Using faecal metabarcoding to examine consumption of crop pests and beneficial arthropods in communities of generalist avian insectivores

Generalist insectivorous birds can provide ecosystem services in agricultural landscapes by consuming arthropod pests, or they can provide disservices when they consume beneficial arthropods. To examine bird impacts on arthropod communities, including pest control services, we need to know which arthropods birds commonly consume. Faecal metabarcoding is an emerging technique that can be used to identify prey from faecal samples, often to the species level. We used faecal metabarcoding to study diets of birds inhabiting the ecotone between soybean fields and adjacent grasslands in a largely agricultural landscape in Illinois, USA, during the summer of 2017. Whereas previous studies have used faecal metabarcoding to compare bird diets among species or among capture sites, we analysed samples from multiple species within a community at replicate sites. We collected and sequenced DNA from 132 faecal samples from 25 bird species captured at six sites. We found that birds consumed an extremely large and varied diet that differed among both species and sites, suggesting that birds were consuming prey opportunistically as available at each site. Of the nine most commonly detected prey species, three are known pests of soybeans. Bird diets also contained significantly more species of herbivorous prey than natural enemies. Finally, we discovered that American Goldfinches Spinus tristis, a highly granivorous species, may consume arthropods more frequently than expected and thus may provide ecosystem services in agricultural landscapes. Our study demonstrates that birds within this system consume a large variety of prey, suggesting that they may be able to respond quickly to pest outbreaks and contribute to agricultural resiliency.     

Population density of the greater mouse-eared bat (Myotis myotis), local diet composition and availability of foraging habitats

We studied the regional variation in population density of Myotis myotis (Borkhausen 1797) in south-eastern Bavaria, Germany, and its relations to diet composition and the availability of potential foraging habitats. We monitored colony size and juvenile mortality from 1991 to 2003, conducted faecal analyses in 1993 and determined land-use patterns around colonies. The numbers of individuals counted in the nursery colonies showed only small fluctuations over the years. However, data on colony size demonstrated a pronounced regional variation. Epigeic arthropods, mainly Carabidae, were the most important prey. The diet included prey taxa of forest as well as grassland habitats. The percentage of those prey taxa in the diet that originated in grassland managed with different intensity varied according to the availability of these potential foraging habitats around the nursery roosts. The calculated population density of the bats was positively correlated to forest area and especially to the area of mixed forest around the nursery roosts. Our results indicate that the availability of foraging habitats is a limiting factor for local population densities in the greater mouse-eared bat.     

Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition?

We investigate using relative amounts of prey DNA recovered from pinniped faeces to obtain diet composition data. Faeces were obtained from captive sea lions being fed a diet containing three fish species (50%, 36% and 14% by mass). Real-time PCR was used to quantify mtDNA in undigested tissue and in the faecal samples. The percent composition of fish mtDNA extracted from tissue corresponded reasonably well to the mass of fish in the mixture. In faecal samples the absolute amount of fish mtDNA recovered varied 100-fold, but the percent composition of the samples was relatively consistent (57.5 ± 9.3%, 19.3 ± 6.6% and 23.2 ± 12.2%). These results indicate there are prey-specific biases in DNA survival during digestion. However, the biases may be less than those commonly observed in conventional diet studies.     

