The effects of pastoral intensification on the feeding interactions of generalist predators in streams.

Land-use change can alter trophic interactions with wide-ranging functional consequences, yet the consequences for aquatic food webs have been little studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft-bodied prey. We used next-generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with increasingly intensive livestock farming. Rhyacophila dorsalis occurred in all streams, whereas D. cephalotes was restricted to low intensities, allowing us to test whether: (i) apparent sensitivity to agriculture in the latter species reflects a more specialized diet and (ii) diet in R. dorsalis varied between sites with and without D. cephalotes. DNA was extracted from dissected gut contents, amplified without blocking probes and sequenced using Ion Torrent technology. Both predators were generalists, consuming 30 prey taxa with a preference for taxa that were abundant in all streams or that increased with intensification. Where both predators were present, their diets were nearly identical, and R. dorsalis's diet was virtually unchanged in the absence of D. cephalotes. The loss of D. cephalotes from more intensive sites was probably due to physicochemical stressors, such as sedimentation, rather than to dietary specialization, although wider biotic factors (e.g., competition with other predatory taxa) could not be excluded. This study provides a uniquely detailed description of predator diets along a land-use intensity gradient, offering new insights into how anthropogenic stressors affect stream communities.

The diet of a nocturnal pelagic predator, the Bulwer's petrel, across the lunar cycle.

The lunar cycle is believed to strongly influence the vertical distribution of many oceanic taxa, with implications for the foraging behaviour of nocturnal marine predators. Most studies to date testing lunar effects on foraging have focused on predator activity at-sea, with some birds and marine mammals demonstrating contrasting behavioural patterns, depending on the lunar-phase. However, to date no study has focused on how the lunar cycle might actually affect predator-prey interactions in the upper layers of the ocean. Here, we tested whether the diet of the predominantly nocturnal pelagic predator, the Bulwer's petrel (Bulweria bulwerii) would change throughout the lunar cycle, using molecular analysis to augment detection and taxonomic resolution of prey collected from stomach-contents. We found no evidence of dietary shifts in species composition or diversity, with Bulwer's petrel always consuming a wide range of mesopelagic species. Other co-variables potentially affecting light availability at-sea, such as percentage of cloud cover, did not confound our results. Moreover, many of the species found are thought not to reach the sea-surface. Our findings reveal that nocturnal predators are probably more specialized than previously assumed, irrespective of ambient-light, but also reveal deficiencies in our current understanding of species vertical distribution and predation-dynamics at-sea.

Hybridization relics complicate barcode-based identification of species in earthworms.

Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.

Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.

Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.

An integrative approach to detect subtle trophic niche differentiation in the sympatric trawling bat species Myotis dasycneme and Myotis daubentonii.

Bats are well known for species richness and ecological diversity, and thus, they provide a good opportunity to study relationships and interaction between species. To assess interactions, we consider distinct traits that are probably to be triggered by niche shape and evolutionary processes. We present data on the trophic niche differentiation between two sympatric European trawling bat species, Myotis dasycneme and Myotis daubentonii, incorporating a wide spectrum of methodological approaches. We measure morphological traits involved in foraging and prey handling performance including bite force, weightlifting capacity and wing morphology. We then measure resulting prey consumption using both morphological and molecular diet analyses. These species closely resemble each other in morphological traits, however, subtle but significant differences were apparent in bite force and lift capacity, which are related to differences in basic body and head size. Both morphological and molecular diet analyses show strong niche overlap. We detected subtle differences in less frequent prey items, as well as differences in the exploitation of terrestrial and aquatic-based prey groups. Myotis dasycneme feeds more on aquatic prey, like Chironomidae and their pupal stages, or on the aquatic moth Acentria ephemerella. Myotis daubentonii feeds more on terrestrial prey, like Brachycera, or Coleoptera. This suggests that these bats use different microhabitats within the habitat where they co-occur.

A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes.

