Environmental DNA enables detection of terrestrial mammals from forest pond water

Mammal dung-dung beetle trophic networks: an improved method based on gut-content DNA

Background

Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding.

Methods

First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity.

Results

We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung-dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2': Ecuador = 0.49; Germany = 0.41).

Conclusion

We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung-dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.

Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons

Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.

Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding

Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.

Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.

Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water

Environmental DNA (eDNA) is an increasingly popular tool in biological and ecological studies. As a biproduct of its increasing use, large number of eDNA samples are being collected and stored, that potentially contain information of many non-target species. One potential use for these eDNA samples is a surveillance and early detection of pathogens and parasites that are otherwise difficult to detect. Echinococcus multilocularis is such a parasite with serious zoonotic concern, and whose range has been expanding. If eDNA samples from various studies can be repurposed in detecting the parasite, it can significantly reduce the costs and efforts in surveillance and early detection of the parasite. We designed and tested a new set of primer-probe for detecting E. multilocularis mitochondrial DNA in environmental medium. Using this primer-probe set, we conducted real-time PCR on repurposed eDNA samples collected from three streams flowing through an area of Japan endemic to the parasite. We detected the DNA of E. multilocularis in one of the 128 samples (0.78%). The discovery suggests that while detecting E. multilocularis using eDNA samples is possible, the rate of detection appear to be very low. However, given the naturally low prevalence of the parasite among wild hosts in endemic areas, the repurposed eDNAs may still be a valid option for surveillance in newly introduced areas with the reduced cost and efforts. Further work is needed to assess and improve the effectiveness of using eDNA for detection of E. multilocularis.

Current research and future directions for realizing the ideal One-Health approach: A summary of key-informant interviews in Japan and a literature review

The COVID-19 pandemic has highlighted the importance of the One Health (OH) approach, which considers the health of humans, animals, and the environment in preventing future pandemics. A wide range of sustainable interdisciplinary collaborations are required to truly fulfill the purpose of the OH approach. It is well-recognized, however, that such collaborations are challenging. In this study, we undertook key-informant interviews with a panel of stakeholders from Japan to identify their perceived needs and challenges related to OH research. This panel included scientists, government officials, journalists, and industry stakeholders. By combining a thematic analysis of these interviews and a literature review, we summarized two key themes pertinent to the effective implementation of OH research: types of required research and systems to support that research. As a technological issue, interviewees suggested the importance of research and development of methodologies that can promote the integration and collaboration of research fields that are currently fragmented. An example of such a methodology would allow researchers to obtain high-resolution metadata (e.g. ecological and wildlife data) with high throughput and then maximize the use of the obtained metadata in research, such as in environmental DNA analysis, database construction, or the use of computational algorithms to find novel viral genomes. In terms of systems surrounding OH research, some interviewees stressed the importance of creating a sustainable research system, such as one that has continuous budget support and allows researchers to pursue their academic careers and interests. These perceptions and challenges held by Japanese stakeholders may be common to others around the world. We hope this review will encourage more researchers and others to work together to create a resilient society against future pandemics.

Under-Appreciated Phylogroup Diversity of Escherichia coli within and between Animals at the Urban-Wildland Interface

Wild animals have been implicated as reservoirs and even "melting pots" of pathogenic and antimicrobial-resistant bacteria of concern to human health. Though Escherichia coli is common among vertebrate guts and plays a role in the propagation of such genetic information, few studies have explored its diversity beyond humans nor the ecological factors that influence its diversity and distribution in wild animals. We characterized an average of 20 E. coli isolates per scat sample (n = 84) from a community of 14 wild and 3 domestic species. The phylogeny of E. coli comprises 8 phylogroups that are differentially associated with pathogenicity and antibiotic resistance, and we uncovered all of them in one small biological preserve surrounded by intense human activity. Challenging previous assumptions that a single isolate is representative of within-host phylogroup diversity, 57% of individual animals sampled carried multiple phylogroups simultaneously. Host species' phylogroup richness saturated at different levels across species and encapsulated vast within-sample and within-species variation, indicating that distribution patterns are influenced both by isolation source and laboratory sampling depth. Using ecological methods that ensure statistical relevance, we identify trends in phylogroup prevalence associated with host and environmental factors. The vast genetic diversity and broad distribution of E. coli in wildlife populations has implications for biodiversity conservation, agriculture, and public health, as well as for gauging unknown risks at the urban-wildland interface. We propose critical directions for future studies of the "wild side" of E. coli that will expand our understanding of its ecology and evolution beyond the human environment. IMPORTANCE To our knowledge, neither the phylogroup diversity of E. coli within individual wild animals nor that within an interacting multispecies community have previously been assessed. In doing so, we uncovered the globally known phylogroup diversity from an animal community on a preserve imbedded in a human-dominated landscape. We revealed that the phylogroup composition in domestic animals differed greatly from that in their wild counterparts, implying potential human impacts on the domestic animal gut. Significantly, many wild individuals hosted multiple phylogroups simultaneously, indicating the potential for strain-mixing and zoonotic spillback, especially as human encroachment into wildlands increases in the Anthropocene. We reason that due to extensive anthropogenic environmental contamination, wildlife is increasingly exposed to our waste, including E. coli and antibiotics. The gaps in the ecological and evolutionary understanding of E. coli thus necessitate a significant uptick in research to better understand human impacts on wildlife and the risk for zoonotic pathogen emergence.

