DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets

DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets

Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.

Food availability aligns with contrasting demographics in populations of an at-risk songbird

Golden-winged Warblers (Vermivora chrysoptera) have become rare across much of their historic breeding range and response to conservation efforts is variable. Evidence from several recent studies suggests that breeding output is a primary driver explaining responses to conservation and it is hypothesized that differences in food availability may be driving breeding output disparity between two subpopulations of the warbler's Appalachian breeding range. Herein, we studied two subpopulations: central Pennsylvania ("central subpopulation"), where breeding productivity is relatively low, and eastern Pennsylvania ("eastern subpopulation"), where breeding productivity is relatively high. To test the food-availability hypothesis in this system, we measured density of caterpillars, plasma lipid metabolites (triglycerides [TRIG; fat deposition] and glycerol [GLYC; fat breakdown]), body mass of adults males, and acquired body mass data for fledglings at 38 sites managed for nesting habitat. Consistent with our prediction, leaf-roller caterpillar density, the group upon which Golden-winged Warblers specialize, was 45× lower in the central subpopulation than the eastern subpopulation. TRIG concentrations were highest within the eastern subpopulation during breeding grounds arrival. The change in TRIG concentrations from the breeding-grounds-arrival stage to the nestling-rearing stage was subpopulation dependent: TRIG decreased in the eastern subpopulation and was constant in the central subpopulation, resulting in similar concentrations during the nestling-rearing stage. Furthermore, GLYC concentrations were higher in the eastern subpopulation, which suggests greater energy demands in this region. Despite this, adult male warblers in the eastern subpopulation maintained a higher average body mass. Finally, fledgling body mass was 16% greater in the eastern subpopulation than the central subpopulation before and after fledging. Collectively, our results suggest that poor breeding success of Golden-winged Warblers in the central subpopulation could be driven by lower availability of primary prey during the breeding season (leaf-roller caterpillars), and this, in turn, limits their response to conservation efforts.

Exploring the biological diversity and source species of medicinal horseflies through metabarcoding

Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy. In this current study, we collected 14 batches, totaling 13,528 individuals, from various provinces in China. Instead of "classic" DNA barcoding strategy, we employed a high-throughput metabarcoding approach to assess the biological composition of crude drug mixtures derived from horseflies. Our analysis identified 40 Amplicon Sequence Variants (ASVs) with similarity percentages ranging from 92% to 100% with 12 previously reported species. Species delimitation methods revealed the presence of 11 Molecular Operational Taxonomic Units (MOTUs), with ten belonging to the Tabanus genus and one to Hybomitra. Tabanus sp6 displayed the highest relative abundance, and its ASVs showed close resemblance to Tabanus pleski. Our investigations revealed that the medicinal batches were biologically composed of 6 to 12 species. Some batches contained ASVs that closely resembled species previously associated with false Tabanus species. In conclusion, our findings offer valuable insights into the biological composition of crude drugs derived from horseflies and have the potential to enhance the quality of these traditional medicines.

The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae

Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications. The application of DNA metabarcoding provides a solution by enabling the determination of the biological source of a large sample. In the current study, we collected 19 batches of Grubs, consisting of 11,539 individuals, from the market and analyzed their biological composition through metabarcoding. We identified 49 Amplicon Sequence Variants (ASVs), 21 of which were Grubs. The 21 ASVs were classified into seven Molecular Operational Taxonomic Units (MOTUs) through species delimitation, which revealed that commercially available Grubs are predominantly sourced from Protaetia brevitarsis seulensis, while species of Rutelinae, Anomala, and Holotrichia were also abundant in some commercial batches. Among the identified ASVs, 28 belonged to non-Grub species and indicated adulteration from different animal families; high abundances of these ASVs were detected for Bombycidae, Tabanidae, and Viviparidae. Our findings underscore the complexity of Grubs' species composition and advocate for a deeper understanding of the wildlife sources contributing to herbal products. This research contributes valuable insights into the molecular identification of Grubs, paving the way for enhanced quality assurance in traditional medicine applications to provide safe and effective medicines for humanity.

