Effects of Jet Fuel Spills on the Microbial Community of Soil

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil⁻¹. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil.     

The Impact of Fe(III)-reducing Bacteria on Uranium Mobility

The ability of specialist prokaryotes to couple the oxidation of organic compounds to the reduction of Fe(III) is widespread in the subsurface. Here microbial Fe(III) reduction can have a great impact on sediment geochemistry, affecting the minerals in the subsurface, the cycling of organic compounds and the mobility of a wide range of toxic metals and radionuclides. The contamination of the environment with radioactive waste is a major concern worldwide, and this review focuses on the mechanisms by which Fe(III)-reducing bacteria can affect the solubility and mobility of one of the most common radionuclide contaminants in the subsurface, uranium. In addition to discussing how these processes underpin natural biogeochemical cycles, we also discuss how these microbial activities can be harnessed for the bioremediation of uranium-contaminated environments.     

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single‐species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.     

Modeling Microbially Induced Carbon Degradation in Redox-Stratified Subsurface Environments: Concepts and Open Questions

The degradation of organic matter, including organic contaminants, in subsurface environments is controlled by the abundances and functional capabilities of the resident microorganisms. As a consequence, modeling approaches simulating the fate of organics and related changes in redox conditions have to account for the effects of microbial activity on the degradation kinetics, as well as for the spatial and temporal distributions of the chemical species (e.g., terminal electron acceptors, nutrients or toxic substances) that control microbial activity. The present paper reviews the principal modeling approaches that are used to simulate the degradation of organic matter in water-saturated porous media. Special attention is devoted to modeling the bioavailability of chemical substrates of microbial reactions, and the sequential occurrence of terminal electron accepting pathways. While the various model approaches found in the literature are capable of reproducing field data sets from various environmental settings, they are rarely compared in terms of performance and predictive ability. Most approaches incorporate simplifications or empirical rate laws, which limit their range of application. Thus, there remains a need for further development of more general, process-based modeling concepts to represent microbially mediated reactive processes.     

Dimensionless parameters to summarize the influence of microbial growth and inhibition on the bioremediation of groundwater contaminants

Monod expressions are preferred over zero- and first-order decay expressions in modeling contaminants biotransformation in groundwater because they better represent complex conditions. However, the wide-range of values reported for Monod parameters suggests each case-study is unique. Such uniqueness restricts the usefulness of modeling, complicates an interpretation of natural attenuation and limits the utility of a bioattenuation assessment to a small number of similar cases. In this paper, four Monod-based dimensionless parameters are developed that summarize the effects of microbial growth and inhibition on groundwater contaminants. The four parameters represent the normalized effective microbial growth rate (η), the normalized critical contaminant/substrate concentration (S*), the critical contaminant/substrate inhibition factor (N), and the bioremediation efficacy (η*). These parameters enable contaminated site managers to assess natural attenuation or augmented bioremediation at multiple sites and then draw comparisons between disparate remediation activities, sites and target contaminants. Simulations results are presented that reveal the sensitivity of these dimensionless parameters to Monod parameters and varying electron donor/acceptor loads. These simulations also show the efficacy of attenuation (η*) varying over space and time. Results suggest electron donor/acceptor amendments maintained at relative concentrations S* between 0.5 and 1.5 produce the highest remediation efficiencies. Implementation of the developed parameters in a case study proves their usefulness.     

