Molecular analysis of predation: a review of best practice for DNA-based approaches

Functional redundancy of weed seed predation is reduced by intensified agriculture

Intensified agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies, however, have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continental-wide study, we assess how functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation at the field scale. We found that ecosystem functions are vulnerable to disturbances in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.

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

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

Predation evaluation of the green lacewing, Chrysopa pallens on the pink tea mite pest, Acaphylla theae (Watt) (Acarina: Eriophyidae)

A better understanding of predator-prey interactions is crucial for the development of biological control strategies. The green lacewing, Chrysopa pallens, is a well-known generalist predator and reportedly functions as one of the most important biological control agents of insect pests. However, information regarding C. pallens' predation on tea plant pests, particularly notorious tea mites, remains largely unknown. In this study, we focused on the predator-prey relationship between C. pallens and an important tea mite pest, Acaphylla theae. We designed species-specific primers for the detection of A. theae DNA and established a PCR-based DNA gut content analysis assay. These results demonstrated that the primers were A. theae-specific and suitable for its molecular identification. The laboratory feeding experiment showed that the detectability success (DS50) of A. theae DNA remaining in C. pallens' guts was 2.9 h. We then performed a molecular detection of field predation, and achieved a 23.53% positive detection rate of A. theae DNA in the guts of field-collected C. pallens. This, for the first time, provides direct evidence that C. pallens can prey on A. theae in tea plantations. Finally, we tested the prey preference and estimated the predation ability of C. pallens on different developmental stages of A. theae. The results revealed that C. pallens had no significant preference for different developmental stages of A. theae. The functional responses of C. pallens' predation on different densities of A. theae at different developmental stages followed a Type II Holling model. The initial attack rate (a') ranged from 0.735 to 0.858 and the handling time (Th) was approximately 0.01. This study is the first to demonstrate the trophic interactions between C. pallens and A. theae and provides evidence for the development of biological control strategies against A. theae using C. pallens as a candidate predator.

DNA metabarcoding of cloacal swabs provides insight into diets of highly migratory sharks in the Mid-Atlantic Bight

The abundances of migratory shark species observed throughout the Mid-Atlantic Bight (MAB) during productive summer months suggest that this region provides critical habitat and prey resources to these taxa. However, the principal prey assemblages sustaining migratory shark biomass in this region are poorly defined. We applied high-throughput DNA metabarcoding to shark feces derived from cloacal swabs across nine species of Carcharhinid and Lamnid sharks to (1) quantify the contribution of broad taxa (e.g., invertebrates, fishes) supporting shark biomass during seasonal residency in the MAB and (2) determine whether the species displayed distinct dietary preference indicative of resource partitioning. DNA metabarcoding resulted in high taxonomic (species-level) resolution of shark diets with actinopterygian and elasmobranch fishes as the dominant prey categories across the species. DNA metabarcoding identified several key prey groups consistent across shark taxa that are likely integral for sustaining their biomass in this region, including Atlantic menhaden (Brevoortia tyrannus), Atlantic mackerel (Scomber scombrus), and benthic elasmobranchs, including skates. Our results are consistent with previously published stomach content data for the shark species of similar size range in the Northwest Atlantic Ocean, supporting the efficacy of cloacal swab DNA metabarcoding as a minimally invasive diet reconstruction technique. The high reliance of several shark species on Atlantic menhaden could imply wasp-waist food-web conditions during the summer months, whereby high abundances of forage fishes sustain a diverse suite of migratory sharks within a complex, seasonal food web.

Testing the effectiveness of different wash protocols to remove body surface contaminants in invertebrate food web studies

Molecular gut content analysis via diagnostic PCR or high-throughput sequencing (metabarcoding) of consumers allows unravelling of feeding interactions in a wide range of animals. This is of particular advantage for analyzing the diet of small invertebrates living in opaque habitats such as the soil. Due to their small body size, which complicates dissection, microarthropods are subjected to whole-body DNA extraction-step before their gut content is screened for DNA of their food. This poses the problem that body surface contaminants, such as fungal spores may be incorrectly identified as ingested food particles for fungivorous species. We investigated the effectiveness of ten methods for body surface decontamination in litter-dwelling oribatid mites using Steganacarus magnus as model species. Furthermore, we tested for potential adverse effects of the decontamination techniques on the molecular detection of ingested prey organisms. Prior to decontamination, oribatid mites were fed with an oversupply of nematodes (Plectus sp.) and postmortem contaminated with fungal spores (Chaetomium globosum). We used diagnostic PCR with primers specific for C. globosum and Plectus sp. to detect contaminants and prey, respectively. The results suggest that chlorine bleach (sodium hypochloride, NaClO, 5%) is most efficient in removing fungal surface contamination without significantly affecting the detection of prey DNA in the gut. Based on these results, we provide a standard protocol for efficient body surface decontamination allowing to trace the prey spectrum of microarthropods using molecular gut content analysis.

Pajda-De La O J, McCary MA. Pattern of seasonal variation in rates of predation between spider families is temporally stable in a food web with widespread intraguild predation

Intraguild predation (IGP)-predation between generalist predators (IGPredator and IGPrey) that potentially compete for a shared prey resource-is a common interaction module in terrestrial food webs. Understanding temporal variation in webs with widespread IGP is relevant to testing food web theory. We investigated temporal constancy in the structure of such a system: the spider-focused food web of the forest floor. Multiplex PCR was used to detect prey DNA in 3,300 adult spiders collected from the floor of a deciduous forest during spring, summer, and fall over four years. Because only spiders were defined as consumers, the web was tripartite, with 11 consumer nodes (spider families) and 22 resource nodes: 11 non-spider arthropod taxa (order- or family-level) and the 11 spider families. Most (99%) spider-spider predation was on spider IGPrey, and ~90% of these interactions were restricted to spider families within the same broadly defined foraging mode (cursorial or web-spinning spiders). Bootstrapped-derived confidence intervals (BCI's) for two indices of web structure, restricted connectance and interaction evenness, overlapped broadly across years and seasons. A third index, % IGPrey (% IGPrey among all prey of spiders), was similar across years (~50%) but varied seasonally, with a summer rate (65%) ~1.8x higher than spring and fall. This seasonal pattern was consistent across years. Our results suggest that extensive spider predation on spider IGPrey that exhibits consistent seasonal variation in frequency, and that occurs primarily within two broadly defined spider-spider interaction pathways, must be incorporated into models of the dynamics of forest-floor food webs.

