Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Abstract

Currently, freshwater zooplankton sampling and identification methodologies have remained virtually unchanged since they were first established in the beginning of the XX century. One major contributing factor to this slow progress is the limited success of modern genetic methodologies, such as DNA barcoding, in several of the main groups. This study demonstrates improved protocols which enable the rapid assessment of most animal taxa inhabiting any freshwater system by combining the use of light traps, careful fixation at low temperatures using ethanol, and zooplankton‐specific primers. We DNA‐barcoded 2,136 specimens from a diverse array of taxonomic assemblages (rotifers, mollusks, mites, crustaceans, insects, and fishes) from several Canadian and Mexican lakes with an average sequence success rate of 85.3%. In total, 325 Barcode Index Numbers (BINs) were detected with only three BINs (two cladocerans and one copepod) shared between Canada and Mexico, suggesting a much narrower distribution range of freshwater zooplankton than previously thought. This study is the first to broadly explore the metazoan biodiversity of freshwater systems with DNA barcodes to construct a reference library that represents the first step for future programs which aim to monitor ecosystem health, track invasive species, or improve knowledge of the ecology and distribution of freshwater zooplankton.

Faunistic survey of the zooplankton community in an oligotrophic sinkhole, Cenote Azul (Quintana Roo, Mexico), using different sampling methods, and documented with DNA barcodes

“…1). A particular case is the planktonic larvae of Mytilopsis, a mollusk also found in Lake Bacalar (Marelli and Berrend, 1978;Elías-Gutiérrez et al, 2018), located about 200 m from Cenote Azul. The nearest possible species is Mytilopsis sallei (Recluz, 1849), described from Lake Izabal, Guatemala, but it should be analyzed in more detail to confirm the identification (Elías-Gutiérrez et al, 2018).…”

“…All samples were sieved and washed with 96% ethanol to extract all water, and finally fixed with 96% ethanol. They were transported on ice from the field, and stored at -18°C for seven days (Prosser et al, 2013;Elías-Gutiérrez et al, 2018).…”

“…These BINS are automated assignments from BOLD and represent putative species (Elías-Gutiérrez et al, 2018).…”

“…Recently, Elías-Gutiérrez et al (2018) demonstrated the usefulness of light traps and DNA barcoding to establish a baseline for the zooplankton in several lakes from Mexico and Canada. Based on this and other experiences, we consider that a combination of potentially complementary sampling gears will provide a more comprehensive picture of the species dwelling in a particular region or habitat (Vásquez-Yeomans et al, 2011;Martínez-Luque et al, 2016;Marrero et al, 2008).…”

“…It is in a good status of conservation and has particular properties of water geochemistry (Perry et al, 2002). It is a famous regional touristic attraction and is vulnerable to anthropogenic perturbations derived from population growth, like other freshwater ecosystems in the region (Elías-Gutiérrez et al, 2007;Elías-Gutiérrez et al, 2018).…”