Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

All in the Details: A First Assessment for the Viability of Metabarcoding in Diet Composition Analysis of African Wild Dogs (Lycaon pictus)

DNA metabarcoding is a contemporary technique in diet composition studies and stands to fill key knowledge gaps left by traditional diet analysis methods. For endangered species such as the African wild dog (Lycaon pictus), the fulfilment of these knowledge gaps presents an opportunity for improved management practices and vulnerability assessments. There are an estimated ~600 African wild dogs remaining in South Africa. These dogs are generally understood to prey upon impala (Aepyceros melampus) and other medium-sized ungulates. Here, we present the first assessment of DNA metabarcoding as a valuable method for diet composition analysis of this highly social carnivore. DNA from faecal samples collected across seven landscape types in the Kruger National Park (KNP) was extracted and used to determine the presence of seven unique prey taxa, including novel species such as the Cape hare (Lepus capensis). Impala was identified as a prey item in all landscape types, complementing the diet preference prediction made with stable isotope analysis using the same samples and existing understanding of wild dog diet. Given recommended improvements, the application of DNA metabarcoding in wild dog diet analysis shows promising prospects for identifying novel prey species and validating previous records of this endangered canids diet.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Unveiling the diet of two generalist stink bugs, Halyomorpha halys and Pentatoma rufipes (Hemiptera: Pentatomidae), through metabarcoding of the ITS2 region from gut content

BACKGROUND

The use of DNA metabarcoding has become an increasingly popular technique to infer feeding relationships in polyphagous herbivores and predators. Understanding host plant preference of native and invasive herbivore insects can be helpful in establishing effective integrated pest management (IPM) strategies. The invasive Halyomorpha halys and native Pentatoma rufipes are piercing-sucking stink bug pests that are known to cause economic damage in commercial fruit orchards.

RESULTS

In this study, we performed molecular gut content analysis (MGCA) on field-collected specimens of these two herbivorous pentatomids using next-generation amplicon sequencing (NGAS) of the internal transcribed spacer 2 (ITS2) barcode region. Additionally, a laboratory experiment was set up where H. halys was switched from a mixed diet to a monotypic diet, allowing us to determine the detectability of the initial diet in a time series of ≤3 days after the diet switch. We detected 68 unique plant species from 54 genera in the diet of two stink bug species, with fewer genera found per sample and a smaller diet breadth for P. rufipes than for H. halys. Both stink bug species generally prefer deciduous trees over gymnosperms and herbaceous plants. Landscape type significantly impacted the observed genera in the diet of both stink bug species, whereas season only had a significant effect on the diet of H. halys.

CONCLUSION

This study provides further insights into the dietary composition of two polyphagous pentatomid pests and illustrates that metabarcoding can deliver a relevant species-level resolution of host plant preference. © 2024 Society of Chemical Industry.

Faecal DNA Metabarcoding for Diet Analysis of Endangered Fish Species, Odontobutis obscurus

Understanding the ecological characteristics of endangered species is essential for their management and conservation. The dark sleeper (Odontobutis obscurus) is a carnivorous freshwater fish that has been designated an endangered species in South Korea because of its highly restricted habitat range and small population size. However, ecological research on prey items for this species remains severely limited globally, posing challenges for establishing conservation measures such as translocation management. In this study, the food sources and feeding strategies of O. obscurus were identified through non-invasive faecal DNA metabarcoding. A total of 24 O. obscurus specimens were collected from Sanyang Stream on Geoje Island, and faecal DNA was amplified using mitochondrial cytochrome c oxidase I (COI) primer. As a result, 13 prey items were identified, comprising fish and benthic invertebrates. Dietary metrics revealed the overall food composition and major food source of O. obscurus, and the Costello method enabled graphical diet analysis, suggesting that O. obscurus is a generalist, feeding on a wide variety of food sources. The food selectivity index suggested that O. obscurus prefers specific prey items, such as genus Misgurnus, Zacco (fish), Radix (gastropod), and Ephemera (mayfly). This molecular method facilitated the diet analysis of an endangered fish species that cannot undergo dissection, providing crucial information for their management, particularly regarding translocation efforts.

Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding

In the global processed seafood industry, disparate actors play different roles along the supply chain, creating multiple opportunities for mistakes, malpractice, and fraud. As a consequence, consumers may be exposed to non-authentic products, which hinder informed purchasing decisions and broader efforts to improve trade transparency and sustainability. Here, we characterised the taxonomic composition of 62 processed seafood products in Italian, British and Albanian retailers, purposefully obtained from different supply routes, using multiple DNA metabarcoding markers. By combining molecular results with metadata reported on labels, we revealed patterns of mislabelling in 24 products (39%) across sampling regions, denoting lack of transparency of processed seafood products based on resources sourced from either Europe or globally. We show that the accuracy of label claims and the mis-represented and underestimated levels of traded biodiversity are largely determined by the management of raw material by global processors. Our study shows that DNA metabarcoding is a powerful and novel authentication tool that is mature for application at different stages of the seafood supply chain to protect consumers and improve the sustainable management of fish stocks.

