Direct PCR meets high-throughput sequencing - metabarcoding of aquatic insect communities without DNA purification DOI Creative Commons
Nina Röder, Klaus Schwenk

Published: Feb. 23, 2023

Aquatic emergent insect communities form an important link between aquatic and terrestrial ecosystems, yet studying them is costly time-consuming as they are usually diverse superabundant. Metabarcoding a valuable tool to investigate arthropod community compositions, however high-throughput applications, such for biomonitoring, require cost-effective user-friendly procedures. To if the labour-intensive DNA purification step can be omitted in metabarcoding, we studied difference detection rates individual read abundance using standard versus direct PCR protocols. with without was performed artificially created of known composition well on natural both dipteran family Chironomidae compare rates, abundances presence-absence composition. We found that here presented novel approach metabarcoding did not alter had minor effect communities. Furthermore, compositions chironomid were highly comparable approaches. In conclusion, showed protocols applied approaches, possible application wider range taxa, enabling us study more efficiently future.

Language: Английский

Next‐generation species delimitation and taxonomy: Implications for biogeography DOI Creative Commons
Miguel Vences, Aurélien Miralles, Christophe Dufresnes

et al.

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(9), P. 1709 - 1722

Published: Feb. 13, 2024

Abstract An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, data are of importance species delimitation. We here review recent developments future perspectives direct relevance biogeographers. The understanding that independently evolving segments population‐level lineages, the rise integrative approaches to delimit such advent high‐throughput sequencing have considerably renewed discipline taxonomy. Using genome‐scale molecular datasets, extent admixture across hybrid zones can now be effectively assessed evolutionary independence lineages inferred, leading more reliable comparable delimitation criteria. Substantially divergent but admixing phylogeographical conveniently named as subspecies, thus avoiding taxonomic oversplitting inflation. At same time, comprehensive DNA barcoding metabarcoding efforts uncovering an enormous proportion undiscovered biotic diversity, we encourage development bioinformatic pipelines combine discovery with diagnosis scientific naming, approach a inventory globe without abandoning established Linnaean system.

Language: Английский

Citations

21
DNA barcodes of the vascular flora of the Altai Mountain Country: type material of the Herbarium ALTB DOI Creative Commons
А. В. Ваганов,

Tatyana A. Sinitsyna,

М. Г. Куцев

et al.

Turczaninowia, Journal Year: 2022, Volume and Issue: 25(4), P. 5 - 11

Published: Nov. 30, 2022

The article presents first data of the work on DNA barcoding type specimens ALTB Herbarium (Barnaul, Russia). Obtained sequences ITS and trnL-trnF, trnH-psbA markers were deposited in NCBI GenBank, corresponding dataset was published GBIF (Global Biodiversity Information Facility).

Language: Английский

Citations

54
Molecular technology in paleontology and paleobiology: Applications and limitations DOI
Ahmed Awad Abdelhady, Barbara Seuß, Sreepat Jain

et al.

Quaternary International, Journal Year: 2024, Volume and Issue: 685, P. 24 - 38

Published: Jan. 25, 2024

Language: Английский

Citations

5
A full‐length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing DOI Creative Commons
Chetan C. Gaonkar, Lisa Campbell

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(4)

Published: April 1, 2024

Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most have utilized short read sequences to assess protist diversity. One limitation of is the low resolution markers. For better taxonomic longer 18S rDNA required because full-length has both conserved and hypervariable regions. In this study, a new primer pair combination was used amplify its efficacy validated with test community then field samples. Full-length obtained Nanopore MinION for from samples were compared Illumina MiSeq V4 V8-V9 reads. Sequences generated high-throughput sequencers Amplicon Sequence Variants (ASVs). Metabarcoding results show high congruency among long reads in annotation at major group level; however, not all taxa could be successfully detected sequences. Based on criteria ≥95% similarity ≥1000 bp query length, 298 genera identified by markers samples, 250 (84%) 18S, while only 226 (76%) 213 (71%) V8-V9. Of total 85 dinoflagellate observed, 19 defined ASVs three 52 diatom genera. The discrepancy due lack taxonomically available reference particular dinoflagellates. Overall, preliminary investigation demonstrates that application approach can successful studies.

