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To investigate the foraging preferences of the Korean water deer (Hydropotes inermis argyropus) from the Janghang wetlands located in Han River estuary in South Korea, we elucidated their diet compositions using DNA extracted from their fecal samples. Samples were collected from the Janghang wetlands from June 2013 to January 2015. For dietary analysis, we amplified the internal transcribed spacer 2 (ITS2) and the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) regions, followed by cloning and sequencing. We were able to detect 20 families and 35 genera of plants from 77 fecal samples, showing that water deer in the Janghang wetlands mainly preferred Salicaceae (27.5%), Fabaceae (17.5%), and Poaceae (14.2%). In winter, the relative frequency of woody plant detection (81.3%) was much higher than that in other seasons. Our results suggest that Korean water deer in Janghang wetlands browse or graze depending on the locally-available plants species in their habitat as intermediate feeders. Non-invasive approaches using fecal samples could be applied to study food webs of various species and ecosystems for conservation and management of wildlife.

Many studies have attempted to find measures for control of cyanobacterial harmful algal blooms (cyanoHABs) caused by Microcystis, Anabaena, and other bloom-forming plankton species. We have investigated allelopathic inhibition of the submerged macrophyte Myriophyllum spicatum on four phytoplankton species of two taxonomic groups: Chlorophyta Selenastrum capricornutum, Scenedesmus obliquus, and cyanobacteria Microcystis aeruginosa (different strains for toxic, non-toxic, the North Han River originated (NHR) and colonies) and Anabaena circinalis. Inhibitions of unicellular cyanobacteria M. aeruginosa were over 50% for three consecutive days from the 3rd to the 5th day of the coexistence. M. spicatum even inhibited M. aeruginosa at a high initial concentration (1.1 mg L−1 Chl-a). Moreover, M. aeruginosa in a mixture of four phytoplankton species (S. capricornutum, S. obliquus, M. aeruginosa and A. circinalis) was selectively inhibited by M. spicatum. The inhibition of toxic, non-toxic, and NHR of Microcystis by M. spicatum were not significantly different. Colonial cyanobacteria strains were mostly not inhibited by M. spicatum.

Crabs live at high densities in intertidal zones with various halophytes in salt marshes. However, the ecological relationships between crabs and halophytes as well as the impacts of herbivorous crabs on the plant distribution are not fully understood. In this study, we identified halophytic plant species consumed by crabs and determined the relative contributions of halophytes and other food sources to the diet. A DNA analysis of stomach contents was used to determine plant food sources for crabs. We found that the dominant crab species Helice tientsinensis consumed Suaeda japonica, even though several halophytes inhabited the study site. These results indicated that H. tientsinensis is a selective feeder. Based on a stable isotope analysis, we observed a dietary shift during crab development. Immature individuals mainly ate soil organic matter, whereas mature individuals showed more diverse food sources. We observed greater plant (S. japonica) consumption by middle-sized crabs than by crabs of other sizes. Our results for the feeding relationship between crabs and plants extend our understanding of the benthic food web in salt marshes.

Background In temperate regions many small mammals including bats hibernate during winter. During hibernation these small mammals occasionally wake up (arouse) to restore electrolyte and water balance. However, field data on water stress and concentration of bodily fluids during hibernation is scarce. Urinary creatinine concentration has long been used to calibrate urinary hormone concentration due to its close correlation with urine concentration. Therefore, by investigating urinary creatinine concentration, we can estimate bodily fluid concentration. In this study, we investigated changes in urinary creatinine from greater horseshoe bats (Rhinolophus ferrumequinum) hibernating in abandoned mineshafts in two regions in South Korea. Results We collected 74 urine samples from hibernating greater horseshoe bats from 2018 to 2019. We found that urinary creatinine concentration was higher in February and March and then declined in April. There were also indications of a sex difference in the pattern of change in creatinine concentration over the three months. Bats in the warmer and less humid mineshaft had higher urinary creatinine concentrations than bats in the colder and more humid mineshaft. Conclusions These results indicate that hibernating bats face water stress as urinary concentration increases during winter and that water stress may vary depending on the microenvironment. Sex differences in behaviour during hibernation may influence arousal frequency and result in sex differences in changes in urinary creatinine concentration as hibernation progresses. Although further behavioural and endocrinal investigations are needed, our study suggests that urinary creatinine concentration can be used as a proxy to estimate the hydration status of bats and the effect of sex and environmental factors on arousal patterns during hibernation.

