Feeding ecology of a bagrid catfish,Mystus tengara (Hamilton, 1822) in the Tanore wetland of Rajshahi,Northwestern Bangladesh

The feeding ecology of Mystus tengara (Hamilton, 1822) was studied in the Tanore wetland of Rajshahi, northwestern Bangladesh from January 2011 to December 2011. In fish purchased from the local market, a total of 14 713 food items were identified in the stomach contents of 3191 M. tengara specimens, an omnivorous catfish with a diversified feeding strategy including cladocerans, copepods, rotifers, gastropods, green algae, diatoms, insects, ‘small fish remains, fish fry and eggs’ and ‘other’ food items. Insects were the most dominant group of prey throughout the year. Seasonal changes in diet composition were due to the availability of prey items and fish size. Ontogenetic changes were noted between the juveniles and adults. The gut contents of M. tengara showed that the food items were from different layers of the water bodies.     

A whole‐genome,radiation hybrid mapping resource of hexaploid wheat

Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole‐genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics‐based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole‐genome using these approaches is nearly impossible. We developed a whole‐genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high‐density single nucleotide polymorphism (SNP) array. At the whole‐genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR₁₅₀₀ with a total map length of 6866 cR₁₅₀₀. The 7296 unique mapping bins provided a five‐ to eight‐fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low‐cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS‐WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high‐quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.     

A false‐positive food chain error associated with a generic predator gut content ELISA

Conventional prey‐specific gut content ELISA (enzyme‐linked immunosorbent assay) and PCR (polymerase chain reaction) assays are useful for identifying predators of insect pests in nature. However, these assays are prone to yielding certain types of food chain errors. For instance, it is possible that prey remains can pass through the food chain as the result of a secondary predator (hyperpredator) consuming a primary predator that had previously consumed the pest. If so, the pest‐specific assay will falsely identify the secondary predator as the organism providing the biological control services to the ecosystem. Recently, a generic gut content ELISA was designed to detect protein‐marked prey remains. That assay proved to be less costly, more versatile, and more reliable at detecting primary predation events than a prey‐specific PCR assay. This study examines the chances of obtaining a ‘false positive’ food chain error with the generic ELISA. Data revealed that the ELISA was 100% accurate at detecting protein‐marked Lygus hesperus Knight (Hemiptera: Miridae) remains in the guts of two (true) primary predators, Hippodamia convergens Guérin‐Méneville (Coleoptera: Coccinellidae) and Collops vittatus (Say) (Coleoptera: Melyridae). However, there was also a high frequency (70%) false positives associated with hyperpredators, Zelus renardii Kolenati (Hemiptera: Reduviidae), that consumed a primary predator that possessed protein‐marked L. hesperus in its gut. These findings serve to alert researchers that the generic ELISA, like the PCR assay, is susceptible to food chain errors.     

Lessons from genome skimming of arthropod‐preserving ethanol

Field‐collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects (from a freshwater habitat and terrestrial habitat) to evaluate the efficiency of DNA transfer from the specimens to the ethanol. In parallel, the specimens themselves were subjected to bulk DNA extraction and shotgun sequencing, followed by assembly of mitochondrial genomes for 39 of 40 species in the two pools. Shotgun sequencing from the ethanol fraction and read‐matching to the mitogenomes detected ~40% of the arthropod species in the ethanol, confirming the transfer of DNA whose quantity was correlated to the biomass of specimens. The comparison of diversity profiles of microbiota in specimen and ethanol samples showed that ‘closed association’ (internal tissue) bacterial species tend to be more abundant in DNA extracted from the specimens, while ‘open association’ symbionts were enriched in the preservative fluid. The vomiting reflex of many insects also ensures that gut content is released into the ethanol, which provides easy access to DNA from prey items. Shotgun sequencing of DNA from preservative ethanol provides novel opportunities for characterizing the functional or ecological components of an ecosystem and their trophic interactions.     