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.

Mink on the brink: comparing survey methods for detecting a critically endangered carnivore, the European mink Mustela lutreola

Monitoring rare and elusive species is critical in guiding appropriate conservation management measures. Mammalian carnivores are challenging to monitor directly, due to their generally nocturnal and solitary lifestyle, and relatively large home ranges. The European mink Mustela lutreola is a critically endangered, small, semi-aquatic carnivore and is one of the most threatened mammal species in Europe. In northern Spain, the European mink population is monitored regionally using different methods and approaches, making assessment of national population status difficult. There is an urgent need to 1) assess the efficacy of survey methods and 2) identify a standard monitoring methodology that can be deployed rapidly and inexpensively over large areas of the mink’s range. We deployed four methods—camera trapping, hair tubes, live trapping, and environmental DNA (eDNA) from water samples—to compare the probability of detecting European mink when present at 25 sampling sites within five 10 × 10 km2, and the economic cost and time required for each method. All four methods successfully detected European mink but the probability of detection varied by method. Camera trapping and hair tubes had the highest probability of detection; however, eDNA and live trapping detected mink in one 10 × 10 km2 where the latter two methods did not. For future European mink monitoring programs, we recommend a combination of at least two methods and suggest that camera traps or hair tubes are combined with live trapping or eDNA (depending on the scale and aims of the study), to gather critical information on distribution, occupancy and conservation status.

Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea)

Brittle stars (class Ophiuroidea) are marine invertebrates comprising approximately 2,100 extant species, and are considered to constitute the most diverse taxon of the phylum Echinodermata. As a non-invasive method for monitoring biodiversity, we developed two new sets of PCR primers for metabarcoding environmental DNA (eDNA) from brittle stars. The new primer sets were designed to amplify 2 short regions of the mitochondrial 16S rRNA gene, comprising a conserved region (111–115 bp, 112 bp on average; named “16SOph1”) and a hyper-variable region (180–195 bp, 185 bp on average; named “16SOph2”) displaying interspecific variation. The performance of the primers was tested using eDNA obtained from two sources: a) rearing water of an 2.5 or 170 L aquarium tanks containing 15 brittle star species and b) from natural seawater collected around Misaki, the Pacific coast of central Japan, at depths ranging from shallow (2 m) to deep (&gt; 200 m) sea. To build a reference library, we obtained 16S rRNA sequences of brittle star specimens collected from around Misaki and from similar depths in Japan, and sequences registered in International Nucleotide Sequence Database Collaboration. As a result of comparison of the obtained eDNA sequences with the reference library 37 (including cryptic species) and 26 brittle star species were detected with certain identities by 16SOph1 and 16SOph2 analyses, respectively. In shallow water, the number of species and reads other than the brittle stars detected with 16SOph1 was less than 10% of the total number. On the other hand, the number of brittle star species and reads detected with 16SOph2 was less than half of the total number, and the number of detected non-brittle star metazoan species ranged from 20 to 46 species across 6 to 8 phyla (only the reads at the “Tank” were less than 0.001%). The number of non-brittle star species and reads at 80 m was less than 10% with both of the primer sets. These findings suggest that 16SOph1 is specific to the brittle star and 16SOph2 is suitable for a variety of marine metazoans. It appears, however, that further optimization of primer sequences would still be necessary to avoid possible PCR dropouts from eDNA extracts. Moreover, a detailed elucidation of the brittle star fauna in the examined area, and the accurate identification of brittle star species in the current DNA databank is required.

Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals

Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals, a guild with many threatened and poorly studied taxa worldwide, within two central New Jersey (USA) woodlands. We evaluated species detected with metabarcoding using two eDNA collection methods (tree bark vs. soil sampling), and compared the performance of two detection methods (qPCR vs. metabarcoding) within a single species. Our survey, which included 94 sampling events at 21 trees, detected 16 species of mammals, representing over 60% of the diversity expected in the area. More DNA was found for the 8 arboreal versus 8 non-arboreal species detected (mean: 2466 vs. 289 reads/sample). Soil samples revealed a generally similar composition, but a lower diversity, of mammal species. Detection rates for big brown bat were 3.4 × higher for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.

Isolation of extended‐spectrum β‐lactamase‐producing Escherichia coli from Japanese red fox ( Vulpes vulpes japonica )

Antimicrobial resistance is a global concern requiring a one‐health approach. Given wild animals can harbor antimicrobial‐resistant bacteria (ARB), we investigated their presence in 11 fecal samples from wild animals using deoxycholate hydrogen sulfide lactose agar with or without cefotaxime (CTX, 1 mg/L). Thus, we isolated CTX‐resistant Escherichia coli from two Japanese red fox fecal samples. One strain was O83:H42‐ST1485‐fimH58 CTX‐M‐55‐producing E. coli carrying the genes aph(3″)‐Ib, aph(3′)‐Ia, aph(6)‐Id, mdf(A), sitABCD, sul2, tet(A), and tet(B), whereas the other was O25:H4‐ST131‐fimH30 CTX‐M‐14‐producing E. coli carrying mdf(A) and sitABCD and showing fluoroquinolone resistance. Thus, the presence of extended‐spectrum β‐lactamase producers in wild foxes suggests a spillover of ARB from human activities to these wild animals.

Parasites and blood-meal hosts of the tsetse fly in Tanzania: a metagenomics study

Background

Tsetse flies can transmit various Trypanosoma spp. that cause trypanosomiasis in humans, wild animals, and domestic animals. Amplicon deep sequencing of the 12S ribosomal RNA (rRNA) gene can be used to detect mammalian tsetse hosts, and the 18S rRNA gene can be used to detect all associated eukaryotic pathogens, including Trypanosoma spp.

Methods

Tsetse flies were collected from the Serengeti National Park (n = 48), Maswa Game Reserve (n = 42), and Tarangire National Park (n = 49) in Tanzania in 2012–13. Amplicon deep sequencing targeting mammal-specific 12S rRNA and 18S rRNA genes was performed to screen the blood-feeding sources of tsetse flies and eukaryotic parasites in tsetse flies, respectively.

Results

12S rRNA gene deep sequencing revealed that various mammals were blood-feeding sources of the tsetse flies, including humans, common warthogs, African buffalos, mice, giraffes, African elephants, waterbucks, and lions. Genes of humans were less frequently detected in Serengeti (P = 0.0024), whereas African buffaloes were detected more frequently as a blood-feeding source (P = 0.0010). 18S rRNA gene deep sequencing showed that six tsetse samples harbored the Trypanosoma gene, which was identified as Trypanosoma godfreyi and Trypanosoma simiae in subsequent ITS1 gene sequencing.

Conclusions

Through amplicon deep sequencing targeting the 12S rRNA and 18S rRNA genes, various mammalian animals were identified as blood-meal sources, and two Trypanosoma species were detected in tsetse flies collected from the Maswa Game Reserve, Serengeti National Park, and Tarangire National Park in Tanzania. This study illustrates the patterns of parasitism of tsetse fly, wild animals targeted by the fly, and Trypanosoma spp. carried by the fly in Tanzania. It may provide essential data for formulating better strategies to control African trypanosomes.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05344-1.

Environmental DNA analysis for macro-organisms: species distribution and more

In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.

Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia

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 amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field 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.

Using Environmental DNA to Detect Whales and Dolphins in the New York Bight

Determining how cetaceans and other threatened marine animals use coastal habitats is critical to the effective conservation of these species. Environmental DNA (eDNA) is an emerging tool that can potentially be used to detect cetaceans over broad spatial and temporal scales. In particular, eDNA may present a useful complementary method for monitoring their presence during visual surveys in nearshore areas, and for co-detecting prey. In conjunction with ongoing visual surveys, we tested the ability of eDNA metabarcoding to detect the presence and identity of cetaceans in the New York Bight (NYB), and to identify fish species (potential prey) present in the area. In almost all cases in which humpback whales and dolphins were visually observed, DNA from these species was also detected in water samples. To assess eDNA degradation over time, we took samples in the same location 15 and 30 min after a sighting in seven instances, and found that eDNA often, but not always, dropped to low levels after 30 min. Atlantic menhaden were detected in all samples and comprised the majority of fish sequences in most samples, in agreement with observations of large aggregations of this important prey species in the NYB. While additional data are needed to better understand how factors such as behavior and oceanographic conditions contribute to the longevity of eDNA signals, these results add to a growing body of work indicating that eDNA is a promising tool to complement visual and acoustic surveys of marine megafauna.