Actinide and metal toxicity to prospective bioremediation bacteria

Bacteria may be beneficial for alleviating actinide contaminant migration through processes such as bioaccumulation or metal reduction. However, sites with radioactive contamination often contain multiple additional contaminants, including metals and organic chelators. Bacteria-based bioremediation requires that the microorganism functions in the presence of the target contaminant, as well as other contaminants. Here, we evaluate the toxicity of actinides, metals and chelators to two different bacteria proposed for use in radionuclide bioremediation, Deinococcus radiodurans and Pseudomonas putida, and the toxicity of Pu(VI) to Shewanella putrefaciens. Growth of D. radiodurans was inhibited at metal concentrations ranging from 1.8 microM Cd(II) to 32 mM Fe(III). Growth of P. putida was inhibited at metal concentrations ranging from 50 microM Ni(II) to 240 mM Fe(III). Actinides inhibited growth at mM concentrations: chelated Pu(IV), U(VI) and Np(V) inhibit D. radiodurans growth at 5.2, 2.5 and 2.1 mM respectively. Chelated U(VI) inhibits P. putida growth at 1.7 mM, while 3.6 mM chelated Pu(IV) inhibits growth only slightly. Pu(VI) inhibits S. putrefaciens growth at 6 mM. These results indicate that actinide toxicity is primarily chemical (not radiological), and that radiation resistance does not ensure radionuclide tolerance. This study also shows that Pu is less toxic than U and that actinides are less toxic than other types of metals, which suggests that actinide toxicity will not impede bioremediation using naturally occurring bacteria.     

Spatial and Resource Factors Influencing High Microbial Diversity in Soil

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.     

Endophytic microorganisms—promising applications in bioremediation of greenhouse gases

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.     

Prediction of growth of Bacillus megaterium spores as affected by gamma radiation dose and spore load

AIMS: To provide data on the interaction of radiation dose (x1) and microbial contamination load (x2), as predictor variables, on the percentage of vials exhibiting growth of Bacillus megaterium spores (y). METHODS AND RESULTS: The influence of a wide range of spore loads (1-50 000 spores of B. megaterium vial-1) and gamma radiation doses (0.2-10 kGy) on the contaminated samples was determined. Each contamination load was studied by adding the specified number of spores to 100 vials containing nutrient broth and exposing them to various doses of gamma radiation. Curves representing the number of contaminated vials against the dose of radiation were sigmoidal in shape and the data showed an indirect relationship. Data were analysed by regression analysis which revealed a significant correlation (R2=0.85). The relationship among the tested variables is exponential and can be described by the following equation: y = 1 - (1 - e(0.0173x(1)))(x(2)) It was also estimated that, for each increase of 1 in the number of spores per vial, there is an increase of 1 in the number of contaminated vials. CONCLUSION: The two variables (x1 and x2) have great influence on the radiation sterilization efficiency and the proposed mathematical model is valid for the prediction of this efficiency. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of the present investigation can be of useful industrial application and can help to set acceptance and rejection limits for the production of materials vulnerable to microbial contamination.     

Radiation-induced carcinogenesis: mechanistically based differences between gamma-rays and neutrons, and interactions with DMBA

Different types of ionizing radiation produce different dependences of cancer risk on radiation dose/dose rate. Sparsely ionizing radiation (e.g. γ-rays) generally produces linear or upwardly curving dose responses at low doses, and the risk decreases when the dose rate is reduced (direct dose rate effect). Densely ionizing radiation (e.g. neutrons) often produces downwardly curving dose responses, where the risk initially grows with dose, but eventually stabilizes or decreases. When the dose rate is reduced, the risk increases (inverse dose rate effect). These qualitative differences suggest qualitative differences in carcinogenesis mechanisms. We hypothesize that the dominant mechanism for induction of many solid cancers by sparsely ionizing radiation is initiation of stem cells to a pre-malignant state, but for densely ionizing radiation the dominant mechanism is radiation-bystander-effect mediated promotion of already pre-malignant cell clone growth. Here we present a mathematical model based on these assumptions and test it using data on the incidence of dysplastic growths and tumors in the mammary glands of mice exposed to high or low dose rates of γ-rays and neutrons, either with or without pre-treatment with the chemical carcinogen 7,12-dimethylbenz-alpha-anthracene (DMBA). The model provides a mechanistic and quantitative explanation which is consistent with the data and may provide useful insight into human carcinogenesis.     