Predicting whether a predator is capable of affecting the dynamics of a prey species in the field implies the analysis of the complete diet of the predator, not simply rates of predation on a target taxon. Here, we employed the Ion Torrent next-generation sequencing technology to investigate the diet of a generalist arthropod predator. A complete dietary analysis requires the use of general primers, but these will also amplify the predator unless suppressed using a blocking probe. However, blocking probes can potentially block other species, particularly if they are phylogenetically close. Here, we aimed to demonstrate that enough prey sequence could be obtained without blocking probes. In communities with many predators, this approach obviates the need to design and test numerous blocking primers, thus making analysis of complex community food webs a viable proposition. We applied this approach to the analysis of predation by the linyphiid spider Oedothorax fuscus in an arable field. We obtained over two million raw reads. After discarding the low-quality and predator reads, the libraries still contained over 61 000 prey reads (3% of the raw reads; 6% of reads passing quality control). The libraries were rich in Collembola, Lepidoptera, Diptera and Nematoda. They also contained sequences derived from several spider species and from horticultural pests (aphids). Oedothorax fuscus is common in UK cereal fields, and the results showed that it is exploiting a wide range of prey. Next-generation sequencing using general primers but without blocking probes provided ample sequences for analysis of the prey range of this spider and proved to be a simple and inexpensive approach.

Dietary competition between the alien Asian Musk Shrew (Suncus murinus) and a re-introduced population of Telfair's Skink (Leiolopisma telfairii).

Re-introduction of rare species to parts of their historical range is becoming increasingly important as a conservation strategy. Telfair's Skinks (Leiolopisma telfairii), once widespread on Mauritius, were until recently found only on Round Island. There it is vulnerable to stochastic events, including the introduction of alien predators that may either prey upon it or compete for food resources. Consequently, skinks have been introduced to Ile aux Aigrettes, another small Mauritian island that has been cleared of rats. However, the island has been invaded by Asian Musk Shrews (Suncus murinus), a commensal species spread by man well beyond its natural Asian range. Our aim was to use next-generation sequencing to analyse the diets of the shrews and skinks to look for niche competition. DNA was extracted from skink faeces and from the stomach contents of shrews. Application of shrew- and skink-specific primers revealed no mutual predation. The DNA was then amplified using general invertebrate primers with tags to identify individual predators, and then sequenced by 454 pyrosequencing. 119 prey MOTUs (molecular taxonomic units) were isolated, although none could be identified to species. Seeding of cladograms with known sequences allowed higher taxonomic assignments in some cases. Although most MOTUs were not shared by shrews and skinks, Pianka's niche overlap test showed significant prey overlap, suggesting potentially strong competition where food resources are limited. These results suggest that removal of the shrews from the island should remain a priority.

Early-season predation on aphids by winter-active spiders in apple orchards revealed by diagnostic PCR.

Aphids are major pests in apple orchards, debilitating the crop and spreading disease. We investigated whether early-season predation by canopy spiders may be effectively controlling aphid numbers in three organic orchards. For this purpose, we monitored the aphid population dynamics from the winter eggs to colony stages and compared this to spider abundances and rates of predation on aphids detected by diagnostic polymerase chain reaction. For the latter, we applied existing general aphid primers. We found that spiders ate colony fundatrices and that aphid numbers were negatively related to spider abundance. Spiders were the main active predators within the orchards when the first colony fundatrices were present, indicating their importance in the early control of aphid populations.

Trophic relationships between predators, whiteflies and their parasitoids in tomato greenhouses: a molecular approach.

