Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Insect root feeders incur negative density-dependent damage across plant species in an alpine meadow

Although herbivores are well known to incur positive density-dependent damage and mortality, thereby likely shaping plant community assembly, the response of belowground root feeders to changes in plant density has seldom been addressed. Locally rare plant species (with lower plant biomass per area) are often smaller with shallower roots than common species (with higher plant biomass per area) in competition-intensive grasslands. Likewise, root feeders are often distributed in the upper soil layers. We hypothesized, therefore, that root feeders would incur negative density (biomass)-dependent damage across plant species. To test this hypothesis, we investigated the diversity and abundance of plant and root feeder species in an alpine meadow and determined the diet of the root feeders using metabarcoding. Across all species, root feeder load decreased with increasing aboveground plant biomass, root biomass, and total plant biomass per area, indicating a negative density dependence of damage across plant species. Aboveground plant biomass per area increased with increasing individual plant biomass and root depth per area across species, suggesting that rare plant species were smaller in size and had shallower root systems compared to common plant species. Both root biomass per area and root feeder biomass per area decreased with soil depth, but the root feeder biomass decreased disproportionately faster compared to root biomass with increasing root depth. Root feeder load decreased with increasing root depth but was not correlated with the feeding preference of root feeder species. Moreover, the prediction derived from a random process incorporating vertical distributions of root biomass and root feeder biomass significantly accounted for interspecific variation in root feeder load. In conclusion, the data indicate that root feeders incur negative density-dependent damage across plant species. On this basis, we suggest that manipulative experiments should be conducted to determine the effect of the negative density-dependent damage on plant community structure and that different types of plant-animal interactions should be concurrently examined to fully understand the effect of plant density on overall herbivore damage across plant species.

Small rodent population cycles and plants - after 70 years, where do we go?

Small rodent population cycles characterise northern ecosystems, and the cause of these cycles has been a long-lasting central topic in ecology, with trophic interactions currently considered the most plausible cause. While some researchers have rejected plant-herbivore interactions as a cause of rodent cycles, others have continued to research their potential roles. Here, we present an overview of whether plants can cause rodent population cycles, dividing this idea into four different hypotheses with different pathways of plant impacts and related assumptions. Our systematic review of the existing literature identified 238 studies from 150 publications. This evidence base covered studies from the temperate biome to the tundra, but the studies were scattered across study systems and only a few specific topics were addressed in a replicated manner. Quantitative effects of rodents on vegetation was the best studied topic, and our evidence base suggests such that such effects may be most pronounced in winter. However, the regrowth of vegetation appears to take place too rapidly to maintain low rodent population densities over several years. The lack of studies prevented assessment of time lags in the qualitative responses of vegetation to rodent herbivory. We conclude that the literature is currently insufficient to discard with confidence any of the four potential hypotheses for plant-rodent cycles discussed herein. While new methods allow analyses of plant quality across more herbivore-relevant spatial scales than previously possible, we argue that the best way forward to rejecting any of the rodent-plant hypotheses is testing specific predictions of dietary variation. Indeed, all identified hypotheses make explicit assumptions on how rodent diet taxonomic composition and quality will change across the cycle. Passing this bottleneck could help pinpoint where, when, and how plant-herbivore interactions have - or do not have - plausible effects on rodent population dynamics.

The positive response of small terrestrial and semi-aquatic mammals to beaver damming

Ecosystem engineers, such as the Eurasian beaver, Castor fiber, transform habitats, thereby creating favourable conditions for other species and increasing biodiversity. Multiple studies have revealed that beaver ponds are valuable habitats for invertebrates and vertebrates, including other mammals, but the impact of watercourse damming on the fauna of small terrestrial rodents and shrews has not yet been documented. We tested the hypothesis that the presence of beaver dams and consequent flooding enrich the small mammal assemblage both quantitatively and qualitatively. We live-trapped small mammals at nine beaver-modified sites on 300-metre transects alongside dammed watercourses, starting from the dam through to the pond to the sections with unmodified lotic conditions. The abundance and species richness of trapped small mammals were highest near the dams and declined with distance. Additionally, five out of 12 trapped species significantly decreased their abundance with linear distance along the shoreline from the dam and none revealed the opposite trend. Four species were more abundant on plots subjected to beaver-related inundation (especially Sorex minutus and Micromys minutus), while none were present solely on uninundated plots. Among the semi-aquatic species, two water shrews benefited from beaver activity in different ways. Neomys milleri occurred only in flooded sections, while N. fodiens preferred unmodified sections, but was the most numerous species closer to the dams, as per known patterns of competitive displacement observed in Central Europe. An important factor affecting small mammals, the herbaceous layer cover, appeared to be interdependent with damming. We provide the first unequivocal evidence that the presence of beaver dams facilitate the abundance and diversity of small mammals, presumably due to increased food abundance, availability of shelter and habitat connectivity. Beaver-created wetlands may act as potential refuges for species most susceptible to the consequences of anthropogenic climate change.