SPECIES IN THE FECES: DNA METABARCODING TO DETECT POTENTIAL GASTROPOD HOSTS OF PARELAPHOSTRONGYLUS TENUIS Consumed By Moose (Alces Alces)

Our understanding of wildlife multihost pathogen transmission systems is often incomplete due to the difficulty of observing contact between hosts. Understanding these interactions can be critical for preventing disease-induced wildlife declines. The proliferation of high-throughput sequencing technologies provides new opportunities to better explore these cryptic interactions. Parelaphostrongylus tenuis, a multihost parasite, is a leading cause of death in some moose (Alces alces) populations threatened by local extinction in the midwestern and northeastern US and southeastern Canada. Moose contract P. tenuis by consuming infected gastropod intermediate hosts, but little is known about which gastropod species moose consume. To gain more insight, we used a genetic metabarcoding approach on 258 georeferenced and temporally stratified moose fecal samples collected May-October 2017-20 from a declining population in the north-central US. We detected moose consumption of three species of gastropods across five positive samples. Two of these (Punctum minutissimum and Helisoma sp.) have been minimally investigated for the ability to host P. tenuis, while one (Zonitoides arboreus) is a well-documented host. Moose consumption of gastropods documented herein occurred in June and September. Our findings prove that moose consume gastropod species known to become infected by P. tenuis and demonstrate that fecal metabarcoding can provide novel insight on interactions between hosts of a multispecies pathogen transmission system. After determining and improving test sensitivity, these methods may also be extended to document important interactions in other multihost disease systems.

Trophic resources of the edaphic microarthropods: A worldwide review of the empirical evidence

Ecosystem sustainable use requires reliable information about its biotic and abiotic structure and functioning. Accurate knowledge of trophic relations is central for the understanding of ecosystem dynamics, which in turn, is essential for food web stability analyzes and the development of sustainable practices. There is a rapid growth in the knowledge on how belowground biodiversity regulates the structure and functioning of terrestrial ecosystems. Although, the available information about trophic relationships is hard to find and fragmented. Most of the information available worldwide about the food resources of soil microarthropods suggested that out of 3105 hits of initial research on this aspect only a total of 196 published works related particular species, genera, and families to particular trophic resources, the majority of them dealing with soils of the Palearctic region. From the 196 publications we extracted 3009 records relating specific taxonomic groups to their trophic resources, 20 percent mention saprophytic fungi as a food resource, 16 percent cite microfauna, 11 percent mention bacteria, 10 percent litter and 8 percent cite Springtails. The available information was highly skewed, the 73.71 percent comes from Acari, and within these, 50.62 percent correspond just to Sarcoptiformes. The literature on Collembola is very scarce and most of the information is on arthropleona. The review also highlights that available research on the use of trophic resources comes from European sites and the information on this aspect from other parts of the soils of the world is still at large but unknown.

Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis

Knowledge of trophic interaction is necessary to understand the dynamics of ecosystems and develop ecosystem-based management. The key data to measure these interactions should come from large-scale diet analyses with good taxonomic resolution. To that end, molecular methods that analyze prey DNA from guts and feces provide high-resolution dietary taxonomic data. However, molecular diet analysis may also produce unreliable results if the samples are contaminated by external sources of DNA. Employing the freshwater European whitefish (Coregonus lavaretus) as a tracer for sample contamination, we studied the possible route of whitefish in beaked redfish (Sebastes mentella) guts sampled in the Barents Sea. We used whitefish-specific COI primers for diagnostic analysis, and fish-specific 12S and metazoa-specific COI primers for metabarcoding analyses of intestine and stomach contents of fish samples that were either not cleaned, water cleaned, or bleach cleaned after being in contact with whitefish. Both the diagnostic and COI metabarcoding revealed clear positive effects of cleaning samples as whitefish were detected in significantly higher numbers of uncleaned samples compared to water or bleach-cleaned samples. Stomachs were more susceptible to contamination than intestines and bleach cleaning reduced the frequency of whitefish contamination. Also, the metabarcoding approach detected significantly more reads of whitefish in the stomach than in intestine samples. The diagnostic analysis and COI metabarcoding detected contaminants in a higher and comparable number of gut samples than the 12S-based approach. Our study underlines thus the importance of surface decontamination of aquatic samples to obtain reliable diet information from molecular data.

Environmental risks of antibiotic resistance genes released from biological laboratories and its control measure

Antibiotic resistance genes (ARGs) are a growing global threat to public health. Biological laboratory wastewater contains large amounts of free ARGs. It is important to assess the risk of free ARGs from biological laboratories and to find appropriate treatments to control their spread. The fate of plasmids in the environment and the effect of different thermal treatments on their persistence activity were tested. The results showed that untreated resistance plasmids could exist in water for more than 24 h (the special 245 bp fragment). Gel electrophoresis and transformation assays showed that the plasmids boiled for 20 min retained 3.65% ± 0.31% transformation activity of the intact plasmids, while autoclaving for 20 min at 121 °C could effectively degrade the plasmids and that NaCl, bovine serum albumin, and EDTA-2Na affected the degradation efficiency of the plasmids during boiling. In the simulated aquatic system, using 10⁶ copy/μL of plasmids after autoclaving, only 10² copies/μL of the fragment after only 1-2 h could be detected. By contrast, boiled plasmids for 20 min were still detectable after plunging them into water for 24 h. These findings suggest that untreated and boiled plasmids can remain in the aquatic environment for a certain time resulting in the risk of disseminating ARGs. However, autoclaving is an effective way of degrading waste free resistance plasmids.

Consumer identity but not food availability affects carabid diet in cereal crops

Understanding trophic interactions in agroecosystems is crucial for harnessing ecosystem services such as pest control, thus enabling a reduction in pesticide use. Carabid beetles (Coleoptera: Carabidae) have the potential to regulate not only insect pests but also weed seeds and slugs. The aim of this study was to investigate the food choice of different carabid species in the experimental setting of a cereal field with varying seed and slug prey availability during the season. In addition to varying food availability, the effects of species identity and season on carabid food choice should also be closely examined. Therefore, the gut contents of 1,120 beetles of eight carabid species were screened for the DNA of plants, aphids, springtails, earthworms and slugs via diagnostic multiplex PCR and a nested metabarcoding approach for plant species identification. Plant DNA was detected far more often (72%) than the various animal prey types (less than 12.5% each). Within the plant detections, 80 weed species were identified in the metabarcoding, with Galinsoga parviflora/quadriradiata (Galinsoga spp.-quickweeds) as the most frequently detected species. Carabid food choice was driven by their species identity and seasonality, while no effect of increased availability of seeds and slugs on their food choice was detected. While weed seeds seem to be an important food source for carabids, their availability does not directly affect the carabid diet. The importance of consumer identity and seasonality highlight the need for a diverse carabid species community for resilient pest control services.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10340-023-01620-w.

DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents

The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.

Intraguild Predation of Hippodamia variegata on Aphid Mummies in Cotton Field

Intraguild predation among arthropod predators in agricultural ecosystems may have a negative impact on biological control. At present, there are few direct reports on trophic relationships among participants of predation in field groups. In this study, we measured the feeding choices of Hippodamia variegata (Goeze) towards mummies with different densities of Aphis gossypii Glover. The dynamics of the occurrence of mummies in the cotton field were investigated over 2017-2019. Singleplex PCR and multiplex PCR were used to detect the predation of 2090 H. variegata individuals on aphids and mummies in Xinjiang cotton field, which revealed the intraguild predation frequency between H. variegata and various parasitoids. There was no obvious feeding preference of H. variegata towards live aphids or mummies, which mainly depended on the relative density of prey. Among the four species of aphids detected in H. variegata, A. gossypii had a high detection rate and was the main prey source of the ladybeetle in the cotton filed. Mostly, ladybeetles consumed parasitoids through mummies, with 6.39% directly feeding on adult parasitoids. H. variegata had strong trophic links to both parasitoids and aphids. We established a food web of aphids-primary parasitoids-hyperparasitoids-H. variegata, which can be used to evaluate the pest control ability of H. variegata from a new perspective.

Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica

Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.

Detectability of Hibiscus Mealybug, Nipaecoccus viridis (Hemiptera: Pseudoccocidae), DNA in the Mealybug Destroyer, Cryptolaemus montrouzieri (Coleoptera: Coccinellidae), and Survey of Its Predators in Florida Citrus Groves

The Hibiscus mealybug, Nipaecoccus viridis (Newstead), has recently established in Florida citrus and become a pest of concern given secondary pest outbreaks associated with management of citrus greening disease. Chemical controls used to manage other citrus arthropod pests are not as effective against N. viridis due to its waxy secretions, clumping behavior, and induced cellular changes to host plant tissue which increase microhabitats. Populations of this mealybug pest are regulated by natural enemies in its native region, but it remains unclear if resident natural enemies in Florida citrus could similarly suppress N. viridis populations. This investigation: 1) established species-specific primers for N. viridis based on the mitochondrial gene Cytochrome-oxidase 1 (COI), 2) determined duration of N. viridis DNA detectability in a known predator, the mealybug destroyer (Cryptolaemus montrouzieri Mulsant), by using identified primers in molecular gut content analysis, and 3) screened field-collected predators for the presence of N. viridis DNA. The detection rate of N. viridis DNA was >50% at 36 h after adult C. montrouzieri feeding but DNA was no longer detectable by 72 h after feeding. Field-collected predators were largely comprised of spiders, lacewings, and C. montrouzieri. Spiders, beetles (primarily C. montrouzieri), and juvenile lacewings were the most abundant predators of N. viridis, with 17.8, 43.5, and 58.3 of field-collected samples testing positive for N. viridis DNA, respectively. Our results indicate that Florida citrus groves are hosts to abundant predators of N. viridis and encourage the incorporation of conservation or augmentative biological control for management of this pest.

Correlation and Influence of Seasonal Variation of Diet with Gut Microbiota Diversity and Metabolism Profile of Chipmunk

Tamias Sibiricus is the only member of the genus Tamias, a significant and vigorous seed distributor and vital food for their predators. No information is known about the strict diet, gut microbiota structure, and metabolism profile of chipmunks and how they diversify seasonally. The above factors, as well as flexibility toward seasonal shifts, are critical in defining its growth rates, health, survivorship, and population stability. This study explored the diet, gut microbiota composition, and chipmunk metabolism. Additionally, the influence of different seasons was also investigated by using next-generation sequencing. Results revealed that seasons strongly affected a diet: streptophyte accounted for 37% in spring, which was lower than in summer (34.3%) and autumn (31.4%). Further, Ascomycota was observed at 43.8% in spring, which reduced to 36.6% in summer and the lowest (31.3%) in autumn. Whereas, nematodes showed maximum abundance from spring (15.8%) to summer (20.6%) and autumn (24.1%). These results signify the insectivorous nature of the chipmunk in summer and autumn. While herbivorous and fungivorous nature in spring. The DNA analysis revealed that chipmunk mainly feeds on fungi, including Aspergillus and Penicillium genus. Similar to diet composition, the microbiome also exhibited highly significant dissimilarity (p < 0.001, R = 0.235) between spring/autumn and spring/summer seasons. Proteobacteria (35.45%), Firmicutes (26.7%), and Bacteroidetes (23.59%) were shown to be the better discriminators as they contributed the most to causing differences between seasons. Moreover, PICRUSt showed that the assimilation of nutrients were also varied seasonally. The abundance of carbohydrates, lipids, nucleotides, xenobiotics, energy, terpenoids, and polyketides metabolism was higher in spring than in other seasons. Our study illustrates that seasonal reconstruction in the chipmunk diet has a significant role in shaping temporal variations in gut microbial community structure and metabolism profile.

Caught on camera: Field imagery reveals the unexpected importance of vertebrates for biological control of the banana weevil (Cosmopolites sordidus Col. Curculionidae)

Understanding of ecological interactions is necessary for the application of biological control. Banana is the second most produced fruit worldwide and the banana weevil (Cosmopolites sordidus) is the most important pest of banana and plantain. Its biological control remains challenging because of the robustness and cryptic behaviour of the adult and the hidden development of larval stages. Researchers therefore tend to favour conservation biological control of this pest. The commonly used methods for measuring the effects of natural enemies on the regulation of this pest focus on invertebrates and may underestimate the role of vertebrates on biological control. Using cameras, we recorded the predation of sentinel adult weevils in banana plots in La Réunion island that differed in weevil infestation levels and in animal biodiversity. To facilitate image analysis, we used background subtraction to isolate moving parts of image sequences and thus detect predators and predation events. Our cameras recorded only vertebrates as predators of adult banana weevils. The most important predator appeared to be the Asian shrew (Suncus murinus), which was responsible for 67% of the predation events. Other predators included the house mouse (Mus musculus), the oriental garden lizard (Calotes versicolor), and the guttural toad (Sclerophrys gutturalis). The exact time of predation events were determined from the images metadata. It was thus possible to identify predator foraging periods that coincided with activity of adult weevils. Our results confirm that images provide useful information for biological and ecological studies. Along with other recent studies, our results suggest that the role of vertebrates in biological control may be underestimated. Based on these results, we advocate for several management implications such as the installation of hedges, grasslands, and ponds to favour these vertebrate predators of the banana weevil, possibly also favouring other vertebrate and invertebrate natural enemies.