The whiteflies Bemisia tabaci Gennadius and Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) are two of the main pests in tomato crops. Their biological control in Mediterranean IPM systems is based on the predators Macrolophus pygmaeus (Rambur) and Nesidiocoris tenuis Reuter (Hemiptera: Miridae), as well as on the parasitoids Eretmocerus mundus (Mercet) and Encarsia pergandiella Howard (Hymenoptera: Aphelinidae). These natural enemies may interact with each other and their joint use could interfere with the biological control of those whitefly pests. Analysis of predator-prey interactions under field conditions is therefore essential in order to optimize whitefly control. Species-specific polymerase chain reaction (PCR)-primers were designed to detect DNA fragments of these whiteflies and parasitoids within both predator species in tomato greenhouses. We demonstrated that both predators feed on both whitefly species, as well as on both parasitoids under greenhouse conditions. Prey molecular detection was possible where prey abundance was very low or even where predation was not observed under a microscope. Whitefly DNA detection was positively correlated with adult whitefly abundance in the crop. However, a significant relationship was not observed between parasitoid DNA detection and the abundance of parasitoid pupae, even though the predation rate on parasitoids was high. This unidirectional intraguild predation (predators on parasitoids) could potentially reduce their combined impact on their joint prey/host. Prey molecular detection provided improved detection of prey consumption in greenhouse crops, as well as the possibility to identify which prey species were consumed by each predator species present in the greenhouse, offering a blueprint with wider applicability to other food webs.

Generalist predators disrupt parasitoid aphid control by direct and coincidental intraguild predation.

Generalist predators and parasitoids are considered to be important regulators of aphids. The former not only feed on these pests, but might also consume parasitoids at all stages of development. This direct or coincidental interference affects the natural control of aphids, the scale of which is largely unknown, and it has rarely been examined under natural conditions. Here, molecular diagnostics were used to track trophic interactions in an aphid-parasitoid-generalist predator community during the build-up of a cereal aphid population. We found that generalist predators, principally carabid and staphylinid beetles as well as linyphiid spiders, had strong trophic links to both parasitoids and aphids. Remarkably, more than 50% of the parasitoid DNA detected in predators stems from direct predation on adult parasitoids. The data also suggest that coincidental intraguild predation is common too. Generalist predators, hence, disrupt parasitoid aphid control, although the levels at which the predators feed on pests and parasitoids seem to vary significantly between predator taxa. Our results suggest that taxon-specific trophic interactions between natural enemies need to be considered to obtain a more complete understanding of the route to effective conservation biological control.

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.

First record of Neoxysomatium brevicaudatum through the non-invasive sampling of Anguis fragilis: complementary morphological and molecular detection.

Relatively few studies have examined the parasite fauna of British reptiles, partly due to the cryptic nature and low population density of these hosts. Here we examined 12 populations of the slow worm Anguis fragilis which, unlike other UK lizards, occurs at locally high population densities. Morphological examination of non-invasively collected faecal samples revealed the presence of Neoxysomatium brevicaudatum and a second unidentified nematode species. Although previously unrecorded from slow worms in the UK, N. brevicaudatum was present in 38% of animals (mean intensity 70.9, range 1-686). Morphological identification was confirmed by sequencing the 18S ribosomal gene. The use of the species-specific, cytochrome oxidase I mitochondrial gene primers proved an efficient alternative to conventional, microscope screening for parasites, although the original identification of N. brevicaudatum was dependent upon morphological characters. Sequencing also identified the second, smaller nematode as belonging to the Rhabdiasidae family: this species was even more common at a prevalence of 83% (mean intensity 102.8, range 1-2000). While increasing our knowledge of the UK macroparasite fauna, this work demonstrates the benefits of a combined morphological-molecular approach.

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.

Predation by beetles (Carabidae, Staphylinidae) on eggs and juveniles of the Iberian slug Arion lusitanicus in the laboratory.