High Resource Overlap and a Consistently Generalised Pattern of Interactions in a Bat-Flower Network in a Seasonally Dry Landscape

Pollination is an ecosystem process that is crucial to maintain biodiversity and ecosystem function. Bats are important pollinators in the tropics and are an integral part of complex plant-pollinator interaction networks. However, network analysis-based approaches are still scarce at the plant species and bat community levels. We used metabarcoding to identify plant taxa present in pollen from fur and faecal samples collected across 1 year from three nectar-feeding bat roosts in central Mexico. We calculated the frequency of occurrence of plant taxa and assembled a zoocentric network of bat-plant interactions. We constructed a year-long network, encompassing the entire period of sampling, two seasonal networks comprising the wet and dry seasons, and six individual networks from sampling at two-month intervals across the year. Four species of nectar-feeding bats interacted with 36 plant species from 16 families. We found highly generalised interaction patterns across networks corresponding with opportunistic feeding behaviour by bats, with little seasonal variation in network structure. There was high resource overlap between bat species, and bats visited a diverse range of plant species even during periods with a high abundance of particular resources in the landscape. The diverse diet of nectar-feeding bats emphasises the importance of floristically rich natural habitats in the landscape to provide reliable foraging resources year-round in a seasonally variable system. While a generalised network structure is thought to increase robustness, further research is necessary to understand how fluctuations in pollinator abundance and diversity in the face of land use and climate change may impact bat-flower networks and the consequences to plant communities.

Using grass inflorescence as source material for biomonitoring through environmental DNA metabarcoding

BACKGROUND

Over the last decade, increasing attention has been directed to using different substrates as sources of environmental DNA (eDNA) in ecological research. Reports on the use of environmental DNA located on the surface of plant leaves and flowers have highlighted the utility of this DNA source in studies including, but not limited to, biodiversity, invasive species, and pollination ecology. The current study assesses grass inflorescence as a source of eDNA for detecting invertebrate taxa.

METHODS AND RESULTS

Inflorescences from four common grass species in a central South African grassland were collected for high-throughput sequencing analysis. Universal COI primers were utilised to detect Metazoan diversity. The sequencing results allowed for the detection of three Arthropoda orders, with most OTUs assigned to fungal taxa (Ascomycota and Basidiomycota). Some biases were detected while observing the relative read abundance (RRA) results.

DISCUSSION

The observed biases could be explained by the accidental inclusion of invertebrate specimens during sample collection and DNA extraction. Primer biases towards the amplified taxa could be another reason for the observed RRA results. This study provided insight into the invertebrate community associated with the four sampled grass species. It should be noted that with the lack of negative field controls, it is impossible to rule out the influence of airborne eDNA on the observed diversity associated with each grass species. The lack of the inclusion of PCR and extraction blanks in the sequencing step, as well as the inclusion of negative field controls, including other areas for refinement were highlighted, and suggestions were provided to improve the outcomes of future studies.

Different coexistence patterns between apex carnivores and mesocarnivores based on temporal, spatial, and dietary niche partitioning analysis in Qilian Mountain National Park, China

Carnivores play key roles in maintaining ecosystem structure and function as well as ecological processes. Understanding how sympatric species coexist in natural ecosystems is a central research topic in community ecology and biodiversity conservation. In this study, we explored intra- and interspecific niche partitioning along spatial, temporal, and dietary niche partitioning between apex carnivores (wolf Canis lupus, snow leopard Panthera uncia, Eurasian lynx Lynx lynx) and mesocarnivores (Pallas's cat Otocolobus manul, red fox Vulpes vulpes, Tibetan fox Vulpes ferrilata) in Qilian Mountain National Park, China, using camera trapping data and DNA metabarcoding sequencing data. Our study showed that apex carnivore species had more overlap temporally (coefficients of interspecific overlap ranging from 0.661 to 0.900) or trophically (Pianka's index ranging from 0.458 to 0.892), mesocarnivore species had high dietary overlap with each other (Pianka's index ranging from 0.945 to 0.997), and apex carnivore and mesocarnivore species had high temporal overlap (coefficients of interspecific overlap ranging from 0.497 to 0.855). Large dietary overlap was observed between wolf and snow leopard (Pianka's index = 0.892) and Pallas's cat and Tibetan fox (Pianka's index = 0.997), suggesting the potential for increased resource competition for these species pairs. We concluded that spatial niche partitioning is likely to key driver in facilitating the coexistence of apex carnivore species, while spatial and temporal niche partitioning likely facilitate the coexistence of mesocarnivore species, and spatial and dietary niche partitioning facilitate the coexistence between apex and mesocarnivore species. Our findings consider partitioning across temporal, spatial, and dietary dimensions while examining diverse coexistence patterns of carnivore species in Qilian Mountain National Park, China. These findings will contribute substantially to current understanding of carnivore guilds and effective conservation management in fragile alpine ecosystems.

Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability

Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing "green" season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons.

Integrating eDNA metabarcoding and citizen science enhances avian ecological research

Research Highlight: Bourbour et al., 2024. Feeding en route: Prey availability and traits influence prey selection by an avian predator on migration. Journal of Animal Ecology. Diet selection plays a key role in the eco-evolutionary dynamics of animals, exhibiting substantial variability across species, environments and seasons. The complex interplay between movement capability, hunting strategies, habitat use, prey traits and availability shapes the foraging patterns of avian predators. However, detailed information on how these birds exploit their extensive territories remains limited. In this study, Bourbour et al. utilised a novel integration of eDNA metabarcoding and citizen science to explore predator-prey interactions between migrating sharp-shinned hawks (Accipiter striatus) and an ephemeral avian prey community along North America's Pacific flyway. The research identified 1396 detections from the diet (65 species) of 588 migrating sharp-shinned hawks. Hawks' diet composition correlated with prey abundance indices sourced from the eBird database throughout the migration season, highlighting the significant impact of prey availability-shaped by migration tendency, flocking behaviour, and habitat-on raptor-songbird interactions. Notably, the study also found significant differences in prey size between male and female hawks, indicating that sexual dimorphism has led to diverse foraging strategies during migration. These findings underscore the potential of combining eDNA metabarcoding with citizen science to deepen our understanding of the foraging ecology of highly mobile and wide-ranging birds, as well as to monitor complex and vast ecosystems.

Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.

Invasive wild pig (Sus scrofa) diets on barrier islands in the southeastern United States

BACKGROUND

Biological invasions are a leading cause of reductions in global biodiversity. Islands are particularly sensitive to invasions, which often result in cascading impacts throughout island communities. Wild pigs (Sus scrofa) are globally invasive and pose threats to numerous taxa and ecosystems, particularly for islands where they have contributed to declines of many endemic species. However, the impacts of wild pig diet on the flora and fauna remain understudied in many island systems.

RESULTS

We used DNA metabarcoding of wild pig fecal samples to quantify the seasonal diet composition of wild pigs on three barrier islands in the southeastern United States. Wild pigs exhibited a diverse diet dominated by plants, but also including marine and terrestrial animals. The diet composition of plants varied seasonally and between islands. Consumption of invertebrates also changed seasonally, with a shift to coastal invertebrates, particularly crabs, in spring and summer. Vertebrates were found in <10% of samples, but spanned broad taxa including amphibians, fish, mammals, and reptiles. Species consumed by wild pigs indicate that wild pigs use a variety of habitats within barrier islands for foraging, including maritime forests, saltmarshes, and beaches.

CONCLUSIONS

An observed shift to beach foraging during sea turtle nesting season suggests wild pigs have potential to hinder nesting success on islands without established management programs. These findings provide insight into the diverse diets of wild pigs on barrier islands and highlight the need for removal of wild pigs from sensitive island ecosystems because of their potential impacts to native plant and animal communities. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Eurasian otters prefer to prey on religious released non-native fish on the Qinghai-Tibetan Plateau

Religious wildlife release is prevalent worldwide, especially in Asia countries. It is one of the anthropogenic pathways to cause biological invasions. Religious fish release is common on the Qinghai-Tibetan Plateau, yet few studies have assessed the influences of religious fish release on local species. In Yushu, a city on the Qinghai-Tibetan Plateau, we interviewed local people, conducted fish trap surveys in local rivers, and examined the diet of Eurasian otters Lutra lutra using a fecal DNA metabarcoding approach. We found that fish release started at least in 1980-1990s in Yushu. Tibetan residents released fish in large amounts and released fish were usually exotic commercial fish purchased from market. Despite such long-term and intensive fish release activities, released fish were few in local rivers. On the other hand, Eurasian otters mainly prey on fish and released fish accounted for ~20% of relative read abundance of prey DNA in otters' diet, indicating their high preference on released fish. Our study suggested that religious fish release may provide additional food resources for otters, whereas otters, as a top predator in local rivers, may deplete non-native fish once they were released and, therefore, reduce the probability of colonization of released fish, although further studies are required to assess otters' impact. Our study revealed otters' diet in Yushu, providing basic information for local otter management and conservation. Furthermore, it represents a case showing that native predators prey on religious released animals, implying a probable direction for controlling invasive species through native predator conservation.

Rodents consuming the same toxic diet harbor a unique functional core microbiome

Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.S. desert southwest from 20 populations (~ 150 individuals) with differential ingestion of creosote bush and analyzed three gut regions (foregut, cecum, hindgut) using16S sequencing and shotgun metagenomics. In each gut region sampled, we found a distinctive set of microbes in individuals feeding on creosote bush that were more abundant than other ASVs, enriched in creosote feeding woodrats, and occurred more frequently than would be predicted by chance. Creosote core members were from microbial families e.g., Eggerthellaceae, known to metabolize plant secondary compounds and three of the identified core KEGG orthologs (4-hydroxybenzoate decarboxylase, benzoyl-CoA reductase subunit B, and 2-pyrone-4, 6-dicarboxylate lactonase) coded for enzymes that play important roles in metabolism of plant secondary compounds. The results support the hypothesis that the ingestion of creosote bush sculpts the microbiome across all major gut regions to select for functional characteristics associated with the degradation of the PSCs in this unique diet.

Diet of Andean leaf-eared mice (Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes

On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ('aolian deposits'). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such plants may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.

Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea

This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.

Multi-dimensional niche differentiation of two sympatric breeding secondary cave-nesting birds in Northeast China using DNA metabarcoding

Niche theory predicts that ecologically similar sympatric species should show differentiation in at least one of the main niche dimensions (time, space, and/or food). Here, we combined observations of breeding timing, nest site selection, and diet (the latter determined using DNA metabarcoding) to analyze the niche overlap and differentiation between two sympatric secondary cavity-nesting birds, the Japanese Tit Parus minor and the Yellow-rumped Flycatcher Ficedula zanthopygia. The results showed that (1) there were significant differences in the first egg laying date, length of the egg laying period, incubation date, and hatching date between tits and flycatchers, and the breeding time of flycatchers peaked later (about 30 days) than that of tits; (2) the two species had a large overlap in nest site selection, although the canopy coverage and shrub density of flycatchers were significantly higher than those of tits; and (3) the niche overlap in diet was minimal, with both species heavily relying on Lepidoptera (39.6% and 63.7% for tits and flycatchers, respectively), but with flycatchers consuming significantly higher percentages of Lepidoptera, Diptera, and Coleoptera than tits. The results indicate that these two sympatric secondary cavity-nesting species have significant niche differentiation in breeding time and diet, but little differentiation in nest site selection.

