Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 3270 - 3288

Опубликована: Авг. 11, 2020

With the growing anthropogenic pressure on marine ecosystems, need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding bulk samples is increasingly being implemented in ecosystem assessments and more cost-efficient less time-consuming than based morphology. However, before raw sequences are obtained from samples, a profound number methodological choices must be made. Here, we critically review recent methods used (including benthic, plankton diet samples) indicate how potential biases can introduced throughout sampling, preprocessing, extraction, marker primer selection, PCR amplification sequencing. From total 64 studies evaluated, our recommendations best practices include to (a) consider DESS as fixative instead ethanol, (b) use DNeasy PowerSoil kit any containing traces sediment, (c) not limit selection COI only, but preferably multiple markers higher taxonomic resolution, (d) avoid touchdown profiles, (e) fixed annealing temperature each pair when comparing across or institutes, (f) minimum three replicates, (g) both negative positive controls. Although implementation still faces several technical complexities, foresee wide-ranging advances near future, including improved bioinformatics assignment, sequencing longer fragments whole-genome information. Despite involved if appropriate controls included along data generation process, it clear that provides valuable tool assessments.

Язык: Английский

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DNA barcoding, an effective tool for species identification: a review

Molecular Biology Reports, Год журнала: 2022, Номер 50(1), С. 761 - 775

Опубликована: Окт. 29, 2022

Язык: Английский

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Towards a multisensor station for automated biodiversity monitoring

Basic and Applied Ecology, Год журнала: 2022, Номер 59, С. 105 - 138

Опубликована: Янв. 7, 2022

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts temperature, transformations land-use, or energy budget systems. While latter processes easily quantifiable, documentation loss biodiversity community structure is more difficult. Changes organismal abundance diversity barely documented. Censuses species usually fragmentary inferred often spatially, temporally ecologically unsatisfactory simple lists for individual study sites. Thus, detrimental global their drivers remain unrevealed. A major impediment to monitoring lack human taxonomic expertise that implicitly required large-scale fine-grained assessments. Another amount personnel associated costs needed cover scales, inaccessibility remote but nonetheless affected areas. To overcome these limitations we propose a network Automated Multisensor stations Monitoring Diversity (AMMODs) pave way new generation assessment centers. This combines cutting-edge technologies with informatics expert systems conserve knowledge. Each AMMOD station autonomous samplers insects, pollen spores, audio recorders vocalizing animals, sensors volatile organic compounds emitted plants (pVOCs) camera traps mammals invertebrates. AMMODs largely self-containing have ability pre-process data (e.g. noise filtering) prior transmission receiver storage, integration analyses. Installation on sites difficult access require sophisticated challenging system design optimum balance between power requirements, bandwidth transmission, service, operation under all environmental conditions years. An important prerequisite automated identification databases DNA barcodes, animal sounds, pVOCs, images used as training identification. thus become key component advance field research policy delivering at an unprecedented spatial temporal resolution.

Язык: Английский

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Future of DNA-based insect monitoring

Trends in Genetics, Год журнала: 2023, Номер 39(7), С. 531 - 544

Опубликована: Март 10, 2023

Язык: Английский

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Towards a global synthesis of Collembola knowledge: challenges and potential solutions

HAL (Le Centre pour la Communication Scientifique Directe), Год журнала: 2020, Номер unknown

Опубликована: Дек. 1, 2020

Collembola are among the most abundant and diverse soil microarthropods, which found in almost all (semi)terrestrial environments often serve as model organisms empirical studies. Diverse data collected on biology ecology of over last century waiting for synthesis studies, while developing technologies may facilitate generation new knowledge. research 2020 is entering stage global this opinion paper we address main challenges that community collembologists facing avenue. We first discuss present status social context taxonomy potential use novel to describe species. then focus aspects ecology, reviewing processes dispersal, environmental biotic filtering, from spatial scale microhabitat globe. also involvement ecosystem proxies, such functional traits, can be used predict roles Finally, provide recommendations how improve collection by using standard methods better handling practices. call (1) integrating morphological descriptions with high-resolution photographs genetic barcodes species user friendly software machine learning approaches deposition structured taxonomic knowledge web platforms; (2) multiscale studies biodiversity distribution processes, especially including dispersal mechanisms; (3) recording sharing functional, not only morphological, trait controlled experiments field surveys; (4) meta-analysis topics Collembola, conservation its diversity, feeding behaviour, protection mechanisms different species, effects land climate change collembolan communities; (5) joint efforts covering gaps knowledge, underexplored regions (predominantly tropics subtropics) methodologies; (6) integration open databases. believe could make ongoing changes society. To progress across these 2040, have established #GlobalCollembola, a distributed-effort community-driven initiative aims abundance, traits literature coordinate key gaps.