Alternative prey mediate intraguild predation in the open field

BACKGROUND

Generalist predators that kill and eat other natural enemies can weaken biological control. However, pest suppression can be disrupted even if actual intraguild predation is infrequent, if predators reduce their foraging to lower their risk of being killed. In turn, predator-predator interference might be frequent when few other prey are available, but less common when herbivorous and detritus-feeding prey are plentiful. We used molecular gut-content analysis to track consumption of the predatory bug Geocoris sp. by the larger intraguild predator Nabis sp., in organic and conventional potato (Solanum tuberosum) fields.

RESULTS

We found that higher densities of both aphids and thrips, two common herbivores, correlated with higher probability of detecting intraguild predation. Perhaps, Nabis foraging for these herbivores also encountered and ate more Geocoris. Surprisingly, likelihood of intraguild predation was not strongly linked to densities of either Nabis or Geocoris, or farming system, suggesting a greater importance for prey than predator community structure. Intriguingly, we found evidence that Geocoris fed more often on the detritus-feeding fly Scaptomyza pallida with increasing predator evenness. This would be consistent with Geocoris shifting to greater foraging on the ground, where S. pallida would be relatively abundant, in the face of greater risk of intraguild predation.

CONCLUSION

Overall, our findings suggest that while herbivorous prey may heighten intraguild predation of Geocoris in the foliage, detritivores might support a shift to safer foraging on the ground. This provides further evidence that prey abundance and diversity can act to either heighten or relax predator-predator interference, depending on prey species identity and predator behavior. © 2022 Society of Chemical Industry.

Alternative prey and farming system mediate predation of Colorado potato beetles by generalists

BACKGROUND

Biological control by generalist predators can be mediated by the abundance and biodiversity of alternative prey. When alternative prey draw predator attacks away from the control target, they can weaken pest suppression. In other cases, a diverse prey base can promote predator abundance and biodiversity, reduce predator-predator interference, and benefit biocontrol. Here, we used molecular gut-content analysis to assess how community composition altered predation of Colorado potato beetle (Leptinotarsa decemlineata (Say)) by Nabis sp. and Geocoris sp. Predators were collected from organic or conventional potato (Solanum tuberosum L.) fields, encouraging differences in arthropod community composition.

RESULTS

In organic fields, Nabis predation of potato beetles decreased with increasing arthropod richness and predator abundance. This is consistent with Nabis predators switching to other prey species when available and with growing predator-predator interference. In conventional fields these patterns were reversed, however, with potato beetle predation by Nabis increasing with greater arthropod richness and predator abundance. For Geocoris, Colorado potato beetle predation was more frequent in organic than in conventional fields. However, Geocoris predation of beetles was less frequent in fields with higher abundance of the detritus-feeding fly Scaptomyza pallida Zetterstedt, or of all arthropods, consistent with predators choosing other prey when available.

CONCLUSION

Alternative prey generally dampened predation of potato beetles, suggesting these pests were less-preferred prey. Nabis and Geocoris differed in which alternative prey were most disruptive to feeding on potato beetles, and in the effects of farm management on predation, consistent with the two predator species occupying complementary feeding niches. © 2021 Society of Chemical Industry.

Dietary preferences and feeding strategies of Colombian highland woolly monkeys

Primates are very selective in the foods they include in their diets with foraging strategies that respond to spatial and temporal changes in resource availability, distribution and quality. Colombian woolly monkeys (Lagothrix lagotricha lugens), one of the largest primate species in the Americas, feed mainly on fruits, but they also eat a high percentage of arthropods. This differs from closely related Atelid species that supplement their diet with leaves. In an 11 month study, we investigated the foraging strategies of this endemic monkey and assessed how resource availability affects dietary selection. Using behavioural, phenological, arthropod sampling and metabarcoding methods, we recorded respectively foraging time, forest productivity, arthropod availability in the forest and arthropod consumption. Scat samples and capturing canopy substrates (i.e. moss, bromeliads, aerial insects) were used for assigning arthropod taxonomy. The most important resource in the diet was fruits (54%), followed by arthropods (28%). Resource availability predicted feeding time for arthropods but not for fruits. Further, there was a positive relationship between feeding time on fruits and arthropods, suggesting that eating both resources during the same periods might work as an optimal strategy to maximize nutrient intake. Woolly monkeys preferred and avoided some fruit and arthropod items available in their home range, choosing a wide variety of arthropods. Geometrid moths (Lepidoptera) were the most important and consistent insects eaten over time. We found no differences in the type of arthropods adults and juveniles ate, but adults invested more time foraging for this resource, especially in moss. Although woolly monkeys are generalist foragers, they do not select their food items randomly or opportunistically.

Microchemical provenancing of prey remains in cormorant pellets reveals the use of diverse foraging grounds

Piscivorous birds in aquatic ecosystems exert predation pressure on fish populations. But the site‐specific impact on fish populations, including stocked and commercially used fish species, remains disputed. One of the key questions for the management of piscivorous birds and fish is determining the origin of prey and thus which fish populations are targeted by the birds. We addressed this question by provenancing otoliths (earstones) of fish obtained from regurgitated pellets of piscivorous birds by otolith microchemistry analysis. We retrieved otoliths from regurgitated pellets of great cormorants (Phalacrocorax carbo sinensis) collected every 2 weeks for 2 years from breeding and roosting colonies at Chiemsee in Bavaria, Germany, and classified them according to family or species. We collected water samples from Chiemsee and potential surrounding foraging grounds. We measured the strontium (Sr) ⁸⁷Sr/⁸⁶Sr isotope ratio and Sr mass fraction of water and otoliths using (laser ablation) inductively coupled plasma‐mass spectrometry. We assigned otoliths from regurgitated pellets to habitat clusters of origin by comparing the Sr isotopic and elemental composition of otoliths and waterbodies. In 36% of cormorant pellets collected at Chiemsee, prey was assigned to waterbodies distinct from Chiemsee. Furthermore, cormorants used different foraging sites during 1 day. Microchemical provenancing of prey remains can contribute to identifying foraging sites of piscivorous birds and to what extend the birds switched among foraging sites.