Sex-specific diet differences in harbor seals (Phoca vitulina) via spatial assortment

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul-out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul-out sites in the inland waters of Washington State and the province of British Columbia during 2012-2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase chain reaction (qPCR). We analyzed 2405 harbor seal scat samples using generalized linear mixed models (GLMMs) to examine the factors influencing harbor seal sex ratio at haul-out sites and permutational multivariate analysis of variance (PERMANOVA) to examine the influence of sex and haul-out site on harbor seal diet composition. We found that the overall sex ratio was 1:1.02 (female:male) with notable spatiotemporal variation. Salmoniformes were about 2.6 times more abundant in the diet of males than in the diet of females, and Chinook salmon comprised ca. three times more of the average male harbor seal's diet than the average female's diet. Based on site-specific sex ratios and diet data, we identified three haul-out sites where Chinook salmon appear to be under high predation pressure by male harbor seals: Cowichan Bay, Cutts Area, and Fraser River. Our study indicates that combining sex-specific pinniped diet data with the sex ratio of haul-out sites can help identify priority sites of conservation concern.

Group 2i Isochrysidales thrive in marine and lacustrine systems with ice cover

Global warming is causing rapid changes to the cryosphere. Predicting the future trajectory of the cryosphere requires quantitative reconstruction of its past variations. A recently identified sea-ice-associated haptophyte, known as Group 2i Isochrysidales, has given rise to a new sea-ice proxy with its characteristic alkenone distributions. However, apart from the occurrence of Group 2i Isochrysidales in regions with sea ice, and the empirical relationship between C37:4 alkenone abundance and sea-ice concentration, little is known about the ecology of these haptophyte species. Here, we systematically mapped the spatial and temporal occurrence of known Group 2i Isochrysidales based on environmental DNA in both marine and lacustrine environments. Our results indicate Group 2i is widely distributed in icy marine and lacustrine environments in both Northern and Southern Hemisphere, but is absent in warm environments. Temporally, Group 2i is part of the sea-ice algae bloom during the cold seasons, in contrast to other Isochrysidales that bloom in open waters during warm seasons. Our results indicate that ice is a prerequisite for the occurrence of the psychrophilic Group 2i haptophytes in marine and lacustrine ecosystems and further affirms its value for past ice reconstructions.

All-you-can-eat buffet: A spider-specialized bat species (Myotis emarginatus) turns into a pest fly eater around cattle

Determining the dietary spectrum of European insectivorous bats over time is the cornerstone of their conservation, as it will aid our understanding of foraging behavior plasticity in response to plummeting insect populations. Despite the global decline in insects, a restricted number of arthropod pest species thrive. Yet past research has overlooked the potential of European bats to suppress pests harmful to woodlands or livestock, in spite of their economic relevance. Here we investigated the diet composition, its breeding season variations and pest consumption of an insectivorous bat species (Myotis emarginatus), at the northern edge of its range (Wallonia, Belgium). We also explored the prey ecology to gain insight into the hunting strategies and foraging habitats of this bat species. We used DNA metabarcoding to amplify two COI markers within 195 bat droppings collected in June, July and August, thereby identifying 512 prey taxa predominated by Diptera, Araneae and Lepidoptera. Overall, in 97% of the samples we detected at least one of the 58 potential pest taxa, 41 of which targeting trees. The June samples were marked by a diet rich in orb-weaver spiders, in accordance with the archetypal diet of M. emarginatus bats. However, during the highly energy demanding July-August parturition and lactation period, roughly 55% of the dropping samples contained two cattle fly pests (Stomoxys calcitrans and Musca domestica). Moreover, among the 88 Diptera species preyed upon by M. emarginatus in July and August, these flies accounted for around 50% of the taxa occurrences. This plasticity-the switch from a spider-rich to a fly-rich diet-seems providential considering the dramatic ongoing drop in insect populations but this involves ensuring bat-friendly cattle farming. Our results revealed that bats widely consume pest entomofauna, thereby highlighting their potential role as allies of forest managers and farmers.

DNA metabarcoding analysis of the bare-nosed wombat (Vombatus ursinus) diet

Wombats are native herbivorous grazers that have adapted to Australia's low-quality forage. Studies on diet selection by bare-nosed wombats (Vombatus ursinus) are limited and are either observational or based on microhistological studies. The current study determined the diet of wombats through DNA metabarcoding across five study sites in New South Wales over a one-year period. Metabarcoding was chosen as it is non-invasive, less time consuming and more specific than traditional techniques. The list of 209 plant species identified as eaten by wombats in this study is much higher than previously reported, with grasses being the most common plant group identified in all samples. Most dietary items identified were introduced plant species. Seasonal differences in plants eaten occurred at four of the five study sites and may reflect dietary abundance and floristic composition at different times of year. Further studies are required to determine if the dietary items differ markedly across the entire range of wombats, and if nutrition influences dietary preferences.

Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR

Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.

Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species

Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.

Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.

Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan

Small islands tend to lack predators because species at higher trophic levels often cannot survive. However, two exceptional top predators-the Iriomote cat Prionailurus bengalensis iriomotensis, and the Crested Serpent Eagle Spilornis cheela perplexus-live on the small Iriomote Island in the Ryukyu Archipelago. To understand how these predators coexist with limited resources, we focused on their seasonal diets between which conflicts are considered to occur. To compare the diets, we used DNA metabarcoding analysis of faecal samples. In the summer, we identified 16 unique prey items from Iriomote cat faecal samples and 15 unique prey items from Crested Serpent Eagle faecal samples. In the winter, we identified 37 and 14, respectively. Using a non-metric multidimensional scaling and a permutational multivariate analysis of variance, our study reveals significant differences in the diet composition at the order level between the predators during both seasons. Furthermore, although some prey items at the species-to-order level overlapped between them, the frequency of occurrence of most prey items differed in both seasons. These results suggest that this difference in diets is one of the reasons why the Iriomote cat and the Crested Serpent Eagle are able to coexist on such a small island.