Measuring biodiversity from DNA in the air

The crisis of declining biodiversity¹ exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential to quantify the causes and consequences of global change. Environmental DNA² has revolutionized aquatic ecology,³ permitting population monitoring⁴ and remote diversity assessments matching or outperforming conventional methods of community sampling.^3-5 Despite this model, similar methods have not been widely adopted in terrestrial ecosystems. Here, we demonstrate that DNA from terrestrial animals can be filtered, amplified, and then sequenced from air samples collected in natural settings representing a powerful tool for terrestrial ecology. We collected air samples at a zoological park, where spatially confined non-native species allowed us to track DNA sources. We show that DNA can be collected from air and used to identify species and their ecological interactions. Air samples contained DNA from 25 species of mammals and birds, including 17 known terrestrial resident zoo species. We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom. Our data demonstrate that airborne eDNA concentrates around recently inhabited areas but disperses away from sources, suggesting an ecology to airborne eDNA and the potential for sampling at a distance. Our findings demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring.

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan

Understanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed a Bufo-specific eDNA assay for detecting an invasive, toxic, and terrestrial toad species Bufo japonicus formosus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. The eDNA assay was field-validated in ponds where B. japonicus were observed, as well as in rivers downstream of the reproductive ponds. Thus, the assay provided us an opportunity to screen watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected toad eDNA at 32 out of 73 sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and 21 sites without such records. And those eDNA detections were from twelve out of 31 river systems in the entire river basin. A Bayesian, multiscale occupancy model supported high eDNA detectability among those sites. These results suggest that the eDNA assay can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

Simple Summary

Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future.

Abstract

Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands

Invasive species are major contributors to global biodiversity decline. Invasive mammalian species (IMS), in particular, have profound negative effects in island systems that contain disproportionally high levels of species richness and endemism. The eradication and control of IMS have become important conservation tools for managing species invasions on islands, yet these management operations are often subject to failure due to knowledge gaps surrounding species- and system-specific characteristics, including invasion pathways and contemporary migration patterns. Here, we synthesize the literature on ways in which genetic and genomic tools have effectively informed IMS management on islands, specifically associated with the development and modification of biosecurity protocols, and the design and implementation of eradication and control programs. In spite of their demonstrated utility, we then explore the challenges that are preventing genetics and genomics from being implemented more frequently in IMS management operations from both academic and non-academic perspectives, and suggest possible solutions for breaking down these barriers. Finally, we discuss the potential application of genome editing to the future management of invasive species on islands, including the current state of the field and why islands may be effective targets for this emerging technology.

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live-trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live-trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap-nights); in addition to 16 pitfall traps (1,408 trap-nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera-days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3-km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample-based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large- and medium-sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community.

eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.

Amazonian mammal monitoring using aquatic environmental DNA

Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.

eDNAir: proof of concept that animal DNA can be collected from air sampling

Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.

Applications of eDNA Metabarcoding for Vertebrate Diversity Studies in Northern Colombian Water Bodies

Environmental DNA metabarcoding is a tool with increasing use worldwide. The uses of such technology have been validated several times for diversity census, invasive species detection, and endangered/cryptic/elusive species detection and monitoring. With the help of this technology, water samples collected (n = 37) from several main river basins and other water bodies of the northern part of Colombia, including the Magdalena, Sinú, Atrato, and San Jorge river basins, were filtered and analyzed and processed using universal 12S primers for vertebrate fauna and NGS. Over 200 native taxa were detected, the majority of them being fish species but also including amphibia, reptiles, and several non-aquatic species of birds and mammals (around 78, 3, 2, 9, and 8%, respectively). Among the matches, vulnerable, and endangered species such as the catfish Pseudoplatystoma magdaleniatum and the Antillean manatee (Trichechus manatus) were detected. The manual revision of the data revealed some geographical incongruencies in classification. No invasive species were detected in the filters. This is, to our knowledge, the first time this technique is used in rivers of the country and this tool promises to bring advances in monitoring and conservation efforts, since its low cost and fast deployment allows for sampling in small periods of time, together with the fact that it can detect a wide range of species, allows for a new way of censing the vertebrate diversity in Colombia. Diversity analysis showed how the species identified using this method point to expected community structure although still much needs to be improved in rates of detection and genomic reference databases. This technique could be used in citizen science projects involving local communities in these regions.