Diet composition and interspecific niche of Taohongling Sika deer (Cervus nippon kopschi) and its sympatric Reeve’s muntjac (Muntiacus reevesi) and Chinese hare (Lepus sinensis) in winter (Animalia, Mammalia)

Species co-existence depends on how organisms utilize their environment and resources. Little is known about the winter diet composition and sympatric co-existence of South China sika deer and its companion species in Taohongling. In this study, high-throughput sequencing and metabarcoding trnL were used to study the diet composition and interspecific relationship including sika deer, Reeve’s muntjac, and Chinese hare. Our results show that 203 genera in 90 families are contained in the diet of sika deer, 203 genera in 95 families for Reeve’s muntjac, and 163 genera in 75 families for Chinese hare. Sika deer fed on Rubus chingii, Loropetalum chinense, and Eurya japonica in winter, accounting for 75.30%; Reeve’s muntjac consumed mainly R. chingii, E. japonica, and Euonymus grandiflorus, accounting for 68.80%, and Chinese hare mainly fed on R. chingii, Smilax china, and Rhus chinensis, accounting for 41.98%. The Shannon index showed no significant difference between groups (p > 0.05). The NMDS analysis found considerable overlap among three species. Sika deer and Reeve’s muntjac consumed similar forage plants but varied greatly in Chinese hare, which occupied the widest choice in winter, resulting in higher diet breadth and increased dietary divergence, thereby reducing competition and facilitating coexistence. The diet niche overlap index among them, as represented by Pianka’s index, ranging from 0.62 between sika deer and Chinese hare to 0.83 between sika deer and Reeve’s muntjac, which indicated a more similar niche and potential competition in closely related species. Our findings provide a new diet perspective of three herbivores, leading to a more comprehensive understanding of resource partitioning and species coexistence.

Seasonal and ontological variation in diet and age-related differences in prey choice, by an insectivorous songbird

The diet of an individual animal is subject to change over time, both in response to short-term food fluctuations and over longer time scales as an individual ages and meets different challenges over its life cycle. A metabarcoding approach was used to elucidate the diet of different life stages of a migratory songbird, the Eurasian reed warbler (Acrocephalus scirpaceus) over the 2017 summer breeding season in Somerset, the United Kingdom. The feces of adult, juvenile, and nestling warblers were screened for invertebrate DNA, enabling the identification of prey species. Dietary analysis was coupled with monitoring of Diptera in the field using yellow sticky traps. Seasonal changes in warbler diet were subtle, whereas age class had a greater influence on overall diet composition. Age classes showed high dietary overlap, but significant dietary differences were mediated through the selection of prey; (i) from different taxonomic groups, (ii) with different habitat origins (aquatic vs. terrestrial), and (iii) of different average approximate sizes. Our results highlight the value of metabarcoding data for enhancing ecological studies of insectivores in dynamic environments.

Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.

Plastid Genome of Equisetum xylochaetum from the Atacama Desert, Chile and the Relationships of Equisetum Based on Frequently Used Plastid Genes and Network Analysis

The modern pteridophyte genus Equisetum is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species Equisetum xylochaetum from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other Equisetum species using network analysis. Equisetum chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that Equisetum is monophyletic, and that E. xylochaetum is more closely related to E. hyemale than to E. arvense. Single-gene phylogenetic estimation and haplotype analysis showed that E. xylochaetum belonged to the subgenus Hippochaete. Single-gene haplotype analysis revealed that E. arvense, E. hyemale, E. myriochaetum, and E. variegatum resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from E. bogotense appeared as a distinct group of haplotypes representing the subgenus Paramochaete that diverged from Hippochaete and Equisetum. In addition, the taxa that were frequently located at the joint region of the map were E. scirpoides and E. pratense, suggesting the presence of some plastome characters among the Equiseum subgenera.

Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding

DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan (Lagopus muta japonica), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015-2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V. uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant s for Japanese rock ptarmigans from July to October. This plant community therefore needs to be conserved in order to protect the food resources of Japanese rock ptarmigans in the region.

The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation

Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data-or similar data such as environmental DNA, microbiomes, or pathobiomes-should be aware of drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.

Rapid PCR-based method for herbivore dietary evaluation using plant-specific primers

Polyphagous pests cause significant economic loss worldwide through feeding damage on various cash crops. However, their diets in agricultural landscapes remain largely unexplored. Pest dietary evaluation in agricultural fields is a challenging task currently approached through visual observation of plant feeding and microscopic identification of semi-digested plant material in pest’s guts. While molecular gut content analysis using metabarcoding approaches using universal primers (e.g., rbcl and trnL) have been successful in evaluating polyphagous pest diet, this method is relatively costly and time-consuming. Hence, there is a need for a rapid, specific, sensitive, and cost-effective method to screen for crops in the gut of pests. This is the first study to develop plant-specific primers that target various regions of their genomes, designed using a whole plant genome sequence. We selected Verticillium wilt disease resistance protein (VE-1) and pathogenesis related protein-coding genes 1–5 (PR-1-5) as our targets and designed species-specific primers for 14 important crops in the agroecosystems. Using amplicon sizes ranging from 115 to 407 bp, we developed two multiplex primer mixes that can separate nine and five plant species per PCR reaction, respectively. These two designed primer mixes provide a rapid, sensitive and specific route for polyphagous pest dietary evaluation in agroecosystems. This work will enable future research to rapidly expand our knowledge on the diet preference and range of crops that pests consume in various agroecosystems, which will help in the redesign and development of new crop rotation regimes to minimize polyphagous pest pressure and damage on crops.

Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

Authentication of garlic (Allium sativum L.) supplements using a trnLUAA mini-barcode

Garlic (Allium sativum), a widely distributed plant with great cultural and medicinal significance, is one of the most popular herbal dietary supplements in Europe and North America. Garlic supplements are consumed for a variety of reasons, including for their purported antihypertensive, antibacterial, and anticarcinogenic effects. The steady increase in the global herbal dietary supplement market paired with a global patchwork of regulatory frameworks makes the development of assays for authentication of these products increasingly important. A DNA mini-barcode assay was developed using the P6 loop of the plastid trnL^UAA intron to positively identify A. sativum products. Analysis of 43 commercially available garlic herbal dietary supplements produced mini-barcode sequences for 33 supplements, all of which contained detectable amounts of A. sativum. The trnL^UAA P6 mini-barcode can be highly useful for specimen identification, particularly for samples that may contain degraded DNA.

Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus

During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship's robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet.

Diet composition of Korean water deer (Hydropotes inermis argyropus) from the Han River Estuary Wetland in Korea using fecal DNA

To investigate the foraging preferences of the Korean water deer (Hydropotes inermis argyropus) from the Janghang wetlands located in Han River estuary in South Korea, we elucidated their diet compositions using DNA extracted from their fecal samples. Samples were collected from the Janghang wetlands from June 2013 to January 2015. For dietary analysis, we amplified the internal transcribed spacer 2 (ITS2) and the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) regions, followed by cloning and sequencing. We were able to detect 20 families and 35 genera of plants from 77 fecal samples, showing that water deer in the Janghang wetlands mainly preferred Salicaceae (27.5%), Fabaceae (17.5%), and Poaceae (14.2%). In winter, the relative frequency of woody plant detection (81.3%) was much higher than that in other seasons. Our results suggest that Korean water deer in Janghang wetlands browse or graze depending on the locally-available plants species in their habitat as intermediate feeders. Non-invasive approaches using fecal samples could be applied to study food webs of various species and ecosystems for conservation and management of wildlife.

Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding

Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defined dietary guilds (e.g., insectivores, carnivores, and frugivores). Apart from these broad guilds, we lack detailed dietary information for many species and therefore have only a limited understanding of interaction networks linking bats and their diet items. In this study, we used DNA metabarcoding of plants, arthropods, and vertebrates to investigate the diets of 25 bat species from the tropical dry forests of Lamanai, Belize. Our results report some of the first detection of diet items for the focal bat taxa, adding rich and novel natural history information to the field of bat ecology. This study represents a comprehensive first effort to apply DNA metabarcoding to bat diets at Lamanai and provides a useful methodological framework for future studies testing hypotheses about coexistence and niche differentiation in the context of modern high-throughput molecular data.

Metagenomics: A viable tool for reconstructing herbivore diet

Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.

Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi

With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan). Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence. Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.

Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities

Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm2). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were Calamagrostis epigejos, Coronilla varia, and Holcus lanatus. For the aboveground part of the vegetation, the season, management intensity, and certain species-with the most prominent being Centaurea rhenana and Cirsium canum-have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, K2O, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies.

Complementarity between microhistological analysis and PCR-capillary electrophoresis in diet analysis of goats and cattle using faecal samples

An evaluation is made of the complementarity between two non-invasive techniques, cuticle microhistological analysis (CMA) and PCR-capillary electrophoresis (PCR-CE) DNA-based analysis, for the determination of herbivore diet composition from faecal samples. Cuticle microhistological analysis is based on the different microanatomical characteristics of the epidermal fragments remaining in the faeces. The PCR-CE technique combines PCR amplification of a trnL(UAA) genomic DNA region with amplicon length determination by CE, with this length being characteristic for each species or taxon. A total of 37 fresh stool samples were analyzed, including 16 from feral goats (Capra hircus) from the Tramuntana mountain range (Mallorca, Baleares) and 11 from Bruna dels Pirineus cattle breed (Bos taurus) from the surrounding Montserrat mountain range (Barcelona, Spain). All the animals were in a free grazing Mediterranean pine habitat, dominated by Aleppo pine (Pinus halepensis). The results showed that both techniques detected a similar number of plant components in the faeces of goats and cows. In the case of goats, a positive correlation was obtained between the percentage of samples in which a particular taxon is detected by CMA and the percentage of samples in which that taxon is detected by PCR-CE. This correlation was not observed in the case of cows. It is concluded that PCR-CE is a fast and reliable method to detect the different plant components in the faeces of herbivores. However, it cannot be considered as an alternative to CMA, but as a complementary method, since both techniques can detect some taxa that are not detected by the other technique. In addition, CMA detected the presence of the different taxa in a greater number of samples, and at the same time, it enables quantitative data to be obtained for plant diet composition. The species of herbivore also seems to influence the results obtained by PCR-CE, so more studies are required to address this aspect.

Resolving Food-Web Structure

Food webs are a major focus and organizing theme of ecology, but the data used to assemble them are deficient. Early debates over food-web data focused on taxonomic resolution and completeness, lack of which had produced spurious inferences. Recent data are widely believed to be much better and are used extensively in theoretical and meta-analytic research on network ecology. Confidence in these data rests on the assumptions ( a) that empiricists correctly identified consumers and their foods and ( b) that sampling methods were adequate to detect a near-comprehensive fraction of the trophic interactions between species. Abundant evidence indicates that these assumptions are often invalid, suggesting that most topological food-web data may remain unreliable for inferences about network structure and underlying ecological and evolutionary processes. Morphologically cryptic species are ubiquitous across taxa and regions, and many trophic interactions routinely evade detection by conventional methods. Molecular methods have diagnosed the severity of these problems and are a necessary part of the cure.

High-resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism

Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary studies, which may be unable to detect subtle intraspecific differentiation in prey consumption. Here, we show the power of multi‐marker metabarcoding to address these issues, focusing on a slightly dimorphic generalist passerine, the black wheatear Oenanthe leucura. Using markers from four genomic regions (18S, 16S, COI, and trnL), we analyzed fecal droppings collected from 93 adult black wheatears during the breeding season. We found that sexes were rather similar in bill and body features, though males had a slightly thicker bill and longer wings and tail than females. Diet was dominated in both sexes by a very wide range of arthropod species and a few fleshy fruits, but the overall diet diversity was higher for males than females, and there was a much higher frequency of occurrence of ants in female (58%) than male (29%) diets. We hypothesize that the observed sexual differentiation was likely related to females foraging closer to their offspring on abundant prey, while males consumed a wider variety of prey while foraging more widely. Overall, our results suggest that dietary sexual differentiation in birds may be more widespread than recognized at present and that multi‐marker DNA metabarcoding is a particularly powerful tool to unveiling such differences.