The origin, connectivity, and individual specialization of island wolves after deer extirpation

Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting on sea otters and other marine resources without ungulate prey, violating this long-held assumption. We address questions about these wolves regarding their origin and fate, degree of isolation, risk of inbreeding depression, and diet specialization by individual and sex. We applied DNA metabarcoding and genotyping by amplicon sequencing using 957 scats collected from 2016 to 2022, and reduced representation sequencing of tissue samples to establish a detailed understanding of Pleasant Island wolf ecology and compare them with adjacent mainland wolves. Dietary overlap was higher among individual wolves on Pleasant Island (Pianka's index mean 0.95 ± 0.03) compared to mainland wolves (0.70 ± 0.21). The individual diets of island wolves were dominated by sea otter, ranging from 40.6% to 63.2% weighted percent of occurrence (wPOO) (mean 55.5 ± 8.7). In contrast, individual mainland wolves primarily fed on ungulates (42.2 ± 21.3) or voles during a population outbreak (31.2 ± 23.2). We traced the origin of the Pleasant Island pack to a mainland pair that colonized around 2013 and produced several litters. After this breeding pair was killed, their female offspring and an immigrant male became the new breeders in 2019. We detected 20 individuals of which 8 (40%) were trapped and killed while two died of natural causes during the 6-year study. Except for the new breeding male, the pedigree analysis and genotype results showed no additional movement to or from the island, indicating limited dispersal but no evidence of inbreeding. Our findings suggest wolves exhibit more flexible foraging behavior than previously believed, and hunting strategies can substantially differ between individuals within or between packs. Nevertheless, anthropogenic and natural mortality combined with limited connectivity to the mainland may inhibit the continued persistence of Pleasant Island wolves.

A CRISPR-based strategy for targeted sequencing in biodiversity science

Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.

High-throughput sequencing and fatty acid profile analyses of the Black Amur bream (Megalobrama terminalis) reveal variation in dietary niche associated with geographic segregation

Fish dietary niche is a core focus, and it reflects the diversity of resources, habitats, or environments occupied by a species. However, whether geographic segregation among different populations triggers dietary diversification and concomitant fish niche shift remains unknown. In the present study, we selected the Black Amur bream (Megalobrama terminalis) is a migratory fish species that plays an important role in the material transfer and energy cycling of river ecosystems, inhabiting southern China drainage with multiple geographic populations. Here, we utilized the combined analyses of 18S rDNA high-throughput sequencing in fish gut contents and fatty acid (FA) in muscle tissues to evaluate potential spatial patterns of habitat and resource use for M. terminalis in three rivers of southern China. Our results showed that prey items of the Xijiang (XR) population (Pearl River) exhibited the highest species diversity and richness among the three geographic populations. Moreover, diet composition of M. terminalis was affected by spatial differences associated with geographic segregation. Analyses of FA biomarkers indicated that the highest levels of C16:0, C18:3n-3, and C18:2n-6c were found in Wanquan (WS) population (Wanquan River). The XR population exhibited a distinct FA profile characterized by higher amounts of arachidonic acid (ARA) and docosahexaenoic acid (DHA). The Moyang (MY) population (Moyang River) acted as the linkage between WS and XR populations and consisted of middle levels of saturated FAs (SFAs) and polyunsaturated FAs (PUFAs). The XR population displayed a greater FA niche width compared with WS population. Furthermore, we observed a close positive relationship between the niche width and α-diversity indices of dietary resources for FA proflies. Our study provides valued information to develop different conservation strategies among different populations and improve fisheries management for M. terminalis and other endemic species in local rivers.

Is the diet cyclic phase-dependent in boreal vole populations?

Herbivorous rodents in boreal, alpine and arctic ecosystems are renowned for their multi-annual population cycles. Researchers have hypothesised that these cycles may result from herbivore-plant interactions in various ways. For instance, if the biomass of preferred food plants is reduced after a peak phase of a cycle, rodent diets can be expected to become dominated by less preferred food plants, leading the population to a crash. It could also be expected that the taxonomic diversity of rodent diets increases from the peak to the crash phase of a cycle. The present study is the first to use DNA metabarcoding to quantify the diets of two functionally important boreal rodent species (bank vole and tundra vole) to assess whether their diet changed systematically in the expected cyclic phase-dependent manner. We found the taxonomic diet spectrum broad in both vole species but with little interspecific overlap. There was no evidence of systematic shifts in diet diversity metrics between the phases of the population cycle in either species. While both species' diet composition changed moderately between cycle phases and seasons, these changes were small compared to other sources of diet variation-especially differences between individuals. Thus, the variation in diet that could be attributed to cyclic phases is marginal relative to the overall diet flexibility. Based on general consumer-resource theory, we suggest that the broad diets with little interspecific overlap render it unlikely that herbivore-plant interactions generate their synchronous population cycles. We propose that determining dietary niche width should be the first step in scientific inquiries about the role of herbivore-plant interactions in cyclic vole populations.

Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores

Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.

Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities

Functional responses describe foraging rates across prey densities and underlie many fundamental ecological processes. Most functional response knowledge comes from simplified lab experiments, but we do not know whether these experiments accurately represent foraging in nature. In addition, the difficulty of conducting multispecies functional response experiments means that it is unclear whether interaction strengths are weakened in the presence of multiple prey types. We developed a novel method to estimate wild predators' foraging rates from metabarcoding data and use this method to present functional responses for wild wolf spiders foraging on 27 prey families. These field functional responses were considerably reduced compared to lab functional responses. We further find that foraging is sometimes increased in the presence of other prey types, contrary to expectations. Our novel method for estimating field foraging rates will allow researchers to determine functional responses for wild predators and address long-standing questions about foraging in nature.

DNA-metabarcoding supports trophic flexibility and reveals new prey species for the Galapagos sea lion

Tropical ecosystems are challenging for pinnipeds due to fluctuating food availability. According to previous research, the Galapagos sea lion (GSL, Zalophus wollebaeki) adopts trophic flexibility to face such conditions. However, this hypothesis comes from studies using traditional methods (hard-parts analysis of scat and isotopic analysis from tissue). We studied the diet of five rookeries in the southeastern Galapagos bioregion (which harbors the highest GSL density), via DNA-metabarcoding of scat samples. The DNA-metabarcoding approach may identify consumed prey with a higher taxonomic resolution than isotopic analysis, while not depending on hard-parts remaining through digestion. Our study included five different rookeries to look for evidence of trophic flexibility at the bioregional level. We detected 98 prey OTUs (124 scats), mostly assigned to bony-fish taxa; we identified novel prey items, including a shark, rays, and several deep-sea fish. Our data supported the trophic flexibility of GSL throughout the studied bioregion since different individuals from the same rookery consumed prey coming from different habitats and trophic levels. Significant diet differentiations were found among rookeries, particularly between Punta Pitt and Santa Fe. Punta Pitt rookery, with a more pronounced bathymetry and lower productivity, was distinguished by a high trophic level and consumption of a high proportion of deep-sea prey; meanwhile, Santa Fe, located in more productive, shallow waters over the shelf, consumed a high proportion of epipelagic planktivorous fish. Geographic location and heterogeneous bathymetry of El Malecon, Española, and Floreana rookeries would allow the animals therein to access both, epipelagic prey over the shelf, and deep-sea prey out of the shelf; this would lead to a higher prey richness and diet variability there. These findings provide evidence of GSL adopting a trophic flexibility to tune their diets to different ecological contexts. This strategy would be crucial for this endangered species to overcome the challenges faced in a habitat with fluctuating foraging conditions.

Interplay of competition and facilitation in grazing succession by migrant Serengeti herbivores

Competition, facilitation, and predation offer alternative explanations for successional patterns of migratory herbivores. However, these interactions are difficult to measure, leaving uncertainty about the mechanisms underlying body-size-dependent grazing-and even whether succession occurs at all. We used data from an 8-year camera-trap survey, GPS-collared herbivores, and fecal DNA metabarcoding to analyze the timing, arrival order, and interactions among migratory grazers in Serengeti National Park. Temporal grazing succession is characterized by a "push-pull" dynamic: Competitive grazing nudges zebra ahead of co-migrating wildebeest, whereas grass consumption by these large-bodied migrants attracts trailing, small-bodied gazelle that benefit from facilitation. "Natural experiments" involving intense wildfires and rainfall respectively disrupted and strengthened these effects. Our results highlight a balance between facilitative and competitive forces in co-regulating large-scale ungulate migrations.

Fecal DNA metabarcoding reveals seasonal and annual variation in willow ptarmigan diet

Understanding spatio-temporal variation in the diet of alpine herbivores is important to predict how a changing climate will affect these species in the future. We examined the spatio-temporal variation in willow ptarmigan (Lagopus l. lagopus) diet using DNA metabarcoding of fecal pellets sampled from winter to early summer over three consecutive years. Furthermore, we assessed how snow cover and vegetation phenology affected diet variation. We also investigated sex differences in diet composition. We identified 18 important diet taxa and the genera Betula, Vaccinium and Empetrum occurred most frequently. Diet composition and richness varied within and between years. Seasonally, there was a shift from a narrow winter diet dominated by trees and dwarf shrubs to a broader spring diet with more nutritious field vegetation. This seasonal progression differed among years. The temporal variation in diet was better explained by day of year than by snow cover and vegetation phenology. Females had a more diverse diet than males, but there were no sex differences in diet composition. Our results demonstrate that metabarcoding of fecal samples provides the opportunity to assess factors affecting diet composition of species in alpine ecosystems in the context of a changing climate.

DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler

Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.

VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.

Molecular analyses of carangid fish diets reveal inter-predation, dietary overlap, and the importance of early life stages in trophic ecology

Carangid fishes are commercially important in fisheries and aquaculture. They are distributed worldwide in both tropical and subtropical marine ecosystems. Their role in food webs is often unclear since their diet cannot be easily identified by traditional gut content analysis. They are suspected to prey on pelagic and benthic species, with clupeiform fishes being important dietary items for some species, though it is unknown whether carangids share food resources or show trophic segregation. Here, we used metabarcoding to overcome traditional challenges of taxonomic approaches to analyze the diet of seven carangid species caught as bycatch in the Brazilian southwest Atlantic sardine fishery. Stomach contents were processed from the following species: Caranx crysos, Caranx latus, Chloroscombrus chrysurus, Hemicaranx amblyrhynchus, Oligoplites saliens, Selene setapinnis, and Trachinotus carolinus. Identified diets were dominated by teleost fishes. The C. latus diet was the most distinct among the seven species, preferentially consuming Engraulis anchoita, but H. amblyrhynchus, O. saliens, and S. setapinnis also showed a trend of predominantly consuming small pelagic fishes. Finally, we found evidence of inter-predation in carangids, especially strong between S. setapinnis and C. crysos, suggesting that consumption of early life stages may result in indirect competition through reduced recruitment in these fishes. These findings provide unprecedented insights into the biodiversity in marine ecosystems, especially the poorly known diet of carangid fishes.

