Effects of consumer surface sterilization on diet DNA metabarcoding data of terrestrial invertebrates in natural environments and feeding trials

Abstract

DNA metabarcoding is an emerging tool used to quantify diet in environments and consumer groups where traditional approaches are unviable, including small‐bodied invertebrate taxa. However, metabarcoding of small taxa often requires DNA extraction from full body parts (without dissection), and it is unclear whether surface contamination from body parts alters presumed diet presence or diversity. We examined four different measures of diet (presence, rarefied read abundance, richness, and species composition) for a terrestrial invertebrate consumer (the spider Heteropoda venatoria) both collected in its natural environment and fed an offered diet item in contained feeding trials using DNA metabarcoding of full body parts (opisthosomas). We compared diet from consumer individuals surface sterilized to remove contaminants in 10% commercial bleach solution followed by deionized water with a set of unsterilized individuals. We found that surface sterilization did not significantly alter any measure of diet for consumers in either a natural environment or feeding trials. The best‐fitting model predicting diet detection in feeding trial consumers included surface sterilization, but this term was not statistically significant (β = −2.3, p‐value = .07). Our results suggest that surface contamination does not seem to be a significant concern in this DNA diet metabarcoding study for consumers in either a natural terrestrial environment or feeding trials. As the field of diet DNA metabarcoding continues to progress into new environmental contexts with various molecular approaches, we suggest ongoing context‐specific consideration of the possibility of surface contamination.

Metabarcoding analysis of different portions of the digestive tract of scorpions (Scorpiones, Arachnida) following a controlled diet regime shows long prey DNA half‐life

“…The hepatopancreas retained prey DNA sequences longest, followed by the mid-gut. This result finds support in similar studies conducted in spiders, where the opisthosoma (the tagma containing the mid-gut and the hepatopancreas) was the best body part to detect DNA of the consumed prey (Krehenwinkel et al, 2017;Macías-Hernández et al, 2018;Miller-ter Kuile et al, 2021).…”

Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds

“…We removed mussel individuals from the sediment and used sterile razor blades to collect a single biofilm sample from the shell of each mussel. Blades were rinsed with 90% ethanol, wiped with a sterile kimwipe, and flame sterilized for 1 min between samples ( Horton et al, 2019 ; Miller-ter Kuile et al, 2021 ). Five shell samples did not successfully sequence (three from A. ligamentina and two from A. plicata ) resulting in a final n of 19.…”

Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts

“…These species respond in composition, diversity, diet and abundance to productivity in this system [15,32]. In this study, we examined trophic patterns for a spider top predator, Heteropoda venatoria , and for spider intermediate predators Keijia mneon , Scytodes longipes and Neoscona theisi , which are all common, habitat generalist, intermediate predator species on the atoll and are predated by H. venatoria [29,30].…”

“…We also considered guano, rather than marine wrack, as a second-end source for (a) only consumers from high-productivity sites and (b) all consumers and found that isotopic trophic position stayed the same. Original explanations of sample processing for diet DNA data are in [29,30], although we adjusted bioinformatics filtering steps that were overly conservative from that original study to capture greater diet diversity, especially among predators. Specifically, while we originally removed all other predator species sequences from any sample that was run on the same sequencing run as those shared species, this step was likely overly conservative given that we followed best practices for both laboratory sample preparation and post-sequence filtering based on negative control samples [34].…”

“…Here, we combine trophic information across two predator groups (top predators and intermediate predators) using two complementary measurements of trophic ecology (diet DNA metabarcoding to capture diet community composition and diet community niche and stable isotope data δ 15 N and δ 13 C to capture trophic position and isotopic niche size) to explore how shifting basal ecosystem productivity alters food web structure. We examine both the isotopic and DNA-based trophic niches along with trophic position of a top predator (the active-hunting spider Heteropoda venatoria (Sparassidae)) and the DNA-based trophic niche of multiple other intermediate predator spiders in the order Araneae (web-building: Neoscona theisi (Araneidae), Keijia mneon (Theridiidae) and the sit-and-wait spider Scytodes longipes (Scytodidae))—which comprise some of the top predator's diet items [29,30]—across two different levels of ecosystem productivity (high and low). We ask (1) does ecosystem productivity alter top predator trophic niches and trophic position, and (2) does ecosystem productivity alter intermediate predator trophic niche?…”