Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

Abstract

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

“…In this study, we considered the correlation between feeding habits and the gut bacterial community of Ensifera to explore the dietary characteristics of the sample with contrasting feeding habits from the perspective of gut PLOS ONE bacterial community. Previous studies have shown that feeding habits could be determined using direct observation for some diurnal insects [63] and DNA sequence analysis was used for identifying gut contents for some insects that have difficulty in directly observing foraging behaviour [64][65][66]. Here, the bacterial community structure in herbivorous, omnivorous and carnivorous Ensifera was focused on, of which different gut bacterial community composition characteristics lacking unique bacteria, even with low abundance was found, and also common bacteria in the two or three feeding habits of Ensifera was found.…”

Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

“…eDNA metabarcoding enables understanding spatial and temporal patterns of fish biodiversity (reviewed in Bálint et al., 2018; Handley et al., 2019), both qualitatively (presence/absence) and quantitatively (abundance/biomass) (Hanfling et al., 2016; Li et al., 2019). The estimation of seasonal species abundance (Bista et al., 2017; Buxton, Groombridge, Zakaria, & Griffiths, 2017), relative species richness (Pont et al., 2018), detection of invasive species (Smart, Tingley, Weeks, van Rooyen, & McCarthy, 2015), vertical distribution patterns associated with latitudinal and depth gradients (Jeunen, 2018; Zintzen, Anderson, Roberts, Harvey, & Stewart, 2017), ancient DNA (Haile et al., 2009; Pedersen et al., 2015), zoonotic disease outbreaks (Sato et al., 2019), and host–microbiome interactions (Deagle, Kirkwood, & Jarman, 2009; Johny, Saidumohamed, Sasidharan, & Bhat, 2018; Van der Reis, Laroche, Jeffs, & Lavery, 2018) that are critical objectives in ecological studies (Gaston, 2000) have all been explored by eDNA‐based approaches. Comparing eDNA metabarcoding success with existing conventional monitoring methods is necessary to validate and calibrate the application of eDNA for conservation biology.…”

Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding

“…Some of the first studies on fecal metabarcoding were published in 2009 ( Figure 1). These studies indicated the effectiveness of fecal metabarcoding on animal diet estimation by conducting a comparison of the results from visual observations of fecal contents and previous diet records of each target species (Deagle, Kirkwood, & Jarman, 2009;Soininen et al, 2009;Valentini et al, 2009). Then, the number of annual publications gradually increased and more than doubled from 2017 to 2018 ( Figure 1).…”