Environmental DNA as an emerging tool in botanical research

Johnson, Mark D.; Freeland, Joanna R.; Parducci, Laura; Evans, Darren M.; Meyer, Rachel S.; Molano‐Flores, Brenda; Davis, Mark A.

doi:10.1002/ajb2.16120

Cited by 11 publications

(7 citation statements)

References 193 publications

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“…Sønstebø et al (2010) already identified the first region of the trnL as a candidate for metabarcoding ancient DNA due to its short size, high coverage, and specificity. We suggest that the combined amplification of this region and the P6 loop with primers c-h lowers the taxonomic resolution unpublished in silico observations, and Johnson, Cox, and Barnes (2019); Johnson et al (2021Johnson et al ( , 2023 while still being compatible with contemporary aquatic plant eDNA studies (Shackleton et al, 2019;Yang et al, 2016).…”

Section: Stratiotes Aloides (Table 1)mentioning

confidence: 63%

“…We encourage fellow (molecular) ecologists and botanists to collaborate in the creation of regional and local barcode databases. Several recent reviews of plant eDNA applications (e.g., Banerjee, Stewart, Dey, et al, 2022; Johnson et al, 2023) and analyses of reference databases and markers (e.g., Kolter & Gemeinholzer, 2021b; Weigand et al, 2019) provide critical guidelines. To support research in this field and improve species identification success, the construction of regional or local DNA BRDs is of utmost importance as they overcome taxonomic gaps in public BRDs.…”

Section: Discussionmentioning

confidence: 99%

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Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

et al. 2023

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Providing reliable, cost‐effective data on species distribution is critical to ensuring biodiversity conservation. However, many species may go unrecorded by conventional surveys, especially in aquatic environments. Environmental DNA (eDNA) barcoding and metabarcoding are alternative approaches that could complete biodiversity estimates based on species observations. While eDNA surveys are being standardized for some animal groups (e.g., fish and amphibians), research on eDNA approaches for freshwater plant communities is just starting to bear fruit. Here, we synthesized the 22 studies that used eDNA barcoding and metabarcoding to survey plant biodiversity in freshwater systems. We present evidence that contemporary aquatic plants (macrophytes) and terrestrial plants can be detected in water and surficial sediment eDNA from lakes and rivers. The phenology (e.g., senescence) of the target taxa strongly influences species detection. The main application of eDNA barcoding targets the monitoring of invasive macrophytes, and barcoding assays are available for 14 taxa. The metabarcoding approach shows a range of applications: the detection of rare macrophytes, catchment‐scale floristic inventories, and sediment fingerprinting. Barcodes on the plastid genome (cpDNA) are preferred for both approaches: matK and trnH‐psbA for barcoding, trnL, and rbcL for metabarcoding. The intergenic transcribed spacer 1 (ITS1) from the nuclear ribosomal DNA (nrDNA) was used for designing eDNA barcoding assays on five invasive macrophytes. In contrast, only three metabarcoding studies used the ITS1 or IST2 with newly designed primers. However, metabarcoding applications should routinely use a multi‐locus approach, combining cpDNA and nrDNA barcodes. Barcode combinations and existing primers need further testing on eDNA samples. We recommend using local barcode reference databases (BRDs), ideally self‐made, to circumvent taxonomic gaps and heterogeneous sequences in public BRDs. Finally, new technologies and developments like droplet digital PCR and hybridisation capture offer new perspectives for eDNA‐based biodiversity monitoring approaches.

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Section: Stratiotes Aloides (Table 1)mentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

et al. 2023

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“…Environmental DNA (eDNA) has been used to assess the taxonomic diversity present in various environmental sources, such as air samples, organismal products (like feces or honey), water, and soils (M. D. Johnson et al, 2023 ), as well as the diversity present in the plant microbiome, i.e., the biotic communities found in or on different plant tissues (Trivedi et al, 2022 ). The combined use of high‐throughput sequencing with eDNA (eDNA metabarcoding, or metagenomics) is further expanding the potential to survey and identify entire communities (Deiner et al, 2017 ).…”

Section: Environmental Dna (Edna)mentioning

confidence: 99%

Emerging methods in botanical DNA/RNA extraction

2023

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“…Brennan et al, 2019), bacteria (Innocente et al, 2017) and fungal spores (Hanson et al 2022a(Hanson et al , 2022b. A recent review by Johnson et al (2023) discussed developments in botanical applications of airborne eDNA detection and highlighted the future potential for advancements in this area, such as monitoring species dispersal, population structures and conservation. Many atmospheric plant studies have focused on wind dispersal and long distance transport of allergenic pollen (e.g.…”

Section: Introductionmentioning

confidence: 99%

Storms facilitate airborne DNA from leaf fragments outside the main tree pollen season

Hanson,

Petch,

Adams-Groom

et al. 2024

Aerobiologia

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Bioaerosols are useful indicators of plant phenology and can demonstrate the impacts of climate change on both local and regional scales (e.g. pollen monitoring/flowering phenology). Analysing bioaerosols with eDNA approaches are becoming more popular to quantify the diversity of airborne plant environmental DNA (eDNA) and flowering season of plants and trees. Leaf abscission from broadleaved trees and other perennial species can also indicate the status of plant health in response to climate. This happens primarily during autumn in response to seasonal growth conditions and environmental factors, such as changing photoperiod and reduced temperatures. During this period biological material is released in larger quantities to the environment. Here, rural bioaerosol composition during late summer and autumn was captured by MiSEQ sequencing of the rRNA internal transcribed spacer 2 (ITS2) region, a common marker for taxonomic variation. Meteorological parameters were recorded from a proximal weather station. The composition of atmospheric taxa demonstrated that deciduous tree DNA forms part of the bioaerosol community during autumn and, for several common broadleaved tree species, atmospheric DNA abundance correlated to high wind events. This suggests that both flowering and autumn storms cause bioaerosols from deciduous trees that can be detected with eDNA approaches. This is an aspect that must be considered when eDNA methods are used to analyse either pollen or other fragments from trees.

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Environmental DNA as an emerging tool in botanical research

Cited by 11 publications

References 193 publications

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

Emerging methods in botanical DNA/RNA extraction

Storms facilitate airborne DNA from leaf fragments outside the main tree pollen season

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