Evaluation of plant contamination in metabarcoding diet analysis of a herbivore

Exploring winter diet, gut microbiota and parasitism in caribou using multi-marker metabarcoding of fecal DNA

In conservation strategies, getting precise and repeatable information on the species' diet and health without relying on invasive or laborious methods is challenging. Here, we developed an efficient and non-invasive workflow for the sequencing and analysis of four taxonomic markers from fecal DNA to characterize the gut microbiota, parasites, and plants and lichens composing the winter diet of caribou (Rangifer tarandus), Canada's most iconic endangered species. Sequencing of the 18S rRNA gene of eukaryotes from seven locations in Manitoba and Saskatchewan, Canada, allowed for the detection of five genera of parasites in caribou feces (including Nematodirella and Parelaphostrongylus) with variable frequency of occurrence depending on sampling location and sex. Our workflow also revealed a rich winter plant and lichen diet in caribou, with respectively 29 and 18 genera identified across all samples through plant and fungal ITS2 sequencing. Relationships between the gut microbiota and both the diet and parasite richness were also identified. Of note, the Central Saskatchewan sampling location was characterized by a clearly distinct gut microbiota which could be linked to an epiphytic lichen-rich diet. Overall, our results showed the potential of this multi-marker DNA metabarcoding workflow as an efficient tool to provide insights into the species biology and ecology.

Differences in Gut Microbes Across Age and Sex Linked to Metabolism and Microbial Stability in a Hibernating Mammal

The gut microbiome has a well-documented relationship with host fitness, physiology, and behavior. However, most of what is known comes from captive animals where diets and environments are more homogeneous or controlled. Studies in wild populations that experience dynamic environments and have natural life history variation are less common but are key to understanding the drivers of variation in the gut microbiome. Here we examine a wild population of yellow-bellied marmots (Marmota flaviventer), an obligate winter hibernator, to quantify multivariate associations between host-associated factors (e.g., age, sex, environmental harshness, and social behavior) and gut microbial composition. Across 5 years and 143 individuals, we found that males had a higher relative abundance of microbes associated with mass gain and cellulose digestion, which suggests a metabolic investment in mass gain (such as phylum Firmicutes and family Lachnospiraceae). By contrast, females had higher relative abundances of microbes associated with inflammation and metabolism (from microbial groups such as Tenericutes and Ruminococcus), possibly reflecting the importance of lactation and offspring investment. Post hoc analyses of lactating females showed a negative relationship with the abundance of microbes associated with mass gain but a positive relationship with microbes associated with metabolic energy, suggesting a trade-off between investment in pups and maternal mass gain. Older animals also had reduced Proteobacteria relative abundance, a phylum associated with reduced inflammation. Results demonstrate that sex and age-based traits, not sociality or environmental harshness, are associated with microbe-mediated metabolism and inflammation in a wild, hibernating mammal.

Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea

This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.

Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.

Noise pollution alters the diet composition of invertebrate consumers both in and beyond a noise-exposed grassland ecosystem

Anthropogenic noise is ubiquitous globally. However, we know little about how the impacts of noise alter fundamental ecosystem properties, such as resource consumption by invertebrate consumers. Using experimental noise manipulation and faecal DNA metabarcoding, we assessed how the direct and cross-trophic indirect effects of noise altered the dietary richness and specializations of omnivorous grasshoppers in a grassland ecosystem. We found that the experimental noise treatment expanded grasshoppers' dietary richness and resulted in dietary generalizations in both noise-exposed and adjacent relatively quieter areas. Unexpectedly, however, these dietary changes were primarily explained by the direct effect of noise not only in the noise-exposed areas but also in the adjacent quieter areas and were relaxed by indirect effects of noise such as reduced birds and predation risk and increased grasshoppers. Our work suggests that noise pollution can be key in explaining the variation of invertebrate consumers' diets across a gradient of noise-exposed environments.

Variation in diet of desert bighorn sheep around parturition: Tradeoffs associated with parturition

