Isolation of Methylophaga spp. from Marine Dimethylsulfide-Degrading Enrichment Cultures and Identification of Polypeptides Induced during Growth on Dimethylsulfide

Abstract

Dimethylsulfide (DMS)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic Emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. Bacterial populations from a broad phylogenetic range were identified in the mixed DMS-degrading enrichment cultures by denaturing gradient gel electrophoresis (DGGE). Sequences of dominant DGGE bands were similar to those of members of the genera Methylophaga and Alcanivorax. Several closely related Methylophaga strains were obtained that were able to grow on DMS as the carbon and energy source. Roseobacter-related populations were detected in some of the enrichment cultures; however, none of the Roseobacter group isolates that were tested were able to grow on DMS. Oxidation of DMS by Methylophaga sp. strain DMS010 was not affected by addition of the inhibitor chloroform or methyl tert-butyl ether, suggesting that DMS metabolism may occur by a route different from those described for Thiobacillus species and other unidentified marine isolates. Addition of DMS and methanethiol to whole-cell suspensions of strain DMS010 induced oxygen uptake when strain DMS010 was grown on DMS but not in cells grown on methanol. The apparent K m s of strain DMS010 for DMS and for methanethiol were 2.1 and 4.6 M, respectively, when grown on DMS. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the biomass of strain DMS010 and analysis of peptide bands by mass spectrometry techniques and N-terminal sequencing provided the first insight into the identity of polypeptides induced during growth on DMS. These included XoxF, a homolog of the large subunit of methanol dehydrogenase for which a biological role has not been identified previously.Dimethylsulfide (DMS) is a volatile organosulfur compound that is emitted from the ocean into the atmosphere, where it represents the most abundant organic sulfur gas (31). Atmospheric oxidation of DMS generates sulfur aerosols that backscatter heat radiation, promote cloud formation, and as a result, cause negative radiative forcing (2). It has been suggested that the effects of DMS-derived aerosols provide a global climate feedback loop that could result in climate cooling (7). DMS is produced mainly by enzymatic cleavage of dimethylsulfoniopropionate (DMSP), an algal metabolite which may have a role in osmoregulation (54) or may constitute an antioxidant system in microalgae (46). Sinks of DMS include photochemical degradation to dimethyl sulfoxide (DMSO) (19), bacterial oxidation of DMS to DMSO (55), and its utilization as a sulfur source by microorganisms (15, 27). Microbial degradation of DMS, however, appears to be the main sink for DMS in the marine environment, often leading to the oxidation of 90% or more of DMS in the ocean surface (3, 26). Bacterial degradation of DMS therefore significantly reduces the amount of DMS in the mixed surface layer that is available for sea-to-air transfer.Growth on DMS as a carbon source has been described for a range of prokaryotes, including ana...

Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences

“…These studies, however, did not assay for the presence of the nitrate reductases narG or napA. No such genes were found in the only available Methylophaga genome sequence from M. thiooxidans DMS010 (GenBank accession number ABXT00000000), and there is no indication as to whether M. thiooxidans could reduce nitrate into nitrite (Schäfer, 2007). Finally, narG or napA, or any other denitrification genes were not detected in M. alcalica or M. marina with the primers used in our study.…”

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling

“…Gentamicin (10 mg ml À 1 ) was added to maintain mutant strains Dtmm::Gm and Dtdm::Gm (Lidbury et al, 2014). For all experiments R. pomeroyi (wild type and mutants) was grown in marine ammonium mineral salts (MAMS) medium (Schäfer, 2007) Figure 1 Proposed model for methylated amine catabolism in the marine bacterium Ruegeria pomeroyi DSS-3. Text in brackets denotes the locus tag of the corresponding gene in R. pomeroyi.…”

“…Text in brackets denotes the locus tag of the corresponding gene in R. pomeroyi. CH 2 ¼ H 4 F, 5,10-methylene tetrahydrofolate; CO 2 , carbon dioxide; DMA, dimethylamine; Dmm, dimethylamine monooxygenase; GMA, gamma-glutamylmethylamide; GmaS, gamma-glutamylmethylamide synthetase; MgdABCD, N-methylglutamate dehydrogenase; MgsABC, N-methylglutamate synthase; MMA, monomethylamine; NMG, N-methylglutamate; TMA, trimethylamine; TMAO, trimethylamine N-oxide; TmoXWV, ATP-dependent TMAO transporter (Lidbury et al, 2014). was modified from Schäfer (2007) (Schäfer, 2007). Vitamins were prepared as described previously (Chen, 2012).…”

Climate relevant trace gases (N2O and CH4) in the Eurasian Basin (Arctic Ocean)

“…Interestingly, several surface stations (ST 4, 5, 8 and 1) displayed CH 4 saturation levels as high as 650%. Although it remains unclear at present how CH 4 is formed in sea ice, it is possible that CH 4 could be produced via the methylotrophic pathway mediated by methylated compounds (Schäfer, 2007;Sun et al, 2011). One candidate for methylated compounds is DMSP and/or DMS, as indicated in the surface water by Damm et al (2010) and Florez-Leiva et al (2013).…”