Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation

Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination

In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ( approximately 50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying gamma- and beta-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa

Polymicrobial bronchopulmonary infections in cystic fibrosis (CF) cause progressive lung damage and death. Although the arrival of Pseudomonas aeruginosa often heralds a more rapid rate of pulmonary decline, there is significant inter-individual variation in the rate of decline, the causes of which remain poorly understood. By coupling culture-independent methods with ecological analyses, we discovered correlations between bacterial community profiles and clinical disease markers in respiratory tracts of 45 children with CF. Bacterial community complexity was inversely correlated with patient age, presence of P. aeruginosa and antibiotic exposure, and was related to CF genotype. Strikingly, bacterial communities lacking P. aeruginosa were much more similar to each other than were those containing P. aeruginosa, regardless of antibiotic exposure. This suggests that community composition might be a better predictor of disease progression than the presence of P. aeruginosa alone and deserves further study.

Developmental microbial ecology of the crop of the folivorous hoatzin

The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adult-fed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with <97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with approximately 1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.

Target amplification for broad spectrum microbial diagnostics and detection

Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.

Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community

Development of cellulosic biofuels from non-food crops is currently an area of intense research interest. Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic composting in a bioreactor to select for a switchgrass-adapted community and to facilitate targeted discovery of glycoside hydrolases. Small-subunit (SSU) rRNA-based community profiles revealed that the microbial community changed dramatically between the initial and switchgrass-adapted compost (SAC) with some bacterial populations being enriched over 20-fold. We obtained 225 Mbp of 454-titanium pyrosequence data from the SAC community and conservatively identified 800 genes encoding glycoside hydrolase domains that were biased toward depolymerizing grass cell wall components. Of these, approximately 10% were putative cellulases mostly belonging to families GH5 and GH9. We synthesized two SAC GH9 genes with codon optimization for heterologous expression in Escherichia coli and observed activity for one on carboxymethyl cellulose. The active GH9 enzyme has a temperature optimum of 50 degrees C and pH range of 5.5 to 8 consistent with the composting conditions applied. We demonstrate that microbial communities adapt to switchgrass decomposition using simulated composting condition and that full-length genes can be identified from complex metagenomic sequence data, synthesized and expressed resulting in active enzyme.

Bacterial community succession and chemical profiles of subtidal biofilms in relation to larval settlement of the polychaete Hydroides elegans

Earlier studies have shown that biofilms can mediate the larval settlement of the polychaete Hydroides elegans and that changes in the bacterial community structure and density of biofilms often alter the larval settlement response. However, the chemical cues that mediate this response remain unknown. In this study, both successional changes in the bacterial community structure and the chemical profiles of subtidal biofilms are described and related to the larval settlement response. Multispecies biofilms were developed on polystyrene Petri dishes and granite rock in the subtidal zone over a period of 20 days. The effects of the substratum and age on the bacterial community structure and chemical profiles of the biofilms were evaluated with two molecular methods (microarray (PhyloChip) and denaturing gradient gel electrophoresis) and with gas chromatography-mass spectrometry, respectively. Both age and substratum altered the bacterial community structures and chemical profiles of the biofilms. Age had a greater effect in shaping the bacterial community structure than did the substratum. In contrast, the type of substratum more strongly affected the chemical profile. Extracts of biofilms of different ages, which developed on different substrata, were tested for the settlement of H. elegans larvae. The extracts induced larval settlement in a biofilm-age-dependent manner, and extracts originating from different substrata of the same age showed no differences in larval settlement. Our results suggest that the larval settlement response cannot be predicted by the overall chemical composition of the biofilm alone.

Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome

Colonization of the infant gut by microorganisms over the first year of life is crucial for development of a balanced immune response. Early alterations in the gastrointestinal microbiota of neonates has been linked with subsequent development of asthma and atopy in older children. Here we describe high-resolution culture-independent analysis of stool samples from 6-month old infants fed daily supplements of Lactobacillus casei subsp. Rhamnosus (LGG) or placebo in a double-blind, randomized Trial of Infant Probiotic Supplementation (TIPS). Bacterial community composition was examined using a high-density microarray, the 16S rRNA PhyloChip, and the microbial assemblages of infants with either high or low LGG abundance were compared. Communities with high abundance of LGG exhibited promotion of phylogenetically clustered taxa including a number of other known probiotic species, and were significantly more even in their distribution of community members. Ecologically, these aspects are characteristic of communities that are more resistant to perturbation and outgrowth of pathogens. PhyloChip analysis also permitted identification of taxa negatively correlated with LGG abundance that have previously been associated with atopy, as well as those positively correlated that may prove useful alternative targets for investigation as alternative probiotic species. From these findings we hypothesize that a key mechanism for the protective effect of LGG supplementation on subsequent development of allergic disease is through promotion of a stable, even, and functionally redundant infant gastrointestinal community.

Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library

Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.

Uranium transformations in static microcosms

Elucidation of complex biogeochemical processes and their effects on speciation of U in the subsurface is critical for developing remediation strategies with an understanding of stability. We have developed static microcosms that are similar to bioreduction process studies in situ under laminar flow conditions or in sediment pores. Uranium L(3)-edge X-ray absorption near-edge spectroscopy analysis with depth in the microcosms indicated that transformation of U(VI) to U(IV) occurred by at least two distinct processes. Extended X-ray absorption fine structure (EXAFS) analysis indicated that initial U(VI) species associated with C- and P-containing ligands were transformed to U(IV) in the form of uraninite and U associated with Fe-bound ligands. Microbial community analysis identified putative Fe(III) and sulfate reducers at two different depths in the microcosms. The slow reduction of U(VI) to U(IV) may contribute the stability of U(IV) within microcosms at 11 months after a decrease in bioreducing conditions due to limited electron donors.

Impact of biostimulated redox processes on metal dynamics in an iron-rich creek soil of a former uranium mining area

Understanding the dynamics of metals and radionuclides in soil environments is necessary for evaluating risks to pristine sites. An iron-rich creek soil of a former uranium-mining district (Ronneburg, Germany) showed high porewater concentrations of heavy metals and radionuclides. Thus, this study aims to (i) evaluate metal dynamics during terminal electron accepting processes (TEAPs) and (ii) characterize active microbial populations in biostimulated soil microcosms using a stable isotope probing (SIP) approach. In biostimulated soil slurries, concentrations of soluble Co, Ni, Zn, As, and unexpectedly U increased during Fe(III)-reduction. This suggests that there was a release of sorbed metals and As during reductive dissolution of Fe(III)-oxides. Subsequent sulfate-reduction was concurrent with a decrease of U, Co, Ni, and Zn concentrations. The relative contribution of U(IV) in the solid phase changed from 18.5 to 88.7% after incubation. The active Fe(III)-reducing population was dominated by delta-Proteobacteria (Geobacter) in (13)C-ethanol amended microcosms. A more diverse community was present in (13)C-lactate amended microcosms including taxa related to Acidobacteria, Firmicutes, delta-Proteobacteria, and beta-Proteobacteria. Our results suggested that biostimulated Fe(III)-reducing communities facilitated the release of metals including U to groundwater which is in contrast to other studies.

Influence of trace erythromycin and eryhthromycin-H2O on carbon and nutrients removal and on resistance selection in sequencing batch reactors (SBRs)

Three sequencing batch reactors (SBRs) were operated in parallel to study the effects of trace erythromycin (ERY) and ERY-H₂O on the treatment of a synthetic wastewater. Through monitoring (1) daily effluents and (2) concentrations of nitrogen (N) and phosphorous (P) in certain batch cycles of the three reactors operated from transient to steady states, the removal of carbon, N, and P was affected negligibly by ERY (100 µg/L) or ERY-H₂O (50 µg/L) when compared with the control reactor. However, through analyzing microbial communities of the three steady state SBRs on high-density microarrays (PhyloChip), ERY, and ERY-H₂O had pronounced effects on the community composition of bacteria related to N and P removal, leading to diversity loss and abundance change. The above observations indicated that resistant bacteria were selected upon exposure to ERY or ERY-H₂O. Short-term batch experiments further proved the resistance and demonstrated that ammonium oxidation (56–95%) was inhibited more significantly than nitrite oxidation (18–61%) in the presence of ERY (100, 400, or 800 µg/L). Therefore, the presence of ERY or ERY-H₂O (at µg/L levels) shifted the microbial community and selected resistant bacteria, which may account for the negligible influence of the antibiotic ERY or its derivative ERY-H₂O (at µg/L levels) on carbon, N, and P removal in the SBRs.

