RESUMEN
BACKGROUND: Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. RESULTS: E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. CONCLUSIONS: Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
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Enterococcus faecium , Animales , Humanos , Filogenia , Enterococcus , Genómica , AntibacterianosRESUMEN
Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16â:â0, summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c), summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c), C12â:â1 3-OH, and C10â:â0 3-OH, while strain G1-23T contained C16â:â0, summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c), and C14â:â0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.
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Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano , Ácidos Grasos , Hibridación de Ácido Nucleico , Filogenia , Pseudoalteromonas , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Ubiquinona , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Pseudoalteromonas/genética , Pseudoalteromonas/clasificación , Pseudoalteromonas/aislamiento & purificación , Phaeophyceae/microbiologíaRESUMEN
A Gram-stain-negative, yellow-pigmented, and facultatively aerobic bacterium, designated strain GPA1T, was isolated from plastic waste landfill soil in the Republic of Korea. The cells were non-motile short rods exhibiting oxidase-negative and catalase-positive activities. Growth was observed at 15-40â°C (optimum, 30â°C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-2.5â% (w/v) NaCl (optimum, 0â%). Menaquinone-7 was the sole respiratory quinone, and iso-C15â:â0, C16â:â1 ω5c, and iso-C17â:â0 3-OH were the major cellular fatty acids (>10â% of the total fatty acids). Phosphatidylethanolamine was identified as a major polar lipid. Phylogenetic analyses based on 16S rRNA gene sequences and 120 concatenated marker protein sequences revealed that strain GPA1T formed a distinct lineage within the genus Chitinophaga. The genome of strain GPA1T was 6078 kb in size with 53.8 mol% G+C content. Strain GPA1T exhibited the highest similarity to Chitinophaga rhizosphaerae T16R-86T, with a 98.6â% 16S rRNA gene sequence similarity, but their average nucleotide identity and digital DNA-DNA hybridization values were 82.5 and 25.9â%, respectively. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain GPA1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga pollutisoli sp. nov. is proposed. The type strain is GPA1T (=KACC 23415T=JCM 36644T).
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Técnicas de Tipificación Bacteriana , Bacteroidetes , Composición de Base , ADN Bacteriano , Ácidos Grasos , Sedimentos Geológicos , Fosfatidiletanolaminas , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Microbiología del Suelo , Vitamina K 2 , ARN Ribosómico 16S/genética , República de Corea , Ácidos Grasos/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Vitamina K 2/análisis , ADN Bacteriano/genética , Sedimentos Geológicos/microbiología , Bacteroidetes/aislamiento & purificación , Bacteroidetes/clasificación , Bacteroidetes/genética , Hibridación de Ácido Nucleico , Instalaciones de Eliminación de Residuos , Genoma BacterianoRESUMEN
Two Gram-stain-negative, facultatively aerobic, and motile rod bacteria, designated as strains KJ51-3T and 15G1-11T, were isolated from marine algae collected in the Republic of Korea. Both strains exhibited catalase- and oxidase-positive activities. Optimum growth conditions for strain KJ51-3T were observed at 30â°C and pH 6.0-8.0, with 1.0-7.0â% (w/v) NaCl, whereas strain 15G1-11T exhibited optimal growth at 30â°C, pH 7.0, and 1.0-5.0â% NaCl. Major fatty acids detected in both strains included C16â:â0, C10â:â0 3-OH and summed features 3 (C16â:â1 ω7c and/or C16â:â1 ω6c) and 8 (C18â:â1 ω7c and/or C18â:â1 ω6c). As for polar lipids, strain KJ51-3T contained phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol, and two unidentified phospholipids, whereas strain 15G1-11T had PE, PG, and an unidentified aminolipid. Ubiquinone-8 was the predominant respiratory quinone in both strains, with minor detection of ubiquinone-9 in strain KJ51-3T. The genomic DNA G+C contents were 44.0âmol% for strain KJ51-3T and 40.5âmol% for strain 15G1-11T. Phylogenetic analyses based on both 16S rRNA gene and genome sequences placed strains KJ51-3T and 15G1-11T into distinct lineages within the genus Marinomonas, most closely related to Marinomonas arctica 328T (98.6â%) and Marinomonas algicola SM1966T (98.3â%), respectively. Strains KJ51-3T and 15G1-11T exhibited a 94.6â% 16S rRNA gene sequence similarity and a 70.7â% average nucleotide identity (ANI), with ANI values of 91.9 and 79.3â% between them and M. arctica 328T and M. algicola SM1966T, respectively, indicating that they represent novel species. In summary, based on their phenotypic, chemotaxonomic, and phylogenetic properties, strains KJ51-3T and 15G1-11T are proposed to represent novel species within the genus Marinomonas, for which the names Marinomonas rhodophyticola sp. nov. (KJ51-3T=KACC 22756T=JCM 35591T) and Marinomonas phaeophyticola sp. nov. (15G1-11T=KACC 22593T=JCM 35412T) are respectively proposed.
