Disturbance legacy of a 100-year flood event: large wood accelerates plant diversity resilience on gravel-bed rivers.

Understanding biodiversity resilience after a major disturbance is a key issue in basic and applied science. Plant diversity in gravel-bed rivers is affected by flood events, which are one of the most effective disturbance agents in the flow regime, affecting species distribution, and ecosystem dynamics. Although disturbance plays a critical role in community assembly mechanisms, how plant diversity recovers after a severe disturbance, such as a 100-year flood event remains unknown. The present study examined how the disturbance legacy of large wood in gravel-bed river ecosystems contributes to the resilience of plant diversity. The present study demonstrated that the resilience of plant species in disturbance legacy sites, namely deposited large wood sites, was higher than that in open habitat sites. Indicator species analysis revealed that perennial plants were the most important indicator species of disturbance legacy sites. These results suggest that perennial species richness contributes to the resilience of high plant diversity across the disturbance legacy sites in this region. After major flood events, land managers often remove large wood and debris jams to avoid secondary disasters, such as embankment collapse. However, we suggest that large wood should be retained on the gravel beds to aid the recovery of biodiversity and ecosystems. Furthermore, understanding the relationships between disturbance legacies and ecosystem resilience can contribute to the formulation of strategies for sustainable ecosystem management and biodiversity conservation in the future.

Estimates of resource transfer via winged adult insects from the hyporheic zone in a gravel-bed river.

Hyporheic zone (HZ) locates below the riverbed providing habitat for macroinvertebrates from where the winged adult insects (i.e., hyporheic insects, HIs) emerge and bring out aquatic resources to the riparian zone. This study estimated mean daily flux as dry biomass (BM), carbon (C), and nitrogen (N) deriving from the dominant HI species Alloperla ishikariana (Plecoptera, Chloroperlidae) for a 4th-order gravel-bed river during the early-summer to summer periods. We hypothesized that HIs were an important contributor in total aquatic resources to the riparian zone. In 2017 and 2018, we set parallelly (May to August) and perpendicularly (June to October) oriented Malaise traps to catch the lateral and longitudinal directional dispersing winged adults of A. ishikariana, and other Ephemeroptera, Plecoptera, Trichoptera, and Diptera from the river and estimated the directional fluxes of them. We further split the directional fluxes as moving away or back to the channel (for lateral) and from down- to upstream or up- to downstream (for longitudinal). Alloperla ishikariana was similar to other Plecoptera species and differed clearly from Ephemeroptera and Trichoptera in directional characteristics of resources flux, suggesting that the extent and directions of HZ-derived resource transfer depend on taxon-specific flight behaviors of HIs. Contributions of A. ishikariana to the riparian zone in total aquatic C and N transfer seasonally varied and were lower in May (5%-6%) and August (2%-4%) and the highest in July (52%-70%). These conservative estimates largely increased (9% in May) after the supplementary inclusion of Diptera (Chironomidae and Tipulidae), part of which were considered HIs. We demonstrated that HZ could seasonally contribute a significant portion of aquatic resources to the riparian zone and highlighted the potential importance of HZ in nutrient balance in the river-riparian ecosystem.

Long-lasting effects of historical land use on the current distribution of mammals revealed by ecological and archaeological patterns.

Past land-use activity has massively altered the environment and vegetation over centuries, resulting in range contractions and expansions of species. When habitat recovery and species recolonization require a long time, the fingerprint of past land use can remain on the current distribution of species. To evaluate millennial-scale effects of land use in Japan, we explained the current ranges of 29 mammalian genera based on three types of archaeological land-use patterns (settlement, ironwork and kiln) considering potential confounding factors. The results indicate that archaeological human activity associated with ironwork and pottery production had severe negative effects on many genera of small and medium-sized mammals. Despite positive effects on some genera, the magnitudes were less than those of the negative effects. The relative importance of archaeological factors on small mammals was greater than those for medium- to-large mammals. The persistent imprint of past land-use patterns was non-negligible, explaining current mammalian diversity. Spatial ecological and archaeological information can provide meaningful insights into long-term socio-ecological processes, which are crucial for the development of sustainable societies in the Anthropocene.

Molecular and histopathological characterization of Cryptosporidium and Eimeria species in bats in Japan.

Bats are potential reservoirs of Cryptosporidium and Eimeria. The genus Cryptosporidium infects various vertebrates and causes a diarrheal disease known as cryptosporidiosis. Many epidemiological studies in wild animals have been performed; however, most of them relied on only PCR-based detection because of the difficulty of performing pathological analyses. Accordingly, the natural host and pathogenicity of Cryptosporidium bat genotypes remain unclear. In this study, we captured Eptesicus nilssonii (Northern bats) in Hokkaido, Japan. Of the three intestinal samples obtained, two were positive for Cryptosporidium spp. and one was positive for Eimeria spp. The corresponding microorganisms were also confirmed histopathologically. We detected the novel Cryptosporidium bat genotype XII and Eimeria rioarribaensis in bat intestine.

