Complementary molecular information changes our perception of food web structure

A highly resolved network reveals the role of terrestrial herbivory in structuring aboveground food webs

Comparative studies suggest remarkable similarities among food webs across habitats, including systematic changes in their structure with diversity and complexity (scale-dependence). However, historic aboveground terrestrial food webs (ATFWs) have coarsely grouped plants and insects such that these webs are generally small, and herbivory is disproportionately under-represented compared to vertebrate predator-prey interactions. Furthermore, terrestrial herbivory is thought to be structured by unique processes compared to size-structured feeding in other systems. Here, we present the richest ATFW to date, including approximately 580 000 feeding links among approximately 3800 taxonomic species, sourced from approximately 27 000 expert-vetted interaction records annotated as feeding upon one of six different resource types: leaves, flowers, seeds, wood, prey and carrion. By comparison to historical ATFWs and null ecological hypotheses, we show that our temperate forest web displays a potentially unique structure characterized by two properties: (i) a large fraction of carnivory interactions dominated by a small number of hyper-generalist, opportunistic bird and bat predators; and (ii) a smaller fraction of herbivory interactions dominated by a hyper-rich community of insects with variably sized but highly specific diets. We attribute our findings to the large-scale, even resolution of vertebrate, insect and plant guilds in our food web.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

New data on trophic associations of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) and lemurs (Primates, Lemuroidea) in Madagascar revealed by metabarcoding

Resource use and diet specialisation of Madagascan dung beetles have been little studied especially concerning the possible associations between specific dung beetle and lemur species. Pilot studies have demonstrated that amplicon sequencing is a promising tool for the lemur inventories. In the present contribution, we report the results of the gut content analysis of three endemic Madagascan dung beetles species: Helictopleurusclouei (Harold), Epilissusapotolamproides (Lebis) and Nanosdubitatus (Lebis). Amplicon metagenomics revealed trophic associations of these species with Eulemursanfordi (Archbold), Eu.fulvus (É.Geoffroy Saint-Hilaire) and Cheirogaleuscrossleyi (Grandidier), respectively. The reads of other mammal species, revealed by the analysis, including putative contaminations, are discussed.

Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar

Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurusfissicollis (Fairmaire), H.giganteus (Harold), Nanosagaboides (Boucomont), and Epilissussplendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔-¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bostaurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.

Cereal Aphid Parasitoids in Europe (Hymenoptera: Braconidae: Aphidiinae): Taxonomy, Biodiversity, and Ecology

Cereals are very common and widespread crops in Europe. Aphids are a diverse group of herbivorous pests on cereals and one of the most important limiting factors of cereal production. Here, we present an overview of knowledge about the taxonomy, biodiversity, and ecology of cereal aphid parasitoids in Europe, an important group of natural enemies contributing to cereal aphid control. We review the knowledge obtained from the integrative taxonomy of 26 cereal aphid primary parasitoid species, including two allochthonous species (Lysiphlebus testaceipes and Trioxys sunnysidensis) and two recently described species (Lipolexis labialis and Paralipsis brachycaudi). We further review 28 hyperparasitoid species belonging to three hymenopteran superfamilies and four families (Ceraphronoidea: Megaspillidae; Chalcidoidea: Pteromalidae, Encyrtidae; Cynipoidea: Figitidae). We also compile knowledge on the presence of secondary endosymbionts in cereal aphids, as these are expected to influence the community composition and biocontrol efficiency of cereal aphid parasitoids. To study aphid-parasitoid-hyperparasitoid food webs more effectively, we present two kinds of DNA-based approach: (i) diagnostic PCR (mainly multiplex PCR), and (ii) DNA sequence-based methods. Finally, we also review the effects of landscape complexity on the different trophic levels in the food webs of cereal aphids and their associated parasitoids, as well as the impacts of agricultural practices and environmental variation.

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.

Early Detection and Identification of Parasitoid Wasps Trichogramma Westwood (Hymenoptera: Trichogrammatidae) in Their Host Eggs Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism

Parasitoid wasps are invaluable agents in pest biological control. Early detection and identification of parasitoid immatures are vital in characterizing parasitoid-host interactions and for evaluating parasitism rates accurately in the field. Trichogramma is the most widely used parasitoid wasp, and several studies have been performed for its molecular identification. However, those studies were mainly focused on Trichogramma adults and rarely on immatures. Here, we report a method to detect and identify Trichogramma larvae in their host eggs. We designed a pair of Trichogramma-specific primers that amplified Trichogramma mtCOI sequences from Corcyra cephalonica (Stainton) eggs parasitized by any of eight Trichogramma species tested but not from nonparasitized eggs of four lepidopteran hosts. This PCR method reliably detected Trichogramma immatures in parasitized eggs as early as 1 h after parasitism. We further developed an RFLP (restriction fragment length polymorphism) assay using restriction enzymes SspI and VspI to differentiate eight Trichogramma species at their immature stage. Overall, we developed a sensitive and reliable PCR-RFLP method to detect and identify immature-stage Trichogramma in their lepidopteran hosts. This method shows promise for conveniently identifying Trichogramma in insectaries and accurately evaluating parasitism rates in the field.

Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.

Distribution Pattern of Woody Plants in a Mountain Forest Ecosystem Influenced by Topography and Monsoons

Many areas are affected by the monsoon because of different sea and land positions. At the same time, the blocking effect of a mountain range forms different habitats on both sides of the mountain range. However, the distribution mechanism of woody plants is unclear in mountain forest ecosystems influenced by topography and monsoons. In this study, 10 plots, each with an area of 1 hm2 (100 m × 100 m), were randomly established on the south and north aspects of a mountain forest. We examined community structure differences and distribution preferences of woody plants on both sides of the mountain. Our findings were as follows: (1) The characteristics of woody plant assemblages differed among various aspects. (2) Network analysis showed that specialization index was 0.186 and modularity index was 0.235, and the torus translation test showed that a total of 45 species were detected to be associated with at least one of the habitats (45/106, 42.45%). (3) The community stability of the south aspect was higher than that of the north aspect. Our findings suggest that the distribution of woody plants among different aspects was specialized and not random in alpine forest ecosystems. This study contributes to a clear understanding of the distribution mechanism of woody plants in mountain forest ecosystems influenced by topography and monsoons.

Evolutionary Ecology of Plant-Arthropod Interactions in Light of the "Omics" Sciences: A Broad Guide

Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities' genetic background and evolution, such knowledge can also help address many current global environmental challenges.

The structure of tropical bat-plant interaction networks during an extreme El Niño-Southern Oscillation event

Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal–plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat–plant network structure during an extreme El Niño‐Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole‐year bat–plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non‐El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability.

Dietary abundance distributions: Dominance and diversity in vertebrate diets

Diet composition is among the most important yet least understood dimensions of animal ecology. Inspired by the study of species abundance distributions (SADs), we tested for generalities in the structure of vertebrate diets by characterising them as dietary abundance distributions (DADs). We compiled data on 1167 population-level diets, representing >500 species from six vertebrate classes, spanning all continents and oceans. DADs near-universally (92.5%) followed a hollow-curve shape, with scant support for other plausible rank-abundance-distribution shapes. This strong generality is inherently related to, yet incompletely explained by, the SADs of available food taxa. By quantifying dietary generalisation as the half-saturation point of the cumulative distribution of dietary abundance (sp50, minimum number of foods required to account for 50% of diet), we found that vertebrate populations are surprisingly specialised: in most populations, fewer than three foods accounted for at least half the diet. Variation in sp50 was strongly associated with consumer type, with carnivores being more specialised than herbivores or omnivores. Other methodological (sampling method and effort, taxonomic resolution), biological (body mass, frugivory) and biogeographic (latitude) factors influenced sp50 to varying degrees. Future challenges include identifying the mechanisms underpinning the hollow-curve DAD, its generality beyond vertebrates, and the biological determinants of dietary generalisation.

Effects of consumer surface sterilization on diet DNA metabarcoding data of terrestrial invertebrates in natural environments and feeding trials

DNA metabarcoding is an emerging tool used to quantify diet in environments and consumer groups where traditional approaches are unviable, including small-bodied invertebrate taxa. However, metabarcoding of small taxa often requires DNA extraction from full body parts (without dissection), and it is unclear whether surface contamination from body parts alters presumed diet presence or diversity.We examined four different measures of diet (presence, rarefied read abundance, richness, and species composition) for a terrestrial invertebrate consumer (the spider Heteropoda venatoria) both collected in its natural environment and fed an offered diet item in contained feeding trials using DNA metabarcoding of full body parts (opisthosomas). We compared diet from consumer individuals surface sterilized to remove contaminants in 10% commercial bleach solution followed by deionized water with a set of unsterilized individuals.We found that surface sterilization did not significantly alter any measure of diet for consumers in either a natural environment or feeding trials. The best-fitting model predicting diet detection in feeding trial consumers included surface sterilization, but this term was not statistically significant (β = -2.3, p-value = .07).Our results suggest that surface contamination does not seem to be a significant concern in this DNA diet metabarcoding study for consumers in either a natural terrestrial environment or feeding trials. As the field of diet DNA metabarcoding continues to progress into new environmental contexts with various molecular approaches, we suggest ongoing context-specific consideration of the possibility of surface contamination.

A dearth of data: fitting parasitoids into ecological networks

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

Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data

DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising -the separation of biological signal from instrument (technical) noise-of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.

