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Microalgal growth-based tests are international standards for ecotoxicity assessment; however, their long exposure times, large sample volumes, and reliance on a single growth-endpoint make them inadequate for rapid toxicity screening. Here, we aimed to develop a rapid and simple ecotoxicological test using the fast-growing green alga Mychonastes afer, with multiple endpoints-growth, lipid content, and photosynthesis. We exposed M. afer to two metals-silver and copper-and two herbicides-atrazine and diuron-for 24 h and identified the most sensitive and reliable endpoints for each toxicant: the maximum electron transport rate (ETR max ) for Ag, Cu and atrazine, and the lipid content for diuron. Lipid content was found to be both a sensitive and reliable biomarker, meeting the effluent limit guidelines in both the Republic of Korea and the USA. The sensitivity of M. afer to Ag and atrazine also closely matched the HC 5 values derived from the species sensitivity distribution approach, confirming its reliability for setting regulatory concentrations of these contaminants. Our calculated predicted no-effect concentration (PNEC) values were similar to established European Union PNECs for Ag, Cu, atrazine, and diuron, underlining the utility of these biological endpoints for ecological risk assessment and regulatory decision making. This method required lower sample volume (2 mL vs 100 mL) and exposure time (24 h vs 72-120 h) than conventional green algal tests, and eliminated the need for labour-intensive cell counting, expensive equipment, and chlorophyll fluorescence measurement expertise. Overall, this M. afer test can be a valuable tool for the rapid screening of wastewater for metals and herbicides, contributing to environmental protection and management practices., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: The Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult., Objective: In this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi., Results: After assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT., Conclusion: The transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping., (© 2024. The Author(s) under exclusive licence to The Genetics Society of Korea.)

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii . The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis . Among the 10 fish genomes, there were significant gene family expansions (8-2387) and contractions (16-2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii .

A Gram-stain-negative, aerobic, oxidase-positive, weakly catalase-positive, motile by means of a single polar flagellum, rod-shaped bacterium designated as strain S2-9 T was isolated from sediment sampled in Wiyang pond, Republic of Korea. Growth of this strain was observed at 10-40 °C (optimum, 35 °C) and pH 5.5-9.5 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % NaCl in Reasoner's 2A broth. The major fatty acids (>10 %) of strain S2-9 T were C 16 : 0 and summed feature 3 (comprising a mixture of C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ). Ubiquinone-8 was detected as the respiratory quinone. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Strain S2-9 T showed the highest 16S rRNA gene sequence similarity to Paucibacter oligotrophus ' CR182 (98.4 %), all type strains of T (98.7 %), followed by ' Paucibacter aquatile ' CR182 (98.4 %), all type strains of Pelomonas species (98.1-98.3 %), Mitsuaria chitosanitabida NBRC 102408 T (97.9 %), Kinneretia asaccharophila KIN192 T (97.8 %), Mitsuaria chitinivorans HWN-4 T (97.4 %), and Paucibacter toxinivorans 2C20 T (97.4 %). Phylogenetic trees based on the 16S rRNA gene and whole-genome sequences showed that strain S2-9 T formed a tight phylogenetic lineage with Paucibacter species (CHU3 T , CR182, and 2C20 T strains were 76.6-79.3% and 19.5-21.5 %, respectively. The genomic DNA G+C content of strain S2-9 T was 68.3 mol%. Notably, genes responsible for both sulphur oxidation and reduction and denitrification were found in the genome of strain S2-9 Paucibacter strains were 76.6-79.3% and 19.5-21.5 %, respectively. The genomic DNA G+C content of strain S2-9 T was 68.3 mol%. Notably, genes responsible for both sulphur oxidation and reduction and denitrification were found in the genome of strain S2-9 T represents a novel species of the genus T is involved in the nitrogen and sulphur cycles in pond ecosystems. Based on the polyphasic taxonomic results, strain S2-9 T represents a novel species of the genus Paucibacter , for which the name Paucibacter sediminis sp. nov. is proposed. The type strain is S2-9 T (= KACC 22267 T = JCM 34541 T ).

Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic conservation data for M. longidorsalis . We analyzed 19 microsatellite loci in six populations of M. longidorsalis in South Korea to characterize their population structure and genetic diversity. The genetic diversity of the microsatellites was 0.741-0.779, which is lower than that of other freshwater fishes. The pairwise genetic differentiation of microsatellite ( F ) values ranged from 0.007 to 0.041, suggesting low genetic differentiation between the populations. The Jojongicheon stream population (CP) had an effective population size of <100. Therefore, conservation efforts are required to prevent inbreeding depression in ST . Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis . Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis .

Background: Staphylococcal cassette chromosome mec type V (SCC mec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCC mec V after transmission from overseas donor strains to Korean recipient strains., Methods: Sixty-three complete MRSA SCC mec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCC mec V strains using publicly available whole-genome data., Results: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCC mec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCC mec V donors., Conclusions: Most Korean SCC mec V strains may have emerged during 2000-2010. A unique MRSA SCC mec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.

This study is the first to report the characterization of Carex pumila genomic information. Assembly of the genome generated a draft of C. pumila based on PacBio Sequel II and Illumina paired-end sequencing, which was assembled from 2941 contigs with an estimated genome size of 0.346 Gb. The estimate of repeats in the genome was 31.0%, and heterozygosity ranged from 0.426 to 0.441%. The integrity evaluation of the assembly revealed 1481 complete benchmarked universal single-copy orthologs (BUSCO) (91.76%), indicating the high quality of the draft assembly. A total of 23,402 protein-coding genes were successfully predicted and annotated in the protein database. UpsetR plots showed that 7481 orthogroups were shared by all species. The phylogenetic tree showed that C. pumila is a close but distant relative of Ananas comosus . C. pumila had greater contraction (3154) than expansion (392). Among the extended gene families, aquaporins have been found to be enriched. Primers for microsatellite markers determined 30 polymorphic markers out of 100. The average number of alleles amplified by these 30 polymorphic markers was 4 to 12, with an average polymorphism information content (PIC) value of 0.660. In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of C. pumila .

Safe drinking water sources are crucial for human health. Consequently, water quality management, including continuous monitoring of water quality and algae at sources, is critical to ensure the availability of safe water for local residents. This study aimed to construct statistical prediction models considering probability distributions relevant to cyanophyte cell counts and compare their prediction performance. In this study, water quality parameters at Juam Lake and Tamjin Lake, representative water sources in the Yeongsan and Seomjin rivers, South Korea, were investigated. We used a water quality monitoring network, algae alert system, and hydraulic and hydrological data measured every 7 days from January 2017 to December 2022 from the Water Environment Information System of the National Institute of Environmental Research. Using data for 2017-2021 as a training set and data for 2022 as a test set, the performances of seven models were compared for predicting cyanophyte cell counts. Environmental factors associated with algae in water sources were observed based on the monitoring data, and a prediction model appropriate for the cyanophyte distribution was generated, which also included the risk of toxicity. The extreme gradient boosting with the random forest model had the best predictive performance for cyanophyte cell counts. The study results are expected to facilitate water quality management in various water systems, including water sources., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Microphysogobio rapidus , an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness ( A = 18.3-18.4, A R = 13.8) compared to those from DC ( A = 11.8, A R = 11.5). The observed heterozygosity among the fish examined ranged from H O = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy-Weinberg equilibrium (HWE) ( p < 0.05). Despite having the largest effective population size ( N e > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341-0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation ( F < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of IS = 0.056-0.053, respectively), which were highly significant ( p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve N e = 61) and showed an inbreeding coefficient close to zero ( p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341-0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation ( F ST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of F ST between fish sampled from the Nam and Deokcheon Rivers revealed significant values ( p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area.

Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea's protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research., (© 2023. The Author(s) under exclusive licence to The Genetics Society of Korea.)

Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE , ndhF , rpl23 , atpF , rps4 , and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.

