Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Krehenwinkel, Henrik; Wolf, Madeline; Lim, Jun Ying; Rominger, Andrew J.; Simison, W. Brian; Gillespie, Rosemary G.

doi:10.1038/s41598-017-17333-x

Cited by 249 publications

(283 citation statements)

References 58 publications

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“…Conventional sampling provides specimens for future research (e.g. PCR amplification biases tend to be predictable within species and can be mitigated with the use of degenerate primers or conserved binding sites (Krehenwinkel et al 2017). DNA metabarcoding, in contrast, allows for the rapid determination of OTUs (roughly analogous to species or genera) and is effective for efficient detection of a very broad range of invertebrate and soil biodiversity.…”

Section: Discussionmentioning

confidence: 99%

“…taxonomic revision of groups) and readily interpretable abundance data (Table 1). This suggests that it is possible to detect shifts in relative abundance of particular organisms, and taxon-specific conversion factors would enable the determination of absolute abundances based on metabarcoding data (Krehenwinkel et al 2017). However, the identification and interpretation of most OTUs is not straightforward.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…In particular, given the importance of being able to assess identity and abundance of all individuals in an entire community, approaches are being developed that allow massive sequencing of entire communities at minimal cost (Krehenwinkel et al 2018). While species richness can be routinely identified by sequencing bulk samples, new approaches also allows estimation of species abundance (Krehenwinkel et al 2017). This in turn allows development of metrics of community stability and turnover in the context of food web structure and species abundance distributions.…”

Section: Target Groups and Biodiversity Monitoring Protocol Selectionmentioning

confidence: 99%

Global Island Monitoring Scheme (GIMS): a proposal for the long-term coordinated survey and monitoring of native island forest biota

et al. 2018

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Islands harbour evolutionary and ecologically unique biota, which are currently disproportionately threatened by a multitude of anthropogenic factors, including habitat loss, 2568 Biodivers Conserv (2018) 27:2567-2586 1 3 invasive species and climate change. Native forests on oceanic islands are important refugia for endemic species, many of which are rare and highly threatened. Long-term monitoring schemes for those biota and ecosystems are urgently needed: (i) to provide quantitative baselines for detecting changes within island ecosystems, (ii) to evaluate the effectiveness of conservation and management actions, and (iii) to identify general ecological patterns and processes using multiple island systems as repeated 'natural experiments'. In this contribution, we call for a Global Island Monitoring Scheme (GIMS) for monitoring the remaining native island forests, using bryophytes, vascular plants, selected groups of arthropods and vertebrates as model taxa. As a basis for the GIMS, we also present new, optimized monitoring protocols for bryophytes and arthropods that were developed based on former standardized inventory protocols. Effective inventorying and monitoring of native island forests will require: (i) permanent plots covering diverse ecological gradients (e.g. elevation, age of terrain, anthropogenic disturbance); (ii) a multiple-taxa approach that is based on standardized and replicable protocols; (iii) a common set of indicator taxa and community properties that are indicative of native island forests' welfare, building on, and harmonized with existing sampling and monitoring efforts; (iv) capacity building and training of local researchers, collaboration and continuous dialogue with local stakeholders; and (v) long-term commitment by funding agencies to maintain a global network of native island forest monitoring plots.

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“…Regarding the source of the duplicate dung samples, while we are confident that each sample in a vial is of the same sheep, we cannot be absolutely certain of this as there is a small chance that two or more animals in a mob could have dropped their dung at the same spot. Additional sampling, and the use of degenerate primers like the rbcL-AM2f primer used in this study, might also help to overcome PCR amplification bias, which can skew the proportion of reads from different taxa in metabarcoding HTS results (Krehenwinkel et al 2017, Pawluczyk et al 2015. In our supplementary study increasing the sensitivity of our analysis by lowering the minimum read depth to 3, the number of families and species recovered in Merinos, Dorpers and goats were higher then when using a minimum read depth of 10, but the relative levels of diversity among taxa were maintained.…”

Section: Discussionmentioning

confidence: 99%

Dropping Hints: Estimating the diets of livestock in rangelands using DNA metabarcoding of faeces

Lee¹,

Alemseged²,

Mitchell³

2018

MBMG

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The introduction of domesticated animals into new environments can lead to considerable ecological disruption, and it can be difficult to predict their impact on the new ecosystem. In this study, we use faecal metabarcoding to characterize the diets of three ruminant taxa in the rangelands of south-western New South Wales, Australia. Our study organisms included goats (Capra aegagrus hircus) and two breeds of sheep (Ovis aries): Merinos, which have been present in Australia for over two hundred years, and Dorpers, which were introduced in the 1990s. We used High-Throughput Sequencing methods to sequence the rbcL and ITS2 genes of plants in the faecal samples, and identified the samples using the GenBank and BOLD online databases, as well as a reference collection of sequences from plants collected in the study area. We found that the diets of all three taxa were dominated by the family Malvaceae, and that the Dorper diet was more diverse than the Merino diet at both the family and the species level. We conclude that Dorpers, like Merinos, are potentially a threat to some vulnerable species in the rangelands of New South Wales.

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Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Cited by 249 publications

References 58 publications

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

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

Global Island Monitoring Scheme (GIMS): a proposal for the long-term coordinated survey and monitoring of native island forest biota

Dropping Hints: Estimating the diets of livestock in rangelands using DNA metabarcoding of faeces

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