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1.
In this study, the results of conventional stomach‐content analysis are compared with the recent DNA metabarcoding approach on faeces to identify fish species consumed by non‐native European catfish Silurus glanis in the Garonne River (south‐western France), with a special emphasis on anadromous prey. Fourteen prey species were identified in the stomach contents or faeces, including four anadromous fish species. Despite higher intestine than stomach emptiness, more species were identified through faecal analysis (11 of 14) than through stomach‐content analysis (five of 14) suggesting that DNA metabarcoding on faeces is an efficient, non‐intrusive technique to study the diet of predatory fishes.  相似文献   

2.
DNA metabarcoding analysis for gut contents has been shown to compensate the disadvantage of traditionally morphological identification and offer higher resolution of prey items in an efficient way. Holland's carp (Spinibarbus hollandi) is a freshwater fish native to southern and eastern Taiwan. In the past two decades, this species has been introduced as a sport fish into the river basins of northern and western Taiwan. The large body size and active predation make it a potential threat for native fishes, but which native species are preyed by Holland's carp remains unknown. In this study, the diet from the gut contents of Holland's carp from the Zhonggang River, an invaded basin, was examined using DNA metabarcoding from 51 individuals and by morphological examinations on 140 samples. Detritus of plants were found in 83.6% samples (117 individuals). Twenty fish species of seven families were identified by DNA metabarcoding, including species of all water layers. Taiwan torrent carp (Acrossocheilus paradoxus) and Rhinogobius spp. are the most common prey items. Based on the results of this study, Holland's carp is considered an opportunistic omnivore because of its diverse diet items, which is an important trait for successful invasive fish species. The population decline of Opsariichthys pachycephalus may not result from the invasion of Holland's carps. Nonetheless, the time lag between successful invasion and the samplings of this study may be a concern because the population size of O. pachycephalus may have declined and become difficult to prey. The Holland's carps consumed the least species in winter; nonetheless, the occurrence frequencies of preys among seasons were not significantly different probably because of limited temperature fluctuation. The smallest Holland's carps consumed the least prey species compared to other size categories, similar to the relationship of prey species number to size of invasive largemouth bass (Micropterus salmoides).  相似文献   

3.
Ecological theory suggests that the coexistence of species is promoted by the partitioning of available resources, as in dietary niche partitioning where predators partition prey. Yet, the mechanisms underlying dietary niche partitioning are not always clear. We used fecal DNA metabarcoding to investigate the diets of seven nocturnal insectivorous bird and bat species. Low diet overlap (2%–22%) supported resource partitioning among all species. Differences in diet corresponded with species identity, prey detection method, and foraging behavior of predators. Insects with ultrasonic hearing capabilities were consumed significantly more often by birds than bats, consistent with an evolved avoidance of echolocating strategies. In turn, bats consumed a greater proportion of noneared insects such as spruce budworms. Overall, our results suggest that evolutionary interactions among bats and moths translate to dietary niche partitioning and coexistence among bats and nocturnal birds.  相似文献   

4.
Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behaviour – yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual‐level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators.  相似文献   

5.
Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genus Ctenomys distributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.  相似文献   

6.
Recent advances in molecular techniques allow us to resolve the diet of unstudied taxa. Odonates are potentially important top‐down regulators of many insects. Yet, to date, our knowledge of odonate prey use is based mainly on limited observations of odonates catching or eating their prey. In this study, we examine the potential use of metabarcoding in establishing the diet of three adult odonate species (Lestes sponsa, Enallagma cyathigerum, and Sympetrum danae) at a site in southwestern Finland. To this purpose, we compared three different methods for extracting DNA from fecal samples: the Macherey‐Nagel Nucleospin XS kit, a traditional salt extraction, and the Zymo Research Fecal Microprep kit. From these extracts, we amplified group‐specific mitochondrial markers (COI and 16S rRNA) from altogether 72 odonate individuals, and compared them to comprehensive reference libraries. The three odonate species show major overlap in diet, with no significant differences between individuals of different size and/or gender, reflecting opportunistic foraging of adult odonates. Of a total of 41 different prey species detected, the most frequently consumed ones were Diptera, with additional records of six other orders. Based on our data, the best DNA extraction method is the traditional salt extraction, as it provides the most information on prey content while also being the most economical. To our knowledge, this is the first study to resolve the species‐level diet of adult odonates. Armed with the appropriate methodological caveats, we are ready to examine the ecological role of odonates in both terrestrial and aquatic food webs, and in transferring subsidies between these two realms.  相似文献   

7.
Environmental conditions in the Chukchi Sea are changing rapidly and may alter the abundance and distribution of marine species and their benthic prey. We used a metabarcoding approach to identify potentially important prey taxa from Pacific walrus (Odobenus rosmarus divergens) fecal samples (n = 87). Bivalvia was the most dominant class of prey (66% of all normalized counts) and occurred in 98% of the samples. Polychaeta and Gastropoda occurred in 70% and 62% of the samples, respectively. The remaining nine invertebrate classes comprised <21% of all normalized counts. The common occurrence of these three prey classes is consistent with examinations of walrus stomach contents. Despite these consistencies, biases in the metabarcoding approach to determine diet from feces have been highlighted in other studies and require further study, in addition to biases that may have arisen from our opportunistic sampling. However, this noninvasive approach provides accurate identification of prey taxa from degraded samples and could yield much-needed information on shifts in walrus diet in a rapidly changing Arctic.  相似文献   

