Explore the vast range of titles available.

Monitoring alien species is critical to their management. However, early detection of invading alien freshwater fish can be challenging due to the difficulty of observing fish in low abundance. Environmental DNA (eDNA) has emerged as a new and potentially more sensitive method for sampling invasive species as compared to conventional methods, but the comparative financial cost is not often assessed. Adoption of eDNA by managers requires studies that showcase its cost‐effectiveness relative to conventional approaches. Here we use eDNA to assist in the management of an aggressive alien fish, the pearl cichlid (Geophagus brasiliensis), that is invading an urban river in south‐western Australia. We applied an occupancy model to survey data collected 6 years apart (2015, 2021) to assess how the species' distribution had changed and to evaluate whether an instream barrier had the potential to limit upstream invasion. To understand the effectiveness of eDNA, we used our model to quantify the relative efficiency (capture probability) of two eDNA sampling methods (active eDNA and passive eDNA) and fyke netting, as well as the number of replicate samples required per site to deliver >95% detection. We coupled the number of replicates needed with the cost per replicate to determine the cost‐efficiency of each method. We found that G. brasiliensis abundance was higher in downstream reaches in both survey years, and there was no evidence that its distribution had changed through time. However, G. brasiliensis was present above the instream barrier. Active eDNA sampling was considerably better at detecting G. brasiliensis than the other methods, making it the most cost‐effective method. Fyke nets came in a close second, and passive eDNA was a very distant third. Our results directly inform management in the study river and broadly highlight the cost‐effectiveness of active eDNA as a freshwater biosecurity tool. Early detection of invading alien freshwater fish can be challenging due to the difficulty observing fish in low abundance. To understand the effectiveness of eDNA sampling, we used our model to quantify the relative efficiency of two eDNA sampling methods (active eDNA, passive eDNA) and fyke netting as well as the number of replicate samples required per site to deliver >95% detection. Active eDNA sampling was considerably better at detecting an invading fish than the other methods making it the most cost‐effective method.

Worldwide, freshwater vertebrate populations are declining with increasing pressure on rivers due to numerous environmental and climatic threats. Environmental DNA (eDNA) could potentially provide a more efficient and non‐invasive mechanism to monitor freshwater systems, either as a complement or in replacement to traditional methods to accurately assess species' distributions. Here, we utilize a hierarchical multispecies N‐mixture model to compare three fish sampling methods: traditional fyke netting and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. We used the fitted model to compare capture probabilities among sampling methods and reveal the sampling effort required to describe the species assemblage. Results indicated that while all methods could detect fish, combined eDNA methodologies detected one more fish species than those caught by fyke netting. In addition, active eDNA sampling produced the highest capture probabilities and more consistently described the entire fish assemblage at any given site. Fyke netting and passive eDNA did not show significant differences in their average capture probabilities, and both methods had lower abilities to capture individual species than active eDNA. Active eDNA also required fewer replicate samples to detect the expected observed richness, and fyke netting required the most replicates. Additionally, a hierarchical multispecies abundance model showed that active environmental DNA (eDNA) sampling is the most effective method for monitoring freshwater fish populations. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting. This study compared three fish sampling methods: traditional fyke netting, and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. The effectiveness of the three different methods of detecting fish was tested with a hierarchical multispecies abundance model fit, with the model used to estimate both detection probability and replication effort required. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting.

Microorganisms represent the most abundant biomass on the planet; however, because of several cultivation technique limitations, most of this genetic patrimony has been inaccessible. Due to the advent of metagenomic methodologies, such limitations have been overcome. Prevailing over these limitations enabled the genetic pool of non-cultivable microorganisms to be exploited for improvements in the development of biotechnological products. By utilising a metagenomic approach, we identified a new gene related to biosurfactant production and hydrocarbon degradation. Environmental DNA was extracted from soil samples collected on the banks of the Jundiaí River (Natal, Brazil), and a metagenomic library was constructed. Functional screening identified the clone 3C6, which was positive for the biosurfactant protein and revealed an open reading frame (ORF) with high similarity to sequences encoding a hypothetical protein from species of the family Halobacteriaceae . This protein was purified and exhibited biosurfactant activity. Due to these properties, this protein was named metagenomic biosurfactant protein 1 (MBSP1). In addition, E. coli Rosetta TM (DE3) strain cells transformed with the MBSP1 clone showed an increase in aliphatic hydrocarbon degradation. In this study, we described a single gene encoding a protein with marked tensoactive properties that can be produced in a host cell, such as Escherichia coli , without substrate dependence. Furthermore, MBSP1 has been demonstrated as the first protein with these characteristics described in the Archaea or Bacteria domains.

We designed a pilot field study to assess relations between sunlight, cyanobacteria, and cyanotoxins. In 2021, we collected day (07:00 h, 10:00 h, 13:00 h, 16:00 h) and night samples (19:00 h, 22:00 h, 01:00 h, 04:00 h) at two locations in Kabetogama Lake, MN, USA. One sample set was collected from the lakeward end of a boat dock and the other on the nearby shoreline. Cyanobacterial phylogenetic eDNA differences over 24 h (pseudo F = 2.0938, p  = 0.127) were not significant. Copies of anatoxin ( anaC ) and microcystin ( mcyE ) synthetase genes varied significantly over the sampling times at the dock (Friedman Χ 2  = 15.01, df  = 7, p  = 0.036; Friedman Χ 2  = 19.22, df  = 7, p  = 0.008) and the shoreline (Friedman Χ 2  = 19.33, df  = 7, p  = 0.007; Friedman Χ 2  = 20.56, df  = 7, p  = 0.005), with the highest anaC counts occurring during the night for both sites. Additionally, the highest total and dissolved microcystin concentrations occurred at night. Despite the proximity of the sampling locations, cyanobacterial phylogenetic eDNA results indicate that the variability between sites (pseudo-F = 27.547, p  = 0.001) were greater than temporal differences over 24 h (pseudo F = 2.0938, p  = 0.127). Understanding the effect of diel and spatial variability may help researchers and resource managers make informed decisions about sampling and potential exposure.