Selection of forage and habitats is driven by nutritional needs of individuals. Some species may sacrifice nutritional quality of forage for the mother in favor of safety of offspring (risk-averse strategy), immediately following parturition. We studied diet quality and forage selection by bighorn sheep before and following parturition to determine how nutritional demands associated with rearing offspring influenced forage acquisition. We used desert bighorn sheep, Ovis canadensis nelsoni, to investigate that potential tradeoff. We captured and radio-collared female bighorn sheep from 2016 to 2018. We used vaginal implant transmitters (VIT)s in pregnant females to identify parturition and to capture and radio-collar neonates to monitor survival of young. We collected fecal samples throughout the breeding season and throughout the year to understand diet quality and composition throughout those temporal periods. We determined diet quality and composition for pre-parturient females, females provisioning offspring, females that lost offspring, and non-pregnant individuals using fecal nitrogen and DNA metabarcoding analyses. Additionally, we compared the diet quality and composition of offspring and adult females during the spring, as well as summer and winter months. Our results indicated differences in diet quality between individuals provisioning offspring and those whose offspring had died. Females that were provisioning dependent young had lower quality diets than those that lost their offspring. Diet composition among those groups was also markedly different; females that had lost an offspring had a more diverse diet than did females with dependent young. Diet quality differed among seasons, wherein offspring and adult females had higher quality diets during the spring months, with decreasing quality as the year progressed. Diet diversity was similar across seasons, although spring months tended to be most diverse. Our results support tradeoffs associated with risk-averse strategies made by adult females associated with parturition. Nutritional quality of forage was linked to provisioning status, indicating that females were trading diet quality for safety of offspring, but those females whose offspring had died selected high quality forages. Those results help explain habitat selection observed in mountain ungulates around parturition and provide further insight into the evolutionary processes and adaptive significance exhibited by those specialized artiodactyls.

Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions

Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.

Evidence-based strategies to navigate complexity in dietary DNA metabarcoding: A reply

It is clearly beneficial to eliminate low-abundance sequences that arise in error during dietary DNA metabarcoding studies, but to purge all low-abundance sequences is to risk eliminating real sequences and complicating ecological analyses. Our prior literature review noted that DNA sequence relative read abundance (RRA) thresholds can help ameliorate false-positive taxon occurrences, but that historical emphasis on this utility has fostered uncertainty about the associated risk of inflating the false-negative rate (Littleford-Colquhoun et al., 2022). To address this, we combined a simulation study and an empirical data set to both illustrate the issue and provide blueprints for simulation studies and sensitivity analyses that can help investigators avoid overcorrecting and thereby bolster confidence in ecological inferences. Awareness of both the costs and the benefits of abundance-filtering is needed because accurately characterizing dietary distributions can be critically important for understanding animal diets, nutrition and trophic networks. Highlighting the need to raise awareness, a critique of our paper emphasized the misleading notion that "false positive interactions between species can present fundamentally incorrect network structures in network ecology, whereas false negatives will provide a correct but incomplete version of the network" (Tercel & Cuff, 2022). Asserting that the reliability of results will be eroded by false positives but resilient to the omission of true positives is risky and runs counter to evidence. Unfortunately, abundance-filtering methods can introduce false negatives at higher rates than they eliminate false positives and thereby undermine the analysis of otherwise reliable sequencing data. Overcorrecting can qualitatively alter and ultimately undermine ecological interpretations.

The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation

Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data-or similar data such as environmental DNA, microbiomes, or pathobiomes-should be aware of drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.

A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples

As one of the most abundant predators of insects in terrestrial ecosystems, spiders have long received much attention from agricultural scientists and ecologists. Do spiders have a certain controlling effect on the main insect pests of concern in farmland ecosystems? Answering this question requires us to fully understand the prey spectrum of spiders. Next-generation sequencing (NGS) has been successfully employed to analyze spider prey spectra. However, the high sequencing costs make it difficult to analyze the prey spectrum of various spider species with large samples in a given farmland ecosystem. We performed a comparative analysis of the prey spectra of Ovia alboannulata (Araneae, Lycosidae) using NGS with individual and mixed DNA samples to demonstrate which treatment was better for determining the spider prey spectra in the field. We collected spider individuals from tea plantations, and two treatments were then carried out: (1) The DNA was extracted from the spiders individually and then sequenced separately (DESISS) and (2) the DNA was extracted from the spiders individually and then mixed and sequenced (DESIMS). The results showed that the number of prey families obtained by the DESISS treatment was approximately twice that obtained by the DESIMS treatment. Therefore, the DESIMS treatment greatly underestimated the prey composition of the spiders, although its sequencing costs were obviously lower. However, the relative abundance of prey sequences detected in the two treatments was slightly different only at the family level. Therefore, we concluded that if our purpose were to obtain the most accurate prey spectrum of the spiders, the DESISS treatment would be the best choice. However, if our purpose were to obtain only the relative abundance of prey sequences of the spiders, the DESIMS treatment would also be an option. The present study provides an important reference for choosing applicable methods to analyze the prey spectra and food web compositions of animal in ecosystems.

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

A fecal sequel: Testing the limits of a genetic assay for bat species identification

DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.