To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.

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Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99?9 %) being found with Bacillus pumilus. However, these isolates share a mere 91?2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA-DNA hybridization showed only 54-66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA-DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36b T (=ATCC BAA-1126 T =NBRC 100820 T ).Spacecraft and associated clean-room assembly-facility surfaces harbour an extremely low biomass (La Duc et al., 2003;Venkateswaran et al., 2001), because of stringent maintenance. However, colonization by micro-organisms specifically adapted to such facility conditions, especially those yet to be cultured and/or characterized, is of major concern to those commissioning modern-day space-related experimentation. The search for extraterrestrial life will rely heavily on validated cleaning and bioreduction strategies to ensure that terrestrial microbial contamination does not compromise the scientific integrity of such missions. It is crucial both to minimize and eradicate such microbial contaminants and to identify and characterize the recurring, prevalent micro-organisms associated with the surfaces of spacecraft and associated environments.Studies have repeatedly shown that extremely resilient, spore-forming members of the genus Bacillus are the most strongly represented micro-organisms in samples collected from spacecraft and facility surfaces (La Duc et al., 2003; Puleo et al., 1977). The extremely oligotrophic, lowhumidity, temperature-controlled conditions of spacecraftassembly facilities appear to select for micro-organisms able to withstand such unfavourable surroundings. During monitoring of the microbial diversity of spacecraftassociated environments over a period of 5 years (1999)(2000)(2001)(2002)(2003)(2004), Bacillus pumilus was found to be the second most domi...

Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.

SummaryIn ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for ~7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80ºC for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80ºC and proliferate at 60ºC. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades: Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.

Shewanella putrefaciens has been considered the main spoilage bacteria of low-temperature stored marine seafood. However, psychrotropic Shewanella have been reclassified during recent years, and the purpose of the present study was to determine whether any of the new Shewanella species are important in fish spoilage. More than 500 H 2 S-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the Baltic Sea during winter or summer time. All strains were identified as Shewanella species by phenotypic tests. Different Shewanella species were present on newly caught fish. During the warm summer months the mesophilic human pathogenic S. algae dominated the H 2 S-producing bacterial population. After iced storage, a shift in the Shewanella species was found, and most of the H 2 S-producing strains were identified as S. baltica. The 16S rRNA gene sequence analysis confirmed the identification of these two major groups. Several isolates could only be identified to the genus Shewanella level and were separated into two subgroups with low (44%) and high (47%) G؉C mol%. The low G؉C% group was isolated during winter months, whereas the high G؉C% group was isolated on fish caught during summer and only during the first few days of iced storage. Phenotypically, these strains were different from the type strains of S. putrefaciens, S. oneidensis, S. colwelliana, and S. affinis, but the high G؉C% group clustered close to S. colwelliana by 16S rRNA gene sequence comparison. The low G؉C% group may constitute a new species. S. baltica, and the low G؉C% group of Shewanella spp. strains grew well in cod juice at 0°C, but three high G؉C Shewanella spp. were unable to grow at 0°C. In conclusion, the spoilage reactions of iced Danish marine fish remain unchanged (i.e., trimethylamine-N-oxide reduction and H 2 S production); however, the main H 2 S-producing organism was identified as S. baltica.

A 17␤-estradiol (E2)-degrading bacterium was isolated from activated sludge in a sewage treatment plant in Tokyo, Japan. The isolate was suggested to be a new Novosphingobium species. Gas chromatography-mass spectrometry and 1 H nuclear magnetic resonance analyses of the metabolites of E2 degradation suggested that no toxic products accumulated in the culture medium.There has been increasing concern recently over the potential of sewage treatment plant (STP) effluent to cause estrogenic effects on aquatic fauna. Widespread sexual disruption, or so-called feminization, is thought to be due to environmental contaminants in the effluent and has been observed for riverine fish in several developed nations, including the United Kingdom, the United States, and Japan (3,4,7,8,10,13). While there still remains some room for discussion about the chemicals that cause this phenomenon, natural estrogens entering the environment through the excretions of humans, domestic or farm animals, and wildlife are thought to be the most likely suspects, because they induce biological effects at environmentally relevant concentrations, on the order of nanograms per liter (12,18,21). Among the natural estrogens, 17␤-estradiol (E2) is the most potent and is found ubiquitously in many water systems (2,9,11,14,24,28). Therefore, it is thought that E2 is responsible for the majority of the estrogenic effects found for STP effluent.Although the fate and behavior of E2 after excretion, during processing in STPs, or following discharge into rivers are not fully understood, there is some evidence supporting the importance of this problem. The efficiency of removal of natural estrogens, including E2, during STP processing is estimated to be 50 to 90%, depending on the facility and the location (2, 14). However, this removal is thought to be mainly due to adsorption of E2 into activated sludge or other factors independent of microbial degradation, because it has been suggested previously that natural steroidal estrogens, including E2, are poorly degraded during STP processing (17,19). Furthermore, the proportion of steroidal estrogens remaining in the effluent is still capable of producing estrogenic effects (18). It has also been reported previously that conjugated E2 (an estrogenically inactive form) excreted from humans and animals is converted back into free E2 (the active form) before or during passage through the STP, suggesting that microbes in the process can cleave the conjugates (16). These facts, considered together with the increasing public consciousness regarding environmental preservation and the views of scientists (19, 26), make it clear that the degradation capabilities and removal efficiencies of STPs need to be improved further. Moreover, recent overpopulation in urban areas may make the feminization problem more serious. These prospects led us to search for microorganisms with strong E2-degrading activity.To find microbes with E2-degrading activity, we collected 11 samples, including 4 soil and 3 water samples from natural en...

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