Structural similarities between biogenic uraninites produced by phylogenetically and metabolically diverse bacteria

While the product of microbial uranium reduction is often reported to be "UO(2)", a comprehensive characterization including stoichiometry and unit cell determination is available for only one Shewanella species. Here, we compare the products of batch uranyl reduction by a collection of dissimilatory metal- and sulfate-reducing bacteria of the genera Shewanella, Geobacter, Anaeromyxobacter, and Desulfovibrio under similar laboratory conditions. Our results demonstrate that U(VI) bioreduction by this assortment of commonly studied, environmentally relevant bacteria leads to the precipitation of uraninite with an approximate composition of UO(2.0), regardless of phylogenetic or metabolic diversity. Coupled analyses, including electron microscopy, X-ray absorption spectroscopy, and powder diffraction, confirm that structurally and chemically analogous uraninite solids are produced. These biogenic uraninites have particle diameters of about 2-3 nm and lattice constants consistent with UO(2.0) and exhibit a high degree of intermediate-range order. Results indicate that phylogenetic and metabolic variability within delta- and gamma-proteobacteria has little effect on biouraninite structure or crystal size under the investigated conditions.

Induction of intestinal Th17 cells by segmented filamentous bacteria

The gastrointestinal tract of mammals is inhabited by hundreds of distinct species of commensal microorganisms that exist in a mutualistic relationship with the host. How commensal microbiota influence the host immune system is poorly understood. We show here that colonization of the small intestine of mice with a single commensal microbe, segmented filamentous bacterium (SFB), is sufficient to induce the appearance of CD4(+) T helper cells that produce IL-17 and IL-22 (Th17 cells) in the lamina propria. SFB adhere tightly to the surface of epithelial cells in the terminal ileum of mice with Th17 cells but are absent from mice that have few Th17 cells. Colonization with SFB was correlated with increased expression of genes associated with inflammation and antimicrobial defenses and resulted in enhanced resistance to the intestinal pathogen Citrobacter rodentium. Thus, manipulation of this commensal-regulated pathway may provide new opportunities for enhancing mucosal immunity and treating autoimmune disease.

Evidence for nitrogen fixation by "Dehalococcoides ethenogenes" strain 195

Genome annotation of the chlorinated ethene-respiring "Dehalococcoides ethenogenes" strain 195 indicated the presence of a complete nitrogenase operon. Here, results from long-term growth experiments, gene expression, and (15)N(2)-isotope measurements confirm that strain 195 is capable of fixing atmospheric dinitrogen when a defined fixed-nitrogen source such as ammonium is unavailable.

Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods

A census of clean room surface-associated bacterial populations was derived from the results of both the cloning and sequencing of 16S rRNA genes and DNA microarray (PhyloChip) analyses. Samples from the Lockheed Martin Aeronautics Multiple Testing Facility (LMA-MTF), the Kennedy Space Center Payload Hazard and Servicing Facility (KSC-PHSF), and the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) clean rooms were collected during the various assembly phases of the Phoenix and Mars Science Laboratory (MSL) spacecraft. Clone library-derived analyses detected a larger bacterial diversity prior to the arrival of spacecraft hardware in these clean room facilities. PhyloChip results were in agreement with this trend but also unveiled the presence of anywhere from 9- to 70-fold more bacterial taxa than cloning approaches. Among the facilities sampled, the JPL-SAF (MSL mission) housed a significantly less diverse bacterial population than either the LMA-MTF or KSC-PHSF (Phoenix mission). Bacterial taxa known to thrive in arid conditions were frequently detected in MSL-associated JPL-SAF samples, whereas proteobacterial lineages dominated Phoenix-associated KSC-PHSF samples. Comprehensive bacterial censuses, such as that reported here, will help space-faring nations preemptively identify contaminant biomatter that may compromise extraterrestrial life detection experiments. The robust nature and high sensitivity of DNA microarray technologies should prove beneficial to a wide range of scientific, electronic, homeland security, medical, and pharmaceutical applications and to any other ventures with a vested interest in monitoring and controlling contamination in exceptionally clean environments.

Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction

Prophage typically are induced to a lytic cycle under stressful environmental conditions or when the host's survival is threatened. However, stress-independent, spontaneous induction also occurs in nature and may be cell density dependent, but the in vivo signal(s) that can trigger induction is unknown. In the present study, we report that acyl-homoserine lactones (AHL), the essential signaling molecules of quorum sensing in many gram-negative bacteria, can trigger phage production in soil and groundwater bacteria. This phenomenon also was operative in a lambda lysogen of Escherichia coli. In model coculture systems, we monitored the real-time AHL production from Pseudomonas aeruginosa PAO1 using an AHL bioluminescent sensor and demonstrated that lambda-prophage induction in E. coli was correlated with AHL production. As a working model in E. coli, we show that the induction responses of lambda with AHL remained unaffected when recA was deleted, suggesting that this mechanism does not involve an SOS response. In the same lambda lysogen we also demonstrated that sdiA, the AHL receptor, and rcsA, a positive transcriptional regulator of exopolysaccharide synthesis, are involved in the AHL-mediated induction process. These findings relate viral reproduction to chemical signals associated with high host cell abundance, suggesting an alternative paradigm for prophage induction.

Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys

Pyrosequencing-based 16S rRNA gene surveys are increasingly utilized to study highly diverse bacterial communities, with special emphasis on utilizing the large number of sequences obtained (tens to hundreds of thousands) for species richness estimation. However, it is not yet clear how the number of operational taxonomic units (OTUs) and, hence, species richness estimates determined using shorter fragments at different taxonomic cutoffs correlates with the number of OTUs assigned using longer, nearly complete 16S rRNA gene fragments. We constructed a 16S rRNA clone library from an undisturbed tallgrass prairie soil (1,132 clones) and used it to compare species richness estimates obtained using eight pyrosequencing candidate fragments (99 to 361 bp in length) and the nearly full-length fragment. Fragments encompassing the V1 and V2 (V1+V2) region and the V6 region (generated using primer pairs 8F-338R and 967F-1046R) overestimated species richness; fragments encompassing the V3, V7, and V7+V8 hypervariable regions (generated using primer pairs 338F-530R, 1046F-1220R, and 1046F-1392R) underestimated species richness; and fragments encompassing the V4, V5+V6, and V6+V7 regions (generated using primer pairs 530F-805R, 805F-1046R, and 967F-1220R) provided estimates comparable to those obtained with the nearly full-length fragment. These patterns were observed regardless of the alignment method utilized or the parameter used to gauge comparative levels of species richness (number of OTUs observed, slope of scatter plots of pairwise distance values for short and nearly complete fragments, and nonparametric and parametric species richness estimates). Similar results were obtained when analyzing three other datasets derived from soil, adult Zebrafish gut, and basaltic formations in the East Pacific Rise. Regression analysis indicated that these observed discrepancies in species richness estimates within various regions could readily be explained by the proportions of hypervariable, variable, and conserved base pairs within an examined fragment.

Biogeochemical changes induced in uranium mining waste pile samples by uranyl nitrate treatments under anaerobic conditions

Response of the subsurface soil bacterial community of a uranium mining waste pile to treatments with uranyl nitrate over different periods of time was studied under anaerobic conditions. The fate of the added U(VI) without supplementation with electron donors was investigated as well. By using 16S rRNA gene retrieval, we demonstrated that incubation with uranyl nitrate for 4 weeks resulted in a strong reduction in and even disappearance of some of the most predominant bacterial groups of the original sample. Instead, a strong proliferation of denitrifying and uranium-resistant populations of Rahnella spp. from Gammaproteobacteria and of Firmicutes occurred. After longer incubations for 14 weeks with uranyl nitrate, bacterial diversity increased and populations intrinsic to the untreated samples such as Bacteroidetes and Deltaproteobacteria propagated and replaced the above-mentioned uranium-resistant groups. This indicated that U(VI) was immobilized. Mössbauer spectroscopic analysis revealed an increased Fe(III) reduction by increasing the incubation time from four to 14 weeks. This result signified that Fe(III) was used as an electron acceptor by the bacterial community established at the later stages of the treatment. X-ray absorption spectroscopic analysis demonstrated that no detectable amounts of U(VI) were reduced to U(IV) in the time frames of the performed experiments. The reason for this observation is possibly due to the low level of electron donors in the studied oligotrophic environment. Time-resolved laser-induced fluorescence spectroscopic analysis demonstrated that most of the added U(VI) was bound by organic or inorganic phosphate phases both of biotic origin.

Dynamic of active microorganisms inhabiting a bioleaching industrial heap of low-grade copper sulfide ore monitored by real-time PCR and oligonucleotide prokaryotic acidophile microarray

The bioleaching of metal sulfide has developed into a very important industrial process and understanding the microbial dynamic is key to advancing commercial bioleaching operations. Here we report the first quantitative description of the dynamic of active communities in an industrial bioleaching heap. Acidithiobacillus ferrooxidans was the most abundant during the first part of the leaching cycle, while the abundance of Leptospirillum ferriphilum and Ferroplasma acidiphilum increased with age of the heap. Acidithiobacillus thiooxidans kept constant throughout the leaching cycle, and Firmicutes group showed a low and a patchy distribution in the heap. The Acidiphilium‐like bacteria reached their highest abundance corresponding to the amount of autotrophs. The active microorganisms in the leaching system were determined using two RNA‐based sensitive techniques. In most cases, the 16S rRNA copy numbers of At. ferrooxidans, L. ferriphilum, At. thiooxidans and F. acidiphilum, was concomitant with the DNA copy numbers, whereas Acidiphilium‐like bacteria and some Firmicutes members did not show a clear correlation between 16S rRNA accumulation and DNA copy numbers. However, the prokaryotic acidophile microarray (PAM) analysis showed active members of Alphaproteobacteria in all samples and of Sulfobacillus genus in older ones. Also, new active groups such as Actinobacteria and Acidobacterium genus were detected by PAM. The results suggest that changes during the leaching cycle in chemical and physical conditions, such as pH and Fe³⁺/Fe²⁺ ion rate, are primary factors shaping the microbial dynamic in the heap.

Characterization and remediation of soils contaminated with uranium

Environmental contamination caused by radionuclides, in particular by uranium and its decay products is a serious problem worldwide. The development of nuclear science and technology has led to increasing nuclear waste containing uranium being released and disposed in the environment. The objective of this paper is to develop a better understanding of the techniques for the remediation of soils polluted with radionuclides (uranium in particular), considering: the chemical forms of uranium, including depleted uranium (DU) in soil and other environmental media, their characteristics and concentrations, and some of the effects on environmental and human health; research issues concerning the remediation process, the benefits and results; a better understanding of the range of uses and situations for which each is most appropriate. The paper addresses the main features of the following techniques for uranium remediation: natural attenuation, physical methods, chemical processes (chemical extraction methods from contaminated soils assisted by various suitable chelators (sodium bicarbonate, citric acid, two-stage acid leaching procedure), extraction using supercritical fluids such as solvents, permeable reactive barriers), biological processes (biomineralization and microbial reduction, phytoremediation, biosorption), and electrokinetic methods. In addition, factors affecting uranium removal from soils are furthermore reviewed including soil characteristics, pH and reagent concentration, retention time.

Treatment of nitric acid-, U(VI)-, and Tc(VII)-contaminated groundwater in intermediate-scale physical models of an in situ biobarrier

Metal and hydrogen ion acidity and extreme nitrate concentrations at Department of Energy legacywaste sites pose challenges for successful in situ U and Tc bioimmobilization. In this study, we investigated a potential in situ biobarrier configuration designed to neutralize pH and remove nitrate and radionuclides from nitric acid-, U-, and Tc-contaminated groundwater for over 21 months. Ethanol additions to groundwater flowing through native sediment and crushed limestone effectively increased pH (from 4.7 to 6.9), promoted removal of 116 mM nitrate, increased sediment biomass, and immobilized 94% of total U. Increased groundwater pH and significant U removal was also observed in a control column that received no added ethanol. Sequential extraction and XANES analyses showed U in this sediment to be solid-associated U(VI), and EXAFS analysis results were consistent with uranyl orthophosphate (UO2)3(PO4)2.4H2O(s), which may control U solubility in this system. Ratios of respiratory ubiquinones to menaquinones and copies of dissimilatory nitrite reductase genes, nirS and nirK, were at least 1 order of magnitude greater in the ethanol-stimulated system compared to the control, indicating that ethanol addition promoted growth of a largely denitrifying microbial community. Sediment 16S rRNA gene clone libraries showed that Betaproteobacteria were dominant (89%) near the source of influent acidic groundwater, whereas members of Gamma- and Alphaproteobacteria and Bacteroidetes increased along the flow path as pH increased and nitrate concentrations decreased, indicating spatial shifts in community composition as a function of pH and nitrate concentrations. Results of this study support the utility of biobarriers for treating acidic radionuclide- and nitrate-contaminated groundwater.

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

Climate change impacts on soil microbial communities could alter the structure of terrestrial ecosystems and biogeochemical cycles of the Earth. We used 16S rRNA gene microarrays to evaluate changes in the composition of grassland soil microbial communities under rainfall amendments simulating alternative climate change scenarios, and to compare these to responses of overlying plants and invertebrates. Following 5 years of rainfall manipulation, soil bacteria and archaea in plots where natural rain was supplemented differed little from ambient controls, despite profound treatment-related changes in the overlying grassland. During the sixth and seventh year, seasonal differences in bacterial and archaeal assemblages emerged among treatments, but only when watering exacerbated or alleviated periods of particularly aberrant conditions in the ambient climate. In contrast to effects on plants and invertebrates, effects on bacteria and archaea did not compound across seasons or years, indicating that soil microbial communities may be more robust than associated aboveground macroorganisms to certain alterations in climate.

Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing

The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. "Candidatus Liberibacter asiaticus" was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of "Candidatus Liberibacter asiaticus" in symptomatic leaves. These data implicate "Candidatus Liberibacter asiaticus" as the pathogen responsible for HLB disease.

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

Avian incubation inhibits growth and diversification of bacterial assemblages on eggs

Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from both treatment groups were dissimilar to one another, as measured by clustering in non-metric dimensional scaling (NMDS) ordination space. After treatment, assemblages of unincubated eggs were similar to one another, but those of incubated eggs were not. Furthermore, assemblages of unincubated eggs were characterized by high abundance of six indicator species while incubated eggs had no indicator species. Bacterial taxon richness remained static on incubated eggs, but increased significantly on unincubated eggs, especially in several families of Gram-negative bacteria. The relative abundance of individual bacterial taxa did not change on incubated eggs, but that of 82 bacterial taxa, including some known to infect the interior of eggs, increased on unincubated eggs. Thus, incubation inhibits all of the relatively few bacteria that grow on eggshells, and does not appear to promote growth of any bacteria.

A bioinformatician's guide to metagenomics

As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

Increasing evidence confirms the crucial role bacteria and archaea play within the coral holobiont, that is, the coral host and its associated microbial community. The bacterial component constitutes a community of high diversity, which appears to change in structure in response to disease events. In this study, we highlight the limitation of 16S rRNA gene (16S rDNA) clone library sequencing as the sole method to comprehensively describe coral-associated communities. This limitation was addressed by combining a high-density 16S rRNA gene microarray with, clone library sequencing as a novel approach to study bacterial communities in healthy versus diseased corals. We determined an increase in diversity as well as a significant shift in community structure in Montastraea faveolata colonies displaying phenotypic signs of White Plague Disease type II (WPD-II). An accumulation of species that belong to families that include known coral pathogens (Alteromonadaceae, Vibrionaceae), bacteria previously isolated from diseased, stressed or injured marine invertebrates (for example, Rhodobacteraceae), and other species (for example, Campylobacteraceae) was observed. Some of these species were also present in healthy tissue samples, but the putative primary pathogen, Aurantimonas corallicida, was not detected in any sample by either method. Although an ecological succession of bacteria during disease progression after causation by a primary agent represents a possible explanation for our observations, we also discuss the possibility that a disease of yet to be determined etiology may have affected M. faveolata colonies and resulted in (or be a result of) an increase in opportunistic pathogens.

Donor-dependent extent of uranium reduction for bioremediation of contaminated sediment microcosms

Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 micromol L(-1) d(-1)). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment

Remediation of uranium-contaminated sediments through in situ stimulation of bioreduction to insoluble UO2 is a potential treatment strategy under active investigation. Previously, we found that newly reduced U(IV) can be reoxidized under reducing conditions sustained by a continuous supply of organic carbon (OC) because of residual reactive Fe(III) and enhanced U(VI) solubilitythrough complexation with carbonate generated through OC oxidation. That finding motivated this investigation directed at identifying a range of OC supply rates that is optimal for establishing U bioreduction and immobilization in initially oxidizing sediments. The effects of OC supply rate, from 0 to 580 mmol of OC (kg of sediment)(-1) year(-1), and OC form (lactate and acetate) on U bioreduction were tested in flow-through columns containing U-contaminated sediments. An intermediate supply rate on the order of 150 mmol of OC (kg of sediment)(-1) year(-1) was determined to be most effective at immobilizing U. At lower OC supply rates, U bioreduction was not achieved, and U(VI) solubilitywas enhanced by complexation with carbonate (from OC oxidation). At the highest OC supply rate, the resulting highly carbonate-enriched solutions also supported elevated levels of U(VI), even though strongly reducing conditions were established. Lactate and acetate were found to have very similar geochemical impacts on effluent U concentrations (and other measured chemical species), when compared at equivalent OC supply rates. While the catalysts of U(VI) reduction to U(IV) are presumably bacteria, the composition of the bacterial community,the Fe-reducing community, and the sulfate-reducing community had no direct relationship with effluent U concentrations. The OC supply rate has competing effects of driving reduction of U(VI) to low-solubility U(IV) solids, as well as causing formation of highly soluble U(VI)-carbonato complexes. These offsetting influences will require careful control of OC supply rates in order to optimize bioreduction-based U stabilization.

Environmental microarray analyses of Antarctic soil microbial communities

Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats.

