Diet of the European bison (Bison bonasus) in a forest habitat estimated by DNA barcoding

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.

Effect of Translocation on Host Diet and Parasite Egg Burden: A Study of the European Bison (Bison bonasus)

For the purpose of nature management and species conservation, European bison (Bison bonasus) are being increasingly reintroduced into nature reserves across Europe. The aim of this study was to investigate European bison's adaptability to new areas through the study of their parasite-EPG (eggs per gram feces) and dietary diversity during twelve months after translocation. We compared the parasite-EPG from introduced European bison in Lille Vildmose, Denmark, with the parasite-EPG from populations from Bornholm, Denmark, and Białowieża Forest, Poland. From March 2021 to February 2022, fecal samples were collected from three populations. Samples from Lille Vildmose were examined through flotation, sedimentation, the Baermann technique, and nanopore sequencing. Fecal samples from Bornholm and Białowieża were examined through flotation and sedimentation. Nanopore sequencing of DNA from 63 European bison's fecal samples collected during March-September in Lille Vildmose identified 8 species of nematodes within the digestive tract of the European bison, with Haemonchus contortus being the most frequently observed. In Lille Vildmose, a significantly higher excretion of nematode-EPG was observed during the summer period than in the spring, autumn, and winter. In addition, monthly differences in the excretion of nematode eggs were found, with this being significantly higher in June than in the months during autumn and winter (October-February). Significant differences in the nematode-EPG were only found between the excretion of nematode eggs in Białowieża Forest when compared to that of Lille Vildmose, with significantly higher excretion in Lille Vildmose (October-November). The results indicate that the development rates for nematodes may be affected by changes in temperature, with increasing temperatures speeding up their development time. Independent of this study design, wildlife vets together with the gamekeepers managing the herd found it necessary to treat the herd with antiparasitics for practical and animal welfare reasons in relation to translocation. Furthermore, 79 plant taxa were identified in the diet of the European bison. The broadest diet was observed in March suggesting that the European bison quickly adapted to their new habitat. The results suggest a seasonal shift in their diet, with this being most apparent from March to April.

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.

Comparative Analysis of In Situ Eukaryotic Food Sources in Three Tropical Sea Cucumber Species by Metabarcoding

Simple Summary

There are large numbers of sea cucumbers naturally inhabiting tropical seas, which play an important ecological role in the habitat through their biological activity. However, despite the diversity of tropical sea cucumbers, until now there have been few studies on their exact eukaryotic food sources. In the present study, we systemically investigated the eukaryotic food sources of three sea cucumber species. We also study the differences of eukaryotic composition among three sea cucumber species and provide new insight into reasons for the differences. The reported information could be valuable in further biological and ecological studies of these species.

Abstract

In this study, the eukaryotic composition of gut contents in three tropical sea cucumber species, Stichopus monotuberculatus, S. chloronotus and Holothuria atra were surveyed and compared by metabarcoding analysis based on 18S rRNA gene V4 region. The sequences were assigned to 21.80 ± 1.07, 22.60 ± 0.68 and 22.40 ± 0.25 different phyla from the gut contents of S. monotuberculatus, S. chloronotus and H. atra, respectively, and those in sediment samples were assigned to 21.00 ± 1.67 phyla. The results of α-diversity showed that surface sediments had a greater eukaryotic diversity than gut contents, yet the guts of sea cucumbers had an enrichment effect on some microorganisms, including Diatomea and Apicomplex. A comparison of the gut eukaryotic community among the three species suggested that the feeding preference was different: S. monotuberculatus fed mainly on Diatomea and Arthropoda, and the other two species had higher Apicomplexa concentrations, which may be due to differences in the morphology of the tentacles and habitat preferences. Moreover, obvious different eukaryotic community composition in the gut contents of the three sea cucumber species and the surrounding sediments also might result from the animals’ selective feeding for sediment patches. The current study filled in gaps about feeding mechanisms of tropical sea cucumbers and provided a basis for further exploring the mechanism about selective feeding and sea cucumber–sediment interaction in the future.