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Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano , Ácidos Grasos , Marinomonas , Fosfolípidos , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Ubiquinona , ARN Ribosómico 16S/genética , Ácidos Grasos/química , ADN Bacteriano/genética , Marinomonas/genética , Marinomonas/aislamiento & purificación , Marinomonas/clasificación , República de Corea , Agua de Mar/microbiologíaRESUMEN
A Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, non-motile, non-flagellated, and coccus-shaped bacterium, strain J2-16T, isolated from a marine green alga, was characterized taxonomically. Strain J2-16T grew at 20-40â°C (optimum, 30â°C), pH 6.0-10.0 (optimum, pH 7.0), and 1.0-4.0â% (w/v) NaCl (optimum, 3.0â%). Menaquinone-7 was identified as the sole respiratory quinone, and major fatty acids (>5â%) were C18â:â1 ω9c, iso-C14â:â0, C14â:â0, anteiso-C15â:â0, C18â:â0, C16â:â0, and C17â:â1 ω8c. The polar lipids of strain J2-16T consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and three unidentified lipids. The genome size of strain J2-16T was 5384 kb with a G+C content of 52.0 mol%. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strain J2-16T formed a distinct phyletic lineage within the genus Coraliomargarita, closely related to Coraliomargarita sinensis WN38T and Coraliomargarita akajimensis DSM 45221T with 16S rRNA gene sequence similarities of 95.7 and 94.4â%, respectively. Average nucleotide identity and digital DNA-DNA hybridization values between strain J2-16T and Coraliomargarita species were lower than 71.2 and 20.0â%, respectively. The phenotypic, chemotaxonomic, and molecular features support that strain J2-16T represents a novel species of the genus Coraliomargarita, for which the name Coraliomargarita algicola sp. nov. is proposed. The type strain is J2-16T (=KACC 22590T=JCM 35407T).
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Técnicas de Tipificación Bacteriana , Composición de Base , Chlorophyta , ADN Bacteriano , Ácidos Grasos , Fosfolípidos , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Vitamina K 2 , ARN Ribosómico 16S/genética , Ácidos Grasos/química , Vitamina K 2/análogos & derivados , Vitamina K 2/análisis , ADN Bacteriano/genética , Hibridación de Ácido Nucleico , Agua de Mar/microbiologíaRESUMEN
Two Gram-stain-negative, rod-shaped bacteria, designated as strains KJ10-1T and KJ40-1T, were isolated from marine brown algae. Both strains were catalase-positive, oxidase-positive, and facultative aerobic. Strain KJ10-1T exhibited optimal growth at 25â°C, pH 7.0, and 3â% NaCl, whereas strain KJ40-1T showed optimal growth at 25â°C, pH 7.0, and 2â% NaCl. The respiratory quinones of strain KJ10-1T were ubiquinone-8, ubiquinone-7, menaquinone-7, and methylated menaquinone-7, while the respiratory quinone of strain KJ40-1T was only ubiquinone-8. As major fatty acids, strain KJ10-1T contained C16â:â0, C17â:â1 ω8c, iso-C15â:â0, and summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c) and strain KJ40-1T contained C16â:â0 and summed features 3 and 8 (C18â:â1 ω7c and/or C18â:â1 ω6c). The major polar lipids in strain KJ10-1T were phosphatidylethanolamine, phosphatidylglycerol, and an unidentified aminolipid, whereas those in strain KJ40-1T were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C contents of strains KJ10-1T and KJ40-1T were 42.1 and 40.8âmol%, respectively. Based on 16S rRNA gene sequences, strains KJ10-1T and KJ40-1T exhibited the closest relatedness to Shewanella saliphila MMS16-UL250T (98.6â%) and Vibrio rumoiensis S-1T (95.4â%), respectively. Phylogenetic analyses, based on both 16S rRNA and 92 housekeeping genes, showed that the strains formed distinct phylogenic lineages within the genera Shewanella and Vibrio. Digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain KJ10-1T and other Shewanella species, as well as between strain KJ40-1T and other Vibrio species, were below the thresholds commonly accepted for prokaryotic species delineation. Based on the phenotypic, chemotaxonomic, and phylogenetic data, strains KJ10-1T and KJ40-1T represent novel species of the genera Shewanella and Vibrio, respectively, for which the names Shewanella phaeophyticola sp. nov. and Vibrio algarum sp. nov. are proposed, respectively. The type strains of S. phaeophyticola and V. algarum are KJ10-1T (=KACC 22589T=JCM 35409T) and KJ40-1T (=KACC 22588T=JCM 35410T), respectively.
