Enhanced ecological indication based on combined planktic and benthic functional approaches in large river phytoplankton ecology

Environmental DNA (eDNA) is a powerful method for assessing the presence and distribution of invasive aquatic species. We used this tool to detect and monitor several invasive crayfishes Procambarus clarkii, Orconectes limosus and Pacifastacus leniusculus present in, or likely to invade, the ponds of the Brenne Regional Natural Park. A previous study showed that the eDNA method was not very efficient in detecting P. clarkii. In the present study, we explored new improvements in the detection of invasive crayfish. We designed specific primers for each crayfish species, and set up an experimental mesocosm approach to confirm the specificity of the primers and the sampling protocol. We analysed samples taken from ponds in 2014 and 2015. We compared two qPCR protocols involving either SybrGreen or TaqMan assays. Using these same primers, we were able to detect crayfish eDNA with both assays during the mesocosm experiment. However, crayfish from field samples could only be detected by performing qPCR with a SybrGreen assay. We successfully monitored the presence of three invasive species of crayfish using eDNA. This method is a powerful tool for establishing the presence or absence of invasive species in various freshwater environments.     

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (<Emphasis Type="Italic">Gymnocephalus cernua</Emphasis>) spread in North America

Detection of invasive species before or soon after they establish in novel environments is critical to prevent widespread ecological and economic impacts. Environmental DNA (eDNA) surveillance and monitoring is an approach to improve early detection efforts. Here we describe a large-scale conservation application of a quantitative polymerase chain reaction assay with a case study for surveillance of a federally listed nuisance species (Ruffe, Gymnocephalus cernua) in the Laurentian Great Lakes. Using current Ruffe distribution data and predictions of future Ruffe spread derived from a recently developed model of ballast-mediated dispersal in US waters of the Great Lakes, we designed an eDNA surveillance study to target Ruffe at the putative leading edge of the invasion. We report a much more advanced invasion front for Ruffe than has been indicated by conventional surveillance methods and we quantify rates of false negative detections (i.e. failure to detect DNA when it is present in a sample). Our results highlight the important role of eDNA surveillance as a sensitive tool to improve early detection efforts for aquatic invasive species and draw attention to the need for an improved understanding of detection errors. Based on axes that reflect the weight of eDNA evidence of species presence and the likelihood of secondary spread, we suggest a two-dimensional conceptual model that management agencies might find useful in considering responses to eDNA detections.     

Unraveling cryptic invasion of a freshwater snail in Chile based on molecular and morphological data

Cryptic species may cause biological invasions to be overlooked leading to underestimation of the potential impacts of invaders on the new ecosystems. Identification of freshwater snails is challenging because of the scarcity of discriminative morphological characters and the limited taxonomic knowledge of some taxa. Here, molecular and morphological analyses were performed to investigate the identity of viable populations of the genus Physa in aquatic ecosystems of different basins in northern and central Chile, including habitats where the native species Physa chilensis and Physa nodulosa have been traditionally recognized. Molecular analyses based on mitochondrial DNA sequences from the small subunit 16S rDNA and cytochrome c oxidase subunit 1 identified all specimens sequenced as belonging to the globally invasive species Physa acuta. Microscopic examination of the radula and morphological observations of the reproductive system were congruent with these findings. Highly divergent haplotypes found in El Salto suggest multiple introductions of different lineages of the invader in this locality. It is clear that for future management planning a more reliable assessment of the status of P. chilensis and P. nodulosa is required.     

Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen,a critically endangered Asian salmonid

For field ecologists, detecting a target species in the wild is a severe bottleneck to understanding its distribution and population status. Recently, environmental DNA (eDNA) techniques have been developed as a noninvasive monitoring tool for aquatic organisms. While applications of eDNA techniques for biomass estimation have been proposed, little is known about an applicable size range of the organisms, which might affect relationships between biomass and eDNA concentration. Here, we investigated eDNA from Sakhalin taimen (Parahucho perryi), a giant salmonid species of northern Japan. This species is critically endangered and difficult to detect in the wild by conventional sampling methods. Using quantitative real-time PCR, we tested correlations between eDNA concentration and fish density using fish with a wide range of ages and body sizes in aquarium experiments. We found that our new primers and probe were truly species-specific, and that the eDNA concentration was significantly correlated with fish density and body size (p < 0.001). Furthermore, based on our calculation, the eDNA concentrations were rather constant among aquaria with fish in different age and size groups when their total weight was adjusted. These results suggest that eDNA concentrations can be an indicator of biomass of Sakhalin taimen, although further research is needed for its application in natural environments.     

California vernal pool endemic responses to hydroperiod,plant thatch,and nutrients

Many endemic large branchiopods inhabit ephemeral freshwater ecosystems, including California vernal pools. Hydroperiod, inundation length, has been well studied in these systems that cycle between aquatic and terrestrial phases, but species’ responses to other ecological processes are still poorly known. For example, temporal (plant thatch from the previous terrestrial phase) and spatial (nutrient runoff) factors may have strong effects on emergence and population densities during the aquatic phase. We examined the effects of hydroperiod stability, thatch, and nutrients on the emergence and density of 4 vernal pool endemic species: Branchinecta lynchi (Anostraca), Linderiella occidentalis (Anostraca), Lepidurus packardi (Notostraca), and Cyzicus californicus (Spinicaudata). A full factorial mesocosm experiment was conducted which measured species densities, along with water quality variables. Hydroperiod and thatch differentially affected 3 of the 4 species based on emergence timing and life cycle. Treatments had effects on many water quality variables, and these variables were correlated with densities. These results highlight how hydroperiod stability along with other processes can affect large branchiopod species in temporary freshwater ecosystems. California vernal pools are a greatly reduced habitat rich in endemic and endangered species (including Branchinecta lynchi and Lepidurus packardi), and therefore, these results have implications for conservation and management.     

Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

The exploitation of non-invasive samples has been widely used in genetic monitoring of terrestrial species. In aquatic ecosystems, non-invasive samples such as feces, shed hair or skin, are less accessible. However, the use of environmental DNA (eDNA) has recently been shown to be an effective tool for genetic monitoring of species presence in freshwater ecosystems. Detecting species in the marine environment using eDNA potentially offers a greater challenge due to the greater dilution, amount of mixing and salinity compared with most freshwater ecosystems. To determine the potential use of eDNA for genetic monitoring we used specific primers that amplify short mitochondrial DNA sequences to detect the presence of a marine mammal, the harbor porpoise, Phocoena phocoena, in a controlled environment and in natural marine locations. The reliability of the genetic detections was investigated by comparing with detections of harbor porpoise echolocation clicks by static acoustic monitoring devices. While we were able to consistently genetically detect the target species under controlled conditions, the results from natural locations were less consistent and detection by eDNA was less successful than acoustic detections. However, at one site we detected long-finned pilot whale, Globicephala melas, a species rarely sighted in the Baltic. Therefore, with optimization aimed towards processing larger volumes of seawater this method has the potential to compliment current visual and acoustic methods of species detection of marine mammals.     

Environmental DNA (eDNA): Powerful technique for biodiversity conservation

Environmental DNA metabarcoding is a non-invasive method for discovering and identifying rare and endangered species in a variety of ecosystems, including aquatic environments, based on the retrieval of genetic traces emitted into the environment by animals. Environmental (e) DNA research has grown in popularity over the last decade as a result of a rise in the number of studies that employ DNA taken from the environment, particularly in freshwater and marine ecosystems. In terms of detecting diversity patterns, we may claim that DNA retrieved from the environment (eDNA) is altering the game. For resource management in fisheries, information on species composition and biomass/abundance of commercially and noncommercially harvested species is critical. The eDNA is a truly non-invasive method that inflicts no damage on the species or habitats under study even during sampling, the eDNA technique never harms any ecosystems or threatened species. This novel molecular method never affects any endangered species or ecosystem during sampling. Environmental DNA analysis has become more widely accepted and is used in the detection of the presence and absence of aquatic macrofauna, such as freshwater and marine fish. This review study may aid researchers in better understanding the current state of eDNA technology. Despite the fact that various scientists have used eDNA to investigate the worldwide biodiversity of aquatic environments, no one in India is focusing on this new technology. We conclude that the eDNA technique has the potential to become a next-generation tool for biodiversity research and aquatic ecosystem conservation.     

