Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough.

A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, most of these archaea have not yet been cultivated, and their physiological and metabolic traits remain unclear. In this study, phylogenetic diversity and distribution profiles of the archaeal genes encoding small subunit (SSU) rRNA, methyl coenzyme A (CoA) reductase subunit A, and the ammonia monooxygenase large subunit were characterized in hydrothermally influenced sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa Trough. Sediment cores were collected at distances of 0.5, 2, or 5 m from a vent emission (90 degrees C). A moderate temperature gradient extends both horizontally and vertically (5 to 69 degrees C), indicating the existence of moderate mixing between the hydrothermal fluid and the ambient sediment pore water. The mixing of reductive hot hydrothermal fluid and cold ambient sediment pore water establishes a wide spectrum of physical and chemical conditions in the microbial habitats that were investigated. Under these different physico-chemical conditions, variability in archaeal phylotype composition was observed. The relationship between the physical and chemical parameters and the archaeal phylotype composition provides important insight into the ecophysiological requirements of uncultivated archaeal lineages in deep-sea hydrothermal vent environments, giving clues for approximating culture conditions to be used in future culturing efforts.

Comprehensive analysis of an Antarctic bacterial community with the adaptability of growth at higher temperatures than those in Antarctica.

To investigate the adaptability to higher temperatures of Antarctic microorganisms persisting in low temperature conditions for a long time, Antarctic lake samples were incubated in several selection media at 25 degrees C and 30 degrees C. The microorganisms did not grow at 30 degrees C; however, some of them grew at 25 degrees C, indicating that the bacteria in Antarctic have the ability to grow at a wide range of temperatures. Total DNA was extracted from these microorganisms and amplified using the bacteria-universal primers. The amplified fragments were cloned, and randomly selected 48 clones were sequenced. The sequenced clones showed high similarity to the alpha-subdivision of the Proteobacteria with specific affinity to the genus Agrobacterium, Caulobacter and Brevundimonas, the ss-subdivision of Proteobacteria with specific affinity to the genus Cupriavidus, and Bacillus of the phylum Firmicutes. These results showed the presence of universal genera, suggesting that the bacteria in the Antarctic lake were not specific to this environment.

Degradation of the seaweed wakame (Undaria pinnatifida) by a composting process with the inoculation of Bacillus sp. HR6.

Disposal of the seaweed wakame (Undaria pinnatifida) by inoculating the halotolerant bacterium Bacillus sp. HR6 was examined in an experimental scale composting system. Strain HR6 was effective in initiating the composting process of wakame, and there was a rapid increase in temperature to over 54.9-55.7 degrees C after 18-20 h. The composting process of wakame could be carried out despite a high NaCl content, 28.2 mg/g, although lower salinity resulted in a shorter lag time and higher weight reduction. In a larger scale composting process with aeration, two peaks of temperature change were found which corresponded well to oxygen consumption and CO2 emission during the process. The pH increased to 8.83 and organic materials were reduced to 93.4% after 72 h. The initial N and C contents were 3.9 and 34.0%, respectively, both of which decreased during the composting process. The changes in the viable cell numbers suggested that strain HR6 predominated before 24 h and other microorganisms including HR6 were present in a mixed state during the later period of composting. The total content of alginate (TA), 32.2% in the initial stage, decreased to 29.2% after 72 h, while water soluble alginate (WSA) increased, indicating that the solubilization and decomposition of alginate had occurred during the composting process.

Identification of a gene induced in conjugation-promoted cells of toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella using differential display analysis.

Marine dinoflagellates Alexandrium tamarense and Alexandrium catenella produce toxins that cause paralytic shellfish poisoning (PSP). A detailed mechanism of encystment is necessary for a better understanding of bloom dynamics and the toxic effect of these organisms. In this study, a cDNA that was up-regulated in conjugation-promoted cells at encystment was identified using differential display. It encoded a polypeptide of 195 amino acids with a molecular weight of 20,900 Da. The deduced amino acid sequence of this cDNA showed 62% similarity with the polypeptide encoded by SPS19, a gene that is activated specifically during spore maturation and spore wall formation in Saccharomyces cerevisiae. Therefore, the cDNA obtained was termed an SPS19 homolog in this study. The expression levels of the SPS19 homolog were highest immediately after the promotion of conjugation and decreased sequentially later, a pattern similar to that of SPS19 in the sporulation of S. cerevisiae in terms of the time of induction and the duration of expression. These similarities between the SPS19 homolog and SPS19 suggested that the putative function of the SPS19 homolog might be an involvement in encystment. RT-PCR showed that the expression of the SPS19 homolog was highest in conjugation-promoted cells but low in vegetative cells. The SPS19 homolog was believed to be expressed constantly in order for cells to respond rapidly to environmental changes and ensure encystment. Characterization of the identified gene might help in understanding the mechanism of encystment.

Species-specific detection and quantification of toxic marine dinoflagellates Alexandrium tamarense and A. catenella by Real-time PCR assay.

A Real-time polymerase chain reaction (PCR) assay was designed and evaluated for rapid detection and quantification of the toxic dinoflagellates Alexandrium catenella and A. tamarense, which cause paralytic shellfish poisoning. Two sets of PCR primers and fluorogenic probes targeting these two species were derived from the sequence of 28S ribosomal DNA. PCR specificity was examined in closely related Alexandrium spp. and many other microalgae. A. catenella-specific primers and probe detected the PCR amplification only from A. catenella strains, and nonspecific signals were not detected from any microalgae. Also, A. tamarense-specific primers and probe also detected the targeted species, suggesting the strict species specificity of each PCR. This assay could detect one cell of each species, showing its high sensitivity. Moreover, using the developed standard curves, A. tamarense and A. catenella could be quantified in agreement with the quantification by optical microscopy. The performance characteristics of species specificity, sensitivity, and rapidity suggest that this method is applicable to the monitoring of the toxic A. tamarense and A. catenella.

Psychroflexus lacisalsi sp. nov., a moderate halophilic bacterium isolated from a hypersaline lake (Hunazoko-Ike) in Antarctica.

A novel gram-negative, aerobic, moderate halophilic, and psychrotolerant bacterium, designated as strain H7(T), was isolated from a hypersaline lake located in Skarvsnes, Antarctica. Cells were filaments with varying lengths. Coccoid bodies developed in old cultures. Growth occurred with 0.5-15% (w/v) NaCl (optimum, 5.8-7.0%), at pH 6.0-10.0 (optimum, pH 7.0-8.0), and at 10-28 degrees C (optimum, 25 degrees C). The strain had a G+C content of 34.9 mol%, which is within the range of 32-36 mol% reported for the genus Psychroflexus. Chemotaxonomic data (major respiratory quinone: MK-6; major fatty acids: aC(15:0), iC(16:0) 3-OH, and aC(15: 1) A) supported the classification of strain H7(T) within the genus Psychroflexus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H7(T) should be assigned to the genus Psychroflexus and has a homology with Psychroflexus salinarum (98.2%), P. sediminis (96.1%), P. torquis (95.2%), P. tropicus (95.8%), and P. gondwanense (92.2%). Strain H7 is not identified as P. salinarum because that DNA-DNA hybridization data were 8.5% between strain H7(T) and P. salinarum. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics, and chemotaxonomic differences supported the view that strain H7(T) represents a novel species of the genus Psychroflexus. The name Psychroflexus lacisalsi is proposed, and the type strain is H7(T) (=JCM 16231(T) =KACC 14089(T)).