Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Holdaway, Robert J.; Wood, Jamie R.; Dickie, Ian A.; Orwin, Kate H.; Bellingham, Peter J.; Richardson, Suzanne M.; Lyver, Phil O'b.; Timoti, Puke; Buckley, Thomas R.

doi:10.20417/nzjecol.41.28

Cited by 27 publications

(26 citation statements)

References 56 publications

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“…Next-generation sequencing metabarcoding has been increasingly recognized as a promising tool for biomonitoring species and complex communities at large scales (Holdaway et al, 2017). In recent cases, it has been applied to plant pathogenic fungi (Merges et al, 2018) and oomycetes (Burgess et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

et al. 2018

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Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

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Section: Discussionmentioning

confidence: 99%

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

et al. 2018

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“…While DNA-based biodiversity assessment methods are not yet in widespread use beyond the microbial world, there are many potential benefits, as well as uncertainties, resulting from their application to a far wider range of organisms, as reviewed in Holdaway et al (2017). For example, traditional observational techniques for biodiversity monitoring can be highly dependent on (and biased by) taxonomic and diagnostic expertise that is in scarce supply worldwide (Paknia et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…Environmental DNA metabarcoding techniques can characterise entire invertebrate communities from a single environmental sample (Bohmann et al 2014;Holdaway et al 2017). DNA metabarcoding analyses involve extraction of DNA from environmental samples such as bulk invertebrates, soil, leaf litter or water and then amplification and sequencing of specific gene regions, grouping of sequences into OTUs based on similarity and identification of OTUs by comparing their sequences to available reference databases (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…However, we need to apply both DNA metabarcoding and conventional methods to the same taxonomic groups to demonstrate and improve the accuracy and reliability of DNA-based methods and to assess the additional value (Ji et al 2013;Holdaway et al 2017). However, we need to apply both DNA metabarcoding and conventional methods to the same taxonomic groups to demonstrate and improve the accuracy and reliability of DNA-based methods and to assess the additional value (Ji et al 2013;Holdaway et al 2017).…”

Section: Introductionmentioning

confidence: 99%

“…DNA metabarcoding analyses involve extraction of DNA from environmental samples such as bulk invertebrates, soil, leaf litter or water and then amplification and sequencing of specific gene regions, grouping of sequences into OTUs based on similarity and identification of OTUs by comparing their sequences to available reference databases (e.g. Yu et al 2012;Bohmann et al 2014;Drummond et al 2015;Holdaway et al 2017). DNA metabarcoding analysis of bulk invertebrate samples (such as malaise trap collections) circumvents time-consuming, costly and demanding microscope-based identifications (Yu et al 2012;Morinière et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques

et al. 2019

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When conserving native biodiversity, it is particularly important to consider invertebrates, a diverse and functionally important component of biodiversity. However, their inclusion in monitoring and conservation planning has lagged behind larger fauna because collecting, sorting and identifying invertebrates using conventional monitoring techniques is often expensive, time consuming and restricted by expertise in diagnostics. Emerging DNA metabarcoding techniques could potentially revolutionise monitoring of invertebrates by providing the ability to characterise entire communities from a single, easily collected environmental sample. We aimed to characterise the invertebrate fauna of an isolated, coastal forest fragment in New Zealand using the same level of financial investment for conventional invertebrate monitoring (pitfall and malaise traps) and a DNA metabarcoding approach applied to two alternative sample types (conventional invertebrate samples and soil samples). The bulk invertebrate and soil DNA metabarcoding methods were able to reproduce ecological patterns observed in the beetle community detected using conventional sampling. The soil DNA metabarcoding method detected a different beetle community and a more diverse array of invertebrate taxa than conventional sampling techniques. DNA metabarcoding offers conservation managers a practical, cost-effective technique for characterising whole invertebrate communities. However, increasing the taxonomic coverage of reference sequence databases (particularly for New Zealand invertebrates) through DNA barcoding efforts should be the focus of future research as it would improve the utility of metabarcoding methods for invertebrate monitoring, which would complement conventional techniques.

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Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Cited by 27 publications

References 56 publications

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques

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