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The strain designated as AN120528

Three bacterial strains isolated from a sediment sample collected at a water depth of 4 m from the Huaihe River in China were characterized. Phylogenetic investigation of the 16S rRNA gene and concatenated housekeeping gene sequences assigned the three novel strains in a highly supported lineage distinct from the published Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes of the three novel strains support their distinctiveness with the type strains of named species. Average nucleotide identity values of the genome sequences (79.9-82.5%) were below the threshold value of 95-96% for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium erythrophlei, Bradyrhizobium jicamae, Bradyrhizobium lablabi, Bradyrhizobium mercantei, Bradyrhizobium elkanii and Bradyrhizobium japonicum. The complete genomes of strains S2-20-1

Microalgae not only serve as raw materials for biofuel but also have uses in the food, pharmaceutical, and cosmetic industries. However, regulated gene expression in microalgae has only been achieved in a few strains due to the lack of genome information and unstable transformation. This study developed a species-specific transformation system for an oleaginous microalga, Ettlia sp. YC001, using electroporation. The electroporation was optimized using three parameters (waveform, field strength, and number of pulses), and the final selection was a 5 kV cm−1 field strength using an exponential decay wave with one pulse. A new strong endogenous promoter CRT (Pcrt) was identified using transcriptome and quantitative PCR analysis of highly expressed genes during the late exponential growth phase. The activities of this promoter were characterized using a codon optimized cyan fluorescent protein (CFP) as a reporter. The expression of CFP was similar under Pcrt and under the constitutive promoter psaD (PpsaD). The developed transformation system using electroporation with the endogenous promoter is simple to prepare, is easy to operate with high repetition, and utilizes a species-specific vector for high expression. This system could be used not only in molecular studies on microalgae but also in various industrial applications of microalgae.

A novel non-phototrophic member of the genus Rhodoferax was obtained from freshwater. The purpose of this study was to analyse the genome of a nonphototrophic strain and propose a new species based on its phylogenetic, genomic, physiological and chemotaxonomic characteristics. The results of phylogenetic analysis based on 16S rRNA gene sequences supports that the strain, designated Gr-4T, has a close relationship to the genus Rhodoferax . The observed average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Gr-4T and its closest related strains were 72.3–74.6 % and 21.9–22.8 %, respectively. These values were much lower than the species separation thresholds for ANI or dDDH of 95–96 and 70 %, respectively, and in fact fall in the intergeneric range. Strain Gr-4T does not contain RuBisCO-related genes, but does contain GS/GOGAT pathway-related genes enabling nitrate ammonification. A polyphasic study and a genomic-level investigation were done to establish the taxonomic status of strain Gr-4T. Based on the phylogenetic, genomic and physiological differences, it is proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax aquaticus sp. nov. with isolate Gr-4T (=KCTC 32394T=JCM 19166T) as the type strain.

A polyphasic taxonomic study was carried out on strains CHu50b-3-2T and CHu40b-3-1 isolated from a 67 cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of the strains were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of two strains with γ-Proteobacteria, which showed the highest pairwise sequence similarities to Lysobacter hankyongensis KTce-2T (96.5 %), Lysobacter pocheonensis Gsoil193T (96.3 %), Lysobacter ginsengisoli Gsoil 357T (96.1 %), Lysobacter solanacearum T20R-70T (96.1 %), Lysobacter brunescens KCTC 12130T (95.4 %) and Lysobacter capsici YC5194T (95.3 %). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus Lysobacter . The major fatty acids were identified as summed feature 9 (iso-C17 : 1 ω9c and/or C18 : 1 10-methyl), iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The respiratory quinone was identified as ubiquinone Q-8. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was determined to be 66.8 mol% (genome) for strain CHu50b-3-2T and 66.4 mol% (HPLC) for strain CHu40b-3-1. Based on the combined genotypic and phenotypic data, we propose that strains CHu50b-3-2T and CHu40b-3-1 represent a novel species of the genus Lysobacter , for which the name Lysobacter profundi sp. nov. is proposed. The type strain is CHu50b-3-2T (=KCTC 72973T=CCTCC AB 2019129T). Besides Lysobacter panaciterrae Gsoil 068T formed a phylogenetic group together with strain Luteimonas aquatica RIB1-20T (EF626688) that is clearly separated from all other known Lysobacter strains. Based on the phylogenetic relationships together with fatty acid compositions, Lysobacter panaciterrae Gsoil 068T should be reclassified as a member of the genus Luteimonas: Luteimonas aquatica comb. nov. (type strain Gsoil 068T=KCTC 12601T=DSM 17927T).

