The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 954, P. 176200 - 176200
Published: Sept. 14, 2024
Language: Английский
Metabarcoding and Metagenomics, Journal Year: 2025, Volume and Issue: 9
Published: Jan. 10, 2025
DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready routine application. However, protocols methods still vary between within countries, limiting their transferability comparability results. In order to overcome this, use diatom requires knowledge sources variability introduced by different steps procedure. Here, we examine how elements procedures contribute European laboratories. A set four experiments were performed focusing on extraction PCR amplification evaluate reproducibility laboratories currently scientific community. Under guidance a reference laboratory, 17 participants from 14 countries in parallel, using same fixed protocol own choice protocol. Experiments each participant standardised biofilm samples (river, lake mock community) investigate potential systematic random errors. Our results revealed successful amongst labs highly similar consistent ecological assessment outcome obtained regardless used participant. We propose an “all one but prove them all” strategy, suggesting that distinct community, as long consistency is proven following minimum standard requirements.
Language: Английский
Citations
2
Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 510 - 510
Published: March 2, 2024
Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, field metagenomics has emerged as powerful tool for studying microbial communities associated cereal crops and their impact on plant health growth. This chapter aims to provide comprehensive overview its enhancing food through exploration beneficial pathogenic interactions. Furthermore, we will examine how integration other tools can effectively address adverse effects security. For this purpose, discuss metagenomic data machine learning providing novel insights into dynamic interactions shaping plant-microbe relationships. We also shed light potential applications leveraging diversity epigenetic modifications improving crop resilience yield sustainability. Ultimately, revolutionized by harnessing between microbiota, paving way sustainable agricultural practices.
Language: Английский
Citations
13
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 1, 2025
Abstract DNA metabarcoding has revolutionised our ability to characterise biodiversity at unprecedented spatial and temporal scales, outperforming most traditional methods for monitoring. However, is not without limitations, in particular regarding the quantitative relationship between sequence read abundances species numerical or biomass (i.e., performance). Variation copy numbers been often pinpointed as a potentially important factor biasing performance but empirical comparisons of number variation across remain rare. Here, we identify chloroplast (cpDNA CNV) plants that could impact studies. Using digital droplet PCR, quantified four common high Arctic plant two tissue types (green tissues roots). The amount cpDNA per unit dry mass varied by 3 (for roots) 7.6 green tissues) among species, up 67 when comparing root from same species. Despite significant differences both roots, pronounced were clearly tested. These findings suggest particularly can be an underestimated impacting reads abundance datasets. We call more extensive CNV referencing efforts wild-ranging improve use research
Language: Английский
Citations
0
Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown
Published: May 15, 2025
ABSTRACT DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species the extract. Here, we amplify sequence a mock community of known composition containing marine fishes cetaceans using four different primer sets variety conditions. We first compare observations two expected based on total genomic target mitochondrial template DNA. find that calibrating concentration most appropriate as it isolates amplification bias; calibration results be attributed both ratios then model remaining approximately 60% explained by inherent species‐specific characteristics. These include primer‐template mismatches, amplicon fragment length, GC content, vary somewhat across Taq polymerases. Finally, investigate how protocols influence regardless changing strongly templates mismatches. Our findings suggest pairs without mismatches targeting narrow taxonomic group yield more repeatable accurate estimates species' true, underlying proportions. identify key factors should considered when designing studies aim apply data quantitatively.
Language: Английский
Citations
0
The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 933, P. 172989 - 172989
Published: May 5, 2024
The study of trophic niche partitioning is great importance for understanding community structure and species coexistence, particularly if these are threatened. Here DNA metabarcoding was used to assess the diet four threatened steppe bird (two bustards two sandgrouses), with aim better their dietary requirements, interactions, potential threats. results showed seasonal interspecific differences in plant diet, greater cultivated plants during autumn winter (around 50 % diet) than spring. Plants genus Convolvulus family Brassicaceae were frequently consumed by all species. In spring, poppies (Papaver spp.) a considerable part could be as source carotenoids or anti-parasitic properties. Furthermore, evidenced among species, marked segregation between bustard and, lesser extent, sandgrouse Diet similarity generally higher from different orders that occur mixed-species flocks (bustard - sandgrouse) same order. This probably related stratification habitat use rather specialisation might prevent competition some extent. However, homogenization resources resulting agricultural intensification pose an important threat, autumn, when weeds scarcer most abundant resource sown seeds, which often treated pesticides.
Language: Английский
Citations
2
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)
Published: July 23, 2024
Abstract Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it challenging produce fast and accurate depiction of due methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative genes that may not correctly represent communities from environmental DNA assessed morphological methods. However, has the potential deliver descriptions provided interpreted validated species‐specific calibrations reference databases. Here, we developed quantitative approach retrieve data assemblages large benthic foraminifera (LBF), photosymbiotic calcifying protists, Indonesian coral reefs are under increasing anthropogenic pressure. To depict diversity, calculated taxon‐specific correction factors reduce biological biases by comparing surface area, biovolume calcite volume, number mitochondrial gene copies seven common LBF species. validate approach, compared calibrated datasets mock samples bulk reef sediment; both sample types were metabarcoded. The calibration significantly improved estimations genus abundance, difference ±5% on average, allowing for comparison past future molecular ones. Our results also highlight application our support monitoring operations capturing fine‐scale processes, such as seasonal pollution‐driven dynamics, require high‐throughput sampling treatment.
Language: Английский
Citations
1
The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 954, P. 176200 - 176200
Published: Sept. 14, 2024
Language: Английский
Citations
0