PCR-based gut content analysis of insect predators: using ribosomal ITS-1 fragments from prey to estimate predation frequency

Efficiency of mitochondrial genes and nuclear Alu elements in detecting human DNA in blood meals of Anopheles stephensi mosquitoes: a time-course study

BACKGROUND

The time required for PCR detection of DNA in human blood meals in vector mosquitoes may vary, depending on the molecular markers used, based on the size and copy number of the amplicons. Detailed knowledge of the blood-feeding behavior of mosquito populations in nature is an essential component for evaluating their vectorial capacity and for assessing the roles of individual vertebrates as potential hosts involved in the transmission of vector-borne diseases.

METHODS

Laboratory experiments were conducted to compare the time course of PCR detection of DNA in human blood meals from individual blood-fed Anopheles stephensi mosquitoes, using loci with different characteristics, including two mitochondrial DNA (mtDNA) genes, cytB (228 bp) and 16S ribosomal RNA (rRNA) (157 bp) and nuclear Alu-repeat elements (226 bp) at different time points after the blood meal.

RESULTS

Human DNA was detectable up to 84-120 h post-blood-feeding, depending on the length and copy number of the loci. Our results suggest that 16S rRNA and Alu-repeat markers can be successfully recovered from human DNA up to 5 days post-blood-meal. The 16S rDNA and Alu-repeat loci have a significantly (P = 0.008) slower decline rate than the cytB locus. Median detection periods (T50) for the amplicons were 117, 113 and 86.4 h for Alu-repeat, 16S rDNA and cytB, respectively, suggesting an inverse linear relationship between amplicon size/copy number and digestion time.

CONCLUSION

This comparative study shows that the Alu-repeat locus is the most efficient marker for time-course identification of human DNA from blood meals in female mosquitoes. It is also a promising tool for determining the anthropophilic index (AI) or human blood index (HBI), i.e. the proportion of blood meals from humans, which is often reported as a relative measure of anthropophagy of different mosquito vectors, and hence a measure of the vector competence of mosquito species collected in the field.

Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding

Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two rations of Chinook salmon (Oncorhynchus tshawytscha) to two piscivorous fish species (largemouth bass [Micropterus salmoides] and channel catfish [Ictalurus punctatus]) held at two different temperatures (15.5 and 18.5°C) and sacrificed at regular intervals up to 120 h from the time of ingestion to quantify the prey contents remaining in the digestive tract. We found that ration size, temperature, and predator species all influenced digestion rate, with some indication that ration size had the largest influence. DNA-based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~12 h for visual analysis vs. ~72 h for molecular analyses). Our study provides evidence that modelling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.

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.

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.

Understanding nutritive need in Harmonia axyridis larvae: Insights from nutritional geometry

The multicolored Asian lady beetle, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae), is an important natural enemy in agricultural ecosystems. In spite of being a carnivore consuming protein-rich preys, the lady beetles often consume carbohydrate-rich food like nectar or honeydew. However, most studies on nutrition regulation of carnivores mainly focus on protein and lipid, two major macronutrients in preys. In this study, nutrition regulation of protein and carbohydrate has been investigated in the 4th instar larvae of H. axyridis using Geometric Framework. We provided the insects two pairs of foods, one a protein-biased one and the second carbohydrate-biased, to determine the intake target. We then confined them to nutritionally imbalanced foods to examine how they regulated food intake to achieve maximal performance. The larvae performed well on the 2 foods that containing the closest P : C ratios to the intake target, but, surprisingly, the lipid content was much lower than that in the choice experiment. The lady beetles seemed to maintain the optimal lipid content by consuming carbohydrate-rich food. Moreover, consuming the carbohydrate-rich food was less metabolically expensive than the protein-rich food. Therefore, switching behavior between plant and animal foods actually reflects their nutritive needs. These findings extended our understanding of predator forage behavior and its influence on food web in ecosystems, and shed light on the role of agri-environment schemes in meeting the nutritional need of predators in field.

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.

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.

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.

Next-generation biological control: the need for integrating genetics and genomics

Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

Using patterns in prey DNA digestion rates to quantify predator diets

Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time- and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half-lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.

Molecular Marker to Identify Diaphorina citri (Hemiptera: Liviidae) DNA in Gut Content of Predators

Diaphorina citri Kuwayama is the vector of the pathogenic bacteria Candidatus Liberibacter spp., the causative agent of Huanglongbing (HLB), the most serious disease of citrus worldwide. Because predatory insects have been historically neglected in biological control programs for D. citri, the impact of generalist predators on D. citri population densities is little understood. A useful tool to evaluate the dynamics of predator-prey interactions is molecular analysis of predators' gut content. We constructed a specific molecular marker to detect D. citri DNA in the gut content of predator insects, for use in estimating the predation rate of field-collected predators in citrus orchards on D. citri. Bioassays of the DNA half-life detection time were carried out with two predatory species, the ladybird beetle Hippodamia convergens Guérin-Méneville and the lacewing Chrysoperla externa (Hagen). The D. citri DNA half-life detection time (DT₅₀) was 6.11 h for H. convergens and 5.46 h for C. externa. One hundred and seven field-collected predators were used for gut-content analysis (52 larvae/adults of ladybirds and 55 larvae of lacewings). The assays showed that 17.3% of ladybirds but no lacewings tested positive for D. citri DNA. These results show that generalist predators can contribute to biological control of D. citri and should be considered for use in pest management programs in citrus orchards.

