Junjiro N. Negishi

Studies validating the efficiency of environmental DNA (eDNA) metabarcoding for hyporheic biodiversity assessment are still limited. Hence, we investigated species diversity in the hyporheic zone beneath gravel bars, focusing on lateral locations along the gravel bar transect and the effects of flooding. We compared the accuracy of metabarcoding with morphological identification, specifically focusing on eDNA metabarcoding and bulk‐sample metabarcoding data to understand the effect of river surface water contamination on eDNA analysis in the hyporheic zone. Despite challenges such as primer bias and surface water contamination, our metabarcoding analysis of both bulk‐sample and eDNA metabarcoding yielded results consistent with morphological identification, providing evidence that the hyporheic zone has a more stable community structure than the river benthic zone in response to flooding. Furthermore, the homogeneity of hyporheic community structures across lateral locations based on eDNA and bulk‐sample metabarcoding suggests that the hyporheic community may be particularly vulnerable to biodiversity loss compared to the river benthic community under extreme flood disturbance. Notably, eDNA metabarcoding demonstrated higher sensitivity for detecting low abundance and elusive taxa compared to both bulk‐sample metabarcoding and morphological identification. Overall, our results highlight the potential of eDNA metabarcoding as a comprehensive, less invasive, and more time‐efficient tool for assessing biodiversity in the hyporheic zone.

Water temperature drives freshwater ecological processes and is increasingly altered by anthropogenic perturbations, particularly dam construction and climate change. Consequently, empirical evaluation of its effects on aquatic organisms is increasingly important. Using a three-year dataset spanning pre-and post-diversion cessation from multiple reaches downstream of a diversion dam in Hokkaido, Japan, we assessed whether diversion-and return flow-induced mainstem thermal gradients structured the distributions of benthic fish with contrasting thermal preferences. We then examined their responses to postcessation thermal perturbations, including a heatwave. Pre-event midsummer thermal maxima significantly shaped the distribution of cold-stenothermic wrinklehead sculpin Cottus nozawae, which was more abundant in cooler reaches, but not that of the eurythermic stone loach Barbatula oreas. C. nozawae showed a partial response two years post-cessation. Its abundance increased in the former bypass reach, and significant differences from adjacent reaches diminished. However, the weakened correspondence between abundance and thermal conditions suggested incomplete recovery. This pattern may reflect limited recovery time or restricted movement caused by in-stream structures. During the heatwave year, C. nozawae abundance increased at most sites despite elevated temperatures, contrasting with its spatial thermal preference. This pattern may reflect enhanced reproduction and fitness at least in the short term. However, individual telemetry, long-term monitoring, and demographic data are needed to evaluate these interpretations. These findings highlight the role of dam-induced thermal heterogeneity in shaping fish communities, the potential of intentional flow re-engineering to facilitate restoration, and the importance of integrating thermal regimes, species-specific thermal niches, and habitat connectivity into dam management.

The signal crayfish, Pacifastacus leniusculus (Dana, 1852), has become established as an invasive species in freshwater ecosystems worldwide, causing severe ecological impacts. While effective control measures are urgently needed, sterilization via pleopod removal may represent a practical option. This study aimed to 1) evaluate the persistence of sterilization achieved through pleopod removal and 2) test whether the procedure could be simplified by unilateral removal (left side only), which approximately halves handling time. Because females rely on pleopods for brooding, we hypothesized that pleopod removal would persistently impair brooding, and that unilateral removal would still produce strong effects. Laboratory experiments were conducted using crayfish collected from the Toyohira River, Sapporo, Hokkaido, Japan between July 2023 and January 2025. Brooding ability declined markedly following pleopod removal. The evidence suggests persistent inhibition of brooding, with egg-carrying reduced by 97.0% in the first reproductive season and showing sustained suppression in the second. This sustained inhibition is attributed to incomplete pleopod regeneration through molting (3.5% in the first year and 40.2% in the second). Females dropped most eggs immediately after oviposition and lost all eggs within two weeks. Partial pleopod removal was technically inadequate, as its sterilization effect relative to effort was inferior to that of complete removal. These findings suggest that complete pleopod removal is a promising sterilization method for invasive crayfish, but further field studies are required to evaluate its effectiveness under natural conditions.

