scholarly journals Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates

2021 ◽  
Vol 5 ◽  
Author(s):  
Barbara R. Leite ◽  
Pedro E. Vieira ◽  
Jesús S. Troncoso ◽  
Filipe O. Costa
Keyword(s):  
Marine Species ◽  
Artificial Substrates ◽  
Species Detection ◽  
Dna Metabarcoding ◽  
Marker Loci ◽  
Single Marker ◽  
Reference Sequences ◽  
Taxonomic Assignments ◽  
Taxonomic Groups ◽  
The Impact

DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the efficiency of two different marker loci (COI and 18S) and three primer pairs in marine species detection through DNA metabarcoding of the macrozoobenthic communities colonizing three types of artificial substrates (slate, PVC and granite), sampled between 3 and 15 months of deployment. To accurately compare detection success between markers, we also compared the representativeness of the detected species in public databases and revised the reliability of the taxonomic assignments. Globally, we recorded extensive complementarity in the species detected by each marker, with 69% of the species exclusively detected by either 18S or COI. Individually, each of the three primer pairs recovered, at most, 52% of all species detected on the samples, showing also different abilities to amplify specific taxonomic groups. Most of the detected species have reliable reference sequences in their respective databases (82% for COI and 72% for 18S), meaning that when a species was detected by one marker and not by the other, it was most likely due to faulty amplification, and not by lack of matching sequences in the database. Overall, results showed the impact of marker and primer applied on species detection ability and indicated that, currently, if only a single marker or primer pair is employed in marine zoobenthos metabarcoding, a fair portion of the diversity may be overlooked.

scholarly journals Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection

2021 ◽  
Vol 5 ◽  
Author(s):  
Laure Van den Bulcke ◽  
Annelies De Backer ◽  
Bart Ampe ◽  
Sara Maes ◽  
Jan Wittoeck ◽  
...  
Keyword(s):  
Rare Species ◽  
Monitoring Methods ◽  
General Belief ◽  
Species Detection ◽  
Methodological Choices ◽  
Pooled Dna ◽  
Dna Metabarcoding ◽  
Low Diversity ◽  
Cost Efficient ◽  
The Impact

DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos.

scholarly journals Alien Marine Species in the Mediterranean - the 100 ‘Worst Invasives’ and their Impact

2006 ◽  
Vol 7 (1) ◽  
pp. 87 ◽  
Author(s):  
N. STREFTARIS ◽  
A. ZENETOS
Keyword(s):  
Alien Species ◽  
Common Ground ◽  
Marine Species ◽  
Management Approach ◽  
Entire Area ◽  
Diffi Cult ◽  
The Mediterranean ◽  
Marine Alien Species ◽  
Taxonomic Groups ◽  
The Impact

A number of marine alien species have been described as invasive or locally invasive in the Mediterranean because of their proliferation, and/or their geographical spread and/or impact on native populations. Based on that information and on the documented impact they have on the biodiversity and socioeconomics of the basin, a preliminary list of the 100 ‘worst’ Invasive Alien Species (IAS) in the Mediterranean has been produced and presented in this work along with details on their impact. Emphasis is given to their impact on socioeconomics (fi sheries/aquaculture, health & sanitation, infrastructure & building), documented for 43 species. Such selection of the ‘worst’ IAS was diffi cult and controversial and is expected to attract much attention and scientifi c criticism since not only can the documentation of the impact of IAS be controversial, but also their inventory can be biased towards the effort and resources devoted to the study of the impact of certain species/taxonomic groups. Thus, while marine plants (phytobenthos and phytoplankton) are fairly well studied, less attention has been paid to the impact of vertebrates and even less to invertebrates. Nevertheless, the list highlights the need for continued research on the issue (monitoring aliens and their impact for an integrated ecosystem based management approach over the entire area). The preliminary list can provide the basis for selecting indicator species within the Mediterranean and thus be the common ground to build cooperation about IAS within countries in the region.

scholarly journals Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

2017 ◽  
Author(s):  
Zhemin Zhou ◽  
Nina Luhmann ◽  
Nabil-Fareed Alikhan ◽  
Christopher Quince ◽  
Mark Achtman
Keyword(s):  
Evaluation Studies ◽  
Species Level ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Reference Databases ◽  
Microbial Strains ◽  
Taxonomic Assignments ◽  
Taxonomic Groups ◽  
Reference Genomes ◽  
Recent Evaluation