Язык: Английский

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DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

Microorganisms, Год журнала: 2021, Номер 9(2), С. 361 - 361

Опубликована: Фев. 12, 2021

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth health. Therefore, the identification, taxonomic characterization determination of role members soil microbial communities have become topics interest. The development continuous improvement high-throughput sequencing platforms further stimulated study complex microbiota soils plants. most frequently used approach to composition, diversity dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with subsequent amplicons. This methodological called DNA metabarcoding. Over last decade, metabarcoding has rapidly emerged as a powerful cost-effective method for description environmental samples. However, this involves several processing steps, each which might introduce significant biases that can considerably compromise reliability output. aim review provide state-of-the-art background knowledge needed make appropriate decisions at step workflow, highlighting crucial steps that, if considered, ensures an accurate standardized studies.

Язык: Английский

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Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data

Molecular Ecology Resources, Год журнала: 2021, Номер 21(6), С. 1772 - 1787

Опубликована: Янв. 27, 2021

Abstract Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation PCR and sequencing artefacts co‐amplification nuclear pseudogenes (NUMTs). The application read abundance thresholds denoising methods is efficient in reducing noise accompanying authentic amplicon sequence variants (ASVs). However, these procedures do not fully account for complex nature concomitant sequences highly variable DNA contribution specimens a metabarcoding sample. We propose, as complement to denoising, Multidimensional Abundance Threshold Evaluation ( metaMATE ) framework, novel approach that allows comprehensive examination multiple dimensions filtering evaluation prevalence unwanted denoised datasets. requires set ASVs input, designates subset being either (mitochondrial haplotypes) or nonauthentic (NUMTs erroneous sequences) comparison external reference data analysing nucleotide substitution patterns. (i) facilitates strategies, which are structured with regard library phylogeny applied range increasing threshold values, (ii) evaluates their performance quantifying collateral effects on removal ASVs. output from decision‐making about required stringency can used improve reliability intraspecific genetic information derived metabarcode data. framework implemented software (available at https://github.com/tjcreedy/metamate ).

Язык: Английский

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Optimizing insect metabarcoding using replicated mock communities

Methods in Ecology and Evolution, Год журнала: 2023, Номер 14(4), С. 1130 - 1146

Опубликована: Фев. 13, 2023

1: Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies its performance not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms presence-absence, abundances, biomass. 2: Here we use mock experiments simple probabilistic model evaluate effect different DNA extraction protocols on performance. Specifically, ask four questions: (Q1) How consistent are recovered profiles across replicate communities?; (Q2) does choice lysis buffer affect recovery original community?; (Q3) estimates affected by differing times homogenization?; (Q4) Is possible obtain adequate abundance through biological spike-ins? 3: We show that quite variable replicates. general, mild protocol better at reconstructing lists approximate counts, while homogenization retrieving biomass composition. Small insects more likely be detected lysates, some tough require detected. Results less replicates lysates than homogenates. Some associated with strong PCR amplification bias, which complicates reconstruction counts. spike-in data, determined roughly 40% standard error homogenates, 50% under ideal conditions. latter case, however, this often requires species-specific reference data generalizes 4: conclude non-destructive, approach shows highest promise presence/absence description community, also allowing future morphological or molecular work material. However, perform composition, particular

Язык: Английский

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From identification to forecasting: the potential of image recognition and artificial intelligence for aphid pest monitoring

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Июль 19, 2023

Insect monitoring has gained global public attention in recent years the context of insect decline and biodiversity loss. Monitoring methods that can collect samples over a long period time independently human influences are particular importance. While these passive collection methods, e.g. suction traps, provide standardized comparable data sets, required to analyze large number trapped specimens is high. Another challenge necessary high level taxonomic expertise for accurate specimen processing. These factors create bottleneck In this context, machine learning, image recognition artificial intelligence have emerged as promising tools address shortcomings manual identification quantification analysis such trap catches. Aphids important agricultural pests pose significant risk several crops cause economic losses through feeding damage transmission plant viruses. It been shown long-term migrating aphids using traps be used make, adjust improve predictions their abundance so viruses spreading more accurately predicted. With increasing demand alternatives conventional pesticide use crop protection, need predictive models growing, basis resistance development measure management. advancing climate change strong influence on total well peak occurrences within year. Using model organism, we demonstrate possibilities systematic potential future technical developments subsequent automated individuals case intelligent forecasting models. an example, show from static images (i.e. advances software). We discuss applications with regard automatic processing prediction

Язык: Английский

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Mitochondrial DNA as a Molecular Marker in Insect Ecology: Current Status and Future Prospects

Annals of the Entomological Society of America, Год журнала: 2021, Номер 114(4), С. 470 - 476

Опубликована: Апрель 22, 2021

Abstract Molecular techniques are powerful tools that can address many research problems in insect ecology. Mitochondrial DNA (mtDNA) is a widely used molecular marker. It easy to use and has favorable biological properties, such as near-neutrality, lack of recombination, clock-like evolutionary rate. However, there some issues involved when using mtDNA data population genetics, species delimitation, estimating the history populations species. Exceptions simplicity mitochondrial inheritance other limitations include small effective sizes, maternal inheritance, complex processes. Combining nuclear markers improve power test phylogenetic phylogeographic hypotheses. We review applications ecology conclude better understanding properties mitochondria essential for application mtDNA.

Язык: Английский

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