Microbacterium elymi KUDC0405 T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405 T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405 T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 μm. Based on 16S rRNA gene sequences, KUDC0405 T was most closely related to Microbacterium bovistercoris NEAU-LLE T (97.8%) and Microbacterium pseudoresistens CC-5209 T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405 T and M. bovistercoris NEAU-LLE T and M. pseudoresistens CC-5209 T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405 T , M. bovistercoris NEAU-LLE T , and M. pseudoresistens CC-5209 T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405 T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C 17:0 and iso-C 16:0 . Strain KUDC0405 T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405 T should be considered a novel species within the genus Microbacterium , for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405 T (=KCTC 49411 T , =CGMCC1.18472 T ).

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6 T , was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0-8.0 (optimum, pH 7.0) and 10-37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6 T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550 T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6 T were iso-C 15:0, iso-C 15 : 1 G and iso-C 17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6 T represents a novel species in a new genus in the family Chitinophagaceae , for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6 T =KCCM 43337 T =NBRC 114336 T ) is proposed.

A strict aerobic bacterium, strain JW14 T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14 T was observed at 20-37 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and in the presence of 0-2.0% NaCl (optimum, 0%). Strain JW14 T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C 15:0 , C 16:0 and iso-C 16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14 T contained meso -diaminopimelic acid. The DNA G+C content of strain JW14 T calculated from the whole genome sequence was 48.1 mol%. Strain JW14 T was most closely related to Paenibacillus graminis DSM 15220 T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14 T formed a distinct phyletic lineage from closely related type strains within the genus Paenibacillus . Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14 T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14 T (=KACC 21840 T =JCM 34279 T ).

The leaf beetle genus Suinzona, consisting of over 20 species, is mainly known for species from Southwest China, and its closely related genus Potaninia, with only two species, is widely distributed in South China and upper Southeast Asia. Despite recent morphological studies, the status of these taxa has long been controversial. Here, we investigated the taxonomic status and phylogenetic relationships of the genera Suinzona and Potaninia within Chrysomelinae using molecular, morphological and ecological data. Molecular phylogenetic analysis supported that they should be regarded as distinct genera, which is consistent with morphological evidence, e.g., well-developed/reduced hind wings. Based on combined evidence from examination of larval and adult morphology, host plants and mitochondrial genomes, we demonstrate that P. cyrtonoides should be placed in the genus Suinzona and that specimens from South Korea represent a new species. Suinzona borowieci sp. nov., occurring in narrow strips of habitat, shows high levels of genetic divergence and distantly related host plants between populations. The population differentiation seems to be correlated with its non-functional wings causing reduced dispersal ability and genetic isolation. Several populations have declined dramatically over the last few decades due to loss of habitat and thus are in need of protection as conservation units.

An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386 T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0-2.5×0.6-0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386 T was within the family Lachnospiraceae . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386 T was Clostridium symbiosum (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386 T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C 16 : 0 and C 14 : 0 . Compared to those of the closely related species, strain SNUG30386 T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386 T represents a novel species within the genus Clostridium , for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386 T (=KCTC 15633 T = JCM 32258 T ).

A red-pigmented bacterial strain, designated KIGAM108 T , within the family Hymenobacteraceae was isolated from zeolite in the Gampo-41 mine of the Gyeongju, Republic of Korea. This strain was a Gram-negative, strictly aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain KIGAM108 T found that it was related to the genus Hymenobacter, with similarities of 96.6, 96.4, 95.5, and 95.0% to H. fastidiosus VUG-A124 T , H. algoricola VUG-A23a T , H. crusticola MIMBbqt21 T , and H. daecheongensis DSM 21074 T , respectively. Strain KIGAM108 T grew in the presence of 0-0.5% (w/v) NaCl at 4-37 °C and pH 6.0-10.0. This isolate contained MK-7 as a respiratory quinone. The polar lipids of strain KIGAM108 T were identified as phosphatidylethanolamine, two unidentified aminophospholipids, one unidentified phospholipid and five unidentified lipids. The major fatty acids profile showed summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c) (22.3%), anteiso-C 15:0 (17.1%), C 16:1 ω5c (13.3%), and iso-C 15:0 (11.0%). The genomic DNA G + C content was 60.0 mol%. Based on the polyphasic taxonomic data, strain KIGAM108 T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter lutimineralis sp. nov. is proposed. The type strain is KIGAM108 T (=KCTC 72263 T =JCM 33444 T ).