CView: A network based tool for enhanced alignment visualization

To date basic visualization of sequence alignments have largely focused on displaying per-site columns of nucleotide, or amino acid, residues along with associated frequency summarizations. The persistence of this tendency to the recent tools designed for viewing mapped read data indicates that such a perspective not only provides a reliable visualization of per-site alterations, but also offers implicit reassurance to the end-user in relation to data accessibility. However, the initial insight gained is limited, something that is especially true when viewing alignments consisting of many sequences representing differing factors such as location, date and subtype. A basic alignment viewer can have potential to increase initial insight through visual enhancement, whilst not delving into the realms of complex sequence analysis. We present CView, a visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. Within the network, nodes are based on the clustering of sequence fragments that span windows placed consecutively along the alignment. Edges are placed between nodes of neighbouring windows where they share sequence identification(s), i.e. different regions of the same sequence(s). Thus, if a node is selected on the network, then the relationship that sequences passing through that node have to other regions of diversity within the alignment can be observed through path tracing. In addition to augmenting visual insight, CView provides export features including variant summarization, per-site residue and kmer frequencies, consensus sequence, alignment dissection as well as clustering; each useful across a range of research areas. The software has been designed to be user friendly, intuitive and interactive. It is open source and an executable jar, source code, quick start, usage tutorial and test data are available (under the GNU General Public License) from https://sourceforge.net/projects/cview/.

Spatial variation in food web structure in a recovering marine ecosystem

Spatial heterogeneity in food web structure and interactions may reconcile spatial variation in population and community dynamics in large marine ecosystems. In order to assess food web contributions to the different community recovery dynamics along the Newfoundland and Labrador shelf ecosystem, we quantified species interactions using stable isotope mixing models and food web metrics within three sub-regions. Representative samples of each species caught in trawls and plankton tows were analyzed for stomach contents and stable isotope ratios (δ15N and δ13C) to parameterize isotope mixing models. Regional variation, highlighted by the diets of three economically important species, was observed such that the southern region demonstrated a variety of trophic pathways of nutrient flow into the higher food web while the diets of fish in the northern regions were typically dominated by one or two pathways via dominant prey species, specifically shrimp (Pandalus sp.) and hyperiids. Food web metrics indicated that the low-diversity northern regions had higher connectance and shorter food chain lengths. This observed regional variation contributes to our understanding of the role of specific forage species to the ecosystem which is an essential contribution towards ecosystem-based management decisions.

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

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.

Data on the diets of Salish Sea harbour seals from DNA metabarcoding

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.

Alternative Prey and Predator Interference Mediate Thrips Consumption by Generalists

Generalist predators’ complex feeding relationships make it difficult to predict their contribution to pest suppression. Alternative prey can either distract predators from attacking pests, weakening biocontrol, or provide food that support larger predator communities to enhance it. Similarly, predator species might both feed upon and complement one another by occupying different niches. Here, we use molecular gut-content analysis to examine predation of western flower thrips (Frankliniella occidentalis) by two generalist predatory bugs, Geocoris sp. and Nabis sp. We collected predators from conventional and organic potato fields that differed in arthropod abundance and composition, so that we could draw correlations between abundance and biodiversity of predators and prey, and thrips predation. We found that alternative prey influenced the probability of detecting Geocoris predation of thrips through a complex interaction. In conventionally-managed potato fields, thrips DNA was more likely to be detected in Geocoris as total abundance of all arthropods in the community increased. But the opposite pattern was found in organic fields, where the probability of detecting thrips predation by Geocoris decreased with increasing total arthropod abundance. Perhaps, increasing abundance (from a relatively low baseline) of alternative prey triggered greater foraging activity in conventional fields, but drew attacks away from thrips in organic fields where prey were consistently relatively bountiful. The probability of detecting Geocoris predation of thrips generally increased with increasing thrips density, but this correlation was steeper in organic than conventional fields. For both Geocoris and Nabis, greater Nabis abundance correlated with reduced probability of detecting thrips DNA; for Nabis this was the only important variable. Nabis is a common intraguild predator of the smaller Geocoris, and is highly cannibalistic, suggesting that predator-predator interference increased with more Nabis present. Complex patterns of thrips predation seemed to result from a dynamic interaction with alternative prey abundance, alongside consistently negative interactions among predators. This provides further evidence that alternative prey and predator interference must be studied in concert to accurately predict the contributions of generalists to biocontrol.

Molecular assays to reliably detect and quantify predation on a forest pest in bats faeces

Targeted molecular methods such as conventional PCR (cPCR) and quantitative PCR (qPCR), combined with species-specific primers and probes, are widely applied for pest species detection. Besides, the potential of qPCR to quantify DNA in samples makes it an invaluable molecular tool to infer the predation levels on specific prey by analysing predators’ stools. Nevertheless, studies on the diet of bats failed to find any empirical relationship, and it remains to be evaluated. Thus, we developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, the pine processionary, Thaumetopoea pityocampa, in bats’ faeces. Further, we empirically compared a range of different known DNA concentrations (input) of the target species mixed with mocks and bat faecal samples against DNA abundances yielded by qPCR (output) for a quantitative assessment. Overall, cPCR showed a lower detection rate than qPCR, but augmenting the replicate effort from one to three replicates led to a greater increase in the detection rate of the cPCR (from 57 to 80%) than the qPCR (from 90 to 99%). The quantitative experiment results showed a highly significant correlation between the input and output DNA concentrations (t = 10.84, p < 0.001) with a mean slope value of 1.05, indicating the accuracy of our qPCR assay to estimate DNA abundance of T. pityocampa in bat faeces. The framework of this study can be taken as a model to design similar assays applicable to other species of interest, such as agricultural pests or insects of public health concern.

A novel molecular diagnostic method for the gut content analysis of Philaenus DNA

Philaenus spumarius is a vector of Xylella fastidiosa, one of the most dangerous plants pathogenic bacteria worldwide. There is currently no control measure against this pathogen. Thus, the development of vector control strategies, like generalist predators, such as spiders, could be essential to limit the spread of this vector-borne pathogen. In this study, a polymerase chain reaction (PCR)-based approach was developed to principally detect DNA of P. spumarius in the spider's gut. Accordingly, 20 primer pairs, targeting the mitochondrial cytochrome oxidase I (COI) and cytochrome b (cytB) genes, were tested for specificity, sensitivity, and efficiency in detecting P. spumarius DNA. Overall, two primer sets, targeting COI gene (COI_Ph71F/COI_Ph941R) and the cytB gene (cytB_Ph85F/cytB_Ph635R), showed the highest specificity and sensitivity, being able to amplify 870 pb and 550 bp fragments, respectively, with P. spumarius DNA concentrations 100-fold lower than that of the DNA of non-target species. Among these two primer sets, the cytB_Ph85F/cytB_Ph635R was able to detect P. spumarius in the spider Xysticus acerbus, reaching 50% detection success 82 h after feeding. The feasibility of this primer set to detect predation of P. spumarius by spiders was confirmed in the field, where 20% of the collected spiders presented positive amplifications.