Environmental DNA (eDNA) metabarcoding has shown great promise as an effective, non‐invasive monitoring method for marine biomes. However, long filtration times and the need for state‐of‐the‐art laboratories are restricting sample replication and in situ species detections. Methodological innovations, such as passive filtration and self‐contained DNA extraction protocols, have the potential to alleviate these issues. We explored the implementation of passive sampling and a self‐contained DNA extraction protocol by comparing fish diversity obtained from active filtration (1 L; 0.45 μm cellulose nitrate [CN] filters) to five passive substrates, including 0.45 μm CN filters, 5 μm nylon filters, 0.45 μm positively charged nylon filters, artificial sponges, and fishing net. Fish diversity was then compared between the PDQeX Nucleic Acid Extractor and the conventional Qiagen DNeasy Blood & Tissue protocol. Experiments were conducted in both a controlled mesocosm and in situ at the Portobello Marine Laboratory, New Zealand. No significant differences in fish diversity were observed among active filtration and more porous passive materials (artificial sponges and fishing net) for both the mesocosm and harbor waters. For the in situ comparison, all passive filter membranes detected a significantly lower number of fish species, resulting from partial sample drop‐out. While no significant differences in fish eDNA signal diversity were observed between either DNA extraction methods in the mesocosm, the PDQeX system was less effective at detecting fish for the in situ comparison. Our results demonstrate that a passive sampling approach using porous substrates can be effectively implemented to capture eDNA from seawater, eliminating vacuum filtration processing. The large variation in efficiency observed among the five substrate types, however, warrants further optimization of the passive sampling approach for routine eDNA applications. The PDQeX system can extract high‐abundance DNA in a mesocosm with further optimization to detect low‐abundance eDNA from the marine environment. This study aims to enhance novel eDNA sampling workflows for biodiversity assessments in marine ecosystems. Specifically, we investigated passive sampling devices as an alternative for timely active filtration and combined it with a novel in‐field extraction protocol. We explored the implementation of both passive sampling and a self‐contained DNA extraction protocol into the eDNA workflow by comparing fish diversity obtained from active filtration (1L; 0.45 µm cellulose nitrate [CN] filters) to five passive capture substrates, including 0.45 µm CN filters, 5 µm nylon filters, 0.45 µm positively charged nylon filters, artificial sponges, and fishing net. In addition, fish diversity was compared between the novel PDQeX Nucleic Acid Extractor and the conventional Qiagen DNeasy Blood & Tissue protocol.

Biosurfactants are amphiphilic molecules that interact with the surfaces of liquids leading to many useful applications. Most biosurfactants have been identified from cultured microbial sources, leaving a largely untapped resource of uncultured bacteria with potentially novel biosurfactant structures. To access the uncultured bacteria, a metagenomic library was constructed in Escherichia coli from environmental DNA within an E. coli , Pseudomonas putida and Streptomyces lividans shuttle vector. Phenotypic screening of the library in E. coli and P. putida by the paraffin spray assay identified a P. putida clone with biosurfactant activity. Sequence analysis and transposon mutagenesis confirmed that an ornithine acyl-ACP N-acyltransferase was responsible for the activity. Although the fosmid was not active in E. coli , overexpression of the olsB gene could be achieved under the control of the inducible T7 promoter, resulting in lyso-ornithine lipid production and biosurfactant activity in the culture supernatants. Screening for activity in more than one host increases the range of sequences that can be identified through metagenomic, since olsB would not have been identified if only E. coli had been used as a host. The potential of lyso-ornithine lipids as a biosurfactant has not been fully explored. Here, we present several biosurfactant parameters of lyso-ornithine lipid to assess its suitability for industrial application.

Environmental pollution is a growing threat to natural ecosystems and one of the world’s most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

Early detection and effective monitoring of aquatic environments are essential for detecting and mitigating potential ecological threats to aquatic organisms and for ensuring the sustainable management of freshwater ecosystems. Passive sampling is an emerging approach for environmental DNA (eDNA) collection in aquatic systems while active sampling involves controlled collection and filtration of water. This study evaluates active and passive sampling methods in a riverine system for detecting eDNA from Atlantic salmon (Salmo salar) and its lethal ectoparasite Gyrodactylus salaris. Sampling was conducted in the Sande River, Vestfold County, Norway. The loop-mediated isothermal amplification (LAMP) method was employed due to its high efficiency and specificity for amplifying target genes. The selected genetic markers were mitochondrial cytochrome B (Cyt B) DNA for S. salar and cytochrome c oxidase 1 (COX1) for G. salaris. The results indicate that host eDNA was readily detected using both sampling methods, whereas detection of G. salaris was more effective using active sampling. These findings provide valuable insight into optimizing eDNA detection protocols for both host and parasite, demonstrating specificity and sensitivity of LAMP in detecting the target organisms. This case study contributes to the development of conservation strategies aimed at preserving Atlantic salmon populations and freshwater biodiversity.