New tools for discovering and characterizing microbial diversity

To discover and characterize microbial diversity, approaches based on new sequencing technologies, novel isolation techniques, microfluidics, and metagenomics among others are being used. These approaches have contributed to discovery of novel genes from environmental samples, to massive characterization of functional and phylogenetic genes and to isolation of members of formerly uncultured yet ubiquitous groups like Verrucomicrobia, Acidobacteria, OP10, and methanogenic Archaea. Cheaper sequencing is key in this process by making available applications that were previously restricted to big research centers, complementing previously available methodologies and potentially replacing some of them. The new tools are reshaping the way we study the environment, increasing the resolution at which microbial communities, their complexities and dynamics, can be studied to reveal their genetic potential and their functional diversity.

In situ long-term reductive bioimmobilization of Cr(VI) in groundwater using hydrogen release compound

The results of a field experiment designed to test the effectiveness of a novel approach for long-term, in situ bioimmobilization of toxic and soluble Cr(VI) in groundwater using a hydrogen release compound (HRC)--a slow release glycerol polylactate--are described. The field experiment was conducted at the Hanford Site (Washington), a U.S. Department of Energy nuclear production facility, using a combination of hydrogeological, geophysical, geochemical, and microbiological measurements and analyses of water samples and sediments. The results of this experiment show that a single HRC injection into groundwater stimulates an increase in biomass, a depletion of terminal electron acceptors O2, NO3-, and SO4(2-), and an increase in Fe2+, resulting in a significant decrease in soluble Cr(VI). The Cr(VI) concentration has remained below the background concentration in the downgradient pumping/ monitoring well, and below the detection limit in the injection well for more than 3 years after the HRC injection. The degree of sustainability of Cr(VI) reductive bioimmobilization under different redox conditions at this and other contaminated sites is currently under study.

Selective progressive response of soil microbial community to wild oat roots

Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.

Effects of organic carbon supply rates on uranium mobility in a previously bioreduced contaminated sediment

Bioreduction-based strategies for remediating uranium (U)-contaminated sediments face the challenge of maintaining the reduced status of U for long times. Because groundwater influxes continuously bring in oxidizing terminal electron acceptors (O2, NO3(-)), it is necessary to continue supplying organic carbon (OC) to maintain the reducing environment after U bioreduction is achieved. We tested the influence of OC supply rates on mobility of previously microbial reduced uranium U(IV) in contaminated sediments. We found that high degrees of U mobilization occurred when OC supply rates were high, and when the sediment still contained abundant Fe(III). Although 900 days with low levels of OC supply minimized U mobilization, the sediment redox potential increased with time as did extractable U(VI) fractions. Molecular analyses of total microbial activity demonstrated a positive correlation with OC supply and analyses of Geobacteraceae activity (RT-qPCR of 16S rRNA) indicated continued activity even when the effluent Fe(II) became undetectable. These data support our hypothesis on the mechanisms responsible for remobilization of U under reducing conditions; that microbial respiration caused increased (bi)carbonate concentration and formation of stable uranyl carbonate complexes, thereby shifted U(IV)/U(VI) equilibrium to more reducing potentials. The data also suggested that low OC concentrations could not sustain the reducing condition of the sediment for much longer time. Bioreduced U(IV) is not sustainable in an oxidizing environment for a very long time.

Prokaryotic community profiles at different operational stages of a Greek solar saltern

A combination of culture-dependent and independent approaches was employed to identify the microbial community structure in a Greek solar saltern. A total of 219 and 132 isolates belonging, respectively, to Bacteria and Archaea, were recovered. All bacterial isolates were phylogenetically related to 43 members of Actinobacteria, Firmicutes and gamma-Proteobacteria. The archaeal isolates were placed within the Halobacteriaceae. At least four groups of isolates represented novel species among the Bacteria. High bacterial diversity, consisting of 417 subfamilies, was revealed using a high-density oligonucleotide microarray (PhyloChip). At the four stages of saltern operation analyzed, the archaeal community consisted of both Crenarchaeota and Euryarchaeota, except for the sediment where Crenarchaeota were not detected. The bacterial community in sediment consisted mainly of gamma-Proteobacteria and Actinobacteria, while, in hypersaline water, it was restricted to a few representatives of Bacteria. Members of alpha-Proteobacteria were the main constituents in saturated brine and crude salt, followed by gamma-Proteobacteria, Actinobacteria and Firmicutes. A large Bacteroidetes and Verrucomicrobia diversity was identified in saturated brine, while delta-Proteobacteria and Cloroflexi were abundant in crude salt. Significant changes in the microbial community structure were detected during a short time period, denoting a rapidly adaptive dynamic ecosystem and viable diversity. Prokaryotic members reported for the first time in solar salterns were identified.