AbstractExploring the genetic diversity of microbes within the environment through metagenomic sequencing first requires classifying these reads into taxonomic groups. Current methods compare these sequencing data with existing biased and limited reference databases. Several recent evaluation studies demonstrate that current methods either lack sufficient sensitivity for species-level assignments or suffer from false positives, overestimating the number of species in the metagenome. Both are especially problematic for the identification of low-abundance microbial species, e. g. detecting pathogens in ancient metagenomic samples. We present a new method, SPARSE, which improves taxonomic assignments of metagenomic reads. SPARSE balances existing biased reference databases by grouping reference genomes into similarity-based hierarchical clusters, implemented as an efficient incremental data structure. SPARSE assigns reads to these clusters using a probabilistic model, which specifically penalizes non-specific mappings of reads from unknown sources and hence reduces false-positive assignments. Our evaluation on simulated datasets from two recent evaluation studies demonstrated the improved precision of SPARSE in comparison to other methods for species-level classification. In a third simulation, our method successfully differentiated multiple co-existing Escherichia coli strains from the same sample. In real archaeological datasets, SPARSE identified ancient pathogens with ≤ 0.02% abundance, consistent with published findings that required additional sequencing data. In these datasets, other methods either missed targeted pathogens or reported non-existent ones. SPARSE and all evaluation scripts are available at https://github.com/zheminzhou/SPARSE.

COMT in major depression - UK candidate gene association study

2011 ◽  
Vol 26 (S2) ◽  
pp. 813-813
Author(s):  
A. Schosser ◽  
M.Y. Ng ◽  
A.W. Butler ◽  
S. Cohen-Woods ◽  
N. Craddock ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Major Depression ◽  
Unipolar Depression ◽  
Candidate Gene Association ◽  
Genetic Overlap ◽  
Haplotypic Association ◽  
Single Marker ◽  
Icd 10 ◽  
System 1 ◽  
The Impact

Catechol-O-methyltransferase (COMT) has a central role in brain dopamine, noradrenalin and adrenalin signaling, and has been suggested to be involved in the pathogenesis and pharmacological treatment of affective disorders. The functional single nucleotide polymorphism (SNP) in exon 4 (Val158Met, rs4680) influences the COMT enzyme activity. The Val158Met polymorphism is a commonly studied variant in psychiatric genetics, and initial studies in schizophrenia and bipolar disorder presented evidence for association with the Met allele. In unipolar depression, while some of the investigations point at an association between the Met/Met genotype and others have found a link between the Val/Val genotype and depression, most of the studies cannot detect any difference in Val158Met allele frequency between depressed individuals and controls.In the present study, we further elucidated the impact of COMT polymorphisms including the Val158Met in MDD. We investigated 1,250 subjects with DSM-IV and/or ICD-10 diagnosis of major depression (MDD), and 1,589 control subjects from UK. A total of 24 SNPs spanning the COMT gene were successfully genotyped using the Illumina HumaHap610-Quad Beadchip (22 SNPs), SNPlex™ genotyping system (1 SNP), and Sequenom MassARRAY® iPLEX Gold (1 SNP). Statistical analyses were implemented using PASW Statistics18, FINETTI (http://ihg.gsf.de/cgi-bin/hw/hwa1.pl), UNPHASED version 3.0.10 program and Haploview 4.0 program.Neither single-marker nor haplotypic association was found with the functional Val158Met polymorphism or with any of the other SNPs genotyped. Our findings do not provide evidence that COMT plays a role in MDD or that this gene explains part of the genetic overlap with bipolar disorder.

Eco Friendly Lighting Options for Offshore Installations and Related Design Challenges

2021 ◽  
Author(s):  
Sathishkumar Pragasam
Keyword(s):  
Migratory Birds ◽  
Feeding Habits ◽  
Reproductive Function ◽  
Marine Species ◽  
Offshore Structures ◽  
Marine Animals ◽  
Artificial Lighting ◽  
Migratory Flight ◽  
Offshore Installations ◽  
The Impact

Abstract The impact of artificial lighting on birds and animals has been a subject of research for many decades. These studies have established that light pollution from offshore facilities result in disturbing effects on migratory birds and marine animals. It is understood from the various studies that light emanating from offshore structures attract birds at night and disorient them during their migratory flight. As they are distracted from their flight path, they are either found trapped by the light that they keep circling around the installations or make them to take shelter in the installations, ultimately making them miss their migratory journey. This results in reduced winter survival and reduced reproduction success. Many birds are also found to die eventually because of bird strike or by getting themselves incinerated in flares. Congregation of birds in offshore installations also lead to risks related to helicopter landing / take-off. It is also observed that artificial light attracts marine species like turtles and fishes, which result in adverse effects like alteration of feeding habits, impacted circadian rhythm and interference with their reproductive function. From the knowledge of aforementioned disruptive effects of artificial lighting, significant efforts have been made to develop lighting systems for offshore installations that are eco-friendly. Various means of mitigating the undesirable effects of artificial lighting in offshore installations are being tried in the last couple of decades.