Inferring the ecological and evolutionary determinants of community genetic diversity

Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.

Temporal change in floral availability leads to periods of resource limitation and affects diet specificity in a generalist pollinator

Generalist species are core components of ecological networks and crucial for the maintenance of biodiversity. Generalist species and networks are expected to be more resilient, and therefore understanding the dynamics of specialization and generalization in ecological networks is a key focus in a time of rapid global change. Whilst diet generalization is frequently studied, our understanding of how it changes over time is limited. Here we explore temporal variation in diet specificity in the honeybee (Apis mellifera), using pollen DNA metabarcoding of honey samples, through the foraging season, over two years. We find that, overall, honeybees are generalists that visit a wide range of plants, but there is temporal variation in the degree of specialization. Temporal specialization of honeybee colonies corresponds to periods of resource limitation, identified as a lack of honey stores. Honeybees experience a lack of preferred resources in June when switching from flowering trees in spring to shrubs and herbs in summer. Investigating temporal patterns in specialization can identify periods of resource limitation that may lead to species and network vulnerability. Diet specificity must therefore be explored at different temporal scales in order to fully understand species and network stability in the face of ecological change.

Using biological traits to assess diet selection: the case of the Pyrenean Desman

Traditionally, researchers have assessed diet selection by comparing consumed versus available taxa. However, taxonomic assignment is probably irrelevant for predators, who likely base their selection on characteristics including prey size, habitat, or behavior. Here, we use an aquatic insectivore, the threatened Pyrenean Desman (Galemys pyrenaicus), as a model species to assess whether biological traits help unravel the criteria driving food and habitat preferences. We reanalyzed data from a previous taxonomy-based study of prey selection in two contrasting streams, one with excellent conservation status and the other affected by diversion for hydropower and forestry. Available and consumed prey were characterized according to nine biological traits, and diet selection was estimated by comparing availability-measured from Surber net samples, and consumption-analyzed by metabarcoding desman feces. Traits offered a biologically coherent image of diet and almost identical selection patterns in both streams, depicting a highly specialized rheophilic predator. Desmans positively selected prey with a preference for fast flow and boulder substrate, indicating their preferred riffle habitat. On the other hand, they positively selected prey with larger but not the largest potential size, living in the water column or the litter, and not inside sediments. They also chose agile prey, swimmers or prey attached to the substrate, prey with high body flexibility, and prey living exposed and clustered in groups. Overall, our results offer a picture of desman diet preference and point to biological traits as being better than taxonomic identity to describe the diet preference of consumers.

Isolated Grauer's gorilla populations differ in diet and gut microbiome

The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.

DNA-based networks reveal the ecological determinants of plant-herbivore interactions along environmental gradients

Understanding the ecological rules structuring the organization of species interactions is a prerequisite to predicting how ecosystems respond to environmental changes. While the ecological determinants of single networks have been documented, it remains unclear whether network ecological rules are conserved along spatial and environmental gradients. To address this gap, we reconstructed 48 plant-herbivore interaction networks along six elevation gradients in the Central European Alps in Switzerland, using DNA metabarcoding on orthoptera faeces. We developed hypotheses on the ecological mechanisms expected to structure interaction networks, based on plant phylogeny, plant abundance, leaf toughness, leaf nitrogen content and plant metabolomics. We show that plant phylogenetic relationships and species abundance have the greatest explanatory power regarding the structure of the ecological networks. Moreover, we found that leaf nitrogen content is a key determinant of interactions in warmer environments, while phenolic compounds and tannins are more important in colder environments, suggesting that determinants of species interactions can shift along environmental gradients. With this work, we propose an approach to study the mechanisms that structure the way species interact with each other between bioregions and ecosystems.

Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes

Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by faecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We examined 420 faecal samples and found different patterns of dietary diversity and composition among the duck species. The pattern also differed between plant and invertebrate food. Dietary niche partitioning was clear in plant food. Large-bodied ducks intensively use crop plants, and other ducks might mediate competition by using terrestrial and aquatic plants that are suitable for their foraging behaviours or microhabitats. Dietary segregation among species was the most apparent in February, when the abundance of foraging ducks was the largest. This study illustrated the complex pattern of dietary niche partitioning of dabbling ducks in agricultural landscapes, which might be difficult to evaluate by conventional approaches. The availability of crop plants, as well as other plant food resources in flooted areas and farmland dikes, may enable ducks to coexist by spatial or behavioural resource partitioning.

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

Deer dietary responses to wildfire: Optimal foraging, individual specialization, or opportunism?