Climate change enhances the negative effects of predation risk on an intermediate consumer

Predators are a major source of stress in natural systems because their prey must balance the benefits of feeding with the risk of being eaten. Although this ‘fear’ of being eaten often drives the organization and dynamics of many natural systems, we know little about how such risk effects will be altered by climate change. Here, we examined the interactive consequences of predator avoidance and projected climate warming in a three‐level rocky intertidal food chain. We found that both predation risk and increased air and sea temperatures suppressed the foraging of prey in the middle trophic level, suggesting that warming may further enhance the top‐down control of predators on communities. Prey growth efficiency, which measures the efficiency of energy transfer between trophic levels, became negative when prey were subjected to predation risk and warming. Thus, the combined effects of these stressors may represent an important tipping point for individual fitness and the efficiency of energy transfer in natural food chains. In contrast, we detected no adverse effects of warming on the top predator and the basal resources. Hence, the consequences of projected warming may be particularly challenging for intermediate consumers residing in food chains where risk dominates predator‐prey interactions.     

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food‐web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high‐resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.     

Predator presence dramatically reduces copepod abundance through condition‐mediated non‐consumptive effects

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Next‐generation sequencing sheds light on intricate regulation of insect gut microbiota

Next‐generation sequencing (NGS) technologies are getting cheaper and easier and hence becoming readily accessible for many researchers in biological disciplines including ecology. In this issue of Molecular Ecology, Sudakaran et al. (2012) show how the NGS revolution contributes to our better and more comprehensive understanding of ecological interactions between gut symbiotic microbiota and the host organism. Using the European red firebug Pyrrhocoris apterus as a model system, they demonstrated that the gut microbiota consists of a small number of major bacterial phylotypes plus other minor bacterial associates. The major bacteria are localized in a specific anoxic section of the midgut and quantitatively account for most of the gut microbiota irrespective of host's geographic populations. The specific gut microbiota is established through early nymphal development of the host insect. Interestingly, the host feeding on different food, namely linden seeds, sunflower seeds or wasp larvae, scarcely affected the symbiont composition, suggesting homoeostatic control over the major symbiotic microbiota in the anoxic section of the midgut. Some of the minor components of the gut microbiota, which conventional PCR/cloning/sequencing approaches would have failed to detect, were convincingly shown to be food‐derived. These findings rest on the robust basis of high‐throughput sequencing data, and some of them could not be practically obtained by conventional molecular techniques, highlighting the significant impact of NGS approaches on ecological aspects of host–symbiont interactions in a nonmodel organism.     

Distribution,feeding habits and morphology of killer whales Orcinus orca in the Caribbean Sea

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Dietary opportunism,resource partitioning,and consumption of coffee berry borers by five species of migratory wood warblers (Parulidae) wintering in Jamaican shade coffee plantations

Diets reflect important ecological interactions, but are challenging to quantify for foliage‐gleaning birds. We used regurgitated stomach samples from five primarily insectivorous species of long‐distance migrant warblers (Parulidae) wintering in two moderate‐elevation shade coffee farms in Jamaica to assess both foraging opportunism and prey resource partitioning. Our results, based primarily on 6120 prey items in 80 stomach samples collected during a one‐week period in March 2000, confirm opportunism. The diets of all five warblers, including American Redstarts (Setophaga ruticilla), Black‐and‐White Warblers (Mniotilta varia), Black‐throated Blue Warblers (S. caerulescens), Northern Parulas (S. americana), and Prairie Warblers (S. discolor), overlapped strongly based on consumption of the same prey types, even many of the same prey species (4 of 10 interspecific overlaps >0.9, range = 0.74–0.97). Moreover, all five species fed on similarly small, often patchily distributed prey, including coffee berry borers (Hypothenemus hampei; Coleoptera, Curculionidae). Nonetheless, permutational multivariate analysis of variance also revealed that the diets of these species differed significantly, primarily with respect to prey mobility (winged vs. sessile); American Redstarts fed on the most mobile prey, and Northern Parulas on the least mobile prey and a relatively restricted set of prey taxa compared to the other four species of warblers. Overall, our results suggest both dietary opportunism consistent with a migratory life‐history, and interspecific resource partitioning consistent with differences in morphology and foraging behavior during a food‐limited season. Having provided evidence of the three necessary conditions, namely intraspecific competition, resource limitation, and interspecific overlap in resource use, the results of our study, in combination with those of other studies, also provide evidence of interspecific competition among wintering migrant insectivores. We thus argue that diffuse interspecific exploitative food competition may be more important than previously recognized.     

