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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 the distribution is urgently needed for its efficient conservation. Here, we used environmental DNA (eDNA) analysis to assess the Japanese giant salamander's distribution in western Japan and, for that purpose, we collected 410 water samples from 12 rivers. We then developed a new eDNA assay for multi-copy nuclear DNA (nuDNA) of the giant salamander and compared the eDNA detectability of the nuDNA marker with that of a previous mitochondrial DNA (mtDNA) marker. Throughout the survey, we detected target eDNA from 162 water samples using either of the markers, which generally corresponded to the known natural distribution of the species. Additionally, the use of the nuDNA marker allowed for higher detection rate of target eDNA than the mtDNA marker. Moreover, the detection rate of target eDNA decreased substantially in water samples with higher conductivity and also partly in those with higher pH, suggesting their negative impacts on the salamander's ecology. Our results demonstrated that eDNA analysis with multi-copy nuDNA marker is highly useful for efficient and sensitive surveillance of Japanese giant salamander's distribution. Our study provided the methodology for efficiently monitoring the Japanese giant salamander's distribution via eDNA analysis and facilitating conservation activities for them. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) analysis can facilitate surveillance of invasive aquatic plant's distribution. However, it is still questionable how accurately eDNA concentration reflects and predicts aquatic plant abundance. Although previous studies investigated relationships between aquatic plant eDNA concentration and their abundance in freshwater environments, the conclusions were not consistent between the studies. Here, a systematic literature search was conducted to summarize previous findings and meta-analyze the relationships between eDNA concentration and aquatic plant abundance. Hierarchical random-effect meta-analyses showed significant positive, but weak, relationships between them (r = 0.45 in average), meaning that eDNA concentration accounted for approximately 20% of the observed variation in plant abundance. Additionally, the relationships tended to be rather stronger in the field than in the laboratory environments, which may be attributed to limited quantifiability and species specificity of plant coverage as abundance metrics, heterogeneous dispersion of plant eDNA particles, and phenology-dependent eDNA production from plant bodies. The finding indicates that aquatic plant eDNA particles could reflect more regional (but not local) abundance, and thus, eDNA-based abundance estimation might be more appropriate at a broader scale (i.e., lower spatial resolution). Further studies focusing on various environmental parameters and plant ecotypes are needed to clarify the relationship. [ABSTRACT FROM AUTHOR]

Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences. [ABSTRACT FROM AUTHOR]

Precise abundance estimation via environmental DNA (eDNA) analysis is challenging because of myriad effects of biotic/abiotic factors on eDNA persistence in water. However, it remains unclarified how the relationship between eDNA concentration and species abundance is influenced by environmental conditions. Warm temperature can accelerate eDNA degradation and its turnover in water, which may make eDNA signals fresher and strengthen the relationship. Here, mathematical models were present to simulate the effect of temperature-dependent eDNA degradation, modeled based on the previous meta-analysis, on the relationship between eDNA concentration and species abundance under different temperature and eDNA production scenarios. The R2 values tended to be higher at warmer temperatures regardless of eDNA production scenarios, although differences in R2 between temperatures were relatively small. Additionally, the R2 values were higher for a smaller variance of eDNA production rate. Furthermore, previous studies regarding the relationship between fish eDNA concentration and their abundance were meta-analyzed and correlation coefficients of the relationship were significantly higher for warmer temperatures. The findings indicated the importance of taking water temperatures into account for better abundance estimation via eDNA, although further technical consideration in the modelling framework was needed. [ABSTRACT FROM AUTHOR]

Understanding environmental DNA (eDNA) persistence and degradation processes is necessary for the precise assessment of species distribution and abundance in marine environments via eDNA. Given the various particle sizes and persistence states of eDNA in water, biphasic degradation of eDNA, composed of its initial rapid and subsequent slower decay, may describe the fate of eDNA more precisely than monophasic degradation. However, it remains unclear which environmental factors influence eDNA decay rates at each decay phase. Here, the factors characterizing the biphasic degradation of eDNA were assessed by re-analyzing the dataset of a previous study, which estimated Japanese jack mackerel (Trachurus japonicus) eDNA decay rates using a monophasic decay model. A biphasic decay model was newly applied to the dataset, and the fitness was compared between decay models. Biphasic models were better fitted to the time-series decreases in Trachurus japonicus eDNA concentrations for all treatment levels. Moreover, eDNA decay rates significantly varied depending on temperature, fish biomass density, and genetic region, though only at the initial rapid phase. These results indicate the importance of microbial and enzymatic degradation of eDNA particles at the initial rapid phase. None of the variables significantly affected eDNA decay rates at the subsequent slower phase, which implies that microbial and enzymatic effect on eDNA degradation may be weakened during the decay phase. Further elucidating the effects of other environmental parameters (e.g., pH, dissolved oxygen, and UV level) on the biphasic eDNA degradation process would be helpful for a more precise understanding of the fate of eDNA considering its various states in water. • Biphasic degradation of eDNA may describe its fate more precisely than monophasic degradation. • The factors characterizing the biphasic degradation of eDNA was assessed by re-analyzing the previous study. • Biphasic models were fitted better to the degradation of Japanese jack mackerel eDNA. • Temperature, fish biomass, and genetic region influenced initial rapid eDNA decays but not subsequent slower decays. [ABSTRACT FROM AUTHOR]