Consistent effects of independent domestication events on the plant microbiota

Current Biology, Journal Year: 2024, Volume and Issue: 34(3), P. 557 - 567.e4

Published: Jan. 16, 2024

The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence a the composition and abundance microbiota. We focused genus Phaseolus, which underwent four independent events within two species (P. vulgaris P. lunatus), providing multiple replicates process spanning thousands years. targeted Phaseolus seeds identify link between domesticated traits bacterial community as have been subject large consistent phenotypic changes during these events. seed communities representative accessions from subpopulations descended each event were analyzed under controlled field conditions. results showed that led similar signatures in independently populations, could be partially explained by selection for common phenotypes. Our therefore microbial offer avenues applying knowledge impact microbiota improve applications agriculture.

Language: Английский

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Three steps towards comparability and standardization among molecular methods for characterizing insect communities

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based large-scale monitoring, to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, provide three recommendations how harmonize efforts biodiversity assessment monitoring via metabarcoding: (i) should adopt use synthetic spike-ins, which will act as positive controls internal standards; (ii) consider using several markers through a multiplex polymerase chain reaction (PCR) approach; (iii) commit publication transparency all protocol-associated metadata standardized fashion. For (i), ready-to-use recipe cytochrome

Language: Английский

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eDNA for monitoring and conserving terrestrial arthropods: Insights from a systematic map and barcode repositories assessments

Insect Conservation and Diversity, Journal Year: 2024, Volume and Issue: 17(4), P. 565 - 578

Published: March 8, 2024

Abstract In the past decade, environmental DNA (eDNA) assays have become an essential tool to investigate species presence with samples from environment instead of collected specimens. eDNA sampling techniques proved their worth in freshwater and marine studies; now, some trends emerge for use terrestrial habitats particularly study arthropods. After a systematic review literature, we illustrate analyse diversity such studies discuss benefits drawbacks. We identified most relevant research themes focused on (i) taxa sample types targeted (ii) details survey scheme. parallel, also assessed available number sequences cytochrome c oxidase subunit I (COI), 16S 18S barcode regions four major (spiders, centipedes, springtails insects) relation diversity. found strong taxonomic geographic biases regarding coverage per barcode. arthropods mainly focuses insect that affect humanity positive or negative way, availability is much higher temperate‐developed countries than tropical ones. Moreover, although high variety are being used, do not assess completeness target nor compare efficacy monitoring technique other well established known traditional techniques. Careful workflow designs comparisons needed before giving any management conservation advice as does come without error. Strengths weaknesses discussed.

Language: Английский

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Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier study, since can be mass-trapped, mass-identified, and semi-mass-quantified into ‘many-row (observation), many-column (species)‘ datasets, with homogeneous error, high resolution, copious environmental-covariate information. These ‘novel community datasets’ let us efficiently generate information on arthropod species distributions, values, uncertainty, magnitude direction human impacts. We use a DNA-based method (barcode mapping) produce an arthropod-community dataset from 121 Malaise-trap samples, combine it 29 remote-imagery layers using deep neural net in joint distribution model. With this approach, we maps for 76 across 225 km 2 temperate-zone forested landscape. visualize fine-scale spatial distributions richness, composition, site irreplaceability. Old-growth forests show distinct composition higher stream courses have highest site-irreplaceability values. ‘sideways biodiversity modelling’ method, demonstrate feasibility mapping at sufficient resolution inform local management choices, while also being efficient enough scale up thousands square kilometres. article is part theme issue ‘Towards toolkit global insect monitoring’.

Language: Английский

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Metagenomics: an emerging tool for the chemistry of environmental remediation

Frontiers in Environmental Chemistry, Journal Year: 2023, Volume and Issue: 4

Published: May 9, 2023

Metagenomics is the study of genetic information, including sequences and genomes microorganisms present in an environment. Since 1998, full-scale application this technique to environmental chemistry has brought significant advances characterization nature chemical composition/distribution contaminants matrices contaminated and/or remediated sites. This been critical selection contributed significantly success biological treatment over years. gone through different phases development, which ranges from initial sequencing strategies next-generation (NGS), a recently developed technology obtain more robust deoxyribonucleic acid (DNA) profile devoid chimeric reduces quality metagenomic data. Therefore, objective review evaluate applications metagenomics understanding dynamics during remediation studies. Also, presents relationship between characteristics properties compounds, forms basis bioremediation could be useful developing predictive models that enhance efficiency. In conclusion, techniques have improved characterisation environment provides correlation for prediction type contaminant expected various matrices.