Host plant use of a polyphagous mirid, Apolygus lucorum: Molecular evidence from migratory individuals

While the host plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA, and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.

Host and Non-host 'Whistle Stops' for Psyllids: Molecular Gut Content Analysis by High-Throughput Sequencing Reveals Landscape-Level Movements of Psylloidea (Hemiptera)

Psyllids (Hemiptera: Psylloidea) are phloem-feeding insects that tend to be highly specific in their host plants. Some species are well-known agricultural pests, often as vectors of plant pathogens. Many pest psyllids colonize agricultural fields from non-crop reproductive hosts or from non-host transitory and winter shelter plants. Uncertainty about which non-crop species serve as sources of psyllids hinders efforts to predict which fields or orchards are at greater risk of being colonized by psyllids. High-throughput sequencing of trnL, trnF, and ITS was used to examine the dietary histories of three pest and two non-pest psyllid species encompassing a diversity of lifecycles: Cacopsylla pyricola (Förster) (Psyllidae), Bactericera cockerelli (Šulc) (Triozidae), Diaphorina citri Kuwayama (Liviidae), Aphalara loca Caldwell (Aphalaridae), and a Cacopsylla species complex associated with Salix (Malphighiales: Salicaceae). Results revealed an unexpectedly high level of feeding on non-host species by all five psyllid species. The identification of the dietary history of the psyllids allowed us to infer their landscape-scale movements prior to capture. Our study demonstrates a novel use for gut content analysis-to provide insight into landscape-scale movements of psyllids-thus providing a means to pinpoint the non-crop sources of pest psyllids colonizing agricultural crops. We observed previously unknown psyllid behaviors during our efforts to develop this method and discuss new research directions for the study of psyllid ecology.

Contribution of predation to the biological control of a key herbivorous pest in citrus agroecosystems

Biological control has traditionally simplified the view of trophic relationships between herbivorous pests and their natural enemies in agriculture. The success or failure of this pest management strategy is still mainly attributed to the ability of a few key natural enemies to suppress the pest density. For example, successful regulation of the California red scale (Aonidiella aurantii), a key citrus pest, is generally credited to specific parasitoids of the Aphytis genus. Currently, research is revealing how herbivore regulation in agroecosystems can be alternatively achieved with a greater number of trophic associations within the system. The goals of the present study were as follows: i) to unravel species-specific trophic links between A. aurantii and its natural enemies in citrus agroecosystems, and ii) to assess their contribution to control of A. aurantii. Predation and parasitism of this herbivorous pest were assessed through exclusion experiments. Species-specific trophic links between this herbivorous pest and its natural enemies were studied using gut-content analysis of field-collected predators employing prey-specific DNA molecular markers. Relative predation rates of the species involved in A. aurantii regulation were estimated. Predation was found to be the main biotic component of A. aurantii mortality, causing reductions of more than 75% in recently settled cohorts. Aonidiella aurantii DNA was detected in the digestive system of 11 species of predators. Generalist and stenophagous predators, mainly associated with other citrus pests such as aphids, proved to be the most important biological control agents of this pest. Complex trophic relationships, such as apparent competition between two key citrus pests, were revealed. The present study highlights the role of predation as biotic mortality factor of key pests in perennial agroecosystems, wherein it is a rich complex of indigenous or naturalized generalist predators that are primarily responsible for this mortality. The results herein presented may therefore offer another perspective on the biological control of one of the key world-wide citrus pests, at least in those regions where specific parasitoids are not able to successfully regulate the scale populations.

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.

Comparing three types of dietary samples for prey DNA decay in an insect generalist predator

The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors; however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, faeces and whole consumers (including their gut contents) at different time points postfeeding. All dietary samples were analysed using multiplex PCR, targeting three different length DNA fragments (128, 332 and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers, prey DNA was detectable significantly longer for all fragment sizes than for faeces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from faeces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and faeces constitute a useful, nonlethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.

Predation by generalist arthropod predators on Apolygus lucorum (Hemiptera: Miridae): molecular gut-content analysis and field-cage assessment

BACKGROUND

The mirid bug Apolygus lucorum (Meyer-Dür) is a principal pest of cotton that also causes great damage to many other crops in China. A study was conducted to assess the mortality of A. lucorum from generalist arthropod predators using both molecular methods and a field-cage trial. The species-specific primer pair for the detection of A. lucorum tissues in predators was designed according to the sequences of the cytochrome oxidase subunit I (COI) gene.