A novel bacterium, strain Seoho-28T, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25–30 °C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order Solirubrobacterales , but sequence similarities to known species were less than 94.7 %. The genomic DNA G+C content of the strain Seoho-28T was 74.2 mol%. Genomic comparisons of strain Seoho-28T with families in the order Solirubrobacterales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8 %, respectively). Strain Seoho-28T contained C16 : 0-iso, C18 : 1 ω9c and C16 : 0 as major fatty acids and MK-7 (H4) as the major quinone. Strain Seoho-28T contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. Meso- and ll-diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28T represents a novel genus and species, Paraconexibacter algicola gen. nov., sp. nov., which belongs to a new family Paraconexibacteraceae in the order Solirubrobacterales and the class Thermoleophilia . The type strain is Seoho-28T (=KCTC 39791T=JCM 31881T).

The genus Gemmobacter grows phototrophically, aerobically, or anaerobically, and utilizes methylated amine. Here, we present two high-quality complete genomes of the strains con4 and con5T isolated from a culture of Anabaena. The strains possess sMMO (soluble methane monooxygenase)-oxidizing alkanes to carbon dioxide. Functional genes for methane-oxidation (prmAC, mimBD, adh, gfa, fdh) were identified. The genome of strain con5T contains nirB, nirK, nirQ, norB, norC, and norG genes involved in dissimilatory nitrate reduction. The presence of nitrite reductase gene (nirK) and the nitric-oxide reductase gene (norB) indicates that it could potentially use nitrite as an electron acceptor in anoxic environments. Taxonomic investigations were also performed on two strains through polyphasic methods, proposing two isolates as a novel species of the genus Gemmobacter. The findings obtained through the whole genome analyses provide genome-based evidence of complete oxidation of methane to carbon dioxide. This study provides a genetic blueprint of Gemmobacter fulva con5T and its biochemical characteristics, which help us to understand the evolutionary biology of the genus Gemmobacter.

A novel Gram-stain-positive bacterial strain, CHu50b-6-2T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148T, Frigoribacterium faeni KACC 20509T and Lysinibacter cavernae DSM 27960T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2T (= KCTC 49081T = JCM 32673T).

Two Gram-stain-negative bacterial strains, DS48-3T and CH68-4T, were isolated from freshwater sediment taken from the Daechung Reservoir, Republic of Korea. Cells of strains DS48-3T and CH68-4T were aerobic, non-motile, non-spore-forming and rod-shaped. Strain DS48-3T was isolated from a sediment surface sample at a depth of 48 m from the Daechung Reservoir and was most closely related to the genus Sphingopyxis according to 16S rRNA gene sequence analysis (94.5–95.9 % similarity). Strain CH68-4T was isolated from the very bottom of a 67-cm-long sediment core collected from Daechung Reservoir at a water depth of 17 m and was most closely related to the genus Sphingopyxis (16S rRNA gene sequence similarity of 93.7–95.0 %). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the two strains formed a separate lineage within the order Sphingomonadales showing similarity values below 95.9 % with their closest phylogenetic neighbours, and sharing 97.3 % similarity with each other. The combined genotypic and phenotypic data showed that strains DS48-3T and CH68-4T could be distinguished from all genera within the family Sphingomonadaceae and represented two distinct species of a novel genus, Aquisediminimonas profunda gen. nov., sp. nov. (type strain DS48-3T=KCTC 52068T=CCTCC AB 2018061T) and Aquisediminimonas sediminicola sp. nov. (type strain CH68-4T=KCTC 62205T=CCTCC AB 2018062T).