Language: Английский

Citations

5
Comparative Analysis of Pasture Composition: DNA Metabarcoding Versus Quadrat‐Based Botanical Surveys in Experimental Grassland Plots DOI Creative Commons
Hannah Vallin, Helen Hipperson, Jan Titěra

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: March 27, 2025

ABSTRACT DNA metabarcoding provides a scalable alternative to traditional botanical surveys, which are often time‐consuming and reliant on taxonomic expertise. Here, we compare with quadrat‐based surveys assess plant species composition in experimental grassland plots under four defoliation regimes (continuous grazing, rotational frequent cutting conservation cutting). Botanical identified 16 taxa, while detected 25 including the dominant Holcus lanatus Lolium perenne . Despite detecting more there were some discrepancies identification, sequence data only able resolve taxa at genus level (e.g., Agrostis spp. instead of capillaris ) potential misidentifications Cardaminopsis helleri vs. Cardamine flexuosa ). However, both methods provided comparable results revealed statistically significant differences between treatments, higher diversity cut versus grazed plots. The semi‐quantitative nature limits its capacity accurately reflect abundance, posing challenges for ecological interpretations where precise quantification is required. it broader view biodiversity can complement methods, offering new opportunities efficient monitoring. findings support integration into assessments, particularly when used alongside techniques. Further refinement bioinformatics tools reference databases will enhance their accuracy reliability, enabling effective monitoring sustainable management practices. This study highlights as valuable tool understanding community responses interventions.

Language: Английский

Citations

0
From Shell to Sequence: Optimizing DNA Extraction and PCR for Pen Shell Identification DOI Open Access
Maria Kamilari, Charikleia Papaioannou,

Antonios A. Augustinos

et al.

Water, Journal Year: 2025, Volume and Issue: 17(8), P. 1162 - 1162

Published: April 13, 2025

Pinna nobilis, an ecologically significant and critically endangered bivalve endemic to the Mediterranean Sea, has been classified as “Critically Endangered” by IUCN due habitat degradation, climate change, mass mortality events caused protozoan parasite Haplosporidium pinnae. Effective conservation efforts require robust molecular tools for species identification genetic monitoring, necessitating development of optimized DNA extraction amplification protocols a non-invasive sampling protocol. In this study, we evaluated multiple methods—Chelex-100, sodium chloride (NaCl) method, modified CTAB protocol, commercial kit, NucleoSpin Tissue Kit—using minute shell fragments from both ethanol-preserved air-dried (dead) samples. We key parameters, including incubation times, temperatures, sample preparation, determine most effective protocol obtaining high-quality suitable downstream applications. Additionally, assessed different PCR strategies, nested semi-nested approaches targeting COI gene marker, enhance identification. To further refine methodology, novel specific primers PCR, improving sensitivity specificity in detecting P. nobilis degraded Our results provide optimized, cost-effective, time-efficient workflow with broad implications genetics, biodiversity recovery programs.

Language: Английский

Citations

0
Machine learning algorithms accurately identify free-living marine nematode species DOI Creative Commons

Simone Brito de Jesus,

Danilo Cândido Vieira, Paula Foltran Gheller

et al.

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e16216 - e16216

Published: Oct. 9, 2023

Identifying species, particularly small metazoans, remains a daunting challenge and the phylum Nematoda is no exception. Typically, nematode species are differentiated based on morphometry presence or absence of certain characters. However, recent advances in artificial intelligence, machine learning (ML) algorithms, offer promising solutions for automating identification, mostly taxonomically complex groups. By training ML models with extensive datasets accurately identified specimens, can learn to recognize patterns nematodes' morphological morphometric features. This enables them make precise identifications newly encountered individuals. Implementing algorithms improve speed accuracy identification allow researchers efficiently process vast amounts data. Furthermore, it empowers non-taxonomists reliable identifications. The objective this study evaluate performance identifying free-living marine nematodes, focusing two well-known genera: Acantholaimus Allgén, 1933 Sabatieria Rouville, 1903.A total 40 60 were considered. measurements obtained from original publications both genera, compilation included information regarding specific characters, as well To assess four employed: Random Forest (RF), Stochastic Gradient Boosting (SGBoost), Support Vector Machine (SVM) linear radial kernels, K-nearest neighbor (KNN) algorithms.For random forest (RF) algorithm demonstrated highest correctly classifying specimens into their respective achieving an rate 93% 100% Sabatieria, only single individual test data was misclassified.These results highlight overall effectiveness identification. Moreover, demonstrates that nematodes be automated, optimizing biodiversity ecological studies, turning more accessible, efficient, scalable. Ultimately will contribute our understanding conservation biodiversity.