8.
Understanding carnivores’ diet is key to understanding their adaptability in a rapidly changing world. However, studying diet of large carnivores is difficult due to their elusive nature. In this study, we performed DNA metabarcoding analyses of 82 putative leopard scats collected from two distinct, but connected, habitat types (rainforest and grassland) in the Udzungwa Mountains, Tanzania. Two mitochondrial markers were used to identify predator and prey. Metabarcoding confirmed that 60 of the collected scats (73%) originated from leopards, and nineteen mammalian prey DNA sequences were identified to species. Using prey size correction factors for leopards, and covariates on habitat type and prey ecology, we investigated whether differences in leopard dietary composition were detectable between habitats. We found that leopards in grassland consumed a larger mean prey size compared with leopards in rainforest. Small prey (<19 kg) constituted >70% of the biomass consumed by leopards in rainforest, while large prey (≥80 kg) were only eaten in grassland. Arboreal species constituted 50% of the biomass consumed by rainforest leopards. Our results highlight the importance of arboreal species in their diet. From a management perspective, we suggest continued protection of all prey species in the protected areas to prevent human–wildlife conflicts.  相似文献   

9.
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.  相似文献   

10.
Knowledge of zooplankton in situ diet is critical for accurate assessment of marine ecosystem function and structure, but due to methodological constraints, there is still a limited understanding of ecological networks in marine ecosystems. Here, we used DNA‐metabarcoding to study trophic interactions, with the aim to unveil the natural diet of zooplankton species under temporal variation of food resources. Several target consumers, including copepods and cladocerans, were investigated by sequencing 16S rRNA and 18S rRNA genes to identify prokaryote and eukaryote potential prey present in their guts. During the spring phytoplankton bloom, we found a dominance of diatom and dinoflagellate trophic links to copepods. During the summer period, zooplankton including cladocerans showed a more diverse diet dominated by cyanobacteria and heterotrophic prey. Our study suggests that copepods present trophic plasticity, changing their natural diet over seasons, and adapting their feeding strategies to the available prey spectrum, with some species being more selective. We did not find a large overlap of prey consumed by copepods and cladocerans, based on prey diversity found in their guts, suggesting that they occupy different roles in the trophic web. This study represents the first molecular approach to investigate several zooplankton–prey associations under seasonal variation, and highlights how, unlike other techniques, the diversity coverage is high when using DNA, allowing the possibility to detect a wide range of trophic interactions in plankton communities.  相似文献   

11.
The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide‐ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in <25% of samples. Some of the taxa identified, such as fish, sharks and rays, clarify previous knowledge of sea lion prey, and some, such as eel taxa and two gastropod species, represent new dietary insights. Even with modest sample sizes, a spatial analysis of taxa and operational taxonomic units found within the scat shows significant differences in diet between many of the sample locations and identifies the primary taxa that are driving this variance. This study provides new insights into the diet of this endangered predator and confirms the efficacy of DNA metabarcoding of scat as a noninvasive tool to more broadly define regional biodiversity.  相似文献   

12.
豹猫(Prionailurus bengalensis)作为北京地区的顶级食肉动物,对于维持食物网结构和生态系统稳定性起到重要的生态作用。对于捕食动物食物构成研究,较为简便的方法是粪样内容物检视法,而粪样残余物DNA鉴定技术具有更为准确细致的优势,但也存在不足,探索不同方法的优势互补,将有助于提高技术应用成效。本研究利用DNA宏条形码技术与粪样内容物分析法,对采集自北京市4个自然保护区的71份豹猫粪样进行食物构成分析,比较两种分析方法的特点,了解豹猫的食物资源利用状况。结果显示,DNA宏条形码技术共鉴别出36种猎物,来自10目22科,4个保护区的豹猫食性具有显著差异,百花山、松山、云蒙山保护区的豹猫食物种类的出现比率均以小型哺乳类为主,其中对鼠类的捕食比例最高,对鸟类的捕食次之,而分布于云峰山保护区的豹猫对鸟类捕食比例最高,对鼠类的捕食次之。粪样内容物分析法鉴别出9类猎物,其中包括昆虫和植物两种DNA宏条形码技术未检出的食物,4个保护区的豹猫食物均以鼠类和鸟类为主,且最多检测出鼠类数量为3只、鸟类2只,次要食物则为植物和昆虫。两种方法均显示北社鼠(Niviventer confucia...  相似文献   

13.
During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.  相似文献   

14.
15.
In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22‐day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)‐ and diatom (Skeletonema marinoi)‐dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow‐through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon‐specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod–prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances.  相似文献   