Knowledge of how aquatic insects use riparian zones can inform the conservation and management of both rivers and riparian zones. This study reports the habitat use and spatial segregation of winged EPT (Ephemeroptera, Plecoptera, Trichoptera) adults in the river channel and riparian zone of the gravel‐bed Satsunai River in Hokkaido, northern Japan. Adult insects were caught using sticky and Malaise traps in the summer of 2019 and 2020. The relative use of forest‐covered and gravel‐covered riparian zones and their edge habitats was examined in relation to above‐water space. Furthermore, the habitat use of the natural forest‐covered riparian zone in two dimensions (i.e., lateral and vertical over 104 and 18 m, respectively) was measured. Ephemeroptera were largely captured above the river channel and showed no preference for forest‐covered or gravel‐covered riparian habitats. In contrast, Plecoptera were caught primarily in the forest‐covered riparian zone. Capture of Trichoptera was moderately higher along the edge of the forest‐covered riparian zone, representing an intermediate response. We identified clear spatial segregation of EPT taxa in lateral and vertical dimensions. Most individuals were caught > 5 m above the ground in forest strata and < 30 m from the channel laterally. At the family level, Plecoptera taxa (Nemouridae and Chloroperlidae) occurred at the medium and lowest height in the vertical dimension. In particular, the numerically dominant Plecoptera family, Chloroperlidae, was most frequently found near the ground (< 5 m height), and was also distributed furthest from the stream (40 m). Other Trichoptera families such as Philopotamidae were found within relatively short distances from the channel. Riparian zones can provide preferable habitat for some EPT adults, with their structural and microclimatic diversity influencing taxon‐specific two‐dimensional distributions. Identification of taxa with high abundance, ease of observation, and laterally extensive use of riparian zones as a useful candidate indicator, in our case Chloroperlidae, could enable the assessment of ecosystem status in the river–riparian continuum and its responses to landscape changes in gravel‐bed river corridors.

The hyporheic zone extends beneath active river channels and gravel bars, serving as crucial habitats for invertebrates, including aquatic insects. This study investigated the emergence of aquatic insects from benthic and subsurface zones through the diverse riverscape features of a gravel‐bed river. Insect emergence during the peak period for hyporheic species, from May to July 2024, was surveyed along a 50‐m section of a gravel bar on the Satsunai River in northern Japan. Emergence traps were positioned above water (WS), at the gravel‐bar edge (GE), and on the gravel‐bar surface (GB) to collect adult insects. Larval communities were sampled from the river channel and subsurface hyporheic pipes in GB to ascertain the insects' habitat affinity for benthic and hyporheic zones. Two Plecoptera taxa, Leuctridae spp. and Alloperla ishikariana , predominated in the hyporheic community (94%), whereas the benthic community comprised a more diverse array of taxa, including Ephemeroptera (74.6%) and Trichoptera (12.3%), based on larval data. Total insect emergence was adjusted for the areal extents of WS, GE, and GB; hyporheic taxa dominated GB (70%) and GE (60%), while benthic taxa dominated WS (82%). Hyporheic taxa utilized gravel‐bar GB and GE for emergence disproportionately more than benthic taxa, likely due to the proximity of their larval habitats beneath the gravel bar and the emergence behavior of dominant Plecoptera by crawling onto land. This study demonstrated insect emergence through three distinct pathways mediated by larval habitats in benthic and hyporheic zones and underscored the critical roles of three riverscape features in supporting the reproduction and biodiversity of aquatic insects in gravel‐bed rivers.

