Improved environmental DNA detection sensitivity of Opisthorchis viverrini using a multi-marker assay.

Opisthorchiasis, caused by the liver fluke Opisthorchis viverrini, is endemic to Southeast Asian countries and constitutes a major health problem as it increases the risk of cholangiocarcinoma. However, owing to the complicated life cycle of O. viverrini, there is no rapid method for monitoring the risk of infection in the environment.

Environmental detection of eumycetoma pathogens using multiplex real-time PCR for soil DNA in Sennar State, Sudan.

Background: Mycetoma is a chronic disease affecting the skin and subcutaneous tissue endemic in the tropical and subtropical regions. Several bacteria and fungi can cause mycetoma, but fungal mycetoma (eumycetoma) is challenging because the treatment requires a combination of a long-term antifungal agent and surgery. Although the transmission route has not yet been elucidated, infection from the soil is a leading hypothesis.

Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens.

Preventing mosquito-borne infectious diseases requires that vector mosquitoes are monitored and controlled. Targeting immature mosquitoes (eggs, larvae, and pupae), which have less mobility than adults, is an effective management approach. However, conducting these surveys is often difficult due to the limitations of morphological classification and survey costs.

Slower growth of farmed eels stocked into rivers with higher wild eel density.

Farmed anguillid eels are frequently stocked into natural fresh waters to enhance eel resources, but little is known about what happens to these eels or their interactions with wild eels after stocking. A recent study observed a depressed survival and growth rate of farmed Japanese eels when they were reared with wild eels, which indicated that wild eels might interfere with the survival and growth of farmed-and-stocked eels through intraspecific competition. To contribute to improving eel stocking efficiency, the growth of farmed-and-stocked Japanese eels was compared among four rivers with different wild eel densities using mark-and-recapture studies.

Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan.

Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Fungal mycetoma and eumycetoma are especially challenging to treat; therefore, prevention, early diagnosis, and early treatment are important, but it is also necessary to understand the geographic distribution of these pathogenic fungi. In this study, we used DNA metabarcoding methodology to identify fungal species from soil samples.

Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami.

Environmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks.

Prevalence of Antimicrobial-Resistant Escherichia coli in Migratory Greater White-Fronted Geese (Anser albifrons) and their Habitat in Miyajimanuma, Japan.

The spread of antimicrobial-resistant bacteria (ARB) in natural environments including wild animals is a concern for public health. Birds cover large areas, and some fly across borders to migrate in large flocks. As a migratory bird, the Greater White-fronted Goose (Anser albifrons) travels to Miyajimanuma, North Japan, each spring and autumn.

Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples.

Alien ant species (Formicidae, Hymenoptera) cause serious damage worldwide. Early detection of invasion and rapid management are significant for controlling these species. However, these attempts are sometimes hindered by the need for direct detection techniques, such as capture, visual observation, or morphological identification.

Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout.

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding.

Sedimentary DNA tracks decadal-centennial changes in fish abundance.

Far too little is known about the long-term dynamics of populations for almost all macro-organisms. Here, we examined the utility of sedimentary DNA techniques to reconstruct the dynamics in the "abundance" of a species, which has not been previously defined. We used fish DNA in marine sediments and examined whether it could be used to track the past dynamics of pelagic fish abundance in marine waters.

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs.

Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly.

Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish.

Water sampling and filtration of environmental DNA (eDNA) analysis have been performed by several different methods, and each method may yield a different species composition or eDNA concentration. Here, we investigated the eDNA of seawater samples directly collected by SCUBA to compare two widely used filtration methods: open filtration with a glass filter (GF/F) and enclosed filtration (Sterivex). We referred to biomass based on visual observation data collected simultaneously to clarify the difference between organism groups.

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan.

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species.

Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA.

The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide-range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp).