Development and application of a DNA metabarcoding method for comprehensive analysis of soil nematode communities

Kawanobe, Masanori; Toyota, Koki; Ritz, Karl

doi:10.1016/j.apsoil.2021.103974

Cited by 21 publications

(19 citation statements)

References 57 publications

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“…However, this does not explain the absence of soil animals in our terra firme samples since these were relatively clay‐free and unflooded. To test this hypothesis, we need further studies in soils with a gradual difference in clay proportion and specific primers targeting nematodes (Kawanobe et al, 2021) alongside morphological examination of the diversity in the samples.…”

Section: Discussionmentioning

confidence: 99%

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

et al. 2021

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Section: Discussionmentioning

confidence: 99%

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

et al. 2021

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“…Due to the functional overlap of the key microbiome predators protists and nematodes, as well as other fauna that perform similar functions (Thakur and Geisen, 2019 ), a separation between metazoans and unicellular organisms would be artificial and provide a biased vision of eukaryotic functional diversity. Like for large protists, nematodes and certainly also rotifers are extracted from the soil matrix before molecular work (Kawanobe et al ., 2021 ). In order to retrieve all microbial‐sized eukaryotic diversity in metabarcoding analyses, huge amounts of soil should be taken.…”

Section: Different Morphologies Change Sampling Protocolsmentioning

confidence: 99%

Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA‐based studies

Lara

Geisen

2022

Environmental Microbiology

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Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.

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“…The biodiversity of nematodes is estimated to be 1-10 million species, but less than 30,000 species have been described using morphology [6]. Recent advances in DNA metabarcoding have fostered the study of nematode biodiversity from a range of environments, highlighting their impressive diversity and the multiple key roles they play [2,3,[7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Ficetola,

Guerrieri,

Cantera

et al. 2024

PLoS ONE

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Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

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Development and application of a DNA metabarcoding method for comprehensive analysis of soil nematode communities

Cited by 21 publications

References 57 publications

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA‐based studies

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

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