To examine the occurrence in other deep-sea bacteria of two amino acid substitutions (Ala-180 and His-229) in malate dehydrogenase (MDH) found previously in the deep-sea piezophilic Moritella sp. strain 2D2, we cloned and sequenced MDH genes of deep-sea piezophilic Moritella and Shewanella strains isolated from intestinal contents of deep-sea fishes, as well as other Moritella species from deep-sea water and sediments: M. marina, M. japonica, and M. yayanosii. The piezophilic Moritella strains had a Val residue or an Ala residue at position 180 and all the Moritella strains except for one had a His residue at position 229. However, four piezophilic-strain-specific substitutions at positions 103, 111, 229, and 283 were found to be completely conserved in the MDH of the intestinal Moritella strains of deep-sea fishes, indicating the substitutions may be habitat-specific. The piezophilic Shewanella strains had a Val residue and a Gln residue at positions 180 and 229, respectively. However, the MDHs of the Shewanella strains had five piezophilic-strain-specific substitutions at positions 61, 65, 107, 161, and 202. Therefore, the enzymatic strategies for responding to deep-sea high pressure environments of the MDHs between the genera Moritella and Shewanella are potentially different. Moreover, homology modeling shows these substitutions found in the MDHs of both genera except for position 229 in the subunit interface are located on the exposed region of the MDH molecules, indicating the substitutions may be related to the hydration state of the molecules.

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A survey was conducted on the isolation and characterization of bacteriocin-producing lactic acid bacteria in soil. Forty-two acid-producing bacterial strains were isolated from 55 soil samples collected in Yamanashi prefecture, Japan. Investigation of antibacterial activities of isolates revealed that three isolates, Lactobacillus animalis C060203, Enterococcus durans C102901 and Leuconostoc mesenteroides subsp. mesenteroides C060204, showed antibacterial activities against the indicator strain of Lactobacillus sakei JCM 1157^T. Bacteriocin from Enterococcus durans C102901 showed different characteristics from the known durancin L28-1A, produced by Enterococcus durans L28-1. Furthermore, this is the first report of a bacteriocin being produced by Lactobacillus animalis. Viewing from the species, bacteriocins from strains C102901 and C060203 showed high possibilities for the novel substances. These significant findings suggest that soil may be a common source for the isolation of novel bacteriocin-producing lactic acid bacteria.

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Five Lactobacillus strains (2 L. gasseri, 2 L. plantarum and 1 L. reuteri) were cultured in modified MRS medium containing fatty acids (FAs) instead of Tween 80 for 24 h at 37°C, to learn the effect of saturated and unsaturated FAs on the Lactobacillus growth. Free FAs included palmitic (16:0), palmitoleic (c9-16:1), stearic (18:0), oleic (c9-18:1), elaidic (t9-18:1), cis-vaccenic (c11-18:1), vaccenic (t11-18:1), linoleic (c9, c12-18:2), conjugated linoleic (c9, t11- and t10, c12-18:2), α-linolenic (c9, c12, c15-18:3), α-eleostearic (c9, t11, t13-18:3), eicosapentaenoic (20:5), and docosahexaenoic (22:6) acids. Among free FAs, oleic acid stimulated the growth of all Lactobacillus strains, whereas palmitoleic acid had almost no affect on the Lactobacillus growth. Saturated FAs such as stearic and palmitic acids inhibited or did not affect the Lactobacillus growth. Polyunsaturated FAs such as α-linolenic, eicosapentaenoic and docosahexaenoic acids strongly inhibited the Lactobacillus growth at 7.6×10⁻⁴ m. Octadecenoic acids such as oleic, elaidic, cis-vaccenic and vaccenic acids remarkably promoted the growth of L. gasseri, regardless of the different double bond positions and configurations. When oleic or cis-vaccenic acid was incubated with L. gasseri, the FAs was transformed to cyclopropane FAs (methyleneoctadecanoic acids) after incorporation into the cells. On the other hand, trans FAs such as elaidic and vaccenic acids incorporated into the cells were not converted to another FAs. Conjugated linoleic and α-eleostearic acids having a trans double bond promoted the Lactobacillus growth. The growth of L. gasseri was also stimulated by trans-rich free FAs from hydrogenated canola and fish oils. These results showed that octadecenoic acid and trans FAs had strong promotion activities for the Lactobacillus growth due to their incorporation into membrane lipids.

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Phylogenetic relationships within the Erythrobasidium clade as a lineage of the urediniomycetous yeasts were examined using partial regions of 18S rDNA, 5.8S rDNA, 26S rDNA, internal transcribed spacers (ITSs), and elongation factor (EF)-1α. Combined data analysis of all segments successfully yielded a reliable phylogeny and confirmed the cohesion of species characterized by Q-10(H₂) as a major ubiquinone. Differences in secondary structure predicted for a variable region in 26S rDNA corresponded to major divergences in the phylogenetic tree based on the primary sequence. The common presence of a shortened helix in this region was considered to be evidence of monophyly for species with Q-10(H₂), Sakaguchia dacryoides, Rhodotorula lactosa, and Rhodotorula lamellibrachiae, although it was not as strongly supported by the combined data tree. The information on intron positions in the EF-1α gene had potential usefulness in the phylogenetic inference between closely related species.

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We have investigated the molecular phylogeny of cold-seep sediments obtained from the Nankai Trough, at depths of about 600, 2,000, and 3,300 m, and compared the microbial diversity profiles of those sediments samples. The γ-Proteobacteria that might function as sulfide oxidizers and the symbiotically related δ-Proteobacteria which might function as sulfate reducers were identified amongst the bacteria from all depths of the sediments. However, anoxic methane oxidizing archaea (ANME) and methanogens were only found in the 600 m deep sediments. These results indicated that the cold-seep microbial sulfur circulation system could be functioning in the shallow seep sediment at a depth of 600 m and the microbial activities at these sites might be more dynamic than at other deeper cold-seep sites.

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