Paenibacillus insulae sp. nov., isolated from soil.

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80(T) was isolated from an island soil. The strain DS80(T) grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11(T) (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403(T)(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1 ω11c. Strain DS80(T) contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80(T) was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80(T) =JCM 17278(T) =KCTC 13833(T)).

Phylogenetic analysis of culturable marine bacteria in sediments from the South Korean Yellow Sea.

Biogeochemical and microbiological characterization of marine sediments taken from the Yellow Sea of South Korea was carried out. One hundred and thirty six bacterial strains were isolated, characterized and phylogenetic relationship was evaluated. The gene sequences of 16S rDNA regions were examined to study the phylogenetic analysis of bacterial community in the marine sediments. Among 136 isolates, 5 bacterial isolates were identified as novel members, remaining 131 isolates were fall into 5 major linkages of bacterial phyla represented as follows: Firmicutes, alpha, gamma-Proteobacteria, High G + C and Bacteroidetes. Bacterial community in sediments mainly dominated by Firmicutes (58.77%) and followed by gamma-Pateobacteria (38.16%). Gamma-Proteobacteria domain highly diverged and mainly consists of the genera Vibrio, Marinobacterium, Photobacterium, Pseudoalteromonas, Oceanisphaera, Halomonas, Alteromonas, Stenotrophomonas and Pseudomonas. Total N and Organic matter content in Yellow Sea of South Korea were relatively high. The Total-N content in the sediments was varied from 177.31 to 1974.96 (mg/kg) and organic matter ranged from 0.82 to 4.23 (g/100 g). The current research work provides clear explanation obtained for the phylogenetic affiliation of the culturable bacterial community in sediments of South Korean Yellow Sea and revealed the relationship with biogeochemical characteristics of the sediments.

Alkaline stress-induced autophagy is mediated by mTORC1 inactivation.

The activation of autophagic pathway by alkaline stress was investigated. Various types of mammalian cells were subjected to alkaline stress by incubation in bicarbonate buffered media in humidified air containing atmospheric 0.04% CO(2) . The induction of autophagy following alkaline stress was evaluated by assessing the conversion of cytosolic LC3-I into lipidated LC3-II, the accumulation of autophagosomes, and the formation of autolysosomes. Colocalization of GFP-LC3 with endolysosomal marker in HeLa GFP-LC3 cells undergoing autophagic process by alkaline stress further demonstrates that autophagosomes triggered by alkaline stress matures into autolysosomes for the lysosome dependent degradation. We found that the inactivation of mTORC1 is important for the pathway leading to the induction of autophagy by alkaline stress since the expression of RhebQ64L, a constitutive activator of mTORC1, downregulates the induction of autophagy after alkaline stress in transfected human 293T cells. These results imply that activation of autophagic pathway following the inactivation of mTORC1 is important cellular events governing alkaline stress-induced cytotoxicity and clinical symptoms associated with alkalosis.

Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204.

The impacts of planted transgenic rice varieties on bacterial communities in paddy soils were monitored using both cultivation and molecular methods. The rice field plot consisted of eighteen subplots planted with two genetically modified (GM) rice and four non-GM rice plants in three replicates. Analysis with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes revealed that the bacterial community structures were quite similar to each other in a given month, suggesting that there were no significant differences in bacterial communities between GM and non- GM rice soils. The bacterial community structures appeared to be generally stable with the seasons, as shown by a slight variation of microbial population levels and DGGE banding patterns over the year. Comparison analysis of 16S rDNA clone libraries constructed from soil bacterial DNA showed that there were no significant differences between GM and non-GM soil libraries but revealed seasonal differences of phyla distribution between August and December. The composition profile of phospholipid fatty acids (PLFA) between GM and non-GM soils also was not significantly different to each other. When soil DNAs were analyzed with PCR by using primers for the bar gene, which was introduced into GM rice, positive DNA bands were found in October and December soils. However, no bar gene sequence was detected in PCR analysis with DNAs extracted from both cultured and uncultured soil bacterial fractions. The result of this study suggested that, in spite of seasonal variations of bacterial communities and persistence of the bar gene, the bacterial communities of the experimental rice field were not significantly affected by cultivation of GM rice varieties.

