Palaemon paucidens has a large population and is an important food source for fish in Lake Biwa, Japan. They are abundant in shallow waters from spring to summer, after which most individuals migrate to offshore deep areas where they remain during autumn and winter. However, some individuals are nonmigratory, remaining in shallow waters over winter. It has been reported that P. paucidens individuals have declined in recent years; a better understanding of its seasonal distribution is needed to manage this species, and basic information on its seasonal distribution is indispensable. We tracked the environmental DNA (eDNA) distribution of P. paucidens in Lake Biwa over a year using a quantitative real‐time polymerase chain reaction method. We collected water samples from offshore (both from the surface and from the benthic) and from shallow shore sites adjacent to the shorelines of the main lake and connecting freshwater lagoons. Offshore sampling took place in summer and winter, and shallow shore and lagoon sampling in all four seasons. During summer, eDNA concentrations were significantly higher in shallow and lagoon areas than offshore bottom sites. Conversely, during winter, eDNA concentrations were higher in offshore bottom sites, and relatively high and low eDNA concentrations in lagoons and shallow shore, respectively. These results most likely reflect the spatial and temporal distribution of this species in Lake Biwa. The eDNA concentrations peaked in early August at shallow shore sites in the main lake, with a significant decline in mid‐October, while low eDNA concentrations were recorded at offshore bottom sites in late August. These results suggest that P. paucidens migrates from shallow waters to offshore bottom sites between early August and mid‐October. These results provide important information for the management of this species.

In recent years, environmental DNA (eDNA) technology has been used in a variety of water environments. Environmental DNA concentrations in marine samples tend to be lower than those in freshwater samples, and few studies have explored methods to improve the recovery yields of eDNA from seawater samples. In this study, we compared different seawater preservation solutions (RNAlater or ATL) to improve eDNA yields. The eDNA concentrations of vertebrate and invertebrate species were compared using species-specific eDNA assays, and the number of detected fish and their compositions were compared using metabarcoding analysis. ATL treatment resulted in significantly higher eDNA yields for both vertebrate and invertebrate species than RNAlater treatment. Metabarcoding analysis revealed non-significant effects of preservation on the number of detected species and species composition. These results suggest that ATL treatment improves DNA yields without changing the species composition compared with the commonly used RNAlater treatment. The findings of this study will reduce false-negative outcomes and provide highly reliable results in future biological surveys. Graphical abstract

As the largest coastal city in China, Shanghai’s rapid development in transportation, tourism, trade, and commerce has facilitated the spread and invasion of non-native aquatic organisms. Aquatic organisms are highly elusive, and once established, eradicating them becomes a challenging task. Currently, our understanding of the invasion risk posed by non-native aquatic species in Shanghai is limited. Therefore, it is imperative to investigate the pathways of introduction, distribution, and dispersion and the invasion risk and impacts of non-native aquatic organisms in Shanghai. This study investigated aquatic organisms in Shanghai’s primary water bodies, including Huangpu River, Suzhou River, and Dianshan Lake. The risk assessment was conducted using the Aquatic Species Invasiveness Screening Kit (AS-ISK), and field monitoring was performed with environmental DNA (eDNA) technology. Results of the risk assessment indicate that among the 21 evaluated species, 9 fall into the medium-to-high-risk category with scores ≥26, while 12 are classified as low-risk with scores <26. The top four species with the highest invasion risk are Gambusia affinis, Pomacea canaliculata, Lepomis macrochirus, and Coptodon zillii. This study identified 54 fish species belonging to seven orders, 16 families, and 42 genera at 16 sampling sites in Shanghai, among which Channa maculata, Micropterus salmoides, and Misgurnus bipartitus are non-native. The results suggest that Shanghai faces a high invasion risk of aquatic species, necessitating enhanced scientific prevention and control measures. Early monitoring is essential for species with medium-to-high invasion risk, and a further evaluation and analysis of the risks associated with introduced fish species already present in Shanghai are recommended for aquaculture practices.

Changes in the thermal structure of lake ecosystems have been documented as a response to climate change, but the dynamics of biomass distribution, which fundamentally determines species conservation, has been less studied. An interdisciplinary approach was used to demonstrate the influence of climate‐driven changes on the environmental DNA (eDNA) distribution of two species (Gymnogobius isaza and Palaemon paucidens) in Lake Biwa, the largest monomictic lake in Japan. In field surveys in 2016–2017 (full water circulation) and 2019 (partial water circulation), eDNA concentrations of these species were measured for 43 and 47 samples, respectively, collected from the lake bottom. The correlative relationship was investigated between species' eDNA concentrations and environmental variables. The species–environment relationship was then applied to species' eDNA distributions under existing and future environments calculated by a lake ecosystem model. Based on differences in the estimated eDNA distributions, we suggest that different species respond differently to climate change. The distribution of G. isaza will expand in the future if full water circulation occurs, although it appears to be independent of water circulation at present. Partial water circulation enlarges the distribution area of P. paucidens, but its eDNA concentrations will be low in the future, regardless of the extent of water circulation. These results indicate that species such as P. paucidens, which is now abundant but vulnerable to climate change, require special attention. Furthermore, our study emphasizes the potential application of interdisciplinary methodologies for improved species conservation.

The lacustrine shrimpPalaemon paucidensundertakes seasonal migration between shallow waters in spring and summer to deep waters in autumn and winter in Lake Biwa in Japan. Previous studies hypothesized that the migration to deep waters was for hibernation. The findings of this study oppose this hypothesis. We showed thatP. paucidensis physiologically active in deep waters during winter; that the carbon stable isotope ratio indicated that the species forages in winter and that there was a difference in food sources between summer and winter; that lipid content was highest in January; and that gene expression activity (as measured by theRNA/DNAratio) remained constant throughout the year. Thus,P. paucidensindividuals that migrate to the bottom are likely to forage in winter, but do not hibernate. Nutrients gained in winter were not reflected in individual growth but may have been allocated to gonadal growth and the production of gametes, suggesting that winter foraging by this species in deep sites contributes to obtain resources for reproductive investment. In addition, we found that both small individuals with no reproductive experience and relatively large females with reproductive experience overwintered, indicating thatP. paucidenshas a life‐cycle that is longer than 1 yr in Lake Biwa.