Best practices in metabarcoding of fungi: From experimental design to results

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(10), P. 2769 - 2795

Published: April 8, 2022

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety ecosystems. Here we provide an overview current best practices in metabarcoding analysis fungal communities, from experimental design through molecular computational analyses. By reanalysing published data sets, demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) recovering diversity, finding is particularly evident for long markers. Additionally, the full-length ITS region allows more accurate placement other eukaryotes compared ITS2 subregion. Finally, show specific methods compositional analyses reliable estimates shifts community structure. We conclude are especially promising integrating into full microbiome broader ecosystem functioning context, recovery novel lineages ancient organisms as well barcoding old specimens including type material.

Language: Английский

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To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

BMC Bioinformatics, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 5, 2021

The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment reads by denoising or clustering methods, which have been wrongly presented as alternatives. It has also suggested that denoised sequence variants should replace clusters basic unit analyses, missing fact are a proxy for species-level entities, in studies. We argue here methods developed and tested ribosomal markers uncritically applied highly variable cytochrome oxidase I (COI) without conceptual operational (e.g., parameter setting) adjustment. COI naturally high intraspecies variability be assessed reported, it is source valuable information. contend not Rather, they complementary both used together pipelines.Using dataset from benthic marine communities, we compared two procedures (based on UNOISE3 DADA2 algorithms), set suitable parameters clustering, these steps different orders. Our results indicated algorithm preserved higher intra-cluster variability. introduce program DnoisE implement taking into account natural (measured entropy) each codon position protein-coding genes. This correction increased number sequences retained 88%. order (denoising clustering) had little influence final outcome.We highlight need combining adequate choice stringency parameters, metabarcoding. present uses coding properties this marker improve step. recommend researchers report their terms (a haplotypes) formed species), avoid collapsing latter single representative. will allow at cluster (ideally equating diversity) level, ease additivity comparability between

Language: Английский

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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 24(5)

Published: Aug. 7, 2023

Abstract Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through require sophisticated processing of high‐throughput sequencing data from taxonomically informative barcodes. Various sets universal and taxon‐specific primers have been developed, extending the usability across archaea, bacteria eukaryotes. Accordingly, multitude analysis tools pipelines also developed. Often, several developed workflows are designed to process same amplicon data, making it somewhat puzzling choose one among plethora existing pipelines. each pipeline its own specific philosophy, strengths limitations, which should be considered depending on aims any study, well bioinformatics expertise user. In this review, we outline input requirements, supported operating systems particular attributes thirty‐two with goal helping users select their projects.

Language: Английский

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Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 289(1973)

Published: April 20, 2022

Increasing speed and magnitude of global change threaten the world's biodiversity particularly coral reef fishes. A better understanding large-scale patterns processes on reefs is essential to prevent fish decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding reconstruct well-known uncover hidden these highly diverse threatened ecosystems. We analysed 226 (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central Southwest Pacific, Coral Triangle Western Indian Ocean) compared those 2047 underwater visual censuses Reef Life Survey 1224 stations. Environmental reveals a higher (16%) biodiversity, with 2650 taxa, 25% more families than surveys. By identifying pelagic, reef-associated crypto-benthic species, eDNA offers fresh view assembly rules across spatial scales. Nevertheless, life survey identified species 47 shared families, which can be due incomplete sequence assignment, possibly combined detection environment, for some species. Combining extensive census novel insights organization richest marine

Language: Английский

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Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites

Environment International, Journal Year: 2023, Volume and Issue: 172, P. 107738 - 107738

Published: Jan. 6, 2023

The Anthropocene is characterized by dramatic ecosystem changes driven human activities. impact of these activities can be assessed different geochemical and paleontological proxies. However, each proxies provides only a fragmentary insight into the effects anthropogenic impacts. It highly challenging to reconstruct, with holistic view, state ecosystems from preindustrial period present day, covering all biological components, prokaryotes multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing trophic levels biodiversity reconstruct two century-natural history in Bagnoli-Coroglio (Gulf Pozzuoli, Tyrrhenian Sea), one most polluted marine-coastal sites Europe. site was seagrass meadows high eukaryotic diversity until beginning 20th century. Then, completely changed, seagrasses associated fauna as well diverse groups planktonic benthic protists being replaced low biota dominated dinophyceans infaunal metazoan species. sedaDNA analysis revealed five-phase evolution area, where appear result multi-level cascade effect impacts industrial activities, urbanization, water circulation land-use changes. allowed infer reference conditions that must considered when restoration actions are implemented.