A Gram-stain-negative, yellow-pigmented, strictly aerobic bacterium, designated strain MaA-Y11 T , was isolated from a culture of Microcystis aeruginosa in the Republic of Korea. Cells were non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain MaA-Y11 T was observed at 25-37 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, 7.0) and in the presence of 0-1.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-Y11 T did not produce flexirubin-type pigments. Strain MaA-Y11 T contained iso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) as major cellular fatty acids and menaquinone-6 as the sole isoprenoid quinone. Phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids were detected as the major polar lipids. The G+C content of the genomic DNA was 37.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MaA-Y11 T formed a phyletic lineage with Flavobacterium lindanitolerans IP-10 T within the genus Flavobacterium . Strain MaA-Y11 T was most closely related to Flavobacterium lindanitolerans IP-10 T , with a 98.85 % 16S rRNA gene sequence similarity, and shared less than 93.87 % sequence similarities with other type strains. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-Y11 T and the type strain of F. lindanitolerans were 87.0 and 32.3 %, respectively. Here, we conclude that strain MaA-Y11 T represents a new species of the genus Flavobacterium , for which the name Flavobacterium microcysteis sp. nov. is proposed. The type strain is MaA-Y11 T (=KACC 21225 T =JCM 33501 T ).

In this study, we isolated a total of 238 culturable putative bacterial endophytes from four Pinus species (Pinus densiflora, P. koraiensis, P. rigida, and P. thunbergii) across 18 sampling sites in Korea. The samples were cultured in de Man Rogosa Sharpe and humic acid-vitamin agar media. These selective media were used to isolate lactic acid bacteria and Actinobacteria, respectively. Analysis using 16S ribosomal DNA sequencing grouped the isolated putative bacterial endophytes into 107 operational taxonomic units (OTUs) belonging to 48 genera. Gamma-proteobacteria were the most abundant bacteria in each sampling site and three tissues (needle, stem and root). The highest OTU richness and diversity indices were observed in the roots, followed by stem and needle tissues. Total metabolites extracted from three isolates (two isolates of Escherichia coli and Serratia marcescens) showed significant nematicidal activity against the pine wood nematode (Bursaphelenchus xylophilus). Our findings demonstrated the potential use of bacterial endophytes from pine trees as alternative biocontrol agents against pine wood nematodes.

Two long-rod-shaped, Gram-stain-positive, obligately anaerobic and non-spore-forming strains, SNUG30099 T and SNUG30370 T , were isolated from faecal samples of healthy Korean subjects. The strains formed circular ivory-coloured colonies on Brain-heart infusion medium supplemented with 0.5% Difco yeast extract (YBHI) agar and cells were approximately 3.5-4.5×0.3-0.4 µm in size. Taxonomic analyses based on 16S rRNA gene sequences distinguished the strains from other species within the family Erysipelotrichaceae. The closest relative of strains SNUG30099 T and SNUG30370 T was Longibaculum muris (92.9 % and 93.6 % similarity, respectively), followed by Clostridium saccharogumia (92.3 % and 92.2 %). Phylogenetic inference also divided the strains into a unique branch that differed from other related strains that belong to the family Erysipelotrichaceae. DNA G+C contents based on the whole genome sequences of strains SNUG30099 T and SNUG30370 T were 29.2 and 30.2 mol%, respectively. Both novel strains possessed meso-diaminopimelic acid as the peptidoglycan, and phosphatidylethanolamine was observed as one of the major polar lipids. The major cellular fatty acid composition was different from those of other related taxa. In addition, the profile of biochemical activities advocated that the strains have distinct characteristics in comparison to other strains. Taken together, a novel genus, named Faecalibacillus gen. nov., is proposed, which includes the type species Faecalibacillus intestinalis sp. nov. for strain SNUG30099 T and Faecalibacillus faecis sp. nov. for strain SNUG30370 T . The type strains of these novel species are SNUG30099 T (=KCTC 15631 T =JCM 32256 T ) and SNUG30370 T (=KCTC 15632 T =JCM 32257 T ).

