Flavihumibacter solisilvae sp. nov., isolated from forest soil.

A Gram-stain-positive, strictly aerobic, yellow colony-forming bacterium, designated strain 3-3(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods without gliding motility, showing oxidase- and catalase-positive reactions. Growth was observed at 20-37 °C (optimum, 28 °C) and pH 5.

Plant RNA virus sequences identified in kimchi by microbial metatranscriptome analysis.

Plant pathogenic RNA viruses are present in a variety of plant-based foods. When ingested by humans, these viruses can survive the passage through the digestive tract, and are frequently detected in human feces. Kimchi is a traditional fermented Korean food made from cabbage or vegetables, with a variety of other plant-based ingredients, including ground red pepper and garlic paste.

A mesophilic, autotrophic, ammonia-oxidizing archaeon of thaumarchaeal group I.1a cultivated from a deep oligotrophic soil horizon.

Soil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.

Microbial successions and metabolite changes during fermentation of salted shrimp (saeu-jeot) with different salt concentrations.

To investigate the effects of salt concentration on saeu-jeot (salted shrimp) fermentation, four sets of saeu-jeot samples with 20%, 24%, 28%, and 32% salt concentrations were prepared, and the pH, bacterial and archaeal abundances, bacterial communities, and metabolites were monitored during the entire fermentation period. Quantitative PCR showed that Bacteria were much more abundant than Archaea in all saeu-jeot samples, suggesting that bacterial populations play more important roles than archaeal populations even in highly salted samples. Community analysis indicated that Vibrio, Photobacterium, Psychrobacter, Pseudoalteromonas, and Enterovibrio were identified as the initially dominant genera, and the bacterial successions were significantly different depending on the salt concentration.

Effect of fumarate reducing bacteria on in vitro rumen fermentation, methane mitigation and microbial diversity.

The metabolic pathways involved in hydrogen (H(2)) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH(4)) emissions by ruminants. H(2) as one of the major substrate for CH(4) production is therefore should be controlled. One of the strategies on reducing CH(4) is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria.

Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.

A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain 5-10(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at 10-37 °C (optimum, 30 °C), at pH 5.

Kimchi microflora: history, current status, and perspectives for industrial kimchi production.

Kimchi, a traditional Korean food made by the fermentation of vegetables, has become popular globally because of its organoleptic, beneficial, and nutritional properties. Spontaneous kimchi fermentation in unsterilized raw materials leads to the growth of various lactic acid bacteria (LAB), which results in variations in the taste and sensory qualities of kimchi products and difficulties in the standardized industrial production of kimchi. Raw materials, kimchi varieties, ingredients, and fermentation conditions have significant effects on the microbial communities and fermentative characteristics of kimchi during fermentation.

Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem.

Methane emissions, along with methanotrophs and methanogens and soil chemical properties, were investigated in a flooded rice ecosystem. Methane emission increased after rice transplantation (from 7.2 to 552 mg day(-1) m(-2) ) and was positively and significantly correlated with transcripts of pmoA and mcrA genes, transcript/gene ratios of mcrA, temperature and total organic carbon.

Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia.

An endophytic, Gram-staining-negative bacterium was isolated from sterilized roots of a plant, Suaeda maritima, growing on tidal flats. Cells of the strain were motile by means of a single polar flagellum and colonies were pigmented light brown. Strain YC6927(T) was able to grow at 15-37 °C (optimum at 28-30 °C) and at pH 5.

Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers.

Comparative genomic and transcriptomic analyses of NaCl-tolerant Staphylococcus sp. OJ82 isolated from fermented seafood.

Bacteria belonging to the Staphylococcus genus reside in various natural environments; however, only disease-associated Staphylococcus strains have received attention while ecological function and physiologies of non-pathogenic strains were often neglected. Because high level of tolerance against NaCl is a common trait of Staphylococcus, we investigated the characteristics of halotolerance in Staphylococcus sp. OJ82 isolated from fermented seafood containing a high concentration of NaCl.

Effects of temperature on microbial succession and metabolite change during saeu-jeot fermentation.

To investigate the effects of temperature on saeu-jeot (shrimp) fermentation, four sets of saeu-jeot samples with approximately 25% (w/v) NaCl were fermented at 10 °C, 15 °C, 20 °C, and 25 °C. The pH values of the 10 °C and 15 °C samples were relatively constant during the entire fermentation period, whereas those of the 20 °C and 25 °C samples gradually decreased after 25 days of fermentation. Quantitative PCR showed that the maximum bacterial abundance was greater in higher temperature samples, and the bacterial abundance in the 10 °C samples steadily decreased during the entire fermentation period.

Photobacterium aestuarii sp. nov., a marine bacterium isolated from a tidal flat.