Determining Rates of Change and Evaluating Group-Level Resiliency Differences in Hyporheic Microbial Communities in Response to Fluvial Heavy-Metal Deposition

Prior field studies by our group have demonstrated a relationship between fluvial deposition of heavy metals and hyporheic-zone microbial community structure. Here, we determined the rates of change in hyporheic microbial communities in response to heavy-metal contamination and assessed group-level differences in resiliency in response to heavy metals. A controlled laboratory study was performed using 20 flowthrough river mesocosms and a repeated-measurement factorial design. A single hyporheic microbial community was exposed to five different levels of an environmentally relevant metal treatment (0, 4, 8, 16, and 30% sterilized contaminated sediments). Community-level responses were monitored at 1, 2, 4, 8, and 12 weeks via denaturing gradient gel electrophoresis and quantitative PCR using group-specific primer sets for indigenous populations most closely related to the α-, β-, and γ-proteobacteria. There was a consistent, strong curvilinear relationship between community composition and heavy-metal contamination (R² = 0.83; P < 0.001), which was evident after only 7 days of metal exposure (i.e., short-term response). The abundance of each phylogenetic group was negatively affected by the heavy-metal treatments; however, each group recovered from the metal treatments to a different extent and at a unique rate during the course of the experiment. The structure of hyporheic microbial communities responded rapidly and at contamination levels an order of magnitude lower than those shown to elicit a response in aquatic macroinvertebrate assemblages. These studies indicate that hyporheic microbial communities are a sensitive and useful indicator of heavy-metal contamination in streams.     

Bioremediation of radioactive waste: radionuclide-microbe interactions in laboratory and field-scale studies

Given the scale of the contamination associated with 60 years of global nuclear activity, and the inherent high financial and environmental costs associated with invasive physical and chemical clean-up strategies, there is an unparalleled interest in new passive in situ bioremediation processes for sites contaminated with nuclear waste. Many of these processes rely on successfully harnessing newly discovered natural biogeochemical cycles for key radionuclides and fission products. Recent advances have been made in understanding the microbial colonization of radioactive environments and the biological basis of microbial transformations of radioactive waste in these settings.     

植物根系分泌物对土壤污染修复的作用及影响机理

生物修复是一种经济环保的土壤修复技术。根系分泌物是利用生物修复污染土壤过程中的关键物质,也是植物与土壤微生物进行物质交换和信息传递的重要载体,在植物响应污染物胁迫中扮演重要角色。研究植物根系分泌物对土壤污染修复的作用和影响机理,是深入理解植物和微生物环境适应机制的重要途径,对促进生物修复污染土壤有重要指导意义。从污染物胁迫对根系分泌物的影响、根系分泌物对土壤污染物环境行为的影响、根系分泌物在调控污染土壤中根际微生物群落结构和多样性中发挥的作用等几个方面综述了根系分泌物对土壤污染修复的影响及内在机制。研究结果表明,根系分泌物在降低重金属对植物的毒性、加速有机污染物降解等方面有非常重要的作用。根系分泌物对土壤微生物的丰度和多样性均有显著影响,其与根际微生物互作在土壤污染物的消减中发挥了重要的调控作用。在此基础上,提出了以往研究中的不足,并对污染物胁迫下根系分泌物未来研究的方向和趋势进行了展望。     

Managing microbial communities in membrane biofilm reactors

Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H₂) or methane (CH₄), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O₂ is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR’s biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community’s structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community’s structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.

     

Current development of the human and environmental contamination in the Bryansk-Gomel Spot after the Chernobyl accident

Up to 1991, it was assumed that after the Chernobyl accident in 1986 the time development of radioactive contamination with regard to environment, foodstuff, and man would decrease due to migration processes in the soil, radioactive decay, and protective measures. This assumption was confirmed by all measurements in the first few years after the accident. Since 1991, however, a change in this development has been observed, as many measurements show stagnation or in some cases even an increase of foodstuff and human contamination. If normalised to an average local ground contamination, only a few groups of foodstuffs (e.g., potatoes) show a slight decrease in radioactivity. In this paper, the time development of radioactive contamination in the Bryansk-Gomel Spot on the basis of measurements since 1991 is presented. The consequences for long-term dose assessment are discussed. Received: 10 November 1998 / Accepted: 20 January 2000     

Utilization of bioremediation processes for the treatment of PAH-contaminated sediments