Despite widespread use as a preservation method, cryopreservation remains recalcitrant for microalgae preservation due to low viability and strain specificity. Herein, a cryopreservation method for Ettlia sp. YC001 was optimized using the following strategies. Cold acclimation at 4 °C for 24 h prior to the freezing procedure enhanced the expression of the cold response pathway and heat-shock proteins, helping to both stabilize the proteins against cold stress and prevent rapid dehydration. Three independent parameters of cryopreservation, the cooling rate, plunge temperature, and thawing temperature, were optimized with various cryoprotectants using a response surface methodology (RSM). Finally, the cellular damage was minimized when using the optimized controlled cooling procedure with an accurate programmable freezer. When applying the optimized conditions, the cell viability of the cryopreserved strain YC001 was > 90% after 1 year. It is believed that the suggested approach can also be applied to other commercial microalgal strains.

A novel non-phototrophic member of the genus

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5T, except for N2O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5T.

The impact of microalgae (including blue-green algae or cyanobacteria) on human life can be both beneficiary and deleterious. While microalgae can be cultivated and used as feedstocks for the production of bioenergy and high value-added products in nutraceuticals, pharmaceuticals, and aquaculture feeds, some microalgae cause harmful algal blooms (HABs) that cause large-scale mortality in aquatic environments around the world. Thus, with the development of microalgal biotechnology and increasing concern about HABs, research on microscopic algae has increased significantly. However, this growth of academic research and application fields has been hindered by difficulties in obtaining axenic cultures. Therefore, this review provides a brief explanation of diverse establishment techniques, along with their strengths and weaknesses, with the hope of facilitating successful axenic cultures. A compilation of research fields and relevant important findings is also presented to clarify the importance of pure algal cultures. Finally, several controversial and sometimes overlooked issues related to the establishment, maintenance, and utilization of axenic cultures are discussed.

Fructophilic behavior in microalgae is a rare trait that could benefit biorefineries by enabling substitution of carbon source with fructose, and our previous study identified that Ettlia sp. prefers fructose relative to glucose. In this study, by analyzing the transcription levels of genes related to sugar transport and the glycolysis pathway, the fructose utilization of Ettlia sp. was investigated. In a fructose-containing medium, the expression levels of fructokinase (EttFRK3) and glucokinase (EttGCK1 and EttGCK2) genes were significantly upregulated in heterotrophic cultivation of Ettlia sp. under fructose supplementation conditions. Further, a sugar transporter (EttSTF11) was significantly upregulated by 3.2-fold in one day, and this increase was analogous to the specific growth rate exhibited by the species. Subsequent cultivation tests with multi-sugar sources also showed a significant upregulation of EttSTF11 relative to other treatments without fructose. A phylogenetic tree derived from the analysis of different transporters of interest identified that EttSTF11 was adjacent to reference fructose transporters with a high bootstrap value of 71. Given that the transmembrane domains of EttSTF11 were analogous to those of reference fructose transporter genes, EttSTF11 appeared to play a critical role in fructose consumption and metabolism in Ettlia sp. This article is protected by copyright. All rights reserved.

Chlamydomonas reinhardtii of the microalgal model species lacks phosphatidylcholine (PC), and PC is replaced by diacylglyceryl N,N,N-trimethylhomoserine (DGTS). DGTS is a betaine lipid that is placed in the endoplasmic reticulum (ER) and is synthesized by a single gene, BTA1. In this study, we aimed to ascertain the turnover between membrane and neutral lipids via BTA1 knockdown transformants. Transgenic lines CrBta-hm13 and CrBta-hm31 were 80% and 60% downregulated in BTA1 gene expression levels, respectively. Both transformants had half the amount of DGTS, which coincided with decreased monogalactosyldiacylglycerol (MGDG), which was increased approximately threefold in neutral lipids. While the reduction of DGTS was shown to arise from inhibition of DGTS synthesis, decreased MGDG was affected by internal stress, such as ER stress, which was induced to have a decreased amount of DGTS in the ER. However, galactolipids, except for MGDG, and phospholipids in the transformants were maintained at similar levels. In the transformants, the molar proportion of C16:4 and C18:3(9,12,15), which are the major fatty acids of MGDG, was significantly increased in triacylglycerol (TAG) because of MGDG degradation. Thus, lipid turnover arising from the downregulation of DGTS and induction of ER stress caused a decrease in DGTS and MGDG, which generated a synergy effect on the accumulation of TAG. This study implies that genetic modification of a membrane lipid synthesis pathway could not only be a suitable approach to target accumulation of TAG, but could also suggest a mechanism for the lipid turnover between membrane lipids and neutral lipids.

