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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Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Microbial Biotechnology, Journal Year: 2024, Volume and Issue: 17(1)

Published: Jan. 1, 2024

Abstract Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic built on genome‐scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher complex interactions occurring among species. Model reconstruction increasingly relies metagenomics, which permits direct characterisation naturally communities that may contain organisms cannot be isolated or cultured. In this review, we provide an overview field modelling its increasing reliance synergy with metagenomics bioinformatics. We survey assigning reconstructing networks from (meta‐)genomes, present variety mathematical fundamentals foster dynamics. emphasise scaling model construction large communities, two important bottlenecks in applicability these models. give current state art metagenome sequencing bioinformatics analysis, focusing genomes Metagenomics benefits tremendously third‐generation sequencing, discuss opportunities long‐read strain‐level eukaryotic metagenomics. aim at providing algorithmic support, together tool application resources, permit bridging gap between modelling.

Language: Английский

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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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A new flow path: eDNA connecting hydrology and biology

Wiley Interdisciplinary Reviews Water, Journal Year: 2024, Volume and Issue: 11(6)

Published: July 29, 2024

Abstract Environmental DNA (eDNA) has revolutionized ecological research, particularly for biodiversity assessment in various environments, most notably aquatic media. analysis allows non‐invasive and rapid species detection across multiple taxonomic groups within a single sample, making it especially useful identifying rare or invasive species. Due to dynamic hydrological processes, eDNA samples from running waters may represent broad contributing areas, which is convenient biomonitoring perspective but also challenging, as knowledge required meaningful biological interpretation. Hydrologists could benefit address unsolved questions, concerning water movement through catchments. While naturally occurring abiotic tracers have advanced our understanding of age distribution catchments, example, current geochemical cannot fully elucidate the timing flow paths landscapes. Conversely, tracers, owing their immense diversity interactions with environment, offer more detailed information on sources stream. The informational capacity tracer, however, determined by ability interpret complex heterogeneity at study site, arguably requires both expertise. As data become increasingly available part campaigns, we argue that accompanying surveys observations enhance processes; identify opportunities, challenges, needs further interdisciplinary collaboration; highlight eDNA's potential bridge between hydrology biology, foster domains. This article categorized under: Science Water > Hydrological Processes Methods Life Nature Freshwater Ecosystems

Language: Английский

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Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities

Annals of Microbiology, Journal Year: 2024, Volume and Issue: 74(1)

Published: Aug. 10, 2024

Abstract Background High-throughput sequencing of the full-length 16S rRNA gene has improved taxonomic classification prokaryotes found in natural environments. However, shorter regions from same gene, like V4-V5 region, can provide more cost-effective high throughput. It is unclear which approach best describes prokaryotic communities underexplored In this study, we hypothesize that high-throughput combined with adequate databases improves description environments comparison a short region gene. Results To test our hypothesis, compared profiles seawater samples Arctic Ocean using: and combination either Genome Taxonomy Database (GTDB) or Silva taxonomy database. Our results show all combinations strategies present similar at higher levels. lower levels, namely family, genus, most notably species level, led to proportions Amplicon Sequence Variants (ASVs) assigned formally valid taxa. Hence, was obtained by GTDB combination, some cases allowed for identification intraspecific diversity ASVs. Conclusions We conclude coupling microbiome profiling ranks. The improvements reported here context scientists discuss microbial community dynamics within solid framework still underrepresented sequences public databases.

Language: Английский

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16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases

Italian Journal of Food Safety, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 16, 2025

The 16S rRNA metabarcoding, based on Next-Generation Sequencing (NGS), is used to assess microbial biodiversity in various matrices, including food. process involves a "dry-lab" phase where NGS data are processed through bioinformatic pipelines, which finally rely taxonomic unit assignment against reference databases assign them at order, genus, and species levels. Today, several public genomic available for the of sequences. In this study, 42 insect-based food products were chosen as models find out how database choice could affect microbiome results matrices. At same time, study aims evaluate most suitable composition these still poorly investigated products. V3-V4 region was sequenced by Illumina technology, R package “DADA2” analysis. After bibliographic search, three (SILVA, RDP, NCBI RefSeq) compared amplicon sequence variant (ASV) percentages different levels diversity indices. SILVA assigned significantly higher percentage ASVs family genus RefSeq RDP. However, no significant differences noted between according α β results. A total 121 genera identified, with 56.2% detected all databases, though some taxa identified only one or two. highlights importance using updated accurate characterization, contributing optimization metabarcoding analysis microbiota studies, novel foods.

