Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

Yang, Chunyan; Wang, Xiaoyang; Miller, Jeremy A.; Blécourt, Marleen de; Ji, Yinqiu; Harrison, Rhett D.; Yu, Douglas W.

doi:10.1016/j.ecolind.2014.06.028

Cited by 85 publications

(90 citation statements)

References 57 publications

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“…Indeed, other groups of taxa that have successfully been the target of eDNA studies in soil samples include nematodes (Porazinska et al 2010;Vervoort et al 2012) and boreal plant communities . Sequencing of genetic material recovered from leaf litter samples has reflected terrestrial arthropod diversity in China and Vietnam (Yang et al 2014). Other examples of whole-community eDNA analyses in aquatic environments include survey of fish species in the Monterey Bay Aquarium, California, USA (Kelly et al 2014b), survey of fish species in aquaria and the Yuma River in Japan , and the detection of fish and bird eDNA in marine water samples in Denmark (Thomsen et al 2012b).…”

Section: Description Of Whole Communitiesmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

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Section: Description Of Whole Communitiesmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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“…Gut and faecal material, collected in 5% of the studies, has been used to analyse the diets of herbivores (Hibert et al 2013), carnivores and carrion feeders (Calvignac-Spencer et al 2013). Several of the 167 DNA metabarcoding studies analysed pools of invertebrate specimens collected in malaise traps (Yu et al 2012;Ji et al 2013;Liu et al 2013;Yang et al 2014) or from soil samples , while others targeted invertebrate DNA extracted directly from soil (McGee & Eaton 2015) or aquatic habitats (Pochon et al 2013;Cowart et al 2015).…”

Section: Study Environmentsmentioning

confidence: 99%

“…Bhadury & Austen 2010;Kanzaki et al 2012) and some arthropod-focused studies (e.g. Pochon et al 2013;Yang et al 2014). The 18S rRNA gene region was similarly amplified in several fungal analyses (e.g.…”

Section: Summary Of Gene Regions Used In Prior Analyses Of Environmenmentioning

confidence: 99%

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

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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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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“…Highly trained specialists are not needed for specimen identification, avoiding this typically labour-intensive process (e.g. Yu et al 2012;Yang et al 2014). Molecular analyses and bioinformatics, while challenging, can be partially or totally automated to process large datasets rapidly.…”

Section: General Benefits Of Dna Metabarcoding and Its Integration Wimentioning

confidence: 99%

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

Holdaway¹,

Wood²,

Dickie³

et al. 2017

NZ J Ecol

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High throughput DNA sequencing technology has enabled entire biological communities to be characterised from DNA derived from pools of organisms, such as bulk-collected invertebrates, or DNA extracted from environmental samples (e.g. soil). These DNA-based techniques have the potential to revolutionise biodiversity monitoring. One approach in particular, DNA metabarcoding, can provide unprecedented taxonomic breadth at a scale not practically achievable through the morphological identification of individual organisms. Here, we assess the current strengths and weaknesses of DNA metabarcoding techniques for biodiversity assessment. We argue that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data. We present a conceptual framework for how this might be done, explore potential applications within national biodiversity assessment frameworks, Maori biodiversity monitoring and the primary sector, and highlight areas of current uncertainty and future research directions. Rapid developments in DNA sequencing technology and bioinformatics will make DNA-based community data increasingly accessible to ecologists, and there needs to be a corresponding shift in research focus from DNA metabarcoding method development and evaluation to real-world applications that provide rich information for a range of purposes, including conservation planning and land management decisions.

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Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

Cited by 85 publications

References 57 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

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

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

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