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 degrees C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37 mW m(-2) with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray and clone library analysis with small subunit ribosomal RNA (16S rRNA) and ribosomal RNA gene (16S rDNA). The results illustrated the dominance (80% of clone library sequences) of the Firmicutes in electricity production. Similarly, rRNA sequences from Firmicutes accounted for 50% of those taxa that increased in relative abundance from current-producing MFCs, implying their functional role in current production. We complemented these analyses by isolating the first organisms from a thermophilic MFC. One of the isolates, a Firmicutes Thermincola sp. strain JR, not only produced more current than known organisms (0.42 mA) in an H-cell system but also represented the first demonstration of direct anode reduction by a member of this phylum. Our research illustrates the importance of using a variety of molecular and culture-based methods to reliably characterize bacterial communities. Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation.

Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure

BACKGROUND, AIM, AND SCOPE

The subsurface at the Oak Ridge Field Research Center represents an extreme and diverse geochemical environment that places different stresses on the endogenous microbial communities, including low pH, elevated nitrate concentrations, and the occurrence of heavy metals and radionuclides, including hexavalent uranium [U(VI)]. The in situ immobilization of U(VI) in the aquifer can be achieved through microbial reduction to relatively insoluble U(IV). However, a high redox potential due to the presence of nitrate and the toxicity of heavy metals will impede this process. Our aim is to test biostimulation of the endogenous microbial communities to improve nitrate reduction and subsequent U(VI) reduction under conditions of elevated heavy metals.

MATERIALS AND METHODS

Column experiments were used to test the possibility of using biostimulation via the addition of ethanol as a carbon source to improve nitrate reduction in the presence of elevated aqueous nickel. We subsequently analyzed the composition of the microbial communities that became established and their potential for U(VI) reduction and its in situ immobilization.

RESULTS

Phylogenetic analysis revealed that the microbial population changed from heavy metal sensitive members of the actinobacteria, alpha- and gamma-proteobacteria to a community dominated by heavy metal resistant (nickel, cadmium, zinc, and cobalt resistant), nitrate reducing beta- and gamma-proteobacteria, and sulfate reducing Clostridiaceae. Coincidentally, synchrotron X-ray absorption spectroscopy analyses indicated that the resulting redox conditions favored U(VI) reduction transformation to insoluble U(IV) species associated with soil minerals and biomass.

DISCUSSION

This study shows that the necessary genetic information to adapt to the implemented nickel stress resides in the endogenous microbial population present at the Oak Ridge FRC site, which changed from a community generally found under oligotrophic conditions to a community able to withstand the stress imposed by heavy metals, while efficiently reducing nitrate as electron donor. Once nitrate was reduced efficient reduction and in situ immobilization of uranium was observed.

CONCLUSIONS

This study provides evidence that stimulating the metabolism of the endogenous bacterial population at the Oak Ridge FRC site by adding ethanol, a suitable carbon source, results in efficient nitrate reduction under conditions of elevated nickel, and a decrease of the redox potential such that sulfate and iron reducing bacteria are able to thrive and create conditions favorable for the reduction and in situ immobilization of uranium. Since we have found that the remediation potential resides within the endogenous microbial community, we believe it will be feasible to conduct field tests.

RECOMMENDATIONS AND PERSPECTIVES

Biostimulation of endogenous bacteria provides an efficient tool for the successful in situ remediation of mixed-waste sites, particularly those co-contaminated with heavy metals, nitrate and radionuclides, as found in the United States and other countries as environmental legacies of the nuclear age.

Novelty and uniqueness patterns of rare members of the soil biosphere

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.

Monitoring aromatic hydrocarbon biodegradation by functional marker genes

The development of biological treatment technologies for contaminated environments requires tools for obtaining direct information about the biodegradation of specific contaminants. The potential of functional gene array analysis to monitor changes in the amount of functional marker genes as indicators of contaminant biodegradation was investigated. A prototype functional gene array was developed for targeting key functions in the biodegradation of naphthalene, toluene and xylenes. Internal standard probe based normalization was introduced to facilitate comparison across multiple samples. Coupled with one-colour hybridization, the signal normalization improved the consistency among replicate hybridizations resulting in better discrimination for the differences in the amount of target DNA. During the naphthalene biodegradation in a PAH-contaminated soil slurry microcosm, the normalized hybridization signals in naphthalene catabolic gene probes were in good agreement with the amount of naphthalene-degradation genes and the production of 14CO2. Gene arrays provide efficient means for monitoring of contaminant biodegradation in the environment.