Assessing the impact of taxon resolution on network structure

Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research vary widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to molecular operational taxonomic units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large data sets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 data sets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied.

Resolving Food-Web Structure

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

Molecular ecology as a tool for understanding pollination and other plant-insect interactions

Advances in molecular ecology offer unprecedented opportunities to understand the ecology and evolution of insects, the complex ways in which they interact and their role in ecosystem functioning. Rapidly developing DNA sequencing technologies are resolving previously intractable questions in taxonomic and functional biodiversity and provide significant potential to determine formerly difficult to observe plant-insect interactions. We provide an overview of the state-of-the-art and critically appraise the range of molecular approaches currently available for the study of insect pollination, host-parasitoid interactions and/or wider food-web studies. Species-interaction data are increasingly being incorporated into ecological network analyses. DNA metabarcoding offers opportunities to scale-up efforts to create large, highly resolved, phylogenetically structured networks within an exciting framework to study pressing questions in ecology and evolution.

Dynamics of a host-parasitoid interaction clarified by modelling and DNA sequencing

It has been hypothesised that the 2-year oscillations in abundance of Xestia moths are mediated by interactions with 1-year Ophion parasitoid wasps. We tested this hypothesis by modelling a 35-year time series of Xestia and Ophion from Northern Finland. Additionally, we used DNA barcoding to ascertain the species diversity of Ophion and targeted amplicon sequencing of their gut contents to confirm their larval hosts. Modelling of the time-series data strongly supported the hypothesised host-parasitoid dynamics and that periodic occurrence of Xestia moths is mediated by Ophion. DNA barcodes revealed that Ophion included five species rather than just one while targeted amplicon sequencing verified that Ophion does parasitise Xestia. At least one Ophion species employs 1-year Syngrapha interrogationis as an alternate host, but it did not detectably affect Xestia-Ophion dynamics. We also demonstrate the previously unrecognised complexity of this system due to cryptic parasitoid diversity.

Arctic terrestrial biodiversity status and trends: A synopsis of science supporting the CBMP State of Arctic Terrestrial Biodiversity Report

This review provides a synopsis of the main findings of individual papers in the special issue Terrestrial Biodiversity in a Rapidly Changing Arctic. The special issue was developed to inform the State of the Arctic Terrestrial Biodiversity Report developed by the Circumpolar Biodiversity Monitoring Program (CBMP) of the Conservation of Arctic Flora and Fauna (CAFF), Arctic Council working group. Salient points about the status and trends of Arctic biodiversity and biodiversity monitoring are organized by taxonomic groups: (1) vegetation, (2) invertebrates, (3) mammals, and (4) birds. This is followed by a discussion about commonalities across the collection of papers, for example, that heterogeneity was a predominant pattern of change particularly when assessing global trends for Arctic terrestrial biodiversity. Finally, the need for a comprehensive, integrated, ecosystem-based monitoring program, coupled with targeted research projects deciphering causal patterns, is discussed.

A DNA Barcoding Survey of an Arctic Arthropod Community: Implications for Future Monitoring

Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.

Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding

An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.

Seeing is believing? Comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures

Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete interaction networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had threefold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, for example, bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.

Approaches to integrating genetic data into ecological networks

As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.

Finding flies in the mushroom soup: Host specificity of fungus-associated communities revisited with a novel molecular method

Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities. Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.

Host specificity of parasitoids (Encyrtidae) toward armored scale insects (Diaspididae): Untangling the effect of cryptic species on quantitative food webs

Host specificity of parasitoids may be measured by various specialization indices to assess the variation of interaction strength among species and the structure of the wider interaction network. However, the conclusions from analyses at the species and network levels may differ, which remains poorly explored. In addition, the recovery of cryptic species of hosts and parasitoids with molecular data may affect the structure of inferred interaction links. We quantified host specificity of hymenopteran parasitoids (family Encyrtidae) on armored scale insects (Hemiptera: Diaspididae) from a wide geographic sampling range across the Chinese Mainland based on both morphological and molecular species delimitation. Mitochondrial COI and nuclear 28S markers detected high cryptic species diversity in the encyrtids and to a lesser degree in the diaspidids, which divided generalist morphospecies into complexes of specialists and generalists. One-to-one reciprocal host-parasite links were increased in the molecular data set, but different quantitative species-level indices produced contrasting estimates of specificity from various one-to-multiple and multiple-to-multiple host-parasite links. Network indices calculated from DNA-based species, compared to morphology-based species definitions, showed lower connectance and generality, but greater specialization and compartmentalization of the interaction network. We conclude that a high degree of cryptic species in host-parasitoid systems refines the true network structure and may cause us overestimating the stability of these interaction webs.