A novel Gram-negative bacterium strain, DRW22-8T, was isolated from fresh water taken at a depth of 22 m at Daechung Reservoir, Republic of Korea. The cells of strain DRW22-8T were aerobic and motile with a single polar flagellum or non-motile (stalked), and formed creamy-white colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the order Rhodobacterales , showing similarity values under 91.8 % with its closest phylogenetic neighbours, Hirschia litorea , Hirschia baltica and Hirschia maritima . The chemotaxonomic results showed Q-10 as the predominant respiratory ubiquinone, three unidentified glycolipids, an unidentified lipid and phosphatidylglycerol as the major polar lipids, and C16 : 0, 11-methyl C18 : 1, C18 : 1 ω7c and/or C18 : 1 ω6c as the major fatty acids. The DNA G+C content was 64.4 mol%. The combined genotypic and phenotypic data showed that strain DRW22-8T could be distinguished from all genera within the family Hyphomonadaceae and represented a novel genus, Asprobacter gen. nov., with the name Asprobacter aquaticus sp. nov., in the family Hyphomonadaceae . The type strain is DRW22-8T (=KCTC 42356T=JCM 30469T).

Two Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacteria, designated strains T2T and T5, were isolated from a culture of Microcystis from Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the new isolates in the class Alphaproteobacteria and, notably, most closely related to Blastomonas aquatica PE 4-5T, Blastomonas natatoria DSM 3183T and Blastomonas ursincola KR-99T showing 99.4 %, 98.2 % and 97.9 % 16S rRNA gene sequence similarities, respectively. The two novel strains shared 100 % similarity with each other. The cells of strains T2T and T5 formed yellow colonies on R2A agar and contained Q-10 as the only ubiquinone, sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids, and C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C17 : 1ω8c and C17 : 0 as the major fatty acids (>5 %). The DNA G+C content of the genomes was determined to be 64.2 mol% for strain T2T and 64.4 mol% for strain T5. The DNA–DNA hybridization values of strains T2T and T5 with B. aquatica PE 4-5T, B. natatoria DSM 3183T, and B. ursincola KR-99T were 19.7–42.4 %. Based on the combined genotypic and phenotypic data, we propose that strains T2T and T5 represent a novel species of the genus Blastomonas , for which the name Blastomonas fulvasp. nov. is proposed. The type strain is T2T (=KCTC 42354T=JCM 30467T).

Water deprivation could be a lethal stress for aquatic and aero-terrestrial organisms. Ettlia sp. is a unicellular photosynthetic freshwater microalga. In the present study, proteomic alterations and physiological characteristics of Ettlia sp. were analyzed to comprehend the molecular changes in dehydrated conditions. Varying levels of dehydration were achieved by incubating drained Ettlia sp. in different relative humidity environments for 24 hours. Using a comparative proteomic analysis, 52 differentially expressed protein spots were identified that could be divided into eight functional groups. The PCA analysis of normalized protein expression values demonstrated a clear segregation of protein expression profiles among different dehydration levels. Identified proteins could be grouped into four clusters based on their expression profiles. Proteins relating to photosynthesis comprised the largest group with 25% of the identified proteins that were decreased in dehydrated samples and belonged to cluster I. The photosynthetic activities were measured with rehydrated Ettlia sp. These results revealed that photosynthesis remained inhibited over extended time in response to dehydration. The expressions of reactive oxygen species (ROS) scavenger proteins increased in strong dehydration and were assigned to cluster III. Carbon metabolism proteins were suppressed, which might limit energy consumption, whereas glycolysis was activated at mild dehydration. The accumulation of desiccation-associated late embryogenesis proteins might inhibit the aggregation of housekeeping proteins. DNA protective proteins were expressed higher in the dehydrated state, which might reduce DNA damage, and membrane-stabilizing proteins increased in abundance in desiccation. These findings provide an understanding of Ettlia's adaptation and survival capabilities in a dehydrated state.