Deer feeding selectivity for invasive plants

Native generalist herbivores might limit plant invasion by consuming invading plants or enhance plant invasion by selectively avoiding them. The role of herbivores in plant invasion has been investigated in relation to plant native/introduced status, however, a knowledge gap exists about whether food selection occurs according to native/introduced status or to species. We tested preference of the native herbivore white-tailed deer (Odocoileus virginianus) for widespread and frequently occurring invasive introduced and native plants in the northeastern United States. Multiple-choice deer preference trials were conducted for the species and relative preference was determined using biomass consumption and feeding behavior. While more native than introduced plant biomass was consumed overall, deer food selection varied strongly by plant species. Results show consistent deer avoidance of several invasive introduced plants (Alliaria petiolata, Berberis thunbergii, and Microstegium vimineum) and a native plant (Dennstaedtia punctilobula). Other invasive introduced plants (Celastrus orbiculatus, Ligustrum vulgare, and Lonicera morrowii) and a native plant (Acer rubrum) were highly preferred. These results provide evidence that herbivore impacts on plant invaders depend on plant species palatability. Consequently, herbivore selectivity likely plays an important role in the invasion process. To the extent that herbivory impacts population demographics, these results suggest that native generalist herbivores promote enemy release of some plant invaders by avoiding them and contribute to biotic resistance of others by consuming them.     

Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.     

A PCR-based analysis of plant DNA reveals the feeding preferences of <Emphasis Type="Italic">Apolygus lucorum</Emphasis> (Heteroptera: Miridae)

The mirid bug Apolygus lucorum (Meyer-Dür) (Heteroptera: Miridae) is a severe pest of cotton and other crops in China. The feeding preferences of this pest are unclear due to its frequent movement among different host plants and the inconspicuous signs of its feeding. Here, we present results of a field trial that used direct observation of bug densities and a PCR-based molecular detection assay to detect plant DNA in bugs to explore relationships between A. lucorum population abundance and its feeding preference between two host plants, Humulus scandens (Loureiro) Merrill and Medicago sativa L. The field-plot samples showed that A. lucorum adults generally prefer flowering host plants. Its density was significantly higher on flowering H. scandens than on seedlings of M. sativa, and a similarly higher bug density was observed on flowering M. sativa than on seedlings of H. scandens. In the laboratory, we designed two pairs of species-specific primers targeting the trnL-F region for H. scandens and M. sativa, respectively. The detectability of plant DNA generally decreased with time post-feeding, and the half-life of plant DNA detection (DS₅₀) in the gut was estimated as 6.26 h for H. scandens and 3.79 h for M. sativa with significant differences between each other. In mirid bugs exposed to seedlings of H. scandens and flowering M. sativa, the detection rate of M. sativa DNA was significantly higher than that of H. scandens. Meanwhile, in mirid bugs exposed to seedlings of M. sativa and flowering H. scandens, a significantly higher detection rate of H. scandens DNA was found. We developed a useful tool to detect the remaining plant food species specifically from the gut of A. lucorum in the current study. We provided direct evidence of its feeding preference between H. scandens and M. sativa at different growth stages, which strongly supported a positive correlation between population abundance and feeding preference of A. lucorum on different plants under field conditions. The findings provide new insights into the understanding of A. lucorum’s feeding preference, and are helpful for developing the strategies to control this pest.     

Do associations between native and invasive plants provide signals of invasive impacts?

