Persistence and renaturation efficiency of thermally treated waste recombinant DNA in defined aquatic microcosms

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

Environmental risks of antibiotic resistance genes released from biological laboratories and its control measure

Antibiotic resistance genes (ARGs) are a growing global threat to public health. Biological laboratory wastewater contains large amounts of free ARGs. It is important to assess the risk of free ARGs from biological laboratories and to find appropriate treatments to control their spread. The fate of plasmids in the environment and the effect of different thermal treatments on their persistence activity were tested. The results showed that untreated resistance plasmids could exist in water for more than 24 h (the special 245 bp fragment). Gel electrophoresis and transformation assays showed that the plasmids boiled for 20 min retained 3.65% ± 0.31% transformation activity of the intact plasmids, while autoclaving for 20 min at 121 °C could effectively degrade the plasmids and that NaCl, bovine serum albumin, and EDTA-2Na affected the degradation efficiency of the plasmids during boiling. In the simulated aquatic system, using 10⁶ copy/μL of plasmids after autoclaving, only 10² copies/μL of the fragment after only 1-2 h could be detected. By contrast, boiled plasmids for 20 min were still detectable after plunging them into water for 24 h. These findings suggest that untreated and boiled plasmids can remain in the aquatic environment for a certain time resulting in the risk of disseminating ARGs. However, autoclaving is an effective way of degrading waste free resistance plasmids.

Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept, and sediment samples

Biomonitoring is vital for establishing baseline data that is needed to identify and quantify ecological change and to inform management and conservation activities. However, biomonitoring and biodiversity assessment in arid environments, which are predicted to cover 56% of the Earth's land surface by 2100, can be prohibitively time consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high-throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human-constructed and natural water sources in a semi-arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S-V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term-granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling that simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.

Effects of Temperature on the Timeliness of eDNA/eRNA: A Case Study of Fenneropenaeus chinensis

Environmental DNA (eDNA) technology has been successfully applied to detect organisms in various aquatic ecosystems. However, eDNA has been proven to exist for a long time in environmental samples. The timeliness of eDNA detection results largely depends on the rate of molecular degradation. Environmental RNA (eRNA) is considered an excellent complementary tool because most researchers believe that RNA degrades faster than DNA in vitro, while, to the best of our knowledge, the number of published articles related to eRNA is very limited. To address an important knowledge gap, this study focused on the response mechanism of eRNA degradation to water temperature change as compared with eDNA. Changes in the concentration of eDNA and eRNA of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene from Fenneropenaeuschinensis were detected at four temperatures (10, 15, 20 and 25 °C). The results showed that the degradation rate of eDNA increased with an increase in temperature. The degradation rate constants ranged from 0.011 to 0.486 h−1 and the degradation time ranged from 8 to 383 h for eDNA. The degradation rate of eRNA changed slightly with an increase in temperature. The degradation rate constants ranged from 0.190 to 0.379 h−1 and the degradation time ranged from 11 to 22 h for eRNA. eRNA showed better stability under temperature change and maintained a faster degradation rate at low temperatures. These results provide answers to the questions of whether eRNA and eDNA degradation rates are fast or slow. Furthermore, this study may suggest the potential superiority of eRNA over eDNA and promote further study of eRNA in future research.

Environmental conditions influence eDNA persistence in aquatic systems

Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.