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (non-cyanobacteria) during cyanobacterial harmful algal blooms (cyanoHABs), samples were collected from the Nakdong River, Korea, from June 2016 to August 2017, and microbial recurrent association network (MRAN) analysis was performed to overcome the limitations of conventional network analysis. Microcystis blooms were tightly linked with Pseudanabaena in summer and were accompanied by significant changes in the non-cyanobacterial community composition (nCCC) compared to non-bloom period. Riverine bacterial communities could be clearly separated into modules that were involved in the formation, maintenance, and decomposition of cyanoHABs. Roseomonas and Herbaspirillum were directly linked with major cyanobacteria and assigned to connector and module hub in cyanoHABs-related modules, respectively. The functional profiles of the cyanoHABs-related modules suggested that nitrate reduction, aerobic ammonia oxidation, fermentation, and hydrocarbon degradation could be increased during the Microcystis bloom periods. In conclusion, MRAN analysis revealed that specific bacteria belonging to cyanoHABs-related module, including connectors and module hubs, appeared to contribute to the development and collapse of cyanoHABs. Therefore, to understand cyanoHABs, a modular microbial perspective may be more helpful than a single bacterial species perspective.

To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.

A novel Gram-stain-negative bacterial strain, CHu64-6-4T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu64-6-4T were aerobic nonmotile and formed colorless colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Oxalobacteraceae, exhibiting 97.2% and 97.1% 16S rRNA gene sequence similarities to Glaciimonas singularis and Paraherbaspirillum soli, respectively. Strain CHu64-6-4T showed less than 74.4% average nucleotide identity compared to the type strains of related genera within the family Oxalobacteraceae. In the UPGMA dendrogram based on the ANI values of genomic sequences, strain CHu64-6-4T formed an evolutionary lineage independent of the genera Glaciimonas and some other taxa. The chemotaxonomic results showed Q-8 as the predominant respiratory ubiquinone, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethnolamine as the major polar lipids, Summed Feature 3 (C16:1ω7c and/or iso-C15:0 2-OH), C16:0, and C18:1ω7c as the major fatty acids, and a DNA G+C content of 62.1 mol%. The combined genotypic and phenotypic data showed that strain CHu64-6-4T could be distinguished from all genera within the family Oxalobacteraceae and represents a novel genus, Lacisediminimonas profundi gen. nov., with the name Lacisediminimonas profundi sp. nov., in the family Oxalobacteraceae. The type strain is CHu64-6-4T (=KCTC 62287T=JCM 32676T).

A polyphasic taxonomic study was carried out on strain EBR-8-1T isolated from a biofilm reactor in Korea. The cells of the strain were Gram-stain negative, non-spore-forming, non-motile, and short rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain with Betaproteobacteria, which showed high pairwise sequence similarities with Pusillimonas noertemannii BN9T (99.1 %), Pusillimonas soli MJ07T (97.3 %), Pusillimonas ginsengisoli DCY25T (97.2 %), and Pusillimonas harenae B201T (96.8 %). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a clear phylogenetic lineage within the genus Pusillimonas. The major fatty acids were identified as C16:0, C17:0 cyclo and C19:0 cyclo ω8c. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. The respiratory quinone was identified as Q-8 and the genomic DNA G+C content was determined to be 63.3 mol%. On the basis of polyphasic evidence, it is proposed that strain EBR-8-1T should be placed in a new species, Pusillimonas caeni sp. nov. The type stain is EBR-8-1T (=KCTC 42353T = JCM 30463T).

Three bacterial strains, designated DS48-6-5T, DS48-6-7 and DS48-6-9, were isolated from a sediment sample taken from Daechung Reservoir (Republic of Korea) at a water depth of 48 m. Cells of the strains were Gram-stain-negative, aerobic, rod-shaped and motile with a single polar flagellum. Comparative 16S rRNA gene sequence studies showed that the three isolates had clear affiliation with Betaproteobacteria and the closest relatives were Rhizobacter bergeniae KCTC 32299T, Rhizobacter dauci DSM 11587T and Rhizobacter fulvus KCTC 12591T with 97.2-97.9 % 16S rRNA gene sequence similarities; the 16S rRNA gene sequence similarities between the three strains were 99.5-100 %. The only isoprenoid quinone of the three strains was ubiquinone-8, and the major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strains DS48-6-5T, DS48-6-7 and DS48-6-9 was 66.7, 67.0 and 66.8 mol%, respectively. DNA-DNA hybridization values of the novel strains with R. bergeniae KCTC 32299T, R. dauci DSM 11587T and R. fulvus KCTC 12591T were 19.3-48.5 %. Based on the evidence from this taxonomic study using a polyphasic approach, it is proposed that strains, DS48-6-5T, DS48-6-7 and DS48-6-9, represent a novel species of the genus Rhizobacter, for which the name Rhizobacter profundi sp. nov. is proposed. The type strain is DS48-6-5T ( = KCTC 42645T = NBRC 111169T).