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Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano , Ácidos Grasos , Phaeophyceae , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Shewanella , Ubiquinona , Vibrio , Vitamina K 2 , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Vibrio/genética , Vibrio/clasificación , Vibrio/aislamiento & purificación , Ubiquinona/análogos & derivados , Shewanella/genética , Shewanella/aislamiento & purificación , Shewanella/clasificación , Phaeophyceae/microbiología , Vitamina K 2/análogos & derivados , Fosfolípidos , Hibridación de Ácido Nucleico , Agua de Mar/microbiologíaRESUMEN
Two Gram-stain-negative, strictly aerobic rods, designated as RMAR6-6T and KMA01T, exhibiting catalase- and oxidase-positive activities, were isolated from marine red algae in the Republic of Korea. Cells of strain RMAR6-6T exhibited flagellar motility, while those of strain KMA01T were non-motile. Strain RMAR6-6T exhibited optimal growth at 30-35°C and pH 7.0-8.0 with 4.0-6.0â% (w/v) NaCl, while strain KMA01T grew optimally at 30-35â°C, pH 7.0-8.0 and 2.0-5.0% NaCl. Both strains shared common major respiratory isoprenoid quinone (ubiquinone-10), cellular fatty acids (C18â:â0, C18:â1 ω7c 11-methyl, C20â:â1 ω7c and summed feature 8) and polar lipids (phosphatidylglycerol, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sulphoquinovosyldiacylglycerol). The genomic DNA G+C contents were 59.0 and 55.0âmol% for strains RMAR6-6T and KMA01T, respectively. With 98.5â% 16S rRNA gene similarity, 75.2 % average nucleotide identity (ANI) and 19.8â% digital DNA-DNA hybridization (dDDH) values, strains RMAR6-6T and KMA01T were identified as representing distinct species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains RMAR6-6T and KMA01T formed distinct phylogenic lineages within the genus Roseibium, most closely related to Roseibium aggregatum IAM 12614T and Roseibium album CECT 5094T, respectively. The ANI and dDDH values between strain RMAR6-6T and R. aggregatum IAM 12614T were 87.5 and 33.3â%, respectively. Similarly, the values between KMA01T and R. album CECT 5094T were 74.2â% (ANI) and 19.3â% (dDDH). Based on phenotypic, chemotaxonomic and molecular characteristics, strains RMAR6-6T and KMA01T represent two novel species of the genus Roseibium, for which the names R. algicola sp. nov. (RMAR6-6T=KACC 22482T=JCM 34977T) and R. porphyridii sp. nov. (KMA01T=KACC 22479T=JCM 34597T) are proposed, respectively.