Diet niche relationships among North American grassland and shrubsteppe birds

Summary We consider the dietary relationships of the numerically dominant breeding bird species in four North American grassland/shrubsteppe habitats, sampled over 2–3 consecutive years. Overall, the diets of these species contained primarily insects: orthopterans comprised 29% of the diet biomass, coleopterans 24%, and lepidopteran larvae 23%, while seeds contributed 15% of the average diet. These diets varied substantially, however, and we evaluated several aspects of this variation. Intersexual differences in diets within a species were few, despite the occurrence of significant sexual size dimorphism in several species. For many species, however, there were substantial shifts in dietary composition between years at a given location; overall, the average between-year similarity of species' dietary composition was 70%. Different species exhibited rather different diet patterns. Horned Larks were relatively omnivorous, had broad diet composition niches, and varied considerably in diets between different locations. Meadowlarks were also broad-niched and geographically variable in their diets, but were the most highly carnivorous of the species we considered. Dietary niche breadths of Grasshopper Sparrows were intermediate, but diet composition was rather stable, both between years and between locations. Chestnut-collared Longspurs exhibited narrow diet niches, but substantial annual variation: each year this species apparently exploited a different but limited set of prey types rather heavily. Larger avian predators generally consumed a broader array of functional groups of prey, but did not differ in the taxonomic variety of their diets from small birds. Variation in diet composition between individuals within local populations was considerable; in most species, an individual contained on the average 30–40% of the prey taxa represented in entire population smaples.Patterns of dietary overlap among species were quite inconsistent from year to year at most locations, although at the shrubsteppe site overlap among all species present was consistently quite high. Relatively few cooccurring species pairs exhibited low diet overlap. The degree of diet niche overlap was unrelated to body size differences of the birds, despite as much as six-fold differences in weight among some coexisting species. Relationships of the bird species on another dimension of the trophic niche, prey size, also differed substantially between sites and years. The ranking of co-occurring species by the mean sizes of the prey they consumed generally did not parallel their rankings by body sizes, and in some cases the smallest and the largest species present ate prey of similar sizes. At the shrubsteppe site, all the breeding species exhibited quite similar frequency distributions of prey sizes in their diets.As species number and diversity increased in the breeding avifaunas, diet niche breadths generally decreased, species packing by prey size decreased, and diet composition niche overlap remained relatively unchanged. These trends are in at least partial agreement with predictions of diffuse competition theory, but the patterns were derived from broad inter-site comparisons of overall site averages, and the relationships generally did not hold within local assemblages of species. In general, our attempts to match values of dietary niche features with site characteristics failed to demonstrate close agreement with the predictions of prevailing ecological theory based upon assumptions of resource limitation and competition. Instead, our findings seem generally most consistent with the suggestion that food is not normally limiting to bird populations in these systems, and individuals and populations are exploiting the food resources in an opportunistic fashion, which leads to considerable individual, between-year, and between-location variation in diet compositions and interspecific overlaps.Our attempts to discern clear relationships that accord with theoretical expectations in these avian assemblages are thwarted by our lack of detailed information on the resource base and by the lack of clear tests that will separate alternative hypotheses of community organization and structuring. We suggest that these complications may compromise the findings of many community studies.     

Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces

Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat samples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition.
Scat samples have been collected from intertidal haul-out sites around the inner Moray Firth, north-east Scotland. We have assessed methods to extract and purify faecal DNA, a combination of DNA from the individual seal, prey items, and gut bacteria, for use in PCR. Controls using faecal and blood samples from the same individual have enabled microsatellite primer sets from four pinniped species to be tested. Approximately 200 scat samples have been examined for species identity and individual matches. This study will provide essential information for the assessment of interactions between seals and commercial or recreational fisheries.     

The food habits of a Malagasy Giant: Hipposideros commersoni (E. Geoffroy, 1813)

Hipposideros commersoni is a large microchiropteran bat endemic to Madagascar. We analysed fragments of its prey from faeces and from underneath feeding perches to describe its diet from four sites. Diet was similar across sites and Coleoptera was the main prey item by percentage volume (75%), followed by Hemiptera (13%). Carabidae and Scarabidae were the most frequent coleopterans found in the diet. Direct observations (n = 3) were made of bats flying short distances from perches along forest trails to prey on Cicadidae ( c. 20 mm in length) located on tree trunks. There were differences in the composition of faecal samples collected form netted bats and pellets collected under feeding perches, with the latter consisting of more Blattoptera (Blattellidae 'cockroaches'). Hipposideros commersoni appears to have a unique foraging behaviour and diet among Malagasy microchiropterans and its preference for certain Coleoptera and other large invertebrates may account for reported seasonal variation in body fattening and activity.     

崂山湾人工鱼礁区星康吉鳗摄食生态及食物网结构

根据2015年4月至2017年1月于崂山湾人工鱼礁区地笼网和延绳钓捕获的279尾星康吉鳗样本,从胃含物组成、食性类型、摄食等级、营养生态位和营养级等方面对其摄食生态进行研究,同时结合海区许氏平鲉、大泷六线鱼、斑头鱼、褐菖鲉、花鲈等9种鱼类的胃含物分析结果,构建人工鱼礁区鱼类关键种的简化食物网模型.食性研究结果表明:星康吉鳗共摄食7类30余种饵料,虾类是其最主要的饵料类群,其次为鱼类和头足类,大泷六线鱼、方氏云鳚、鹰爪虾、玉筋鱼和日本鼓虾等是其优势饵料.星康吉鳗的饵料生物组成随肛长和季节发生显著变化.四季均以鱼类和虾类为主,春季胃含物中包括头足类,秋季包括头足类和蟹类,冬季亦有蟹类出现.肛长≤120 mm的星康吉鳗主要摄食鱼卵和鹰爪虾,120~130 mm肛长组主要摄食玉筋鱼和日本鼓虾,肛长>130 mm的星康吉鳗主要摄食大泷六线鱼和方氏云鳚.其摄食强度也随季节和肛长而变化,空胃率的季节性差异显著,平均胃饱满系数的季节性差异不显著,不同肛长组的空胃率和平均胃饱满系数均不存在显著差异.人工鱼礁区简化食物网结构显示:鱼类关键种的营养级均在3级以上,星康吉鳗的营养级为4.636,处于海区食物网的最顶端.虾类、蟹类、端足类和软体动物等是鱼类关键种的主要饵料,甲壳类、方氏云鳚、大泷六线鱼和玉筋鱼是高营养级鱼类花鲈和星康吉鳗的主要饵料.     