Seasonal changes in the environment often strongly influence biological communities. In environmental transition zones, or ecotones, the environment fluctuates over time between two different types of environments and the seasonal change is more pronounced. Although emphasis has been placed on the spatial variation of biota along environmental gradients, seasonal change has not been well studied despite the seasonal nature of many ecotones. In this study, we investigated seasonal shifts in aquatic community structures of floodplain waterbodies characterised as transitions between lotic and lentic environments, and further investigated the biological processes behind the shift. We observed a clear seasonal shift of community structure in floodplain waterbodies. From the spring snowmelt season to the summer low flow season, the aquatic community structure was largely driven by the hydrological connectivity to the river, represented as the timing of the lotic–lentic transition during the seasonal flood recession. In contrast, after a few months of summer low flow period, the effect weakened over time, and the communities were structured based more on the basis of the local environment. The seasonal shift was largely explained by the change in amphibian and aquatic insect larvae, the main members of the floodplain aquatic assemblage, which metamorphose and emerge from the water during the summer period and then redistribute in different ways more strongly influenced by local environmental factors such as water body size, temperature and dissolved oxygen levels. Given that biota in ecotones occupy the habitat for a limited time due to the severe environmental fluctuations, such seasonal changes as we observed in this study may be widespread in ecotones. Landscape and local environmental conditions could alternately shape community structures in different seasons. Further attention to the temporal aspects of community structure is needed for community studies and for conservation.

Urbanization transforms natural river channels, and surface water of some rivers disappeared over time. How and whether the subsurface domains of the original waterways and aquifers connecting them (a phantom of historical landscape) are functional is not known. This study examined the effects of tributary groundwater inflow on the response of river–riparian organisms in an alluvial mainstem river in northern Japan, where the tributary disappeared over the course of urban landscape transformation. A 2.8‐km lowland segment of the mainstem gravel‐bed river was examined for water properties and the river–riparian food web. In addition, watershed‐wide water sampling was conducted to isotopically distinguish several types of groundwater that contributed to the hyporheic water in the study segment. Altitude had a clear effect on the hydrogen/oxygen stable isotope ratios in the river water collected across the watershed. Groundwater unique both in chemical and isotopic signatures occurred in several spots within the study segment, and its properties resembled and its upwelling locations matched groundwater from a tributary river whose surface channel disappeared 60 years ago. Positive numerical increases in abundance and/or a sign of nitrogen transfer in river–riparian communities (algae, invertebrates and riparian trees) originating from groundwater high in nitrate with elevated nitrogen stable isotope ratios were found. We demonstrated that tributary groundwater with unique chemical properties manifested by an urban watershed river network continued to have trophic effects on biota across the river–riparian boundary in the mainstem river, even after urbanization transformed the tributary into a phantom river. We highlighted the legacy effects of landscape transformation in the subsurface domain and the significance of scrutinizing the past landscape and hydrological connectivity at the watershed scale in urban environments.

How hyporheic invertebrates at relatively shallow depths cope with floods and sediment movements that involve vertical and horizontal distribution shifts is not well known. This study examined the responses of macroinvertebrate communities in both benthic and hyporheic zone (30–50 cm deep from the riverbed) to a flow release at a fine temporal resolution (a few hours prior to and four days after an artificially caused flood) of a gravel-covered point bar so that immediate responses to the event can be described. Hyporheic communities exhibited little change during the flood, whereas benthic communities exhibited substantial decreases in total abundance. Most strikingly, at the taxon level, numerically dominant hyporheic species at relatively shallow depths, Alloperla ishikariana, increased substantially in the hyporheic zone, and its increase was positively correlated with deposited sediment depth (up to 45 cm). This study suggests that flood-induced sediment deposition drives rapid invertebrate colonization of the hyporheic zone. This can be perceived as refuge use of the benthic zone by hyporheic species in association with sediment deposits, which is a new conceptual framework for explaining how hyporheic invertebrates can persist through flood events by adapting to dynamic sediment movements. Experiments using artificial floods provide promising opportunities for challenging hyporheic studies.