When to use next generation sequencing or diagnostic PCR in diet analyses

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

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

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.

Effects of red ginseng extract on gut microbial distribution

Background

Red ginseng extract boosts immunity against inflammation and cancer in the human body. However, studies on the effects of red ginseng extract on the gut microbiome remain unexplored.

Methods

In 2019, the positive effects and changes in the gut microbiome after administering 1 pack (3 g) of red ginseng extract per day to 53 adults aged 40 to 75 for 24 weeks were investigated. The gut microbial environment changes were qualitatively and quantitatively analyzed using next-generation sequencing and real-time polymerase chain reaction technology.

Results

On comparing and analyzing alpha diversity and beta diversity, the microbial pattern showed significant differences (OTUs p = 0.003, chao1 p < 0.001, Bray-Curtis p = 0.001) before and after ingestion of red ginseng extract, indicating that gut microbial richness increased after ingestion. Moreover, after comparing and analyzing the gut microbiome's differences after red ginseng extract intake, significant differences were noted between three strains at the phylum level and among 57 strains at the genus level.

Conclusion

This study proposes the potential use of red ginseng extract as a prebiotic after confirming its positive effects, including increasing gut microbiome richness, reducing harm to the gut microbiome, and increasing the number of some strains in the gut microbiome.

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

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

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

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

Assessment of the biocontrol potential of natural enemies against psyllid populations in a pear tree orchard during spring

BACKGROUND

Modern pest control management systems are based on the support of naturally occurring arthropod predators, as it has been shown that such predators offer an important ecosystem service. However, most naturally occurring arthropod predators are generalists (euryphagous). Their role in the biological control of specific pests has been recognized but remains poorly studied. Here, we focused on the naturally occurring arthropod predators of psyllids - the main insect pest of pear trees. We investigated the abundance of psyllids and all of their potential enemies in an abandoned pear orchard on a weekly basis from early spring to early summer. In addition, employing polymerase chain reaction diagnostics and specific primers, we investigated the predation rate on psyllids in all predators collected.

RESULTS

We found four predatory groups: spiders were the most abundant (60%, N = 756), followed by coccinellid beetles, anthocorid bugs and cantharid beetles. Anthocorids and spiders had the highest predation rates among the predatory groups. Among spiders, >50% of foliage-dwelling spiders (belonging to the genera Philodromus and Clubiona; N = 206) were positive for psyllids and showed a numerical response to the abundance of psyllids.

CONCLUSION

We conclude that foliage-dwelling spiders are, of the four groups, the most important natural enemies of psyllids on pear trees during spring in Central Europe, as they outnumber specialized Anthocoris bugs. © 2021 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.

Revealing the Diet of Generalist Insect Predators in Strawberry Fields: Not Only Pests, But Other Predators Beware

Generalist invertebrate predators contribute to pest management in agriculture, providing an important ecosystem service, particularly in organically managed fields. DNA-based methods to study food webs and feeding interactions in unrestricted field conditions have transformed dietary analysis of generalist predators. In this study, we used MiSeq next-generation sequencing (NGS) technology and universal arthropod primers to investigate the diet of several generalist insect predators collected in commercial organic Florida strawberry fields from November 2017 to March 2018. Of 12 predator insect taxa, Geocoris spp. (Say) (Hemiptera: Geocoridae) was the most abundant early in the growing season (November) and was collected consistently until the end of the season (early March). DNA sequences from 105 predator samples were matched to 44 arthropod families, and of these, 17 were categorized as pest families, 10 as nonpest or nonpredator families, and 17 as predator families. Drosophilidae was the most detected pest family, and Dolichopodidae was the most detected predator family. Prey diversity differed among the predators. Chrysoperla spp. (Neuroptera: Chrysopidae) consumed more prey earlier in the season than did other predators, whereas the other predators consumed a greater diversity of other predators regardless of month. Our results showed a high amount of intraguild predation, but also that predators are contributing to pest suppression in organic strawberries and providing an important biological control service in Florida organic strawberries.

