Toshifumi Minamoto's research while affiliated with Kobe University and other places

Publications (223)

Preprint
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Japanese giant salamander ( Andrias japonicus ) is one of the largest amphibian species in the world and an iconic species in Japan. However, as its distribution has recently declined across the country, rapid and extensive monitoring of its distribution is urgently required for its efficient conservation. Here, we used environmental DNA (eDNA) ana...
Article
The accuracy of environmental DNA (eDNA) methods developed as innovative biological monitoring technologies can be improved by considering the ecological characteristics of a target species. In this study, we performed an aquarium experiment and field surveys to establish an effective eDNA method for an endangered Japanese bagrid catfish (Pseudobag...
Article
During spawning activity, fish release large amounts of sperm and eggs into the water, which has been assumed to cause an increase in environmental DNA (eDNA) levels and nuclear DNA/mitochondrial DNA ratios. To test whether these assumptions are valid and whether nuclear and mitochondrial eDNA analysis can be used to monitor the spawning activity o...
Article
In biological monitoring using environmental DNA (eDNA) in the sea, there is a concern that the distribution of eDNA may change depending on the sampling location and timing because the flow changes are large. Therefore, it is important to understand the influence of current flow in the selection of sampling locations and timings of eDNA monitoring...
Article
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Antimicrobial resistance is a global concern requiring a one‐health approach. Given wild animals can harbor antimicrobial‐resistant bacteria (ARB), we investigated their presence in 11 fecal samples from wild animals using deoxycholate hydrogen sulfide lactose agar with or without cefotaxime (CTX, 1 mg/L). Thus, we isolated CTX‐resistant Escherichi...
Article
Determining the timing and location of spawning is critical for the conservation and management of aquatic species. Environmental DNA (eDNA) analysis can be used to monitor fish spawning activity by detecting peaks in eDNA concentrations and nuclear DNA (nuDNA)/mitochondrial DNA (mtDNA) ratios; however, the duration and diffusion distance of high c...
Article
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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 an...
Article
Full-text available
Estimating abundance or biomass using eDNA metabarcoding is a powerful emerging tool that may provide an alternative to conventional laborious methods for biological monitoring. However, inferring aquatic macroorganism abundance or biomass using eDNA concentrations remains challenging, especially in lotic environments, because of several potential...
Preprint
Changes in the thermal structure of lake ecosystems have been documented as a precursor of climate change, but the dynamics of biomass distribution, which fundamentally determines species conservation, have been less studied. An interdisciplinary approach was used to demonstrate the influence of climate-driven changes on the biomass distribution of...
Preprint
Underwater sediments are a natural archive of biological information. Reconstruction of past fauna has been conducted for various taxonomic groups using morphological remains and DNA derived from these remains. However, information on past occurrences of fish species, the top predator of lake ecosystems, could have been reproduced only in exception...
Article
Farmed anguillid eels are frequently stocked into natural freshwaters 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...
Article
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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 b...
Article
The pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon are economically important fishery resources in Japan. The catching of these fish species has decreased owing to environmental pollution and habitat loss caused by human impacts. We developed species-specific primer–probe sets to detect and quantify environmental DNA (...
Article
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Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians' ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA...
Article
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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 D...
Article
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The terrestrialization of floodplains has become a concern to river managers and ecologists because it has degraded habitats for floodplain-dependent organisms. We examined the temporal distributions of the endangered deepbody bitterling (Acheilognathus longipinnis) throughout its life history, which is an autumn-spawning annual fish spending its e...
Article
This study aimed at characterizing the distribution of black sea bream Acanthopagrus schlegelii, a major target fish of commercial and recreational fishing, using environmental DNA (eDNA). Twelve survey stations were aligned along an inshore-offshore axis in Tango Bay, southwestern Japan. Water samples were taken from the surface and bottom layers...
