Microbial growth with vapor-phase substrate

Phase-specific stable isotope fractionation effects during combined gas-liquid phase exchange and biodegradation

Stable isotope fractionation of toluene under dynamic phase exchange was studied aiming at ascertaining the effects of gas-liquid partitioning and biodegradation of toluene stable isotope composition in liquid-air phase exchange reactors (Laper). The liquid phase consisted of a mixture of aqueous minimal media, a known amount of a mixture of deuterated (toluene-d) and non-deuterated toluene (toluene-h), and bacteria of toluene degrading strain Pseudomonas putida KT2442. During biodegradation experiments, the liquid and air-phase concentrations of both toluene isotopologues were monitored to determine the observable stable isotope fractionation in each phase. The results show a strong fractionation in both phases with apparent enrichment factors beyond -800‰. An offset was observed between enrichment factors in the liquid and the gas phase with gas-phase values showing a stronger fractionation in the gas than in the liquid phase. Numerical simulation and parameter fitting routine was used to challenge hypotheses to explain the unexpected experimental data. The numerical results showed that either a very strong, yet unlikely, fractionation of the phase exchange process or a - so far unreported - direct consumption of gas phase compounds by aqueous phase microorganisms could explain the observed fractionation effects. The observed effect can be of relevance for the analysis of volatile contaminant biodegradation using stable isotope analysis in unsaturated subsurface compartments or other environmental compartment containing a gas and a liquid phase.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Headspace Passive Dosing of Volatile Hydrophobic Organic Chemicals from a Lipid Donor-Linking Their Toxicity to Well-Defined Exposure for an Improved Risk Assessment

High hydrophobicity and volatility of chemicals often lead to substantial experimental challenges but were here utilized in headspace passive dosing (HS-PD) to establish and maintain exposure: the pure chemical served as a passive dosing donor for controlling exposure at saturation, whereas triglyceride oil containing the chemical was used to control lower exposure levels. These donor solutions were added to glass inserts placed in the closed test systems. Mass balance calculations confirmed a dominant donor capacity for all chemicals except isooctane. This HS-PD method was applied to algal growth inhibition and springtail lethality tests with terpenes, alkanes, and cyclic siloxanes. Headspace concentrations above the lipid donors were measured for three chemicals to determine their chemical activity, using saturated vapor as the analytical standard and thermodynamic reference. Toxicity was related to chemical activity and calculated concentrations in membranes at equilibrium with the lipid donor. For both tests and all chemicals, toxic effects were observed within or above the reported range for baseline toxicity, meaning that no excess toxicity was observed. The toxicity of siloxanes was markedly higher to the terrestrial springtail than the aquatic algae, which is consistent with a more efficient mass transfer of these volatile hydrophobic chemicals in air compared to water.

Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter

Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.

Limited recovery of soil microbial activity after transient exposure to gasoline vapors

During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation.

Biodegradation of vapor-phase toluene in unsaturated porous media: Column experiments

Biodegradation of organic chemicals in the vapor phase of soils and vertical flow filters has gained attention as promising approach to clean up volatile organic compounds (VOC). The drivers of VOC biodegradation in unsaturated systems however still remain poorly understood. Here, we analyzed the processes controlling aerobic VOC biodegradation in a laboratory setup mimicking the unsaturated zone above a shallow aquifer. The setup allowed for diffusive vapor-phase transport and biodegradation of three VOC: non-deuterated and deuterated toluene as two compounds of highly differing biodegradability but (nearly) identical physical and chemical properties, and MTBE as (at the applied experimental conditions) non-biodegradable tracer and internal control. Our results showed for toluene an effective microbial degradation within centimeter VOC transport distances despite high gas-phase diffusivity. Degradation rates were controlled by the reactivity of the compounds while oxic conditions were found everywhere in the system. This confirms hypotheses that vadose zone biodegradation rates can be extremely high and are able to prevent the outgassing of VOC to the atmosphere within a centimeter range if compound properties and site conditions allow for sufficiently high degradation rates.

Numerical modeling analysis of VOC removal processes in different aerobic vertical flow systems for groundwater remediation

Vertical flow systems filled with porous medium have been shown to efficiently remove volatile organic contaminants (VOCs) from contaminated groundwater. To apply this semi-natural remediation strategy it is however necessary to distinguish between removal due to biodegradation and due to volatile losses to the atmosphere. Especially for (potentially) toxic VOCs, the latter needs to be minimized to limit atmospheric emissions. In this study, numerical simulation was used to investigate quantitatively the removal of volatile organic compounds in two pilot-scale water treatment systems: an unplanted vertical flow filter and a planted one, which could also be called a vertical flow constructed wetland, both used for the treatment of contaminated groundwater. These systems were intermittently loaded with contaminated water containing benzene and MTBE as main VOCs. The highly dynamic but permanently unsaturated conditions in the porous medium facilitated aerobic biodegradation but could lead to volatile emissions of the contaminants. Experimental data from porous material analyses, flow rate measurements, solute tracer and gas tracer test, as well as contaminant concentration measurements at the boundaries of the systems were used to constrain a numerical reactive transport modeling approach. Numerical simulations considered unsaturated water flow, transport of species in the aqueous and the gas phase as well as aerobic degradation processes, which made it possible to quantify the rates of biodegradation and volatile emissions and calculating their contribution to total contaminant removal. A range of degradation rates was determined using experimental results of both systems under two operation modes and validated by field data obtained at different operation modes applied to the filters. For both filters, simulations and experimental data point to high biodegradation rates, if the flow filters have had time to build up their removal capacity. For this case volatile emissions are negligible and total removal can be attributed to biodegradation, only. The simulation study thus supports the use of both of these vertical flow systems for the treatment of groundwater contaminated with VOCs and the use of reactive transport modeling for the assessment of VOCs removal and operation modes in these high performance treatment systems.

