Characterization of multiple-substrate utilization by anthracene-degrading Mycobacterium frederiksbergense LB501T

Water Stress-Driven Changes in Bacterial Cell Surface Properties

Increased drought intensity and frequency exposes soil bacteria to prolonged water stress. While numerous studies reported on behavioral and physiological mechanisms of bacterial adaptation to water stress, changes in bacterial cell surface properties during adaptation are not well researched. We studied adaptive changes in cell surface hydrophobicity (CSH) after exposure to osmotic (NaCl) and matric stress (polyethylene glycol 8000 [PEG 8000]) for six typical soil bacteria (Bacillus subtilis, Arthrobacter chlorophenolicus, Pseudomonas fluorescens, Novosphingobium aromaticivorans, Rhodococcus erythropolis, and Mycobacterium pallens) covering a wide range of cell surface properties. Additional physicochemical parameters (surface chemical composition, surface charge, cell size and stiffness) of B. subtilis and P. fluorescens were analyzed to understand their possible contribution to CSH development. Changes in CSH caused by osmotic and matric stress depend on strain and stress type. CSH of B. subtilis and P. fluorescens increased with stress intensity, R. erythropolis and M. pallens exhibited a generally high but constant contact angle, while the response of A. chlorophenolicus and N. aromaticivorans depended on growth conditions and stress type. Osmotically driven changes in CSH of B. subtilis and P. fluorescens are accompanied by increasing surface N/C ratio, suggesting an increase in protein concentration within the cell wall. Cell envelope proteins thus presumably control bacterial CSH in two ways: (i) by increases in the relative density of surface proteins due to efflux of cytoplasmic water and subsequent cell shrinkage, and (ii) by destabilization of cell wall proteins, resulting in conformational changes which render the surface more hydrophobic. IMPORTANCE Changes in precipitation frequency, intensity, and temporal distribution are projected to result in increased frequency and intensity of droughts and heavy rainfall events. Prolonged droughts can promote the development of soil water repellency (SWR); this impacts the infiltration and distribution of water in the soil profile, exposing soil microorganisms to water stress. Exposure to water stress has recently been reported to result in increased cell surface hydrophobicity. However, the mechanism of this development is poorly understood. This study investigates the changes in the physicochemical properties of bacterial cell surfaces under water stress as a possible mechanism of increased surface hydrophobicity. Our results improve understanding of the microbial response to water stress in terms of surface properties, the variations in stress response depending on cell wall composition, and its contribution to the development of SWR.

Differences in the properties of extracellular polymeric substances responsible for PAH degradation isolated from Mycobacterium gilvum SN12 grown on pyrene and benzo[a]pyrene

This study aimed to evaluate the differences in the characteristics of extracellular polymeric substances (EPSs) secreted by Mycobacterium gilvum SN12 (M.g. SN12) cultured on pyrene (Pyr) and benzo[a]pyrene (BaP). A heating method was used to extract EPSs from M.g. SN12, and the composition, emulsifying activity, and morphology of EPS extracts were investigated. Results showed that EPS extracts varied significantly with Pyr or BaP addition to the bacterial cultures. The concentration of proteins and carbohydrates, the main components of the EPS extracts, first increased and then decreased, with an increase in the concentration of Pyr (0-120 mg L^-1) and BaP (0-120 mg L^-1). A similar trend was observed for the emulsifying activity of the EPS extracts. EPSs extracted from all cultures exhibited a compact structure with a smooth surface, except for EPSs extracted from BaP-grown M.g. SN12, which revealed a more fragile and softer surface. These findings suggest that Pyr and BaP had different influences on the properties of isolated EPSs, providing insights into the mechanism underlying polycyclic aromatic hydrocarbons (PAHs) biodegradation by some EPS-secreting bacteria. To the best of our knowledge, this is the first report on the texture profile of EPS samples extracted from M.g. SN12 grown on PAHs.

Draft Whole-Genome Sequence of the Anthracene-Degrading Strain Mycolicibacterium frederiksbergense LB501T, Isolated from a Polycyclic Aromatic Hydrocarbon-Contaminated Soil

Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities.

Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

Biophysical methods to quantify bacterial behaviors at oil-water interfaces

Motivated by the need for improved understanding of physical processes involved in bacterial biodegradation of catastrophic oil spills, we review biophysical methods to probe bacterial motility and adhesion at oil-water interfaces. This review summarizes methods that probe bulk, average behaviors as well as local, microscopic behaviors, and highlights opportunities for future work to bridge the gap between biodegradation and biophysics.