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.

Connectivity dynamics in Irish mudflats between microorganisms including Vibrio spp., common cockles Cerastoderma edule, and shorebirds

Shellfish, including the key species the common cockle Cerastoderma edule, living and feeding in waters contaminated by infectious agents can accumulate them within their tissues. It is unknown if microbial pathogens and microparasites can subsequently be transmitted via concomitant predation to their consumers, including shorebirds. The objective of this study was to assess if pathogens associated with C. edule could be detected seasonally in the faeces of shorebirds that feed on C. edule and in the physical environment (sediment) in which C. edule reside, along the Irish and Celtic Seas. Two potentially pathogenic global groups, Vibrio and Haplosporidia, were detected in C. edule. Although Haplosporidia were not detected in the bird faeces nor in the sediment, identical strains of Vibrio splendidus were detected in C. edule and bird faecal samples at sites where the oystercatcher Haematopus ostralegus and other waders were observed to be feeding on cockles. Vibrio spp. prevalence was seasonal and increased in C. edule and bird faecal samples during the warmer months, possibly due to higher seawater temperatures that promote the replication of this bacteria. The sediment samples showed an overall higher prevalence of Vibrio spp. than the bird faecal and C. edule samples, and its detection remained consistently high through the sites and throughout the seasons, which further supports the role of the sediment as a Vibrio reservoir. Our findings shed light on the fact that not all pathogen groups are transmitted from prey to predator via feeding but bacteria such as V. splendidus can be. As most of the wading birds observed in this study are migratory, the results also indicate the potential for this bacterium to be dispersed over greater geographic distances, which will have consequences for areas where it may be introduced.

A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples

As one of the most abundant predators of insects in terrestrial ecosystems, spiders have long received much attention from agricultural scientists and ecologists. Do spiders have a certain controlling effect on the main insect pests of concern in farmland ecosystems? Answering this question requires us to fully understand the prey spectrum of spiders. Next-generation sequencing (NGS) has been successfully employed to analyze spider prey spectra. However, the high sequencing costs make it difficult to analyze the prey spectrum of various spider species with large samples in a given farmland ecosystem. We performed a comparative analysis of the prey spectra of Ovia alboannulata (Araneae, Lycosidae) using NGS with individual and mixed DNA samples to demonstrate which treatment was better for determining the spider prey spectra in the field. We collected spider individuals from tea plantations, and two treatments were then carried out: (1) The DNA was extracted from the spiders individually and then sequenced separately (DESISS) and (2) the DNA was extracted from the spiders individually and then mixed and sequenced (DESIMS). The results showed that the number of prey families obtained by the DESISS treatment was approximately twice that obtained by the DESIMS treatment. Therefore, the DESIMS treatment greatly underestimated the prey composition of the spiders, although its sequencing costs were obviously lower. However, the relative abundance of prey sequences detected in the two treatments was slightly different only at the family level. Therefore, we concluded that if our purpose were to obtain the most accurate prey spectrum of the spiders, the DESISS treatment would be the best choice. However, if our purpose were to obtain only the relative abundance of prey sequences of the spiders, the DESIMS treatment would also be an option. The present study provides an important reference for choosing applicable methods to analyze the prey spectra and food web compositions of animal in ecosystems.

Application of species-specific primers to estimate the in situ diet of Bythotrephes [Cladocera, Onychopoda] in its native European range via molecular gut content analysis

The study of invasive species often focuses on regions of recent introduction rather than native habitats. Understanding an invasive species in its natural environment, however, can provide important insights regarding the long-term outcome of invasions. In this study we investigated the diet of the invasive spiny water flea, Bythotrephes longimanus, in two Austrian perialpine lakes, where it is native. The gut contents of wild-caught Bythotrephes individuals were estimated by quantitative polymerase chain reaction, targeting species-specific fragments of the barcoding region of the cytochrome c oxidase I gene of potential prey. The observed prey spectrum of Bythotrephes in the study lakes consisted primarily of Eudiaptomus gracilis and Diaphanosoma brachyurum. The Daphnia longispina complex, Leptodora kindtii and Mesocyclops leuckarti also contributed to the diet. Results indicate that Bythotrephes is a generalist feeder with a preference for epilimnetic prey.

Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey

Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.

Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions

The use of sensitive methods is key for the detection of target taxa from trace amounts of environmental DNA (eDNA) in a sample. In this context, digital PCR (dPCR) enables direct quantification and is commonly perceived as more sensitive than endpoint PCR. However, endpoint PCR coupled with capillary electrophoresis (celPCR) potentially embodies a viable alternative as it quantitatively measures signal strength after PCR in Relative Fluorescence Units (RFU). Provided comparable levels of sensitivity are reached, celPCR permits the development of cost-efficient multiplex reactions, enabling the simultaneous detection of several target taxa. Here, we compared the sensitivity of singleplex and multiplex celPCR to dPCR for species-specific primer pairs amplifying mitochondrial DNA (COI) of fish species occurring in European freshwaters by analyzing dilution series of tissue extracts as well as field-collected water samples. Both singleplex and multiplex celPCR and dPCR displayed comparable sensitivity with reliable positive amplifications starting at two to 10 target DNA copies per μl extract. celPCR was suitable for quantifying target DNA and direct inference of copy numbers from RFU was possible after accounting for primer effects in linear mixed-effects models and calibration via dPCR. Furthermore, multiplex celPCR and dPCR were successfully used for the detection and quantification of fish-eDNA in field-collected water samples, confirming the results of the dilution series experiment and exemplifying the high sensitivity of the two approaches. The possibility of detection and quantification via multiplex celPCR is appealing for the cost-efficient screening of high sample numbers. The present results confirm the sensitivity of this approach thus enabling its application for future eDNA-based monitoring efforts.