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Ácidos Grasos , Gammaproteobacteria , Composición de Base , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Cloruro de Sodio , Análisis de Secuencia de ADN , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , NucleótidosRESUMEN
Two Gram-stain-negative, obligately aerobic, motile rod bacteria, designated as G2-5T and G20-9T, exhibiting catalase- and oxidase-positive activities, were isolated from the phycosphere of a Chondrus species, a marine red alga. Strain G2-5T exhibited optimal growth at 30â°C and pH 5.0-6.0 and in the presence of 0.5-1.0% NaCl. In contrast, strain G20-9T demonstrated optimal growth at 25â°C and pH 6.0 and in the presence of 0.5-1.5% NaCl. Both strains contained ubiquinone-10, summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c), C18â:â0 and 11-methyl-C18â:â1 ω7c, and diphosphatidylglycerol and phosphatidylglycerol as the major respiratory isoprenoid quinone, cellular fatty acids and polar lipids, respectively. The genomic DNA G+C contents were 57.2âmol% for strain G2-5T and 57.5âmol% for strain G20-9T. Strains G2-5T and G20-9T exhibited 98.2â% 16S rRNA gene sequence similarity, along with 82.3â% average nucleotide identity (ANI) and 25.0â% digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G2-5T and G20-9T formed distinct phylogenic lineages within the genus Devosia. Strains G2-5T and G20-9T were most closely related to Devosia limi DSM 17137T and Devosia beringensis S02T with 97.7 and 96.9â% 16S rRNA gene sequence similarities, respectively. The ANI and dDDH values between strains G2-5T and G20-9T and other Devosia species were lower than 73.9 and 19.2â%, respectively, suggesting that they constitute novel species within the genus Devosia. Based on their distinct phenotypic, chemotaxonomic, and molecular characteristics, strains G2-5T and G20-9T represent two novel species of the genus Devosia, for which the names Devosia rhodophyticola sp. nov. (G2-5T=KACC 22601T=JCM 35404T) and Devosia algicola sp. nov. (G20-9T=KACC 22650T=JCM 35405T) are proposed, respectively.
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Gammaproteobacteria , Rhodophyta , Composición de Base , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Cloruro de Sodio , Análisis de Secuencia de ADN , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , NucleótidosRESUMEN
A Gram-stain-positive, non-spore-forming, and obligate anaerobic bacteria designated strain CBA3647T was isolated from a horse faecal sample in Jeju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA3647T formed a distinct phyletic lineage from closely related species within the genus Peptostreptococcus. Based on comparative analysis of 16S rRNA gene sequences, Peptostreptococcus anaerobius ATCC 27337T is most closely related to strain CBA3647T with a 16S rRNA gene similarity of 98.31â%, while similarity to other type strains is below 98.0â%. The genomic DNA G+C content of strain CBA3647T was 30.0 mol%. The digital DNA-DNA hybridization values between strain CBA3647T and the six Peptostreptococcus species were equal to or less than 24â%. Cells were non-motile and oval-shaped cocci with catalase-positive and oxidase-negative activities. Growth occurred at 20-40â°C (optimum, 35â°C), pH 6-8 (optimum, pH 7), and in the presence of 0-2â% (w/v) NaCl (optimum, 1â%). Strain CBA3647T contained C14â:â0 iso and C16â:â0 as major fatty acids. Phenotypic, chemotaxonomic, and molecular properties of strain CBA3647T suggest that it represents a novel species in the genus Peptostreptococcus, which has been named Peptostreptococcus equinus sp. nov. The type strain is CBA3647T (=KACC 22891T= JCM 35846T).
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Ácidos Grasos , Peptostreptococcus , Animales , Caballos , Composición de Base , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , HecesRESUMEN
Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.
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Aflatoxinas , Aspergillus oryzae , Aspergillus flavus/metabolismo , Filogenia , Aspergillus oryzae/genética , Aspergillus oryzae/metabolismo , Aflatoxinas/genética , GenómicaRESUMEN
Heme, a porphyrin ring complexed with iron, is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Several microbial groups are known to lack the de novo heme biosynthetic pathway and therefore require exogenous heme from the environment. These heme auxotroph groups are largely limited to pathogens, symbionts, or microorganisms living in nutrient-replete conditions, whereas the complete absence of heme biosynthesis is extremely rare in free-living organisms. Here, we show that the acI lineage, a predominant and ubiquitous free-living bacterial group in freshwater habitats, is auxotrophic for heme, based on the experimental or genomic evidence. We found that two recently cultivated acI isolates require exogenous heme for their growth. One of the cultured acI isolates also exhibited auxotrophy for riboflavin. According to whole-genome analyses, all (n = 20) isolated acI strains lacked essential enzymes necessary for heme biosynthesis, indicating that heme auxotrophy is a conserved trait in this lineage. Analyses of >24,000 representative genomes for species clusters of the Genome Taxonomy Database revealed that heme auxotrophy is widespread across abundant but not-yet-cultivated microbial groups, including Patescibacteria, Marinisomatota (SAR406), Actinomarinales (OM1), and Marine groups IIb and III of Euryarchaeota Our findings indicate that heme auxotrophy is a more common phenomenon than previously thought, and may lead to use of heme as a growth factor to increase the cultured microbial diversity.
