scholarly journals Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11619
Author(s):  
Jon T. Hestetun ◽  
Anders Lanzén ◽  
Thomas G. Dahlgren
Keyword(s):  
Sediment Sample ◽  
Benthic Communities ◽  
Alpha Diversity ◽  
Environmental Dna ◽  
Sampling Bias ◽  
Coi Gene ◽  
Morphological Identification ◽  
Sampling Station ◽  
Sediment Samples ◽  
Diversity Assessment

Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.

scholarly journals Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

2021 ◽  
Vol 8 ◽  
Author(s):  
Franck Lejzerowicz ◽  
Andrew John Gooday ◽  
Inés Barrenechea Angeles ◽  
Tristan Cordier ◽  
Raphaël Morard ◽  
...  
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Benthic Communities ◽  
Experimental Studies ◽  
Alpha Diversity ◽  
Environmental Dna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Data Resource ◽  
Dna And Rna

The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.

scholarly journals Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Parisa Soltan-Alinejad ◽  
Javad Rafinejad ◽  
Farrokh Dabiri ◽  
Piero Onorati ◽  
Olle Terenius ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Morphological Identification ◽  
Species Determination ◽  
Important Species ◽  
Mitochondrial Markers ◽  
12S Rdna ◽  
Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

scholarly journals Molecular Characterisation using 16S rRNA and COI Gene Sequences in Hard Ticks of Gwalior, India

2020 ◽  
Vol 5 (3) ◽  
pp. 173-179
Author(s):  
Pooja Ghosh ◽  
Sachin Tikar ◽  
Mahendra K. Gupta ◽  
D Sukumaran
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Tick Infestation ◽  
Rhipicephalus Sanguineus ◽  
Total Sample ◽  
Domestic Animals ◽  
Coi Gene ◽  
Morphological Identification ◽  
Surveillance Studies ◽  
Global Threat

Tick infestation in humans and animals represents a global threat for different tick-borne diseases. In the present study, the ticks from the Gwalior region of India have been mapped to create a database of tick diversity. We explored 773 ticks collected from domestic animals and vegetation in Gwalior. Animals were screened visually, and ticks were collected manually, whereas the flag-drag method was used to collect ticks from the vegetation. The 16S rRNA and cytochrome oxidase I (COI) genes of tick samples were amplified and purified for sequencing and respective phylogenetic trees were constructed. The ticks were morphologically identified using taxonomical keys, revealing the presence of five genera in the region: Hyalomma, Haemaphysalis, Rhipicephalus, Boophilus, and Nosomma. Hyalomma spp. (Hy. annatolicum and Hy. marginatum) were the most abundant accounting for 69.598% of the total sample, followed by Rhipicephalus sanguineus (17.335%), Rhipicephalus microplus (7.115%), Haemaphysalis sp. (5.692%), and Nosomma monstrotum (0.258%). The tick sequences were submitted to the GenBank database. Phylogenetic analysis confirmed the morphological identification at the species level. The combination of molecular and morphological analyses of the ticks supported the result obtained with each method, thus providing more reliable estimates for continued surveillance studies.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

scholarly journals Identification of Megaselia scalaris (Diptera : Phoridae) based on morphology and mitochondrial 16S rRNA and COI gene sequences

2016 ◽  
Vol 25 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Mohammad Shamimul Alam ◽  
Khandaker Asif Ahmed ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
Model Organism ◽  
Coi Gene ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
Mitochondrial Coi ◽  
Molecular Approaches ◽  
Megaselia Scalaris ◽  
Rrna Sequences

Megaselia scalaris (Diptera: Phoridae), commonly known as scuttle fly, is widely distributed all over the world. It is easily cultured in the laboratory condition making it a potential model organism. Besides, it has forensic importance. However, no report from Bangladesh could be retrieved about this fly. So, in the present study, identification of this species was attempted using both morphological and molecular approaches. Characteristics of male hypopygium and legs played key roles in morphological identification. To strengthen identification, mitochondrial COI and 16S rRNA gene fragments were amplified and sequenced. Blast search at NCBI provided highest hits to available COI and 16S rRNA sequences of M. scalaris. A neighbor joining phylogenetic tree was built using sequences of respective COI gene region to show its relationship among other closely related dipteran flies. Dhaka Univ. J. Biol. Sci. 25(2): 149-159, 2016 (July)

Analysis of Pesticide Residues by Chemical Derivatization. VI. Analysis of Ten Acid Herbicides in Sediment1

1983 ◽  
Vol 66 (4) ◽  
pp. 1023-1028
Author(s):  
Hing-Biu Lee ◽  
Alfred S Y Chau
Keyword(s):  
Sediment Sample ◽  
Detection Limits ◽  
Chemical Derivatization ◽  
Multiresidue Analysis ◽  
Organic Extract ◽  
Sediment Samples ◽  
Routine Monitoring ◽  
Liquid Chromatographic ◽  
Acid Herbicides ◽  
Better Than

Abstract A sensitive gas-liquid chromatographic (GLC) method was developed for multiresidue analysis of 10 acid herbicides in sediment. An acidified sediment sample was extracted 3 times with acetonehexane. The combined organic extract was partitioned with acidified water to remove aqueous coextractives. To produce low detection limits for all herbicides including MCPA and MCPB for routine monitoring purposes, pentaf luorobenzyl esters were formed before GLC analysis. Recoveries of all herbicides from fortified sediment samples were better than 80% at the levels studied. Practical detection limits of this method were 10-25 μg/kg (ppb).

scholarly journals Exploring unknown life stages of Arctic Tanytarsini (Diptera: Chironomidae) with DNA barcoding

Zootaxa ◽  
2011 ◽  
Vol 2743 (1) ◽  
pp. 27 ◽  
Author(s):  
ELISABETH STUR ◽  
TORBJØRN EKREM
Keyword(s):  
Dna Barcoding ◽  
Coi Gene ◽  
Morphological Identification ◽  
Life Stages ◽  
Larval Morphology ◽  
Gene Sequences ◽  
Larval Stages ◽  
Identification Keys ◽  
Close Resemblance ◽  
First Results

We present the first results from a project on Spitsbergen and Bear Island where the ultimate goal is to provide genetic and morphological identification keys to all species. Five Tanytarsini species have been recorded from Svalbard. By sequencing partial COI gene sequences, we have associated larvae of all of these, and describe the hitherto undescribed larval stages of Microspectra insignilobus Kieffer, M. radialis Goetghebuer and Tanytarsus heliomesonyctios Langton. We also present keys to larva, pupa and imagines of all Tanytarsini species found on Svalbard and discuss larval morphology in relationship to characters preserved in subfossil material. Of particular interest is the mandible and mentum of T. heliomsonyctios which show close resemblance to the tentatively associated larvae of Corynocera oliveri Lindeberg. An overview over Tanytarsus species with “lugens-type” larvae is given and the phylogenetic value of mandibular accessory teeth is briefly discussed.

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