Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: effects of sampling protocols and primer choice

Castro, Lyda R.; Meyer, Rachel S.; Shapiro, Beth; Shirazi, Sabrina; Cutler, Samuel; Lagos, Ana Milena; Quiroga, Sigmer

doi:10.1007/s10750-021-04576-z

Cited by 23 publications

(22 citation statements)

References 73 publications

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“…Recently, Castro et al ( 2021) compared the recovered community composition from DNA extracted directly from sediment cores with two meiofauna extraction methods commonly used in metabarcoding studies, namely (1) separation of meiofaunal specimens from sediment by flotation and centrifugation with Ludox and (2) separation of meiofaunal specimens from sediment by decantation of specimens with MgCl 2 . The community composition recovered through direct DNA extraction from sediment differed strongly from that obtained with the isolation techniques (Castro et al, 2021). Isolation of specimens with Ludox or MgCl 2 led to more taxa and meiofaunal species compared to DNA extraction directly from sediment (Castro et al, 2021).…”

Section: Sample Collection and Pre-treatmentmentioning

confidence: 90%

“…Isolation of specimens with Ludox or MgCl 2 led to more taxa and meiofaunal species compared to DNA extraction directly from sediment (Castro et al, 2021). Differences were also found amongst isolation techniques, as some genera belonging to the phyla of platyhelminthes, annelids, mollusks, xenacoelomorpha, gastrotrichs, and nematodes were found in a lower abundance in samples obtained through MgCl 2 decantation relative to Ludox flotation (Castro et al, 2021).…”

Section: Sample Collection and Pre-treatmentmentioning

confidence: 97%

“…Hence, as sample type significantly affects both the OTU richness and taxonomic composition of meiofaunal communities (Brannock and Halanych, 2015;Haenel et al, 2017;Nascimento et al, 2018;Castro et al, 2021), a greater consideration should be given to the choice of sample and DNA extraction workflow. Indeed, any extraction method will lead to a bias toward taxonomic groups that are more easily isolated with the chosen technique.…”

Section: Sample Collection and Pre-treatmentmentioning

confidence: 99%

“…Indeed, any extraction method will lead to a bias toward taxonomic groups that are more easily isolated with the chosen technique. Therefore, if the goal is to maximize recovery of taxa, a combination of isolation methods is the best option (Castro et al, 2021).…”

Section: Sample Collection and Pre-treatmentmentioning

confidence: 99%

“…However, the degenerate LoboR1 primer (Lobo et al, 2013) is a promising reverse primer in combination with the mlCOIintF forward primer, as it uncovered a higher diversity compared to the degenerate reverse primer dgHCO2198 (Haenel et al, 2017). This combination was used and recommended in several meiofaunal community studies (Haenel et al, 2017;Fais et al, 2020a,b;Castro et al, 2021). Additionally, inosine bases present in the widely used jgHCO2198 reverse primer may impair the performance of highfidelity polymerases commonly used for PCR amplification in metabarcoding studies (Jungbluth et al, 2020).…”

Section: Selection Of Primer Pairsmentioning

confidence: 99%

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

Gielings

Fais²,

Fontaneto

et al. 2021

Front. Mar. Sci.

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

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Section: Sample Collection and Pre-treatmentmentioning

confidence: 90%

Section: Sample Collection and Pre-treatmentmentioning

confidence: 97%

Section: Sample Collection and Pre-treatmentmentioning

confidence: 99%

Section: Sample Collection and Pre-treatmentmentioning

confidence: 99%

Section: Selection Of Primer Pairsmentioning

confidence: 99%

See 3 more Smart Citations

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

Gielings

Fais²,

Fontaneto

et al. 2021

Front. Mar. Sci.

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Environmental DNA as an emerging tool in botanical research

Johnson

Freeland

Parducci

et al. 2023

American J of Botany

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Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems. K E Y W O R D Sancient botanical eDNA, aquatic botanical eDNA, botanical eDNA, eDNA, organism derived botanical eDNA, review

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Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California

Lin

Simons

Harrigan

et al. 2021

Ecological Applications

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Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system‐level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi‐scalar community‐level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel‐2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.

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Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: effects of sampling protocols and primer choice

Cited by 23 publications

References 73 publications

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

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

Environmental DNA as an emerging tool in botanical research

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California

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