Predicting the ecological impacts of large-dam removals on a river network based on habitat-network structure and flow regimes.

Large dams provide vital protection and services to humans. However, an increasing number of large dams worldwide are old and not operating properly. The removal of large dams has excellent potential to restore habitat connectivity and flow regimes; therefore, projecting the related ecological consequences is an emerging need for water resource and ecosystem management. However, no modeling methods are currently available for such projections at the basin scale. We devised a scheme that integrates changes in flow regimes and habitat network structure into a basin-scale impact assessment of removal of large dams and applied it to the Nagara-Ibi Basin, Japan. We used a graph-theoretical approach and a hydrological model, to quantify changes in habitat availability for 11 freshwater fishes at the basin scale under multiple removal scenarios. We compared these results with the change predicted using a conventional scheme that considered only changes to the habitat network due to dam removal. Our proposed scheme revealed that an increase in flow variability associated with dam removal projected both positive and negative effects on basin-scale habitat availability, depending on the focal species, endangered species had a negative response to dam removal. In contrast, the conventional approach projected only positive effects for all species. This difference in the outcomes indicates that large-dam removal can have negative and positive effects on watershed restoration due to changes in flow regimes. Our results also suggest the effect of removal of large dams may depend on the dams and their locations. Our study is the first step in projecting ecological trade-offs associated with the removal of large dams on riverscapes at the basin scale and provides a foundation for future process-based watershed restoration.

Establishment and characterization of a cell line derived from Eptesicus nilssonii.

Bats of the genus Eptesicus have several non-retroviral RNA virus-derived sequences in their genomes, among which an endogenous bornavirus-like L element, named eEBLL-1, was suggested to encode functional proteins in the hosts. However, the function of eEBLL-1 remains unclear due to a lack of appropriate investigation tools, such as cultured cells expressing eEBLL-1. Here, we established a continuous cell line, named HAMOI-EnK cells, from kidney of Eptesicus nilssonii. HAMOI-EnK cells are robust and could be passaged for at least 10 months. eEBLL-1 in the genomes of HAMOI-EnK cells retains an intact open reading frame. Additionally, eEBLL-1 is transcribed in the sense-orientation in cells. To our knowledge, this is the first report to demonstrate that eEBLL-1 is transcribed in cultured cells.

An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus.

Endogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Here, we demonstrate that bats of the genus Eptesicus have preserved for more than 11.8 million years an EBLL element named eEBLL-1, which has an intact open reading frame of 1,718 codons. The eEBLL-1 coding sequence revealed that functional motifs essential for mononegaviral RdRp activity are well conserved in the EBLL-1 genes. Genetic analyses showed that natural selection operated on eEBLL-1 during the evolution of Eptesicus. Notably, we detected efficient transcription of eEBLL-1 in tissues from Eptesicus bats. To the best of our knowledge, this study is the first report showing that the eukaryotic genome has gained a riboviral polymerase gene from an ancient virus that has the potential to encode a functional RdRp.

The Distribution of Cool Spots as Microrefugia in a Mountainous Area.

It has recently been proposed that microrefugia played an important role in species survival during past climate change events. However, the current distributions of microrefugia remain largely unknown. Wind-hole sites are areas affected by preferential flows of cool air generated in interstitial spaces created by rock fragments or colluvia. Alpine plant species occurring in lowland wind-hole sites isolated from alpine zones may be relicts of the last glacial period. Hokkaido, northern Japan, is known to contain many wind-hole sites in which alpine plant species can occur. Here we surveyed 55 wind-hole sites in the Kitami region, eastern Hokkaido, and observed two alpine plant species (lingonberry, Vaccinium vitis-idaea, and Labrador tea, Rhododendron groenlandicum ssp. diversipilosum var. diversipilosum) in 14 wind-hole sites. Statistical modeling showed that wind-hole sites are likely to occur in areas with high maximum slope angles and volcanic rock cover, and concave surfaces. Our predictions of wind-hole site distributions suggest that such topographic conditions are common in our study area, and that many undiscovered wind-hole sites exist. Ignoring microhabitats may greatly underestimate species distributions in topographically complex regions, and dispersed cool spots may also function as stepping stones and temporal habitats for cold-adapted species. Because these localized unique habitats usually occur in economically unproductive sites, identifying and protecting potential microrefugia (cool spots) would be a robust and cost-effective mitigation of climate change impacts.