Arion lusitanicus has become a major pest species in western Norway in the last few years. This species originates from southern Europe but has been spread by humans over large parts of central and northern Europe during recent decades. Slugs have traditionally been controlled by the use of molluscicides; but, as these may have serious ecological side effects, biological control of slugs is highly desirable. Potential biological control agents include nematodes, gastropods and arthropods. In laboratory experiments, we tested whether five common predator beetles would feed on eggs and juveniles of A. lusitanicus. The species Carabus nemoralis, Nebria brevicollis, Pterostichus melanarius and Pterostichus niger (Carabidae) as well as Staphylinus erythropterus (Staphylinidae) were tested, of which only P. melanarius has been tested on A. lusitanicus previously. Nebria brevicollis did not feed on slug eggs or newly hatched slugs, but the remaining four species all killed and ate a large proportion of the eggs and hatchlings offered. Both P. melanarius and P. niger also destroyed A. lusitanicus eggs and hatchlings under conditions emulating those in the field. Prey size choice experiments were conducted by feeding C. nemoralis, P. niger and S. erythropterus on different sizes of A. lusitanicus. Carabus nemoralis was also given a choice between two slug species, A. lusitanicus and Deroceras reticulatum. A significant preference for slugs smaller than one gram was evident for C. nemoralis, while the other beetles struggled much more to overcome the mucus of juvenile slugs. No significant preference was found between A. lusitanicus and D. reticulatum as prey for C. nemoralis. We also discuss the feasibility of biological control of A. lusitanicus using beetle predators.

Endoparasitism in cereal aphids: molecular analysis of a whole parasitoid community.

Insect parasitoids play a major role in terrestrial food webs as they are highly diverse, exploit a wide range of niches and are capable of affecting host population dynamics. Formidable difficulties are encountered when attempting to quantify host-parasitoid and parasitoid-parasitoid trophic links in diverse parasitoid communities. Here we present a DNA-based approach to effectively track trophic interactions within an aphid-parasitoid food web, targeting, for the first time, the whole community of parasitoids and hyperparasitods associated with a single host. Using highly specific and sensitive multiplex and singleplex polymerase chain reaction, endoparasitism in the grain aphid Sitobion avenae (F) by 11 parasitoid species was quantified. Out of 1061 aphids collected during 12 weeks in a wheat field, 18.9% were found to be parasitized. Parasitoids responded to the supply of aphids, with the proportion of aphids parasitized increasing monotonically with date, until the aphid population crashed. In addition to eight species of primary parasitoids, DNA from two hyperparasitoid species was detected within 4.1% of the screened aphids, with significant hyperparasitoid pressure on some parasitoid species. In 68.2% of the hyperparasitized aphids, identification of the primary parasitoid host was also possible, allowing us to track species-specific parasitoid-hyperparasitoid links. Nine combinations of primary parasitoids within a single host were found, but only 1.6% of all screened aphids were multiparasitized. The potential of this approach to parasitoid food web research is discussed.

Do functional traits improve prediction of predation rates for a disparate group of aphid predators?

Aphid predators are a systematically disparate group of arthropods united on the basis that they consume aphids as part of their diet. In Europe, this group includes Araneae, Opiliones, Heteroptera, chrysopids, Forficulina, syrphid larvae, carabids, staphylinids, cantharids and coccinellids. This functional group has no phylogenetic meaning but was created by ecologists as a way of understanding predation, particularly for conservation biological control. We investigated whether trait-based approaches could bring some cohesion and structure to this predator group. A taxonomic hierarchy-based null model was created from taxonomic distances in which a simple multiplicative relationship described the Linnaean hierarchies (species, genera, etc.) of fifty common aphid predators. Using the same fifty species, a functional groups model was developed using ten behavioural traits (e.g. polyphagy, dispersal, activity, etc.) to describe the way in which aphids were predated in the field. The interrelationships between species were then expressed as dissimilarities within each model and separately analysed using PROXSCAL, a multidimensional scaling (MDS) program. When ordinated using PROXSCAL and then statistically compared using Procrustes analysis, we found that only 17% of information was shared between the two configurations. Polyphagy across kingdoms (i.e. predatory behaviour across animal, plant and fungi kingdoms) and the ability to withstand starvation over days, weeks and months were particularly divisive within the functional groups model. Confirmatory MDS indicated poor prediction of aphid predation rates by the configurations derived from either model. The counterintuitive conclusion was that the inclusion of functional traits, pertinent to the way in which predators fed on aphids, did not lead to a large improvement in the prediction of predation rate when compared to the standard taxonomic approach.

Molecular analysis of predation on parasitized hosts.