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Agua Dulce/microbiología , Hemo/metabolismo , Archaea/genética , Archaea/metabolismo , Bacterias/genética , Bacterias/metabolismo , Biodiversidad , Vías Biosintéticas , Ecosistema , Genoma Bacteriano , RiboflavinaRESUMEN
Eco-friendly reagents derived from plants represent a promising strategy to mitigate the occurrence of toxic cyanobacterial blooms. The use of an amentoflavone-containing Selaginella tamariscina extract (STE) markedly decreased the number of Microcystis aeruginosa cells, thus demonstrating significant anti-cyanobacterial activity. In particular, the Microcystis-killing fraction obtained from pulverized S. tamariscina using hot-water-based extraction at temperatures of 40 °C induced cell disruption in both axenic and xenic M. aeruginosa. Liquid chromatographic analysis was also conducted to measure the concentration of amentoflavone in the STE, thus supporting the potential M. aeruginosa-specific killing effects of STE. Bacterial community analysis revealed that STE treatment led to a reduction in the relative abundance of Microcystis species while also increasing the 16S rRNA gene copy number in both xenic M. aeruginosa NIBR18 and cyanobacterial bloom samples isolated from a freshwater environment. Subsequent testing on bacteria, cyanobacteria, and algae isolated from freshwater revealed that STE was not toxic for other taxa. Furthermore, ecotoxicology assessment involving Aliivibrio fischeri, Daphnia magna, and Danio rerio found that high STE doses immobilized D. magna but did not impact the other organisms, while there was no change in the water quality. Overall, due to its effective Microcystis-killing capability and low ecotoxicity, aqueous STE represents a promising practical alternative for the management of Microcystis blooms.
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Microcystis , Extractos Vegetales , Selaginellaceae , Microcystis/efectos de los fármacos , Selaginellaceae/química , Animales , Extractos Vegetales/farmacología , Daphnia/efectos de los fármacos , Floraciones de Algas Nocivas , ARN Ribosómico 16S , Agua Dulce/microbiologíaRESUMEN
In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang. Through gene inventory analysis based on the high-quality reference genome of S. fibuligera, new genes involved in cellulose degradation and volatile aroma biosynthesis and applicable to the production of novel valuable enzymes and chemicals can be discovered. The integrated genomic and transcriptomic analysis of Hyphopichia yeasts, which exhibit strong halotolerance, provides insights into the novel mechanisms of salt and osmo-stress tolerance for survival in fermentation environments with a low-water activity and high-concentration salts. In addition, Jang yeast isolates, such as D. hansenii, show probiotic potential for the industrial application of yeast species beyond fermentation starters to diverse human health sectors.
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Glycine max , Vino , Humanos , Filogenia , Levaduras/genética , Fermentación , Genómica , República de CoreaRESUMEN
A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0â% (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15â:â0, iso-C15â:â0, iso-C14â:â0 and iso-C16â:â0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8âmol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0â% 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.
