Display omitted
•eDNA metabarcoding was gradually applied to investigating estuarine fish diversity.•156 fish taxa were detected by eDNA metabarcoding and gillnetting.•Significant/highly significant ...seasonal differences were found for both methods.•More species obtained by eDNA than gillnetting, with significant differences.
Non-destructive and cost-effective fish diversity monitoring approaches are needed for the management and protection of estuarine ecosystems. Environmental DNA (eDNA) technology is a promising, environmentally friendly technology that has been applied in fish diversity studies in estuarine ecosystems. In this study, we investigated the seasonal composition, diversity, and structure of fish community in the Pearl River Estuary (PRE) using eDNA technology and gillnetting. We identified 156 fish in the PRE, including 26 orders, 58 families, 93 genera, and 115 species according to eDNA technology. And eDNA technology provided more taxonomic composition information in the PRE than did gillnetting. Significant or highly significant seasonal differences in fish community composition and structure were detected between the wet and dry seasons. Fifteen and eight genus-level indicator taxa differed significantly between the two seasons according to eDNA technology and gillnetting, respectively. However, the significant differences detected in this study suggest that some taxa did not overlap between the two approaches. Therefore, fish diversity monitoring in the PRE should include a combination of eDNA technology and gillnetting for comprehensive fish community data analysis. Our findings have important implications for fish community monitoring and estuarine ecosystem management.
Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth of new information on the distribution of species. ...However, eDNA methods have limited application for estimating population‐level metrics. Environmental RNA (eRNA) has the potential to address ecological questions by gathering population demographic information from environmental media but may be challenging to detect and analyze. We developed gene‐specific eRNA assays targeting keratin‐associated genes in two focal species, American bullfrogs (Lithobates catesbeianus) and tiger salamanders (Ambystoma mavortium) to answer an important question in amphibian management: whether species detections represent breeding populations versus transitory adults. We performed an extensive laboratory validation with amphibians housed across development stages, where we collected 95 and 127 environmental samples for bullfrogs and salamanders, respectively. Both assays were highly specific to the larval stage and amplified with high sensitivity (90% in bullfrog and 88.4% in tiger salamander samples). We then applied our validated assays to multiple natural systems. When larvae were present, we found 74.1% overall detection in bullfrog field samples and 70.8% and 48.5% overall detection in field samples from ponds with A. macrodactylum and A. californiense larvae, correlating with eDNA detection rates. When only adults were present, we did not detect larvae‐specific eRNA in A. macrodactylum ponds, despite high eDNA detection rates. Although much work is ahead for optimizing assay design, sampling and filtering methods, we demonstrate that eRNA can successfully be used to discern life stages with direct application for ecology and conservation management.
see also the Perspective by Robert M. Hechler and Melania E. Cristescu
Environmental DNA (eDNA) metabarcoding is a relatively new monitoring tool featuring in an increasing number of applications such as the facilitation of the accurate and cost effective detection of ...species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA metabarcoding to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of metabarcoding markers reflect the true species' identity, (b) test the sensitivity under different abundance levels and environmental noise and (c) establish a low-cost sequencing method to enable the bulk processing of field samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to sterile pre-filtered and unfiltered seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNA surveys in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we were able to identify two parasites (
and
to species level, whereas the microalgae species
, and
could be assigned correctly only to the genus level. Illumina and Ion Torrent provided near identical results in terms of community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the difference in relative abundance between treatments in 4 out of 5 species when samples were exposed to the unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA metabarcoding offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is as accurate as Illumina in determining differences in their relative abundance between samples.