The widespread contamination of aquatic sediments by polycyclic aromatic hydrocarbons (PAHs) has created a need for cost-effective remediation processes. Many common PAHs are biodegradable, leading to studies investigating the potential of sediment bioremediation. This article reviews several factors that currently complicate the implementation of sediment bioremediation processes: the effect of complex mixtures of contaminants on the rate and extent of degradation observed, the bioavailability of PAHs in sorbed- and nonaqueous-phase, and methods being evaluated to enhance degradation/availability (surfactant-enhanced solubility, nutrient addition, and bioaugmentation). Received 13 November 1995/ Accepted in revised form 23 July 1996     

Sediment quality of North Carolina estuaries: an integrative assessment of sediment contamination, toxicity, and condition of benthic fauna

Sediment quality of North Carolina estuaries was evaluated using synoptic data on sediment chemistry, toxicity, and macroinfaunal community structure from 175 subtidal stations sampled during the summers of 1994–1997. The study area included Currituck, Albemarle, and Pamlico Sounds; estuarine portions of major rivers (e.g., Chowan, Roanoke, Tar-Pamlico, Neuse, New, Cape Fear); and numerous smaller tributaries and coastal embayments between the Virginia and South Carolina borders. A probabilistic sampling design permitted statistical estimation of the spatial extent of degraded versus non-degraded condition across these estuaries. Over half (54 ± 7%) of the surveyed area had high sediment quality characterized by healthy benthic assemblages and low levels of sediment contamination and toxicity. The remaining 46% showed evidence of significant stress in one or more of the above sediment-quality-triad components. While this is a sizable area, portions of it (27 ± 6%) were represented by sites with no connection between presence of stressors and adverse biological responses. Only 19% of the total area showed evidence of an impaired benthos coupled to significant pollution exposure (high sediment contamination, toxicity, or both). Impaired benthic condition was more closely linked to sediment contamination than to low dissolved oxygen (based on instantaneous oxygen measurements). The most pervasive contaminants were the metals arsenic, mercury, chromium, and nickel; the pesticides lindane, dieldrin, DDT, and DDT derivatives; and total PCBs. Degraded condition in all three components of the sediment quality triad co-occurred in <10% of the study area, suggesting that strong contaminant-induced effects on the benthos are limited to a small (yet ecologically significant) percentage of total estuarine area. The spatial extent of sediment contamination and toxicity was much less in these estuaries in comparison to other U.S. coastal regions where similar studies have been performed.     

Medical management of the acute radiation syndrome

The acute radiation syndrome (ARS) occurs after whole-body or significant partial-body irradiation (typically at a dose of >1 Gy). ARS can involve the hematopoietic, cutaneous, gastrointestinal and the neurovascular organ systems either individually or in combination.There is a correlation between the severity of clinical signs and symptoms of ARS and radiation dose. Radiation induced multi-organ failure (MOF) describes the progressive dysfunction of two or more organ systems over time. Radiation combined injury (RCI) is defined as radiation injury combined with blunt or penetrating trauma, burns, blast, or infection. The classic syndromes are: hematopoietic (doses >2–3 Gy), gastrointestinal (doses 5–12 Gy) and cerebrovascular syndrome (doses 10–20 Gy). There is no possibility to survive after doses >10–12 Gy.The Phases of ARS are—prodromal: 0–2 days from exposure, latent: 2–20 days, and manifest illness: 21–60 days from exposure.Granulocyte-colony stimulating factor (G-CSF) at a dose of 5 μg/kg body weight per day subcutaneously has been recommended as treatment of neutropenia, and antibiotics, antiviral and antifungal agents for prevention or treatment of infections.If taken within the first hours of contamination, stable iodine in the form of nonradioactive potassium iodide (KI) saturates iodine binding sites within the thyroid and inhibits incorporation of radioiodines into the gland.Finally, if severe aplasia persists under cytokines for more than 14 days, the possibility of a hematopoietic stem cell (HSC) transplantation should be evaluated.This review will focus on the clinical aspects of the ARS, using the European triage system (METREPOL) to evaluate the severity of radiation injury, and scoring groups of patients for the general and specific management of the syndrome.     

Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), ¹³⁷Cs, and ⁹⁹Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ~10⁴ CFU g⁻¹, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of ¹³⁷Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 μCi of ¹³⁷Cs g⁻¹) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.