Article
Paddy ecosystems are among the most biodiversity-rich ecosystems, but they can be degraded by field consolidation or the abandonment of rice cultivation. Snakes are the top predators in paddy ecosystems; therefore, understanding the distribution of snakes is important for the conservation of paddy biodiversity. Traditionally, surveys of snakes have...
Article
1. The COVID-19 pandemic is an outstanding global threat for both human health and well-being. Under the pandemic, green spaces are known to mitigate the physical/mental stress of urban people. However, it remains unclarified how blue spaces such as coastal and river areas play a role in healing urban people's health and well-being during the pande...
Article
Environmental DNA (eDNA) has been utilized for the detection of target species, and its application in biomass estimation has great potential. However, there are several factors that may hinder this application, such as species-specific eDNA emission, interspecific interactions, and the effect of feeding. In this experiment, we quantified eDNA emis...
Article
The utilization of environmental DNA(eDNA) is being considered as a new method for monitoring seagrass beds. In field surveys, the amount of eDNA of seagrass was below the minimum limit of quantification by using the conventional method that is often performed in freshwater areas for animals. In this study, we assumed water sample condition with a...
Preprint
Full-text available
Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians ecological traits (e.g., nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA...
Preprint
Full-text available
Introduction: 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 cla...
Article
Full-text available
Aim Although at least five Tylototriton species were recorded in Thailand, only Tylototriton verrucosus is registered as a protected species under the Wildlife Preservation and Protection Act in Thailand. Populations of T. uyenoi are now severely declining, caused by anthropogenic activities. As intense human pressure is having profound effects on...
Article
Environmental DNA (eDNA) analysis allows noninvasive and cost‐effective monitoring of macroorganisms' distribution and composition in aquatic ecosystems. Benzalkonium chloride (BAC) is an inexpensive and simple preservative for eDNA in water samples and has been used in many eDNA studies for preventing its degradation during transportation. However...
Article
In the biomonitoring using environmental DNA (eDNA) analysis, the suppression of eDNA degradation has been an important issue to estimate accurately the presence of target species and their eDNA concentrations. A recently proposed eDNA preservation technique requires only the addition of benzalkonium chloride (BAC) to water samples and has been use...
Article
Full-text available
Environmental DNA (eDNA) analysis is a revolutionary tool for non-invasive, cost-effective, and highly sensitive monitoring of species distribution and abundance; however, there remain some uncertainties related to eDNA detection and quantification, as well as limitations in terms of its ecological interpretation. Although these may be elucidated b...
Article
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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 kep...
Article
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. To i...
Article
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Recently, environmental DNA (eDNA) metabarcoding techniques have been applied to biodiversity investigations in aquatic ecosystems. However, no study has yet tested whether this technique is effective for water bodies in which extensive algal blooms break out. In this study, fish eDNA metabarcoding was carried out in Lake Taihu, which experiences e...
Article
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Dam‐mediated biological invasions are a serious problem all over the world. Once established in reservoirs, the invasive species have catastrophic impacts on the river ecosystems downstream, and thus, rapid monitoring of invasive species is an urgent issue for the effective removal of them and the conservation management of native ecosystems. Here,...
Article
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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. In this study, w...
Article
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A lack of reliable tools for determining the presence and distribution of fish species can impede understanding of predator–prey interactions and fishery management. Conventional fish survey methods are invasive, and can be size or species selective. Combining netting and electrofishing is a current method used to monitor fish species in Phayao Lak...
Article
Outbreaks of bacterial cold-water disease (BCWD), caused by Flavobacterium psychrophilum, are widespread in Japan, especially among ayu Plecoglossus altivelis. There are few investigations of F. psychrophilum in river water, and its seasonal distribution has not been clarified. We aimed to identify the spatiotemporal dynamics of F. psychrophilum an...
Article
The recent development of the environmental DNA (eDNA) technique has dramatically facilitated investigations of the distribution and abundance of macroorganisms in the natural environment. Various real‐time polymerase chain reaction (PCR)‐based methods have been proposed for the detection and quantification of eDNA by independent researchers or gro...
