scholarly journals Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.)

2021 ◽  
Author(s):  
Karen L. Bell ◽  
Kathryn L. Batchelor ◽  
Matt Bradford ◽  
Adam McKeown ◽  
Stewart L. Macdonald ◽  
...  
Keyword(s):  
Diet Analysis ◽  
Flying Foxes ◽  
Dna Metabarcoding

scholarly journals MEDITERATRI project - assessing the trophic ecology of predatory arthropods in Mediterranean agriculture via DNA metabarcoding diet analyses

2019 ◽  
Vol 2 ◽  
Author(s):  
Lucija Šerić Jelaska ◽  
Barbara Anđelić ◽  
Mišel Jelić ◽  
Tomislav Kos
Keyword(s):  
Pest Management ◽  
Trophic Ecology ◽  
Arable Land ◽  
Carabid Beetles ◽  
Diet Analysis ◽  
Gut Contents ◽  
Dna Metabarcoding ◽  
Potential Benefits ◽  
Diet Analyses ◽  
Predatory Arthropods

A type of management and the use of pesticides in arable land may negatively affect a range of soil biota and thus their food webs important for ecosystem functioning. By analysing trophic interactions we could reveal the extent of potential benefits that certain organisms can provide in biocontrol and maintaining healthy ecosystems. To evaluate the role of predatory arthropods within olive orchards and vineyards under Integrated Pest Management (IPM) and Ecological Pest Management (EPM) we collected carabid beetles together with other dominant predatory arthropods in the field (e.g. ladybugs, antlions, spiders, centipedes) and subdued the individuals to molecular gut content analyses using NGS. DNA metabarcoding diet analysis approach allowed detecting a wide variety of taxa from gut contents of the predators. In addition, using ICP-MS and LC-MS/MS we quantified Cu, pesticides and its residues in soil and animals representing different trophic guilds. Since concentrations of some toxic compounds detected in carabids body were negatively correlated with those in the soil, we aim to identify a potential vector for possible transfer of toxicants to general predators via predation. The results contribute to the risk assessment of proliferation of detected chemical compounds including copper in the ecosystem and to the knowledge on the overall field sustainability of predatory invertebrates to maximize their role in pest control. The study was conducted under the project activity of HRZZ – Mediteratri.

A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare

2018 ◽  
Vol 88 ◽  
pp. 31-42 ◽  
Author(s):  
Maria Buglione ◽  
Valeria Maselli ◽  
Daniela Rippa ◽  
Gabriele de Filippo ◽  
Martina Trapanese ◽  
...  
Keyword(s):  
Pilot Study ◽  
Diet Analysis ◽  
Non Invasive ◽  
Dna Metabarcoding

scholarly journals Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding

2021 ◽  
Author(s):  
Melissa R. Ingala ◽  
Nancy B. Simmons ◽  
Claudia Wultsch ◽  
Konstantinos Krampis ◽  
Kaiya L. Provost ◽  
...  
Keyword(s):  
Diet Analysis ◽  
Fecal Dna ◽  
Dna Metabarcoding ◽  
Neotropical Bats ◽  
Molecular Diet Analysis

scholarly journals Using DNA metabarcoding to decipher the diet plant component of mammals from the Eastern Mediterranean region

2021 ◽  
Vol 5 ◽  
Author(s):  
Liliane Boukhdoud ◽  
Carole Saliba ◽  
Lillian D. Parker ◽  
Nancy Rotzel McInerney ◽  
Rhea Kahale ◽  
...  
Keyword(s):  
Eastern Mediterranean ◽  
Species Conservation ◽  
Eastern Mediterranean Region ◽  
Diet Analysis ◽  
Mammal Species ◽  
Plant Component ◽  
Dna Metabarcoding ◽  
Conservation Projects ◽  
Plant Families ◽  
Plant Animal Interactions

Longevity of species populations depends largely on interactions among animals and plants in an ecosystem. Predation and seed dispersal are among the most important interactions necessary for species conservation and persistence, and diet analysis is a prerequisite tool to evaluate these interactions. Understanding these processes is crucial for identifying conservation targets and for executing efficient reforestation and ecological restoration. In this study, we applied a scat DNA metabarcoding technique using the P6-loop of the trnL (UAA) chloroplastic marker to describe the seasonal plant diet composition of 15 mammal species from a highly biodiverse Lebanese forest in the Eastern Mediterranean. We also recovered plant seeds, when present, from the scats for identification. The mammal species belong to 10 families from 5 different orders. More than 133 plant species from 54 plant families were detected and identified. Species from the Rosaceae, Poaceae, Apiaceae, Fabaceae, Fagaceae and Berberidaceae families were consumed by the majority of the mammals and should be taken into consideration in future reforestation and conservation projects. Our results showed that the DNA metabarcoding approach provides a promising method for tracking the dietary plant components of a wide diversity of mammals, yielding key insights into plant-animal interactions inside Lebanon’s forests.

scholarly journals Use of DNA metabarcoding of bird pellets in understanding raptor diet on the Qinghai-Tibetan Plateau of China

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Charlotte E. Hacker ◽  
Brandon D. Hoenig ◽  
Liji Wu ◽  
Wei Cong ◽  
Jingjing Yu ◽  
...  
Keyword(s):  
Niche Partitioning ◽  
Bird Species ◽  
Diet Analysis ◽  
Sample Type ◽  
Plateau Pika ◽  
Dna Metabarcoding ◽  
Eagle Owl ◽  
Dietary Niche ◽  
Saker Falcon ◽  
Expected Values

