Evaluating the efficacy of restoration plantings through DNA barcoding of frugivorous bird diets

Significant biomagnification of methylmercury in songbird nestlings through a rice-based food web: Insights from stable mercury isotopes

To elucidate the sources and transfer of mercury (Hg) in terrestrial food chains, particularly in heavily Hg-contaminated rice paddy ecosystems, we collected rice leaves, invertebrates, and Russet Sparrow nestlings from a clear food chain and analyzed the dietary compositions and potential Hg sources using stable Hg isotopes coupled with a Bayesian isotope mixing model (BIMM). Our findings indicated that MeHg exposure is dominant through the dietary route, with caterpillars, grasshoppers, and katydids being the main prey items, while the less provisioned spiders, dragonflies, and mantises contributed the most of the Hg to nestlings. We found minimal MIF but certain MDF in this terrestrial food chain and identified two distinct MeHg sources of dietary exposure and maternal transfer. We firstly found that the dietary route contributed substantially (almost tenfold) more MeHg to the nestlings than maternal transfer. These findings offer new insights into the integration of Hg from the dietary route and maternal transfers, enhancing our understanding of fluctuating Hg exposure risk during the nestling stage. Our study suggested that Hg isotopes combined with BIMM is an effective approach for tracing Hg sources in birds and for gaining in-depth insight into the trophic transfers and biomagnification of MeHg in food chains.

A global systematic review of frugivorous animal tracking studies and the estimation of seed dispersal distances

Seed dispersal is one of the most important ecosystem functions globally. It shapes plant populations, enhances forest succession, and has multiple, indirect benefits for humans, yet it is one of the most threatened processes in plant regeneration, worldwide. Seed dispersal distances are determined by the diets, seed retention times and movements of frugivorous animals. Hence, understanding how we can most effectively describe frugivore movement and behaviour with rapidly developing animal tracking technology is key to quantifying seed dispersal. To assess the current use of animal tracking in frugivory studies and to provide a baseline for future studies, we provide a comprehensive review and synthesis on the existing primary literature of global tracking studies that monitor movement of frugivorous animals. Specifically, we identify studies that estimate dispersal distances and how they vary with body mass and environmental traits. We show that over the last two decades there has been a large increase in frugivore tracking studies that determine seed dispersal distances. However, some taxa (e.g. reptiles) and geographic locations (e.g. Africa and Central Asia) are poorly studied. Furthermore, we found that certain morphological and environmental traits can be used to predict seed dispersal distances. We demonstrate that flight ability and increased body mass both significantly increase estimated seed dispersal mean and maximum distances. Our results also suggest that protected areas have a positive effect on mean seed dispersal distances when compared to unprotected areas. We anticipate that this review will act as a reference for future frugivore tracking studies, specifically to target current taxonomic and geographic data gaps, and to further explore how seed dispersal relates to key frugivore and fruit traits.

The mercury flow through a terrestrial songbird food chain in subtropical pine forest: Elucidated by Bayesian isotope mixing model and stable mercury isotopes

In order to comprehend the transfer of inorganic mercury (IHg) and methylmercury (MeHg) within food chains in terrestrial pine forests, we collected samples of Great Tit nestlings, common invertebrates, plants, and soil in a subtropical pine forest and used Bayesian isotope mixing model analysis, Hg daily intake, and stable Hg isotopes to elucidate the flow of MeHg and IHg in these food chains. Results indicate that caterpillars and cockroaches are the predominant prey items for nestlings, accounting for a combined contribution of 81.5%. Furthermore, caterpillars, cockroaches, and spiders were found to contribute the most (∼80%) of both IHg and MeHg that dietary accumulated in nestlings. The provisoned invertebrates tend to supply more IHg and diluting the proportion of MeHg as total Hg (MeHg%). Notably, nestling feathers displayed the highest Δ199Hg values but a relatively lower MeHg%, suggesting an imbalanced incorporation of Hg from maternal transfer and dietary accumulation during the nestling stage. This study highlights the efficacy of nestlings as indicators for identifying Hg sources and transfers in avian species and food chains. However, caution must be exercised when using Hg isotope compositions in growing feathers, and the contribution of maternally transferred Hg should not be ignored.

eDNA Metabarcoding- and Microscopic Analysis for Diet Determination in Waterfowl, a Comparative Study in Vejlerne, Denmark

Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another.

Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration

Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.

Anticholesterolemic Activity of Three Vegetal Extracts (Artichoke, Caigua, and Fenugreek) and Their Unique Blend

