Component 1: non-destructive DNA extractions on individuals

The first component of this study aimed to determine whether a non-destructive DNA extraction can be used to obtain DNA from whole individuals from common freshwater macroinvertebrate orders/subclasses (Fig. 1A). To test this, we included a small experiment (Experiment 1a) that examined the incubation time required for specimens to be immersed in extraction buffer to obtain DNA without destruction of morphological characters, followed by a second broader experiment (Experiment 1b) to see how the method performed on individuals from multiple families covering 15 common orders/classes/subclasses.

(A) Individual non-destructive DNA extraction (Extraction 1) followed by a Chelex extraction (Extraction 2) performed on single specimens from 15 different macroinvertebrate orders (Component 1). (B) Comparison of the detection of taxa via metabarcoding by using three DNA extraction based on non-destructive processing, homogenization of whole small taxa and dissection of all taxa (Component 2). (C) Comparison of the detection of taxa via metabarcoding from six field collected samples stored in different ethanol concentration, and temperatures an with varying levels of diversity. Drawings by Melissa Carew.

A total genomic extraction (Extraction 1; Fig. 1A), which is commonly used to prepare samples for HTS (e.g., Elbrecht, Peinert & Leese, 2017), was used to obtain DNA from whole and intact invertebrate specimens. For extraction, ethanol was removed using a pipette from microcentrifuge tubes containing individual specimens, then 180 µL T1 buffer and 25 µL of proteinase K (extraction buffer) from the Nucleospin DNA extraction kit (Macherey-Nagel Inc. Bethlehem, PA, USA) were added. We tested the whether the presence of ethanol interfered with the DNA extraction by soaking several specimens overnight in TE buffer prior to extraction, but found no difference in successful amplification between soaked specimens and those with ethanol removed just prior to extraction (Table S1). Specimens were then incubated in the extraction buffer at 56 °C. Based on other studies (Rowley et al., 2007; Castalanelli et al., 2010; Porco et al., 2010), we incubated specimens for 1 hr in the extraction buffer, but also tested a subset of taxa for 30 mins and/or 3 hrs depending on their levels of sclerotization (Tables S1 and S2). The extraction buffer was removed and placed into a new 1.5 ml microcentrifuge tube for DNA extraction using a Nucleospin DNA extraction kit (Macherey-Nagel Inc. Bethlehem, PA, USA) following the manufacturer’s instructions. After extraction buffer removal, absolute ethanol was added to microcentrifuge tubes containing whole specimens to preserve them for subsequent Chelex extraction and taxonomic identification. The condition of specimens was inspected under a dissecting microscope (Leica Microsystem and Instruments, Wetzlar, Germany).

A Chelex extraction (Extraction 2; Fig. 1A) was then performed to establish if two extractions of the same specimen was possible, i.e., an initial extraction intended for metabarcoding followed by an extraction intended for individual DNA barcoding. The material used for Chelex extraction varied among taxonomic groups, depending on how specimens needed to be prepared for identification (Table S2) but followed the methods of Carew, Pettigrove & Hoffmann (2003).

The success of both DNA extractions was determined by amplification of the DNA barcode region (Hebert et al., 2003) using the primer set HCOI2198/LCOI1490 from (Folmer et al., 1994) according to Carew & Hoffmann (2015), as this primer set was known to amplify the majority of taxa considered in the study. Some DNA barcode amplicons isolated with DNA extraction methods were sequenced to ensure that the intended species were extracted. Sequencing reactions were performed in both directions using an ABI 3730XL capillary sequencer (Applied Biosystems, Foster City, California, USA) with sequencing reactions and runs performed by Macrogen (Seoul, Korea).

After DNA extraction, taxa were identified to the lowest possible level using relevant taxonomic keys (see Hawking, 2000). In most instances this was species, but for some groups we had difficultly identifying species due to a lack of keys, expertise or because specimens were immature or damaged (e.g., most Ephemeroptera were missing legs/cerci prior to being processed).

All macroinvertebrate specimens used for these experiments were collected using a 250 µm net from riffle and pool habitats from several streams/rivers around the greater Melbourne area (Victoria, Australia) and stored in 100% ethanol at −20 °C until required.