RESULTS

A total of 2096 generalist predators that consisted of ladybeetles, lacewings and spiders were collected, and A. lucorum remains were detected using the designed primers. Only 1.6% of these predators contained A. lucorum DNA, with the highest positive proportion (6.1%) for Harmonia axyridis larvae. In the field-cage experiment, the daily predation rates of second-instar A. lucorum nymphs by H. axyridis adults and larvae were 4.7 and 5.2% respectively.

CONCLUSIONS

The overall low positive proportion of generalist predators with A. lucorum DNA detected using the molecular method, combined with the low predation rate in the field-cage experiment, indicated that the primary generalist predators likely had a limited role in the suppression of A. lucorum in the field. © 2016 Society of Chemical Industry.

Analysis of digestion of rice planthopper by Pardosa pseudoannulata based on CO-I gene

In order to systematically study the predatory behavior and digestion regularity of spiders, real-time fluorescence quantification PCR technique was used to detect the number of CO-I genes in Pardosa pseudoannulata after it preyed on rice planthoppers in different temperatures within different periods. At 28 °C, 0, 1, 2, 4, 8, 16, and 24 h after P. pseudoannulata preyed on rich planthopper, DNA was extracted from cephalothorax and abdomen of P. pseudoannulata. Routine PCR and real-time fluorescence PCR techniques were employed for CO-I gene amplification. The results show that: The prey liquid was temporarily stored in the sucking stomach of the spider head within 2 h after prey, and gradually transferred to the midgut of the abdomen with the prolongation of time. After 4 h, CO-I gene residues of rice planthopper in the cephalothorax gradually decreased. The CO-I gene of rice planthopper was basically transferred to the abdomen after 16 h. During 0–1 h, food contained in abdominal midgut and other digestive organs was very small, CO-I gene detection was not obvious. Over time, food entered into the midgut from the sucking stomach for digestion. During 2–4 h, CO-I gene amount increased, at 2–4 h, detected CO-I gene residue reached the peak; but rapidly declined after 8, 16, and 24 h, even it is still detectable. The results at different temperatures reveal that: As the temperature increased from 26 °C to 32 °C, CO-I gene residues of rich planthopper in cephalothorax and abdomen of P. pseudoannulata gradually decreased, which indicated that the digestion rate increased with the increase of temperature with some range. However, when the temperature continued to increase to 34 °C, the digestion rate decreased.

Overcoming PCR Inhibition During DNA-Based Gut Content Analysis of Ants

Generalist predators play an important role in many terrestrial systems, especially within agricultural settings, and ants (Hymenoptera: Formicidae) often constitute important linkages of these food webs, as they are abundant and influential in these ecosystems. Molecular gut content analysis provides a means of delineating food web linkages of ants based on the presence of prey DNA within their guts. Although this method can provide insight, its use on ants has been limited, potentially due to inhibition when amplifying gut content DNA. We designed a series of experiments to determine those ant organs responsible for inhibition and identified variation in inhibition among three species (Tetramorium caespitum (L.), Solenopsis invicta Buren, and Camponotus floridanus (Buckley)). No body segment, other than the gaster, caused significant inhibition. Following dissection, we determined that within the gaster, the digestive tract and crop cause significant levels of inhibition. We found significant differences in the frequency of inhibition between the three species tested, with inhibition most evident in T. caespitum The most effective method to prevent inhibition before DNA extraction was to exude crop contents and crop structures onto UV-sterilized tissue. However, if extracted samples exhibit inhibition, addition of bovine serum albumin to PCR reagents will overcome this problem. These methods will circumvent gut content inhibition within selected species of ants, thereby allowing more detailed and reliable studies of ant food webs. As little is known about the prevalence of this inhibition in other species, it is recommended that the protocols in this study are used until otherwise shown to be unnecessary.

Detection of seed DNA in regurgitates of granivorous carabid beetles

Granivory can play a pivotal role in influencing regeneration, colonization as well as abundance and distribution of plants. Due to their high abundance, nutrient content and longevity, seeds are an important food source for many animals. Among insects, carabid beetles consume substantial numbers of seeds and are thought to be responsible for a significant amount of seed loss. However, the processes that govern which seeds are eaten and are therefore prevented from entering the seedbank are poorly understood. Here, we assess if DNA-based diet analysis allows tracking the consumption of seeds by carabids. Adult individuals of Harpalus rufipes were fed with seeds of Taraxacum officinale and Lolium perenne allowing them to digest for up to 3 days. Regurgitates were tested for the DNA of ingested seeds at eight different time points post-feeding using general and species-specific plant primers. The detection of seed DNA decreased with digestion time for both seed species, albeit in a species-specific manner. Significant differences in overall DNA detection rates were found with the general plant primers but not with the species-specific primers. This can have implications for the interpretation of trophic data derived from next-generation sequencing, which is based on the application of general primers. Our findings demonstrate that seed predation by carabids can be tracked, molecularly, on a species-specific level, providing a new way to unravel the mechanisms underlying in-field diet choice in granivores.

