An Overview of DNA-Based Applications for the Assessment of Benthic Macroinvertebrates Biodiversity in Mediterranean Aquatic Ecosystems

Abstract

The loss of aquatic biodiversity is increasing at a rapid rate globally. There is a worldwide effort to protect, preserve and restore aquatic ecosystems. For efficient biodiversity monitoring and reliable management tools, comprehensive biodiversity data are required. The abundance and species diversity of benthic macroinvertebrates are commonly used as indicators of the aquatic ecosystem condition. Currently, macroinvertebrate species biodiversity assessment is based on morpho-taxonomy, which could be enhanced by recent advances in DNA-based tools for species identification. In particular, DNA metabarcoding has the potential to identify simultaneously many different taxa in a pool of species and to improve aquatic biomonitoring significantly, especially for indicator species. This review is focused on the current state of DNA-based aquatic biomonitoring using benthic macroinvertebrates in the Mediterranean region.

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

“…Moreover, the success of the eDNA metabarcoding is based on the availability of efficient primer sets for the amplification of several taxa in a given sample (Elbrecht et al 2017;Tzafesta et al 2021). However, only 26% of NIS occurring in the Mediterranean Sea appear to have publicly available COI primers.…”

“…Consistent biological records can provide a better understanding of the distribution of marine species, their expansion range, and the arrival of new NIS in the Mediterranean basin (Mannino et al 2019;Bariche et al 2020). A promising approach for the identification of species and biomonitoring of ecosystems is the use of molecular tools such as DNA barcoding, metabarcoding and environmental DNA (Pawlowski et al 2018;Specchia et al 2020;Pinna et al 2021;Tzafesta et al 2021). DNA barcoding refers to a single species identification with the use of a short DNA fragment, while in the metabarcoding technique the DNA is extracted from a sample containing more than one organism/species, amplified and sequenced by Next Generation Sequencing (NGS) (Ji et al 2013;Deiner et al 2017).…”

“…This technique can efficiently be applied for assessing the presence and the distribution of NIS that are hard to detect. Also, it may result in a perfect tool for monitoring and preventing new NIS arrivals, for instance, by analysing the genetic content of ballast waters and monitoring it in water exchanges between different regions (Bariche et al 2020;Tzafesta et al 2021).…”

Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment

“…In general, appraisals of biodiversity should take into consideration that the target units may remain undetected, despite being present in the study area ( Ficetola et al, 2015 ; Roussel et al, 2015 ; Beng & Corlett, 2020 ; Tzafesta et al, 2021 ). While this understanding was certainly developed before eDNA surveys, biodiversity assessment based on eDNA has added some extra dimensions to the types of potentially erroneous observations.…”

Revealing cryptic diversity and population divergence in subtropical aphids throughDNAbarcoding

“…An attractive aspect of DNA barcoding is that it is not influenced by phenotype plasticity and can be used at any life stage (Hebert et al, 2003). The barcode sequences can also be widely used in revealing ecological and evolutionary relationships between and within species (Li, Chen, et al, 2021; Smith et al, 2008), monitoring biological invasions (Dejean et al, 2012), assessing ecosystem biodiversity (Tzafesta et al, 2021) and commercial applications such as quality inspection of biological products (Tnah et al, 2019).…”