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Ácidos Grasos , Rhodophyta , Composición de Base , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , ADN Bacteriano/genética , Técnicas de Tipificación BacterianaRESUMEN
A Gram-stain-positive, spore-forming and facultative aerobic bacterium, designated C11T, was isolated from mountain soil collected in the Republic of Korea. The cells were motile rods with peritrichous flagella, and positive for catalase and oxidase activities. Strain C11T grew at 15-45 °C (optimum, 30-37 °C) and pH 6.0-8.0 (optimum, pH 6.0) and in the presence of 0-1â% (w/v) NaCl (optimum, 0.5â%). Strain C11T contained menaquinone-7 as the sole isoprenoid quinone and iso-C15â:â0, iso-C16â:â0 and anteiso-C15â:â0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The G+C content of the genomic DNA was 38.8âmol%. Strain C11T was most closely related to Neobacillus drentensis IDA1967T and Mesobacillus foraminis CV53T, with 98.0 and 97.7â%, 71.7 and 69.9â%, and 20.1 and 20.3â% 16S rRNA gene sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain C11T was included in a phyletic lineage with members of the genus Neobacillus but was distinct from members of the genus Mesobacillus. Phenotypic, chemotaxonomic and molecular properties suggested that strain C11T represents a novel species of the genus Neobacillus, for which the name Neobacillus terrae sp. nov. is proposed. The type strain is C11T (=KACC 21661T=JCM 33943T).
Asunto(s)
Bacillaceae , Ácidos Grasos , Ácidos Grasos/química , Fosfolípidos/química , Suelo , Filogenia , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Composición de Base , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Bacillaceae/genéticaRESUMEN
Two Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38T, that were isolated from soil and freshwater, respectively, were taxonomically characterized. Both strains optimally grew at 30 °C and pH 7.0 in Reasoner's 2A medium and contained ubiquinone-8 as the sole respiratory quinone. As major fatty acids (>10â%), strain BLT contained iso-C15â:â0 and summed features 3 and 9 (comprising iso-C15â:â0 2-OH and/or C16â:â1 ω7c/ω6c and iso-C17â:â1 ω9c and/or C16â:â0 10-methyl, respectively), whereas strain W38T contained iso-C15â:â0, iso-C16â:â0 and summed feature 9. Diphosphatidylglycerol and phosphatidylmonomethylethanolamine as major polar lipids and phosphatidylethanolamine and phosphatidylglycerol as minor polar lipids were detected in both strains. The DNA G+C contents of strains BLT and W38T were 68.3 and 65.3â%, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strains BLT and W38T formed a tight phylogenetic lineage with Tahibacter species, and they shared 98.8â% 16S rRNA gene sequence similarity and 75.5â% average nucleotide identity (ANI) and 16.6â% digital DNA-DNA hybridization (dDDH) values, indicating that they are different species. Strains BLT and W38T were most closely related to Tahibacter caeni BUT-6T and Tahibacter aquaticus PYM5-11T with 97.7 and 98.0â% 16S rRNA gene sequence similarities, respectively. ANI and dDDH values between strain BLT and T. caeni BUT-6T and between strain W38T and T. aquaticus DSM 21667T were 78.5 and 21.6% and 75.3 and 21.0â%, respectively. Based on their phenotypic, chemotaxonomic and genomic properties, strains BLT and W38T represent two different novel species of the genus Tahibacter, for which the names Tahibacter soli sp. nov. and Tahibacter amnicola sp. nov. are proposed. The type strains of T. soli and T. amnicola are BLT (=KACC 22831T=JCM 35402T) and W38T (=KACC 22832T=JCM 35749T), respectively.
Asunto(s)
Ácidos Grasos , Fosfolípidos , Ácidos Grasos/química , Fosfolípidos/química , Filogenia , ARN Ribosómico 16S/genética , Suelo , ADN Bacteriano/genética , Análisis de Secuencia de ADN , Composición de Base , Técnicas de Tipificación Bacteriana , Agua DulceRESUMEN
Two Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive and non-motile rod-shaped bacteria, strains D2-3T and G9-8T, were isolated from a marine red alga. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. As the major cellular fatty acids (>5.0â%), D2-3T contained C16â:â0, 11-methyl-C18â:â1ω7c, summed feature 3 (C16â:â1ω7c and/or C16â:â1ω6c), and summed feature 8 (C18â:â1ω7c and/or C18â:â1ω6c), whereas G9-8T contained C16â:â0, 11-methyl-C18â:â1ω7c, C12â:â1 3-OH, and summed feature 8. The DNA G+C contents of D2-3T and G9-8T were 54.4â% and 56.0â%, respectively. As the major polar lipids, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipid, aminolipid and lipid were identified from both strains, and phosphatidylcholine was additionally detected from G9-8T only. The 16S rRNA gene sequence similarity of D2-3T and G9-8T was 98.5â% and their digital DNA-DNA hybridization (DDH) value was 19.1â%. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that D2-3T and G9-8T formed respectively distinct phylogenetic lineages within the genus Octadecabacter. D2-3T and G9-8T were most closely related to Octadecabacter ascidiaceicola RA1-3T and Octadecabacter antarcticus 307T, with 98.9â% and 98.5â% 16S rRNA gene sequence similarities, respectively, and digital DDH values between D2-3T and O. ascidiaceicola and between G9-8T and O. antarcticus were 18.3â% and 19.5â%, respectively. Phenotypic, chemotaxonomic and molecular features support the hypothesis that D2-3T and G9-8T represent two novel species of the genus Octadecabacter, for which the names Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov. are proposed. The type strains of O. algicola and O. dasysiphoniae are D2-3T (=KACC 22493T =JCM 34969T) and G9-8T (=KACC 22488T =JCM 34973T), respectively.