Specific detection of the floodwater mosquitoes Aedes sticticus and Aedes vexans DNA in predatory diving beetles

Floodwater mosquitoes (Diptera: Culicidae) are associated with periodically flooded wet meadows, marshes, and swamps in floodplains of major rivers worldwide, and their larvae are abundant in the shallow parts of flooded areas. The nuisance caused by the blood-seeking adult female mosquitoes motivates mosquito control. Larviciding with Bacillus thuringiensis israelensis is considered the most environmentally safe method. However, some concern has been raised whether aquatic predatory insects could be indirectly affected by this reduction in a potential vital prey. Top predators in the temporary wetlands in the River Dalälven floodplains are diving beetles (Coleoptera: Dytiscidae), and Aedes sticticus and Ae. vexans are the target species for mosquito control. For detailed studies on this aquatic predator-prey system, we developed a polymerase chain reaction (PCR) assay for detection of mosquito DNA in the guts of medium-sized diving beetles. Primers were designed for amplifying short mitochondrial DNA fragments of the cytochrome C oxidase subunit I (COI) gene in Ae. sticticus and Ae. vexans, respectively. Primer specificity was confirmed and half-life detectability of Ae. sticticus DNA in diving beetle guts was derived from a feeding and digestion experiment. The Ae. sticticus DNA within diving beetle guts was detected up to 12 h postfeeding, and half-life detectability was estimated to 5.6 h. In addition, field caught diving beetles were screened for Ae. sticticus and Ae. vexans DNA and in 14% of the diving beetles one or both mosquito species were detected, showing that these mosquito species are utilized as food by the diving beetles.

Knowing your enemies: Integrating molecular and ecological methods to assess the impact of arthropod predators on crop pests

The importance of natural enemies as the foundation of integrated pest management (IPM) is widely accepted, but few studies conduct the manipulative field experiments necessary to directly quantify their impact on pest populations in this context. This is particularly true for predators. Studying arthropod predator-prey interactions is inherently difficult: prey items are often completely consumed, individual predator-prey interactions are ephemeral (rendering their detection difficult) and the typically fluid or soft-bodied meals cannot be easily identified visually within predator guts. Serological techniques have long been used in arthropod predator gut-contents analysis, and current enzyme linked immunosorbent assays (ELISA) are highly specific and sensitive. Recently, polymerase chain reaction (PCR) methods for gut-contents analysis have developed rapidly and they now dominate the diagnostic methods used for gut-contents analysis in field-based research. This work has identified trophic linkages within food webs, determined predator diet breadth and preference, demonstrated the importance of cannibalism and intraguild predation within and between certain taxa, and confirmed the benefits (predator persistence) and potential disadvantages (reduced feeding on pest species) of the availability of alternative nonpest prey. Despite considerable efforts to calibrate gut-contents assays, these methods remain qualitative. Available techniques for predator gut-contents analysis can provide rapid, accurate, cost-effective identification of predation events. As such, they perfectly compliment the ecological methods developed to directly assess predator impacts on prey populations but which are imperfect at identifying the key predators. These diagnostic methods for gut-contents analysis are underexploited in agricultural research and they are almost never applied in unison with the critical field experiments to measure predator impact. This paper stresses the need for a combined approach and suggests a framework that would make this possible, so that appropriate natural enemies can be targeted in conservation biological control.

Molecular screening and predation evaluation of the key predators of Conopomorpha sinensis Bradley (Lepidoptera: Gracilariidae) in litchi orchards

Conopomorpha sinensis Bradley (Lepidoptera: Gracilariidae) is one of the major fruit borer pests of litchi and longan in Southern China. Although chemical control is effective, alternative, biorational strategies are preferable, and should be developed. Predators play an important role in the biological control of agricultural pests, but an accurate method for the evaluation of predation in agriculture has not yet been developed. Here, we report a new, specific primer pair to amplify a C. sinensis cytochrome c oxidase subunit I (COI) sequence fragment that can be used to detect consumption of C. sinensis by its predators. C. sinensis DNA was found in several arthropods collected in the field, including the important C. sinensis predators M enochilus sexmaculata (Coccinellidae), Leucauge magnifica (Tetragnathidae), Propylea japonica (Coccinellidae), and Oxyopes sertatus (Oxyopidae). The detection rates of C. sinensis COI DNA in these predators were 39.3, 36.4, 27.3, and 27.2%, respectively. Laboratory consumption and hunting capacity analysis of M. sexmaculata and P. japonica adults indicated that they exhibit a Holling type II functional response on C. sinensis eggs under field temperatures. A polymerase chain reaction digestion analysis of M. sexmaculata and P. japonica adults after consumption of a single C. sinensis egg indicated that positive detection decreased with the extension of digestion time, and estimated prey DNA half-lives were 16.3 h in M. sexmaculata and 6.0 h in P. japonica. These data serve to characterize two major predators of C. sinensis with potential for biological control of C. sinensis in litchi orchards.