Fecal DNA metabarcoding helps characterize the Canada jay's diet and confirms its reliance on stored food for winter survival and breeding

Accurately determining the diet of wild animals can be challenging if food items are small, visible only briefly, or rendered visually unidentifiable in the digestive system. In some food caching species, an additional challenge is determining whether consumed diet items have been previously stored or are fresh. The Canada jay (Perisoreus canadensis) is a generalist resident of North American boreal and subalpine forests with anatomical and behavioural adaptations allowing it to make thousands of arboreal food caches in summer and fall that are presumably responsible for its high winter survival and late winter/early spring breeding. We used DNA fecal metabarcoding to obtain novel information on nestling diets and compiled a dataset of 662 published and unpublished direct observations or stomach contents identifications of natural foods consumed by Canada jays throughout the year. We then used detailed natural history information to make informed decisions on whether each item identified to species in the diets of winter adults and nestlings was best characterized as 'likely cached', 'likely fresh' (i.e., was available as a non-cached item when it appeared in a jay's feces or stomach), or 'either possible'. Of the 87 food items consumed by adults in the winter, 39% were classified as 'likely cached' and 6% were deemed to be 'likely fresh'. For nestlings, 29% of 125 food items identified to species were 'likely cached' and 38% were 'likely fresh'. Our results support both the indispensability of cached food for Canada jay winter survival and previous suggestions that cached food is important for late winter/early spring breeding. Our work highlights the value of combining metabarcoding, stomach contents analysis, and direct observations to determine the cached vs. non-cached origins of consumed food items and the identity of food caches, some of which could be especially vulnerable to degradation through climate change.

Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps

A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet.

Exploring and validating observations of non-local species in eDNA samples

The development of DNA-based methods in recent decades has opened the door to numerous new lines of research in the biological sciences. While the speed and accuracy of DNA methodologies are clearly beneficial, the sensitivity of these methods has the adverse effect of increased susceptibility to false positives resulting from contamination in field or lab. Here, we present findings from a metabarcoding study on the diet of and food availability for five insectivorous birds, in which multiple lepidopteran species not known to occur locally were discovered. After describing the pattern of occurrences of these non-local species in the samples, we discuss various potential origins of these sequences. First, we assessed that the taxonomic assignments appeared reliable, and local occurrences of many of the species could be plausibly ruled out. Then, we looked into the possibilities of natural environmental contamination, judging it to be unlikely, albeit impossible to fully falsify. Finally, while dissimilar combinations of non-local species' occurrences across the samples did not initially suggest lab contamination, we found overlap with taxa and sequences handled in the same lab, which was undoubtedly not coincidental. Even so, not all exact sequences were accounted for in these locally conducted studies, nor was it clear if these and other sequences could remain detectable years later. Although the full explanation for the observations of non-local species remains inconclusive, these findings highlight the importance of critical examination of metabarcoding results, and showcase how species-level taxonomic assignments utilizing comprehensive reference libraries may be a tool in detecting potential contamination events, and false positives in general.

Assessment of the diet of the critically endangered northern hairy-nosed wombat (Lasiorhinus krefftii) using DNA metabarcoding

Invasive buffel grass (Cenchrus ciliaris) is considered a threat to the critically endangered northern hairy-nosed wombat (Lasiorhinus krefftii; NHW). Buffel grass outcompetes native grasses, reducing availability of native food items for NHW, and causes more intense fires due to the large volumes of dead matter it produces. Previous studies suggested buffel grass was increasing in the diet; however, the diet of the NHW has not been reassessed for over two decades and was limited to Epping Forest National Park, with the population at Richard Underwood Nature Refuge having never been assessed. The recently released 2022 Recovery Action Plan for the species outlined objectives to assist its conservation and recommended the impact of buffel grass on the species' diet be investigated. This study aimed to determine: (1) which plant species are being consumed by the NHW; (2) the differences in the diet between sites; (3) differences between seasons; and (4) the abundance of buffel grass in the diet. The diet was assessed using DNA metabarcoding of scat samples collected from both sites from winter 2020 to spring 2021. Site and season significantly affected the diet of the NHW. Buffel grass dominated the diet and has increased in the diet since past assessments. The findings of this study will support population and habitat management of the critically endangered NHW. Enhanced knowledge of dietary items consumed at both sites will also assist efforts to locate additional sites suitable for translocation.

