Burkholderia species are free-living bacteria with a versatile metabolic lifestyle. The genome of B. fungorum LB400 is predicted to encode three different pathways for formaldehyde oxidation: an NAD-linked, glutathione (GSH)-independent formaldehyde dehydrogenase; an NAD-linked, GSH-dependent formaldehyde oxidation system; and a tetrahydromethanopterin-methanofuran-dependent formaldehyde oxidation system. The other Burkholderia species for which genome sequences are available, B. mallei, B. pseudomallei, and B. cepacia, are predicted to contain only the first two of these pathways. The roles of the three putative formaldehyde oxidation pathways in B. fungorum LB400 have been assessed via knockout mutations in each of these pathways, as well as in all combinations of knockouts. The resulting mutants have the expected loss of enzyme activities and exhibit defects of varying degrees of severity during growth on choline, a formaldehyde-producing substrate. Our data suggest that all three pathways are involved in formaldehyde detoxification and are functionally redundant under the tested conditions.

In order to validate a gel free quantitative proteomics assay for the model methylotrophic bacterium Methylobacterium extorquens AM1, we examined the M. extorquens AM1 proteome under single carbon (methanol) and multi-carbon (succinate) growth, conditions that have been studied for decades and for which extensive corroborative data have been compiled. In total, 4,447 proteins from a database containing 7,556 putative ORFs from M. extorquens AM1 could be identified with two or more peptide sequences, corresponding to a qualitative proteome coverage of 58%. Statistically significant non-zero (log2 scale) differential abundance ratios of methanol/succinate could be detected for 317 proteins using summed ion intensity measurements and 585 proteins using spectral counting, at a q-value cut-off of 0.01, a measure of false discovery rate. The results were compared to recent microarray studies performed under equivalent chemostat conditions. The M. extorquens AM1 studies demonstrated the feasibility of scaling up the multidimensional capillary HPLC tandem mass spectrometry approach to a prokaryotic organism with a proteome more than three times the size of microbes we have investigated previously, while maintaining a high degree of proteome coverage and reliable quantitative abundance ratios.

A new bacterial isolate from a methylamine enrichment culture is described, representing a novel species of facultatively methylotrophic bacteria. The non-motile bacterium is Gram-negative, replicates by budding and does not form endospores. The isolate utilizes methylated amines, as well as a variety of monosaccharides, disaccharides, amino acids, organic acids, aromatic compounds and alcohols as substrates, but does not utilize methanol. Growth factors are not required, although yeast extract stimulates growth. The major components of the fatty acid profile are C 18 : 1 v7c, C 19 : 0 cyclo and C 16 : 0 . The dominant cellular phospholipids are phosphatidyl acid, phosphatidylcholine and phosphatidylethanolamine. The G+C content of the DNA is 65?7±0?3 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the novel isolate belongs to the a-Proteobacteria and is closely related to the only representative of the genus Labrys, Labrys monachus (97?4 % sequence similarity). However, the level of DNA-DNA relatedness with L. monachus is less than 3 %, justifying the placement of this isolate into a novel species of the genus Labrys. The name Labrys methylaminiphilus sp. nov. is proposed (type strain JLW10 T =ATCC BAA-1080 T =DSM 16812 T ).Methylotrophs are a group of bacteria capable of metabolizing compounds containing no carbon-carbon bonds as sole sources of carbon and energy. These bacteria are ubiquitous in the biosphere and have been isolated from a wide variety of natural habitats including plants, soils and freshwater and marine sediments (Anthony, 1982). Methylotrophs play an important role in biogeochemical cycling and possess a potential for use in bioremediation (Pol et al., 1994; De Marco et al., 2004). We are studying a specific habitat that is rich in methylotrophic activity: the sediment of Lake Washington at a depth of about 60 m (Kuivila et al., 1988;Costello & Lidstrom, 1999). Until recently, research at this site has focused primarily on methanotroph populations (Auman et al., 2000;Costello & Lidstrom, 1999) and no survey of broader methylotroph presence has been conducted. This study focused on enrichment, isolation and taxonomic description of methylamine-utilizing bacteria from Lake Washington sediment. One of these isolates, a novel facultative methylotroph, is described. Sediment samples were collected on 21 July 2003, off the RV Clifford Barnes from a 63 m-deep site in Lake Washington, Seattle, WA, USA (47 u 38?0759 N 122 u 15?9939 W) using a box core that allowed collection of undisturbed sediment. Sediment cores were taken to a depth of approximately 20 cm and subsectioned into layers approximately 1?5 cm thick. Samples were transported to the laboratory on ice and used immediately. One millilitre samples of the upper 1?0 cm of the sediment cores were inoculated into 250 ml flasks containing 50 ml 0?26 salts medium (Harder et al., 1973) supplemented with 0?01 % methylamine (w/v) and were incubated for 6-8 days at room temperature with shaking (125 r.p.m.). In subsequent enrichments, ...

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The anthelmintic agent methyl 5(6)-butyl-2-benzimidazolecarbamate (Parbendazole) was transformed to two of its animal metabolites, methyl 5(6)-(4-hydroxybutyl)-2-benzimidazolecarbamate and methyl 5(6)-3-(carboxypropyl)-2-benzimidazolecarbamate, by the filamentous fungus Cunninghamella bainieri ATCC 9244. The transformation pathway was shown to be through the 4-hydroxybutyl product to the 3-carboxypropyl product. The reaction favored accumulation of the latter product.