Mesozooplankton grazing on picocyanobacteria in the Baltic Sea as inferred from molecular diet analysis

Our current knowledge on the microbial component of zooplankton diet is limited, and it is generally assumed that bacteria-sized prey is not directly consumed by most mesozooplankton grazers in the marine food webs. We questioned this assumption and conducted field and laboratory studies to examine picocyanobacteria contribution to the diets of Baltic Sea zooplankton, including copepods. First, qPCR targeting ITS-1 rDNA sequence of the picocyanobacteria Synechococcus spp. was used to examine picocyanobacterial DNA occurrence in the guts of Baltic zooplankton (copepods, cladocerans and rotifers). All field-collected zooplankton were found to consume picocyanobacteria in substantial quantities. In terms of Synechococcus quantity, the individual gut content was highest in cladocerans, whereas biomass-specific gut content was highest in rotifers and copepod nauplii. Moreover, the gut content in copepods was positively related to the picocyanobacteria abundance and negatively to the total phytoplankton abundance in the water column at the time of sampling. This indicates that increased availability of picocyanobacteria resulted in the increased intake of this prey and that copepods may rely more on picoplankton when food in the preferred size range declines. Second, a feeding experiments with a laboratory reared copepod Acartia tonsa fed a mixture of the picocyanobacterium Synechococcus bacillaris and microalga Rhodomonas salina confirmed that copepods ingested Synechococcus, even when the alternative food was plentiful. Finally, palatability of the picocyanobacteria for A. tonsa was demonstrated using uptake of ¹³C by the copepods as a proxy for carbon uptake in feeding experiment with ¹³C-labeled S. bacillaris. These findings suggest that, if abundant, picoplankton may become an important component of mesozooplankton diet, which needs to be accounted for in food web models and productivity assessments.

Parsing handling time into its components: implications for responses to a temperature gradient

The functional response is a key element of predator-prey interactions, and variations in its parameters influence interaction strength and population dynamics. Recent studies have used the equation of the metabolic theory of ecology (MTE) to quantify the effect of temperature on the parameter Th, called "handling time," and then predict the responses of predators and communities to climate change. However, our understanding of the processes behind Th and how they vary with temperature remains limited. Using a ladybeetle-aphid system, we compared estimates of Th to direct observations of handling time across a temperature gradient. We found estimated Th values to be greater than observed Th values, suggesting that predation rate is not limited by the time available for handling prey. We next estimated the corrected digestion time, i.e., digestion time corrected for gut capacity, by subtracting observed to estimated Th values. We finally plotted the relationships between temperature and handling or digestion rates. As predicted by MTE, the corrected digestion rate increased exponentially with warming whereas, in contrast to MTE prediction, the relationship between handling rate and temperature was hump shaped. The parameter Th is thus confusing because it combines handling and digestive processes that have different thermal responses. This may explain why general patterns in the relationship between Th and temperature have been difficult to identify in previous studies.

Resolving multiple host use of an emergent pest of cotton with microsatellite data and chloroplast markers (Creontiades dilutus Stål; Hemiptera, Miridae)

Following the global uptake of transgenic cotton several Hemipteran pests have emerged as primary targets for pesticide control. Previous research on one such emergent pest: the green mirid, Creontiades dilutus, indicated differential use of two crop hosts, cotton (Gossypium hirsutum, Malvaceae) and lucerne (alfalfa) (Medicago sativa, Fabaceae). We tested the hypothesis that this apparent demographic independence of lucerne and cotton inhabiting mirids is the result of cryptic species being associated with these two crops. We assessed gene flow using microsatellite markers across adjacent cotton and lucerne crops at three geographically separated sites (up to 900 km apart). We also analysed the recent feeding behaviour of these insects by amplifying chloroplast markers from their gut contents. We find high gene flow between these two crops (mean pair wise F ST between host plants=0.0141 within localities), and no evidence of cryptic species. Furthermore, the gut analyses revealed evidence of substantial recent movement between these two crops. We discuss the implications of these results for interpreting multiple host use in this species and setting future research priorities for this economically important pest.