Language: Английский

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Ecosystem type drives soil eukaryotic diversity and composition in Europe

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(19), P. 5706 - 5719

Published: July 14, 2023

Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited spatial scale. Here, we analyzed an unprecedented amount of observational data soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into impact wide range environmental conditions (climatic edaphic) community composition structure. We found that fungi, protists, rotifers, tardigrades, nematodes, arthropods, annelids was predominantly shaped by type (annual permanent croplands, managed unmanaged grasslands, coniferous broadleaved woodlands), higher observed croplands than less intensively systems, such as woodlands. Also more specialized eukaryotes, while between homogeneous compared other ecosystems. The high proportion overlapping taxa ecosystems also indicates DNA has accumulated from previous land uses, hence mimicking transformations occurring Europe last decades. This strong ecosystem-type influence linked properties, particularly, pH richness annelids, plant-available phosphorus drove nematodes. Furthermore, organic carbon total nitrogen ratio crucially explained possibly decades agricultural inputs. Our results highlighted importance long-term variables rather measured time sampling shaping communities, which reinforces need include those addition future monitoring programs conservation efforts.

Language: Английский

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Environmental DNA metabarcoding shows potential for monitoring meiofauna and marine nematodes diversity in mangrove ecosystems in China

Ecological Indicators, Journal Year: 2025, Volume and Issue: 170, P. 113134 - 113134

Published: Jan. 1, 2025

Language: Английский

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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: April 12, 2021

Abstract Despite representing one of the largest biomes on earth, biodiversity deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches careful choice environmental substrate. Here, we aimed to optimize genetic assessment prokaryote (16S), protistan (18S V4), metazoan V1–V2, COI) communities, by evaluating strategies sediment aboveground water, deployed simultaneously at deep-sea site. For sediment, while size-class sorting through sieving had no significant effect total detected alpha diversity resolved similar taxonomic compositions phylum level all markers studied, it effectively increased detection meiofauna phyla. large volumes obtained from an in situ pump (~ 6000 L) significantly more than 7.5 L collected boxes. However, being limited larger mesh sizes (> 20 µm), only captured a fraction microbial diversity, boxes allowed access pico- nanoplankton. More importantly, communities characterized water samples differed those whatever volume used, both sample types shared between 3 8% molecular units. Together, these results underline that may be recommended when targeting metazoans, does not represent alternative benthic diversity.

Language: Английский

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DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review

Frontiers in Marine Science, Journal Year: 2021, Volume and Issue: 8

Published: Sept. 30, 2021

Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous ecologically important inhabitants of benthic marine ecosystems. Their high species richness rapid response to environmental change make them promising targets for ecological biomonitoring studies. However, diversity patterns meiofauna remain poorly known due challenges identification using classical morphological methods. DNA metabarcoding is a powerful tool overcome this limitation. Here, we review approaches used studies on meiobenthos with the aim facilitating researchers informed decisions implementation meiofaunal biodiversity monitoring. We found that applied methods vary greatly studies, concluded further explicit comparisons protocols needed apply as standard assessing community composition. Key aspects require additional consideration include: (1) comparability sample pre-treatment methods; (2) integration different primers molecular markers both mitochondrial cytochrome c oxidase subunit I (COI) nuclear 18S rRNA genes maximize taxon recovery; (3) precise standardized description sampling allow comparison replication; (4) evaluation testing bioinformatic pipelines enhance By enhancing various currently analyses, will improve long-term integrative potential surveying meiofauna.

Language: Английский

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Assessment of benthic invertebrate diversity and river ecological status along an urbanized gradient using environmental DNA metabarcoding and a traditional survey method

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 806, P. 150587 - 150587

Published: Sept. 27, 2021

Language: Английский

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