Predation on parasitized hosts can significantly affect natural enemy communities, and such intraguild predation may indirectly affect control of herbivore populations. However, the methodological challenges for studying these often complex trophic interactions are formidable. Here, we evaluate a DNA-based approach to track parasitism and predation on parasitized hosts in model herbivore-parasitoid-predator systems. Using singleplex polymerase chain reaction (SP-PCR) to target mtDNA of the parasitoid only, and multiplex PCR (MP-PCR) to additionally target host DNA as an internal amplification control, we found that detection of DNA from the parasitoid, Lysiphlebus testaceipes, in its aphid host, Aphis fabae, was possible as early as 5 min. post parasitism. Up to 24 h post parasitism SP-PCR proved to be more sensitive than MP-PCR in amplifying parasitoid DNA. In the carabid beetles Demetrias atricapillus and Erigone sp. spiders, fed with aphids containing five-day-old parasitoids, parasitoid and aphid DNA were equally detectable in both predator groups. However, when hosts containing two-day-old parasitoids were fed to the predators, detection of parasitoid prey was possible only at 0 h (immediately after consumption) and up to 8 h post consumption in carabids and spiders, respectively. Over longer periods of time, post-feeding prey detection success was significantly higher in spiders than in carabid beetles. MP-PCR, in which parasitoid and aphid DNA were simultaneously amplified, proved to be less sensitive at amplifying prey DNA than SP-PCR. In conclusion, our study demonstrates that PCR-based parasitoid and prey detection offers an exciting approach to further our understanding of host-parasitoid-predator interactions.

The effects of temperature on detection of prey DNA in two species of carabid beetle.

PCR-based techniques to investigate predator-prey trophic interactions are starting to be used more widely, but factors affecting DNA decay in predator guts are still poorly understood. Here, we investigated the effects of time since feeding, temperature and amplicon size on the detectability of prey DNA in the gut content of two closely related predator species. Cereal aphids, Sitobion avenae, were fed to the carabid beetles Pterostichus melanarius and Nebria brevicollis. Beetles were allowed to digest their meal at 12 degrees C, 16 degrees C and 20 degrees C, and batches of beetles were subsequently frozen at time periods from 0-72 h after feeding. Aphid DNA was detected within beetles' gut contents using primers amplifying fragments of 85, 231, 317 and 383 bp. Prey DNA detection rates were significantly higher in N. brevicollis than in P. melanarius, indicating fundamental dissimilarities in prey digestion capacities. High temperatures (20 degrees C) and large amplicons (383 bp) significantly decreased detection rates. The shortest amplicon gave the highest prey DNA detection success, whereas no differences were observed between the 231 bp and the 317 bp fragment. Our results indicate that factors such as ambient temperature, predator taxon and amplicon size should all be considered when interpreting data derived from PCR-based prey detection. Correction for such factors should make calculation of predation rates in the field more accurate and could help us to estimate when predation events occur in the field.

Impact of abiotic factors on predator-prey interactions: DNA-based gut content analysis in a microcosm experiment.

The effects of predators on prey populations can be modified by a number of abiotic factors. Here, we investigated the combined and separate effects of rain and ground-dwelling predators on aphid populations in a microcosm experiment lasting for 21 days, using PCR to analyse the gut content of the predators. Rain significantly dislodged aphids from shoots and ears by 57% and 25%, respectively. The gut content analysis showed that more predators consumed aphids in the rain treatment than without rain, indicating higher availability of aphids to ground-dwelling predators after rain. However, no synergistic effects of rain and ground-dwelling predators on aphid population development could be demonstrated. Rain alone significantly decreased aphid populations by 27%, suggesting that this is a significant mortality factor. Predators alone had no significant effect on aphid numbers, but the gut content analyses showed aphid consumption also in the no-rain treatments, indicating that aphids were available to the predators on the soil surface even without rain. Our results suggest that weather conditions such as rain can modify predator-prey interactions in the field. Employing PCR-based predator gut content analyses proved to be useful as trophic links could be directly verified.