The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach

Background

The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities.

Methods

DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians).

Results

Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior.

Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival

In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept

Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been widely applied to humans. Here, we present data derived from sequencing of a chloroplast DNA marker (the P6 loop of the trnL [UAA] intron) in stool samples collected from 11 individuals consuming both controlled and freely selected diets. The DNA metabarcoding strategy resulted in successful PCR amplification in about 50% of samples, which increased to a 70% success rate in samples from individuals eating a controlled plant-rich diet. Detection of plant taxa among sequenced samples yielded a recall of 0.86 and a precision of 0.55 compared to a written diet record during controlled feeding of plant-based foods. The majority of sequenced plant DNA matched common human food plants, including grains, vegetables, fruits, and herbs prepared both cooked and uncooked. Moreover, DNA metabarcoding data were sufficient to distinguish between baseline and treatment diet arms of the study. Still, the relatively high PCR failure rate and an inability to distinguish some dietary plants at the sequence level using the trnL-P6 marker suggest that future methodological refinements are necessary. Overall, our results suggest that DNA metabarcoding provides a promising new method for tracking human plant intake and that similar approaches could be used to characterize the animal and fungal components of our omnivorous diets.

IMPORTANCE Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Assessment of seasonal variation of diet composition in rodents using DNA barcoding and Real-Time PCR

The study of animal diet and feeding behaviour is a fundamental tool for the illustration of the ecological role of species in the ecosystem. However, size and quality of food intake samples make it hard for researchers to describe the diet composition of many small species. In our study, we exploited genomic tools for the analysis of the diet composition of the Savi’s pine vole (Microtus savii) using DNA barcoding and qPCR techniques for the identification of ingested plant species retrieved from stomach contents. In contrast with previous studies, we found that, despite being a fossorial species, the Savi’s pine vole is a selective feeder that undergoes intense superficial activity in search for food. In addition, our study shows that with a a priori knowledge of the candidate plant species included in animal diet, qPCR is a powerful tool to assess presence/absence, frequency of occurrence and electivity of ingested species. We conclude that this approach offers new opportunities to implement the analysis of food selection in small animals, thereby revealing a detailed picture of plant-animal interactions.

Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists

The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxonomic resolution and biases. Here, we test the use of a mix of universal and specific markers, provide criteria to integrate multi‐marker metabarcoding data and a python script to implement such criteria and produce a single list of taxa ingested per sample. We then compare the results of dietary analysis based on morphological methods, single markers, and the proposed combination of multiple markers. The study was based on the analysis of 115 faeces from a small passerine, the Black Wheatears (Oenanthe leucura). Morphological analysis detected far fewer plant taxa (12) than either a universal 18S marker (57) or the plant trnL marker (124). This may partly reflect the detection of secondary ingestion by molecular methods. Morphological identification also detected far fewer taxa (23) than when using 18S (91) or the arthropod markers IN16STK (244) and ZBJ (231), though each method missed or underestimated some prey items. Integration of multi‐marker data provided far more detailed dietary information than any single marker and estimated higher frequencies of occurrence of all taxa. Overall, our results show the value of integrating data from multiple, taxonomically overlapping markers in an example dietary data set.

Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates: A case study with Pyrenean chamois

The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) and emerging DNA-based methods being the most relevant. In this work, we refined and optimized a qualitative DNA-based approach combining PCR amplification of long trnL(UAA) and ITS2 fragments and capillary electrophoresis (PCR-CE), instead of short trnL(UAA) fragments and massive sequencing technologies commonly reported. To do so, we developed a controlled diet assay using a stabled Pyrenean chamois specimen (Rupicapra pyrenaica pyrenaica), which included representative herbaceous and shrubby plant species. We also assessed the impact of sample freshness on the diet determination of this mountain caprinae by exposing faecal samples to the outdoor environment for three weeks. Faecal samples from both experiments were analysed by qualitative PCR-CE and semi-quantitative CMA in order to compare the pros and cons of both approaches. Our results show that all of the offered plant species were detected by both methodologies although CMA over-detected shrubs compared to herbaceous species. At the same time, sample degradation due to sustained climate exposure is a limiting factor for molecular analysis, but not for CMA. Taken all together, our results suggest that the qualitative information obtained by CMA and PCR-CE can be interchangeable when faecal samples are fresh (less than one week after deposition) but, afterwards, molecular analysis underestimates diet composition probably due to DNA degradation. CMA, however, can accurately be used at least three weeks after defecation. Moreover, by combining the results of simultaneous PCR amplification of two complementary genes, this optimized PCR-CE methodology provides a reliable, feasible and more affordable alternative for multiple and routine analyses of complex samples. Neither CMA nor PCR-CE seems to solve comprehensively the quatification of herbivore diets and thus further research needs to be done.