Molecular gut content analysis indicates the inter- and intra-guild predation patterns of spiders in conventionally managed vegetable fields

Inter- and intra-guild interactions are important in the coexistence of predators and their prey, especially in highly disturbed vegetable cropping systems with sporadic food resources. Assessing the dietary range of a predator taxon characterized by diverse foraging behavior using conventional approaches, such as visual observation and conventional molecular approaches for prey detection, has serious logistical problems. In this study, we assessed the prey compositions and compare the dietary spectrum of a functionally diverge group of predators-spiders-to characterize their trophic interactions and assess biological control potential in Brassica vegetable fields. We used high-throughput sequencing (HTS) and biotic interaction networks to precisely annotate the predation spectrum and highlight the predator-predator and predator-prey interactions. The prey taxa in the gut of all spider families were mainly enriched with insects (including dipterans, coleopterans, orthopterans, hemipterans, and lepidopterans) with lower proportions of arachnids (such as Araneae) along with a wide range of other prey factions. Despite the generalist foraging behavior of spiders, the community structure analysis and interaction networks highlighted the overrepresentation of particular prey taxa in the gut of each spider family, as well as showing the extent of interfamily predation by spiders. Identifying the diverse trophic niche proportions underpins the importance of spiders as predators of pests in highly disturbed agroecosystems. More specifically, combining HTS with advanced ecological community analysis reveals the preferences and biological control potential of particular spider taxa (such as Salticidae against lepidopterans and Pisauridae against dipterans), and so provides a valuable evidence base for targeted conservation biological control efforts in complex trophic networks.

A barcoding-based scat-analysis assessment of Eurasian otter Lutra lutra diet on Kinmen Island

While it is well known that Eurasian otters principally feed on fishes and crustaceans, their detailed diet taxonomies are not fully understood. This is partly due to their nocturnal behavior and the limited resolving power of traditional morphological identification from scat. A suitable, reliable molecular method for diet studies is therefore needed.I performed a series of Sanger-sequencing reactions, utilizing nine primer sets for Eurasian otter diet research. These are mainly based on the barcoding concept to determine the taxonomic composition of spraints. The primer sets target different types of animals, amplifying each separately. This procedure was used to detect the prey contents of 64 spraint samples collected from Kinmen Island. Through high-resolution gel electrophoresis and sequencing, it was evident that PCR products could be successfully amplified by the different primer sets and from spraint samples comprising multiple prey species.Extracted DNA from all spraint samples was PCR-amplified with 9 primer sets. In total, 16 prey types were identified across all 64 samples. Fourteen were identified at the species level.The aim of this study was to develop and apply a novel diet research method to Eurasian otters. Eight of the primers are universal primers designed for COI segments of different animal groups, and one primer set was designed specifically for tilapia groups. This method can be applied to study the diets of not only Kinmen Eurasian otter populations, but also other Eurasian otter populations and other small carnivorous animals.

A dearth of data: fitting parasitoids into ecological networks

Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.

Exploratory analysis reveals arthropod consumption in 10 lemur species using DNA metabarcoding

Arthropods (insects, spiders, etc.) can fulfill major nutritional requirements for primates, particularly in terms of proteins, fats, vitamins, and minerals. Yet, for many primate species we know very little about the frequency and importance of arthropod consumption. Traditional methods for arthropod prey identification, such as behavioral observations and fecal dissections, offer limited taxonomic resolution and, as a result, underestimate true diversity. Metabarcoding arthropod DNA from primate fecal samples provides a promising but underused alternative. Here, we inventoried arthropod prey diversity in wild lemurs by sequencing two regions of the CO1 gene. Samples were collected opportunistically from 10 species of lemurs inhabiting three national parks in southern Madagascar using a combination of focal animal follows and live trapping. In total, we detected arthropod DNA in 98 of the 170 fecal samples analyzed. Although all lemur species included in these analyses showed evidence of arthropod consumption, those within the family Cheirogaleidae appeared to consume the highest frequency and diversity of arthropods. To our knowledge, this study presents the first evidence of arthropod consumption in Phaner pallescens, Avahi peyrierasi, and Propithecus verreauxi, and identifies 32 families of arthropods as probable food items that have not been published as lemur dietary items to date. Our study emphasizes the importance of arthropods as a nutritional source and the role DNA metabarcoding can play in elucidating an animal's diet.

Flower strips as a bridge habitat facilitate the movement of predatory beetles from wheat to maize crops

BACKGROUND

Generalist predators play a key role in the biocontrol of insect pests in agricultural systems. However, predators are subject to frequent mortality events due to periodic disturbance regimes such as crop planting and harvest, which inevitably affect the population development of predators. Conservation of predators in this critical period is important for double-cropping systems such as winter wheat and summer maize, the most widely used cropping system in North China.

RESULTS

Planting Cnidium monnieri flower strips at field borders could not only serve as a bridge habitat to conserve the dominant predator Propylaea japonica in wheat fields during harvest but also help the predator immigrate to adjacent maize fields. The predator abundance was 7-fold higher on flower strips than that on natural vegetation strips during the wheat postharvest period and before the maize plant emergence for about a month, and its abundance in maize fields planted with flower strips was nearly 2-fold higher than that in maize fields planted with natural vegetation strips. Moreover, 77.56% of predators that entered maize fields were proven to originate from flower strips.

CONCLUSION

Our findings provided evidence that manipulating flower strips as a bridge habitat in wheat-maize rotation fields could conserve P. japonica during crop phenophase changes, and we quantitatively testified that the proportion of this predator in maize fields derived from flower strips. In practice, such a strategy may also be applied in other double-cropping and triple-cropping systems. © 2020 Society of Chemical Industry.

Predation on Drosophila suzukii within Hedges in the Agricultural Landscape

Simple Summary

Drosophila suzukii is an invasive species that feeds and reproduces on various cultivated and wild fruits and moves between agricultural and semi-natural habitats, such as hedges and forest patches. These semi-natural habitats are known to harbor a diverse community of natural enemies of pests. When we exposed D. suzukii pupae in dry and humid hedges, we found that on average 44% of them were predated within four days. The most common predators in the hedges were earwigs, spiders, and ants. Using a molecular assay that detects the DNA of D. suzukii in the gut of predators, we could show that 3.4% of the sampled earwigs, 1.8% of the spiders, and one predatory bug had fed on D. suzukii. This small proportion may be due to methodological constraints. However, the overall predation rate helps to reduce D. suzukii populations, in particular in hedges that are scarce of host fruits.

Abstract

The invasive Drosophila suzukii feeds and reproduces on various cultivated and wild fruits and moves between agricultural and semi-natural habitats. Hedges in agricultural landscapes play a vital role in the population development of D. suzukii, but also harbor a diverse community of natural enemies. We investigated predation by repeatedly exposing cohorts of D. suzukii pupae between June and October in dry and humid hedges at five different locations in Switzerland. We sampled predator communities and analyzed their gut content for the presence of D. suzukii DNA based on the COI marker. On average, 44% of the exposed pupae were predated. Predation was higher in dry than humid hedges, but did not differ significantly between pupae exposed on the ground or on branches and among sampling periods. Earwigs, spiders, and ants were the dominant predators. Predator communities did not vary significantly between hedge types or sampling periods. DNA of D. suzukii was detected in 3.4% of the earwigs, 1.8% of the spiders, and in one predatory bug (1.6%). While the molecular gut content analysis detected only a small proportion of predators that had fed on D. suzukii, overall predation seemed sufficient to reduce D. suzukii populations, in particular in hedges that provide few host fruit resources.

