Environmental DNA as a non-invasive alternative for surveying aquatic communities in tank bromeliads

Bromeliad phytotelmata: the first scientometric study

“…Advances in metagenomics and next-generation sequencing have revolutionized the molecular field, and these methods are important tools for biodiversity studies, decreasing the time, expense and resources spent on traditional survey methods (Klymus et al, 2017). Studies using eDNA allow researchers to identify species of amphibians not sampled by traditional sampling methods, for example, in bromeliads (Lopes et al, 2021). From this type of study, new possibilities for molecular research have emerged, which have been even more widely applied to studies of organisms.…”

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil

“…We are also using these sequences as an additional line of evidence to describe and revalidate species (e.g., de Sá et al 2015, Gazoni et al 2021, to flag groups of species where species diversity could be underestimated (Walker, et al 2018, Sabbag et al 2018, or even identifying invasive species (Melo et al 2014). In addition to COI and 16S reference sequences, we have also been adding information on the 12S gene fragment to our databases, including data from environmental DNA studies of monitoring endangered species (e.g., Lopes et al 2021a, Lopes et al 2021b, see below), and complete mitogenome sequences from studies of systematics and evolution (e.g., Lyra et al 2021). Besides supporting this variety of studies, DNA barcoding is also being used as an important tool for identifying mislabeled tissues in biological collections (Lyra et al 2017), serving as support for the selection of specimens for multilocus phylogenies and genomic studies.…”

“…All information provided by our pilot project (Lopes et al 2017) was essential to guide our next studies aiming to search for DNA traces of 43 target amphibian species of conservation concern in Brazil, from species last registered in 1910 to species with historical records of severe population declines (Lopes et al 2021a, Lopes et al 2021b, C. M. Lopes unpublished data). We filtered water samples from streams, rivers, puddles, ponds, rocky seeps, and tank bromeliads from 13 localities distributed in the Brazilian Atlantic Forest and adjacent Cerrado grasslands.…”

“…An extensive 12S mitochondrial sequence reference database was constructed to analyze the eDNA data, filling an important gap of sequences from species and geographical areas underrepresented in public databases. We successfully detected DNA traces of four declined anuran species (Crossodactylus timbuhy, Hylodes ornatus, Hylodes regius, and Vitreorana eurygnatha); two locally disappeared (Phasmahyla exilis and Phasmahyla guttata); and one species that has not been seen since 1968 (putatively assigned to Phantasmarana bocainensis) (Lopes et al 2021b) (Figure 3). Our results recovered so far highlight the value of applying eDNA in conservation biology, to evaluate persistence and distribution of threatened species in their natural environment, and to improve accuracy of red lists.…”