We characterized the complete sequence of the mitochondrial genome of the freshwater green algal strain YC001, known as ‘Ettlia sp.', which is of great interest for biofuel production. The size of the mitogenome was 52,489 base pairs (bp), with 49.0% GC content. It consisted of 49 mitochondrial genes typical of the Chlorophyceae, including 16 protein-coding genes, 27 transfer RNA genes and six ribosomal RNA genes as well as three introns within cox1 (6832 bp), rnl4 (1805 bp) and cob (1107 bp). We determined that YC001 is a species of Coelastrella on the basis of molecular phylogenetic analyses and microscopic observations. A unique feature of this mitogenome is the presence of three different types of inverted repeats between trnL and trnI and between nad4 and cox1 as well as the presence of orf215, orf755 and one additional copy of the trnM gene, all of which enable a comparison with an available sister taxon, Acutodesmus obliquus.

The establishment of an axenic culture of microalgae is essential step in understanding its physiology, genetics, and ecology. However, culturing of microalgae is usually accompanied by complex and variable associated prokaryotic and eukaryotic microorganisms. Conventional approaches used for obtaining axenic cultures of microalgae are time-consuming and often involve difficulties in maintaining and preserving axenicity. In this study, we developed a procedure for establishing an axenic culture of Ettlia sp. YC001 and demonstrate that we maintained the axenic culture through subculture in the long term. Three sequential treatments, an antibiotic cocktail, serial dilution, and plate spreading, were applied to strain YC001 and we confirmed axenicity using molecular and physiological methods. The bacterial community associated with strain YC001 was investigated to select antibiotics for their specific elimination. The xenic culture (1 × 106 cells/mL) was treated with the antibiotic cocktail-5 (AC-5), carbendazim, chloramphenicol, imipenem, rifampicin, and tetracycline for 3 days, followed by serial dilution up to 1 × 102 cells and spreading on agar plates. The pure colonies were analyzed using denaturing gradient gel electrophoresis (DGGE), fluorescence-activated cell sorting (FACS), and scanning electron microscopy (SEM). The procedure we developed can be applied to other strains of microalgae for the establishment of axenic cultures.

A novel Gram-stain negative, rod-shaped and motile bacterial strain, designated strain Seoho-38T, was isolated from a eutrophic lake in South Korea. Polyphasic taxonomic studies were performed to investigate the taxonomic position of the new isolate. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain Seoho-38T formed a distinct cluster with Nevskia ramosa Soe1T, Nevskia persephonica G6M-30T, Nevskia soli GR15-1T, Nevskia terrae KIS13-15T and Nevskia aquatilis F2-63T with bootstrap resampling value of 100%. Of those Nevskia strains, the new isolate shows high sequence similarity with N. ramosa Soe1T (98.7%) and N. persephonica G6M-30T (97.2%), and values lower than 96.5% with the other type strains. The new isolate was observed to grow aerobically in 0–1.5% (w/v) NaCl (optimum 0%), at pH 7.0–9.0 (optimum pH 7.0) and temperature 15–36 °C (optimum 20–30 °C) on R2A medium. DNA–DNA relatedness values between strain Seoho-38T and the type strains of reference species in the genus Nevskia were

A polyphasic taxonomic study was carried out on strains PB105T and PB108 isolated from a grass soil in Korea. The cells of the strains were Gram-stain negative, non-spore-forming, non-motile, and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of these strains with Bacteroidetes, which showed high pairwise sequence similarities with Hymenobacter algoricola VUG-A23aT (99.2%), Hymenobacter fastidiosus VUG-A124aT (97.4%), and Hymenobacter daecheongensis Dae14T (96.9%). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus Hymenobacter. The major fatty acids were identified as C15:0 iso, C15:0 anteiso, C16:1 ω5c, C15:0 iso 3-OH, C17:0 iso 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t), and summed feature 4 (C17:1 anteiso B and/or C17:1 iso I). The major cellular polar lipids were identified as phosphatidylethanolamine, an unidentified aminolipid, and two unidentified lipids. The respiratory quinone was identified as MK-7 and the genomic DNA G+C content was determined to be 64.5 mol% for strain PB105T and 64.1 mol% for strain PB108. DNA–DNA hybridization value of type strain PB105T with H. algoricola VUG-A23aT was 32.3% (reciprocal 39.2). Based on the combined genotypic and phenotypic data, we propose that strains PB105T and PB108 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter daejeonensis sp. nov. is proposed. The type strain is PB105T (= KCTC 52579T = JCM 31885T).