Abstract Background Diet analysis is essential to understanding the functional role of large bird species in food webs. Morphological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity. DNA metabarcoding has the ability to circumvent these issues, but has yet to be done. Methods We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces, China. Results We detected four raptor species [Eurasian Eagle Owl (Bubo bubo), Saker Falcon (Falco cherrug), Steppe Eagle (Aquila nipalensis), and Upland Buzzard (Buteo hemilasius)] and 11 unique prey species across 10 families and 4 classes. Mammals were the greatest detected prey class with Plateau Pika (Ochotona curzoniae) being the most frequent. Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479, respectively, while expected values were 1.312 ± 0.266 and 0.485 ± 0.086. For Eurasian Eagle Owl, observed values were 1.202 and 0.565, while expected values were 1.502 ± 0.340 and 0.580 ± 0.114. Interspecific dietary niche partitioning between the two species was not detected. Conclusions Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species. More work is needed to understand how raptor diets vary locally, and the mechanisms that enable exploitation of similar dietary resources. This approach has wide ranging applicability to other birds of prey, and demonstrates the power of using DNA metabarcoding to study species noninvasively.

scholarly journals Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

2019 ◽  
Author(s):  
Aimee Massey ◽  
Gretchen Roffler ◽  
Tessa Vermeul ◽  
Jennifer Allen ◽  
Taal Levi
Keyword(s):  
Dna Sequences ◽  
Rare Species ◽  
Prey Species ◽  
Castor Canadensis ◽  
Black Bear ◽  
Diet Analysis ◽  
High Rate ◽  
Diet Diversity ◽  
Full Diet ◽  
Dna Metabarcoding

AbstractDNA metabarcoding has become a powerful technique for identifying species and profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and correct mistaken identification error in diet studies. However, the extent to which molecular approaches agree with traditional approaches is unknown for many species. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be overestimated with mechanical sorting methods because of the failure to account for the full diet diversity of these wolves. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves appear to have a more diverse diet with greater occurrence of rare species than previously described including 14 prey species that contribute to wolf diet. Metabarcoding is an effective method for profiling carnivore diet and enhances our knowledge concerning the full diversity of wolf diets, even in the extremely wet conditions of southeast Alaska, which can lead to DNA degradation. Given the increasingly efficient and cost-effective nature of collecting eDNA, we recommend incorporating these molecular methods into field-based projects to further examine questions related to increased use of alternate prey coinciding with changes in abundance of primary prey and habitat alteration.

scholarly journals Prey partitioning between sympatric canid species revealed by DNA metabarcoding

2019 ◽  
Author(s):  
Yue Shi ◽  
Yves Hoareau ◽  
Ellie Reese ◽  
Samuel K. Wasser
Keyword(s):  
Trophic Interactions ◽  
Diet Composition ◽  
Niche Overlap ◽  
Diet Analysis ◽  
Apex Predators ◽  
Fine Grained ◽  
Carnivore Species ◽  
Snowshoe Hares ◽  
Dna Metabarcoding ◽  
Canid Species

AbstractThe recovery of apex predators relies on restoring the full suite of trophic interactions within the ecosystem. Diet analysis with DNA metabarcoding technology can help deliver insights into these trophic interactions with fine-grained resolution. The recovery of wolves in Washington state offers an excellent case to study the trophic cascade impacts of the apex predators on the ecosystem and explore prey partitioning between sympatric canid species. We used DNA metabarcoding technology on scats to characterize the diet composition and its spatiotemporal variations of wolves and coyotes and quantified the diet niche overlap between these two canid species in northeastern Washington. In total, 19 different prey taxa were detected. Frequency of occurrence data showed that wolves primarily preyed upon deer (Odocoileus sp.) (47.47%) and moose (Alces alces) (42.42%). Coyotes also consumed moose (30.10%) and deer (21.36%), but snowshoe hares (Lepus americanus) were the most common prey (61.17%) in their diet. There were significant spatial variations in the wolf diet composition (p = 0.001) with wolves in the Dirty Shirt pack range consuming more moose (71.43%). Coyotes showed significant spatial and temporal dietary variations (season: p = 0.037; pack: p = 0.003; pack:season p = 0.043). Our data suggested that coyotes use ungulate carrion subsidies from wolves as food resources. DNA metabarcoding with fecal DNA provides an excellent noninvasive tool to characterize diet profile at the fine-grained level and can be applied to other carnivore species to help understand the impacts of recovery of apex predators on the local ecosystems.

scholarly journals DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion ( Neophoca cinerea )

2017 ◽  
Vol 7 (14) ◽  
pp. 5435-5453 ◽  
Author(s):  
Tina E. Berry ◽  
Sylvia K. Osterrieder ◽  
Dáithí C. Murray ◽  
Megan L. Coghlan ◽  
Anthony J. Richardson ◽  
...  
Keyword(s):  
Diet Analysis ◽  
Sea Lion ◽  
Neophoca Cinerea ◽  
Australian Sea Lion ◽  
Dna Metabarcoding

Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

2020 ◽  
Vol 29 (16) ◽  
pp. 3143-3153
Author(s):  
Carla Martins Lopes ◽  
Marta De Barba ◽  
Frédéric Boyer ◽  
Céline Mercier ◽  
Daniel Galiano ◽  
...  
Keyword(s):  
Niche Overlap ◽  
Diet Analysis ◽  
Subterranean Rodents ◽  
Ecological Specialization ◽  
Dna Metabarcoding

A pilot study on the use of DNA metabarcoding for diet analysis in a montane amphibian population from North Africa

2021 ◽  
pp. 1-7
Author(s):  
Ana Pereira ◽  
Mohamed Amine Samlali ◽  
Abderrahim S’Khifa ◽  
Tahar Slimani ◽  
D James Harris
Keyword(s):  
Pilot Study ◽  
North Africa ◽  
Diet Analysis ◽  
Amphibian Population ◽  
Dna Metabarcoding
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