Our newly designed primers were evaluated for the molecular analysis of specific groups of the sqr gene encoding sulfide : quinone reductase (SQR) in sediment environments. Based on the phylogenetic analysis, we classified the sqr sequences into six groups. PCR primers specific for each group were developed. We successfully amplified sqr-like gene sequences related to groups 1, 2 and 4 from diverse sediments including a marine sediment (SW), a tidal flat (TS), a river sediment (RS) and a lake sediment (FW). We recovered a total of 82 unique phylotypes (based on a 95 % amino acid sequence similarity cutoff) from 243 individual sqr-like gene sequences. Phylotype richness varied widely among the groups of sqr-like gene sequences (group 1.group 2.group 4) and sediments (SW.TS.RS.FW). Most of the sqr-like gene sequences were affiliated with the Proteobacteria clade and were distantly related to the reference sqr gene sequences from cultivated strains (less than~80 % amino acid sequence similarity). Unique sqr-like gene sequences were associated with individual sediment samples in groups 1 and 2. This molecular tool has also enabled us to detect sqr-like genes in a sulfuroxidizing enrichment from marine sediments. Collectively, our results support the presence of previously unrecognized sqr gene-containing micro-organisms that play important roles in the global biogeochemical cycle of sulfur. INTRODUCTIONSulfide, the most reduced form of inorganic sulfur, occurs in sediment environments, where it is generated from anaerobic sulfate-reducing bacteria (Detmers et al., 2001;Sorensen et al., 1981). Besides chemical oxidation, microorganisms are involved in the oxidation of sulfide at oxicanoxic interfaces; this reaction initiates the first step of the sulfur oxidation process (Cytryn et al., 2005;Jorgensen, 1982) and produces sulfate or sulfur as the major oxidation product (Friedrich, 1998;Ruepp et al., 2000;She et al., 2001;Theissen et al., 2003).The oxidation of sulfide to sulfate is mediated by membrane-bound electron-transport systems. Two main enzymic systems participating in the initial step have been intensively studied to understand the mechanism of sulfide oxidation. The electrons from sulfide enter the electrontransport chain either at the level of c-type cytochromes, via a sulfide : cytochrome c reductase (FCC) (Kusai & Yamanaka, 1973a, b, c; Lyric & Suzuki, 1970a, b, c), or at the level of quinone via a sulfide : quinone reductase (SQR) (Nubel et al., 2000;Schutz et al., 1997Schutz et al., , 1998Schutz et al., , 1999. FCC was suggested to play an essential role in sulfide oxidation in vivo, and found in a number of chemotrophic and phototrophic sulfide-oxidizing bacteria (Griesbeck et al., 2000;Schutz et al., 1999). However, it is not obligatory in sulfide oxidation since FCC does not occur in a variety of sulfide-oxidizing bacteria, and appears to be dispensable in the micro-organisms in which it is present (Brune, 1995). For example, disruption of the fcc gene in Chromatium vinosum did not have any signifi...

A taxonomic study was carried out on an isolate, strain NO2 T , from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Gammaproteobacteria and was most closely related to Glaciecola mesophila KMM 241 T and Glaciecola polaris LMG 21857 T (98.6 and 98.0 % 16S rRNA gene sequence similarity, respectively). The isolate was Gram-negative, aerobic and slightly halophilic and grew in 2-8 % NaCl and at 7-30 6C. Strain NO2 T shared some physiological and biochemical properties with G. mesophila KMM 241 T and G. polaris LMG 21857 T . The G+C content of the genomic DNA of strain NO2 T was 45 mol%. Strain NO2 T possessed C 16 : 0 , summed feature 4 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH) and summed feature 7 (C 18 : 1 v9c/v12t/v7c) as the major cellular fatty acids. DNA-DNA relatedness data indicated that strain NO2 T represents a distinct species that is separate from G. mesophila and G. polaris. On the basis of polyphasic evidence, it is proposed that strain NO2 T (=KCTC 12755 T =LMG 23762 T ) represents the type strain of a novel species, Glaciecola agarilytica sp. nov.The genus Glaciecola accommodates aerobic, slightly halophilic bacteria and, at the time of writing, includes four species, Glaciecola punicea and Glaciecola pallidula (Bowman et al., 1998), Glaciecola mesophila (Romanenko et al., 2003) and Glaciecola polaris (Van Trappen et al., 2004). During screening, a novel agar-digesting bacterial strain, NO2 T , detected by the occurrence of pitting around colonies, was isolated from marine sediment of the East Sea, Korea, and selected for further characterization by a polyphasic approach. Strain NO2 T was isolated using a natural seawater agar medium, prepared using seawater of the East Sea. For solidification, 1.5 % (w/v) agarose was added to seawater before autoclaving. A sediment sample was placed in a sterile conical tube and serially diluted with filtersterilized (0.22 mm pore size, Millipore) natural seawater. An aliquot of each dilution was spread onto the agar medium and incubated at 17 u C for 4 weeks. Agar-digesting colonies were transferred onto new plates and subjected to an additional incubation for 2 days at 25 u C. Cultured strains were preserved at 270 uC as suspensions in marine broth (Difco) containing 20 % (w/v) glycerol.Bacterial genomic DNA was extracted using a commercial genomic DNA extraction kit (Bioneer). The 16S rRNA gene was amplified from chromosomal DNA using the universal bacterial primer set 9F and 1512R and the purified PCR products were sequenced by Solgent Co. Ltd (Daejeon, Korea) (Yoon et al., 1998). The full 16S rRNA gene sequences were compiled using SeqMan software (DNASTAR). 16S rRNA gene sequences of related taxa were obtained from the GenBank database. Sequence alignments were performed using the CLUSTAL_X program (Thompson et al., 1997) and gaps were edited in the BioEdit program (Hall, 1999). Evolutionary distances were calculated using the two-parameter model of Kimura (1983). Phylogene...

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