Article
Full-text available
The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA...
Article
Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states...
Article
Full-text available
Environmental DNA (eDNA) techniques have the potential to become useful tools for investigating the distribution and biomass of aquatic organisms. Additionally, Unmanned Aerial Vehicle (UAV) photos have recently been applied to evaluate vegetation cover. We tested the ability of eDNA techniques to evaluate the distribution and biomass of an invasiv...
Article
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Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to monitor invasive fish species. As an alternative (or complementary) tool for biodiversity monitoring, eDNA metabarcoding had been used to detect species in aquariums, which represents an important transit avenue for introducing non-indigenous species with high popu...
Article
Antimicrobial‐resistant bacteria and resistance determinants are of great concern to human and veterinary medicine worldwide. This article is protected by copyright. All rights reserved.
Article
Full-text available
Background The importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown feathe...
Article
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As an alternative/supplement to conventional biodiversity survey methods, environmental DNA (eDNA) analysis has developed rapidly during the past decade, and is widely used for the biomonitoring of wildlife. However, the interpretation of eDNA results has been limited to the presence/absence or biomass/abundance of the target species because of unc...
Article
Full-text available
The diversity and the abundance of amphibians have dramatically declined globally over the past 30 years, and the monitoring and conservation of their habitats is essential. However, traditional methods such as bait trapping and mark-recapture are costly, and morphological identification usually requires a high level of taxonomic expertise. Here, s...
Article
Full-text available
In recent years, biodiversity loss has become one of the most serious environmental issues worldwide, especially in aquatic ecosystems. To avoid diversity loss, it is necessary to monitor biological communities, and environmental DNA (eDNA) metabarcoding has been developed as a rapid, noninvasive, and cost-effective method for aquatic biodiversity...
Article
Full-text available
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, H...
Article
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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 pa...
Preprint
Full-text available
Although environmental DNA (eDNA) metabarcoding is acknowledged to be an exceptionally useful and powerful tool for monitoring surveys, it has limited applicability, particularly for nationwide surveys. To evaluate the performance of eDNA metabarcoding in broad-scale monitoring, we examined the effects of species ecological/biological traits and ec...
Conference Paper
Environmental DNA (eDNA) analysis allows information to be obtained about the identification of aquatic species. Seagrass DNA can be detected in sampled water which contains exocrine secretions from the fine pores on the leaf surface. We developed a seagrass monitoring method based on the eDNA analysis. The results show that the concentration of eD...
Article
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Background Freshwater ecosystems are rapidly declining. The Siberian salamander ( Salamandrella keyserlingii ) which inhabits the Kushiro marsh in Hokkaido, Japan has lost some habitat due to human activity. There are many challenges associated with conventional monitoring methods, including cost, the need for specialist personnel, environmental im...
Article
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Environmental DNA (eDNA)‐based assessments of macro‐organisms have now become an essential approach for biomonitoring. eDNA survey methods have a number of advantages over conventional survey methods. However, the value of the data that will accumulate would be greatly enhanced by standardizing the analysis methods, which would allow us to compare...
Article
Environmental DNA (eDNA) is a useful tool for biological monitoring of a target species by detecting DNA contained in environmental samples. However, the suppression of eDNA degradation after sample collection is a major issue when estimating the presence of a target species. Recently, benzalkonium chloride (BAC) was shown to dramatically suppress...
Article
Full-text available
Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost‐effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal...
Article
We report a novel species-specific primer set for detection of the endangered botiid loach Parabotia curtus in environmental waters. A primer test using DNA extracted from tissues of P. curtus and four other loach species indicated its high specificity to P. curtus. Application of the primer set to field samples collected throughout the year in a n...
