Biology

A taxonomic study was carried out on an isolate, strain NO2 T , from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Gammaproteobacteria and was most closely related to Glaciecola mesophila KMM 241 T and Glaciecola polaris LMG 21857 T (98.6 and 98.0 % 16S rRNA gene sequence similarity, respectively). The isolate was Gram-negative, aerobic and slightly halophilic and grew in 2-8 % NaCl and at 7-30 6C. Strain NO2 T shared some physiological and biochemical properties with G. mesophila KMM 241 T and G. polaris LMG 21857 T . The G+C content of the genomic DNA of strain NO2 T was 45 mol%. Strain NO2 T possessed C 16 : 0 , summed feature 4 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH) and summed feature 7 (C 18 : 1 v9c/v12t/v7c) as the major cellular fatty acids. DNA-DNA relatedness data indicated that strain NO2 T represents a distinct species that is separate from G. mesophila and G. polaris. On the basis of polyphasic evidence, it is proposed that strain NO2 T (=KCTC 12755 T =LMG 23762 T ) represents the type strain of a novel species, Glaciecola agarilytica sp. nov.

A taxonomic study was carried out on two isolates, strains BL1 T and BL11, from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that these isolates clearly affiliated with the Gammaproteobacteria. BL1 T and BL11 were most closely related to Oceanisphaera litoralis KMM 3654 T (97?6 and 97?7 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains BL1 T and BL11 was 99?7 %. The two isolates were Gram-negative, aerobic, moderately halophilic, and grew in 0?5-8?0 % NaCl and at 4-42 6C. Strains BL1 T and BL11 shared some physiological and biochemical properties with O. litoralis KMM 3654 T , although they differed in that BL1 T and BL11 were able to utilize ethanol, proline and alanine. The G+C contents of the genomic DNA of strains BL1 T and BL11 were 56?6 and 57?1 mol%, respectively. Both strains possessed C 16 : 1 v7c and/or iso-C 15 : 0 2-OH, C 16 : 0 and C 18 : 1 v7c as the major fatty acids. DNA-DNA relatedness data indicated that strains BL1 T and BL11 represent a genomic species that is separate from O. litoralis KMM 3654 T . On the basis of polyphasic evidence, it is proposed that strain BL1 T (=KCTC 12522 T =DSM 17589 T ) represents the type strain of a novel species, Oceanisphaera donghaensis sp. nov.

Our newly designed primers were evaluated for the molecular analysis of specific groups of the sqr gene encoding sulfide : quinone reductase (SQR) in sediment environments. Based on the phylogenetic analysis, we classified the sqr sequences into six groups. PCR primers specific for each group were developed. We successfully amplified sqr-like gene sequences related to groups 1, 2 and 4 from diverse sediments including a marine sediment (SW), a tidal flat (TS), a river sediment (RS) and a lake sediment (FW). We recovered a total of 82 unique phylotypes (based on a 95 % amino acid sequence similarity cutoff) from 243 individual sqr-like gene sequences. Phylotype richness varied widely among the groups of sqr-like gene sequences (group 1.group 2.group 4) and sediments (SW.TS.RS.FW). Most of the sqr-like gene sequences were affiliated with the Proteobacteria clade and were distantly related to the reference sqr gene sequences from cultivated strains (less than~80 % amino acid sequence similarity). Unique sqr-like gene sequences were associated with individual sediment samples in groups 1 and 2. This molecular tool has also enabled us to detect sqr-like genes in a sulfuroxidizing enrichment from marine sediments. Collectively, our results support the presence of previously unrecognized sqr gene-containing micro-organisms that play important roles in the global biogeochemical cycle of sulfur.

Erratum to: Microb EcolDOI 10.1007/s00248-011-9860-5In the original version of this article, Fig. 2a was incorrectly provided. The correct Figure appears below: Figure 2Effect of environmental factors and microbial community composition, as measured by the DGGE banding patterns. a Archaea. b Bacteria. Canonical correspondence analysis (CCA) ordination diagram of microbial communities associated with the environmental variables of chlorophyll a (bottom water and transition layer, respectively), sedimentation rate, total nitrogen (TN), total carbon (TC), total inorganic carbon (TIC), total organic carbon (TOC), calcium carbonate (CaCO3), and carbon/nitrogen ratio (C/N). The stations were indicated as closed diamond, 176; open circle, 178; cross, 180; closed circle, 182; closed triangle, 184; closed square, 186; open triangle, 188

Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase α-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0–1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1 × 107 to 4.9 × 107 per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.

A critical step in the process of metagenome analysis is to screen for clones that contain specific genes among a large number of clones. To form one of the sequence-based screening tools of a metagenome library, we designed a format of microarray [metagenome microarray (MGA)] that is arrayed with fosmid library clone DNA samples on a glass slide. We evaluated the MGA using random prime labeled fluorescent probes prepared from PCR products of the target gene and found that we could obtain specific hybridization signals only for the fosmid clone that contained the target gene. We found that the detection limit of the MGA was c. 10 ng μL−1 of fosmid clone DNA, and that the MGA-based hybridization was quantitative within a concentration range of 10–200 ng μL−1 of fosmid clone DNA. We used the MGA successfully to identify two fosmid clones that contained 16S rRNA genes from a fosmid library from the sediment of the East Sea, Korea. In conclusion, we have demonstrated that the MGA can be used for screening for fosmid clones containing specific genes in a metagenome library, and that this technology has potential application as a high-throughput metagenome screening tool.