Suspension-feeding mechanisms of the armoured sea cucumber Psolus chitinoides Clark

The armoured sea cucumber Psolus chitinoides Clark feeds on suspended particulate matter by means of tentacle ensnarement and the adhesive papillae of the tentacle buds. The latter provide the only ‘sticky’ surface on the feeding tentacles. Electron microscope preparations of the tentacle tips show the adhesive papillae to be comprised of both stout, warty papillary cells which appear to secrete the adhesive material used in the capture of food, and slender, uniciliated cells which may function to disengage food from the tentacle papillae during ingestion. Tentacular response to olfactory and mechanical stimuli together with ultrastructural evidence indicate that the papular cells may also function in a sensory capacity.     

The effect of zooplankton abundance on feeding behaviour and prey size selection in Atlantic salmon,Salmo salar,alevins1

In an experiment on the effect of zooplankton density on feeding behaviour and prey size selection in Atlantic salmon (Salmo salar) alevins, total behavioural activity (feeding, social, ambiguous) was positively related to prey abundance up to a density of 350 items 1^?1, after which activity peaked. Feeding error (missed attacks and/or rejected ingestions) increased with prey density. The likelihood that an alevin would attack an item upon which it had binocularly fixed (no. bites/no. visual fixes) peaked at densities of 270 items 1^?1 and then declined. Feeding success (no. ingestions per bite or per fixation) also peaked and then declined. Changes in success were reflected in total number of items found in the gut. At high prey abundance (608 items 1^?1) only 0.5 – 0.9 mm copepods were preferred components of alevin diets. Over all prey densities, preferred sizes of cladocerans and copepods did not overlap. These results may reflect a perceptual constraint (at high zooplankton densities) on alevin feeding behaviour.     

Differences in foraging ecology determine variation in visual fields in ibises and spoonbills (Threskiornithidae)

Variations in visual field topography among birds have been interpreted as adaptations to the specific perceptual challenges posed by the species’ foraging ecology. To test this hypothesis we determined visual field topography in four bird species which have different foraging ecologies but are from the same family: Puna Ibis Plegadis ridgwayi (probes for prey in the soft substrates of marsh habitats), Northern Bald Ibis Geronticus eremita (surface pecks for prey in dry terrestrial habitats), African Spoonbill Platalea alba and Eurasian Spoonbill Platalea leucorodia (bill‐sweeps for prey in shallow turbid waters). All four species employ tactile cues provided by bill‐tip organs for prey detection. We predicted that the visual fields of these species would show general features similar to those found in other birds whose foraging is guided by tactile cues from the bill (i.e. bill falling outside the frontal binocular field and comprehensive visual coverage of the celestial hemisphere). However, the visual fields of all four species showed general features characteristic of birds that take food directly in the bill under visual guidance (i.e. a narrow and vertically long binocular field in which the projection of the bill tip is approximately central and with a blind area above and behind the head). Visual fields of the two spoonbills were very similar but differed from those of the ibises, which also differed between themselves. In the spoonbills, there was a blind area below the bill produced by the enlarged spatulate bill tip. We discuss how these differences in visual fields are related to the perceptual challenges of these birds’ different foraging ecologies, including the detection, identification and ingestion of prey. In particular we suggest that all species need to see binocularly around the bill and between the opened mandibles for the identification of caught prey items and its transport to the back of the mouth. Our findings support the hypothesis that sensory challenges associated with differences in foraging ecology, rather than shared ancestry or the control of locomotion, are the main determinants of variation in visual field topography in birds.     

Hypotheses and trends on how body size affects trophic interactions in a guild of South American killifishes

A chief structuring force in food webs is the hierarchy of trophic interactions, where bigger animals feed on smaller ones. The anatomic and physiological explanations of why body size determines this hierarchy are embodied within the concept of gape limitation. The relaxation of gape limitation and an increase in energetic demands due to predators' larger body size determine the size and diversity of prey species. However, these patterns may be related to further trends in trophic interactions with body size, which have been less considered. Specifically, the passive incorporation of prey should involve a nested distribution of prey among predator size classes. However, predators avoid smaller resources because of their low energy return, with a clumped distribution of prey potentially generating modular organization with qualitative changes in prey identity (e.g. zooplankton, macroinvertebrates and fishes). Finally, size‐mediated interactions (such as direct and indirect competition) may cause predators of similar body size to differentiate among prey organisms, resulting in a checkerboard distribution of prey identity. Consequently, nestedness, modularity and checkerboard distributions of prey among predators of different size classes should form emergent network structures that are directly related to clear ecological mechanisms. We analyse these predictions in a killifish guild, where trends in trophic positions, prey richness, evenness and the number of energy sources systematically scale with body size. We found significant nestedness and segregation in diet among different size classes, supporting the progressive incorporation of prey items coupled with prey differentiation among similar classes. However, we also detected an ‘anti‐modular’ trend, which contradicts theoretical expectations and previous results. We hypothesize that this anti‐modularity is determined by the high biodiversity of the system and the continuous representation of prey size classes. These results reinforce the concept of size‐mediated interactions and its connection with community biodiversity as a main structuring force of food webs.     

