Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.     

Microbial Isotopic Fractionation of Perchlorate Chlorine

Perchlorate contamination can be microbially respired to innocuous chloride and thus can be treated effectively. However, monitoring a bioremediative strategy is often difficult due to the complexities of environmental samples. Here we demonstrate that microbial respiration of perchlorate results in a significant fractionation (~−15‰) of the chlorine stable isotope composition of perchlorate. This can be used to quantify the extent of biotic degradation and to separate biotic from abiotic attenuation of this contaminant.     

Factors That Influence Microbial Contamination of Fluids Associated with Hemodialysis Machines

Studies were conducted on the microbiological quality of fluids associated with different types of dialysis systems located in six dialysis centers and 14 homes. Included were (i) single-pass systems employing either parallel flow (Kiil or Gambro) or capillary cartridge dialyzers and (ii) recirculating single-pass and batch recirculating systems using coil dialyzers. Microbiological assays were performed on the water used to prepare dialysis fluid, the concentrated dialysate, and either pre- and postdialyzer dialysate (single-pass systems) or the dialysate contained in storage reservoirs and recirculating cannisters (recirculating systems). The levels of microbial contamination consisting of gram-negative bacteria were directly related to the type of dialysis system, method of water treatment, distribution system, and in some instances, the type of dialyzer. Recirculating single-pass and batch recirculating systems consistently contained significantly higher levels of contamination than single-pass systems. These results were directly related to the design of recirculating systems which permits carbon- and nitrogen-containing waste products dialyzed from the patient to accumulate, be used as nutrients by microorganisms, and subsequently allow for 2- to 4-log increases in contamination levels during a dialysis treatment. In contrast, levels of contamination in single-pass machines were related more to the quality of the water used to prepare dialysis fluid and the adequacy of cleaning and disinfection procedures than to the design of the system.     

Intestinal Microbial Ecology and Environmental Factors Affecting Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.     

Abiotic Environmental Factors Affecting the Formation of Microbial Biofilms

Biofilms are aform of existence of bacteria in the environment, due to which bacteria can expand the boundaries of their habitats during contamination of different surfaces under diverse conditions. The most important environmental factors affecting biofilms are discussed. These factors include temperature, osmolarity, the concentration of ferrous iron ions, the availability of nutrients, the quality of materials on which biofilms are formed, and light and theambient acidity.     

Bacterial Perchlorate Reduction in Simulated Reverse Osmosis Rejectate

Reverse osmosis (RO) is capable of removing perchlorate (ClO₄ ^?) from contaminated groundwater and producing potable effluent; however, RO does not destroy ClO₄ ^?, but collects it in a concentrated waste stream (rejectate) that must be treated or disposed of appropriately. A packed bed bioreactor, inoculated with the pure culture perclace, was tested for its ability to remove ClO₄ ^? from a simulated RO rejectate. Perchlorate concentrations were lowered from 5 mg/L to <0.004 mg/L with a residence time of 0.8 h. In addition, this system removed 98% of ClO₄ ^? from a twice-concentrated rejectate with an influent ClO₄ ^? concentration of 8 mg/L and a residence time of 2.0 h. In both experiments, nitrate (NO₃ ^?) was removed simultaneously with ClO₄ ^? from an initial concentration as high as 900 mg/L NO₃ to below 4 mg/L. Despite the efficiency of ClO₄ ^? removal, the system suffered from clogging due to the high total dissolved solids (TDS) of the twice-concentrated rejectate.     

Factors That Control the Chemistry of the LOV Domain Photocycle

Algae, plants, bacteria and fungi contain Light-Oxygen-Voltage (LOV) domains that function as blue light sensors to control cellular responses to light. All LOV domains contain a bound flavin chromophore that is reduced upon photon absorption and forms a reversible, metastable covalent bond with a nearby cysteine residue. In Avena sativa LOV2 (AsLOV2), the photocycle is accompanied by an allosteric conformational change that activates the attached phototropin kinase in the full-length protein. Both the conformational change and formation of the cysteinyl-flavin adduct are stabilized by the reduction of the N5 atom in the flavin’s isoalloxazine ring. In this study, we perform a mutational analysis to investigate the requirements for LOV2 to photocycle. We mutated all the residues that interact with the chromophore isoalloxazine ring to inert functional groups but none could fully inhibit the photocycle except those to the active-site cysteine. However, electronegative side chains in the vicinity of the chromophore accelerate the N5 deprotonation and the return to the dark state. Mutations to the N414 and Q513 residues identify a potential water gate and H₂O coordination sites. These residues affect the electronic nature of the chromophore and photocycle time by helping catalyze the N5 reduction leading to the completion of the photocycle. In addition, we demonstrate that dehydration leads to drastically slower photocycle times. Finally, to investigate the requirements of an active-site cysteine for photocycling, we moved the nearby cysteine to alternative locations and found that some variants can still photocycle. We propose a new model of the LOV domain photocycle that involves all of these components.     