How Do Richness and Composition of Diet Shape Trace Metal Exposure in a Free-Living Generalist Rodent, Apodemus sylvaticus

Exposure of terrestrial mammals to chemical contaminants like trace metals (TMs) is considered to be mainly based on trophic transfer. Although relationships between TM transfer to animals and identity of contaminated food have been studied, the variation of the TM transfer with respect to diet diversity has been poorly documented. In this study, the oral exposure to TMs of wood mice Apodemus sylvaticus was investigated with respect to both the number of different items, i.e., diet richness, and the identity of items determined by metabarcoding from their stomach content, i.e., diet composition. The results showed that consuming Salicaceae, a known cadmium accumulator plant family, significantly increased exposure to cadmium and zinc. However, an increase in diet richness minimized exposure to cadmium when mice consumed Salicaceae items. This strongly suggests that TM accumulator items can lead to a high oral exposure to TMs but that such high exposure due to TM accumulator items can be " diluted" by diet richness due to other low accumulator items. Our results clearly indicate that both the presence of certain items in the diet and diet richness are important determinants of exposure to TMs in generalist animals, which matches the predictions of the " diet dilution hypothesis".

Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs

The decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats (Rattus rattus) and endemic frogs (Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi, is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill-trapping and subjected to three methods of diet analysis (one morphological and two DNA-based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA-based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.

Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices

The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.

Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic "barcode" primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.

The effect of plant identity and mixed feeding on the detection of seed DNA in regurgitates of carabid beetles

Carabids are abundant in temperate agroecosystems and play a pivotal role as biocontrol agents for weed seed and pest regulation. While there is good knowledge regarding their effects on invertebrate pests, direct evidence for seed predation in the field is missing. Molecular approaches are ideally suited to investigate these feeding interactions; however, the effects of an omnivorous diet, which is characteristic for many carabid species, and seed identity on the detection success of seed DNA has not yet been investigated. In a series of feeding experiments, seeds of six different Central European weed species were fed to beetles of the species Pseudoophonus rufipes, to determine post-feeding seed DNA detection rates and how these are affected by plant identity, meal size, and chemical seed composition. Moreover, we investigated the effect of a mixed diet of seeds and mealworm on prey DNA detection. Four out of six seed species were detectable for up to five days after consumption, and seed species identity significantly affected post-feeding detection rates. Detectability was negatively influenced by protein content and seed mass, whereas oil content and meal size had a positive effect. The mixed diet led to both increased detection rates and post-feeding detection intervals of seed DNA. This suggests that mixed feeding leads to an enhancement of food detection intervals in carabid beetles and that seed identity, their chemical composition, and meal size can affect DNA detection of consumed seeds. These aspects and potential implications of this non-invasive approach are discussed as they can become highly relevant for interpreting field-derived data.

A metabarcoding approach for the feeding habits of European hake in the Adriatic Sea

European hake (Merluccius merluccius) is one of the most economically important fish for the Mediterranean Sea. It is an important predator of deep upper shelf slope communities currently characterized by growth overexploitation: the understanding of hake's diet might support next generation management tools. However, all current European hake diet studies depend on the morphological identification of prey remains in stomach content, with consequent limitations. In this study, we set up a metabarcoding approach based on cytochrome oxidase I PCR amplification and Miseq Illumina paired-end sequencing of M. merluccius stomach content remains and compared the results to classic morphological analyses. A total of 95 stomach contents of M. merluccius sampled in the North-Central Adriatic Sea were analyzed with both the metabarcoding and morphological approaches. Metabarcoding clearly outperformed the morphological method in the taxonomic identification of prey describing more complex trophic relationships even when considering the morphological identification of 200 stomach contents. Statistical analysis of diet composition revealed a weak differentiation among the hake's size classes, confirming an opportunistic feeding behavior. All the analyses performed showed the presence of a core of shared prey among the size classes and a cloud of size-specific prey. Our study highlights the exceptional potential of metabarcoding as an approach to provide unprecedented taxonomic resolution in the diet of M. merluccius and potentially of other marine predators, due to the broad-spectrum of detection of the primers used. A thorough description of these complex trophic relationships is fundamental for the implementation of an ecosystem approach to fisheries.

