Leen Bastiaens

Isolation of Adherent Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Bacteria Using PAH-Sorbing Carriers

ABSTRACT Two different procedures were compared to isolate polycyclic aromatic hydrocarbon (PAH)-utilizing bacteria from PAH-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which PAHs were supplied as crystals and (ii) a new method in which PAH degraders were enriched on and recovered from hydrophobic membranes containing sorbed PAHs. Both techniques were successful, but selected from the same source different bacterial strains able to grow on PAHs as the sole source of carbon and energy. The liquid enrichment mainly selected for Sphingomonasspp., whereas the membrane method exclusively led to the selection ofMycobacterium spp. Furthermore, in separate membrane enrichment set-ups with different membrane types, three repetitive extragenic palindromic PCR-related Mycobacterium strains were recovered. The new Mycobacterium isolates were strongly hydrophobic and displayed the capacity to adhere strongly to different surfaces. One strain, Mycobacterium sp. LB501T, displayed an unusual combination of high adhesion efficiency and an extremely high negative charge. This strain may represent a new bacterial species as suggested by 16S rRNA gene sequence analysis. These results indicate that the provision of hydrophobic sorbents containing sorbed PAHs in the enrichment procedure discriminated in favor of certain bacterial characteristics. The new isolation method is appropriate to select for adherent PAH-degrading bacteria, which might be useful to biodegrade sorbed PAHs in soils and sludge.

Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

ABSTRACT Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

Ten Year Performance Evaluation of a Field-Scale Zero-Valent Iron Permeable Reactive Barrier Installed to Remediate Trichloroethene Contaminated Groundwater

The Monkstown zero-valent iron permeable reactive barrier (ZVI PRB), Europes oldest commercially-installed ZVI PRB, had been treating trichloroethene (TCE) contaminated groundwater for about 10 years on the Nortel Network site in Northern Ireland when cores from the reactive zone were collected in December, 2006. Groundwater data from 2001-2006 indicated that TCE is still being remediated to below detection limits as the contaminated groundwater flows through the PRB. Ca and Fe carbonates, crystalline and amorphous Fe sulfides, and Fe (hydr)oxides have precipitated in the granular ZVI material in the PRB. The greatest variety of minerals is associated with a approximately 1-2 cm thick, slightly cemented crust on top (up-gradient influent entrance) of the ZVI section of the PRB and also with the discontinuous cemented ZVI material ( approximately 23 cm thick) directly below it. The greatest presence of microbial communities also occurred in the up-gradient influent portion of the PRB compared to its down-gradient effluent section, with the latter possibly due to less favorable conditions (i.e., high pH, low oxygen) for microbial growth. The ZVI filings in the down-gradient effluent section of the PRB have a projected life span of >10 years compared with ZVI filings from the continuous to discontinuous cemented up-gradient ZVI section (upper approximately 25 cm) of the PRB, which may have a life span of only approximately 2-5 more years. Supporting Information from applied, multi-tracer testing indicated that restricted groundwater flow is occurring in the upper approximately 25 cm of the ZVI section and preferential pathways have also formed in this PRB over its 10 years of operation.

Influence of the carbon/nitrogen/phosphorus ratio on polycyclic aromatic hydrocarbon degradation by Mycobacterium and Sphingomonas in soil

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the environment is often limited due to unfavorable nutrient conditions for the bacteria that use these PAHs as sole source of carbon and energy. Mycobacterium and Sphingomonas are 2 PAH-degrading specialists commonly present in PAH-polluted soil, but not much is known about their specific nutrient requirements. By adding different inorganic supplements of nitrogen (N) and phosphorus (P), affecting the overall carbon/nitrogen/phosphorus ratio of soil in soil slurry degradation tests, we investigated the impact of soil inorganic N and P nutrient conditions on PAH degradation by PAH-degrading Sphingomonas and Mycobacterium strains. The general theoretically calculated C/N/P ratio of 100/10/1 (expressed in moles) allowed rapid PAH metabolization by Sphingomonas and Mycobacterium strains without limitation. In addition, PAH-degradation rate and extent was not affected when ca. ten times lower concentrations of N and P were provided, indicating that Sphingomonas and Mycobacterium strains are capable of metabolizing PAHs under low nutrient conditions. Nor does PAH-degradation seem to be affected by excesses of N and P creating an imbalanced C/N/P ratio. However, supplements of N and P salts increased the salinity of soil slurry solutions and seriously limited or even completely blocked biodegradation.

Elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by Sphingomonas sp. LB126.

The metabolic pathway of the PAH fluorene and the cometabolic pathway of the PAHs phenanthrene, fluoranthene, anthracene and dibenzothiophene in Sphingomonas sp. LB126 were examined. To our knowledge this is the first study on the cometabolic degradation of the three-ring PAHs phenanthrene, anthracene and the four-ring PAH fluoranthene by a fluorene-utilizing species. Metabolism of fluorene was shown to proceed via the 9-fluorenone pathway to form o-phthalic acid and protocatechuic acid. The cometabolic mono-hydroxylation found for phenanthrene, fluoranthene and anthracene shows similarity with the hydroxylation of fluorene. Several mono- and dihydroxy products and ring-cleavage products were identified for phenanthrene, fluoranthene and anthracene. It appeared that the cometabolism of those three compounds is a non-specific process, in contrast to the metabolism of fluorene. For dibenzothiophene the metabolites dibenzothiophene-5-oxide and dibenzothiophene-5,5-dioxide were identified; these compounds appeared to be the products of a dead-end pathway. Since apart from dibenzothiophene no metabolites were found in very high concentrations for any of the other substrates, complete degradation is suggested, even for the cometabolic degradation of phenanthrene, fluoranthene and anthracene.

Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Dynamics of an Oligotrophic Bacterial Aquifer Community during Contact with a Groundwater Plume Contaminated with Benzene, Toluene, Ethylbenzene, and Xylenes: an In Situ Mesocosm Study

ABSTRACT An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contamination.

Evaluation of the intrinsic methyl tert-butyl ether (MTBE) biodegradation potential of hydrocarbon contaminated subsurface soils in batch microcosm systems.

Eleven soil samples (contaminated and non-contaminated top soils and aquifers) from seven different locations in Belgium were examined in lab-scale batch microcosms simulating in situ conditions for their indigenous capacity to biodegrade methyl tert-butyl ether (MTBE). The effect of implementing nutrients or additional oxygen and of the presence of co-contaminants on MTBE degradation was investigated. All soils showed rapid degradation of benzene. On the other hand, only one site, historically contaminated with oxygenated fuel, provided soil samples showing relatively fast MTBE biodegradation. These soil samples originated from four different depths from the vadose and saturated zone. MTBE degradation kinetics differed between the samples of the saturated and non-saturated zone and depended on the implemented conditions. MTBE-biodegradation in the samples from the non-saturated zone started after a very short lag-phase (<7 days), while long lag-phases (up to 270 days) were obtained with the other samples. Addition of extra nutrients stimulated MTBE degradation kinetics in microcosms containing the saturated soil samples while inhibiting effects were seen in the case of non-saturated soil samples. In contrast, implementing dissolved oxygen concentrations of 9.5 and 11.5 mg l(-1) led to lower degradation kinetics compared to 8 mg l(-1) in microcosms containing saturated soil samples, while stimulating effects were seen with the non-saturated soil samples. Addition of an extra carbon source like benzene or propane did increase in general the MTBE first order degradation rate constant. Differences in the eubacterial community composition between these depth samples were confirmed based on denaturing gradient gel electrophoresis (DGGE) patterns of PCR-amplified 16S rRNA gene fragments. The results of the presented study indicate that an aerobic MTBE biodegradation potential is not omnipresent in Belgian sub-soils.

A transcriptional luxAB reporter fusion responding to fluorene in Sphingomonas sp. LB126 and its initial characterisation for whole-cell bioreporter purposes.

The promoter probe mini-Tn5-luxAB-tet was used to create a luxAB transcriptional fusion responding to fluorene in the fluorene utilising bacterium Sphingomonas sp. LB126. The mutant strain, named L-132, was impaired in fluorene utilisation and strongly emitted light upon addition of fluorene to the growth medium. L-132 was initially characterised and examined for its potential use as a whole-cell biosensor in the perspective of quantifying fluorene in environmental samples. Activity of the reporter gene as a response to fluorene was detectable after 30 min and was optimal after 4 h. A linear response to fluorene concentrations within the water solubility range was achieved, with a detection limit of 200 microg per litre. Besides fluorene, L-132 weakly responded to the polycyclic aromatic hydrocarbons phenanthrene and dibenzothiophene, whereas strong responses were obtained with 9-fluorenone, 9-hydroxyfluorene, phthalic acid and protocatechuic acid. The latter four compounds are metabolites formed in course of fluorene degradation, which suggested that a fluorene metabolite rather than fluorene itself was the true inducer of the luxAB fusion in L-132.

Corrosion rate estimations of microscale zerovalent iron particles via direct hydrogen production measurements.

In this study, the aging behavior of microscale zerovalent iron (mZVI) particles was investigated by quantifying the hydrogen gas generated by anaerobic mZVI corrosion in batch degradation experiments. Granular iron and nanoscale zerovalent iron (nZVI) particles were included in this study as controls. Firstly, experiments in liquid medium (without aquifer material) were performed and revealed that mZVI particles have approximately a 10-30 times lower corrosion rate than nZVI particles. A good correlation was found between surface area normalized corrosion rate (RSA) and reaction rate constants (kSA) of PCE, TCE, cDCE and 1,1,1-TCA. Generally, particles with higher degradation rates also have faster corrosion rates, but exceptions do exists. In a second phase, the hydrogen evolution was also monitored during batch tests in the presence of aquifer material and real groundwater. A 4-9 times higher corrosion rate of mZVI particles was observed under the natural environment in comparison with the aquifer free artificial condition, which can be attributed to the low pH of the aquifer and its buffer capacity. A corrosion model was calibrated on the batch experiments to take into account the inhibitory effects of the corrosion products (dissolved iron, hydrogen and OH(-)) on the iron corrosion rate.