Geographical and intrapopulation variation in the diet of a threatened marine predator,Pontoporia blainvillei (Cetacea)

Understanding diet variation is a major concern when developing conservation guidelines for threatened species, especially for marine predators whose prey availability can be reduced by commercial fisheries. Diet can vary in geographically structured populations due to variation in prey availability and within a location due to the effects of season, sex, age, and individual. However, these sources of variation are seldom considered together in dietary studies. We analyzed diet variation at the geographical and intrapopulation levels in the franciscana dolphin (Pontoporia blainvillei) by analyzing samples of stomach contents from individuals incidentally caught by artisanal fisheries. We investigated the geographical (Northern, Central, and Southern regions of the São Paulo State coast, Brazil) and intrapopulation effects of season, sex, and age. We used the leave‐one‐out cross‐validation method to test for significance of the proportional similarity index, which measures the overlap between diet compositions. We found that diet varied across different levels, from the geographical to the individual level, including the effects of season, sex, and age. Diet variation as a function of age suggests an ontogenetic diet shift. Our findings indicate that ecological processes within local stocks should inform management at the local geographic scale. Evidence for ecological differences between franciscana stocks is of great significance for the conservation of this threatened species.     

Prey use of wetland benthivorous sunfishes: ontogenetic, interspecific and seasonal variation

The intensity of competitive interactions between fishes is partly determined by prey use and ontogenetic niche shifts. In a wetland where distinct habitat shifts are missing we compared prey use of three generalist benthivorous sunfishes to look for evidence of ontogenetic, interspecific, and “seasonal” variation in prey composition. Diet analysis revealed evidence of diet ontogeny in warmouth (Lepomis gulosus, 30–152 mm standard length, SL), but not in bluespotted sunfish (Enneacanthus gloriosus, 30–47 mm SL) or dollar sunfish (Lepomis marginatus, 30–60 mm SL). Bluespotted and dollar sunfishes consumed small dipteran and amphipod prey and had similar diets in both seasons suggesting a potential for strong interspecific competition. In the dry season, warmouth shifted from using smaller insect prey to larger decapod and fish prey with increasing size. This shift to prey types that were little used by the other species reduced dietary niche overlap with the other sunfishes. After drought and re-flooding (in the wet season), decapods and small fish were less abundant in the wetland and the warmouth ontogenetic shift was less distinct. When matched for gape width, prey composition differed between warmouth and both dollar and bluespotted sunfishes in the wet season, suggesting differences in sunfish foraging modes, but prey use differences were less clear in the dry season when prey were abundant. Both warmouth ontogenetic diet shifts and seasonal variation in prey use (probably mediated by prey abundance) had strong influences on diet overlap and therefore the potential for intra- and interspecific competition between sunfishes in this wetland ecosystem.     

Seasonal variation in the diet of Redshank Tringa totanus in the Odiel Marshes,southwest Spain: a comparison of faecal and pellet analysis

Capsule Redshank diet from southern Europe during migration shows spatial and seasonal variations.

Aims To assess seasonal variation in Redshank diet at a major passage site, and to compare data derived from analysing pellets or faeces.

Methods At the Odiel Marshes in 2001, pellets from spring migration (39), autumn migration (121) and midwinter (15) were analysed, together with faecal samples from autumn (84).

Results The abundance of different invertebrate groups in pellets varied between seasons. In spring, Chironomus salinarius pupae and larvae dominated by volume, followed by Ephydridae larvae and the beetle Paracymus aenus. Polychaetes and molluscs dominated in autumn, and isopods in midwinter. In autumn, chironomid larvae, Mesembryanthemum nodiflorum seeds and Artemia cysts were relatively more abundant in faeces, whereas polychaetes, isopods, molluscs and cestode cysticercoids were more abundant in pellets. Harder and/or larger items were thus relatively more abundant in pellets than faeces. Pellet analysis gave more emphasis to mudflat prey, and faeces to saltpan prey.