Evaluation of plant contamination in metabarcoding diet analysis of a herbivore

Fecal DNA metabarcoding is currently used in various fields of ecology to determine animal diets. Contamination of non-food DNA from complex field environments is a considerable challenge to the reliability of this method but has rarely been quantified. We evaluated plant DNA contamination by sequencing the chloroplast trnL P6 loop region from food-controlled geese feces. The average percentage of contaminant sequences per sample was 1.86%. According to the results of generalized linear models, the probability of contamination was highest in samples placed in wet soil. The proportion of contaminant sequences was lowest at the earliest sampling point and was slightly higher in samples placed in open conditions. Exclusion of rare OTUs (operational taxonomic units) was effective for obtaining reliable dietary data from the obtained sequences, and a 1% cutoff reduced the percentage of contaminated samples to less than 30%. However, appropriate interpretation of the barcoding results considering inevitable contamination is an important issue to address. We suggest the following procedures for fecal sampling and sequence data treatment to increase the reliability of DNA metabarcoding diet analyses: (i) Collect samples as soon as possible after deposition, (ii) avoid samples from deposits on wet soil, and (iii) exclude rare OTUs from diet composition estimations.

Next-generation sequencing analysis of Pardosa pseudoannulata's diet composition in different habitats

Spiders are the most common and predominant predators in terrestrial ecosystems. The predatory behavior of spiders affects the energy flow across the food web within an ecosystem. Traditiaonal methods for analyzing spider diets such as field observation, anatomy and faeces analysis are not suitable for spider experiments due to spiders’ special dietary behavior. The molecular method based on the specific primers of prey DNA seems to be inefficient either in spite of its wide application in diet analysis. As the next-generation sequencing (NGS) technology becomes prevalent in many different areas, several cases of the NGS-based analysis of mammal diets have been published. This study analyzed the diet differences of Pardosa pseudoannulata (Araneae: Lycosidae) in four habitats (a wetland, a tea plantation, an alpine meadow and a paddy field) by using the NGS technology, combined with the DNA barcode method. The results suggested that the Pardosa pseudoannulata feed on a broad range of prey, and 7 orders and 24 families of insects were detected in the four investigated habitats. Moreover, it is found that the diet diversity of Pardosa pseudoannulata is greatly influenced by their living environments and seasons. In a nutshell, this study established an NGS-based methodology for spider diets analysis, and the results provided some basic materials to inform the protection and utilization of the Pardosa pseudoannulata as a potential eco-friendly predator against pests.

Does pollution influence small mammal diet in the field? A metabarcoding approach in a generalist consumer

Mammals are mainly exposed to trace metals (TMs) via consuming contaminated food. Several studies have demonstrated relationships between metal concentrations in food and in animal tissues. However, potential effects of TMs on feeding behaviour of wildlife have been poorly documented under field conditions, despite experimental evidence showing that food selection is impacted by resource contamination. Here, we test the hypothesis that the diet of a generalist rodent, the wood mouse (Apodemus sylvaticus), is altered by soil TM contamination in the field. Wood mice were sampled in spring and in autumn along a gradient of soil contamination in the surroundings of a former smelter located in northern France. Available resources in the field were inventoried, and the diet of the animals was analysed using DNA "metabarcoding." We demonstrated that (a) relationship between the resource richness in the diet and their richness in the field was altered by soil metal contamination. Wood mice specialized their diet along the gradient of soil metal contamination for both plant and invertebrate resources in spring. We also showed that (b) preference for Salicaceae, a plant family accumulating metals, decreased when soil contamination increased. These results suggest that environmental TM pollution could act as a force modulating trophic interactions in terrestrial food webs, thereby affecting wildlife exposure to contaminants by trophic route.