A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding

Molecular Ecology Resources, Год журнала: 2024, Номер 24(5)

Опубликована: Май 11, 2024

The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are available many species. This is a particular issue when complex communities such as wildlife parasites or terrestrial aquatic free-living communities. We have used markerDB to produce four databases of distinct regions the rRNA cistron: 18S gene, 28S ITS-1 intergenic spacer region spanning ITS-1_5.8S_ITS-2. These comprise 2645, 254, 13,461 10,107 unique full-length representing 1391, 204, 1837 1322 species, respectively. comparative analysis illustrates complementary value also reveals better representation Clade III, IV V than I II nematodes in each case. Although database includes largest number sequences, provides widest taxonomic coverage. developed PrimerTC, tool assess primer sequence conservation across any database, applied it evaluate large previously published cistron primers. identified sets primers that currently provide broadest coverage marker phylum. new resources will facilitate more comprehensive using either short-read long-read sequencing platforms. Further, PrimerTC simple WebApp guide PCR design genetic and/or group beyond

Язык: Английский

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More intraguild prey than pest species in arachnid diets may compromise biological control in apple orchards

Basic and Applied Ecology, Год журнала: 2021, Номер 57, С. 1 - 13

Опубликована: Окт. 4, 2021

Understanding the full diet of natural enemies is necessary for evaluating their role as biocontrol agents, because many enemy species do not only feed on pests but also other enemies. Such intraguild predation can compromise pest control if consumed are actually better than predators. In this study, we used gut metabarcoding to quantify diets all common arachnid in Swedish and Spanish apple orchards. For purpose, designed new primers that reduce amplification predators while retaining high prey groups. Results suggest most arachnids consume a large range putative proportion enemies, where latter constitute almost third sequences. Intraguild varied between regions, with larger content heteropteran bugs guts from orchards, orchard types. There was tendency cursorial spiders have more web spiders. Two groups may be overlooked important agents orchards seem theridiid opilionids, had several small-bodied gut. These results thus provide guidance what should targets management actions, even though additional information needed direct indirect interactions occurring complex arthropod food webs fruit

Язык: Английский

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Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments

Ecological Indicators, Год журнала: 2021, Номер 129, С. 107916 - 107916

Опубликована: Июнь 22, 2021

Due to a high number of specialized species and unique environmental conditions, alpine spring ecosystems are particularly vulnerable change human impact. Therefore, the assessment ecosystem integrity through habitat monitoring over long periods time is particular importance, especially in protected areas. Bioindication by conventional includes sampling whole communities morphological identification. This approach, however, brings along major drawbacks such as invasiveness, low reproducibility, specificity relatively time-consuming. To overcome these issues, we developed targeted bioindicator eDNA detection approach for representative freshwater macroinvertebrate compared results with sampling. Macroinvertebrates 15 springs, located Swiss National Park UNESCO biosphere reserve Engiadina Val Müstair, were sampled using hand-net morphologically identified. We selected six spring-bound species: Hygrobates norvegicus, Partnunia steinmanni, Dictyogenus fontium, Protonemura lateralis, Lithax niger, Wormaldia occipitalis designed novel, species-specific qPCR primers hydrolysis probes. Spring was collected filtering 1.5 l water cellulose nitrate filter funnels DNA extracts screened species. Results showed congruence between qPCR-based detection. The assay targeting L. niger less sensitive performance samples decreased other species, indicating necessity careful indicator choice evaluation. newly eDNA-based protocols allow detecting springs represent non-invasive, specific, cost- time-effective alternative biomonitoring approaches. Particularly areas Park, implementation filtered can be beneficial fosters sustainable assessment.

Язык: Английский

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Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

GigaScience, Год журнала: 2022, Номер 11

Опубликована: Янв. 1, 2022

Abstract Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond global change. However, large-scale syntheses may be compromised if workflows differ from each other. There are ongoing efforts improve standardization the reporting inventory harmonization at stage metabarcode has yet addressed. A modular framework harmonized generation a pathway navigate complex structure terrestrial metazoan biodiversity. Here, through our collective expertise practitioners, method developers, researchers leading initiatives we seek initiate generation, arthropod module. We develop initial set submodules covering 5 main steps generation: (i) sample acquisition; (ii) processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, sequencing; (v) sequence metadata deposition, providing backbone To achieve this, identified key points harmonization, reviewed current state art, distilled existing knowledge within submodules, thus promoting best practice by guidelines recommendations reduce universe methodological options. advocate adoption further development encourage modules other fractions step toward synthesis harmonization.

Язык: Английский

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Using DNA Metabarcoding to Identify Floral Visitation by Pollinators

Diversity, Год журнала: 2022, Номер 14(4), С. 236 - 236

Опубликована: Март 24, 2022

The identification of floral visitation by pollinators provides an opportunity to improve our understanding the fine-scale ecological interactions between plants and pollinators, contributing biodiversity conservation promoting ecosystem health. In this review, we outline various methods which can be used identify visitation, including plant-focused insect-focused methods. We reviewed literature covering ways in DNA metabarcoding has been answer questions relating plant use discuss findings research. present detailed methodological considerations for each step workflow, from sampling through amplification, finally bioinformatic analysis. Detailed guidance is provided researchers utilisation these techniques, emphasising importance standardisation improving reliability results. Future opportunities directions using molecular analyse plant–pollinator are then discussed.

Язык: Английский

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