A Gram-staining-negative, motile, weakly halophilic and facultatively aerobic bacterium, designated strain YA11(T), was isolated from tidal flat sediment at Yeongam Bay, South Korea. Strain YA11(T) grew at 10-30 °C (optimum, 20 °C), at pH 6.0-10.

Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis.

DNA stable isotope probing and metagenomic sequencing were used to assess the metabolic potential of iron-reducing bacteria involved in anaerobic aromatic hydrocarbon degradation in oil spill-affected tidal flats. In a microcosm experiment, (13) C-toluene was degraded with the simultaneous reduction of Fe(III)-NTA, which was also verified by quasi-stoichiometric (13) C-CO2 release. The metabolic potential of the dominant member affiliated with the genus Desulfuromonas in the heavy DNA fraction was inferred using assembled scaffolds (designated TF genome, 4.

A proposal to unify two subspecies of Staphylococcus equorum: Staphylococcus equorum subsp. equorum and Staphylococcus equorum subsp. linens.

Twelve isolates from jeotgal, a Korean high-salt-fermented seafood, identified as Staphylococcus equorum were compared by phenotypic and genotypic methods to determine their precise taxonomic identities at the subspecies level. Four strains and three strains had complete 16S rRNA gene sequence matches with S. equorum subsp.

Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat.

A Gram-stain-negative, non-spore-forming, facultatively anaerobic bacterium, designated strain SC18(T), was isolated from a tidal flat of Suncheon bay in South Korea. Cells were rod-shaped and motile by means of a polar flagellum. Cells were catalase-, oxidase- and β-haemolysis-positive.

Pyrosequencing-based analysis of the bacterial community in Korean traditional seafood, ojingeo jeotgal.

Jeotgal fermentation is dependent upon a diverse microbial community, although a detailed understanding of its microbial composition is limited to a relatively small number of jeotgal. Pyrosequencing-based bacterial community analysis was performed in fermented squid, ojingeo jeotgal. Leuconostoc was identified as the predominant bacterial genus, with Bacillus and Staphylococcus also accounting for a large proportion of the bacterial community.

Aquamicrobium aestuarii sp. nov., a marine bacterium isolated from a tidal flat.

A Gram-negative, strictly aerobic, motile bacterium with flagella, designated strain G210(T), was isolated from a crude-oil-contaminated tidal flat of the Taean coast in South Korea. Cells were non-spore-forming, ovoid rods showing catalase- and oxidase-positive reactions. Growth of strain G210(T) was observed between 15 and 45 °C (optimum, 30-35 °C) and between pH 5.

Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima.

A novel bacterial strain, YC6899(T), was isolated from the root of Suaedae maritima growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899(T) grew optimally at a salinity of 2-4 %, at 25-37 °C and at pH 6.

Roseovarius lutimaris sp. nov., isolated from a marine tidal flat.

A novel Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain 112(T), was isolated from a tidal flat at Taean, Korea. Cells were catalase- and oxidase-positive ovoids to rods and did not produce bacteriochlorophyll a. Optimum growth of strain 112(T) was observed at 30 °C, at pH 6.

Microbial succession and metabolite changes during fermentation of dongchimi, traditional Korean watery kimchi.

Dongchimi, one of the most common types of watery kimchi in Korea, was prepared using radish and its pH values, microbial cell numbers, bacterial communities, and metabolites were monitored periodically to investigate the fermentation process of watery kimchi. The bacterial abundance increased quickly during the early fermentation period and the pH values concurrently decreased rapidly without any initial pH increase. After 15 days of fermentation, the bacterial abundance decreased rapidly with the increase of Saccharomyces abundance and then increased again with a decrease of Saccharomyces abundance after 40 days of fermentation, suggesting that bacteria and Saccharomyces have a direct antagonistic relationship.

Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation.

Barcode-based 16S rRNA gene pyrosequencing showed that the kimchi microbiome was dominated by six lactic acid bacteria (LAB), Leuconostoc (Lc.) mesenteroides, Lactobacillus (Lb.) sakei, Weissella (W.

Microbial succession and metabolite changes during long-term storage of Kimchi.

Kimchi is often stored for a long period of time for a diet during the winter season because it is an essential side dish for Korean meals. In this study pH, abundance of bacteria and yeasts, bacterial communities, and metabolites were monitored periodically to investigate the fermentation process of kimchi for 120 d. Bacterial abundance increased quickly with a pH decrease after an initial pH increase during the early fermentation period.

Brevibacterium jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.

A Gram-staining-positive, aerobic, non-motile bacterium, designated strain SJ5-8(T), was isolated from seau-jeot (shrimp jeotgal), a traditional fermented seafood in South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain SJ5-8(T) was observed at 10-37 °C (optimum, 30 °C), at pH 6.