A polyphasic taxonomic study was carried out on strain EBR-4-1T, which was isolated from a biofilm reactor in the Republic of Korea. The cells of the strain were Gram-stain-negative, non-spore-forming, motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain to the Alphaproteobacteria , and it was most closely related to Chelatococcus daeguensis CCUG 54519T, Chelatococcus sambhunathii HT4T, and Chelatococcus asaccharovorans DSM 6462T with 16S rRNA gene sequence similarities to the type strains of these species of 98.8 %, 98.7 %, and 96.3 %, respectively. The G+C content of the genomic DNA of strain EBR-4-1T was 68.7 mol%. Phenotypic and chemotaxonomic data [Q-10 as the major ubiquinone; C19 : 0cycloω8c, C18 : 1 2-OH, and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids] supported the affiliation of strain EBR-4-1T to the genus Chelatococcus . On the basis of the polyphasic evidence, it is proposed that strain EBR-4-1T should be assigned to a new species, Chelatococcus caeni sp. nov. The type strain is EBR-4-1T ( = KCTC 32487T = JCM 30181T).

A novel Gram-stain-negative, rod-shaped and non-motile bacterial strain, designated strain Seoho-37T, was isolated from a eutrophic lake in South Korea. Polyphasic studies were performed to investigate the taxonomic position of the new isolate. The isolate grew aerobically with 0–1.0 % (w/v) NaCl (optimum 0 %), at pH 6.0–10.0 (optimum pH 7.0–9.0) and at temperatures of 15–36 °C (optimum 25–30 °C) on R2A medium. In the phylogenetic analysis of 16S rRNA gene sequences, strain Seoho-37T formed a clear cluster with the strains of Reyranella graminifolii , Reyranella massiliensis and Reyranella soli with a bootstrap resampling value of 100 %. DNA–DNA relatedness between strain Seoho-37T and the type strains of each species in the genus Reyranella was

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated M23T, was isolated from a laboratory culture of a bloom-forming cyanobacterium, Microcystis , which was isolated from a eutrophic lake in Korea. The strain grew optimally without NaCl and at 25–30 °C on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the genus Silanimonas , with the highest similarity to Silanimonas lenta DSM 16282T (98.5 %). DNA–DNA relatedness between strain M23T and the closely related species in the genus Silanimonas was

Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.

The microbial community in eutrophic freshwater sediment was investigated from a 67-cm-deep sediment core collected from the Daechung Reservoir in South Korea, where cyanobacterial blooms have occurred annually for the past 30 years. The majority of core sediments were characterized by dark-grayish, fine-grained mud with abundant gas-escaped and thinly laminated layers. Intervals of summer and winter seasons were represented by periodic peaks of geochemical profiles of parameters such as grain size and relative carbon mass ratios to various nutrients such as nitrogen, sulfur, and phosphorus. In bacteria, Proteobacteria (66.6%) was the most prevalent phylum, followed by Chloroflexi (8.9%), Bacteroidetes (5.1%), and Spirochaetes (2.6%). Archaea were also abundant, representing approximately half of the total prokaryotes in the sediments. Notably, three Bacteria (Sulfuricurvum, Sideroxydans, and Gallionella) and one Archaea (Thermoplasmata) accounted for 43.4% and 38.4% of the total bacteria and archaea, respectively, implying that iron and sulfur oxidizing microorganisms dominate in this eutrophic freshwater sediment. These results indicate that 1) eutrophic freshwater lakes in monsoon climates undergo a stratified sedimentary process with seasonal and annual variations in geochemical and microbial profiles, and 2) the microbial oxidative metabolism of iron and sulfur is notably active in sediments from a eutrophic lake.