Selecting Bacteria Candidates for the Bioaugmentation of Activated Sludge to Improve the Aerobic Treatment of Landfill Leachate

In this study, a multifaceted approach for selecting the suitable candidates for bioaugmentation of activated sludge (AS) that supports leachate treatment was used. To determine the exploitation of 10 bacterial strains isolated from the various matrices for inoculating the AS contaminated with the Kalina pond leachate (KPL), their degradative potential was analyzed along with their aptitude to synthesize compounds improving remediation of pollutants in wastewater and ability to incorporate into the AS flocs. Based on their capability to degrade aromatic compounds (primarily catechol, phenol, and cresols) at a concentration of 1 mg/mL and survive in 12.5% of the KPL, Pseudomonas putida OR45a and P. putida KB3 can be considered to be the best candidates for bioaugmentation of the AS among all of the bacteria tested. Genomic analyses of these two strains revealed the presence of the genes encoding enzymes related to the metabolism of aromatic compounds. Additionally, both microorganisms exhibited a high hydrophobic propensity (above 50%) and an ability to produce biosurfactants as well as high resistance to ammonium (above 600 µg/mL) and heavy metals (especially chromium). These properties enable the exploitation of both bacterial strains in the bioremediation of the AS contaminated with the KPL.

Biofilm formation as a microbial strategy to assimilate particulate substrates

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Phenotypic Adaptations Help Rhodococcus erythropolis Cells during the Degradation of Paraffin Wax

During crude oil extraction, the reduction in temperature and pressure results in the precipitation of paraffin wax that contains 20-40 carbon chain hydrocarbons. The paraffin wax may accumulate inside production tubes, pipelines, and processing facilities, and also in tankers during petroleum transportation. There are few bacterial strains that are able to degrade solid substrates. In the present study, the biodegradation of paraffin is evaluated using Rhodococcus erythropolis cells. This bacterium is able to grow using paraffin wax from an oil refinery plant as the sole carbon source. The cells grow as a thick biofilm over the solid substrate, make scale-like structures that increase the area of the initially smooth surface of paraffin, produce biosurfactants, and become more negatively charged than ethanol- or glucose-grown cells. When paraffin wax is supplied as microparticles, to increase the cell-substrate contact area and to simulate paraffin precipitation, the cells also adjust the composition of the fatty acids of the phospholipids of the cellular membrane to decrease its fluidity and paraffin biodegradation increases considerably. The study suggests that the phenotypic adaptation of R. erythropolis cells may be used to degrade paraffin wax under real conditions.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.

Immediate response mechanisms of Gram-negative solvent-tolerant bacteria to cope with environmental stress: cis-trans isomerization of unsaturated fatty acids and outer membrane vesicle secretion

Bacteria have evolved an array of adaptive mechanisms enabling them to survive and grow in the presence of different environmental stresses. These mechanisms include either modifications of the membrane or changes in the overall energy status, cell morphology, and cell surface properties. Long-term adaptations are dependent on transcriptional regulation, the induction of anabolic pathways, and cell growth. However, to survive sudden environmental changes, bacterial short-term responses are essential to keep the cells alive after the occurrence of an environmental stress factor such as heat shock or the presence of toxic organic solvents. Thus far, two main short-term responses are known. On the one hand, a fast isomerization of cis into trans unsaturated fatty leads to a quick rigidification of the cell membrane, a mechanism known in some genera of Gram-negative bacteria. On the other hand, a fast, effective, and ubiquitously present countermeasure is the release of outer membrane vesicles (OMVs) from the cell surface leading to a rapid increase in cell surface hydrophobicity and finally to the formation of cell aggregates and biofilms. These immediate response mechanisms just allow the bacteria to stay physiologically active and to employ long-term responses to assure viability upon changing environmental conditions. Here, we provide insight into the two aforementioned rapid adaptive mechanisms affecting ultimately the cell envelope of Gram-negative bacteria.

Sorption, transport and biodegradation - An insight into bioavailability of persistent organic pollutants in soil

Contamination of soils with persistent organic pollutants (POPs), such as organochlorine pesticide, polybrominated diphenyl ethers, halohydrocarbon, polycyclic aromatic hydrocarbons (PAHs) is of increasing concern. Microbial degradation is potential mechanism for the removal of POPs, but it is often restricted by low bioavailability of POPs. Thus, it is important to enhance bioavailability of POPs in soil bioremediation. A series of reviews on bioavailability of POPs has been published in the past few years. However, bioavailability of POPs in relation to soil organic matter, minerals and soil microbes has been little studied. To fully understand POPs bioavailability in soil, research on interactions of POPs with soil components and microbial responses in bioavailability limitation conditions are needed. This review focuses on bioavailability mechanisms of POPs in terms of sorption, transport and microbial adaptation, which is particularly novel. In consideration of the significance of bioavailability, further studies should investigate the influence of various bioremediation strategies on POPs bioavailability.