16.
Optimal foraging theory suggests that avian parents should prefer the most energetically efficient (largest) prey items when delivering food to offspring at a central place. However, during periods of high demand, selectivity of prey may decline, leading to the delivery of smaller and/or less nutritious items. We compared foraging trade‐offs between great tits (Parus major) which had a wider feeding niche than blue tits (Cyanistes caeruleus). We also compared the foraging efficiency of cross‐fostered young, which had learned the spatial foraging niche and prey size of the foreign species, to that of control conspecifics. Mean delivery rates did not differ between control and cross‐fostered parents of either species but as delivery rates increased, prey size declined for both species and both treatment groups. However, across the range of increasing delivery rates, parents were able to increase the total biomass of prey delivered. Cross‐fostering did not alter the proportion of different prey taxa in the diet, but cross‐fostered birds shifted the size of the prey taken to that of their foster species. Consistent with their broader feeding niche, great tits, but not blue tits, incorporated more unpalatable items (flies) as delivery rates increased. Although great tits foraged less efficiently in the blue tit niche, paradoxically, blue tits seem to deliver more prey biomass when foraging in the great tit niche.  相似文献   

17.
Sympatric cryptic species, characterized by low morphological differentiation, pose a challenge to understanding the role of interspecific competition in structuring ecological communities. We used traditional (morphological) and novel molecular methods of diet analysis to study the diet of two cryptic bat species that are sympatric in southern England (Plecotus austriacus and P. auritus) (Fig. 1). Using Roche FLX 454 (Roche, Basel, CH) high-throughput sequencing (HTS) and uniquely tagged generic arthropod primers, we identified 142 prey Molecular Operational Taxonomic Units (MOTUs) in the diet of the cryptic bats, 60% of which were assigned to a likely species or genus. The findings from the molecular study supported the results of microscopic analyses in showing that the diets of both species were dominated by lepidopterans. However, HTS provided a sufficiently high resolution of prey identification to determine fine-scale differences in resource use. Although both bat species appeared to have a generalist diet, eared-moths from the family Noctuidae were the main prey consumed. Interspecific niche overlap was greater than expected by chance (O(jk) = 0.72, P < 0.001) due to overlap in the consumption of the more common prey species. Yet, habitat associations of nongeneralist prey species found in the diets corresponded to those of their respective bat predator (grasslands for P. austriacus, and woodland for P. auritus). Overlap in common dietary resource use combined with differential specialist prey habitat associations suggests that habitat partitioning is the primary mechanism of coexistence. The performance of HTS is discussed in relation to previous methods of molecular and morphological diet analysis. By enabling species-level identification of dietary components, the application of DNA sequencing to diet analysis allows a more comprehensive comparison of the diet of sympatric cryptic species, and therefore can be an important tool for determining fine-scale mechanisms of coexistence.  相似文献   

18.
Globally urban areas are expanding rapidly and this usually has negative effects on biodiversity. Despite this, some species manage to persist in urban areas, as is the case with African Crowned Eagles Stephanoaetus coronatus in KwaZulu-Natal, South Africa. As relatively little is known about African Crowned Eagle nestling diet, especially about how it changes with nestling age, we investigated this with nest camera-traps. We analysed temporal changes in prey composition and biomass delivery during the nestling stage. We also recorded which adults provisioned and attended the nest. The main prey fed to nestlings were Rock Hyrax Procavia capensis and Hadeda Ibis Bostrychia hagedash. Adult males did most of the food provisioning, especially at the start of the nestling period. We found a decrease in total prey number and biomass with nestling age. This may be caused by changing requirements of nestlings. Furthermore, delivering fewer prey at later nestling stages may be a facilitating mechanism to enhance fledging of the nestling. Although the total number of prey brought to the nest decreased, we found an increase in numbers of Vervet Monkey Chlorocebus pygerythrus in the diet with nestling age. This indicated an increase in larger prey being delivered to the nests as the nestling aged. We suggest that this could be caused by increased participation in hunting by the larger female as her nest attendance time decreased as the nestling aged. We conclude with emphasising the importance of protecting the Durban Metropolitan Open Space System (D’MOSS) zones for the persistence of this Near Threatened raptor species, and populations of its prey in urban areas for its breeding success.  相似文献   

19.
Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red‐shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~10 000 (0.014%) and ~44 000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast ‘barcodes’ for angiosperms. The results were compared with ‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.  相似文献   

20.
Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the necessity to understand their diet for conservation, the trophic ecology of many arachnid species has not been sufficiently studied. In the case of the wandering spider, Phoneutria boliviensis F. O. Pickard‐Cambridge, 1897, only field and laboratory observational studies on their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of P. boliviensis. By DNA metabarcoding of the cytochrome c oxidase subunit I (COI), we detected and identified 234 prey items (individual captured by the spider) belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of P. boliviensis with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that P. boliviensis feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera, and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences were also observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of P. boliviensis, particularly when predation records in the field cannot be established or quantified using direct observation.  相似文献   

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