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Yoamel Milin&#x;García Robert Young Mary Madden Erin Bullas&#x;Appleton Robert H. Hanner 《Ecology and evolution》2021,11(5):1999
Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and invasive pest biosurveillance programs. The introduction of insect pests considered invasive alien species (IAS) into a non‐native range poses a threat to native plant health. The early detection of IAS can allow for prompt actions by regulating authorities, thereby mitigating their impacts. In the present study, we optimized and validated a fast and cost‐effective eDNA metabarcoding protocol for biosurveillance of IAS and characterization of insect and microorganism diversity. Forty‐eight traps were placed, following the CFIA''s annual forest insect trapping survey, at four locations in southern Ontario that are high risk for forest IAS. We collected insects and eDNA samples using Lindgren funnel traps that contained a saturated salt (NaCl) solution in the collection jar. Using cytochrome c oxidase I (COI) as a molecular marker, a modified Illumina protocol effectively identified 2,535 Barcode Index Numbers (BINs). BINs were distributed among 57 Orders and 304 Families, with the vast majority being arthropods. Two IAS (Agrilus planipennis and Lymantria dispar) are regulated by the Canadian Food Inspection Agency (CFIA) as plant health pests, are known to occur in the study area, and were identified through eDNA in collected traps. Similarly, using 16S ribosomal RNA and nuclear ribosomal internal transcribed spacer (ITS), five bacterial and three fungal genera, which contain species of regulatory concern across several Canadian jurisdictions, were recovered from all sampling locations. Our study results reaffirm the effectiveness and importance of integrating eDNA metabarcoding as part of identification protocols in biosurveillance programs. 相似文献
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Toshifumi Minamoto 《DNA research》2022,29(3)
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. 相似文献
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Alexander Van Nynatten Kavishka S. Gallage Nathan K. Lujan Nicholas E. Mandrak Nathan R. Lovejoy 《Molecular ecology resources》2023,23(6):1319-1333
Detection of invasive species is critical for management but is often limited by challenges associated with capture, processing and identification of early life stages. DNA metabarcoding facilitates large-scale monitoring projects to detect establishment early. Here, we test the use of DNA metabarcoding to monitor invasive species by sequencing over 5000 fishes in bulk ichthyoplankton samples (larvae and eggs) from four rivers of ecological and cultural importance in southern Canada. We were successful in detecting species known from each river and three invasive species in two of the four rivers. This includes the first detection of early life-stage rudd in the Credit River. We evaluated whether sampling gear affected the detection of invasive species and estimates of species richness, and found that light traps outperform bongo nets in both cases. We also found that the primers used for the amplification of target sequences and the number of sequencing reads generated per sample affect the consistency of species detections. However, these factors have less impact on detections and species richness estimates than the number of samples collected and analysed. Our analyses also show that incomplete reference databases can result in incorrectly attributing DNA sequences to invasive species. Overall, we conclude that DNA metabarcoding is an efficient tool for monitoring the early establishment of invasive species by detecting evidence of reproduction but requires careful consideration of sampling design and the primers used to amplify, sequence and classify the diversity of native and potentially invasive species. 相似文献
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Forrest W. Lefler David E. Berthold H. Dail Laughinghouse IV 《Journal of phycology》2023,59(3):470-480
Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well-known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq ( https://zenodo.org/record/7569105 ), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full-length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences. 相似文献
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Ariane Atteia;Béatrice Bec;Camille Gianaroli;Ophélie Serais;Isaure Quétel;Franck Lagarde;Angélique Gobet; 《Molecular ecology resources》2024,24(1):e13887