The food web in a subterranean ecosystem is driven by intraguild predation

Trophic interactions of cave arthropods have been understudied. We used molecular methods (NGS) to decipher the food web in the subterranean ecosystem of the Ardovská Cave (Western Carpathians, Slovakia). We collected five arthropod predators of the species Parasitus loricatus (gamasid mites), Eukoenenia spelaea (palpigrades), Quedius mesomelinus (beetles), and Porrhomma profundum and Centromerus cavernarum (both spiders) and prey belonging to several orders. Various arthropod orders were exploited as prey, and trophic interactions differed among the predators. Linear models were used to compare absolute and relative prey body sizes among the predators. Quedius exploited relatively small prey, while Eukoenenia and Parasitus fed on relatively large prey. Exploitation of eggs or cadavers is discussed. In contrast to previous studies, Eukoenenia was found to be carnivorous. A high proportion of intraguild predation was found in all predators. Intraspecific consumption (most likely cannibalism) was detected only in mites and beetles. Using Pianka's index, the highest trophic niche overlaps were found between Porrhomma and Parasitus and between Centromerus and Eukoenenia, while the lowest niche overlap was found between Parasitus and Quedius. Contrary to what we expected, the high availability of Diptera and Isopoda as a potential prey in the studied system was not corroborated. Our work demonstrates that intraguild diet plays an important role in predators occupying subterranean ecosystems.

Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina

Despite strong support from the media, the reintroduction of animals into natural environments does not always achieve its goal. Alouatta caraya is the primate species facing the greatest hunting pressure due to the illegal pet trade in Argentina. Confiscations of this species are common, as is the voluntary surrender of animals by owners no longer able or willing to care for them. These animals ultimately arrive at rehabilitation centers and, in many cases, are released into natural environments that may differ from the original sites where they were captured. Until recently, the lack of genetic analysis of the individuals involved led to biased relocation decisions. We followed the reintroduction of 12 A. caraya individuals in a protected area (Isla Palacio, Misiones, Argentina). The presence of potential predators such as pumas (Puma concolor) and jaguars (Panthera onca) in this area was confirmed by camera traps, footprints and feces. After the disappearance of four A. caraya at the reintroduction site, we investigated the applicability of genetic assignment tests based on genotypic data to accurately identify predated individuals. Genetic analyses allowed us to determine the predator species (P. onca) and to identify the predated individuals as two of the reintroduced animals. This procedure is promising for identifying the remains of predated individuals, and can contribute to the design of reintroduction policies based on scientific evidence.

Plant-herbivorous insect networks: who is eating what revealed by long barcodes using high-throughput sequencing and Trinity assembly

Interactions between plants and insects are among the most important life functions for all organism at a particular natural community. Usually a large number of samples are required to identify insect diets in food web studies. Previously, Sanger sequencing and next generation sequencing (NGS) with short DNA barcodes were used, resulting in low species-level identification; meanwhile the costs of Sanger sequencing are expensive for metabarcoding together with more samples. Here, we present a fast and effective sequencing strategy to identify larvae of Lepidoptera and their diets at the same time without increasing the cost on Illumina platform in a single HiSeq run, with long-multiplex-metabarcoding (COI for insects, rbcL, matK, ITS and trnL for plants) obtained by Trinity assembly (SHMMT). Meanwhile, Sanger sequencing (for single individuals) and NGS (for polyphagous) were used to verify the reliability of the SHMMT approach. Furthermore, we show that SHMMT approach is fast and reliable, with most high-quality sequences of five DNA barcodes of 63 larvae individuals (54 species) recovered (full length of 100% of the COI gene and 98.3% of plant DNA barcodes) using Trinity assembly (up-sized to 1015 bp). For larvae diets identification, 95% are reliable; the other 5% failed because their guts were empty. The diets identified by SHMMT approach are 100% consistent with the host plants that the larvae were feeding on during our collection. Our study demonstrates that SHMMT approach is reliable and cost-effective for insect-plants network studies. This will facilitate insect-host plant studies that generally contain a huge number of samples.

Fish as predators and prey: DNA-based assessment of their role in food webs

Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.

DNA diet profiles with high-resolution animal tracking data reveal levels of prey selection relative to habitat choice in a crepuscular insectivorous bird

Given the global decline of many invertebrate food resources, it is fundamental to understand the dietary requirements of insectivores. We give new insights into the functional relationship between the spatial habitat use, food availability, and diet of a crepuscular aerial insectivore, the European Nightjar (Caprimulgus europaeus) by relating spatial use data with high-throughput sequencing (HTS) combined with DNA metabarcoding. Our study supports the predictions that nightjars collect a substantial part of their daily nourishment from foraging locations, sometimes at considerable distance from nesting sites. Lepidopterans comprise 65% of nightjars' food source. Nightjars tend to select larger species of Lepidoptera (>19 mm) which suggests that nightjars optimize the efficiency of foraging trips by selecting the most energetically favorable-larger-prey items. We anticipate that our findings may shed additional light on the interactions between invertebrate communities and higher trophic levels, which is required to understand the repercussions of changing food resources on individual- and population-level processes.

Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)

In the UK, the native European otter (Lutra lutra) and invasive American mink (Neovison vison) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in decline due to population control and probable interspecific interaction with the otter. We explored the potential of DNA metabarcoding for investigating diet and niche partitioning between these mustelids. Otter spraints (n = 171) and mink scats (n = 19) collected from three sites (Malham Tarn, River Hull and River Glaven) in northern and eastern England were screened for vertebrates using high-throughput sequencing. Otter diet mainly comprised aquatic fishes (81.0%) and amphibians (12.7%), whereas mink diet predominantly consisted of terrestrial birds (55.9%) and mammals (39.6%). The mink used a lower proportion (20%) of available prey (n = 40 taxa) than the otter and low niche overlap (0.267) was observed between these mustelids. Prey taxon richness of mink scats was lower than otter spraints and beta diversity of prey communities was driven by taxon turnover (i.e. the otter and mink consumed different prey taxa). Considering otter diet only, prey taxon richness was higher in spraints from the River Hull catchment and beta diversity of prey communities was driven by taxon turnover (i.e. the otter consumed different prey taxa at each site). Studies using morphological faecal analysis may misidentify the predator as well as prey items. Faecal DNA metabarcoding can resolve these issues and provide more accurate and detailed dietary information. When scaled up across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink.