scholarly journals DNA metabarcoding quantifies relative abundances of arthropod taxa in songbird diets: validation with camera-recorded diets

2021 ◽  
Author(s):  
Yvonne Verkuil ◽  
Marion Nicolaus ◽  
Richard Ubels ◽  
Maurine Dietz ◽  
Jelmer Samplonius ◽  
...  
Keyword(s):  
Diet Composition ◽  
Arthropod Community ◽  
Cytochrome Oxidase Subunit ◽  
Free Living ◽  
Faecal Samples ◽  
Dna Metabarcoding ◽  
Lower Intestine ◽  
Quantitative Analyses ◽  
Ecological Applications ◽  
Relative Abundances

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of faecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free-living animals. This study validates that DNA metabarcoding of faeces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify relative abundances of dietary taxa. Validation was done with the hole-nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size-adjusted counts of food items delivered to nestlings were used to approximate provided biomass of prey orders and families and subsequently nestling faeces were assessed through DNA metabarcoding. To explore potential effects of digestion, stomach and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera-recorded taxa. Overall, and in each replicate year (N = 3), the relative abundances of size-adjusted prey counts and COI read numbers correlated at R=0.85 (CI:0.68-0.94) at order level and at R=0.75 (CI:0.67-0.82) at family level. Similarity in arthropod community composition between stomach and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.

Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin

2020 ◽  
Vol 47 (6) ◽  
pp. 509
Author(s):  
Melanie J. Young ◽  
Ludovic Dutoit ◽  
Fiona Robertson ◽  
Yolanda van Heezik ◽  
Philip J. Seddon ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Diet Composition ◽  
Pcr Primers ◽  
Fish Prey ◽  
Genus Level ◽  
Faecal Samples ◽  
Significant Difference ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
Diet Assessment

Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.

Seasonal and between-year variations in the diet of harbour seals in the Moray Firth, Scotland

1996 ◽  
Vol 74 (6) ◽  
pp. 1110-1121 ◽  
Author(s):  
D. J. Tollit ◽  
P. M. Thompson
Keyword(s):  
Diet Composition ◽  
Gadus Morhua ◽  
Prey Species ◽  
Temporal Variations ◽  
Short Term ◽  
Harbour Seals ◽  
Faecal Samples ◽  
Poor Indicator ◽  
Moray Firth ◽  
Merlangius Merlangus

Predictions concerning the effect of seals upon prey stocks require an understanding of temporal variations in diet composition. This study examined the extent of between-year and seasonal variations in the diet of harbour seals (Phoca vitulina) from the Moray Firth, Scotland, between 1989 and 1992. Analyses of fish otoliths and cephalopod beaks collected from 1129 faecal samples were used to derive estimates of the contribution made by each of 35 prey species, based on the number and mass consumed. The key prey, by mass, were sand eels (Ammodytidae) (47%), lesser octopus (Eledone cirrhosa) (27%), whiting (Merlangius merlangus) (6%), flounder (Platichthys flesus) (5%), and cod (Gadus morhua) (4%). Between-year and seasonal fluctuations in the contributions of these species were observed. Sand eels contributed 86–20% in summer and 91–49% in winter. Lesser octopus contributed 0–62% in summer and < 5% in winter, whilst whiting and cod contributed 2–34% in winter and 1–4% in summer. In contrast to 1988, clupeids were unimportant in winter. Differences in diet composition appeared to reflect local changes in the availability of food, especially overwintering clupeids. Results indicate that dietary information obtained from short-term studies can be a poor indicator of subsequent diet composition and should be treated with caution when used to predict the effect of seals on prey populations.

scholarly journals Molecular survey of Besnoitia spp. (Apicomplexa) in faeces from European wild mesocarnivores in Spain. Short running title: Molecular survey of Besnoitia spp in faeces from wild carnivores.

2021 ◽  
Author(s):  
David González-Barrio ◽  
Pamela C. Köster ◽  
Miguel Habela ◽  
Manuel Martín-Pérez ◽  
José Fernández-García ◽  
...  
Keyword(s):  
Definitive Host ◽  
Red Foxes ◽  
Besnoitia Besnoiti ◽  
Free Living ◽  
Wild Carnivores ◽  
Molecular Survey ◽  
Faecal Samples ◽  
Bovine Besnoitiosis ◽  
Western Spain ◽  
Free Ranging

Numerous studies have unsuccessfully tried to unravel the definitive host of the coccidian parasite Besnoitia besnoiti. Cattle infections by B. besnoiti cause a chronic and debilitating condition called bovine besnoitiosis that has emerged in Europe during the last two decades, mainly due to limitations in its control associated to the absence of vaccines and therapeutical tools. Although the exact transmission pathway of B. besnoiti is currently unknown, it is assumed that the parasite might have an indirect life cycle with a carnivore as definitive host. Current lack of studies in wildlife might underestimate the importance of free-living species in the epidemiology of B. besnoiti. Thus, the aim of the present study is to assess the presence of Besnoitia spp. in free-ranging mesocarnivores in Spain. DNA was searched by PCR on faeces collected from wild carnivores as a first approach to determine which species could be considered as potential definitive host candidates in further research. For this purpose, a total of 352 faecal samples from 12 free-living wild carnivore species belonging to the Canidae, Felidae, Herpestidae, Mustelidae, Procyonidae, and Viverridae families were collected in seven Spanish regions. PCR testing showed that Besnoitia spp. DNA was present in four faecal samples from red foxes collected in western Spain, an area with the greatest density of extensively reared cattle and associated to high incidence of bovine besnoitiosis in the country. To date, this is the first report of a Besnoitia besnoiti-like sequence (99.57% homology) from carnivore faeces in a worldwide context. Red foxes might contribute to the epidemiology of B. besnoiti, although further studies, mostly based on bioassay, would be needed to elucidate the accuracy and extent of these interesting findings.

scholarly journals The ability of the n-alkane technique to estimate intake and diet choice of sheep

2003 ◽  
Vol 77 (2) ◽  
pp. 319-327 ◽  
Author(s):  
R.M. Lewis ◽  
A.M. Magadlela ◽  
N.S. Jessop ◽  
G.C. Emmans
Keyword(s):  
Diet Composition ◽  
Restricted Feeding ◽  
Diet Choice ◽  
Residual Standard Deviation ◽  
Extra Information ◽  
Faecal Samples ◽  
Two Component ◽  
Ad Libitum ◽  
Log Linear ◽  
Significant Diurnal Variation

AbstractThis study assessed the efficacy of the n-alkane technique to estimate intake and diet composition in animals given single foods or a choice of two. In the first experiment intakes of pelleted ryegrass and lucerne, given either alone or as a choice, were measured in lambs housed indoors in individual pens. Each of the three feeding treatments was given to 12 lambs at two degrees of maturity (0·30 and 0·45 of estimated mature sizes). The 12 lambs were constituted as three replicates of the two sexes of each of two breeds. The measured intakes were compared with those estimated using the n-alkanes C31and C33, found naturally in the foods, and C32, which was given as a dose. On the choice treatment diet composition was estimated using a non-negative least squares procedure and data on C31and C33alone. The agreement between actual and predicted intake was good:R2of 0·938 for log-linear regression with a residual standard deviation of 0·0845. Intake of lucerne when offered alone was slightly yet significantly over-predicted. The proportion of ryegrass in the diet was also accurately predicted (R2of 0·950 and residual s.d. of 0·0398). Using the data on C27and C29, in addition to that on C31and C33, gave a poorer agreement with the observed diet compositions. The low and similar levels of C27in the two foods meant that this n-alkane provided little extra information that could be used to estimate diet composition. In a second experiment faecal samples were collected every 4 hours over a 24-h period in six lambs on ad libitum, and in six lambs on a restricted quantity, of pelleted ryegrass. There was no significant diurnal variation in the ratios of either C31or C33to C32on either ad libitum or restricted feeding. The time of faecal collection within a day should not therefore affect the reliability of the predictions. The study confirmed the value of using n-alkanes in methods to determine the intake of forages by sheep, and that the time of faecal collection within the day does not affect the reliability of these predictions. The results also confirm the utility of the n-alkane method for estimating diet choice, at least with two-component mixtures.

scholarly journals Cartography of Free-Living Amoebae in Soil in Guadeloupe (French West Indies) Using DNA Metabarcoding

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 440
Author(s):  
Yann Reynaud ◽  
Célia Ducat ◽  
Antoine Talarmin ◽  
Isabel Marcelino
Keyword(s):  
West Indies ◽  
Hot Springs ◽  
Soil Samples ◽  
Microbial Pathogens ◽  
Potential Threat ◽  
Free Living ◽  
Dna Metabarcoding ◽  
Different Temperatures ◽  
Les Saintes ◽  
Enrichment Step

Free-living amoebae (FLA) are ubiquitous protists. Pathogenic FLA such as N. fowleri can be found in hot springs in Guadeloupe, soil being the origin of this contamination. Herein, we analyzed the diversity and distribution of FLA in soil using a targeted metataxonomic analysis. Soil samples (n = 107) were collected from 40 sites. DNA was extracted directly from soil samples or from FLA cultivated at different temperatures (30, 37 and 44 °C). Metabarcoding studies were then conducted through FLA 18SrDNA amplicons sequencing; amplicon sequence variants (ASV) were extracted from each sample and taxonomy assigned against SILVA database using QIIME2 and SHAMAN pipelines. Vermamoeba were detected in DNA extracted directly from the soil, but to detect other FLA an amoebal enrichment step was necessary. V. vermiformis was by far the most represented species of FLA, being detected throughout the islands. Although Naegleria were mainly found in Basse-Terre region, N. fowleri was also detected in Grand Terre and Les Saintes Islands. Acanthamoeba were mainly found in areas where temperature is approx. 30 °C. Vannella and Vahlkampfia were randomly found in Guadeloupe islands. FLA detected in Guadeloupe include both pathogenic genera and genera that can putatively harbor microbial pathogens, therefore posing a potential threat to human health.

scholarly journals Exploration and prevalence of gastrointestinal worm in buffalo from West Java, Central Java, East Java and Lombok, Indonesia

2016 ◽  
Vol 1 (1) ◽  
pp. 1-15
Author(s):  
Wahyudin Abd. Karim ◽  
Achmad Farajallah ◽  
Bambang Suryobroto
Keyword(s):  
Gastrointestinal Parasites ◽  
Free Living ◽  
West Java ◽  
Mcmaster Technique ◽  
Central Java ◽  
Total Prevalence ◽  
Faecal Samples

The studies of parasites in buffaloes have not been widely explored. The aim of the present study was to explore the prevalence of gastrointestinal worm infection in buffaloes. The fresh faecal samples were collected from 89 buffaloes and observed by a modified McMaster technique. The faecal of buffaloes were collected in Bogor, Demak, East Java, and Lombok. The results of identification on gastrointestinal parasites show that there were one cestode and eight nematode. The total prevalence and infestation of cestodes and nematodes was found highest in Bogor. The prevalence and infestation of differences in geographical conditions were found highest in Bogor. The prevalence of gastrointestinal worm in males were highest than female, whereas for larger was found in females. The prevalence of gastrointestinal worms was found at age 1 year, whereas a larger infestation was found at the age of 1-5 years. The calculation of FEC in Bogor was 840 EPG, in Demak 375 EPG, in East Java 570 EPG and in Lombok 13 EPG. This study informed that there were nine genera of gastrointestinal worm found in Java and five genera in Lombok. Types larvae were found six i.e Strongyloides, Haemonchus, Cooperia, Oesophagostomum, Bunostomum and free living larvae.

scholarly journals Parasites of Myocastor coypus – a Comparison in Farm Animals and Their Feral Counterparts

2018 ◽  
Vol 49 (1) ◽  
pp. 21-25
Author(s):  
S. Nechybová ◽  
I. Langrová ◽  
E. Tůmová
Keyword(s):  
Czech Republic ◽  
Nematode Species ◽  
Farm Animals ◽  
Myocastor Coypus ◽  
Free Living ◽  
The Czech Republic ◽  
Faecal Samples ◽  
Nematode Eggs ◽  
Mcmaster Method ◽  
Feral Animals

Abstract The parasitic status in the coypus (nutrias) Myocastor coypus, both farm-bred or free-living on river banks in the Czech Republic, was determined. Faecal samples were collected from 200 coypus originating from 11 farms (farm-bred animals) and from 20 individuals living at 14 natural localities (feral animals). Faeces were examined for nematode eggs and coccidian oocysts using the McMaster method. The evaluation of faeces from farm-bred coypus indicated infection with the following parasites: Trichuris sp., Strongyloides sp., Trichostrongylus sp., Eimeria seidelli, Eimeria nutriae, Eimeria coypi, and Eimeria myopotami. Free-living feral rodents harboured Eimeria nutriae, E. coypi, Strongyloides sp. and in one case also Trichuris sp. An additional visceral examination of 20 coypus originating from five farms revealed two nematode species in the gastrointestinal tracts, namely Trichuris myocastoris and Strongyloides myopotami. The study indicated that feral coypus are far less parasitized than their captive counterparts.

Evaluating the impacts of metabarcoding primer selection on DNA characterization of diet in an aerial insectivore, the Purple Martin

The Auk ◽  
2021 ◽  
Author(s):  
Anna M Forsman ◽  
Brandon D Hoenig ◽  
Stephanie A Gaspar ◽  
Jason D Fischer ◽  
Joe Siegrist ◽  
...  
Keyword(s):  
Diet Composition ◽  
Foraging Ecology ◽  
Molecular Technique ◽  
Insectivorous Birds ◽  
Alpha And Beta Diversity ◽  
Primer Selection ◽  
Aerial Insectivore ◽  
Dna Metabarcoding ◽  
The Usa ◽  
Primer Sets

Abstract DNA metabarcoding is a molecular technique frequently used to characterize diet composition of insectivorous birds. However, results are sensitive to methodological decisions made during sample processing, with primer selection being one of the most critical. The most frequently used DNA metabarcoding primer set for avian insectivores is ZBJ. However, recent studies have found that ZBJ produces significant biases in prey classification that likely influence our understanding of foraging ecology. A new primer set, ANML, has shown promise for characterizing insectivorous bat diets with fewer taxonomic biases than ZBJ, but ANML has not yet been used to study insectivorous birds. Here, we evaluate the ANML primer set for use in metabarcoding of avian insectivore diets through comparison with the more commonly used ZBJ primer set. Fecal samples were collected from both adult and nestling Purple Martins (Progne subis subis) at 2 sites in the USA and 1 site in Canada to maximize variation in diet composition and to determine if primer selection impacts our understanding of diet variation among sites. In total, we detected 71 arthropod prey species, 39 families, and 10 orders. Of these, 40 species were uniquely detected by ANML, whereas only 11 were uniquely detected by ZBJ. We were able to classify 54.8% of exact sequence variants from ANML libraries to species compared to 33.3% from ZBJ libraries. We found that ANML outperformed ZBJ for PCR efficacy, taxonomic coverage, and specificity of classification, but that using both primer sets together produced the most comprehensive characterizations of diet composition. Significant variation in both alpha- and beta-diversity between sites was found using each primer set separately and in combination. To our knowledge, this is the first published metabarcoding study using ANML primers to describe avian diet, and also the first to directly compare results returned by ANML and ZBJ primer sets.

scholarly journals Endoparasitic Insights of Free-Living Fin (Balaenoptera physalus), Humpback (Megaptera novaeangliae) and North Atlantic Right Whales (Eubalaena glacialis) from Eastern Canadian Waters

2020 ◽  
Author(s):  
S. Kleinertz ◽  
L. M. R. Silva ◽  
S. Köpper ◽  
C. Hermosilla ◽  
C. Ramp
Keyword(s):  
North Atlantic ◽  
Eubalaena Glacialis ◽  
Balaenoptera Physalus ◽  
Free Living ◽  
Baleen Whales ◽  
Non Invasive ◽  
Faecal Samples ◽  
Zoonotic Parasite ◽  
North Atlantic Right Whales ◽  
Parasite Infections

Abstract Purpose To date, little is still known on parasite infections affecting free-living large whale populations worldwide. Data presented should be considered as a baseline study for future monitoring surveys on endoparasites affecting whales, thereby enhancing investigations on impacts of zoonotic parasitoses not only on vulnerable or endangered baleen whale population health but also on public health. Methods The presented study is a first report on gastrointestinal parasites infecting different free-living baleen whales inhabiting East Canadian waters using non-invasive methods. Individual faecal samples from fin (n = 3; Balaenoptera physalus), humpback (n = 4; Megaptera novaeangliae) and North Atlantic right whales (n = 1; Eubalaena glacialis) were collected without animal disturbance, within their natural habitats on an ecological expedition during annual surveys in summer 2017. Faecal samples were assessed by standardized diagnostic methods, such as sodium acetate acetic formalin (SAF) technique, carbol fuchsin-stained faecal smears, Giardia/Cryptosporidium coproantigen ELISAs and were applied for further identification. Results Parasitological infections included three different potentially zoonotic parasite species, one protozoa (Entamoeba spp.) and two metazoans (Diphyllobothriidae gen. sp., Ascaridida indet.). No positive Giardia/Cryptosporidium coproantigen ELISA could be found in the studied whales. Conclusion This study adds to the current knowledge of intestinal and zoonotic parasite infections of vulnerable to partly endangered free-ranging baleen whales. Only few or no parasitological studies exist for these whale species, usually dealing with only one dead specimen. We call for more research in this field especially for the importance of conservation of free-living marine mammals using non-invasive methods.

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