Microsatellite markers from a fresh water yellow catfish, Pseudobagrus fulvidraco , were developed by whole-genome sequencing in the Ion S5 system. Of the 40 chosen sets of microsatellite markers, with tetra-repeat and penta-repeat motifs, from a total 19,743 sequence, only 13 markers were successfully applied in 78 individual fish sampled to detect genomic variability from four natural populations of Korea. On an average, the number of alleles per marker was 6.7. The observed heterozygosity varied from 0.048 to 0.810. Twelve microsatellite markers conformed to Hardy-Weinberg equilibrium and none exhibited significant linkage disequilibrium. In yellow catfish, genetic differentiation among four natural populations was further supported by F ST < 0.05) and STRUCTURE analysis. The microsatellite markers identified could facilitate genetic diversity and population structure studies and thus aid in conservation of the yellow catfish.P < 0.05) and STRUCTURE analysis. The microsatellite markers identified could facilitate genetic diversity and population structure studies and thus aid in conservation of the yellow catfish.

A yellow-coloured, Gram-strain-negative, non-motile, cocci-shaped, strictly aerobic bacterium, designated HZ-65 T , was isolated from hyporheic freshwater in the Republic of Korea. Strain HZ-65 T grew at 15-37 °C (optimum, 25-30 °C), pH 5.5-9.0 (optimum, pH 7.0) and 0-0.5 % NaCl (w/v; optimum at 0 % NaCl). Phylogenetic analysis based on the 16S rRNA gene showed that strain HZ-65 T is a member of family Opitutaceae and is closely related to Opitutus terrae PB90-1 T (94.0 % similarity), Cephaloticoccus primus CAG34 T (93.0 %), and Cephaloticoccus capnophilus CV41 T (92.7 %), while the similarities to other Opitutaceae-type strains were lower than 90.0 %. The DNA G+C content was 62.2 mol% and the quinone present was menaquinone-7. The predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, and iso-C16 : 0, representing 70 % of the total fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Analysis of the HZ-65 T genome revealed the presence of 300 genes that are involved in carbohydrate-active enzymes, which indicates the metabolic potential to degrade polysaccharides. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain HZ-65 T represents a novel species in a new genus within the family Opitutaceae, for which the name Nibricoccus aquaticus gen. nov., sp. nov., is proposed. The type strain of Nibricoccus aquaticus is HZ-65 T (KACC 19333 T =NBRC 112907 T ).

The mature larvae of the nominotypical subgenus Gonioctena Chevrolat, 1836 are redescribed and illustrated: G. coreana (Bechyně, 1948), G. gracilicornis (Kraatz, 1879), G. jacobsoni (Ogloblin Medvedev, 1956), and G. viminalis (Linnaeus, 1758). The tubercular pattern, chaetotaxy, and shape of tarsugulus were used as diagnostic characters for the species determination of Gonioctena s. str. larvae. The literature on larval morphology of each species has been summarized. Furthermore, the biology, behavior, and host plant are presented. Ovoviviparity is newly reported in G. coreana.

A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1 T , was isolated from soil in South Korea. Cells of strain D1 T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1 T formed a phyletic lineage with Sphingobacterium hotanense XH4 T within the genus Sphingobacterium. Strain D1 T was most closely related to S. hotanense XH4 T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603 T (97.2 %), and the DNA-DNA relatedness level between strain D1 T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1 T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1 T (=KACC 18595 T =JCM 31225 T ).

