Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(2)

Published: Nov. 28, 2023

Abstract The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, future directions the field. Key research areas include understanding drivers microbiome community assembly, linking composition to host genetics, exploring microbial functions, transience spatial partitioning, disentangling non‐bacterial components microbiome. Methodological such as quantifying absolute abundances, sequencing complete genomes, utilizing novel statistical approaches, are also useful tools for complex diversity patterns. Our aims encourage robust practices studies inspire researchers explore next frontier this rapidly changing

Language: Английский

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Comparing diversity and structure of freshwater fish assemblages using environmental DNA and gillnetting methods: A case study of a large deep reservoir in East China

Ecological Indicators, Journal Year: 2024, Volume and Issue: 166, P. 112538 - 112538

Published: Aug. 27, 2024

Language: Английский

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Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT The detection of environmental DNA (eDNA) has revolutionized aquatic species monitoring, yet interpreting eDNA data remains challenging due to gaps in our understanding ecology (i.e., origin, state, transport, and fate) variability how methods are applied across the literature. A crucial aspect complexity is that a heterogeneous mix components vary size other properties, thereby influencing interactions with environment diverse ways. In this study, we explore interplay between three particle sizes (the physical dimension eDNA‐containing particles) two molecule lengths (DNA base pairs) flowing water systems. Specifically, elucidated mechanisms governing removal different using set 24 recirculating mesocosms where varied light substrate conditions. Consistent previous observations, findings revealed substantial differences small large particles. biofilm‐colonized substrate, found higher rates for smaller particles, but larger particles were removed more quickly presence any substrate. Importantly, also biofilm removes longer molecules faster, shedding on probable mechanism underlying longstanding association biofilm. Despite colonization faster molecules, analyzed (86 387 exhibited somewhat consistent behavior. combination, observations highlight an important predictor fate, fate shows few varying lengths. Furthermore, work suggests conclusions regarding from studies utilizing short markers applicable metabarcoding applications, which typically use marker

Language: Английский

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Active or passive? A multi-marker approach to compare active and passive eDNA sampling in riverine environments

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 974, P. 179247 - 179247

Published: March 29, 2025

Language: Английский

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Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics

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

Published: April 1, 2025

Environmental DNA (eDNA) metagenomics sequences all molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels false positives negatives, this approach is underexplored as a tool for biodiversity monitoring across tree life, particularly non-microscopic eukaryotes. We SeqIDist, framework that combines multilocus BLAST matches against several reference databases followed by an analysis sequence identity distribution patterns disentangle while revealing new increasing accuracy metagenomic approaches. tested SeqIDist on eDNA dataset riverine site compared results those obtained with metabarcoding benchmarking purposes. start characterising biological community (~2000 taxa) life at low taxonomic show higher sensitivity than discovering diversity. limited representation whole genome can lead positives. For eukaryotes, data often consist few sparse, anonymous scattered genome, making metagenome assembly methods unfeasible. Finally, we infer source residency time using read length distributions measure decay status. The opens discussion archived its implementation long-term planetary scale.

Language: Английский

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Parameterizing the particle size distribution of environmental DNA provides insights into its improved availability from the water

Environmental Monitoring and Assessment, Journal Year: 2025, Volume and Issue: 197(5)

Published: April 8, 2025

Language: Английский

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Vertical distribution of free and multi-fraction environmental DNA in a controlled aquatic system: insights into dispersal dynamics and sampling implications

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

Published: April 10, 2025

Language: Английский

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Spatial dispersal of environmental DNA particles in lentic and marine ecosystems: An overview and synthesis

Ecological Indicators, Journal Year: 2025, Volume and Issue: 174, P. 113469 - 113469

Published: April 15, 2025

Language: Английский

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Metabarcoding Versus Species‐Specific Primers to Estimate Salmo trutta Biomass and Density in Mountain Streams

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) is a cost‐efficient, noninvasive method to monitor fish populations, but the quantitative aspect of this technique (e.g., estimating biomass or densities) remains underexplored. Few studies have established relationships between concentration and biomass/density. Here, we investigate relationship eDNA (copies per liter) trout densities estimated by electrofishing in mountain streams Picos de Europa National Park (Spain). We assessed effectiveness inferring biomass/density using 18S rRNA (18S) cytochrome c oxidase I (COI) metabarcoding, PCR with COI‐specific Salmo trutta primer, each performed different datasets from same sampling points. Salmonidae positively correlates density. Both specific‐COI markers showed significant increase as density rose surveys. However, general COI did not exhibit relationships, despite providing greater taxonomic resolution at species level. Further analysis exploring biomass/densities across size classes (fry, juvenile, adult) revealed that juvenile contributed most observed concentration–biomass/density relationship. Our results suggest when an appropriately selected can reliably indicate these where dominant species. Although similar trends, it had lower explanatory power. This study highlights importance integrating framework metabarcoding for ecological monitoring biodiversity assessments. Factors such amplicon length, genetic region, marker specificity, class influence sequencing reads data. methodology could aid conservation management populations other communities, though further research needed extend assess detection reliability.

Language: Английский

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Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems

Ecological Indicators, Journal Year: 2023, Volume and Issue: 156, P. 111171 - 111171

Published: Oct. 31, 2023

Language: Английский

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