Impact of Polymer Colonization on the Fate of Organic Contaminants in Sediment

Plastic pellets and microbes are important constitutes in sediment, but the significance of microbes colonizing on plastic pellets to the environmental fate and transport of organic contaminants has not been adequately recognized and assessed. To address this issue, low-density polyethylene (LDPE), polyoxymethylene (POM) and polypropylene (PP) slices were preloaded with dichlorodiphenyltrichloroethanes (DDTs), polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) and incubated in abiotic and biotic sediment microcosms. Images from scanning electron microscope, Lysogeny Broth agar plates and confocal laser scanning microscope indicated that all polymer slices incubated in biotic sediments were colonized by microorganisms, particularly the LDPE slices. The occurrence of biofilms induced higher dissipation rates of DDTs and PAHs from the LDPE slice surfaces incubated in the biotic sediments than in the abiotic sediments. Plastic colonization on LDPE slice surfaces enhanced the biotransformation of DDT and some PAHs in both marine and river sediments, but had little impact on PCBs. By comparison, PP and POM with unique properties were shown to exert different impacts on the physical and microbial activities as compared to LDPE. These results clearly demonstrated that the significance of polymer surface affiliated microbes to the environmental fate and behavior of organic contaminants should be recognized.

Enhanced biodegradation of PAHs in historically contaminated soil by M. gilvum inoculated biochar

The inoculation of rice straw biochar with PAH-degrading Mycobacterium gilvum (1.27 × 10¹¹ ± 1.24 × 10¹⁰ cell g^-1), and the subsequent amendment of this composite material to PAHs contaminated (677 mg kg^-1) coke plant soil, was conducted in order to investigate if would enhance PAHs biodegradation in soils. The microbe-biochar composite showed superior degradation capacity for phenanthrene, fluoranthene and pyrene. Phenanthrene loss in the microbe-biochar composite, free cell alone and biochar alone treatments was, respectively, 62.6 ± 3.2%, 47.3 ± 4.1% and non-significant (P > 0.05); whereas for fluoranthene loss it was 52.1 ± 2.3%; non-significant (P > 0.05) and non-significant (P > 0.05); and for pyrene loss it was 62.1 ± 0.9%; 19.7 ± 6.5% and 13.5 ± 2.8%. It was hypothesized that the improved remediation was underpinned by i) biochar enhanced mass transfer of PAHs from the soil to the carbonaceous biochar "sink", and ii) the subsequent degradation of the PAHs by the immobilized M. gilvum. To test this mechanism, a surfactant (Brij 30; 20 mg g^-1 soil), was added to impede PAHs mass transfer to biochar and sorption. The surfactant increased solution phase PAH concentrations and significantly (P < 0.05) reduced PAH degradation in the biochar immobilized M. gilvum treatments; indicating the enhanced degradation occurred between the immobilized M. gilvum and biochar sorbed PAHs.

Heterogenic response of prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces

Tons of anthropogenic silver nanoparticles (AgNPs) are assumed to be released into the environment due to their use in many consumer products. AgNPs are known to be toxic toward microorganisms and thus may harm their specific functions in ecosystems. Here we explore the impact of AgNPs on functioning of single cells in microbial populations at doses typically found in anthropogenic environments. The response of single cells to AgNPs was analyzed by flow cytometry and using the fluorescent dyes propidium iodide and DiBAC₄ (3) as markers for cell membrane disintegration and depolarization, respectively. The effects of 10-nm and 30-nm AgNPs on three bacterial species (Mycobacterium frederiksbergense, Pseudomonas putida, and Escherichia coli) showed that the populations split into affected cells and others not showing any malfunction, with varying abundances depending on strains and cell growth states. Further, the dissolution of AgNPs measured with 3 KDa ultrafiltration and inductively coupled plasma-mass-spectrometry to distinguish particle-related effects from toxicity of dissolved Ag revealed that Ag ions were the principal toxicant. AgNP aggregate formation was followed by dynamic light scattering and the aggregates' attachment to cell surfaces was visualized by transmission electron microscopy and scanning electron microscopy-energy dispersive X-ray spectroscopy. An increased AgNP-affected cell fraction relative to the Ag ion impact was identified. The study shows that individual cells in a population cope differently with AgNP induced stress by evolving heterogeneous phenotypes. The response is linked to cell death and cell energy depletion depending on cell type and cell growth states. The attachment of AgNP aggregates to cell surfaces seems to amplify the heterogeneous response. © 2017 International Society for Advancement of Cytometry.

Effects of rhamnolipids on the cell surface characteristics of Sphingomonas sp. GY2B and the biodegradation of phenanthrene

The mechanism of the interaction of rhamnolipids on strain GY2B.

Adaptive response of Rhodococcus opacus PWD4 to salt and phenolic stress on the level of mycolic acids

Mycolata form a group of Gram-positive bacteria with unique cell envelope structures that are known for their high tolerance against antibiotics and both aromatic and aliphatic hydrocarbons. An important part of the unique surface structure of the mycolata is the presence of long chain α-alkyl-β-hydroxy fatty acids, the mycolic acids. In order to investigate the adaptive changes in the mycolic acid composition, we investigated the composition of mycolic acids during the response both to osmotic stress caused by NaCl and to 4-chlorophenol in Rhodococcus opacus PWD4. This bacterium was chosen as it is known to adapt to different kinds of stresses. In addition, it is a potential biocatalyst in bioremediation as well as for biotechnological applications. In the present study, cells of R. opacus PWD4, grown in liquid cultures, responded to toxic concentrations of NaCl by increasing the ratio between mycolic acids and membrane phospholipid fatty acids (MA/PLFA-ratio). Cells reacted to both NaCl and 4-chlorophenol by decreasing both the average chain length and the unsaturation index of their mycolic acids. These changes in mycolic acid composition correlated with increases in cell surface hydrophobicity and saturation of membrane fatty acids, demonstrating the relation between mycolic acid and phospholipid synthesis and their contribution to cell surface properties of R. opacus PWD4.