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.

Selective collection of long fragments of environmental DNA using larger pore size filter

Environmental DNA (eDNA) can exist in water with various sizes and states. Among them, relative to extra-cellular DNA, intra-cellular DNA such as cell and tissue fragments can mainly be detected at larger size fractions, and may be protected from enzymatic DNA degradation processes. Here, we verified the hypothesis that the selective collection of such large-sized eDNA enhances the efficiency of capturing less-degraded eDNA, based on a tank experiment using Japanese Jack Mackerel (Trachurus japonicus) as a model species. We concentrated different volumes of rearing water using the filters with different pore sizes (0.7 μm and 2.7 μm), and quantified the copy number of short and long mitochondrial and short nuclear DNA fragments of target species in water samples. As a result, the ratio of long to short eDNA concentrations was higher in the larger pore size filter, which would support our stated hypothesis. In addition, the ratio of nuclear to mitochondrial eDNA was lower in the larger pore size filter. These results imply a difference in the persistence of nuclear and mitochondrial DNA between intra- and extra-cellular environments. Moreover, larger filter pore size did not necessarily decrease the yields of eDNA, and there was little difference in yields in smaller filtration volumes. The findings of this study indicate the potential to select information from eDNA signals by focusing on eDNA of specific size and state, which may contribute to efficient utilization of the information on species taxonomy and physiology in water samples.

Leveraging eDNA to expand the study of hybrid zones

Hybrid zones are important windows into ecological and evolutionary processes. Our understanding of the significance and prevalence of hybridization in nature has expanded with the generation and analysis of genome‐spanning data sets. That said, most hybridization research still has restricted temporal and spatial resolution, which limits our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue that rapidly advancing environmental DNA (eDNA) methodology could be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), refine and geographically expand sampling density, and collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real‐time biological tracking of hybrid zones, and eDNA provides broad, but as yet untapped, potential to address eco‐evolutionary questions.

Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment

Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3) and 41 (dada2) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA-based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods. Our results suggest that eDNA-based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

Blood meal sources and bacterial microbiome diversity in wild-caught tsetse flies

Tsetse flies are the vectors of African trypanosomiasis affecting 36 sub-Saharan countries. Both wild and domestic animals play a crucial role in maintaining the disease-causing parasites (trypanosomes). Thus, the identification of animal reservoirs of trypanosomes is vital for the effective control of African trypanosomiasis. Additionally, the biotic and abiotic factors that drive gut microbiome diversity in tsetse flies are primarily unresolved, especially under natural, field conditions. In this study, we present a comprehensive DNA metabarcoding approach for individual tsetse fly analysis in the identification of mammalian blood meal sources and fly bacterial microbiome composition. We analyzed samples from two endemic foci, Kafue, Zambia collected in June 2017, and Hurungwe, Zimbabwe sampled in April 2014 (pilot study) and detected DNA of various mammals including humans, wild animals, domestic animals and small mammals (rat and bat). The bacterial diversity was relatively similar in flies with different mammalian species DNA, trypanosome infected and uninfected flies, and female and male flies. This study is the first report on bat DNA detection in wild tsetse flies. This study reveals that small mammals such as bats and rats are among the opportunistic blood meal sources for tsetse flies in the wild, and the implication on tsetse biology and ecology needs to be studied.

Are bacteria potential sources of fish environmental DNA?

The environmental DNA (eDNA) method is being increasingly applied in various environments. Although eDNA undergoes rapid degradation in aqueous environments, it has been detected in streams up to 10 km downstream from its source. As environmental bacteria can uptake free DNA, transfer their genetic traits, and amplify, there is a potential risk that they, rather than a target aquatic species, could become a source of measured eDNA. This study examined whether bacteria with incorporated fish DNA could be such a source by investigating the detectability of fish DNA generated by bacteria inhabiting river water and riverbed sediment. We attempted to detect common carp (Cyprinus carpio) eDNA in stream water and sediment samples and the DNA of common carp produced by bacterial colonies (Escherichia coli, total coliform, and heterotrophic bacteria) cultured from the samples. The eDNA was detected in the environmental samples but the carp DNA from the targeted bacteria was rarely detected in both water and riverbed sediment samples. Our results suggest that the risk of bacterium-induced false positive detection for fish eDNA is negligible.