Impact of host plant resistance on the tritrophic interactions between wheat genotypes, Schizaphis graminum (Homoptera: Aphididae), and Coccinella septempunctata (Coleoptera: Coccinellidae) using molecular methods

The objective of the current study was to evaluate the impact of wheat resistance on digestibility of Schizaphis graminum (Rondani) in the Coccinella septempunctata L. gut. Four wheat genotypes including an ancient wheat species (Einkorn) and three Iranian wheat genotypes (Azadi, Ommid, and Moghan2) were used. Einkorn was found to be a highly resistant species, while Azadi, Ommid, and Moghan2 were characterized as resistant, semiresistant, and susceptible genotypes, respectively, based on some biological parameters of S. graminum on these plants. Adult C. septempunctata starved for 24 h were fed one S. graminum reared on the selected wheat genotypes. A semiquantitative polymerase chain reaction technique using specific primers for the gene cytochrome oxidase II (COII) of S. graminum showed a significant effect of plant resistance on S. graminum DNA disappearance time. The DNA half-lives of S. graminum fed on Einkorn, Azadi, Ommid, and Moghan2 in C. septempunctata gut was 3.3, 3.6, 4.8, and 6.7 h, respectively. The findings suggest that digestibility of S. graminum fed on resistant plant genotypes is higher than those fed on susceptible plants because of the lighter weights and smaller sizes of the first. This phenomenon could result in faster ingestion of S. graminum by C. septempunctata on these resistant plants. It is also possible that some metabolites found differentially in Einkorn and Azadi genotypes may have affected S. graminum quality as a food for C. septempunctata.

Analyzing spatial patterns linked to the ecology of herbivores and their natural enemies in the soil

Modern agricultural systems can benefit from the application of concepts and models from applied ecology. When understood, multitrophic interactions among plants, pests, diseases and their natural enemies can be exploited to increase crop production and reduce undesirable environmental impacts. Although the understanding of subterranean ecology is rudimentary compared to the perspective aboveground, technologies today vastly reduce traditional obstacles to studying cryptic communities. Here we emphasize advantages to integrating as much as possible the use of these methods in order to leverage the information gained from studying communities of soil organisms. PCR-based approaches to identify and quantify species (real time qPCR and next generation sequencing) greatly expand the ability to investigate food web interactions because there is less need for wide taxonomic expertise within research programs. Improved methods to capture and measure volatiles in the soil atmosphere in situ make it possible to detect and study chemical cues that are critical to communication across trophic levels. The application of SADIE to directly assess rather than infer spatial patterns in belowground agroecosystems has improved the ability to characterize relationships between organisms in space and time. We review selected methodology and use of these tools and describe some of the ways they were integrated to study soil food webs in Florida citrus orchards with the goal of developing new biocontrol approaches.

Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms

Predation is often difficult to observe or quantify for species that are rare, very small, aquatic or nocturnal. The assessment of such species' diet can be conducted using molecular methods that target prey DNA remaining in predators' guts and faeces. These techniques do not require high taxonomic expertise, are applicable to soft-bodied prey and allow for identification at the species level. However, for generalist predators, the presence of mixed prey DNA in guts and faeces can be a major impediment as it requires development of specific primers for each potential prey species for standard (Sanger) sequencing. Therefore, next generation sequencing methods have recently been applied to such situations. In this study, we used 454-pyrosequencing to analyse the diet of Powelliphantaaugusta, a carnivorous landsnail endemic to New Zealand and critically endangered after most of its natural habitat has been lost to opencast mining. This species was suspected to feed mainly on earthworms. Although earthworm tissue was not detectable in snail faeces, earthworm DNA was still present in sufficient quantity to conduct molecular analyses. Based on faecal samples collected from 46 landsnails, our analysis provided a complete map of the earthworm-based diet of P. augusta. Predated species appear to be earthworms that live in the leaf litter or earthworms that come to the soil surface at night to feed on the leaf litter. This indicates that P. augusta may not be selective and probably predates any earthworm encountered in the leaf litter. These findings are crucial for selecting future translocation areas for this highly endangered species. The molecular diet analysis protocol used here is particularly appropriate to study the diet of generalist predators that feed on liquid or soft-bodied prey. Because it is non-harmful and non-disturbing for the studied animals, it is also applicable to any species of conservation interest.

Effectiveness of annealing blocking primers versus restriction enzymes for characterization of generalist diets: unexpected prey revealed in the gut contents of two coral reef fish species

Characterization of predator-prey interactions is challenging as researchers have to rely on indirect methods that can be costly, biased and too imprecise to elucidate the complexity of food webs. DNA amplification and sequencing techniques of gut and fecal contents are promising approaches, but their success largely depends on the ability to amplify the taxonomic array of prey consumed and then match prey amplicons with reference sequences. When little a priori information on diet is available or a generalist predator is targeted, versatile primer sets (also referred to as universal or general primers) as opposed to group- or species-specific primer sets are the most powerful to unveil the full range of prey consumed. However, versatile primers are likely to preferentially amplify the predominant, less degraded predator DNA if no manipulation is performed to exclude this confounding DNA template. In this study we compare two approaches that eliminate the confounding predator template: restriction digestion and the use of annealing blocking primers. First, we use a preliminary DNA barcode library provided by the Moorea BIOCODE project to 1) evaluate the cutting frequency of commercially available restriction enzymes and 2) design predator specific annealing blocking primers. We then compare the performance of the two predator removal strategies for the detection of prey templates using two versatile primer sets from the gut contents of two generalist coral reef fish species sampled in Moorea. Our study demonstrates that blocking primers should be preferentially used over restriction digestion for predator DNA removal as they recover greater prey diversity. We also emphasize that a combination of versatile primers may be required to best represent the breadth of a generalist's diet.

