Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to ...disentangle study‐specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta‐analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for <200 bp sequences in the available literature means this relationship was not assessed with longer sequences (e.g. >800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta‐analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments.
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.
The fish biodiversity of the Beagle Channel is insufficiently assessed, poorly managed, and threatened by exotic species. Novel, rapid, and cost-effective DNA-based approaches are valuable for ...understanding fish communities and biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing fish species composition by analyzing water samples from three sites along the Beagle Channel in the extreme south of Argentina. Fish biodiversity was estimated using high-throughput sequencing of 12S rRNA amplicons. First, a local reference database was generated, including 12S sequences of 48 spp. In total, 31 environmental sequences were recovered, belonging to 11 families, 15 genera, and 22 species. Six eDNA sequences did not match any species in our database. Multivariate analyses indicated that the relative species composition differed significantly among the sampled sites. However, the most abundant species detected were consistent with historical data on fish species recorded in the sites sampled. In conclusion, eDNA metabarcoding is sensitive, reliable, and suitable for studies on the presence and distribution of fish species in the area. We further strengthen the potential of eDNA metabarcoding as a biomonitoring tool.
•EDNA metabarcoding method detects abundant and rare species of the Beagle Channel.•The list of species reported for the Beagle Channel has been updated.•Information for the 12S rRNA gene was enriched with Southern-Hemisphere fish species.
Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may ...assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.
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•5 µm filter pore size is preferable for capturing eDNA from human blood in freshwater.•8 µm filter pore is more suitable for capturing human skin cells in freshwater.•Amount of eDNA from human blood and skin cells in freshwater is reduced over time.•Filter sizes of 8 µm, 5 µm, and 1.2 µm filters recommended for unknown eDNA source.
The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling ...approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6–18 h for open mesocosms versus 18–48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0–0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.
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•We investigated how eDNA particle sizes traveled under varying substrate and light.•In stream mesocosms, small eDNA particles traveled farther than large eDNA particles.•Light, potentially impacting algae, may increase eDNA removal by benthic biofilms.•eDNA particle size distribution could estimate organism location and abundance.
Collembola are abundant and have significant roles in the soil ecosystem. Therefore, the phenotypic endpoints of Collembola population or community have been used as an effective bioindicator for ...assessing soil quality. Since the identification and counting the collembolans in the soil is a laborious and costly procedure, environmental DNA (eDNA)‐based biomonitoring was proposed as an analysis tool of collembolan species found in the soil. In this study, standard primer sets for the species‐specific eDNA analysis using Allonychiurus kimi, a soil bioindicator species was selected. Then, the primers were tested for specificity and sensitivity from the soil samples. Two different eDNA samples were tested: (1) eDNA samples were extracted from the soil with A. kimi individuals (intra‐organismal eDNA). (2) The samples from the soil without A. kimi individuals (extra‐organismal eDNA). The two primers were confirmed in their sensitivity and specificity to the two types of eDNA samples selected. Ct‐values from both intra‐ and extra‐organismal eDNA showed the significant correlations to the number of inoculated A. kimi (adj. R2 = 0.7453–0.9489). These results suggest that in excretion, egg, and other exuviae had a significant effect on eDNA analysis from soil samples taken. Furthermore, our results suggest that environmental factors should be considered when analyzing eDNA collected from soil.
In this study, standard primer sets for the species‐specific eDNA analysis using Allonychiurus kimi, a soil bioindicator species was selected. Then, the primers were tested for specificity and sensitivity from the soil samples. Two primers were confirmed in their sensitivity and specificity to the two eDNA samples selected. Ct‐values from both intra‐ and extra‐organismal eDNAs showed the significant correlations to the number of inoculated A. kimi. These results suggest that in excretion, egg, and other exuviae had a significant effect on eDNA analysis from soil samples taken.
