Metabarcoding of soil environmental DNA to estimate plant diversity globally

Abstract

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods.MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data.ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region.DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Navigating the Aerosolized Frontier: A Comprehensive Review of Bioaerosol Research Post-COVID-19

“…This technique has been commonly used in aquatic ecosystems to assess biodiversity, such as in fish, amphibians [143], and bacterial antibiotic resistance genes (ARGs) [144]. Terrestrial ecosystems have also been assessed using eDNA, including terrestrial vertebrate diversity and global plant diversity using soil eDNA and pollen DNA [145,146]. However, the application of eDNA technology in bioaerosol studies lags behind due to several challenges.…”

Niche types and community assembly

“…These data were used by both Davison et al (2021 and Bebber and Chaloner (2022) to investigate the abiotic niche attributes of AM fungi. We further incorporated recently published metabarcoding data describing other eukaryotes (targeting fungi using ITS and plants using trnL) and prokaryotes (16S rDNA) from the same soil samples (Vasar et al, 2023;Vasar, Davison, Sepp, Mucina, et al, 2022). All of the raw metabarcoding data are available from NCBI Bioproject PRJNA659159.…”

Development of an Environmental DNA Assay for Prohibited Matter Weed Amazon Frogbit (Limnobium laevigatum)

“…Despite being broadly applied in monitoring of animal species, the application of eDNA in weed biosecurity is limited [12,13]. Several studies used a metabarcoding approach for biodiversity analyses to investigate the plant communities using soil [14], dust [15] and honey [16] samples. Additionally, qPCR-based targeted species detection methods have been developed for various aquatic weeds, such as Hydrilla verticillata (L.f.)…”