Testing a novel agri‐environment scheme based on the ecology of the target species,Montagu's Harrier Circus pygargus

Farmland birds are in steep decline and agri‐environment schemes (AES) to counteract these biodiversity losses are expensive and inefficient. Here we test a novel AES, ‘Birdfields’, designed using detailed ecological knowledge of the target species, Montagu's Harrier Circus pygargus. Current AES, such as field margins, that aim to improve foraging conditions (i.e. vole densities) for harriers are inefficient, as prey are difficult to capture in tall set‐aside habitat. ‘Birdfields’ combines strips of set‐aside to boost vole numbers and strips of alfalfa, as voles are accessible after alfalfa has been harvested. We found that vole numbers were generally highest in set‐aside. Montagu's Harriers fitted with GPS‐loggers used ‘Birdfields’ intensively after mowing, preferring mown to unmown strips. Thus, prey availability appeared more important than prey abundance. Thus, ‘Birdfields’, as a targeted AES for Montagu's Harriers, is more effective than previous AES due to increased prey accessibility. An additional advantage of ‘Birdfields’ is that it is considerably cheaper, due to the harvest of alfalfa. We advocate that AES should always include monitoring and research activities, aiming at a more adaptive conservation approach.     

From Puffins to Plankton: A DNA-Based Analysis of a Seabird Food Chain in the Northern Gulf of Maine

The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis.     

Molecular identification of the prey range of the invasive Asian paper wasp

The prey range of the invasive Asian paper wasp, Polistes chinensis antennalis, was studied using molecular diagnostics. Nests of paper wasps were collected from urban residential and salt marsh habitats, larvae were removed and dissected, and DNA in the gut of the paper wasp larvae was amplified and sequenced with cytochrome c oxidase subunit I (COI). Seventy percent of samples (211/299) yielded medium‐to high‐quality sequences, and prey identification was achieved using BLAST searches in BOLD. A total of 42 taxa were identified from 211 samples. Lepidoptera were the majority of prey, with 39 taxa from 91% of samples. Diptera was a relatively small component of prey (three taxa, 19 samples). Conclusive species‐level identification of prey was possible for 67% of samples, and genus‐level identification, for another 12% of samples. The composition of prey taken was different between the two habitats, with 2.5× more native prey species being taken in salt marsh compared with urban habitats. The results greatly extend the prey range of this invasive species. The technique is a more effective and efficient approach than relying on the collection of “prey balls”, or morphological identification of prey, for the study of paper wasps.     

Food quality affects the expression of antimicrobial peptide genes upon simulated parasite attack in the larvae of greater wax moth

Predator‐prey interactions are an important evolutionary force affecting the immunity of the prey. Parasitoids and mites pierce the cuticle of their prey, which respond by activating their immune system against predatory attacks. Immunity is a costly function for the organism, as it often competes with other life‐history traits for limited nutrients. We tested whether the expression of antimicrobial peptides (AMP) of the larvae of the greater wax moth Galleria mellonella (L.) (Lepidoptera: Pyralidae) changes as a consequence of insertion of a nylon monofilament, which acts like a synthetic parasite. The treatment was done for larvae grown on a high‐quality vs. a low‐quality diet. The expression of Gloverin and 6‐tox were upregulated in response to the insertion of the nylon monofilament. The expression of 6‐tox, Cecropin‐D, and Gallerimycin were significantly higher in the ‘low‐quality diet’ group than in the ‘high‐quality diet’ group. As food quality seems to affect AMP gene expression in G. mellonella larvae, it should always be controlled for in studies on bacterial and fungal infections in G. mellonella.