Unfiltered and filtered water samples can be used to collect environmental DNA (eDNA). We developed the novel "Preserve, Precipitate, Lyse, Precipitate, Purify" (PPLPP) workflow to efficiently ...extract eDNA from Longmire's preserved unfiltered and filtered water samples (44-100% recovery). The PPLPP workflow includes initial glycogen-aided isopropanol precipitation, guanidium hypochlorite and Triton X-100-based lysis, terminal glycogen-aided polyethylene glycol precipitation, and inhibitor purification. Three novel eDNA assays that exclusively target species invasive to Australia were also developed: Tilapia_v2_16S concurrently targets
(Mozambique tilapia) and
(spotted tilapia) while R.marina_16S and C.caroliniana_matK discretely target
(cane toad) and
(fanwort), respectively. All 3 assays were validated
before
and
validations using PPLPP workflow extracted samples. PPLPP workflow was concurrently validated
and
using all 3 assays.
validations demonstrated that
) glycogen inclusion increased extracellular DNA recovery by ∼48-fold compared with glycogen exclusion,
) swinging-bucket centrifugation for 90 min at 3270
is equivalent to fixed-angle centrifugation for 5-20 min at 6750
, and
) Zymo OneStep Inhibitor Removal Kit, Qiagen DNeasy PowerClean Pro Cleanup Kit, and silica-Zymo double purification provide effective inhibitor removal.
validation demonstrated 95.8 ± 2.8% (mean ± SEM) detectability across all 3 target species in Longmire's preserved unfiltered and filtered water samples extracted using the PPLPP workflow (without phenol:chloroform:isoamyl alcohol purification) after 39 d of incubation at room temperature and 50°C. PPLPP workflow is recommended for future temperate and tropical eDNA studies that use Longmire's to preserve unfiltered or filtered water samples.
Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the ...laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2‐week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol–chloroform–isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.
As one of the nine primary non-ferrous metal smelting bases in China, Daye Lake basin was polluted due to diverse human activities. But so far the pollution status and related ecological risks of ...this region have not been detailly investigated. In current study, pollutants including heavy metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in eight sediment samples from Daye Lake were quantified. 18S rRNA gene sequencing was employed to profile the nematode community structure within these sediments. Model organism Caenorhabditis elegans (C. elegans) were further applied for a comprehensive ecological risk assessment of Daye Lake. Notably, Cadmium (Cd) was identified as a key driver of ecological risk, reaching an index of 1287.35. At sample point S4, OCPs particularly p,p'-DDT, displayed an extreme ecological risk with a value of 23.19. Cephalobidae and Mononchida showed strong sensitivity to pollutant levels, reinforcing their suitability as robust bioindicators. The composite pollutants in sampled sediments caused oxidative stress in C. elegans, with gene Vit-2 and Mtl-1 as sensitive biomarkers. By employing the multiple analysis methods, our data can offer valuable contributions to environmental monitoring and health risk assessment for composite polluted areas.
Advances and Discoveries in Myxozoan Genomics Alama-Bermejo, Gema; Holzer, Astrid S.
Trends in parasitology,
June 2021, 2021-Jun, 2021-06-00, 20210601, Letnik:
37, Številka:
6
Journal Article
Recenzirano
Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, ...and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first ‘omic’ datasets have now become the main resource for a better understanding of host–parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data.
The first myxozoan genome assembly was published in 2015, and myxozoan genomics has since become a rapidly progressing field, with limitations due to DNA contamination from largely polyploid fish hosts.Myxozoan genomes are amongst the smallest metazoan genomes on Earth with important gene reductions and loss of basic biological functions such as DNA methylation and, in one case, the mitochondrial genome.The evolutionary history of myxozoans appears to confirm a sister relationship of the Myxozoa and Polypodium hydriforme but their old age and derived genome characteristics obscure evolutionary analyses.The first metagenomic study using aquatic eDNA highlights the importance of using genomic approaches for uncovering the strongly underestimated myxozoan biodiversity.Comparative transcriptomics highlighted protease-encoding genes as candidate gene groups for therapeutics and vaccine design.
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