Conclusion Pellet and faecal analysis give different results for wader diet, and it is useful to combine the two methods. However, they show significant correlations both in diet range and rank abundance of prey items. Redshank diet shows much seasonal and spatial variation in southern Europe.     

Partitioning the effects of livestock farming on the diet of an aerial insectivorous passerine,the Barn Swallow Hirundo rustica

Capsule The presence of farm animals increases the amount of larger insect prey (mainly large Diptera and Coleoptera) and decreases the proportion of smaller prey (Hymenoptera).

Aims To determine the relationships between presence of farm animals and diversity of diet of nestling Barn Swallows from 52 colonies located at sites with and without livestock.

Methods Diet was determined on the basis of faecal analysis. We used two approaches to quantify livestock based on their spatial distribution – a breeding site-focused approach and a village-focused approach.

Results Our results show a relationship between the presence of livestock and the size, number and composition of insect prey detected in the diet of nestling Barn Swallows. The results from the two approaches we used in our study were broadly consistent, although effects varied according to the number and types of animal being raised. The presence of domestic animals increases the amount of larger prey (mainly larger Diptera and Coleoptera) and decreases the proportion of smaller prey (Hymenoptera species). The effect of individual livestock species, mainly pigs and poultry alone, was considerably higher than the effects of pooling livestock species from Principal Component Analysis.

Conclusion Our results imply that Barn Swallows were foraging beyond the immediate area of the farm buildings in which they nest, suggest considerable adaptability in the species' diet and further emphasize the ecological role that livestock play in providing a source of prey of a required size rather specific identity. Furthermore, a statistically significant positive effect of average mass of prey (which is a direct consequence of the presence of cattle at a breeding site) on colony size suggests that livestock farming provides a more profitable prey community, which may ultimately increase local populations of Barn Swallow.     

Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection.     

黄海中部高眼鲽的摄食及随体长的变化

对2004年1月-2005年10月在黄海中部采集的622尾高眼鲽样品的胃含物进行分析.结果表明：高眼鲽摄食的食物种类包括11类38种,其中甲壳类和瓣鳃类为优势饵料类群,共占食物相对重要性指数百分比的99%;食物中的优势饵料种类为太平洋磷虾、脊腹褐虾和樱蛤.与20世纪80年代相比,黄海高眼鲽的摄食强度下降,食物组成发生了较大的变化;鱼类不再是优势饵料类群,鳀鱼在食物中所占的比例明显下降.通过聚类分析和列联表检验等方法对高眼鲽摄食随体长的变化进行研究,结果表明：体长在51～370 mm范围内的高眼鲽的摄食强度没有显著的体长变化,但不同体长组摄食的食物种类有一定差异.＜119 mm的主要以磷虾类和底层虾类为食;体长在120～199 mm的除以磷虾类和底层虾类为主要食物外,还摄食相当比例的瓣鳃类和鱼类;＞200 mm的则主要摄食底层虾类和鱼类,磷虾类所占比例减小.     

Offshore insular variation in the diet of the Taiwanese bamboo viper Trimeresurus stejnegeri (Schmidt)

Dietary data were ascertained for 229 T. stejnegeri (snout vent length >300mm) from 36 localities throughout the main island of Taiwan and the outlying Orchid (Lanyu) and Green (Ludau) Islands. Twenty nine percent of the snakes were devoid of any prey, and of the snakes containing prey, 43% of the cases were unidentifiable. This relatively large proportion of unidentifiable prey items (observed in the hindgut) may reflect either rapid digestion of amphibian prey and/or rapid venting of feces as an evolutionary adaptation to arboreal life. Trimeresurus stejnegeri appears euryphagous, taking primarily amphibians, but additionally reptilian, mammalian and insect prey. There was no discrepancy in prey composition based on comparisons of where the prey item was recorded in the digestive tract. No sexual variation in diet composition was evident, although males were more likely to contain prey than females, indicating the utilisation of different foraging strategies on similar sympatric prey items. Variation in diet composition was observed between mainland Taiwan and offshore islands, which is most likely the result of differences in prey availability.     

