scholarly journals eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Louise Nørgaard ◽  
Carsten Riis Olesen ◽  
Kristian Trøjelsgaard ◽  
Cino Pertoldi ◽  
Jeppe Lund Nielsen ◽  
...  

AbstractWith an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as “biodiversity capsules” and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.

2021 ◽  
Author(s):  
Physilia Ying Shi Chua ◽  
Youri Lammers ◽  
Emmanuel Menoni ◽  
Torbjørn Ekrem ◽  
Kristine Bohmann ◽  
...  

ABSTRACTConservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47 = 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies’ diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.


2021 ◽  
Author(s):  
Masayuki K. Sakata ◽  
Mone U. Kawata ◽  
Atsushi Kurabayashi ◽  
Takaki Kurita ◽  
Masatoshi Nakamura ◽  
...  

Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians ecological traits (e.g., nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA released into the environment-allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160-311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata, and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set Amph16S had the highest resolution among the tested sets. Finally, we applied Amph16S to actual metabarcoding and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kleopatra Leontidou ◽  
Despoina Vokou ◽  
Anna Sandionigi ◽  
Antonia Bruno ◽  
Maria Lazarina ◽  
...  

AbstractMonitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.


Author(s):  
Elena I. Sarapultseva ◽  
Darya V. Uskalova ◽  
Ksenya V. Ustenko

Despite the fact that there are still conflicting opinions about the damage caused by modern wireless communication technologies, most scientists report on the negative biological effects of low-intensity radio frequency electromagnetic radiation at different levels of the organization of live nature. There is no doubt that there is a need not only for a sanitary and hygienic assessment of man-made electromagnetic effects on humans, but also for an environmental assessment for biota. The purpose of the study was to assess the potential environmental risk of electromagnetic impact in the centimeter range on natural ecosystems. The initial data were the authors' own results in the field of radiobiology of non-ionizing radiation, as well as published of other researchers. The article analyzes the biological effects of radio frequency electromagnetic fields detected in organisms of different systematic groups and levels of organization. The data on the non-thermal biological effects of electromagnetic fields indicate a high sensitivity of different species to this factor. The analyzed research results emphasize the need to take into account the features of non-thermal effects of electromagnetic radiation on biota, since these radiations can have a negative impact on different hierarchical levels in natural ecosystems.


2014 ◽  
Vol 36 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Maciej Korczyński ◽  
Ewa Krasicka-Korczyńska

Abstract Cypripedium calceolus is considered an endangered species in the territory of Poland. Population of this rare species, situated at Lake Kwiecko (Western Pomerania), was regularly monitored in the years 1986-2013. The studied population has been under the permanent influence of the nearby hydroelectric power plant for almost 45 years. The field observations showed that the power plant had no negative impact on the condition of Cypripedium calceolus population. An indication of its good condition was, among others, an increase in the size - from 150 to 350 specimens within the study period.


2021 ◽  
Vol 2021 (23) ◽  
pp. 237-250
Author(s):  
Anatolii Morozov ◽  
◽  
Tetiana Morozova ◽  
Inessa Rutkovska ◽  
◽  
...  