High mycobacterial diversity in recreational lakes

Although nontuberculous mycobacteria (NTM) are natural inhabitants of freshwater ecosystems, few studies have focused on their distribution in these habitats. Thus, the knowledge about the abundance as well as the composition of NTM remains limited and patchy in these environments. In this context, a prospective study was performed to identify favourable habitats for mycobacteria in two recreational lakes. Mycobacterial density and diversity were measured using quantitative real-time PCR and the MiSeq Illumina platform. For both lakes, five compartments were investigated, i.e. water column, air-water interface, sediment, epilithon and epiphyton biofilms. Nontuberculous mycobacteria were detected in all compartments in large densities and displayed a remarkable diversity. NTM were dominated by fast-growing species. Lakes and compartments appeared to shape mycobacteria assemblage composition as well as their densities. In both lakes, some OTUs assigned to the species level were identified as related to known opportunistic pathogens.

A bio-hybrid material for adsorption and degradation of phenanthrene: bacteria immobilized on sawdust coated with a silica layer

Membrane permeability of bacteria immobilized in silica-coated sawdust was increased, and its metabolic activity toward Phe was enhanced.

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea

Bacterial colonization of marine plastic litter (MPL) is known for over four decades. Still, only a few studies on the plastic colonization process and its influencing factors are reported. In this study, seafloor MPL was sampled at different locations across the Belgian part of the North Sea to study bacterial community structure using 16S metabarcoding. These marine plastic bacterial communities were compared with those of sediment and seawater, and resin pellets sampled on the beach, to investigate the origin and uniqueness of plastic bacterial communities. Plastics display great variation of bacterial community composition, while each showed significant differences from those of sediment and seawater, indicating that plastics represent a distinct environmental niche. Various environmental factors correlate with the diversity of MPL bacterial composition across plastics. In addition, intrinsic plastic-related factors such as pigment content may contribute to the differences in bacterial colonization. Furthermore, the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization, and may confound comparisons of free-floating plastics. Our studies provide insights in the factors that shape plastic bacterial colonization and shed light on the possible role of plastic as transport vehicle for bacteria through the aquatic environment.

Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS

The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.

Experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene)

Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested it with three aerobic phenanthrene (PHE) degraders: Novosphingobium pentaromativorans US6-1, Sphingomonas sp. EPA505, and Sphingobium yanoikuyae B1. PHE was present as microcrystals, providing non-limiting conditions for growth. Total PHE and protein concentration were tracked over 6-12 days. The model was fitted to the test results for the rates of dissolution, metabolism, and growth. The strains showed similar efficiency, with vmax values of 12-18 g dw g(-1) d(-1), yields of 0.21 g g(-1), maximum growth rates of 2.5-3.8 d(-1), and decay rates of 0.04-0.05 d(-1). Sensitivity analysis with the model shows that (i) retention in crystals or NAPLs or by sequestration competes with biodegradation, (ii) bacterial growth conditions (dissolution flux and resulting chemical activity of substrate) are more relevant for the final state of the system than the initial biomass, and (iii) the desorption flux regulates the turnover in the presence of solid-state, sequestered (aged), or NAPL substrate sources.

Biodegradation of MC252 oil in oil:sand aggregates in a coastal headland beach environment

Unique oil:sand aggregates, termed surface residue balls (SRBs), were formed on coastal headland beaches along the northern Gulf of Mexico as emulsified MC252 crude oil mixed with sand following the Deepwater Horizon spill event. The objective of this study is to assess the biodegradation potential of crude oil components in these aggregates using multiple lines of evidence on a heavily-impacted coastal headland beach in Louisiana, USA. SRBs were sampled over a 19-month period on the supratidal beach environment with reasonable control over and knowledge of the residence time of the aggregates on the beach surface. Polycyclic aromatic hydrocarbons (PAHs) and alkane concentration ratios were measured including PAH/C30-hopane, C2/C3 phenanthrenes, C2/C3 dibenzothiophenes and alkane/C30-hopane and demonstrated that biodegradation was occurring in SRBs in the supratidal. These biodegradation reactions occurred over time frames relevant to the coastal processes moving SRBs off the beach. In contrast, submerged oil mat samples from the intertidal did not demonstrate chemical changes consistent with biodegradation. Review and analysis of additional biogeochemical parameters suggested the existence of a moisture and nutrient-limited biodegradation regime on the supratidal beach environment. At this location, SRBs possess moisture contents <2% and molar C:N ratios from 131–323, well outside of optimal values for biodegradation in the literature. Despite these limitations, biodegradation of PAHs and alkanes proceeded at relevant rates (2–8 year⁻¹) due in part to the presence of degrading populations, i.e., Mycobacterium sp., adapted to these conditions. For submerged oil mat samples in the intertidal, an oxygen and salinity-impacted regime is proposed that severely limits biodegradation of alkanes and PAHs in this environment. These results support the hypothesis that SRBs deposited at different locations on the beach have different biogeochemical characteristics (e.g., moisture, salinity, terminal electron acceptors, nutrient, and oil composition) due, in part, to their location on the landscape.