Language: Английский

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FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(7), P. e0286272 - e0286272

Published: July 19, 2023

Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers cost-effective relatively fast method characterizing community samples. However, the methodology applied varies greatly among studies, thus complicating design repeatable monitoring schemes. Here we describe non-destructive metabarcoding protocol that is optimized high-throughput processing Malaise trap samples other The details process from obtaining up to submitting libraries sequencing. It divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring wet-weight biomass concentration preservative performing lysis preserving material future work; 3) DNA extraction purification; 4) Library preparation relies on readily available reagents materials. For steps require expensive infrastructure, such as purification robots, suggest alternative low-cost solutions. use this yields assessment number species present given sample, their relative read abundances overall biomass. To date, successfully more than 7000 obtained Sweden Madagascar. We demonstrate data yield using small subset these

Language: Английский

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Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods

Metabarcoding and Metagenomics, Journal Year: 2023, Volume and Issue: 7

Published: Nov. 23, 2023

Biodiversity is declining at alarming rates worldwide and large-scale monitoring urgently needed to understand changes their drivers. While classical taxonomic identification of species time labour intensive, the combination with DNA-based methods could upscale activities achieve larger spatial coverage increased sampling effort. However, challenges remain for when number individuals per and/or biomass estimates are required. Several methodological advancements exist improve potential DNA metabarcoding abundance analysis, which however need further evaluation. Here, we discuss laboratory, as well some bioinformatic adjustments workflows regarding estimation from arthropod community samples. Our review includes pre-laboratory processing such specimen photography, laboratory use spike-in an internal standard like correction factors. We conclude that photography coupled currently promises greatest estimates, but approaches spike-ins factors promising pursue further.

Language: Английский

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The best of two worlds: toward large‐scale monitoring of biodiversity combining COI metabarcoding and optimized parataxonomic validation

Ecography, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 4, 2025

In a context of unprecedented insect decline, it is critical to have reliable monitoring tools measure species diversity and their dynamic at large‐scales. High‐throughput DNA‐based identification methods, particularly metabarcoding, were proposed as an effective way reach this aim. However, these methods are subject multiple technical limitations, resulting in unavoidable false‐positive false‐negative detection. Moreover, metabarcoding does not allow estimation abundance given sample, which key document detect population declines or range shifts large scales. To overcome obstacles, we propose here human‐assisted molecular (HAMI) approach, framework based on combination image‐based parataxonomic validation outputs recording abundance. We assessed the advantages using HAMI over exclusive use approach by examining 492 mixed beetle samples from biodiversity initiative conducted throughout France. On average, 23% missed when relying exclusively percent being consistently higher species‐rich samples. Importantly, 20% identified molecular‐only approaches correspond false positives linked cross‐sample contaminations mis‐identified barcode sequences databases. The methodologies significantly reduces intrinsic biases recovers data. This also enables users engage virtuous circle database improvement through specimens associated with missing incorrectly assigned barcodes. As such, fills important gap toolbox available for fast

Language: Английский

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Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It most commonly used for species identification, phylogenetic analysis expansion of reference libraries. GS can be applied single or composite DNA samples representing multiple species; the latter termed metagenome (MGS). GS/MGS shows promise effective approach environmental (eDNA) studies, but it currently limited ancient sedimentary samples. There potential expand this methodology other eDNA sources, including water, soil airborne In paper, we introduce briefly review its current applications. We discuss benefits challenges using assay eDNA. a promising technology could broaden studies if some methodological addressed.

Language: Английский

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No attenuation of fish and mammal biodiversity declines in the Guiana Shield

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 971, P. 179021 - 179021

Published: March 1, 2025

Real-time biodiversity monitoring should provide more resolved data to quantify shifts in ecological communities progressively altered by anthropogenic disturbances. Identifying trends requires a rapid and efficient inventory method that enables the collection delivery of high-resolution within short intervals. Using aquatic environmental DNA (eDNA), we investigated spatiotemporal changes fish mammal along Maroni River French Guiana. We compared spatial between two years, separated four-year interval, during which an increase disturbances was observed. To evaluate changes, examined impact these on both taxonomic functional diversity. Our findings revealed that, while did not result major decline, it continued drive alterations community richness. Communities underwent their structure, with experiencing decline extreme traits, lost redundancy generalist functions experienced reduction strategies. In context small-scale disturbances, highlight necessity long-term, short-interval capture reorganisation under stress.

Language: Английский

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