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Filogenia , Rhodobacteraceae , Rhodophyta , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Fosfolípidos , Rhodophyta/microbiología , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Ubiquinona/química , Rhodobacteraceae/clasificación , Rhodobacteraceae/aislamiento & purificaciónRESUMEN
A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10-37 °C (optimum, 25-30 °C) and pH 6.0-9.0 (optimum, pH 8.0), and in the presence of 0-0.5â% (w/v) NaCl (optimum, 0â%). Strain U1T contained iso-C15â:â0, C16â:â0, C16â:â1 ω5c and summed feature 3 (comprising C16â:â1 ω6c and/or C16â:â1 ω7c) as the major cellular fatty acids (>5â%) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5âmol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter. Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9â%). Average nucleotide identity and digital DNA-DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6â% and 18.9â%, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).
Asunto(s)
Cytophagaceae , Ácidos Grasos , Ácidos Grasos/química , Suelo , Filogenia , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Composición de Base , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADNRESUMEN
Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from species of the marine algae Chondrus and Ulva, respectively. Both strains optimally grew at 30â°C, pH 7.0 and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain G2-23T contained summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c), C16â:â0 and summed feature 3 (iso-C15â:â0 2-OH and/or C16â:â1 ω7c/ω6c) as major cellular fatty acids, and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol and an unidentified phospholipid (PL) as major polar lipids. Strain J2-29T contained summed feature 8, C18â:â1 ω7c 11-methyl and C16â:â0 as major cellular fatty acids and PE, PME, PG and PL as major polar lipids. The genomic DNA G+C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9â% 16S rRNA gene sequence similarity, 79.8â% average nucleotide identity (ANI) and 22.8â% digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and dDDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3â%, respectively, suggesting that they represent novel species of the genus Hoeflea. In summary, based on their phenotypic, chemotaxonomic and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T=KACC 22714T=JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T=KACC 22715T=JCM 35549T), respectively, are proposed.
Asunto(s)
Gammaproteobacteria , Phyllobacteriaceae , Composición de Base , Ácidos Grasos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Fosfolípidos , NucleótidosRESUMEN
A Gram-stain-negative and facultative aerobic bacterium, strain 16-MAT, was isolated from seawater of Yellow Sea in South Korea. Cells were catalase- and oxidase-positive and non-motile rods. Growth occurred at 4-37 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, 8.0), and in the presence of 0-7.0% NaCl (optimum, 3â%). Strain 16-MAT contained ubiquinone-8 as the sole isoprenoid quinone, C16â:â0 and summed feature three as the major fatty acids (>10â%), and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids. The genome size and DNA G+C content of strain 16-MAT were 3.69 Mb and 46.0 mol%, respectively. Strain 16-MAT was most closely related to Alishewanella alkalitolerans LNK-7.1T with a 97.9â% 16S rRNA gene sequence similarity. A phylogenomic tree based on whole genome sequences showed that strain 16-MAT formed a phylogenetic lineage within the genus Alishewanella. Based on the phenotypic, chemotaxonomic, and molecular analyses, strain 16-MAT represents a novel species of the genus Alishewanella, for which the name Alishewanella maricola is proposed. The type strain is 16-MAT (=KACC 22238T =JCM 34596T).