Little is known about the archaeal diversity of fermented seafood; most of the earlier studies of fermented food have focused on lactic acid bacteria (LAB) in the fermentation process. In this study, the archaeal and bacterial diversity in seven kinds of fermented seafood were culture-independently examined using barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) methods. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers, using different primers for Archaea or Bacteria. Because PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results were compared with the results of the barcoded pyrosequencing analysis. A total of 13 372 sequences were retrieved from 15 898 pyrosequencing reads and were analyzed to evaluate the diversity of the archaeal and bacterial populations in seafood. The most predominant types of archaea and bacteria identified in the samples included extremely halophilic archaea related to the family Halobacteriaceae; various uncultured mesophilic Crenarchaeota, including Crenarchaeota Group I.1 (CG I.1a and CG I.1b), Marine Benthic Group B (MBG-B), and Miscellaneous Crenarchaeotic Group (MCG); and LAB affiliated with genus Lactobacillus and Weissella. Interestingly, numerous uncultured mesophilic Crenarchaeota groups were as ubiquitous in the fermented seafood as in terrestrial and aquatic niches; the existence of these Crenarchaeota groups has not been reported in any fermented food. These results indicate that the archaeal populations in the fermented seafood analyzed are diverse and include the halophilic and mesophilic groups, and that barcoded pyrosequencing is a promising and cost-effective method for analyzing microbial diversity compared with conventional approaches.

Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multipledisplacement amplification (MDA), an isothermal whole-genome amplification method with 29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

During a previous study on the molecular interaction between commensal bacteria and host gut immunity, two novel bacterial strains, A911T and G707 T , were isolated from the gut of Drosophila melanogaster. In this study, these strains were characterized in a polyphasic taxonomic study using phenotypic, genetic, and chemotaxonomic analyses. We show that the strains represent novel species in the family Acetobacteraceae. Strain G707T , a highly pathogenic organism, represents a new species in the genus Gluconobacter, "Gluconobacter morbifer" sp. nov. (type strain G707 ‫؍‬ KCTC 22116 T ‫؍‬ JCM 15512 T ). Strain A911 T , dominantly present in the normal Drosphila gut community, represents a novel genus and species, designated "Commensalibacter intestini" gen. nov., sp. nov. (type strain A911 ‫؍‬ KCTC 22117 T ‫؍‬ JCM 15511 T ).

A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).

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Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella The genus Alishewanella is one of the major branches of the family Alteromonadaceae and was first proposed by Fonnesbech Vogel et al. (2000) to accommodate Alishewanella fetalis, isolated from an autopsy of a human fetus in 1992. Recently, another species, Alishewanella aestuarii, from a marine environment, has been reported (Roh et al., 2009). Here, we describe a third novel species that belongs to the genus Alishewanella, isolated from a traditional fermented food in Korea. Strain MS1T was isolated from gajami sikhae (jeotgal), which is a traditional fermented food in Korea. A sample of gajami sikhae was diluted 10 26 -fold with PBS and cultured on R2A agar (Difco). The 16S rRNA gene sequence was amplified by the colony PCR method with PCR Pre-Mix (Intron Biotechnology) and two universal primers for bacteria (Baker et al., 2003). The PCR products were sequenced with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems) after purification according to the manufacturer's instructions. The reaction mixtures were analysed with an automated system (ABI Prism 3730XL DNA Analyzer; Applied Biosystems) and the 16S rRNA gene sequences were assembled with SEQMAN (DNASTAR). Comparison of the 16S rRNA gene sequence of strain MS1T with those deposited in GenBank revealed that strain MS1T belongs to the genus Alishewanella in the phylum Proteobacteria and that its 16S rRNA gene sequence shares 98.67 and 98.04 % similarity with the sequences of A. aestuarii B11 T and A. fetalis CCUG 30811 T , respectively. The 16S rRNA gene sequence of the isolate was aligned with those of reference strains by using the multiple-sequence alignment program CLUSTAL X (1.83) (Thompson et al., 1997). The phylogenetic relationships between strain MS1T and the representative type strains of Alishewanella species were defined by MEGA4 (Tamura et al., 2007). In the randomly generated neighbour-joining, maximum-parsimony and maximumlikelihood consensus trees constructed from 1000, 1000 and 300 bootstrap replicates, respectively (Felsenstein, 1981;Kluge & Farris, 1969;Saitou & Nei, 1987), strain MS1T formed a monophyletic clade that was separate Abbreviation: TMAO, trimethylamine oxide.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MS1 T is EU817498.