Increasing impacts of wildfire on arid regions of the world fuelled by climate change highlight the need to better understand how natural communities respond to fire. We took advantage of a large (1660-km2 ) wildfire that erupted in northern California during an in-progress study of black-tailed deer (Odocoileus hemionus columbianus) to investigate deer use of and diets within burned and unburned habitats before and after the fire. We compared deer diet breadth to predictions of optimal foraging theory, the niche variation hypothesis, and opportunistic (i.e., generalist) foraging expectations under the assumption that overall availability and diversity of forage in burned areas declined immediately after the fire and increased as the plant community recovered in the next 3 years after the fire. We used faecal pellet counts to document space use and metabarcoding to study diet during pre-fire, post-fire, and recovery periods. Pellet counts supported predictions that deer increased use of unburned sites and reduced use of burn sites after the fire and began to return to burned sites in subsequent sampling years. Diet diversity did not differ significantly between control and burn sites before the fire, but was lower in burn than control sites post-fire (p < .001), when and where diet was dominated by oak (Quercus spp). In contrast, during subsequent years, diet diversity was higher (including more herbaceous plants) in burn than control sites (p < .05). In contrast to predictions of optimal foraging and niche variation hypotheses, individual deer foraged as generalists for which changes in dietary niche breadth paralleled fire-induced changes in diversity of the plant community.

Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant-pollinator networks

Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant-pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations. Individual pollinators often carry pollen from multiple plant species, and therefore we expected MB to reveal a more diverse and complex network structure. We used two gene regions (ITS2 and trnL) to identify plant species present in the pollen loads of 154 insect pollinator specimens from three alpine habitats and construct MB networks, and compared them to networks based on observations alone. We compared species and interaction turnover across space for both types of networks, and evaluated their differences for plant phylogenetic diversity and beta diversity. We found significant structural differences between the two types of networks; notably, MB networks were much less specialized but more diverse than observation networks, with MB detecting many cryptic plant species. Both approaches revealed that alpine pollination networks are very generalized, but we estimated a high spatial turnover of plant species (0.79) and interaction rewiring (0.6) as well as high plant phylogenetic diversity (0.68) driven by habitat differences based on the larger diversity of plant species and species interactions detected with MB. Overall, our findings show that habitat and microclimatic heterogeneity drives diversity and fine-scale spatial turnover of alpine plant-pollinator networks.

DNA metabarcoding reveals consumption of diverse community of amphibians by invasive wild pigs (Sus scrofa) in the southeastern United States

Invasive wild pigs (Sus scrofa) are one of the most widespread, destructive vertebrate species globally. Their success can largely be attributed to their generalist diets, which are dominated by plant material but also include diverse animal taxa. Wild pigs are demonstrated nest predators of ground-nesting birds and reptiles, and likely pose a threat to amphibians given their extensive overlap in wetland use. DNA metabarcoding of fecal samples from 222 adult wild pigs culled monthly from 2017 to 2018 revealed a diverse diet dominated by plant material, with 166 plant genera from 56 families and 18 vertebrate species identified. Diet composition varied seasonally with availability for plants and was consistent between sexes. Amphibians were the most frequent vertebrate group consumed and represented the majority of vertebrate species detected, suggesting amphibians are potentially vulnerable to predation by wild pigs in our study region. Mammal, reptile, and bird species were also detected in pig diets, but infrequently. Our results highlight the need for research on the impacts of wild pigs on amphibians to better inform management and conservation of imperiled species.

Metabarcoding dietary analysis in the insectivorous bat Nyctalusleisleri and implications for conservation

In this study, we aim to uncover diet preferences for the insectivorous bat Nyctalusleisleri (Leisler's bat, the lesser noctule) and to provide recommendations for conservation of the species, based on the analysis of prey source habitats. Using a novel guano trap, we sampled bat faeces at selected roosts in a forest in Germany and tested two mitochondrial markers (COI and 16S) and three primer pairs for the metabarcoding of bat faecal pellets. We found a total of 17 arthropod prey orders comprising 358 species in N.leisleri guano. The most diverse orders were Lepidoptera (126 species), Diptera (86 species) and Coleoptera (48 species), followed by Hemiptera (28 species), Trichoptera (16 species), Neuroptera (15 species) and Ephemeroptera (10 species), with Lepidoptera species dominating in spring and Diptera in summer. Based on the ecological requirements of the most abundant arthropod species found in the bat guano, we propose some recommendations for the conservation of N.leisleri that are relevant for other insectivorous bat species.

Aerospace-foraging bats eat seasonably across varying habitats

Recent research has confirmed the efficiency of insectivorous bats as pest suppressors, underlining the ecological services they offer in agroecosystems. Therefore, some efforts try to enhance bat foraging in agricultural landscapes by acting upon environmental factors favouring them. In this study, we monitored a Miniopterus schreibersii colony, in the southern Iberian Peninsula. We intensively sampled their faeces and analysed them by metabarcoding to describe how the bent-winged bat diet would change with time, and to test whether their most-consumed prey would seasonally depend on different landscapes or habitats. Our results confirm that M. schreibersii are selective opportunist predators of moths, dipterans, mayflies, and other fluttering insects, shifting their diet to temporary peaks of prey availability in their foraging range, including both pest and non-pest insects. Supporting our hypothesis, throughout the year, M. schreibersii consume insects linked to diverse open habitats, including wetlands, grassland, diverse croplands, and woodland. The importance of each prey habitat varies seasonally, depending on their insect phenology, making bats indirectly dependent on a diverse landscape as their primary prey source. Bats' predation upon pest insects is quantitatively high, consuming around 1610 kg in 5 months, of which 1467 kg correspond to ten species. So, their suppression effect may be relevant, mainly in patchy heterogeneous landscapes, where bats' foraging may concentrate in successive outbursts of pests, affecting different crops or woodlands. Our results stress that to take advantage of the ecosystem services of bats or other generalist insectivores, keeping the environmental conditions they require to thrive, particularly a heterogeneous landscape within the colony's foraging area, is crucial.