Marine biodiversity is threatened by human activities. To understand the changes happening in aquatic ecosystems and to inform management, detailed, synoptic monitoring of biodiversity across large ...spatial extents is needed. Such monitoring is challenging due to the time, cost, and specialized skills that this typically requires. In an unprecedented study, we combined citizen science with eDNA metabarcoding to map coastal fish biodiversity at a national scale. We engaged 360 citizen scientists to collect filtered seawater samples from 100 sites across Denmark over two seasons (1 p.m. on September 29th 2019 and May 10th 2020), and by sampling at nearly the exact same time across all 100 sites, we obtained an overview of fish biodiversity largely unaffected by temporal variation. This would have been logistically impossible for the involved scientists without the help of volunteers. We obtained a high return rate of 94% of the samples, and a total richness of 52 fish species, representing approximately 80% of coastal Danish fish species and approximately 25% of all Danish marine fish species. We retrieved distribution patterns matching known occurrence for both invasive, endangered, and cryptic species, and detected seasonal variation in accordance with known phenology. Dissimilarity of eDNA community compositions increased with distance between sites. Importantly, comparing our eDNA data with National Fish Atlas data (the latter compiled from a century of observations) we found positive correlation between species richness values and a congruent pattern of community compositions. These findings support the use of eDNA-based citizen science to detect patterns in biodiversity, and our approach is readily scalable to other countries, or even regional and global scales. We argue that future large-scale biomonitoring will benefit from using citizen science combined with emerging eDNA technology, and that such an approach will be important for data-driven biodiversity management and conservation.
Abstract Bioaerosols are useful indicators of plant phenology and can demonstrate the impacts of climate change on both local and regional scales (e.g. pollen monitoring/flowering phenology). ...Analysing bioaerosols with eDNA approaches are becoming more popular to quantify the diversity of airborne plant environmental DNA (eDNA) and flowering season of plants and trees. Leaf abscission from broadleaved trees and other perennial species can also indicate the status of plant health in response to climate. This happens primarily during autumn in response to seasonal growth conditions and environmental factors, such as changing photoperiod and reduced temperatures. During this period biological material is released in larger quantities to the environment. Here, rural bioaerosol composition during late summer and autumn was captured by MiSEQ sequencing of the rRNA internal transcribed spacer 2 (ITS2) region, a common marker for taxonomic variation. Meteorological parameters were recorded from a proximal weather station. The composition of atmospheric taxa demonstrated that deciduous tree DNA forms part of the bioaerosol community during autumn and, for several common broadleaved tree species, atmospheric DNA abundance correlated to high wind events. This suggests that both flowering and autumn storms cause bioaerosols from deciduous trees that can be detected with eDNA approaches. This is an aspect that must be considered when eDNA methods are used to analyse either pollen or other fragments from trees.
Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Touch or trace DNA samples from surfaces and objects deemed ...to have been contacted are frequently collected. However, a person of interest may not leave any traces on contacted surfaces, for example, if wearing gloves. A novel means of sampling human DNA from air offers additional avenues for DNA collection. In the present study, we report on the results of a pilot study into the prevalence and persistence of human DNA in the air. The first aspect of the pilot study investigates air conditioner units that circulate air around a room, by sampling units located in four offices and four houses at different time frames post‐cleaning. The second aspect investigates the ability to collect human DNA from the air in rooms, with and without people, for different periods of time and with different types of collection filters. Results of this pilot study show that human DNA can be collected on air conditioner unit surfaces and from the air, with air samples representing the more recent occupation while air conditioner units showing historic use of the room.
•Long-read sequencing is a suitable platform for tracking natural microbial dynamics.•Chlorophyll-a concentration shapes bacterioplankton communities.•Bloom’s microbiome changes with the bloom stage ...and cyanobacteria species.
Understanding spatial and temporal heterogeneity in ecosystems is essential to forecasting the effects of environmental changes. Freshwater microbes, including cyanobacteria, play a crucial role in food-web structures and biochemical processes, yet can exhibit substantial heterogeneity through space and time. They also act as powerful indicators of natural and human-induced stress due to their high metabolic and rapid response to environmental change. The formation of cyanobacteria blooms can be particularly important due to the potential production of toxins that are harmful to humans and wildlife. While high water temperatures and high nutrients are largely recognized as triggers of cyanobacterial bloom formation, there is growing evidence of the role of its associated microbiome in bloom formation. The inability to accurately forecast cyanobacteria blooms is challenged by uncertainty in the degree to which microbial diversity, and bloom forming taxa in particular, exhibit spatial heterogeneity and how spatial heterogeneity varies seasonally or between lakes spanning the trophic gradient. Here, we used long-read sequencing of the 16S rRNA gene to quantify variations in microbial spatiotemporal dynamics over the course of an ice-free season between two lakes that varied substantially in trophic status. Our results showed that the microbial community composition of eutrophic Chautauqua Lake was seasonally and spatially structured; however, during bloom events we observed lower diversity and a homogeneous community dominated by Microcystis and enriched with Gammaproteobacteria. In oligotrophic Lake George, seasonality rather than the basin of origin played a major role in structuring the microbial community; however, there was a significant difference between basins when controlling for the temporal effect and was linked to a South-to-North anthropogenic gradient. This study provides a solid foundation for exploiting long-read sequencing of prokaryotes and couples sequencing with traditional water quality monitoring to assess microbial dynamics (e.g., cyanobacteria bloom microbiome) and the effect of local and global stressors.
