Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools

Abstract

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Environmental DNA for biomonitoring

“…Gleason et al (2021) show that bulk DNA metabarcoding more accurately represents the local stream macroinvertebrate community, with water eDNA data being overwhelmed by non-metazoan sequences. The same difference was observed when comparing bulk DNA to water eDNA and morphological inventories of pond macroinvertebrates (Harper et al, 2021). However, the authors consider both approaches as complementary and suggest that they should be combined for comprehensive assessment of the invertebrate community.…”

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

“…Since the earliest study published in 2010 [58], there has been a steep growth during the following years in the number of papers published on the theme, with most studies published between 2016 and 2020 (Figure 1). An overview of the studies indicates that metabarcoding-targeting benthic macroinvertebrates have been widely used in ecological assessments in aquatic ecosystems, for example, to assess (1) the effects of contaminants in urbanized, industrialized, and agricultural stream and estuarine areas (e.g., [15,27,39,[58][59][60][61][62][63][64][65]), (2) the effects of stream fragmentation due to dams [66], (3) longterm effects of pesticides [67], oil spills [68], or offshore oil and gas drilling activities [40,69,70], or (4) the effects of invasive species (e.g., invasive algae [71] and crucian carp [72]). It has also proven to be a reliable tool to characterize archive collections of specimens [73], to estimate intraspecific genetic diversity [74], to early detect and monitor invasive species [42,[75][76][77], to be used in the biomonitoring of sea-based fish farms [78,79], and to identify large biogeographic patterns [80,81] and new molecular and cryptic metazoan diversity, in particular in marine ecosystems [55,[81][82][83][84].…”

“…The location of the sampled regions has been mostly concentrated in the Palearctic, Nearctic (Northern Hemisphere), and Australasia, with a few studies in the Antarctic and IndoMalay (Southern Hemisphere) and absent in Neotropics and Afrotropics (Figure 2). In fresh waters, most studies pertained to the macroinvertebrate fauna of watercourses (rivers or streams, e.g., [23,85,86,88]), and a smaller amount in ponds (e.g., [60,72,89]), wetlands (e.g., [54,90,91]), lakes (e.g., [61,92]), or reservoirs (e.g., [57]), whereas in marine waters, most studies were conducted in open coastal regions (e.g., [80,[93][94][95][96]), with a few in the deep sea [87,97]. In transitional waters, studies have been performed in estuaries (e.g., [15,27,39,58]) and also in coastal lagoons [98].…”

“…Sediment sieving has been often employed to separate bulk organisms from the environmental matrix (i.e., 0.5 mm to 2 mm mesh size, e.g., [15,22,66,107]), and slicing into layers is often used to subsample marine sediments from different depths [39,87,97] (Table S2). Bulk organisms sieving in different size fractions (e.g., marine: >106 µm to >2 mm, [41,55,81,93,111]), sorting into different size categories (fresh waters, 2.5 mm to >10 mm) [72,112], or detecting by the naked eye [86,109], has been performed to improve the detection of smaller sized organisms before DNA extraction, but at an extra cost of an increase in sample processing time. A feasible option may be sorting samples into basic taxonomic groups that require little taxonomic knowledge (e.g., Annelida, Arthropoda, Mollusca) and less time effort, and that can greatly improve the recovery of taxa through DNA metabarcoding [113].…”

“…The choice of the primers can highly affect the recovered diversity through metabarcoding approaches because metabarcoding results can be particularly affected by the affinity of the primers with the target sequences [78,80,93], the completeness of reference libraries [80] and reference databases used, and the algorithms used to assign taxonomy [43]. If possible, in silico evaluations and the use of mock communities of known compositions should be used to validate the primers that work better for the target groups and the purpose of the study [72,137,138]. For instance, in marine waters, the DNA from mollusks has been reportedly found to have poor mismatches with broad-coverage primers targeting both COI [80,93,139] and 18S [78] regions, but Cowart et al [22] found a high success of mollusks detection through DNA metabarcoding by using Folmer primers (LCO1490/HCO21982).…”