Biofilm formation of a bacterial consortium on linuron at micropollutant concentrations in continuous flow chambers and the impact of dissolved organic matter

Bacterial multispecies biofilms are catalysts for pollutant degradation in aqueous ecosystems. Their activity in systems where xenobiotics occur as micropollutants (μg L(-1) level) and natural dissolved organic matter provides carbon and energy instead remains uncharacterized. Biofilm formation of a bacterial consortium consisting of the linuron-degrading Variovorax sp. WDL1 and metabolite-degrading strains Comamonas sp. WDL7 and Hyphomicrobium sp. WDL6 at micropollutant linuron concentrations and the impact of auxiliary carbon sources on degradation and biofilm composition were investigated. Biofilms formed at concentrations of 1000, 100, and 10 μg L(-1) linuron. The highest biomass, organized in mixed-species mounds, was observed at 1000 μg L(-1) linuron, while at 100 and 10 μg L(-1) , thin layers of cells occurred. Linuron removal efficiencies decreased from c. 85% when fed with 100 and 1000 μg L(-1) linuron to 30% in case of 10 μg L(-1) linuron due to reduced specific activity. Biofilms grown on 10 μg L(-1) linuron were subsequently fed with easily and less degradable carbon sources in addition to 10 μg L(-1) linuron. Although co-feeding with more degradable C-sources increased biofilm biomass, linuron removal remained 30%. Calculations based on biofilm volume measurements pointed toward reduced specific activity, compensated by a higher biomass. Uncertainties about biofilm heterogeneity and cell volume can undo this explanation.

Practical considerations and challenges involved in surfactant enhanced bioremediation of oil

Surfactant enhanced bioremediation (SEB) of oil is an approach adopted to overcome the bioavailability constraints encountered in biotransformation of nonaqueous phase liquid (NAPL) pollutants. Fuel oils contain n-alkanes and other aliphatic hydrocarbons, monoaromatics, and polynuclear aromatic hydrocarbons (PAHs). Although hydrocarbon degrading cultures are abundant in nature, complete biodegradation of oil is rarely achieved even under favorable environmental conditions due to the structural complexity of oil and culture specificities. Moreover, the interaction among cultures in a consortium, substrate interaction effects during the degradation and ability of specific cultures to alter the bioavailability of oil invariably affect the process. Although SEB has the potential to increase the degradation rate of oil and its constituents, there are numerous challenges in the successful application of this technology. Success is dependent on the choice of appropriate surfactant type and dose since the surfactant-hydrocarbon-microorganism interaction may be unique to each scenario. Surfactants not only enhance the uptake of constituents through micellar solubilization and emulsification but can also alter microbial cell surface characteristics. Moreover, hydrocarbons partitioned in micelles may not be readily bioavailable depending on the microorganism-surfactant interactions. Surfactant toxicity and inherent biodegradability of surfactants may pose additional challenges as discussed in this review.

Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation

The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response.

Influence of mass transfer on stable isotope fractionation

Biodegradation of contaminants is a common remediation strategy for subsurface environments. To monitor the success of such remediation means a quantitative assessment of biodegradation at the field scale is required. Nevertheless, the reliable quantification of the in situ biodegradation process it is still a major challenge. Compound-specific stable isotope analysis has become an established method for the qualitative analysis of biodegradation in the field and this method is also proposed for a quantitative analysis. However, to use stable isotope data to obtain quantitative information on in situ biodegradation requires among others knowledge on the influence of mass transfer processes on the observed stable isotope fractionation. This paper reviews recent findings on the influence of mass transfer processes on stable isotope fractionation and on the quantitative interpretation of isotope data. Focus will be given on small-scale mass transfer processes controlling the bioavailability of contaminants. Such bioavailability limitations are known to affect the biodegradation rate and have recently been shown to affect stable isotope fractionation, too. Theoretical as well as experimental studies addressing the link between bioavailability and stable isotope fractionation are reviewed and the implications for assessing biodegradation in the field are discussed.

Marine crude-oil biodegradation: a central role for interspecies interactions

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.

Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods

Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.