Spatial variation in abundance of prey and diet of trumpeter (Pelates sexlineatus: Teraponidae) associated with Zostera capricorni seagrass meadows

Abstract The diet of juveniles of Pelates sexlineatus was examined at six estuaries, separated by tens to hundreds of kilometres, and two sites within each estuary, separated by hundreds of metres to kilometres. Fish were collected in Zostera capricorni seagrass meadows along the coast of New South Wales (Australia). Spatial variability in diet was compared with the abundance of prey. Pelates sexlineatus had a broad diet (27 different prey) but generally preferred crustaceans (harpacticoid copepods, gammarid amphipods, ostracods and tanaids), although at some sites other prey items were important (e.g. polychaetes, nematodes and foraminiferans). Composition of the diet varied among estuaries and between sites. Proportional representation of the different size of prey eaten by the three sizes of juveniles (40‐ 54 , 55–74 and 75–94 mm standard length) was similar. Fish generally preferred prey smaller than 1 mm. Abundance of prey also varied at both spatial scales. At five of the 12 sites, there was a significant correlation between abundance of prey in the seagrass meadows and abundance of prey in the diet. Variation in the composition of the diet was partly explained by spatial variation in abundance of prey. When crustaceans were not abundant in the seagrass, P. sexlineatus had a broad diet, taking both benthic and planktonic prey items. It is concluded therefore that trophic linkages between P. sexlineatus and benthic invertebrates may vary greatly with spatial scales from hundreds of metres to hundreds of kilometres, and are strongly related to availability of prey in seagrass habitats.     

Body size and tree species composition determine variation in prey consumption in a forest‐inhabiting generalist predator

Trophic interactions may strongly depend on body size and environmental variation, but this prediction has been seldom tested in nature. Many spiders are generalist predators that use webs to intercept flying prey. The size and mesh of orb webs increases with spider size, allowing a more efficient predation on larger prey. We studied to this extent the orb‐weaving spider Araneus diadematus inhabiting forest fragments differing in edge distance, tree diversity, and tree species. These environmental variables are known to correlate with insect composition, richness, and abundance. We anticipated these forest characteristics to be a principle driver of prey consumption. We additionally hypothesized them to impact spider size at maturity and expect shifts toward larger prey size distributions in larger individuals independently from the environmental context. We quantified spider diet by means of metabarcoding of nearly 1,000 A. diadematus from a total of 53 forest plots. This approach allowed a massive screening of consumption dynamics in nature, though at the cost of identifying the exact prey identity, as well as their abundance and putative intraspecific variation. Our study confirmed A. diadematus as a generalist predator, with more than 300 prey ZOTUs detected in total. At the individual level, we found large spiders to consume fewer different species, but adding larger species to their diet. Tree species composition affected both prey species richness and size in the spider''s diet, although tree diversity per se had no influence on the consumed prey. Edges had an indirect effect on the spider diet as spiders closer to the forest edge were larger and therefore consumed larger prey. We conclude that both intraspecific size variation and tree species composition shape the consumed prey of this generalist predator.     

The diet of the diadem leaf-nosed bat Hipposideros diadema: confirmation of a morphologically-based prediction of carnivory

The diet of Hipposideros diadema was investigated over three seasons at two sites on Cape York Peninsula, Australia using faecal analysis (at both sites) and prey remains identification (at one site). The possibility that this species feeds on terrestrial vertebrates, a behaviour here referred to as carnivory, was suggested by the similarity of three of its morphological features with those of eight of the 10 species of bats known to exhibit carnivory.
The study confirmed that H. diadema is at least occasionally carnivorous. Bird feathers were found in faeces at both sites; however, their occurrence was limited to a collection of faecal pellets from the early dry season at Iron Range and a single pellet from the wet season at Chillagoe. The birds taken could not be identified to family or species. Coleoptera, Lepidoptera and various orthopteroid orders were the main insect taxa in faecal pellets. The frequency of these taxa in the diet varied significantly among the three seasons at both sites. Analysis of prey remains indicated that large, hard-bodied insects, mainly cerambycid and scarabaeid beetles and acridid grasshoppers, particularly the locust Gastrimargus musicus , were taken frequently. The mean length of intact beetle elytra collected below roosts was 18.0 mm. No vertebrate material was found in prey remains. Hipposideros diadema is similar to several other bats which exhibit carnivory in preying infrequently on vertebrates. The term 'partial carnivore' or 'occasional carnivore' is suggested for these species.     

Gradients in richness and turnover of a forest passerine's diet prior to breeding: A mixed model approach applied to faecal metabarcoding data

Rather little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding, we provide the most comprehensive analysis of a passerine's diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39 site and 2° latitudinal transect in Scotland. Faecal samples were collected in 2014–2015 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon‐rich prey order. Here, we present a statistical approach for estimation of gradients and intersample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model‐based estimation of repeatability, taxon richness and Jaccard indices. We found that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.