BackgroundThe genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.ResultsThe genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.ConclusionsD. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.

Background: Alicyclobacillus acidoterrestris is a key spoilage causing bacterium commonly found in fruit juices and purees. Commercial real-time PCR based assays to detect this organism are available, but reportedly require 48 hours of enrichment for detection. The underlying hypothesis of this study was that fruit juice and puree characteristics influence the enrichment requirements of this organism, and that in some matrices, the organism can be detected within 24 hours even when present at low initial contamination. Thirteen different store-purchased fruit juice and purees were inoculated with 10 CFU/ml of Alicyclobacillus acidoterrestris. The inoculated samples were enriched for 24 and 48 h. Aliquots from the un-enriched, 24 hour, and 48 hour enriched samples were taken, total community DNA extracted, and the real-time PCR assay performed using commercially available kits. Results: A. acidoterrestris was detected by real-time PCR within 24 h of enrichment in most matrices (except ketchup and orange concentrate) even from a low starting concentration (10 CFU/ml). Juice and puree samples with high soluble solids contents (i.e. Brix values) required longer incubation periods for lower A. acidoterrestris Ct values.