Hepatic-related diseases, in particular hyperlipidemia and hypercholesterolemia, are a thorn on the side of the national health institutes around the globe. Indeed, liver lipid and cholesterol dysregulation could lead to atherosclerotic plaque formation and cardiovascular diseases. Currently, statin administration and monacolin K consumption are the main therapies proposed to counter this alarming connection, but relevant side effects are known. To overcome this issue, safe nutraceutical formulations and/or vegetal extracts, endowed with anticholesterolemic activity, could be instrumental in hypercholesterolemia prevention and treatment. In the present work, the anticholesterolemic efficacy of three vegetal extracts used in traditional medicine (artichoke, caigua, and fenugreek), their unique blend (ACFB), and the monacolin K-containing red yeast extract (RYR), was investigated with an in vitro approach based on hepatic cell line HepG2. The impact on cholesterol of the three extracts, their blend, and RYR were investigated by determining hepatocyte total and free cholesterol and bile acids biosynthesis. According to our results, the anticholesterolemic activity of the vegetal extracts was confirmed, and a novel choleretic activity of caigua extract was evidenced. ACFB showed to be safer than RYR while showing a similar effect on total and free cholesterol and bile acids synthesis compared to it. The anticholesterolemic activity of the blend was obtained with lower vegetal extract concentrations compared with the single vegetal extract, potentially indicating an additive effect between the extracts. In conclusion, the vegetal extracts and their blend, ACFB, are safe and are endowed with anticholesterolemic activity, potentially providing complementary therapies to the statin-based ones for hyperlipidemia and hypercholesterolemia-related complications.

Rapid Identification of Common Poisonous Plants in China Using DNA Barcodes

Toxic plants have been a major threat to public health in China. However, identification and tracing of poisoned species with traditional methods are unreliable due to the destruction of plant morphology by cooking and chewing. DNA barcoding is independent of environmental factors and morphological limitations, making it a powerful tool to accurately identify species. In our study, a total of 83 materials from 26 genera and 31 species of 13 families were collected and 13 plant materials were subjected to simulated gastric fluid digestion. Four markers (rbcL, trnH-psbA, matK, and ITS) were amplified and sequenced for all untreated and mock-digested samples. The effectiveness of DNA barcoding for the identification of toxic plants was assessed using Basic Local Alignment Search Tool (BLAST) method, PWG-Distance method, and Tree-Building (NJ) method. Except for the matK region, the amplification success rate of the remaining three regions was high, but the sequencing of trnH-psbA and ITS was less satisfactory. Meanwhile, matK was prone to be more difficult to amplify and sequence because of simulated gastric fluid. Among the three methods applied, BLAST method showed lower recognition rates, while PWG-Distance and Tree-Building methods showed little difference in recognition rates. Overall, ITS had the highest recognition rate among individual loci. Among the combined loci, rbcL + ITS had the highest species recognition rate. However, the ITS region may not be suitable for DNA analysis of gastric contents and the combination of loci does not significantly improve species resolution. In addition, identification of species to the genus level is sufficient to aid in the clinical management of most poisoning events. Considering primer versatility, DNA sequence quality, species identification ability, experimental cost and speed of analysis, we recommend rbcL as the best single marker for clinical identification and also suggest the BLAST method for analysis. Our current results suggest that DNA barcoding can rapidly identify and trace toxic species and has great potential for clinical applications. In addition, we suggest the creation of a proprietary database containing morphological, toxicological and molecular information to better apply DNA barcoding technology in clinical diagnostics.

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.

The decline of the Turtle Dove: Dietary associations with body condition and competition with other columbids analysed using high-throughput sequencing

Dietary changes linked to the availability of anthropogenic food resources can have complex implications for species and ecosystems, especially when species are in decline. Here, we use recently developed primers targeting the ITS2 region of plants to characterize diet from faecal samples of four UK columbids, with particular focus on the European turtle dove (Streptopelia turtur), a rapidly declining obligate granivore. We examine dietary overlap between species (potential competition), associations with body condition in turtle doves and spatiotemporal variation in diet. We identified 143 taxonomic units, of which we classified 55% to species, another 34% to genus and the remaining 11% to family. We found significant dietary overlap between all columbid species, with the highest between turtle doves and stock doves (Columba oenas), then between turtle doves and woodpigeons (Columba palumbus). The lowest overlap was between woodpigeons and collared doves (Streptopelia decaocto). We show considerable change in columbid diets compared to previous studies, probably reflecting opportunistic foraging behaviour by columbids within a highly anthropogenically modified landscape, although our data for nonturtle doves should be considered preliminary. Nestling turtle doves in better condition had a higher dietary proportion of taxonomic units from natural arable plant species and a lower proportion of taxonomic units from anthropogenic food resources such as garden bird seed mixes and brassicas. This suggests that breeding ground conservation strategies for turtle doves should include provision of anthropogenic seeds for adults early in the breeding season, coupled with habitat rich in accessible seeds from arable plants once chicks have hatched.

Bioprospecting on invasive plant species to prevent seed dispersal

The most anthropized regions of the world are characterized by an impressive abundance of invasive plants, which alter local biodiversity and ecosystem services. An alternative strategy to manage these species could be based on the exploitation of their fruits in a framework of bioprospecting to obtain high-added value compounds or phytocomplexes that are useful for humans. Here we tested this hypothesis on three invasive plants (Lonicera japonica Thunb., Phytolacca americana L., and Prunus serotina Ehrh.) in the Po plain (northern Italy) which bear fruits that are highly consumed by frugivorous birds and therefore dispersed over large distances. Our biochemical analyses revealed that unripe fruit shows high antioxidant properties due to the presence of several classes of polyphenols, which have a high benchmark value on the market. Fruit collection for phytochemical extraction could really prevent seed dispersal mediated by frugivorous animals and produce economic gains to support local management actions.

Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification

Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.