword(s):  
Rrna Genes ◽  
Biodiversity Monitoring ◽  
Standard Tool ◽  
Dna Metabarcoding ◽  
High Species Richness ◽  
Pre Treatment ◽  
18S Rrna Genes ◽  
Key Aspects ◽  
Response To Environmental Change

Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous and ecologically important inhabitants of benthic marine ecosystems. Their high species richness and rapid response to environmental change make them promising targets for ecological and biomonitoring studies. However, diversity patterns of benthic marine meiofauna remain poorly known due to challenges in species identification using classical morphological methods. DNA metabarcoding is a powerful tool to overcome this limitation. Here, we review DNA metabarcoding approaches used in studies on marine meiobenthos with the aim of facilitating researchers to make informed decisions for the implementation of DNA metabarcoding in meiofaunal biodiversity monitoring. We found that the applied methods vary greatly between researchers and studies, and concluded that further explicit comparisons of protocols are needed to apply DNA metabarcoding as a standard tool for assessing benthic meiofaunal community composition. Key aspects that require additional consideration include: (1) comparability of sample pre-treatment methods; (2) integration of different primers and molecular markers for both the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 18S rRNA genes to maximize taxon recovery; (3) precise and standardized description of sampling methods to allow for comparison and replication; and (4) evaluation and testing of bioinformatic pipelines to enhance comparability between studies. By enhancing comparability between the various approaches currently used for the different aspects of the analyses, DNA metabarcoding will improve the long-term integrative potential for surveying and biomonitoring marine benthic meiofauna.

scholarly journals PriSeT: Efficient De Novo Primer Discovery

2020 ◽  
Author(s):  
Marie Hoffmann ◽  
Michael T. Monaghan ◽  
Knut Reinert
Keyword(s):  
De Novo ◽  
Dna Barcode ◽  
Rrna Genes ◽  
Reference Database ◽  
Homologous Sequence ◽  
Dna Metabarcoding ◽  
Primer Sets ◽  
18S Rrna Genes ◽  
Eukaryotic Organisms ◽  
Freshwater Plankton

AbstractMotivationDNA metabarcoding is a commonly applied technique used to infer the species composition of environmental samples. These samples can comprise hundreds of organisms that can be closely or very distantly related in the taxonomic tree of life. DNA metabarcoding combines polymerase chain reaction (PCR) and next-generation sequencing (NGS), whereby a short, homologous sequence of DNA is amplified and sequenced from all members of the community. Sequences are then taxonomically identified based on their match to a reference database. Ideally, each species of interest would have a unique DNA barcode. This short, variable sequence needs to be flanked by relatively conserved regions that can be used as primer binding sites. Appropriate PCR primer pairs would match to a broad evolutionary range of taxa, such that we only need a few to achieve high taxonomic coverage. At the same time however, the DNA barcodes between primer pairs should be different to allow us to distinguish between species to improve resolution. This poses an interesting optimization problem. More specifically: Given a set of references ℛ = {R1, R2, …, Rm}, the problem is to find a primer set P balancing both: high taxonomic coverage and high resolution. This goal can be captured by filtering for frequent primers and ranking by coverage or variation, i.e. the number of unique barcodes. Here we present the software PriSeT, an offline primer discovery tool that is capable of processing large libraries and is robust against mislabeled or low quality references. It tackles the computationally expensive steps with linear runtime filters and efficient encodings.ResultsWe first evaluated PriSeT on references (mostly 18S rRNA genes) from 19 clades covering eukaryotic organisms that are typical for freshwater plankton samples. PriSeT recovered several published primer sets as well as additional, more chemically suitable primer sets. For these new sets, we compared frequency, taxon coverage, and amplicon variation with published primer sets. For 11 clades we found de novo primer pairs that cover more taxa than the published ones, and for six clades de novo primers resulted in greater sequence (i.e., DNA barcode) variation. We also applied PriSeT to 19 SARS-CoV-2 genomes and computed 114 new primer pairs with the additional constraint that the sequences have no co-occurrences in other taxa. These primer sets would be suitable for empirical testing.Availabilityhttps://github.com/mariehoffmann/[email protected]