•Artificial light at night (ALAN) causes light pollution, affecting organisms.•This study investigated the effect of ALAN on wild-fish ecology.•The ALAN treatment level used in this study did not ...alter the species composition.•Location had a greater effect on fish habitat selection than ALAN in this study.•Carnivorous species may be affected more by ALAN than other fish.
The use of artificial light at night (ALAN) has been increasing globally and has been reported to affect a wide range of organisms. However, the effects of ALAN on wild fish communities remain unknown. In this study, we investigated the effects of ALAN on the species distribution and composition of a fish community in a canal. We hypothesized that the fish species composition in areas subjected to ALAN would differ from that in the control area. To test this hypothesis, we conducted a three-week manipulative field experiment in which real-world ALAN conditions were simulated by illuminating the water surface at night using LED lights for two weeks. During the experiment, water samples were collected from ALAN and control conditions four times a week, from which environmental DNA (eDNA) were extracted. Additionally, the number of arthropods in the ALAN and control environments was recorded daily to investigate whether ALAN impacts distribution patterns of fish prey, which may have indirect effect on fish through changed prey-predator relationships. Collected water samples were analyzed using eDNA metabarcoding with MiFish primers and real-time PCR targeting six fish species to obtain qualitative and quantitative data on fish species composition. We compared the fish species composition data between the ALAN and control environments. Our results suggest that ALAN did not significantly influence the overall fish species composition and that the sampling location had a more significant impact. Our findings also point to the possibility that the effect of ALAN on habitat selection may vary depending on the diet of the individual fish. Overall, the effect of ALAN on fish was less significant than expected. By combining eDNA methods with manipulative field experiment, this study shows the applicability of eDNA methods in investigating the effect of pollutants and offers a promising area for future investigation.
Display omitted
Marine stock assessments or biodiversity monitoring studies, which historically relied on extractive techniques (e.g., trawl or grab surveys), are being progressively replaced by non-extractive ...approaches. For instance, species abundance indices can be calculated using data obtained from high-definition underwater cameras that enable to identify taxa at low taxonomical level. In biodiversity studies, environmental DNA (eDNA) has proven to be a useful tool for characterising fish species richness. However, several marine phyla remain poorly represented in reference gene databases or release limited amounts of DNA, restricting their detection. The absence of amplification of some invertebrate taxa might also reflect primer bias. We here explore and compare the performance of eDNA and image data in describing the marine communities of several sites in the Bay of Biscay. This was achieved by deploying a remotely operated vehicle to both record images and collect seawater samples. A total of 88 taxa were identified from the eDNA samples and 121 taxa from the images. For both methods, the best characterised phylum was Chordata, with 29 and 27 Actinopterygii species detected using image versus eDNA, respectively. Neither Bryozoa nor Cnidaria was detected in the eDNA samples while the phyla were easily identifiable by imagery. Similarly, Asteroidea (Echinodermata) and Cephalopoda (Mollusca) were scarcely detected in the eDNA samples but present on the images, while Annelida were mostly identified by eDNA (18 taxa vs 7 taxa from imagery). The complementary community descriptions we highlight from these two methods therefore advocate for using both eDNA and imagery in tandem in order to capture the macroscopic biodiversity of bentho-demersal marine communities.
•We compare the performance of eDNA and imagery in describing the marine communities.•88 taxa were identified from the eDNA samples and 121 taxa from the images.•Actinopterygii species were the best characterised for both methods.•Neither Bryozoa nor Cnidaria were detected in the eDNA samples contrary to Annelida.•eDNA and imagery should be used in tandem to capture the biodiversity.
The coastline of Sub‐Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are ...threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science‐based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade‐off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade‐off could be partly resolved by applying our new data‐merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA‐based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub‐Saharan Africa.
PDF
