Armando Espinosa Prieto

RESEARCH, TEACHING, or OTHER INTERESTS

Ecology, Plant Science, Ecological Modeling, Management, Monitoring, Policy and Law

Scopus Publications

A comparative analysis of eDNA metabarcoding and field surveys: Exploring freshwater plant communities in rivers
Armando Espinosa Prieto, Laurent Hardion, Nicolas Debortoli, Thibaut Bournonville, Thibaut Mathot, Jonathan Marescaux, Etienne Chanez, Cybill Staentzel, and Jean-Nicolas Beisel
Elsevier BV



Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding
Armando Espinosa Prieto, Laurent Hardion, Nicolas Debortoli, and Jean‐Nicolas Beisel
Wiley
AbstractAs the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi‐marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior‐supported primers for immediate applications. The ITS2 was the best‐performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.


Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding
Armando Espinosa Prieto, Jean‐Nicolas Beisel, Pieternel Verschuren, and Laurent Hardion
Wiley
AbstractProviding 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.


An infraspecific dimension of bioindication? Comparison between genotypes and ecological distribution of Potamogeton coloratus
Laurent Hardion, Etienne Chanez, Cybill Staentzel, Isabelle Combroux, Jean-Nicolas Beisel, Armando Espinosa Prieto, Henry Béral, Michèle Trémolières, and Corinne Grac
Elsevier BV