Do invasive plant species act more as “passengers” or drivers of ecological change in native plant communities? Snapshot studies based on correlations at the site scale ignore longer-term dynamics and variation in how particular invaders affect particular native species. We analyzed patterns of co-occurrence between three invading species (Alliaria petiolata, Lonicera x bella, and Rhamnus cathartica) and 70 native plant species in 94 southern Wisconsin forests at two scales to test four hypotheses. Surveys at these sites in the 1950s and again in the 2000s allowed us to assess how initial plant diversity and site conditions affected subsequent patterns of invasion. Sites with more native species in the 1950s experienced fewer invasions of Lonicera and Rhamnus. However, this result may reflect the fact that more fragmented habitat patches supported both fewer species in the 1950s and more invasions. At the site-level, few negative correlations exist between invasive and native species’ abundances. Sites with higher Alliaria densities in the 2000s, however, support fewer native species and lower populations of several declining natives. Rhamnus-invaded sites support lower populations of two increasing species. Association (C-score) analyses detect more associations and more negative associations at the 1 m² scale than at the site scale. Most strong associations between invasive and increasing native species are positive while those with declining natives are often negative. Species restricted to specialized habitats rarely co-occur with invaders. Alliaria has more negative associations at fragmented sites where it is more abundant and invasions may be older. Fine-scale invasive-native associations were stronger, easier to detect, and less consistent than those detectable at the site-level. Thus, screening large numbers of local associations using observational data may allow us to identify particular invasive-native interactions worth further investigation. Although invading plants sometimes act as passive passengers, increasing in tandem with certain native plants in response to disturbed fragmented habitats, they may also contribute to the declines we observe in many native species. Monitoring invasions would allow us to assess whether local associations serve to predict subsequent invasive species impacts.     

Histological evidence that diploid hybrids of <Emphasis Type="Italic">Cobitis taenia</Emphasis> and <Emphasis Type="Italic">C. elongatoides</Emphasis> (Teleostei,Cobitidae) develop into fertile females and sterile males

Rising temperatures likely affect the trophic interactions in temperate regions as global warming progresses. An open question is how a temperature rise may affect consumer pressure and plant abundance in shallow aquatic ecosystems, where most consumers are omnivorous. Interestingly, herbivory (plant-eating) is more prevalent toward low latitudes in ectotherms such as fish and aquatic invertebrates, and this may be temperature driven. We used pond snails (Lymnaea stagnalis L.) as a model aquatic ectotherm species and tested their consumption of both animal prey (Gammarus pulex L.) and plant material (Potamogeton lucens L.) at three different temperatures (15, 20, and 25°C). Higher temperatures led to higher consumption rates by the omnivore on both plant food and animal prey when fed separately. When the food was offered simultaneously, the pond snails consistently preferred animal prey over plant material at all tested temperatures. However, the omnivore did consume plant material even though they had enough animal prey available to them. Based on our experiments, we conclude that with increasing temperatures, L. stagnalis will only increase their consumption rates but not change food preference. Further studies are needed to test the generality of our findings across aquatic species to predict the effect of warming on aquatic plant consumption.     

Detection of invasive freshwater fish species using environmental DNA survey

Invasive species are one of the most significant problem in freshwater ecosystems. Most common non-native freshwater species in Turkish freshwater fish fauna are Prussian Carp (Carassius gibelio), North African Catfish (Clarias gariepinus), Nile Tilapia (Oreochromis niloticus) and Topmouth Gudgeon (Pseudorasbora parva).Recent studies showed that environmental DNA could be used to detect target species inhabiting the ecosystem with higher precision and less effort compared to traditional field surveys. In this study, eDNA approach was used to investigate non-native freshwater fish species from fifteen different locations of Upper Sakarya Basin. eDNA was successfully extracted from the water samples of locations where the species were visually observed. Mean amplification rate of eDNA was calculated as 77.03%.This study is the first environmental DNA study used in detection of four of the most common invasive freshwater fish species. Results clearly indicating that eDNA surveys could be used as an important molecular tool to monitor invasive fish species in freshwater ecosystems.     