Molecular evidence of facultative intraguild predation by Monochamus titillator larvae (Coleoptera: Cerambycidae) on members of the southern pine beetle guild

The southern pine bark beetle guild (SPBG) is arguably the most destructive group of forest insects in the southeastern USA. This guild contains five species of bark beetles (Coleoptera: Curculionidae: Scolytinae): Dendroctonus frontalis, Dendroctonus terebrans, Ips avulsus, Ips calligraphus, and Ips grandicollis. A diverse community of illicit receivers is attracted to pheromones emitted by the SPBG, including the woodborers Monochamus carolinensis and Monochamus titillator (Coleoptera: Cerambycidae). These woodborers have been traditionally classified as resource competitors; however, laboratory assays suggest that larval M. carolinensis may be facultative intraguild predators of SPBG larvae. This study used polymerase chain reaction (PCR)-based molecular gut content analyses to characterize subcortical interactions between M. titillator and members of the SPBG. The half-lives of SPBG DNA were estimated in the laboratory prior to examining these interactions in the field. A total of 271 field-collected M. titillator larvae were analyzed and 26 (9.6 %) tested positive for DNA of members of the SPBG. Of these larvae, 25 (96.2 %) tested positive for I. grandicollis and one (3.8 %) for I. calligraphus. Failure to detect D. terebrans and D. frontalis was likely due to their absence in the field. I. avulsus was present, but primers developed using adult tissues failed to amplify larval tissue. Results from this study support the hypothesis that larval Monochamus spp. are facultative intraguild predators of bark beetle larvae. Additionally, this study demonstrates the capabilities of PCR in elucidating the interactions of cryptic forest insects and provides a tool to better understand mechanisms driving southern pine beetle guild population fluctuations.

Detecting aphid predation by earwigs in organic citrus orchards using molecular markers

Aphids (Hemiptera: Aphidoidea) can damage citrus trees via direct damage to leaves and flowers or via the indirect transmission of viruses. Predators such as the European earwig, Forficula auricularia Linnaeus (Dermaptera: Forficulidae), may assist in keeping aphid populations under control in citrus orchards. Group-specific primers were developed to detect aphid DNA in earwigs, in order to determine earwig predation rates in aphids in Mediterranean organic citrus trees. These primers were designed in accordance with the alignment of comparable sequences of aphids and earwigs, and they amplified a 224 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) region. Following the consumption of three to five Aphis spiraecola Patch, aphid DNA was still detectable in 50% of earwigs one day after the ingestion. When predation was evaluated in the field, aphid DNA was detected in earwigs in May, June and July but not in April and August. The most interesting result is that of May, when aphid abundance was very low but 30% of the earwigs tested positive for aphid DNA. This finding suggests that earwigs are important aphid predators in citrus orchards, as they probably alter aphid dynamics as a result of early seasonal pressure on this pest.

Molecular interrogation of the feeding behaviour of field captured individual insects for interpretation of multiple host plant use

The way in which herbivorous insect individuals use multiple host species is difficult to quantify under field conditions, but critical to understanding the evolutionary processes underpinning insect–host plant relationships. In this study we developed a novel approach to understanding the host plant interactions of the green mirid, Creontiades dilutus, a highly motile heteropteran bug that has been associated with many plant species. We combine quantified sampling of the insect across its various host plant species within particular sites and a molecular comparison between the insects' gut contents and available host plants. This approach allows inferences to be made as to the plants fed upon by individual insects in the field. Quantified sampling shows that this “generalist” species is consistently more abundant on two species in the genus Cullen (Fabaceae), its primary host species, than on any other of its numerous listed hosts. The chloroplast intergenic sequences reveal that C. dilutus frequently feeds on plants additional to the one from which it was collected, even when individuals were sampled from the primary host species. These data may be reconciled by viewing multiple host use in this species as an adaptation to survive spatiotemporally ephemeral habitats. The methodological framework developed here provides a basis from which new insights into the feeding behaviour and host plant relationships of herbivorous insects can be derived, which will benefit not only ecological interpretation but also our understanding of the evolution of these relationships.