Sequential membrane filtration of water samples is commonly used to monitor the diversity of aquatic microbial eukaryotes. This capture method is efficient to focus on specific taxonomic groups within a size fraction, but it is time-consuming. Centrifugation, often used to collect microorganisms from pure culture, could be seen as an alternative to capture microbial eukaryotic communities from environmental samples. Here, we compared the two capture methods to assess diversity and ecological patterns of eukaryotic communities in the Thau lagoon, France. Water samples were taken twice a month over a full year and sequential filtration targeting the picoplankton (0.2–3 μm) and larger organisms (>3 μm) was used in parallel to centrifugation. The microbial eukaryotic community in the samples was described using an environmental DNA approach targeting the V4 region of the 18S rRNA gene. The most abundant divisions in the filtration fractions and the centrifugation pellet were Dinoflagellata, Metazoa, Ochrophyta, Cryptophyta. Chlorophyta were dominant in the centrifugation pellet and the picoplankton fraction but not in the larger fraction. Diversity indices and structuring patterns of the community in the two size fractions and the centrifugation pellet were comparable. Twenty amplicon sequence variants were significantly differentially abundant between the two size fractions and the centrifugation pellet, and their temporal patterns of abundance in the two fractions combined were similar to those obtained with centrifugation. Overall, centrifugation led to similar ecological conclusions as the two filtrated fractions combined, thus making it an attractive time-efficient alternative to sequential filtration. 相似文献
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赤水河是长江上游少有的仍保持自然流态的大型一级支流,是长江鱼类重要的繁衍场和珍稀物种的保护地,摸清其鱼类多样性现状及鱼类群落结构特征对赤水河水生态恢复评估极为重要。于2021年9月对赤水河流域开展了鱼类多样性、分布及其特征调查,全流域共设置52个采样点,采用环境DNA技术采集并研究了赤水河鱼类的组成及其分布。结果显示通过环境DNA方法共调查到鱼类6目18科62属77种,包含16种长江特有鱼类。以鲤形目为主,占总数的87.87%。赤水河鱼类食性以杂食性和肉食性鱼类为主,群落结构上,处于下层水环境鱼类较多;赤水河鱼类优势种为宽鳍鱲(Y=0.205)、西昌华吸鳅(Y=0.085)、麦穗鱼(Y=0.068)、乌苏拟鲿(Y=0.033)、云南光唇鱼(Y=0.027);赤水河上游和下游鱼类群落(P<0.01)和Shannon-Wiener指数差异均显著(P<0.05)。海拔、流速、pH、电导率和温度是影响赤水河鱼类多样性的主要环境因素。为环境DNA技术在赤水河鱼类多样性调查中的应用提供了探索性研究,将有助于赤水河生物多样性的保护。 相似文献
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《Evolutionary Applications》2018,11(6):891-905
Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models’ performances through simulations. We tested 1,050 parameter sets on 18S sequences from 20 AIS to determine optimal parameters for each research goal. We tested optimized pipelines’ performances (detectability and sensitivity) by computationally inoculating sequences of 20 AIS into ten bulk zooplankton samples from ports across Canada. We found that optimal parameter selection generally depends on the research goal. However, regardless of research goal, we found that metazoan 18S sequences produced by 454 pyrosequencing should be trimmed to 375–400 bp and sequence quality filtering should be relaxed (1.5 ≤ maximum expected error ≤ 3.0, Phred score = 10). Clustering and denoising were only viable for estimating species richness, because these processing steps made some species undetectable at low sequence abundances which would not be useful for early detection of AIS. With parameter sets optimized for early detection of AIS, 90% of AIS were detected with fewer than 11 target sequences, regardless of whether clustering or denoising was used. Despite developments in next‐generation sequencing, sequence processing remains an important issue owing to difficulties in balancing false‐positive and false‐negative errors in metabarcoding data. 相似文献
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Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments. 相似文献
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Arial J. Shogren Jennifer L. Tank Scott P. Egan Diogo Bolster Tenna Riis 《Freshwater Biology》2019,64(8):1467-1479
- Sampling water for environmental DNA (eDNA) is an emerging tool for documenting species presence without direct observation, allowing for earlier detection and faster response than conventional sampling methods in aquatic ecosystems.
- However, current understanding of how eDNA is transported in streams and rivers remains imprecise, with uncertainty of how the unique transport properties of eDNA may influence the interpretation of a positive detection. To test the utility of eDNA sensing in flowing waters, we compared quantitative eDNA analyses to zebra mussel density surveys in a Danish river.
- Although flowing water complicates the relationships between eDNA production, transport, and removal, we found weak but positive relationships between eDNA concentration, zebra mussels, and biophysical parameters. For example, while zebra mussel densities were only moderately predicted by eDNA concentrations, eDNA was most strongly influenced by nutrient concentrations and water velocity. These results may be used to inform future sampling strategies, where hydrological variables could better constrain eDNA fate.
- We also modelled estimates for net eDNA transport, retention, and degradation to estimate the relative importance of these processes for removing eDNA from the water column. In our study system, physical retention accounted for c. 70% of removal when compared to degradation alone, making it an important process to consider when assessing downstream eDNA transport.