Thermophilic Microbial Metal Reduction

Thermophilic microorganisms can reduce Fe(III), Mn(IV), Cr(VI), U(VI), Tc(VII), Co(III), Mo(VI), Au(I, III), and Hg(II). Ferric iron and Mn(IV) can be used as electron acceptors during growth; the physiological role of the reduction of the other metals is unclear. The process of microbial dissimilatory reduction of Fe(III) is the most thoroughly studied. Iron-reducing prokaryotes have been found in virtually all of the recognized types of terrestrial ecosystems, from hot continental springs to geothermally heated subsurface sediments. Thermophilic iron reducers do not belong to a phylogenetically homogenous group and include representatives of many bacterial and archaeal taxa. Iron reducing thermophiles can couple Fe(III) reduction with oxidation of a wide spectrum of organic and inorganic compounds. In the thermophilic microbial community, they can fulfil both degradative and productive functions. Thermophilic prokaryotes probably carried out global reduction of metals on Earth in ancient times, and, at the same time, they are promising candidates for use in modern biotechnological processes.     

Use of Stochastic Models To Assess the Effect of Environmental Factors on Microbial Growth

We present a novel application of a stochastic ecological model to the study and analysis of microbial growth dynamics as influenced by environmental conditions in an extensive experimental data set. The model proved to be useful in bridging the gap between theoretical ideas in ecology and an applied problem in microbiology. The data consisted of recorded growth curves of Escherichia coli grown in triplicate in a base medium with all 32 possible combinations of five supplements: glucose, NH₄Cl, HCl, EDTA, and NaCl. The potential complexity of 2⁵ experimental treatments and their effects was reduced to 2² as just the metal chelator EDTA, the presumed osmotic pressure imposed by NaCl, and the interaction between these two factors were enough to explain the variability seen in the data. The statistical analysis showed that the positive and negative effects of the five chemical supplements and their combinations were directly translated into an increase or decrease in time required to attain stationary phase and the population size at which the stationary phase started. The stochastic ecological model proved to be useful, as it effectively explained and summarized the uncertainty seen in the recorded growth curves. Our findings have broad implications for both basic and applied research and illustrate how stochastic mathematical modeling coupled with rigorous statistical methods can be of great assistance in understanding basic processes in microbial ecology.     

Biological Control of Hog Waste Odor through Stimulated Microbial Fe(III) Reduction

Odor control and disposal of swine waste have inhibited expansion of swine production facilities throughout the United States. Swine waste odor is associated primarily with high concentrations of volatile fatty acids (VFAs). Here, we demonstrate that stimulated Fe(III) reduction in hog manure can rapidly remove the malodorous compounds and enhance methane production by 200%. As part of these studies, we enumerated the indigenous Fe(III)-reducing population in swine waste and identified members of the family Geobacteraceae as the dominant species. These organisms were present at concentrations as high as 2 × 10⁵ cells g⁻¹. Several pure cultures of Fe(III) reducers, including Geobacter metallireducens, Geobacter humireducens, Geobacter sulfurreducens, Geobacter grbiciae, Geothrix fermentans, and Geovibrio ferrireducens, readily degraded some or all of the malodorous VFAs found in swine manure. In contrast, Shewanella algae did not degrade any of these compounds. We isolated an Fe(III) reducer, Geobacter strain NU, from materials collected from primary swine waste lagoons. This organism degraded all of the malodorous VFAs tested and readily grew in swine waste amended with Fe(III). When raw waste amended with Fe(III) was inoculated with strain NU, the VFA content rapidly decreased, corresponding with an almost complete removal of the odor. In contrast, the raw waste without Fe(III) or strain NU showed a marked increase in VFA content and a rapid pH drop. This study showed that Fe(III) supplementation combined with appropriate bioaugmentation provides a simple, cost-effective approach to deodorize and treat swine waste, removing a significant impediment to the expansion of pork production facilities.     

Environmental Factors Associated with the Eukaryotic Microbial Diversity of Ulleungdo Volcanic Island in South Korea

Microbiology - Ulleungdo is a volcanic island with an oceanic climate seasonally affected by warm and cold currents. The freshwater ecosystems of Ulleungdo Island act as an ecological indicator...     

Distribution of Microbial Arsenic Reduction,Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations

The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.     

Effects of Environmental Factors on Microbial Populations in Brackish Waters off the Southern Coast of Finland

The roles played by environmental factors in seasonal changes in microbial populations were investigated in the Tvärminne area, off the southern coast of Finland. Surface-layer samples were collected at 1- or 2-week intervals in 1976-78, and 14 microbiological and 10 environmental parameters were determined. Stepwise multiple regression analysis was used to explain seasonal variation in the microbiological parameters. Separate analyses were made of the data from the open-water and ice-cover periods. In analyses of data from both periods, the environmental factors included accounted for a significant proportion of the variation in the parameters for community respiration (90%) and bacterial spores (80%), and a smaller proportion (60 to 65%) of the variation in total counts of bacteria and plate counts of psychrophiles and yeasts. Lower values (40 to 55%) were obtained for the variation in the other microbiological parameters. The environmental factors with maximal contributions were organic matter, water temperature, chlorophyll a, and salinity, but rainfall and winds also explained part of the variation in some microbiological parameters. In the winter analysis the results differed from those obtained for the other seasons, the variation being governed by parameters indicating freshwater outflows, namely, humic matter, salinity, water temperature (positive regression coefficient), and rainfall (negative regression coefficient).