Diet composition of wild columbiform birds: next-generation sequencing of plant and metazoan DNA in faecal samples

Accurate knowledge of a species' diets is fundamental to understand their ecological requirements. Next-generation sequencing technology has become a powerful and non-invasive tool for diet reconstruction through DNA metabarcoding. Here, we applied those methods on faecal samples of Common Woodpigeons Columba palumbus, European Turtle Doves Streptopelia turtur, and Stock Doves C. oenas to investigate their dietary composition. By applying primer pairs targeting both the ITS2 region of plant nuclear DNA and the mitochondrial COI region of metazoan DNA, we provide a complete picture of the food ingested and estimate the dietary overlap between the columbiform species during the breeding season. Animal DNA was present very rarely, and a diverse range of plants from the class Spermatopsida dominated the diet, with Asteraceae, Brassicaceae, Cucurbitaceae, Fabaceae, and Poaceae as the most frequently represented families. Generally, we detected a variability between species but also amongst individual samples. Plant species already known from previous studies, mainly visual analyses, could be confirmed for our individuals sampled in Germany and the Netherlands. Our molecular approach revealed new plant taxa, e.g. plants of the families Malvaceae for Woodpigeons, Lythraceae for Turtle Doves, and Pinaceae for Stock Doves, not found in previous studies using visual analyses. Although most of the plant species observed were of wild origin, the majority of cultivated plants found were present in higher frequencies of occurrence, suggesting that cultivated food items likely constitute an important part of the diet of the studied species. For Turtle Doves, a comparison with previous studies suggested regional differences, and that food items (historically) considered as important part of their diet, such as Fumitory Fumaria sp. and Chickweed Stellaria media, were missing in our samples. This indicates that regional variations as well as historic and current data on diet should be considered to plan tailored seed mixtures, which are currently proposed as an important management measure for conservation of the rapidly declining Turtle Dove.

Environmental abundances of the non-native round goby Neogobius melanostomus influence feeding of native fish predators

The authors assessed the importance of the round goby Neogobius melanostomus as prey for three native predatory fish species, Atlantic cod Gadus morhua, European perch Perca fluviatilis and northern pike Esox lucius, in a northern and southern area of the Baltic Proper, using a combination of visual analysis and DNA metabarcoding of predator stomach contents. To explore the influence of environmental abundances of N. melanostomus on predation, they related the occurrence of N. melanostomus in predator diets to its abundance in survey fishing. Gadus morhua and E. lucius in the southern area showed the highest tendency to feed on N. melanostomus when it was abundant, as N. melanostomus occurred in up to 100% of stomachs and constituted up to 88% of the total diet volume proportion. The diet contribution of N. melanostomus was associated with N. melanostomus abundances for G. morhua and E. lucius, and when N. melanostomus was abundant, these predators exhibited lower prey richness and a higher degree of piscivory. G. morhua and P. fluviatilis also fed less on crustacean prey when N. melanostomus was abundant. The high importance of N. melanostomus in diets of native fish predators may modify indirect interactions between N. melanostomus and native prey species in invaded coastal communities.

Aircraft surveys for air eDNA: probing biodiversity in the sky

Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.

Future of DNA-based insect monitoring

Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).

The importance of population contextual data for large-scale biomonitoring using an apex predator: The Tawny Owl (Strix aluco)

Top predators are often used as sentinel species in contaminant monitoring due to their exposure and vulnerability to persistent, bioaccumulative and, in some cases, biomagnificable contaminants. Some of their ecological traits can vary in space and time, and are known to influence the contamination levels and therefore information on ecological traits should be used as contextual data for correct interpretation of large-scale contaminant spatial patterns. These traits can explain spatiotemporal variation in contaminant exposure (traits such as diet and dispersal distances) or contaminant impacts (traits such as population trend and clutch size). The aim of our research was to review the spatial variation in selected contextual parameters in the Tawny Owl (Strix aluco), a species identified by the COST Action European Raptor Biomonitoring Facility as one of the most suitable candidates for pan-European biomonitoring. A considerable variation in availability of published and unpublished contextual data across Europe was found, with diet being the most extensively studied trait. We demonstrate that the Tawny Owl is a suitable biomonitor at local scale but also that taking spatial variation of other contextual data (e.g. diet) into account is necessary. We found spatial gaps in knowledge about the species ecology and biology in Southern Europe, along with gaps in certain population parameters (e.g. population trends) in several countries. Based on our findings, we proposed a minimal recommended scheme for monitoring of population contextual data as one of the first steps towards a pan-European monitoring scheme using the Tawny Owl.