Uptake and toxicity of polycyclic aromatic hydrocarbons in terrestrial springtails--studying bioconcentration kinetics and linking toxicity to chemical activity

Passive dosing applies a polymer loaded with test compound(s) to establish and maintain constant exposure in laboratory experiments. Passive dosing with the silicone poly(dimethylsiloxane) was used to control exposure of the terrestrial springtail Folsomia candida to six polycyclic aromatic hydrocarbons (PAHs) in bioconcentration and toxicity experiments. Folsomia candida could move freely on the PAH-loaded silicone, resulting in exposure via air and direct contact. The bioconcentration kinetics indicated efficient uptake of naphthalene, anthracene, and pyrene through air and (near) equilibrium partitioning of these PAHs to lipids and possibly the waxy layer of the springtail cuticle. Toxicities of naphthalene, phenanthrene, and pyrene were related to chemical activity, which quantifies the energetic level and drives spontaneous processes including diffusive biouptake. Chemical activity-response relationships yielded effective lethal chemical activities (La50s) well within the expected range for baseline toxicity (0.01-0.1). Effective lethal body burdens for naphthalene and pyrene exceeded the expected range of 2 to 8 mmol kg(-1) fresh weight, which again indicated the waxy layer to be a sorbing phase. Finally, chemical activities were converted into equilibrium partitioning concentrations in lipids yielding effective lethal concentrations for naphthalene and phenanthrene in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Passive dosing was a practical approach for tightly controlling PAH exposure, which in turn provided new experimental possibilities and findings.

Walking the tightrope of bioavailability: growth dynamics of PAH degraders on vapour-phase PAH

Microbial contaminant degradation may either result in the utilization of the compound for growth or act as a protective mechanism against its toxicity. Bioavailability of contaminants for nutrition and toxicity has opposite consequences which may have resulted in quite different bacterial adaptation mechanisms; these may particularly interfere when a growth substrate causes toxicity at high bioavailability. Recently, it has been demonstrated that a high bioavailability of vapour‐phase naphthalene (NAPH) leads to chemotactic movement of NAPH‐degrading Pseudomonas putida (NAH7) G7 away from the NAPH source. To investigate the balance of toxic defence and substrate utilization, we tested the influence of the cell density on surface‐associated growth of strain PpG7 at different positions in vapour‐phase NAPH gradients. Controlled microcosm experiments revealed that high cell densities increased growth rates close (< 2 cm) to the NAPH source, whereas competition for NAPH decreased the growth rates at larger distances despite the high gas phase diffusivity of NAPH. At larger distance, less microbial biomass was likewise sustained by the vapour‐phase NAPH. Such varying growth kinetics is explained by a combination of bioavailability restrictions and NAPH‐based inhibition. To account for this balance, a novel, integrated ‘Best Equation’ describing microbial growth influenced by substrate availability and inhibition is presented.

Simplified MPN method for enumeration of soil naphthalene degraders using gaseous substrate

We describe a simplified microplate most-probable-number (MPN) procedure to quantify the bacterial naphthalene degrader population in soil samples. In this method, the sole substrate naphthalene is dosed passively via gaseous phase to liquid medium and the detection of growth is based on the automated measurement of turbidity using an absorbance reader. The performance of the new method was evaluated by comparison with a recently introduced method in which the substrate is dissolved in inert silicone oil and added individually to each well, and the results are scored visually using a respiration indicator dye. Oil-contaminated industrial soil showed slightly but significantly higher MPN estimate with our method than with the reference method. This suggests that gaseous naphthalene was dissolved in an adequate concentration to support the growth of naphthalene degraders without being too toxic. The dosing of substrate via gaseous phase notably reduced the work load and risk of contamination. The result scoring by absorbance measurement was objective and more reliable than measurement with indicator dye, and it also enabled further analysis of cultures. Several bacterial genera were identified by cloning and sequencing of 16S rRNA genes from the MPN wells incubated in the presence of gaseous naphthalene. In addition, the applicability of the simplified MPN method was demonstrated by a significant positive correlation between the level of oil contamination and the number of naphthalene degraders detected in soil.