Mite composition in nests of the Japanese wood mouse, Apodemus speciosus (Rodentia: Muridae)

Acari is a diverse group of arthropods that include well-known parasites of animals. Rodents, particularly, serve as common hosts of mites and ticks, transmitting pathogens to domestic animals and humans. Understanding the ecological dynamics between parasites and rodent hosts is crucial for ecosystem management. Due to limited knowledge about the life history of ectoparasites in wild mouse nests, we collected four nests of Apodemus speciosus, the most common rodent species in the wild areas of Japan, along with soil samples near the nests to study arthropod communities. Mites overwhelmingly populated the mouse nests, comprising approximately 90% of all arthropods, while both mites and collembolans were prevalent in soil. Various species identified in our study, such as those from the families Laelapidae, Pygmephoridae, Cheyletidae, Trombiculidae, Glycyphagidae, and Thyrisomidae align with known ectoparasites or species found in the nests of other rodent species, but most parasitic species were never collected in the surrounding soil except for trombiculids. The dominance of mites in mouse nests suggests selective preference for inhabiting these host environments, although the exact reasons driving this dominance remain unclear. Further investigations into the food web within mouse nests will aid in characterising faunal composition and understanding the ecological interaction among rodents, mites, and other nest symbionts.

Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes

Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by faecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We examined 420 faecal samples and found different patterns of dietary diversity and composition among the duck species. The pattern also differed between plant and invertebrate food. Dietary niche partitioning was clear in plant food. Large-bodied ducks intensively use crop plants, and other ducks might mediate competition by using terrestrial and aquatic plants that are suitable for their foraging behaviours or microhabitats. Dietary segregation among species was the most apparent in February, when the abundance of foraging ducks was the largest. This study illustrated the complex pattern of dietary niche partitioning of dabbling ducks in agricultural landscapes, which might be difficult to evaluate by conventional approaches. The availability of crop plants, as well as other plant food resources in flooted areas and farmland dikes, may enable ducks to coexist by spatial or behavioural resource partitioning.

Phoretic behavior of the pseudoscorpion Megachernes ryugadensis on the Japanese wood mouse Apodemus speciosus

Phoresy is a passive transportation behavior where one organism (phoront) disperses to a new location by attaching to another organism. Pseudoscorpions are arthropod predators that mainly live in soil, subterranean habitats, and under tree bark. Some species also live in animal nests and engage in phoresy on small mammals, suggesting close associations with these animals. However, the relationship between phoretic pseudoscorpions and hosts as well as the ecological significance of phoresy remain largely unexplored. Here, to understand the function of phoresy of Megachernes ryugadensis, phoretic on small mammals, their phoretic behavior was investigated in a deciduous forest in northern Japan; individual-level dynamics of phoresy were examined by over 3-year mark-recapture surveys that concurrently marked the host and phoront; and host characteristics, such as sex and age class, were analyzed based on a 2-year small mammal trapping survey. The primary host species was the abundant Japanese wood mouse Apodemus speciosus. Out of 132 pseudoscorpions marked, 5 were recaptured approximately 1 month later. No pseudoscorpions were recaptured within the same census period (3-4 days) when they were marked, indicating that phoresy events last less than one night, and pseudoscorpions are unlikely to engage in phoresy again within a few weeks of their initial engagement. Furthermore, analysis of host characteristics revealed a tendency for female mice and adult individuals to have a higher probability of being hosts compared with males and subadults, respectively. Based on the findings in this and previous studies, the function of phoresy in this species is discussed.

How much do field mice prefer dwarf bamboo seeds? Two-choice experiments between seeds of Sasa borealis and several tree species on the forest floor

Bambusoideae is a taxon of mass-flowering monocarpic perennials with a long life cycle. Forest ecosystems are affected by Bambusoideae seeding and death events in various ways, including an increased abundance of Apodemus spp. The utilization and preference of dwarf bamboo seeds over tree seeds by field mice remain elusive. Therefore, we aimed to determine whether field mice prefer dwarf bamboo to tree seeds. We examined one dwarf bamboo species (Sasa borealis) against four tree species with varying acorn/fruit traits (Castanea crenata, Quercus crispula, Fagus crenata, and Lindera triloba). The seeds were placed in a container in a forest among dead S. borealis culms, with an automatic camera monitoring the setup. The examined seeds were mainly foraged by two field mouse species, Apodemus speciosus and Apodemus argenteus, with preference in the following order: C. crenata, L. triloba, S. borealis, F. crenata, and Q. crispula. Our findings indicated that during S. borealis mast seeding years, predation pressure on F. crenata and Q. crispula seeds could be considerably reduced. This suggests that mast seeding might disrupt the normal pattern of survival, and seed dispersal patterns, potentially altering the forest vegetation composition.

Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding

DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan (Lagopus muta japonica), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015-2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V. uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant s for Japanese rock ptarmigans from July to October. This plant community therefore needs to be conserved in order to protect the food resources of Japanese rock ptarmigans in the region.

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents

Host-microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.

DNA metabarcoding dietary analyses of the wood mouse Apodemus speciosus on Innoshima Island, Japan, and implications for primer choice

We used DNA metabarcoding to assess the seasonal diets of the large Japanese wood mouse, Apodemus speciosus (Muridae, Rodentia), in forest edges adjacent to citrus orchards on Innoshima Island, Japan. We used one chloroplast and three mitochondrial DNA barcoding markers to determine mouse diets. Among the various plant and invertebrate diets, A. speciosus typically consumed Chinese cork oak (Quercus variabilis) in early spring (likely acorns preserved during winter) and gypsy moths (Lymantria dispar, a forest pest) in late spring and summer. In addition, we found that A. speciosus also preyed on orchard pests, including the gutta stink bug and other potentially harmful invertebrates. The season during which A. speciosus preyed on stink bugs corresponded with the harvest of orchard products. This study revealed several of the ecological roles of A. speciosus within the boundary zone between forest and human ecosystems. Furthermore, based on the performance of various mitochondrial markers in dietary profiling of invertebrate food items, we recommend the multi-locus DNA metabarcoding method to comprehensively assess the diet of A. speciosus.

Molecular assessment of dietary niche partitioning in an endemic island radiation of tropical mammals

Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here, we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.

Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus

During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship's robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet.

Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding

Ecological theory postulates that niches of co‐occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely‐related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra‐ and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat‐driven. The two most‐closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly‐related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.

Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination

Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we sampled (n = 288) two species pairs of Apodemus mice that occur in sympatry in habitats affected by the Chernobyl and Fukushima nuclear accidents, these comparisons provide an opportunity for a general assessment of the effects of exposure to environmental contamination (radionuclides) on gut microbiota across host phylogeny and geographical areas. In general agreement with our hypothesis, analyses of bacterial 16S rRNA gene sequences revealed that radiation exposure alters the gut microbiota composition and structure in three of the four species of Apodemus mice. The notable lack of an association between the gut microbiota and soil radionuclide contamination in one mouse species from Fukushima (A. argenteus) probably reflects host "radiation escape" through its unique tree-dwelling lifestyle. The finding that host ecology can modulate effects of radiation exposure offers an interesting counterpoint for future analyses into effects of radiation or any other toxic exposure on host and its associated microbiota. Our data show that exposure to radionuclide contamination is linked to comparable gut microbiota responses across multiple species of rodents.

Cold temperature improves tannin tolerance in a granivorous rodent

The foraging ecology of mammalian herbivores is regulated in part by their ability to detoxify plant secondary metabolites (PSM). Ambient temperature has been shown to alter liver function in rodents and the toxicity of some PSMs, but little is known about the physiological and nutritional consequences of consuming PSMs at different ambient temperatures. Furthermore, the effect of ambient temperature on the response of mammals to the most ubiquitous class of PSM, tannins, is unknown. We measured the effect of temperature and tannin intake on liver function, and the subsequent effect on the tannin tolerance of wild Japanese wood mice, Apodemus speciosus. The experiment involved acclimation to one of two ambient temperatures (10°C or 20°C) followed by acclimation to a diet of acorns (6.2% tannin DW). Liver function was measured both before and after acclimation to acorns by measuring the clearance time of a hypnotic agent. Finally, the mice were fed only acorns in a 5-day feeding experiment to assess their tolerance to tannin in the diet. Acclimation to acorns had a significant effect on liver function, but the direction of this effect was dependent on ambient temperature. Acorn consumption improved the liver function of wood mice at 10°C, but reduced liver function at 20°C, revealing a complex relationship between ambient temperature and tannin intake on liver function. Furthermore, mice with better liver function, indicated by faster clearance of the hypnotic agent, exhibited higher protein digestibility on an acorn-only diet, indicative of higher tannin tolerance. These results suggest that environmental temperature plays a significant role in the tolerance of A. speciosus to tannins, providing new insight into their seasonal feeding behaviour and winter ecology. We contend that cold-induced tannin tolerance may help to explain the population dynamics of mammalian herbivores with seasonal changes in the tannin content of their diet, and inform predictions about the response of these animals to a changing climate.

The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus

Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.