The Eurasian oystercatcher (Haematopus ostralegus), Near Threatened in the IUCN red list, was designated classified endangered species II by the Ministry of Environment of Korea and a Natural Monument (No. 326) by the Cultural Heritage Administration of Korea. In this study, the complete mitochondrial genome (16,798 bp) of H. ostralegus was determined for the first time, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region. The overall base composition was A (31.4%), C (31.3%), G (13.8%), and T (23.5%), so the percentage of A and T (54.9%) was slightly higher than that of G and C. A phylogenetic analysis using concatenated mitogenomes revealed that the family Haematopodidae has a closer relationship with the family Recurvirostridae and H. ostralegus and H. ater clustered together. The results are expected to provide useful resources for species identification and further phylogenetic studies of genus Haematopus.

Additional file 1: Figure S1. Daily ambient temperature, TA (a) and relative humidity, RH (b) of A1 and H1 in 2019. Figure S2. Ambient temperature (top) and relative humidity (bottom) at the nearest weather stations in Cheonan (CA) and Yeonggwang (YG) in 2018 and 2019. The nearest weather station to A1 (Anseong) is 17.6km away in Cheonan (N36°45’45.576” E127°17’33.071), and for H1 (Hampyeong), it is 18.2km away in Yeonggwang (N35°17’1.932” E126°28’39.071”). Temperature data were collected by the automatic weather system (AWS) managed by the Korean Government ( https://data.kma.go.kr/ ). Figure S3. Creatinine concentrations in 2018 and 2019 (N = 74). Lines in boxes: the median, the top and bottom of boxes: the first and third quartiles, dots: creatinine concentration of each urine from females (circle) and males (triangle).

Background Ikonnikov’s whiskered bat (Myotis ikonnikovi) is found throughout the Korean Peninsula, as well as in Kazakhstan, Russia, Mongolia, China, and Japan. It is small-sized and primarily inhabits old-growth forests. The decrease and fragmentation of habitats due to increased human activity may influence the genetic structure of bat populations. This study was designed to elucidate the population genetic structure of M. ikonnikovi using mitochondrial genes (cytochrome oxidase I and cytochrome b). Results The results showed that M. ikonnikovi populations from Korea have high genetic diversity. Although genetic differentiation was not detected for the COI gene, strong genetic differentiation of the Cytb gene between Mt. Jeombong and Mt. Jiri populations was observed. Moreover, the results indicated that the gene flow of the maternal lineage may be limited. Conclusions This study is the first to identify the genetic population structure of M. ikonnikovi. We suggest that conservation of local populations is important for sustaining the genetic diversity of the bat, and comprehensive studies on factors causing habitat fragmentation are required.

Additional file 1: Table S1. Primers used in the present study [Akmali et al. 2015; Irwin et al. 1991; and Vrijenhoek 1994]. Table S2. Slatkin’s linearized FST for COI (above the diagonal) and for Cytb (below the diagonal) across four populations of Myotis ikonnikovi in Korea.

We investigated the feeding preferences of the White-cheeked Starling Spodiopsar cineraceus in Korean village groves during the breeding season by means of a fecal dietary analysis using a non-invasive molecular approach. A total of 529 fecal samples were collected from four different study sites, 113 of them (21.4% of all fecal samples) were identified as those of S. cineraceus. Analysis showed that the starling's diet mostly consisted of animal matter (64.5%), but also contained vegetable matter (32.7%). Terrestrial prey, such as insects and spiders, constituted the largest proportion (65.2%) of species in the diet, although aquatic organisms (26.1%) were also important. Most of the seeds detected in feces were of mulberries, with detection rates rising to 68.1% by the end of May and remaining high until mid-June. Our results suggest that higher water levels in paddy fields due to irrigation could potentially act as an impediment to bird feeding, particularly for small birds such as S. cinerace...