scholarly journals A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations

2018 ◽  
Vol 115 (48) ◽  
pp. 12229-12234 ◽  
Author(s):  
Joan Cáliz ◽  
Xavier Triadó-Margarit ◽  
Lluís Camarero ◽  
Emilio O. Casamayor
Keyword(s):  
High Elevation ◽  
Rrna Genes ◽  
Source Tracking ◽  
Seasonal Patterns ◽  
Air Mass ◽  
Back Trajectories ◽  
Long Term Ecological Research ◽  
Airborne Microbes ◽  
18S Rrna Genes

Airborne microbes (bacteria, archaea, protists, and fungi) were surveyed over a 7-y period via high-throughput massive sequencing of 16S and 18S rRNA genes in rain and snow samples collected fortnightly at a high-elevation mountain Long-Term Ecological Research (LTER) Network site (LTER-Aigüestortes, Central Pyrenees, Spain). This survey constitutes the most comprehensive mountain-top aerobiology study reported to date. The air mass origins were tracked through modeled back-trajectories and analysis of rain water chemical composition. Consistent microbial seasonal patterns were observed with highly divergent summer and winter communities recurrent in time. Indicative microbial taxa were unveiled as a forensic signature, and ubiquitous taxa were observed as common atmosphere inhabitants, highlighting aerosols as a potentially successful mechanism for global microbial dispersal. Source-tracking analyses identified freshwater, cropland, and urban biomes as the most important sources for airborne bacteria in summer, while marine and forest biomes prevailed in winter, in agreement with air mass retrotrajectories and the prevailing general and regional atmospheric circulation.

EELS characterization of “Smut” layer films on steel surface prepared for chrome plating by anodic etching

1995 ◽  
Vol 53 ◽  
pp. 538-539
Author(s):  
E Y. Wang ◽  
J. T. Cherian ◽  
A. Madsen ◽  
R. M. Fisher
Keyword(s):  
Steel Surface ◽  
Surface Preparation ◽  
Treatment Method ◽  
Chrome Plating ◽  
Transmission Electron ◽  
Alloy Steels ◽  
Pre Treatment ◽  
Hard Chrome ◽  
Electron Energy Loss

Many steel parts are electro-plated with chromium to protect them against corrosion and to improve their wear-resistance. Good adhesion of the chrome plate to the steel surface, which is essential for long term durability of the part, is extremely dependent on surface preparation prior to plating. Recently, McDonnell Douglas developed a new pre-treatment method for chrome plating in which the steel is anodically etched in a sulfuric acid and hydrofluoric acid solution. On carbon steel surfaces, this anodic pre-treatment produces a dark, loosely adhering material that is commonly called the “smut” layer. On stainless steels and nickel alloys, the surface is only darkened by the anodic pre-treatment and little residue is produced. Anodic pre-treatment prior to hard chrome plating results in much better adherence to both carbon and alloy steels.We have characterized the anodic pre-treated steel surface and the resulting “smut” layer using various techniques including electron spectroscopy for chemical analysis (ESCA) on bulk samples and transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) on stripped films.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

scholarly journals An Overview of DNA-Based Applications for the Assessment of Benthic Macroinvertebrates Biodiversity in Mediterranean Aquatic Ecosystems

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 112
Author(s):  
Eftychia Tzafesta ◽  
Francesco Zangaro ◽  
Valeria Specchia ◽  
Maurizio Pinna
Keyword(s):  
Benthic Macroinvertebrates ◽  
Aquatic Ecosystems ◽  
Biodiversity Monitoring ◽  
Biodiversity Data ◽  
Management Tools ◽  
Aquatic Biodiversity ◽  
Current State ◽  
Dna Metabarcoding ◽  
Ecosystem Condition ◽  
Macroinvertebrate Species

The loss of aquatic biodiversity is increasing at a rapid rate globally. There is a worldwide effort to protect, preserve and restore aquatic ecosystems. For efficient biodiversity monitoring and reliable management tools, comprehensive biodiversity data are required. The abundance and species diversity of benthic macroinvertebrates are commonly used as indicators of the aquatic ecosystem condition. Currently, macroinvertebrate species biodiversity assessment is based on morpho-taxonomy, which could be enhanced by recent advances in DNA-based tools for species identification. In particular, DNA metabarcoding has the potential to identify simultaneously many different taxa in a pool of species and to improve aquatic biomonitoring significantly, especially for indicator species. This review is focused on the current state of DNA-based aquatic biomonitoring using benthic macroinvertebrates in the Mediterranean region.

Volume reduction of produced water generated from natural gas production process using membrane technology

2000 ◽  
Vol 41 (10-11) ◽  
pp. 117-123 ◽  
Author(s):  
C. Visvanathan ◽  
P. Svenstrup ◽  
P. Ariyamethee
Keyword(s):  
Natural Gas ◽  
Produced Water ◽  
Hollow Fibre ◽  
Gas Production ◽  
Oil And Grease ◽  
Natural Gas Production ◽  
Pre Treatment ◽  
Selection Of ◽  
Spiral Wound

This paper presents a case study of a natural gas production site covering various technical issues related to selection of an appropriate Reverse Osmosis (RO) system. The long-term field experience indicates the necessity of the selection of appropriate pretreatment systems for fouling-free RO operational conditions. The produced water has a variety of impurities such as oil and grease, process chemicals used for corrosion and scaling control, and dehydration of natural gas, etc. This situation leads to a complicated and extremely difficult task for a membrane specialist to design RO systems, especially the pre-treatment section. Here as part of the pretreatment selection, two types of UF membrane modules viz. spiral wound and hollow fibre, with MWCO of 8000 and 50,000 Dalton respectively, were tested in parallel with NF membranes of the spiral wound type with MWCO 200 Dalton. The UF permeate is used as feed for RO compatibility testing. Both configurations of UF failed to be compatible, due to irreversible fouling of the RO membrane. The NF membrane, however, showed interesting results, due to membrane stability in terms of cleaning and fouling. The NF plant with 50% capacity gave a recovery of 75% and the RO plant gave a recovery of 60% versus the expected 92–95%. The long-term tests have indicated that the reminder of the membranes could be installed to achieve full capacity of the plant. This study also demonstrates the importance of selection of proper pre-treatment set-up for the RO system design.

scholarly journals Eucaryotic Diversity in a Hypersaline Microbial Mat

2007 ◽  
Vol 74 (1) ◽  
pp. 329-332 ◽  
Author(s):  
Leah M. Feazel ◽  
John R. Spear ◽  
Alicia B. Berger ◽  
J. Kirk Harris ◽  
Daniel N. Frank ◽  
...  
Keyword(s):  
18S Rrna ◽  
Microbial Mat ◽  
Rrna Genes ◽  
Clone Libraries ◽  
18S Rrna Genes

ABSTRACT To determine the eucaryotic diversity of the hypersaline Guerrero Negro microbial mat, we amplified 18S rRNA genes from DNA extracted from this mat and constructed and analyzed clone libraries. The extent of eucaryotic diversity detected was remarkably low, only 15 species among 890 clones analyzed. Six eucaryotic kingdoms were represented, as well as a novel cluster of sequences. Nematode sequences dominated the clone libraries.

scholarly journals Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 189
Author(s):  
Kinga Kęska ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska ◽  
Małgorzata Czernicka
Keyword(s):  
Stress Tolerance ◽  
De Novo ◽  
Average Length ◽  
Marker Genes ◽  
Long Term Memory ◽  
Low Oxygen ◽  
Waterlogging Tolerance ◽  
Pre Treatment ◽  
Waterlogging Treatment

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.

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