Flower preferences and pollen transport networks for cavity-nesting solitary bees: Implications for the design of agri-environment schemes

Floral foraging resources are valuable for pollinator conservation on farmland, and their provision is encouraged by agri-environment schemes in many countries. Across Europe, wildflower seed mixtures are widely sown on farmland to encourage pollinators, but the extent to which key pollinator groups such as solitary bees exploit and benefit from these resources is unclear. We used high-throughput sequencing of 164 pollen samples extracted from the brood cells of six common cavity-nesting solitary bee species (Osmia bicornis, Osmia caerulescens, Megachile versicolor, Megachile ligniseca, Megachile centuncularis and Hylaeus confusus) which are widely distributed across the UK and Europe. We documented their pollen use across 19 farms in southern England, UK, revealing their forage plants and examining the structure of their pollen transport networks. Of the 32 plant species included currently in sown wildflower mixes, 15 were recorded as present within close foraging range of the bees on the study farms, but only Ranunculus acris L. was identified within the pollen samples. Rosa canina L. was the most commonly found of the 23 plant species identified in the pollen samples, suggesting that, in addition to providing a nesting resource for Megachile leafcutter bees, it may be an important forage plant for these species. Higher levels of connectance and nestedness were characteristic of pollen transport networks on farms with abundant floral resources, which may increase resilience to species loss. Our data suggest that plant species promoted currently by agri-environment schemes are not optimal for solitary bee foraging. If a diverse community of pollinators is to be supported on UK and European farmland, additional species such as R. canina should be encouraged to meet the foraging requirements of solitary bees.

High Redundancy as well as Complementary Prey Choice Characterize Generalist Predator Food Webs in Agroecosystems

Food web structure influences ecosystem functioning and the strength and stability of associated ecosystem services. With their broad diet, generalist predators represent key nodes in the structure of many food webs and they contribute substantially to ecosystem services such as biological pest control. However, until recently it has been difficult to empirically assess food web structure with generalist predators. We utilized DNA-based molecular gut-content analyses to assess the prey use of a set of generalist invertebrate predator species common in temperate agricultural fields. We investigated the degree of specialization of predator-prey food webs at two key stages of the cropping season and analysed the link temperature of different trophic links, to identify non-random predation. We found a low level of specialization in our food webs, and identified warm and cool links which may result from active prey choice or avoidance. We also found a within-season variation in interaction strength between predators and aphid pests which differed among predator species. Our results show a high time-specific functional redundancy of the predator community, but also suggest temporally complementary prey choice due to within-season succession of some predator species.

DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs

BACKGROUND

Understanding feedback between above- and below-ground processes of biological communities is a key to the effective management of natural and agricultural ecosystems. However, as above- and below-ground food webs are often studied separately, our knowledge of material flow and community dynamics in terrestrial ecosystems remains limited.

RESULTS

We developed a high-throughput sequencing method for examining how spiders link above- and below-ground food webs as generalist predators. To overcome problems related to DNA-barcoding-based analyses of arthropod-arthropod interactions, we designed spider-specific blocking primers and Hexapoda-specific primers for the selective PCR amplification of Hexapoda prey sequences from spider samples. By applying the new DNA metabarcoding framework to spider samples collected in a temperate secondary forest in Japan, we explored the structure of a food web involving 15 spider species and various taxonomic groups of Hexapoda prey. These results support the hypothesis that multiple spider species in a community can prey on both above- and below-ground prey species, potentially coupling above- and below-ground food-web dynamics.

CONCLUSIONS

The PCR primers and metabarcoding pipeline described in this study are expected to accelerate nuclear marker-based analyses of food webs, illuminating poorly understood trophic interactions in ecosystems.

Landscape configuration affects herbivore-parasitoid communities in oilseed rape

It is crucial to consider the effects of large-scale drivers on species presences and ecological interactions to understand what structures communities. In our study, we investigated how the species composition and the potential interaction networks of herbivore and parasitoid communities in oilseed rape fields are affected by agricultural landscape characteristics. Insect communities of 26 winter oilseed rape fields in southern Sweden were captured in water traps over a continuous time span of 30 ± 2 days. In total, 31% of the variation in the composition of herbivore host communities was explained by a combination of the surrounding oilseed rape area in the study year and the previous year and distance to the nearest forest. The oilseed rape area in the study year and distance to forest also explained 14% of the variation in the composition of parasitoid communities. Distance to the nearest forest together with the area of oilseed rape in the previous year explained 45% of the variation in asymmetry of interaction webs. These results indicate that several measures of landscape configuration are important both for the composition of host and parasitoid communities and also for the structure of interaction networks. Our results support the view that it is an appropriate strategy to cultivate oilseed rape in landscapes that are far away from forests, in order to minimize recolonization by pest species and at the same time to attract parasitoid species from the open landscape.