Plasmids are important “vehicles” for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

bTreatment of Pseudomonas aeruginosa PAO1 flow biofilms with a D-amino acid mixture caused significant reductions in cell biomass by 75% and cell viability by 71%. No biofilm disassembly occurred, and matrix production increased by 30%, thereby providing a thick protective cover for remaining viable or persister cells.T he multifactorial tolerance of surface-attached complex microbial communities known as biofilms apparently renders conventional treatment strategies ineffective. Biofilms persist and are hard to eradicate because of mechanisms that involve restricted penetration of antimicrobials, differential physiological activity, presence of phenotypic variants and persisters, efflux systems, and enhanced repair systems (1, 2). Unless anti-biofilm strategies are able to block these tolerance mechanisms, biofilms will continue to exert detrimental effects, especially in the hospital and industrial settings.Since D-amino acids are synthesized and released by many bacterial species, including the opportunistic human pathogen Pseudomonas aeruginosa, and have been shown to lack significant toxicity, the idea of using them to combat biofilm-associated infections is highly attractive (3). Recent findings reveal that D-amino acids regulate bacterial cell wall remodeling in stationary phase and cause biofilm dispersal in aging bacterial communities (3, 4). Incorporation of a D-amino acid mixture (D-leucine, D-methionine, D-tryptophan, and D-tyrosine) into the peptidoglycan has also been reported to induce biofilm disassembly in Bacillus subtilis (5). In standing cultures, exogenous D-amino acids prevent biofilm formation in some bacterial strains (5). To date, there are no reports on the susceptibility of flow chamber-grown biofilms to D-amino acids. Flow-chamber biofilm systems not only simulate more physiologically relevant biofilm environments but also allow nondestructive, real-time, high-resolution characterization and quantification of live biofilm structures and development. Hence, in the present study, we investigated whether a Damino acid mixture could affect P. aeruginosa PAO1 biofilms grown under flow conditions using a multichannel microdevice flow system. With the use of confocal laser scanning microscopy (CLSM) and COMSTAT (6), we determined the effect of exogenous D-amino acid mixture on the structure, development, and viability of P. aeruginosa PAO1 flow biofilms.Pseudomonas aeruginosa strain PAO1 with the green fluorescent protein (GFP)-expressing plasmid pMRP9-1 (7) was used to enable detection of cells by CLSM. Cultures for inoculation of the microdevice were prepared in Luria-Bertani (LB) medium supplemented with 300 g ml Ϫ1 carbenicillin for plasmid maintenance as described previously (8) but at 30°C. Biofilms were grown in the microdevice at 30°C supplied with 1/3-diluted LB medium at an 11-ml h Ϫ1 flow rate. The multichannel microdevice flow system was assembled and prepared as described previously (8). In brief, this autoclavable, once-through, continuous-culture system consists of a stainless...

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Ammonia inhibition of methane fermentation is one of the leading causes of failure of anaerobic digestion reactors. In a batch anaerobic digestion reactor with 429 mM NH3-N/L of ammonia, the addition of 25 mM phosphate resulted in an increase in methane production rate. Similar results were obtained with the addition of disodium phosphate in continuous anaerobic digestion using an upflow anaerobic sludge blanket (UASB) reactor. While methane content and production rate decreased in the presence of more than 143 mM NH3-N/L of ammonium chloride in UASB, the addition of 5 mM disodium phosphate suppressed ammonia inhibition at 214 mM NH3-N/L of ammonium chloride. The addition prevented acetate/propionate accumulation, which might be one of the effects of the phosphate on the ammonia inhibition. The effects on the microbial community in the UASB reactor was also assessed, which was composed of Bacteria involved in hydrolysis, acidogenesis, acetogenesis, and dehydrogenation, as well as Archaea carrying out methanogenesis. The change in the microbial community was observed by ammonia inhibition and the addition of phosphate. The change indicates that the suppression of ammonia inhibition by disodium phosphate addition could stimulate the activity of methanogens, reduce shift in bacterial community, and enhance hydrogen-producing bacteria. The addition of phosphate will be an important treatment for future studies of methane fermentation.

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