Language: Английский

Citations

7
Synthesis of Silver Nanoparticles from Ganoderma Species and Their Activity against Multi Drug Resistant Pathogens DOI

Iffraz Ali Syed,

Iqbal Ahmad Alvi, Muhammad Fiaz

et al.

Chemistry & Biodiversity, Journal Year: 2023, Volume and Issue: 21(4)

Published: Nov. 6, 2023

The widespread and indiscriminate use of broad-spectrum antibiotics leads to microbial resistance, which causes major problems in the treatment infectious diseases. However, advances nanotechnology using mushrooms have opened up new domains for synthesis nanoparticles against multidrug-resistant pathogens. Mushooms recently attracted attention are exploited food medicinal purposes. current study focuses on molecular identification, characterization biologically synthesized silver by X-ray diffraction (XRD) spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), UV-Vis spectroscopy scanning electron microscopy (SEM) antibacterial analysis extract (AgNPs) from Ganoderma resinaceum multidrug resistant microbes. Accurate identification is key utilizing them benefit humans. morphological time consuming, tedious may be prone error. Molecular techniques quick reliable tools that useful mushroom taxonomy. Blast results showed G. (GU451247) obtained Pakistan was 97 % same recognized China as well India. antimicrobial potential composite AgNPs high efficacy pathogenic Staphylococcus aureus (ZOI 23 mm) K. pneumonia 20 mm), Pseudomonas aeruginosa 24 E. fecalis A. baumannii 10 (MDR) mm). XRD evaluation revealed crystalline composition NPs with diameter 45 nm. obsorption peaked 589 nm confirmed presence AgNPs. SEM cubic morphology FTIR containing C=O (O=C-H) stretching hydrogen, carbonyl amide groups. promising minimum inhibitory concentration (MIC) at 2 mg MDR strains. observed efficient they need less quantities prevent bacterial growth. In view challenges developing variable shape size various other methods, tuning via can a wonderful approach resolve existing hurdles.

Language: Английский

Citations

7
Comparison of Metabarcoding Techniques for Dietary Assessment in Herbivores and Omnivores DOI Creative Commons

Nur Hartini Sariyati,

Hidayah Haris,

Farah Farhana Ramli

et al.

BIO Web of Conferences, Journal Year: 2024, Volume and Issue: 94, P. 01002 - 01002

Published: Jan. 1, 2024

Dietary assessment plays a crucial role in comprehending the ecological dynamics and nutritional needs of herbivores omnivores. The metabarcoding technique has emerged as potent tool for exploring dietary composition these animals. However, various techniques have been developed, each with its own advantages limitations. This study aims to compare performance different omnivores diet. We systematically reviewed 159 published manuscripts Scopus Google Scholar, thematic analysis was conducted across several categories, including marker, platform, database utilized. Preliminary findings reveal significant variations among two animal groups. trnL gene exhibited higher taxonomic resolution herbivorous species, whereas combination 'trnL + 16s rRNA' superior omnivorous species. Illumina platform most commonly used method analyzing diets both omnivores, primary reference being National Centre Biotechnology Information (NCBI). offers valuable insights into strengths limitations optimizing protocols, facilitating more precise reliable diet analyses within

Language: Английский

Citations

1
DNA Barcoding and its Applications DOI
Gholamreza Abdi,

Shubhi Singh,

Sahithya Selvakumar

et al.

Published: Jan. 1, 2024

Language: Английский

Citations

1