Evidence-Based Decision Making to Underpin the Thresholds in New Zealand's Craft Risk Management Standard: Biofouling on Vessels Arriving to New Zealand

2017 ◽  
Vol 51 (2) ◽  
pp. 76-88 ◽  
Author(s):  
Eugene Georgiades ◽  
Daniel Kluza
Keyword(s):  
Risk Management ◽  
New Zealand ◽  
Best Management Practices ◽  
Management Practices ◽  
Marine Species ◽  
Evidence Based ◽  
Management Standard ◽  
Antifouling Coatings ◽  
Slime Layer ◽  
Taxonomic Groups

AbstractVessel biofouling is a significant pathway for the introduction of nonindigenous marine species (NIMS). New Zealand is the first nation to regulate the vessel biofouling pathway, with controls scheduled to come into force in May 2018. The Craft Risk Management Standard (CRMS): Biofouling on Vessels Arriving to New Zealand specifies the hull fouling thresholds that vessels must meet; and here, we present the evidence-based decisions that underpin these thresholds.Under the CRMS, a vessel must arrive in New Zealand with a “clean hull,” the thresholds for which are governed by the intended duration of a vessel's stay in New Zealand. For example, long-stay (≥21 days) vessels must meet a more stringent standard of hull cleanliness due to the increased likelihood of release and establishment of NIMS. While setting a clean hull threshold at “slime layer only” can be tractable when vessels operate within the specifications of antifouling coatings, incidental amounts of macrofouling can establish even under the best management practices. Because of such instances, the thresholds within the CRMS were designed to allow for the presence of some macrofouling species, albeit with restrictions to minimize biosecurity risk. These thresholds are intended to limit species richness and to prevent successful reproduction and settlement of the allowed taxonomic groups while considering the practicality and feasibility of implementation.The difficulties of managing biofouling on different areas of the hull are acknowledged within these thresholds. For example, a greater tolerance of macrofouling has been allowed for niche areas due to the difficulties in preventing biofouling on these areas.

scholarly journals Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

2020 ◽  
Vol 8 ◽  
Author(s):  
Zacchaeus G. Compson ◽  
Beverly McClenaghan ◽  
Gregory A. C. Singer ◽  
Nicole A. Fahner ◽  
Mehrdad Hajibabaei
Keyword(s):  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Individual Species ◽  
Biodiversity Assessment ◽  
Occupancy Models ◽  
Widespread Adoption ◽  
Sampling Protocols ◽  
Dna Metabarcoding ◽  
Global Biodiversity ◽  
Taxonomic Groups

Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.

scholarly journals Ground-truthing Phylotype Assignments for Antarctic Invertebrates

DNA Barcodes ◽  
2017 ◽  
Vol 5 (1) ◽  
pp. 1-13
Author(s):  
Paul Czechowski ◽  
Laurence Clarke ◽  
Alan Cooper ◽  
Mark Stevens
Keyword(s):  
18S Rdna ◽  
High Throughput Sequencing ◽  
Antarctic Soils ◽  
Reference Information ◽  
Artificial Dna ◽  
Terrestrial Habitats ◽  
Ground Truthing ◽  
Taxonomic Assignments ◽  
Taxonomic Groups ◽  
Biodiversity Information

AbstractBiodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, hence DNA-based metabarcoding methods are well suited for their study. We compared taxonomy assignments of a high throughput sequencing metabarcoding approach using one ribosomal DNA (18S rDNA) and one mitochondrial DNA (cytochrome c oxidase subunit I - COI) marker with morphological reference data. Specifically, we compared metabarcoding or morphological taxonomic assignments on multiple taxonomic levels in an artificial DNA blend containing Australian invertebrates, and in seven extracts of Antarctic soils containing known micro-faunal taxa. Avoiding arbitrary application of metabarcoding analysis parameters, we calibrated those parameters with metabarcoding data from non-Antarctic soils. Metabarcoding approaches employing 18S rDNA and COI markers enabled detection of small and cryptic Antarctic invertebrates, and on low taxonomic ranks 18S data outperformed COI data in this respect. Morphological taxonomy determination did not outperform metabarcoding approaches. Our study demonstrates how barcoding markers can be tested prior to their application to specific taxonomic groups, and that taxonomy fidelity of markers needs to be validated in relation to environment, taxa, and available reference information.

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