Effects of rhamnolipids on cell surface hydrophobicity of PAH degrading bacteria and the biodegradation of phenanthrene

The effects of rhamnolipids produced by Pseudomonas aeruginosa ATCC9027 on the cell surface hydrophobicity (CSH) and the biodegradation of phenanthrene by two thermophilic bacteria, Bacillus subtilis BUM and P. aeruginosa P-CG3, and mixed inoculation of these two strains were investigated. Rhamnolipids significantly reduced the CSH of the hydrophobic BUM and resulted in a noticeable lag period in the biodegradation. However, they significantly increased the CSH and enhanced the biodegradation for the hydrophilic P-CG3. In the absence of rhamnolipids, a mixed inoculation of BUM and P-CG3 removed 82.2% of phenanthrene within 30 days and the major contributor of the biodegradation was BUM (rapid degrader) while the growth of P-CG3 (slow degrader) was suppressed. Addition of rhamnolipids promoted the surfactant-mediated-uptake of phenanthrene by P-CG3 but inhibited the uptake through direct contact by BUM. This resulted in the domination of P-CG3 during the initial stage of biodegradation and enhanced the biodegradation to 92.7%.

Novel Polyoxyethylene-Containing Glycolipids Are Synthesized in Corynebacterium matruchotii and Mycobacterium smegmatis Cultured in the Presence of Tween 80

The addition of polyoxyethylene sorbitan monooleate (Tween 80) to a culture of mycobacteria greatly influences cell permeability and sensitivity to antibiotics but very little is known regarding the underlying mechanism. Here we show that Corynebacterium matruchotii (surrogate of mycobacteria) converts Tween 80 to a structural series of polyoxyethylenic acids which are then used to form novel series-2A and series-2B glycolipids. Minor series-3 glycolipids were also synthesized. The polyoxyethylenic acids replaced corynomycolic acids in the cell wall. Correspondingly the trehalose dicorynomycolate content was reduced. MALDI mass spectrometry, MS-MS, ¹H-NMR, and ¹³C-NMR were used to characterize the series-2 glycolipids. Series-2A glycolipid is trehalose 6-C_36:2-corynomycolate-6′-polyoxyethylenate and series-2B glycolipid is trehalose 6-C_36:2-corynomycolate-6′-furan ring-containing polyoxyethylenate. Mycobacterium smegmatis grown in the presence of Tween 80 also synthesizes series-2 type glycolipids. The synthesis of these novel glycolipids in corynebacteria and mycobacteria should result in gross changes in the cell wall permeability and drug sensitivity.

Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria

Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low ( approximately 10(2) ppb; approximately 1 muM) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing

Motivated by the finding that Pseudomonas knackmussii B13 but not Rhodococcus opacus 1CP grows in the absence of externally provided CO(2), we investigated the assimilation of (13)CO(2) into active cells cultivated with non-labelled glucose as sole energy substrate. (13)C found in the bulk biomass indicated a substantial but different CO(2) assimilation by Pseudomonas and Rhodococcus, respectively (3500 per thousand and 2600 per thousand). Cellular fatty acids were labelled from -15 per thousand to 470 per thousand and amino acids from 500 per thousand to 24,000 per thousand demonstrating clear differences between various compound classes. 'You are what you eat plus 1 per thousand' is therefore only valid for the average bulk C without specific isotope signature deviation of the external CO(2) or carbonates. Odd-numbered and 10-methyl fatty acids, which are much more abundant in Rhodococcus or other Gram-positive bacteria, were up to fivefold higher enriched in (13)C relative to the Pseudomonas fatty acids. A high-level growth-phase-independent, labelling of the oxaloacetate-derived amino acids indicated heterotrophic CO(2) fixation by anaplerotic reactions known to replenish the tricarboxylic acid cycle. Although both strains assimilate CO(2) via similar general pathways, Rhodococcus depends to a much higher extent on carboxylations reactions with external CO(2) owing to the formation of odd-numbered fatty acids. As a general consequence, heterotrophic fixation of CO(2) should be taken into account in investigations of degradation experiments using isotope tracer compounds.

Differential responses of eubacterial, Mycobacterium, and Sphingomonas communities in polycyclic aromatic hydrocarbon (PAH)-contaminated soil to artificially induced changes in PAH profile

Recent reports suggest that Mycobacterium is better adapted to soils containing poorly bioavailable polycyclic aromatic hydrocarbons (PAHs) compared to Sphingomonas. To study this hypothesis, artificial conditions regarding PAH profile and PAH bioavailability were induced in two PAH-contaminated soils and the response of the eubacterial, Mycobacterium, and Sphingomonas communities to these changed conditions was monitored during laboratory incubation. Soil K3663 with a relatively high proportion of high molecular weight PAHs was amended with phenanthrene or pyrene to artificially change the soil into a soil with a relatively increased bioavailable PAH contamination. Soil AndE with a relatively high proportion of bioavailable low molecular weight PAHs was treated by a single-step Tenax extraction to remove the largest part of the easily bioavailable PAH contamination. In soil K3663, the added phenanthrene or pyrene compounds were rapidly degraded, concomitant with a significant increase in the number of phenanthrene and pyrene degraders, and minor and no changes in the Mycobacterium community and Sphingomonas community, respectively. However, a transient change in the eubacterial community related to the proliferation of several gamma-proteobacteria was noted in the phenanthrene-amended soil. In the extracted AndE soil, the Sphingomonas community initially developed into a more diverse community but finally decreased in size below the detection limit. Mycobacterium in that soil never increased to a detectable size, while the eubacterial community became dominated by a gamma-proteobacterial population. The results suggest that the relative bioavailability of PAH contamination in soil affects bacterial community structure but that the behavior of Mycobacterium and Sphingomonas in soil is more complex than prospected from studies on their ecology and physiology.