Cryptophytes are ubiquitous and one of the major phototrophic components in marine plankton communities. They often cause red tides in the waters of many countries. Understanding the bloom dynamics of cryptophytes is, therefore, of great importance. A critical step in this understanding is unveiling their trophic modes. Prior to this study, several freshwater cryptophyte species and marine Cryptomonas sp. and Geminifera cryophila were revealed to be mixotrophic. The trophic mode of the common marine cryptophyte species, Teleaulax amphioxeia has not been investigated yet. Thus, to explore the mixotrophic ability of T. amphioxeia by assessing the types of prey species that this species is able to feed on, the protoplasms of T. amphioxeia cells were carefully examined under an epifluorescence microscope and a transmission electron microscope after adding each of the diverse prey species. Furthermore, T. amphioxeia ingestion rates heterotrophic bacteria and the cyanobacterium Synechococcus sp. were measured as a function of prey concentration. Moreover, the feeding of natural populations of cryptophytes on natural populations of heterotrophic bacteria was assessed in Masan Bay in April 2006. This study reported for the first time, to our knowledge, that T. amphioxeia is a mixotrophic species. Among the prey organisms offered, T. amphioxeia fed only on heterotrophic bacteria and Synechococcus sp. The ingestion rates of T. amphioxeia on heterotrophic bacteria or Synechococcus sp. rapidly increased with increasing prey concentrations up to 8.6×10 6 cells ml -1 , but slowly at higher prey concentrations. The maximum ingestion rates of T. amphioxeia on heterotrophic bacteria and Synechococcus sp. reached 0.7 and 0.3 cells predator -1  h -1 , respectively. During the field experiments, the ingestion rates and grazing coefficients of cryptophytes on natural populations of heterotrophic bacteria were 0.3-8.3 cells predator -1 h -1 and 0.012-0.033d -1 , respectively. Marine cryptophytes, including T. amphioxeia, are known to be favorite prey species for many mixotrophic and heterotrophic dinoflagellates and ciliates. Cryptophytes, therefore, likely play important roles in marine food webs and may exert a considerable potential grazing impact on the populations of marine bacteria., (Copyright © 2017 Elsevier B.V. All rights reserved.)

A novel Gram-stain-negative, non-spore-forming, orange-pigmented bacterium, designated strain SS2-56T, was isolated from sediment of the Nakdong River in Sangju-si, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate SS2-56T belongs to the family Chitinophagaceae, and was most closely related to Lacibacter daechungensis H32-4T (96.6 % similarity) and Lacibacter cauensis NJ-8T (96.1 %). Strain SS2-56T contained menaquinone 7 (MK-7) as a respiratory quinone and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as major fatty acids. The major polar lipids of strain SS2-56T were phosphatidylethanolamine, one unidentified aminophospholipid and four unidentified lipids. The DNA G+C content was 43.8 mol%. Phenotypic, chemotaxonomic and phylogenetic evidence clearly indicates that strain SS2-56T represents a novel species of the genus Lacibacter, for which the name Lacibacter nakdongensis sp. nov. is proposed. The type strain is SS2-56T (=KCTC 52160T=JCM 31372T).

A Gram-stain-negative, motile by gliding, non-spore-forming and oval-shaped bacterial strain designated T1-10T was isolated from pine forest soil, and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 6-7 and in the presence of 0-1 % (w/v) (optimum, 0 %) NaCl. Flexirubin-type pigments were produced. On the basis of 16S rRNA gene sequence similarity, strain T1-10T was assigned to the genus Taibaiella of the phylum Bacteroidetes, and the most closely related species was Taibaiella koreensis THG-DT86T with 97.11 % sequence similarity, but the strain formed an independent lineage in the phylogenetic tree. The genomic DNA G+C content of strain T1-10T was 42.5 mol%. The main cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The only isoprenoid quinone detected in the strain was MK-7, and the major polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminophospholipids. Strain T1-10T could be distinguished from related species by physiological and biochemical properties. Phenotypic and phylogenetic data supported that strain T1-10T represents a novel species of the genus Taibaiella, for which the name Taibaiella soli sp. nov. is proposed (type strain T1-10T=KCTC 42277T=JCM 31014T).

A Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90 %, while levels of similarity to other related taxa were less than 93.08 %. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15 : 1 G, iso-C15 : 0 and a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0 mol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T ( = KCTC 42060T = JCM 19844T).