Effectiveness of TaqMan probes for detection of fish eggs and larvae in the stomach contents of a teleost predator

Experiments were conducted on the ability of TaqMan molecular probes to detect plaice Pleuronectes platessa DNA from eggs, and cod Gadus morhua DNA from eggs and larvae following ingestion by a teleost predator, whiting Merlangius merlangus. Estimated half-life detection rate (T50) for eggs was 31 h, and 26 h for larvae, with some positive detections occurring even after visual inspection indicated complete gut clearance. Because TaqMan probes are taxon specific, the results presented demonstrate that this technique can provide a means of rapid and unambiguous detection of predation by teleosts on fish eggs and larvae.

Suction sampling as a significant source of error in molecular analysis of predator diets

The molecular detection of predation is a fast growing field, allowing highly specific and sensitive detection of prey DNA within the gut contents or faeces of a predator. Like all molecular methods, this technique is prone to potential sources of error that can result in both false positive and false negative results. Here, we test the hypothesis that the use of suction samplers to collect predators from the field for later molecular analysis of predation will lead to high numbers of false positive results. We show that, contrary to previous published work, the use of suction samplers resulted in previously starved predators testing positive for aphid and collembolan DNA, either as a results of ectopic contamination or active predation in the collecting cup/bag. The contradictory evidence for false positive results, across different sampling protocols, sampling devices and different predator-prey systems, highlights the need for experimentation prior to mass field collections of predators to find techniques that minimise the risk of false positives.

Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA

DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.

Using group-specific PCR to detect predation of mayflies (Ephemeroptera) by wolf spiders (Lycosidae) at a mercury-contaminated site

Bioaccumulation of contaminants can occur across ecosystem boundaries via transport by emergent aquatic insects. In the South River, Virginia, USA, aquatic mercury has contaminated songbirds nesting in adjacent riparian forests. Spiders contribute the majority of mercury to these songbirds' diets. We tested the hypothesis that massive annual mayfly emergences provide a vector for mercury from river sediments to the Lycosid spiders most frequently eaten by contaminated songbirds. We designed mayfly-specific PCR primers that amplified mtDNA from 76% of adult mayflies collected at this site. By combining this approach with an Agilent 2100 electrophoresis system, we created a highly sensitive test for mayfly predation by Lycosids, commonly known as wolf spiders. In laboratory spider feeding trials, mayfly DNA could be detected up to 192h post-ingestion; however, we detected no mayfly predation in a sample of 110 wolf spiders collected at the site during mayfly emergence. We suggest that mayfly predation is not an important mechanism for dietary transfer of mercury to wolf spiders and their avian predators at the South River. Instead, floodplain soil should be considered as a potential proximate source for mercury in the terrestrial food web.

Who is eating what: diet assessment using next generation sequencing

The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.

Molecular analysis of predation by carabid beetles (Carabidae) on the invasive Iberian slug Arion lusitanicus

The invasive Iberian slug, Arion lusitanicus, is spreading through Europe and poses a major threat to horticulture and agriculture. Natural enemies, capable of killing A. lusitanicus, may be important to our understanding of its population dynamics in recently invaded regions. We used polymerase chain reaction (PCR) to study predation on A. lusitanicus by carabid beetles in the field. A first multiplex PCR was developed, incorporating species-specific primers, and optimised in order to amplify parts of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of large Arion slugs, including A. lusitanicus from the gut contents of the predators. A second multiplex PCR, targeting 12S rRNA mtDNA, detected predation on smaller Arion species and the field slug Deroceras reticulatum. Feeding trials were conducted to measure the effects of digestion time on amplicon detectability. The median detection times (the time at which 50% of samples tested positive) for A. lusitanicus and D. reticulatum DNA in the foreguts of Carabus nemoralis were 22 h and 20 h, respectively. Beetle activity-densities were monitored using pitfall traps, and slug densities were estimated using quadrats. Predation rates on slugs in the field by C. nemoralis in spring ranged from 16-39% (beetles positive for slug DNA) and were density dependent, with numbers of beetles testing positive being positively correlated with densities of the respective slug species. Carabus nemoralis was shown to be a potentially important predator of the alien A. lusitanicus in spring and may contribute to conservation biological control.

The ubiquity of intraguild predation among predatory arthropods

Intraguild predation (IGP) occurs when one predator species attacks another predator species with which it competes for a shared prey species. Despite the apparent omnipresence of intraguild interactions in natural and managed ecosystems, very few studies have quantified rates of IGP in various taxa under field conditions. We used molecular analyses of gut contents to assess the nature and incidence of IGP among four species of coccinellid predators in soybean fields. Over half of the 368 predator individuals collected in soybean contained the DNA of other coccinellid species indicating that IGP was very common at our field site. Furthermore, 13.2% of the sampled individuals contained two and even three other coccinellid species in their gut. The interaction was reciprocal, as each of the four coccinellid species has the capacity to feed on the others. To our knowledge, this study represents the most convincing field evidence of a high prevalence of IGP among predatory arthropods. The finding has important implications for conservation biology and biological control.