Growth and physiological response of Arthrobacter protophormiae RKJ100 toward higher concentrations of o-nitrobenzoate and p-hydroxybenzoate

Bioremediation of sites that are heavily contaminated with pollutant chemicals is a challenge as most of the microorganisms cannot tolerate higher concentrations of toxic compounds. Only a few strains of the genus Pseudomonas have been studied for their tolerance toward the higher concentrations of aromatic pollutant compounds, a phenomenon that is accompanied by various physiological changes. In the present study we have characterized the growth response and physiological changes (adaptations) of a Gram-positive bacterium, Arthrobacter protophormiae RKJ100, toward the higher concentrations of two aromatic compounds, viz. o-nitrobenzoate (ONB) and p-hydroxybenzoate (PHB). Arthrobacter protophormiae RKJ100 could utilize 30 mM ONB and 50 mM PHB as sole sources of carbon and energy. It was capable of growth on higher concentrations of ONB (up to 200 mM) and PHB (up to 150 mM) when the cells were pre-exposed to lower concentrations of these compounds. The adaptive responses shown by the organism during growth on higher concentrations of these compounds were evident from significant changes in cellular fatty acid profiles. In addition, Bacterial Adhesion To Hydrocarbon (BATH) assay and scanning electron microscopy showed substantial increase in cell surface hydrophobicity and decrease in cell size of A. protophormiae RKJ100 when grown on ONB and PHB as compared to succinate-grown cells.

Carbon conversion efficiency and limits of productive bacterial degradation of methyl tert-butyl ether and related compounds

The utilization of the fuel oxygenate methyl tert-butyl ether (MTBE) and related compounds by microorganisms was investigated in a mainly theoretical study based on the Y(ATP) concept. Experiments were conducted to derive realistic maintenance coefficients and K(s) values needed to calculate substrate fluxes available for biomass production. Aerobic substrate conversion and biomass synthesis were calculated for different putative pathways. The results suggest that MTBE is an effective heterotrophic substrate that can sustain growth yields of up to 0.87 g g(-1), which contradicts previous calculation results (N. Fortin et al., Environ. Microbiol. 3:407-416, 2001). Sufficient energy equivalents were generated in several of the potential assimilatory routes to incorporate carbon into biomass without the necessity to dissimilate additional substrate, efficient energy transduction provided. However, when a growth-related kinetic model was included, the limits of productive degradation became obvious. Depending on the maintenance coefficient m(s) and its associated biomass decay term b, growth-associated carbon conversion became strongly dependent on substrate fluxes. Due to slow degradation kinetics, the calculations predicted relatively high threshold concentrations, S(min), below which growth would not further be supported. S(min) strongly depended on the maximum growth rate mu(ma)(x), and b and was directly correlated with the half maximum rate-associated substrate concentration K(s), meaning that any effect impacting this parameter would also change S(min). The primary metabolic step, catalyzing the cleavage of the ether bond in MTBE, is likely to control the substrate flux in various strains. In addition, deficits in oxygen as an external factor and in reduction equivalents as a cellular variable in this reaction should further increase K(s) and S(min) for MTBE.

Influences of polycyclic aromatic hydrocarbons (PAHs) on soil microbial community composition with or without vegetation

Uptake of three polycyclic aromatic hydrocarbons (PAHs), naphthalene (NAP), phenanthrene (PHN), and pyrene (PYR), from soils by ryegrass, white clover and soybean were investigated in an 8-week pot experiment. The microbial phospholipid-fatty-acid (PLFA) patterns in PAHs-contaminated soil were analyzed. Contamination with PAHs inhibited the soil microbial activity. In non-vegetated soils, the total PLFA showed 87% reduction on the addition of PAHs after an 8-week incubation compared to the PAH-free soil; the concentrations of NAP, PHN, and PYR in soils showed 19.4%, 25.5% and 24.3% reduction, respectively, due mainly to the evaporative loss and microbial degradation. In vegetated soils, the reduction of added NAP and PHN levels was not related to the plant biomass nor to the total PLFA. However, the reduction in PYR concentrations in soil mediated by soybean growth was much pronounced than those by ryegrass or white clover growth, but thisis not related to the total microbial biomass as revealed by PLFAs. The principal-component analysis (PCA) of the PLFA signatures revealed significant changes in the PLFA pattern in PAH-spiked soils when different vegetations were planted. Using the PLFA as a biomarker, it was found that the Gram-negative bacteria were more sensitive to PAHs than Gram-positive bacteria and fungi.

Effect of inoculum pretreatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil

The survival and effectiveness of a bioaugmentation strain in its target environment depend not only on physicochemical parameters in the soil but also on the physiological state of the inoculated organism. This study examined the effect of variations in inoculum pretreatment on the survival, metabolic activity (measured as rRNA content) and polycyclic aromatic hydrocarbon (PAH)-catabolic gene expression of Sphingobium yanoikuyae B1 in an aged PAH-contaminated soil. RNA denaturing gradient gel electrophoresis analysis showed stable colonization of PAH-contaminated soil by S. yanoikuyae B1 after four pretreatments (growth in complex or minimal medium, starvation, or acclimation to phenanthrene). By contrast, extractable CFUs decreased with time for all four treatments, and significantly faster for Luria Bertani-grown inocula, suggesting that these cells adhered strongly to soil particles while remaining metabolically active. Pretreatment of the inoculum had a dramatic effect on the expression of genes specific to the PAH-degradation pathway. The highest levels of bphC and xylE expression were seen for inocula that had been precultivated on complex medium, and degradation of PAHs was significantly enhanced in soils treated with these inocula. The results suggest that using complex media instead of minimal media for cultivating bioaugmentation inocula may improve the subsequent efficiency of contaminant biodegradation in the soil.

Energetics and surface properties of Pseudomonas putida DOT-T1E in a two-phase fermentation system with 1-decanol as second phase

The solvent-tolerant strain Pseudomonas putida DOT-T1E was grown in batch fermentations in a 5-liter bioreactor in the presence and absence of 10% (vol/vol) of the organic solvent 1-decanol. The growth behavior and cellular energetics, such as the cellular ATP content and the energy charge, as well as the cell surface hydrophobicity and charge, were measured in cells growing in the presence and absence of 1-decanol. Although the cells growing in the presence of 1-decanol showed an about 10% reduced growth rate and a 48% reduced growth yield, no significant differences were measured either in the ATP and potassium contents or in the energy charge, indicating that the cells adapted completely at the levels of membrane permeability and energetics. Although the bacteria needed additional energy for adaptation to the presence of the solvent, they were able to maintain or activate electron transport phosphorylation, allowing homeostasis of the ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities and more negative cell surface charges were observed in cells grown in the presence of 1-decanol. Both reactions occurred within about 10 min after the addition of the solvent and were significantly different after killing of the cells with toxic concentrations of HgCl2. This adaptation of the surface properties of the bacterium to the presence of solvents seems to be very similar to previously observed reactions on the level of lipopolysaccharides, with which bacteria adapt to environmental stresses, such as heat shock, antibiotics, or low oxygen content. The results give clear physiological indications that the process with P. putida DOT-T1E as the biocatalyst and 1-decanol as the solvent is a stable system for two-phase biotransformations that will allow the production of fine chemicals in economically sound amounts.

Distribution of the Mycobacterium community and polycyclic aromatic hydrocarbons (PAHs) among different size fractions of a long-term PAH-contaminated soil

Summary Mycobacterium is often isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil as degraders of PAHs. In model systems, Mycobacterium shows attachment to the PAH substrate source, which is considered to be a particular adaptation to low bioavailability as it results into increased substrate flux to the degraders. To examine whether PAH-degrading Mycobacterium in real PAH-contaminated soils, in analogy with model systems, are preferentially associated with PAH-enriched soil particles, the distribution of PAHs, of the PAH-mineralizing capacity and of Mycobacterium over different fractions of a soil with an aged PAH contamination was investigated. The clay fraction contained the majority of the PAHs and showed immediate pyrene- and phenanthrene-mineralizing activity upon addition of (14)C-labelled pyrene or phenanthrene. In contrast, the sand and silt fractions showed a lag time of 15-26 h for phenanthrene and 3-6 days for pyrene mineralization. The maximum pyrene and phenanthrene mineralization rates of the clay fraction expressed per gram fraction were three to six times higher than those of the sand and silt fractions. Most-probable-number (MPN)-polymerase chain reaction demonstrated that Mycobacterium represented about 10% of the eubacteria in the clay fraction, while this was only about 0.1% in the sand and silt fractions, indicating accumulation of Mycobacterium in the PAH-enriched clay fraction. The Mycobacterium community composition in the clay fraction represented all dominant Mycobacterium populations of the bulk soil and included especially species related to Mycobacterium pyrenivorans, which was also recovered as one of the dominant species in the eubacterial communities of the bulk soil and the clay fraction. Moreover, Mycobacterium could be identified among the major culturable PAH-degrading populations in both the bulk soil and the clay fraction. The results demonstrate that PAH-degrading mycobacteria are mainly associated with the PAH-enriched clay fraction of the examined PAH-contaminated soil and hence, that also in the environmental setting of a PAH-contaminated soil, Mycobacterium might experience advantages connected to substrate source attachment.