Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria

Comparative 16S rRNA sequencing was used to evaluate phylogenetic relationships among selected strains of ammonia- and nitrite-oxidizing bacteria. All characterized strains were shown to be affiliated with the proteobacteria. The study extended recent 16S rRNA-based studies of phylogenetic diversity among nitrifiers by the comparison of eight strains of the genus Nitrobacter and representatives of the genera Nitrospina and Nitrospina. The later genera were shown to be affiliated with the delta subdivision of the proteobacteria but did not share a specific relationship to each other or to other members of the delta subdivision. All characterized Nitrobacter strains constituted a closely related assemblage within the alpha subdivision of the proteobacteria. As previously observed, all ammonia- oxidizing genera except Nitrosococcus oceanus constitute a monophyletic assemblage within the beta subdivision of the proteobacteria. Errors in the 16S rRNA sequences for two strains previously deposited in the databases by other investigators (Nitrosolobus multiformis C-71 and Nitrospira briensis C- 128) were corrected. Consideration of physiology and phylogenetic distribution suggested that nitrite-oxidizing bacteria of the alpha and gamma subdivisions are derived from immediate photosynthetic ancestry. Each nitrifier retains the general structural features of the specific ancestor's photosynthetic membrane complex. Thus, the nitrifiers, as a group, apparently are not derived from an ancestral nitrifying phenotype

Erosion probability for biofilm modeling: analysis of trends

This study presents the strengths and weaknesses of a biofilm erosion probability algorithm that can be used in cellular automaton and individual-based biofilm simulation models. The erosion probability is calculated using data on localized biofilm mechanical properties, expressed through the composite biofilm Young's modulus-a measure of biofilm strength that varies in time and space-and on fluid hydrodynamic shear stress. Analysis of trends shows that biofilm detachment is the process that results from the competition between biofilm strength and hydrodynamic shear stress exerted on it by the fluid, with hydrodynamics being more important when biofilm strength is low and vice versa. From the modeling sample analyzed in this study, it is evident that for biofilms with cluster and mushroom formations, erosion probabilities are lower in the crevices formed between two clusters-where substrate is depleted-and higher at the top of the clusters where there is fresh biomass growth. When compared to other detachment methodologies extensively used by biofilm modeling researchers, such as the detachment speed that is a function of the square of the distance to the solid substratum, it is proved that the probability of erosion algorithm would give similar results

Subsurface interactions of actinide species and microorganisms : implications for the bioremediation of actinide-organic mixtures.

By reviewing how microorganisms interact with actinides in subsurface environments, we assess how bioremediation controls the fate of actinides. Actinides often are co-contaminants with strong organic chelators, chlorinated solvents, and fuel hydrocarbons. Bioremediation can immobilize the actinides, biodegrade the co-contaminants, or both. Actinides at the IV oxidation state are the least soluble, and microorganisms accelerate precipitation by altering the actinide's oxidation state or its speciation. We describe how microorganisms directly oxidize or reduce actinides and how microbiological reactions that biodegrade strong organic chelators, alter the pH, and consume or produce precipitating anions strongly affect actinide speciation and, therefore, mobility. We explain why inhibition caused by chemical or radiolytic toxicities uniquely affects microbial reactions. Due to the complex interactions of the microbiological and chemical phenomena, mathematical modeling is an essential tool for research on and application of bioremediation involving co-contamination with actinides. We describe the development of mathematical models that link microbiological and geochemical reactions. Throughout, we identify the key research needs

Radiotoxicity of neptunium(V) and neptunium(V)-nitrilotriacetic acid (NTA) complexes towards Chelatobacter heintzii

The objective of this work was to investigate the toxicity mechanisms of neptunium and the neptunium-NTA complex towards Chelatobacter heintzii. The results show that metal toxicity of aquo NpO{sub 2}{sup +} may significantly limit growth of Cl heintzii at free metal ion concentrations greater than {approx} 10{sup {minus}5} M. However, neptunium concentrations {ge} 10{sup {minus}4} M do not cause measurable radiotoxicity effects in C. heintzii when present in the form of a neptunium-NTA complex or colloidal/precipitated neptunium-phosphate. The neptunium-NTA complex, which is stable under aerobic conditions, is destabilized by microbial degradation of NTA. When phosphate was present, degradation of NTA led to the precipitation of a neptunium-phosphate phase

Mathematical modeling of the effects of aerobic and anaerobic chelate bioegradation on actinide speciation.

Biodegradation of natural and anthropogenic chelating agents directly and indirectly affects the speciation, and, hence, the mobility of actinides in subsurface environments. We combined mathematical modeling with laboratory experimentation to investigate the effects of aerobic and anaerobic chelate biodegradation on actinide [Np(IV/V), Pu(IV)] speciation. Under aerobic conditions, nitrilotriacetic acid (NTA) biodegradation rates were strongly influenced by the actinide concentration. Actinide-chelate complexation reduced the relative abundance of available growth substrate in solution and actinide species present or released during chelate degradation were toxic to the organisms. Aerobic bio-utilization of the chelates as electron-donor substrates directly affected actinide speciation by releasing the radionuclides from complexed form into solution, where their fate was controlled by inorganic ligands in the system. Actinide speciation was also indirectly affected by pH changes caused by organic biodegradation. The two concurrent processes of organic biodegradation and actinide aqueous chemistry were accurately linked and described using CCBATCH, a computer model developed at Northwestern University to investigate the dynamics of coupled biological and chemical reactions in mixed waste subsurface environments. CCBATCH was then used to simulate the fate of Np during anaerobic citrate biodegradation. The modeling studies suggested that, under some conditions, chelate degradation can increase Np(IV) solubility due to carbonate complexation in closed aqueous systems