Propidium monoazide (PMA) is a highly selective dye that penetrates only membrane-compromised, dead microbial cells and inhibits both DNA extraction and amplification. PMA has been widely used for discrimination between living and dead microbial cells; however, the application of PMA in phytoplankton studies has been limited. In this study, we attempted to evaluate its applicability for the discrimination of viable phytoplankton. We tested PMA on seven phytoplankton species, Microcystis aeruginosa, Anabaena sp., Aphanizomenon sp., Synechocystis sp., Cryptomonas ovata, Scenedesmus obliquus, and Nitzschia apiculata as representatives of the major phytoplankton taxa Cyanobacteria (first four species), Chlorophyta, Cryptophyta, and Bacillariophyta, respectively. Our results showed that application of PMA to phytoplankton living in freshwater has the potential to distinguish viable from dead cells as in microbial studies. Particularly, PMA differentiated viable from dead cells in cyanobacterial species rather than in other phytoplankton taxa under our experimental conditions. However, our results also showed that it may be necessary to adjust various conditions affecting PMA treatment efficiency to expand its applicability to other phytoplankton. Although all factors contributing to the effects of PMA could not be evaluated, our study showed the applicability of PMA-based molecular approaches, which can be convenient quantitative methods for distinguishing living from dead phytoplankton in freshwater ecosystems. Setting optimal treatment conditions for other phytoplankton species may increase the efficacy of PMA-based molecular approaches.

We conducted a 7-d co-existence experiment to verify the inhibitory activity of an aquatic vascular plant,Myriophyllum spicatum, on the cyanobacteriumMicrocystis aeruginosa, and to screen for allelopathic compounds. Plants were placed on a modified solid M4 medium whileM. aeruginosa was cultured in an L16 liquid medium. Our treatments included rearingMyriophyllum spicatum alone (Plant-Only; PO) or withMicrocystis aeruginosa (Plant-Cyanobacteria; PCB), as well as an untreated control, or plates with the cyanobacterium alone. In the PCB treatment,M. aeruginosa became transparent in three replicates on the 6th day and in four replicates on Day 7. To make the distinction inMyriophyllum spicatum metabolites between the PO and PCB treatments, we obtained 13 m/z profiles using a 15 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Principle component analyses were performed on those profiles, from which we obtained accurate mass values for selected peaks that had most negative loadings on the first principal component and most positive loadings on the second principal component: 282.06983 and 283.06836. We identified those peaks as C7H17N5O3S2 and C10H12N4O6, respectively. The Dictionary of Natural Products database suggests that the latter is either oxanosine or xanthosine.

To establish molecular monitoring for the phytoplankton community in aquatic ecosystems, we analysed the terminal restriction fragment length polymorphism (T-RFLP) of small subunit ribosomal RNA gene (18S rDNA) sequences of nuclear genomes from the algal strains of culture collections and environmental samples of two freshwater reservoirs (Sangcheon reservoir and Seoho reservoir, Korea). Terminal restriction fragment (T-RF) length database was also constructed from twelve strains of algal culture collections to annotate and identify the phytoplankton species from T-RFLP profiles. Algal species in reservoirs were identified and monitored through the colony sequencing and T-RF length patterns of 18S rRNA. In this study, 41 unique clones were identified from two reservoirs including Chlorophyta, Cryptophyta, and Alveolata. In the case of Cryptomonas sp., we found significant linear relationships between T-RF peak areas and biovolumes by cell counting. Our results suggest that T-RFLP analysis can be a fast and quantitative monitoring tool for species changes in phytoplankton communities.

To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.

We estimated monthly and annual secondary productivity of pelagic zooplankton in Lake Paldang and Lake Cheongpyong. Secondary productivity was calculated by combining estimated zooplankton biomass and biomass-specific productivity for each site and depth from March to November 2008. In addition to somatic production, we measured production of eggs and exuviae for three dominant species: Daphnia galeata, Bosmina longirostris, Cyclops sp. In terms of biomass, B. longirostris was dominant in Lake Paldang in April and May, B. longirostris showed explosive biomass growth, especially in May. In June and July, B. longirostris and D. galeata were both dominant. Lake Cheongpyeong showed much lower zooplankton biomass than Lake Paldang. In August, there was little or no biomass in both lakes probably due to heavy rain. The Gyeongan River contributed most of the secondary productivity and B. longirostris contributed the most secondary productivity in Lake Paldang. D. galeata also contributed in the Gyeongan River, the South Han River and at the Paldang Dam in spring and fall. Overall, Lake Cheongpyeong showed lower secondary productivity than Lake Paldang. B. longirostris made the largest contribution to secondary productivity in the Cheongpyeong Dam area while D. galeata contributed the most near Nami Island. Somatic production constituted ~80% of the total secondary productivity (the sum of somatic, egg and exuvia production) for D. galeata and B. longirostris. Although production-to-biomass (P/B) ratios were usually