Microcosm study for revegetation of barren land with wild plants by some plant growth-promoting rhizobacteria.

Growth promotion of wild plants by some plant growth-promoting rhizobacteria (PGPR) was examined in the microcosms composed of soils collected separately from a grass-covered site and a nongrass-covered site in a lakeside barren area at Lake Paro, Korea. After sowing the seeds of eight kinds of wild plants and inoculation of several strains of PGPR, the total bacterial number and microbial activity were measured during 5 months of study period, and the plant biomasses grown were compared at the end of the study. Acridine orange direct counts in the inoculated microcosms, 1.3-9.8 x 10(9) cells x g soil(-1) in the soil from the grass-covered area and 0.9-7.2 x 10(9) cells x g soil(-1) in the soil from the nongrass-covered site, were almost twice higher than those in the uninoculated microcosms. The number of Pseudomonas sp., well-known bacteria as PGPR, and the soil dehydrogenase activity were also higher in the inoculated soils than the uninoculated soils. The first germination of sowed seeds in the inoculated microcosm was 5 days earlier than the uninoculated microcosm. Average lengths of all plants grown during the study period were 26% and 29% longer in the inoculated microcosms starting with the grass-covered soil and the nongrass-covered soil, respectively, compared with those in the uninoculated microcosms. Dry weights of whole plants grown were 67-82% higher in the inoculated microcosms than the uninoculated microcosms. Microbial population and activity and growth promoting effect by PGPR were all higher in the soils collected from the grass-covered area than in the nongrass-covered area. The growth enhancement of wild plants seemed to occur by the activities of inoculated microorganisms, and this capability of PGPR may be utilized for rapid revegetation of some barren lands.

Revegetation of a lakeside barren area by the application of plant growth-promoting rhizobacteria.

The growth stimulation of wild plants by several bacterial species showing plant growth-promoting capabilities was examined in a barren lakeside area at Lake Paro, Korea. Microbial numbers and activities in the field soil were monitored for 73 days after inoculation of the bacteria. The acridine orange direct counts for the total soil bacterial populations ranged between 2.0-2.3x10(9) cells/g soil and 1.4-1.8x10(9) cells/g soil in the inoculated and uninoculated soils, respectively. The numbers of Pseudomonas spp., which is known as a typical plant growth-promoting rhizobacteria, and the total microbial activity were higher in the inoculated soil compared to those in the uninoculated soil. The average shoot and root lengths of the wild plants grown in the inoculated soil were 17.3 cm and 12.4 cm, respectively, and longer than those of 11.4 cm and 8.5 cm in the uninoculated soil. The total dry weight of the harvested wild plants was also higher in the inoculated soil (42.0 g) compared to the uninoculated soil (35.1 g). The plant growth-promoting capabilities of the inoculated bacteria may be used for the rapid revegetation of barren or disturbed land, and as biofertilizer in agriculture.

Strombidinopsis jeokjo n. sp. (ciliophora: choreotrichida) from the coastal waters off western Korea: morphology and small subunit ribosomal DNA gene sequence.

The planktonic ciliate Strombidinopsis jeokjo n. sp. is described from Quantitative Protargol-Stained (QPS) preparations, and the sequence of the small subunit rDNA (SSU rDNA) from cultured cells is reported. This species is ovoid and bluntly tapered towards the posterior. The ranges (and mean +/- standard deviation, n = 31) of cell length, cell width, and oral diameter of the QPS-stained specimens were 100-190 microm (149 +/- 25), 60-105 microm (79 +/- 13), and 55-80 microm (64 +/- 5), respectively. Fifteen to seventeen external oral polykinetids had oral membranelle cilia 20-35 microm long. Twenty-six to twenty-eight somatic kineties were equally spaced around the cell body and extended from the oral to the posterior regions with 23-44 dikinetids per kinety. Both kinetosomes of each kinetid bore cilia 3-7 microm long. Strombidinopsis jeokjo had two ovoid macronuclei of 25-38 microm x 12-15 microm. When properly aligned, the sequence of the SSU rDNA of S. jeokjo (GenBank Accession No. AJ628250) was approximately 2% different from that of an unidentified Strombidinopsis species (GenBank Accession No. AF399132-AF399135), the closest species in the SSU rDNA sequence.