Article
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Many techniques have been developed to investigate the interactions between plants and herbivorous insects in natural environments and are generally used to determine either (a) which plant species are eaten by a specific herbivorous insect or (b) which herbivorous insect species are herbivores of a specific plant. The former problem is usually add...
Article
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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 locat...
Article
Full-text available
Environmental DNA (eDNA) can exist in water with various sizes and states. Among them, relative to extra-cellular DNA, intra-cellular DNA such as cell and tissue fragments can mainly be detected at larger size fractions, and may be protected from enzymatic DNA degradation processes. Here, we verified the hypothesis that the selective collection of...
Article
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Although populations of anguillid eels have declined remarkably in recent decades, monitoring data on the spatial and temporal variation in their dynamics are often limited, particularly for tropical eel species. As there are often sympatries of multiple eel species in tropical rivers, identifying eel species based solely on morphological character...
Article
Full-text available
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 gla...
Article
Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivel...
Article
Full-text available
Aqueous environmental DNA (eDNA) analysis has been applied to the monitoring of various ecosystems and taxa, and the characteristics of aqueous eDNA have been previously studied. In contrast, although sedimentary eDNA has been used to restore past information, the characteristics of sedimentary eDNA are not well understood. In this study, we compar...
Article
Full-text available
Environmental DNA (eDNA) analysis has been used as a cost-efficient and non-invasive tool for monitoring invasive and threatened species. Previous studies typically involve two approaches; species-specific detection via PCR and multiple species detection via metabarcoding. However, the former could be costly when several species are targeted, and t...
Article
Environmental DNA (eDNA) is DNA collected directly from environmental samples (soil, sediment, water, air, etc.) rather than from individual organisms. When organisms interact with the environment, DNA is released and accumulates in the environment. Hence, eDNA analysis facilitates efficient detection and monitoring of species in aquatic ecosystems...
Article
The utilization of environmental DNA(eDNA) is being considered as a new method for monitoring seagrass beds. To understand the change in eDNA corresponding to seasonal variations in seagrass, the growth of Zostera marina inhabiting inside a water tank along with the amount of eDNA were investigated for fifteen months. Furthermore, investigations we...
Article
Full-text available
Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of sp...
Article
Full-text available
In recent years, the prevalence and infection intensity of Schistosoma japonicum in endemic areas of the Philippines have significantly decreased due to yearly population-based treatment strategies, yet transmission rates remain high and uninterrupted. An important indicator of active disease transmission is the presence of Schistosoma japonicum an...
Preprint
Full-text available
Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish ( Plecoglossus altivelis altive...
Article
Full-text available
Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear...
Article
Full-text available
Monitoring reproductive migration is essential for the conservation of anadromous species. Shishamo smelt (Spirinchus lanceolatus) is endemic to Hokkaido, the northernmost large island in Japan. S. lanceolatus is an anadromous species that is known to migrate into rivers for a very short period in early winter. While this species has a special valu...
Article
Full-text available
Real‐time PCR has been widely employed in environmental DNA (eDNA) surveys to detect and quantify target species. The biggest obstacle in real‐time PCR based eDNA assays is the inhibition of PCR amplification that results in false‐negative detection and uncertainty of quantification. Here, we aimed to evaluate inhibition resistance of PCR reagents...
Article
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Abstract Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) provide a noninvasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate...
Article
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Background: The perpetuation of schistosomiasis japonica in the Philippines depends to a major extent on the persistence of its intermediate host Oncomelania hupensis quadrasi, an amphibious snail. While the malacological survey remains the method of choice in determining the contamination of the environment as evidenced by snails infected with sc...
Article
Background: The perpetuation of schistosomiasis japonica in the Philippines depends to a major extent on the persistence of its intermediate host Oncomelania hupensis quadrasi, an amphibious snail. While the malacological survey remains the method of choice in determining the contamination of the environment as evidenced by snails infected with sch...
Article
Full-text available
In the original publication the text in right column of page 330, the sequences of primers were incorrectly published as.