Early detection of a highly invasive bivalve based on environmental DNA (eDNA)

Management of non-indigenous invasive species (NIS) is challenging owing in part to limitations of early detection and identification. The advent of environmental DNA (eDNA) techniques provides an efficient way to detect NIS when their abundance is extremely low. However, eDNA-based methods often suffer from uncertain detection sensitivity, which requires detailed testing before applying these methods in the field. Here we developed an eDNA tool for early detection of the highly invasive golden mussel, Limnoperna fortunei, based on the mitochondrial cytochrome c oxidase subunit I gene (COI). Further, we tested technical issues, including sampling strategy and detection sensitivity, based on a laboratory experiment. We then applied the method to field samples collected from water bodies in China where this mussel has or is expected to colonize. Results showed that the detection limit varied extensively among our newly developed primer pairs, ranging from 4 × 10^?2 to 4 × 10^?6 ng of total genomic DNA. Laboratory detection was affected by the availability of eDNA (i.e., both mussel abundance and incubation time). Detection capacity was higher in laboratory samples containing re-suspended matter from the bottom layer versus that collected from the surface. Among 25 field sites, detection was 100% at sites with high mussel abundance and as low as 40% at sites with low abundance when tested using our most sensitive primer pair. Early detection of NIS present at low abundance in nature requires not only sensitive primers, but also an optimized sampling strategy to reduce the occurrence of false negatives. Careful selection and detailed testing of primer pairs ensures effective eDNA-based species detection in surveillance and management programs.     

An invasive plant provides refuge to native plant species in an intensely grazed ecosystem

Invasion by exotic plant species and herbivory can individually alter native plant species diversity, but their interactive effects in structuring native plant communities remain little studied. Many exotic plant species escape from their co-evolved specialized herbivores in their native range (in accordance with the enemy release hypothesis). When these invasive plants are relatively unpalatable, they may act as nurse plants by reducing herbivore damage on co-occurring native plants, thereby structuring native plant communities. However, the potential for unpalatable invasive plants to structure native plant communities has been little investigated. Here, we tested whether presence of an unpalatable exotic invader Opuntia ficus-indica was associated with the structure of native plant communities in an ecosystem with a long history of grazing by ungulate herbivores. Along 17 transects (each 1000 m long), we conducted a native vegetation survey in paired invaded and uninvaded plots. Plots that harboured O. ficus-indica had higher native plant species richness and Shannon–Wiener diversity H′ than uninvaded plots. However, mean species evenness J was similar between invaded and uninvaded plots. There was no significant correlation between native plant diversity and percentage plot cover by O. ficus-indica. Presence of O. ficus-indica was associated with a compositional change in native community assemblages between paired invaded and uninvaded plots. Although these results are only correlative, they suggest that unpalatable exotic plants may play an important ecological role as refugia for maintenance of native plant diversity in intensely grazed ecosystems.     

Environmental DNA quantification in a spatial and temporal context: a case study examining the removal of brook trout from a high alpine basin

Analysis of aquatic environmental DNA (eDNA) is a promising tool to determine species distribution, abundance, and biomass. Understanding how the amount of eDNA collected is affected by spatial and temporal processes needs to become better understood before eDNA quantification can be used in species management. In this study, we analyzed how the amount of eDNA changed across space and time in a high mountain basin where nonnative fish were being removed. We sampled from restoration (sites with fish removal activities; n?=?6) and control sites (sites with no fish removal activities where fish were present; n?=?3) and found the number and biomass of fish removed were related to the quantities of DNA collected and not related to site position within the drainage. Our results indicate that the amount of eDNA collected in an open system can provide an index of population size despite inherent complications of analyzing a spatially connected and temporally dynamic watershed. However, there are complications when applying these methods in species management: (1) small increases in eDNA density corresponded to large increases in trout density; (2) eDNA and traditional field techniques disproportionately target certain life stages, complicating comparisons between techniques; and (3) eDNA index values may need to be calibrated when sampling different species, life stages, environments, and habitats. We call for further research before this process can be used in a management context.     

The impact of invasive knotweed species (<Emphasis Type="Italic">Reynoutria</Emphasis> spp.) on the environment: review and research perspectives

I conducted an exhaustive literature review on Japanese knotweeds s.l. (including Reynoutria japonica, R. sachalinensis and R. ×bohemica), especially on the effects of these invasive plants on biodiversity and ecological processes or the chemical and physical characteristics of invaded habitats. A total of 44 studies have been published, the earliest in 2005, in peer-reviewed journals. Most studies were conducted in Europe, the others in the USA. Invasive knotweeds have major negative impacts on native plants, while the abundant litter produced and the deep rhizome system alter soil chemistry to the benefit of the invaders. However, the effects of knotweeds on other groups of species vary, with a combination of losers (soil bacteria, most arthropods and gastropods, some frogs and birds) and winners (most fungi, detritivorous arthropods, aquatic shredders, a few birds). This literature review highlights significant knowledge gaps of the effects of knotweeds on biodiversity (vertebrates) and ecological processes (ecohydrology). To what extent knotweed invasions have an impact on the population dynamics of native plants and animals on a regional to national scale remains to be verified. Although there is some evidence that knotweed invasions have negative effects on the environment, the research to date remains modest and a more extensive effort is needed to better define the environmental impacts of these plant invaders.     

Using environmental DNA and occupancy modelling to identify drivers of eastern hellbender (Cryptobranchus alleganiensis alleganiensis) extirpation

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Patterns of microbial food webs in Mediterranean shallow lakes with contrasting nutrient levels and predation pressures

Hygraula nitens is a New Zealand native moth with aquatic larvae that feed on submerged aquatic plants. The larvae have been mainly observed using native Potamogeton and Myriophyllum species as a food source, although some studies reported larvae feeding on the alien macrophytes Hydrilla verticillata, Lagarosiphon major and Ceratophyllum demersum. Experimental mesocosm studies showed larvae had a major effect on H. verticillata, C. demersum, L. major, Elodea canadensis and Egeria densa. In both no choice and choice experiments H. nitens larvae showed a clear preference for and the highest consumption of C. demersum, while the native macrophyte Myriophyllum triphyllum ranked fourth out of five alien and two native plant species, indicating a preference of the larvae for alien macrophytes. Additional choice experiments using C. demersum, sampled from different waters in NZ, illustrated that there was a clear difference in H. nitens preference for plants based on their source. However although C. demersum had the lowest leaf dry matter content (LDMC) compared with the other macrophytes, neither the LDMC nor leaf carbon, nitrogen, phosphorus or total phenolic contents alone could explain the preferences of H. nitens, and we conclude that food choice is based on a combination of these and/or additional factors.     

Native granivores reduce the establishment of native grasses but not invasive <Emphasis Type="Italic">Bromus tectorum</Emphasis>

Seed predation can structure plant communities by imposing strong population controls on some species but not others. In this context, studies from various ecosystems report that native granivores selectively forage for seeds from native species over seeds from exotic invaders, which could disproportionately favor the establishment of invaders and facilitate their dominance in communities. However, few studies have connected selective foraging for native seeds to differential patterns of establishment among native and invasive species. Thus, the extent to which preferential foraging for native seeds favors the establishment of invasive plants is unclear. Here, we used experimental seed additions and exclosure treatments at five field sites distributed across?≈?80,000 km² of the Great Basin Desert, USA to compare the effects of rodent foraging on the establishment of less-preferred cheatgrass (Bromus tectorum—an annual species native to Eurasia that is exotic and highly invasive across the Great Basin) and four species of more-preferred native grasses that commonly co-occur with cheatgrass. Rodent foraging reduced the establishment of each native species by at least 80% but had no effect on the establishment of cheatgrass, and this finding was consistent across study sites. Our results suggest that selective foraging for native species may favor the establishment of cheatgrass over native grasses, potentially exacerbating one of the most extensive plant invasions in North America.