Language: Английский

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A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020

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

Published: Jan. 31, 2025

Molecular methods such as DNA/eDNA metabarcoding have emerged useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with for genetic marine hard-bottom benthic communities. Here, we present data our first campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved 2018-2020 across 15 observatories along coasts Europe adjacent regions. describe open-access set (image, metadata) explore show its potential ecological research. Our analysis shows that recovered more than 60 eukaryotic phyla capturing diversity up ~5500 amplicon sequence variants ~1800 operational taxonomic units, ~250 ~50 species per observatory cytochrome c oxidase subunit I (COI) 18S rRNA marker genes, respectively. Further, detected threatened, vulnerable non-indigenous often targeted biological monitoring. while deployment duration does not drive estimates, effort sequencing depth do. recommend should be at least 3-6 months during main growth season use resources efficiently possible post-sequencing curation is applied enable statistical comparison entities. suggest used programs long-term research encourage adoption ARMS-MBON protocols.

Language: Английский

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Metacommunity Theory and Metabarcoding Reveal the Environmental, Spatial and Biotic Drivers of Meiofaunal Communities in Sandy Beaches

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

Published: March 20, 2025

ABSTRACT Understanding the processes that shape community assembly is a critical focus of ecology. Marine benthic meiofauna, microscopic invertebrates inhabiting sediment environments, play important roles in ecosystem functioning but have been largely overlooked metacommunity studies due to lack data. In this study, we quantify relative contributions environmental filtering, spatial processes, and biotic associations structuring meiofaunal communities. We applied Generalised Dissimilarity Modelling (GDM) Joint Species Distribution (JSDM) an extensive metabarcoding dataset comprising 550 samples collected from sandy beaches along over 650 km Dutch German North Sea coast. Our findings reveal associations, followed by factors, particularly distance low tide line grain size, are primary drivers meiofauna turnover, highlighting influence sharp gradients. Spatial factors indicating dispersal limitations no major impact on composition, supporting assumption organisms strong capabilities. JSDM results demonstrate while species sorting key driver assembly, most environmentally distinct (‘extreme’) sites, whereas significantly both similar dissimilar habitats, emphasising need incorporate interactions into models assembly. By providing insights structure, our study highlights importance gradients shaping biodiversity patterns underscores potential for approaches enhance understanding other ecosystems with small, highly diverse, understudied taxa.

Language: Английский

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A Confidence Scoring Procedure for eDNA Metabarcoding Records and Its Application to a Global Marine Fish Dataset

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

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is changing the way biodiversity surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into monitoring programs public databases. Although it widely recognized that records require interpretation light taxonomy biogeography, there remains a range perceptions about how thoroughly should be evaluated which ones reported. Here, we present modular procedure, available as an R script, uses set five steps to assess confidence species‐level by assigning them score from 0 5. This procedure includes evaluations known geographic distribution each taxon, taxonomic resolution marker used, regional completeness reference database, diversification rate, map taxon. We tested on large‐scale marine fish dataset (572 samples) covering 15 ecoregions worldwide, poles tropics, using teleo mitochondrial 12S ribosomal gene. Our analysis revealed broad variation average among regions, with highest scores occurring along European Eastern Atlantic coasts. Generalized linear models applied record covariates highlighted significant influences latitude species richness low (< 2.5). The polar regions notably displayed high proportions scores, probably due limited databases marker. conclude only (> 2.5) medium (2.5) relatively low‐confidence correspond further investigation may after inspection ensure high‐quality records.

Language: Английский

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Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology

Environmental Microbiome, Journal Year: 2025, Volume and Issue: 20(1)

Published: March 27, 2025

Abstract Background Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant long-term epidemiological records of grapevine downy mildew, a major caused by oomycete Plasmopara viticola . Results We found that certain microbial taxa were consistently more abundant in plots lower incidence severity community composition could predict severity. Microbial diversity was not strongly linked to records, suggesting is related abundance specific taxa. These key identified topsoil, where pathogen’s oospores overwinter, phyllosphere, zoospores infect leaves. By contrast, leaf endosphere, mycelium develops, contained few interest. Surprisingly, microbiota better predictor than microbiota, microbiome be indicator dynamics this primarily aerial disease. Conclusion Our study integrates data profiles healthy plants reveal fungi bacteria relevant for biocontrol mildew. The resulting database provides valuable resource designing consortia potential activity. framework applied other crop systems guide development strategies reduce pesticide use agriculture.

Language: Английский

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