A critical step in the process of metagenome analysis is to screen for clones that contain specific genes among a large number of clones. To form one of the sequence-based screening tools of a metagenome library, we designed a format of microarray [metagenome microarray (MGA)] that is arrayed with fosmid library clone DNA samples on a glass slide. We evaluated the MGA using random prime labeled fluorescent probes prepared from PCR products of the target gene and found that we could obtain specific hybridization signals only for the fosmid clone that contained the target gene. We found that the detection limit of the MGA was c. 10 ng mL À1 of fosmid clone DNA, and that the MGA-based hybridization was quantitative within a concentration range of 10-200 ng mL À1 of fosmid clone DNA. We used the MGA successfully to identify two fosmid clones that contained 16S rRNA genes from a fosmid library from the sediment of the East Sea, Korea.

Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188–178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier–proximal zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers, station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers.

This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus.

The Chinese many-toothed snake (Sibynophis chinensis) is an endangered species in South Korea. To determine its reproductive activity, here we captured a gravid S. chinensis from Mulyeongari Oreum Wetland Conservation Area, Jeju Island, on May 27, 2018, and reared it at Animal Taxonomy and Morphology Laboratory, Jeju National University, South Korea. The snake oviposited a clutch of six eggs between June 12 and 20, 2018, with an average size of 24.86 ± 1.36 mm in length and 9.86 ± 0.49 mm in width, which were artificially incubated at a constant temperature of 27 °C. After incubating for 34–41 days, five of these six eggs successfully hatched. Average snout-vent length (SVL), tail length (TL), and body weight (BW) of hatchlings were 136.5 ± 5.17 mm, 47.76 ± 2.80 mm, and 1.66 ± 0.12 g, respectively. This study observed the reproductive activity of S. chinensis and characterized its eggs and hatchlings for the first time, providing valuable information for the long-term conservation p...

Background Sika deer, Cervus nippon , were originally introduced to South Korea from Japan and Taiwan for commercial farming purposes. Unfortunately, they were released into the wild during religious events and have since begun to impact the native ecosystem and species endemic to South Korea. The study of activity patterns can improve our understanding of the environmental impact of non-native species and their association with sympatric species. Using camera traps, we studied the diel and seasonal activity patterns of non-native sika deer and quantified the temporal overlap with sympatric mammalian species in the Muljangori-oreum wetlands of Hallasan National Park, South Korea. Results A total of 970 trap events were recorded for five mammalian species from nine locations during the camera-trap survey. Siberian roe deer ( Capreolus pygargus tianschanicus ) had the highest number of recorded events (72.0%), followed by sika deer ( Cervus nippon ) (16.2%), wild boar ( Sus scrofa ) (...

Background: Sika deer, Cervus nippon, were originally introduced to South Korea from Japan and Taiwan for commercial farming purposes. Unfortunately, they were released into the wild during religious events and have since begun to impact the native ecosystem and species endemic to South Korea. The study of activity patterns can improve our understanding of the environmental impact of non-native species and their association with sympatric species. Using camera traps, we studied the diel and seasonal activity patterns of non-native sika deer and quantified the temporal overlap with sympatric mammalian species in the Muljangori-oreum wetlands of Hallasan National Park, South Korea. Results: A total of 970 trap events were recorded for five mammalian species from nine locations during the camera-trap survey. Siberian roe deer (Capreolus pygargus tianschanicus) had the highest number of recorded events (72.0%), followed by sika deer (Cervus nippon) (16.2%), wild boar (Sus scrofa) (5.0%)...

Understanding the ecology of species at risk is extremely important for their conservation and management. Due to land clearing for urban expansion, agriculture, and the import of pets, several snake species including the red-tongue viper (Gloydius ussuriensis) on Jeju Island of South Korea, have become threatened. We studied morphology, distribution, habitat characteristics, diet, and reproduction of red-tongue viper to provide a higher understanding of species ecology. This species on average reach 242–580 mm snout-vent length and is found in a wide range of habitat from mountain forest to lowland areas. Adult snakes prey almost entirely on amphibians followed by mammals and centipedes. The mating usually takes place in spring and birth takes place in autumn. This study points out the major threats and ill-information if addressed will not only contribute to the conservation efforts but also improve the negative attitudes that people hold toward these fascinating animals. The ecol...

Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jej...

Nutria (Myocastor coypus) are semi-aquatic rodents that were introduced in South Korea for commercial farming but significantly damaged aquatic ecosystems. Understanding nutria ecological behavior is essential for developing effective control and eradication strategies to mitigate their impacts. Thus, this study aimed to investigate the home range and activity patterns of 24 nutria (12 males and 12 females) in the Macdo wetland in South Korea from 2015–2016 through radio tracking. The average minimum convex polygon home range of the nutria was 0.29 ± 0.55 km2, with a 95% kernel density estimation (KDE) home range of 0.43 ± 0.85 km2 and a 50% KDE home range of 0.05 ± 1.1 km2. The home range of males was larger than that of females; however, the winter home range of females was as large as that of males. The home range also varied seasonally, with the smallest observed in winter. The nutria showed crepuscular and nocturnal activity patterns throughout the year, with no significant dif...