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Kayoko Fukumori;Natsuko I. Kondo;Ayato Kohzu;Kenji Tsuchiya;Hiroshi Ito;Taku Kadoya; 《Ecology and evolution》2024,14(3):e11091
In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL−1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions. 相似文献
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Tristan Milhau Alice Valentini Nicolas Poulet Nicolas Roset Pauline Jean Coline Gaboriaud Tony Dejean 《Journal of fish biology》2021,98(2):387-398
As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species. 相似文献
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Nathan T. Evans Brett P. Olds Mark A. Renshaw Cameron R. Turner Yiyuan Li Christopher L. Jerde Andrew R. Mahon Michael E. Pfrender Gary A. Lamberti David M. Lodge 《Molecular ecology resources》2016,16(1):29-41
Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance. 相似文献
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Johan Pansu Richard C. Winkworth Fran?oise Hennion Ludovic Gielly Pierre Taberlet Philippe Choler 《Biology letters》2015,11(9)
During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems. 相似文献
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Ryan P. Kelly 《Molecular ecology resources》2016,16(1):10-12
The arc of reception for a new technology or method – like the reception of new information itself – can pass through predictable stages, with audiences’ responses evolving from ‘I don't believe it’, through ‘well, maybe’ to ‘yes, everyone knows that’ to, finally, ‘old news’. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. ‘Macrobial’ biologists and ecologists – those accustomed to dealing with species they can see and count – have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. ( 2015 ) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species’ biomasses. The strength and slope of this association vary for each species and each primer set – further evidence that there is no universal parameter linking recovered DNA to species abundance – but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: ‘Yes, but how many are there?’ 相似文献
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Kristy Deiner Holly M. Bik Elvira Mächler Mathew Seymour Anaïs Lacoursière‐Roussel Florian Altermatt Simon Creer Iliana Bista David M. Lodge Natasha de Vere Michael E. Pfrender Louis Bernatchez 《Molecular ecology》2017,26(21):5872-5895
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. 相似文献
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S. V. Turanov;M. A. Koltsova;O. A. Rutenko; 《Ecology and evolution》2024,14(7):e11631
Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode. 相似文献
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Sarsha Gorissen Jacqueline Mallinson Matthew Greenlees Richard Shine 《Austral ecology》2015,40(2):170-177
The Blue Mountains water skink (Eulamprus leuraensis; Scincidae) is restricted to less than 40 fragmented swamp sites, all within the Blue Mountains and Newnes Plateau areas of New South Wales, Australia. Climate change is expected to increase fire frequency in the area, potentially degrading habitat quality for this endangered reptile. We quantified lizard abundances in 12 swamps using standardized surveys, and constructed a Global Information System (GIS) database to determine fire‐histories for each swamp since 1967. The abundance of Blue Mountains water skinks was negatively correlated with fire frequency, but not with time since fire. Indirect impacts of fire (mediated via shifts in vegetation density, moisture levels, prey availability and post‐fire predation) may be more important than direct effects in these cool, moist habitats. Although lizards were less common in swamps close to urban areas, and less common in frequently burnt areas, viable populations of this endangered reptile still persist even in anthropogenically disturbed swamps and in swamps that have experienced up to four fires in 20 years. Future research could usefully extend these analyses to other swamps in the locality, and explore the broader impacts of fire regimes on the distinctive flora and fauna of this threatened ecological community. 相似文献
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Bruno H. Saranholi Karen G. Rodriguez-Castro Carolina S. Carvalho Samira Chahad-Ehlers Carla C. Gestich Sónia C. S. Andrade Patrícia D. Freitas Pedro M. Galetti Jr 《Molecular ecology resources》2023,23(8):1790-1799
Ingested-derived DNA (iDNA) from insects represents a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a diverse diet and are widely distributed. Because of these advantages, the use of iDNA for detecting mammals has gained increasing attention. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals with a small sampling effort in a semi-controlled area, a zoo that houses native and non-native species. We compared mosquitoes and flies regarding the number of mammal species detected, the amount of mammal sequence reads recovered, and the flight distance range for detecting mammals. We also verified if the combination of two mini-barcodes (12SrRNA and 16SrRNA) would perform better than either mini-barcode alone to inform local mammal biodiversity from iDNA. To capture mosquitoes and flies, we distributed insect traps in eight sampling points during 5 days. We identified 43 Operational Taxonomic Units from 10 orders, from the iDNA of 17 mosquitoes and 46 flies. There was no difference in the number of species recovered per individual insect between mosquitoes and flies, but the number of flies captured was higher, resulting in more mammal species recovered by flies. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers would allow a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our assay proved to be efficient for mammal detection, considering the high number of species detected with a reduced sampling effort. 相似文献