c Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (؎standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ؎ 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean. D imethylsulfoniopropionate (DMSP), the precursor of dimethylsulfide (DMS), is mainly produced by marine phytoplankton, marine macroalgae, and a few angiosperms in the ocean (1-3) and is an important carbon and sulfur source for marine bacteria (4). After DMSP has been released, it is mainly assimilated and degraded by marine bacteria (5, 6). Phytoplankton and their predators also degrade DMSP to a certain extent (7,8). Once incorporated into bacterial cells, DMSP is degraded via two major pathways: a demethylation pathway involving DMSP demethylase, encoded by dmdA (9), and a cleavage pathway involving several different ddd (DMSP-dependent DMS) (dddD, dddL, dddP, dddQ, dddY, and dddW) genes (10-15). dmdA, the first DMSP degradation gene identified, is the most widely distributed DMSP degradation gene. It was reported that approximately 60% of marine bacteria in the open ocean and coastal waters contain this gene (16). dmdA genes, which are found mainly in members of the SAR11, SAR116, Gammaproteobacteria, and Roseobacter clades (16-19), can be grouped into five clades and 14 subclades based on the genes' nucleotide sequences (16,20).In the cleavage pathway, bacteria transform DMSP to DMS. Aerosols formed from the oxidati...
A novel bacterium, strain Seoho-28T, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25–30 °C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order Solirubrobacterales , but sequence similarities to known species were less than 94.7 %. The genomic DNA G+C content of the strain Seoho-28T was 74.2 mol%. Genomic comparisons of strain Seoho-28T with families in the order Solirubrobacterales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8 %, respectively). Strain Seoho-28T contained C16 : 0-iso, C18 : 1 ω9c and C16 : 0 as major fatty acids and MK-7 (H4) as the major quinone. Strain Seoho-28T contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. Meso- and ll-diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28T represents a novel genus and species, Paraconexibacter algicola gen. nov., sp. nov., which belongs to a new family Paraconexibacteraceae in the order Solirubrobacterales and the class Thermoleophilia . The type strain is Seoho-28T (=KCTC 39791T=JCM 31881T).
A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8 T , was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8 T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53 T . The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C 15 : 1 G, iso-C 15 : 0 and iso-C 17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name et al., 2013). In this study, a novel bacterial strain assigned as SK-8 T was isolated from coastal surface seawater of Misaki, Japan and the taxonomic position was investigated using a polyphasic approach.Surface water was collected from a depth of 20 cm near the pier of Misaki Marine Biological Station, University of Tokyo (358 09.59 N 1398 36.59 E), Aburatsubo Inlet, Misaki, Kanagawa Prefecture, Japan. Aliquots (100 ml) of seawater were plated onto 1/10-strength ZoBell agar medium [0.5 g peptone, 0.1 g yeast extract, 15 g agar in 1 l of 80 % aged natural seawater (80 % seawater+20 % water, aged for at least one year)] and incubated at 20 8C for 4 days. Routine cultivation for subsequent characterizations were performed on half-strength marine agar 2216 (Difco) supplemented with 1.0 % NaCl (w/v) at 25 8C, hereby known as 1/2 MA. The isolate was maintained at 280 8C as a suspension in half-strength marine broth 2216 (Difco) supplemented with 1.0 % NaCl (w/v), containing glycerol (20 %, w/v). Cell morphology was examined according to Børsheim et al. (1990). After staining for 30 s with 2 % uranyl acetate, grids were examined at 675 000 magnification at an acceleration voltage of 80 kV using a JEM-1400EX transmission electron microscope (JEOL); at least 50 fields were selected for examination. Gliding motility was observed under light microscopy (BX60; Olympus). Gram staining was performed according to instructions provided in the Gram Stain kit (BD). Temperature (4 8C, 10-30 8C at 5 8C intervals, 37 8C and 45 8C) and salt tolerance were determined using 1/2 MA with different concentrations of NaCl (0-1 % at 0.05 % intervals, 1-8 % at 1 % intervals and 10-15 % at 5 % intervals, w/v) and Abbreviations: ML, maximum-likelihood; MP, maximum-parsimony; NJ, neighbour-joining.3Present address:
Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase ( dddD and dddP ) and DMSP demethylase ( dmdA ) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.
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