Introduction.The main environmental risks posed by roads are population depletion (deaths on roads) and barrier effects (habitat fragmentation). Barrier effects - animals avoid crossing roads, which leads to a decrease in the size and quality of habitat, optimal population size, reduced ability to find food and partner, increased genetic structuring and local extinction (Forman et al. 2003; Andrews et al. 2015; van der Ree et al. 2015). These risks against the background of other stressors, in particular the presence of invasive species, pollution, pesticide use, climate change, plant and animal diseases, may threaten the survival of populations.This issue is especially relevant for herpetofauna due to their biological characteristics. In particular, reptiles and amphibians move slowly, are too small (for drivers to see), do not avoid roads, and in cold periods roads attract amphibians (thermoregulation) because the coating absorbs and retains heat (Case and Fisher 2001; Jochimsen et al. 2004).The principle of ensuring ecological continuity is to identify priority efforts to mitigate environmental risks for animals and reduce the negative impact of the transport complex as a spatial barrier and source of pollution by introducing a number of technical means (eco-crossings, screens, embankments, landscaping). As it is not possible to change the environmental risks on all roads and for all species at present, it is necessary to identify the most vulnerable species, assess the risks to populations and the need for mitigation based on analysis of road density and traffic intensity.Problem Statement. With the advent of land transport there was a progressive environmental problem - the transformation of landscapes, it first appeared in countries with developed road infrastructure in Western Europe and the United States, and quickly spread around the globe (Ellenberg, et al., 1981; Fetisov, 1999; Zagorodnyuk, 2006, Ilyukh, Khokhlov, 2012). Numerous publications by both foreign and domestic authors are devoted to the study of the impact of transport infrastructure. Special attention of European authors is paid to the study of the phenomenon of fragmentation of natural ecosystems. In Europe, there is a network of experts and institutions of IENE, which is studying the possibility of implementing preventive measures for landscape fragmentation, promotes the development of transport infrastructure in accordance with environmental requirements, by creating a safe, environmentally sustainable European transport infrastructure.The ecological trail of the road network significantly exceeds its length (Vozniuk, 2014). This is due to the effects of, in particular, mortality on the roads of mammals, reptiles, reptiles (Forman et al. 2003), landscape fragmentation (roads divide the area into isolated areas, with low populations (sometimes below the minimum), so such populations lose genetic diversity and may become extinct locally), the loss of habitats of species and a decrease in the level of connectivity. In addition to these obvious effects, noise and vibration pollution are added, which inhibit the ability of reptiles, birds and mammals to detect prey or avoid predators (Forman et al. 2003), disturbed light regime (Rich and Longcore 2006). Roads contribute to the development of soil erosion processes, the spread of invasive and introduced species (300-800 seeds/m2 per year are transported to roadside ecotones by vehicles (Von der Lippe and Kowarik 2007), which contributes to the formation of local pseudo-populations), create obstacles and sources. (Forman et al. 2003).Purpose. Substantiation of the principle of ecological continuity regarding the negative impact of transport infrastructure on natural ecosystems and search for possible ways to minimize and prevent such impact.Materials and methods. The main research methods are the application of theoretical general scientific approaches to study: analysis and synthesis of international and domestic scientific and theoretical works, EU documentation (charters, design requirements), Ukrainian legal framework, literature sources; collection and analysis of statistical data to identify the dangers of the impact of road infrastructure on biodiversity and determine the value of the natural landscape.Results. The result is an analysis of the scientific literature on the negative impact of transport infrastructure on animals, systematization of the main impacts for the preparation of methodological documents for organizations planning and designing transport infrastructure in Ukraine to reduce the negative impact.Conclusions. The principle of ensuring ecological continuity is to minimize the negative consequences for the environment. In particular, by leveling the spatial barrier of the public highway. When laying a road through natural ecosystems, it is necessary to build transitions and passages for animals. In this case, their density and type must correspond to the natural rank of the territory. The construction of crossings for animals should be mandatory for all types of roads that cross ecological corridors. This is especially true for smaller roads, completely devoid of any transitions for animals, noise shields (on such roads are more likely to hit animals). An important point is the need to plan preventive methods at the planning stage of road construction. The analysis of the European experience shows that the negative impact of transport infrastructure on biota can be solved by consolidating the efforts of road transport specialists and specialists in the field of nature protection.Keywords:motor road,wildlife crossing, biodiversity, road infrastructure, ecological continuity


2019 ◽  
Vol 29 (1) ◽  
pp. 148-152 ◽  
Author(s):  
Caterina Maria Antognazza ◽  
J. Robert Britton ◽  
Caitlin Potter ◽  
Elizabeth Franklin ◽  
Emilie A. Hardouin ◽  
...  

2019 ◽  
Vol 32 (1) ◽  
pp. 26-40 ◽  
Author(s):  
Paul Shrivastava ◽  
Laszlo Zsolnai ◽  
David Wasieleski ◽  
Mark Stafford-Smith ◽  
Thomas Walker ◽  
...  

The Anthropocene era is characterized by a pronounced negative impact of human and social activities on natural ecosystems. To the extent finance, economics and management underlie human social activities, we need to reassess these fields and their role in achieving global sustainability. This article briefly presents the scientific evidence on accelerating impacts of human activities on nature, which have resulted in breach of planetary boundaries and onset of global climate change. It offers some potential leverage points for change toward sustainability stewardship by highlighting the important role of finance and economics in addressing climate change. We examine the role of financial stakeholders in addressing planetary boundaries and offer a modified stakeholder theory, from which we propose future directions for finance in the Anthropocene.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.


2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Irina A. Tarasenko ◽  
Alexander V. Zin’kov ◽  
Aleksei S. Kholodov ◽  
Muhammad Riaz ◽  
Valeriy I. Petukhov ◽  
...  

Elevated contents of hazardous elements in natural ecosystems are often associated with human activities. Significant quantities of these elements, including heavy metals, are concentrated in tailings. The goal of the study was to assess the mineralogical and geochemical features of the old tailings of the decommissioned Krasnorechenskaya concentrating mill (located in Primorsky Krai, Russian Federation), which was processing complex tin-polymetallic and silver-lead-zinc ores, the chemical features of tailings pond waters, and the extent of environmental impact on the nearby Rudnaya river. In addition to the analysis of rock and water samples, the software modeling of the water-rock-gas system was carried out. In the study area, the minerals and rocks undergo changes that lead to the formation of highly mineralized, acidic waters saturated with various elements. In the tailings ponds, the maximum permissible concentrations were exceeded for Zn, Cd, Cu, Mg, Fetotal, Pb, Mn, Al, As, Co, Be, Sr, Ni, and Ba. The drainage from the tailings pond tripled the total mineralization of the Rudnaya river relative to the background values. However, the intoxication of the ecosystem by tailing products is partially inhibited by the secondary minerals in the tailings ponds. The negative impact is of a local nature, and 500 m downstream the concentration of many of the above elements is reduced. Despite this, the system that forms the chemical composition of highly mineralized waters is far from the equilibrium state. The oxidation of sulfides, dissolution of other minerals, and migration of oxidation and hydrolysis products will continue affecting the environment. In this regard, it is necessary to conduct environmental monitoring and undertake activities aimed at the recovery of mature concentration tailings or at suppressing the activity of hazardous elements by the conservation of tailings ponds.


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