High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

Echeverría‐Galindo, Paula; Anslan, Sten; Frenzel, Peter; Künzel, Sven; Vences, Miguel; Pérez, Liseth; Börner, Nicole; Kang, Wengang; Schwarz, Anja; Wang, Junbo; Peng, Ping; Zhu, Liping; Schwalb, Antje

doi:10.1002/edn3.222

Cited by 6 publications

(3 citation statements)

References 81 publications

(124 reference statements)

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“…Out of all master mixes screened and validated in this study, the Platinum Direct PCR Universal Master Mix generated reproducible results for all samples tested in this study. In the past, the Platinum Direct PCR Universal Master Mix kit has been used by researchers for the isolation of DNA from seafood specimens (i.e., ostracode) and subsequent PCR amplification ( Echeverría-Galindo et al, 2021 ). This master mix is designed to facilitate PCR amplification directly from tissue samples.…”

Section: Discussionmentioning

confidence: 99%

Rapid PCR-lateral flow assay for the onsite detection of Atlantic white shrimp

Kwawukume

Velez

Williams³

et al. 2023

Food Chemistry: Molecular Sciences

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Section: Discussionmentioning

confidence: 99%

Rapid PCR-lateral flow assay for the onsite detection of Atlantic white shrimp

Kwawukume

Velez

Williams³

et al. 2023

Food Chemistry: Molecular Sciences

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“…With the development of next-generation sequencing technologies (Glenn, 2011;Metzker, 2010;Shendure and Ji, 2008), metabarcoding has shown a great potential for reconstructing long-term changes in different biological groups. Several sets of universal PCR primers suitable for sedaDNA studies have been designed for plants (Taberlet et al, 2007), mammals (Giguet-Covex et al, 2014), fish (Miya et al, 2015), fungi (Seeber et al, 2022), diatoms (Stoof-Leichsenring et al, 2012), ostracods (Echeverría-Galindo et al, 2021), and bacteria (Belle and Parent, 2019). Metabarcodes amplified by these primers offer the opportunity to identify the target groups at high taxonomic levels (e.g., species level), and the bias in taxonomic resolution between different taxa can be further complemented by specific primers.…”

Section: Methodological Opportunities and Limitations Of Sedadna Appr...mentioning

confidence: 99%

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

Jia

Anslan

Chen

et al. 2022

Quaternary Science Reviews

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“…A recent study about plant DNA preservation in the sediments suggested that lakes with pH 7-9 and conductivities with 100-500 μS/cm may have better preservation of sedimentary DNA compared to lakes with higher or lower values of latter measures (Jia et al, 2021). However, sedimentary DNA studies to identify diatom (Kang et al, 2021) and ostracod (Echeverría-Galindo et al, 2021) communities indicated the potential of DNA metabarcoding in the environmental settings of the lake Nam Co with conductivity >1,400 μS/cm and pH ~9. Although the overall diatom community patterns matched well between morphological and DNA-based identification methods in the study by Kang et al (2021), it also indicated that the diatom species with fragile valves may be missed via microscopical analyses due to the dissolution effect.…”

Section: Introductionmentioning

confidence: 99%

Compatibility of Diatom Valve Records With Sedimentary Ancient DNA Amplicon Data: A Case Study in a Brackish, Alkaline Tibetan Lake

et al. 2022

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Lake sediments represent valuable and widely used archives for tracking environmental and biotic changes over time. Past aquatic communities are traditionally studied via morphological identification of the remains of organisms. However, molecular identification tools, such as DNA metabarcoding, have revolutionized the field of biomonitoring by enabling high-throughput and fast identification of organisms from environmental samples (e.g., sediments and soil). Sedimentary ancient DNA (sedaDNA) metabarcoding, an approach to track the biodiversity of target organisms from sediment cores, spanning thousands of years, has been successfully applied in many studies. However, researchers seldom explore how well the signals from sedaDNA data correlate with the fossil records of target organisms. This information is essential to infer past environmental conditions and community changes of bioindicators when the increasingly popular molecular identification method, metabarcoding, is desired instead of a morphological identification approach. In this study, we explore the correlations of diatom valve records across the last ∼940 years with the diatom sedaDNA metabarcoding data from the same sediment core from lake Nam Co (Tibetan Plateau). Overall, the results from valve vs. sedaDNA data revealed concordant diatom richness as well as community patterns. However, several mismatches in the diatom taxonomic composition existed between the data sets. In general, sedaDNA data harbored much higher diatom diversity, but due to the lack of reference sequences in public databases, many molecular units (amplicon sequence variants) remained unclassified to lower taxonomic levels. As our study lake, Nam Co, is characterized by brackish water and alkaline pH, some likely cases for the observed taxonomic composition mismatches may be due to a valve dissolution issue. Nevertheless, significant drivers for the diatom richness and community structure largely corresponded between data sets. Both valve and sedaDNA data demonstrated similar breakpoints for historical diatom community shifts. A particularly strong shift in the diatom community structure occurred after ∼1950 CE, which may be associated with abrupt environmental changes on the Tibetan Plateau. Altogether, our study indicates that environmentally driven signals reflected by the diatom communities are successfully recovered via microfossil as well as molecular identification methods.

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High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 6 publications

References 81 publications

Rapid PCR-lateral flow assay for the onsite detection of Atlantic white shrimp

Rapid PCR-lateral flow assay for the onsite detection of Atlantic white shrimp

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

Compatibility of Diatom Valve Records With Sedimentary Ancient DNA Amplicon Data: A Case Study in a Brackish, Alkaline Tibetan Lake

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