The curious and neglected soft-bodied meiofauna: Rouphozoa (Gastrotricha and Platyhelminthes)

Gastrotricha and Platyhelminthes form a clade called Rouphozoa. Representatives of both taxa are main components of meiofaunal communities, but their role in the trophic ecology of marine and freshwater communities is not sufficiently studied. Traditional collection methods for meiofauna are optimized for Ecdysozoa, and include the use of fixatives or flotation techniques that are unsuitable for the preservation and identification of soft-bodied meiofauna. As a result, rouphozoans are usually underestimated in conventional biodiversity surveys and ecological studies. Here, we give an updated outline of their diversity and taxonomy, with some phylogenetic considerations. We describe successfully tested techniques for their recovery and study, and emphasize current knowledge on the ecology, distribution and dispersal of freshwater gastrotrichs and microturbellarians. We also discuss the opportunities and pitfalls of (meta)barcoding studies as a means of overcoming the taxonomic impediment. Finally, we discuss the importance of rouphozoans in aquatic ecosystems and provide future research directions to fill in crucial gaps in the biology of these organisms needed for understanding their basic role in the ecology of benthos and their place in the trophic networks linking micro-, meio- and macrofauna of freshwater ecosystems.

Nourished, Exposed Beaches Exhibit Altered Sediment Structure and Meiofaunal Communities

To retain recreational uses and shoreline protection, a large proportion of ocean beaches have been, and continue to be, nourished. Adding sand from subtidal and terrestrial sources to nourish beaches rarely re-creates the original sediment structure of the beach. Numerous studies have demonstrated that meiofaunal communities are altered by changes in sediment composition in low-energy substrates, therefore, we have explored whether beach nourishment has affected exposed, ocean beach meiofaunal communities. Since the early 2000s, we have conducted a series of sampling and experimental studies on meiofauna and sediments on nourished beaches in coastal North Carolina USA that had been sampled previously in the early 1970s, prior to any beach nourishment. Most of our studies consider meiofauna at the level of major taxa only. However, a few studies examine free-living flatworm (turbellarian) species in detail because of the existence of historical studies examining this group. Comparison of contemporary results to historical data and of heavily nourished versus lightly nourished beaches reveals extensive changes to beach sediment structure and meiofaunal community composition, indicating that the beaches are a more heterogeneous habitat than in the past. The effects of these substantial physical and biological changes to the production of beach ecosystem services are unlikely to be inconsequential.

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

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

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.

When to use next generation sequencing or diagnostic PCR in diet analyses

Next‐generation sequencing (NGS) is increasingly used for diet analyses; however, it may not always describe diet samples well. A reason for this is that diet samples contain mixtures of food DNA in different amounts as well as consumer DNA which can reduce the food DNA characterized. Because of this, detections will depend on the relative amount and identity of each type of DNA. For such samples, diagnostic PCR will most likely give more reliable results, as detection probability is only marginally dependent on other copresent DNA. We investigated the reliability of each method to test (a) whether predatory beetle regurgitates, supposed to be low in consumer DNA, allow to retrieve prey sequences using general barcoding primers that co‐amplify the consumer DNA, and (b) to assess the sequencing depth or replication needed for NGS and diagnostic PCR to give stable results. When consumer DNA is co‐amplified, NGS is better suited to discover the range of possible prey, than for comparing co‐occurrences of diet species between samples, as retested samples were repeatedly different in prey detections with this approach. This shows that samples were incompletely described, as prey detected by diagnostic PCR frequently were missed by NGS. As the sequencing depth needed to reliably describe the diet in such samples becomes very high, the cost‐efficiency and reliability of diagnostic PCR make diagnostic PCR better suited for testing large sample‐sets. Especially if the targeted prey taxa are thought to be of ecological importance, as diagnostic PCR gave more nested and consistent results in repeated testing of the same sample.