Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase

Bacterial coenzyme B12-dependent 2-hydroxyisobutyryl-CoA mutase (HCM) is a radical enzyme catalyzing the stereospecific interconversion of (S)-3-hydroxybutyryl- and 2-hydroxyisobutyryl-CoA. It consists of two subunits, HcmA and HcmB. To characterize the determinants of substrate specificity, we have analyzed the crystal structure of HCM from Aquincola tertiaricarbonis in complex with coenzyme B12 and the substrates (S)-3-hydroxybutyryl- and 2-hydroxyisobutyryl-CoA in alternative binding. When compared with the well studied structure of bacterial and mitochondrial B12-dependent methylmalonyl-CoA mutase (MCM), HCM has a highly conserved domain architecture. However, inspection of the substrate binding site identified amino acid residues not present in MCM, namely HcmA Ile(A90) and Asp(A117). Asp(A117) determines the orientation of the hydroxyl group of the acyl-CoA esters by H-bond formation, thus determining stereospecificity of catalysis. Accordingly, HcmA D117A and D117V mutations resulted in significantly increased activity toward (R)-3-hydroxybutyryl-CoA. Besides interconversion of hydroxylated acyl-CoA esters, wild-type HCM as well as HcmA I90V and I90A mutant enzymes could also isomerize pivalyl- and isovaleryl-CoA, albeit at >10 times lower rates than the favorite substrate (S)-3-hydroxybutyryl-CoA. The nonconservative mutation HcmA D117V, however, resulted in an enzyme showing high activity toward pivalyl-CoA. Structural requirements for binding and isomerization of highly branched acyl-CoA substrates such as 2-hydroxyisobutyryl- and pivalyl-CoA, possessing tertiary and quaternary carbon atoms, respectively, are discussed.

A whole cell bioreporter approach to assess transport and bioavailability of organic contaminants in water unsaturated systems

Bioavailability of contaminants is a prerequisite for their effective biodegradation in soil. The average bulk concentration of a contaminant, however, is not an appropriate measure for its availability; bioavailability rather depends on the dynamic interplay of potential mass transfer (flux) of a compound to a microbial cell and the capacity of the latter to degrade the compound. In water-unsaturated parts of the soil, mycelia have been shown to overcome bioavailability limitations by actively transporting and mobilizing organic compounds over the range of centimeters. Whereas the extent of mycelia-based transport can be quantified easily by chemical means, verification of the contaminant-bioavailability to bacterial cells requires a biological method. Addressing this constraint, we chose the PAH fluorene (FLU) as a model compound and developed a water unsaturated model microcosm linking a spatially separated FLU point source and the FLU degrading bioreporter bacterium Burkholderia sartisoli RP037-mChe by a mycelial network of Pythium ultimum. Since the bioreporter expresses eGFP in response of the PAH flux to the cell, bacterial FLU exposure and degradation could be monitored directly in the microcosms via confocal laser scanning microscopy (CLSM). CLSM and image analyses revealed a significant increase of the eGFP expression in the presence of P. ultimum compared to controls without mycelia or FLU thus indicating FLU bioavailability to bacteria after mycelia-mediated transport. CLSM results were supported by chemical analyses in identical microcosms. The developed microcosm proved suitable to investigate contaminant bioavailability and to concomitantly visualize the involved bacteria-mycelial interactions.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Cytometric patterns reveal growth states of Shewanella putrefaciens

Bacterial growth is often difficult to estimate beyond classical cultivation approaches. Low cell numbers, particles or coloured and dense media may disturb reliable growth assessment. Further difficulties appear when cells are attached to surfaces and detachment is incomplete.

Therefore, flow cytometry was tested and used for analysis of bacterial growth on the single-cell level. Shewanella putrefaciens was cultivated as a model organism in planktonic or biofilm culture. Materials of smooth and rough surfaces were used for biofilm cultivation. Both aerobic and anaerobic as well as feast and famine conditions were applied. Visualization of growth was also done using Environmental Scanning and Phase Contrast Microscopy. Bioinformatic tools were applied for data interpretation.

Cytometric proliferation patterns based on distributions of DNA contents per cell corresponded distinctly to the various lifestyles, electron acceptors and substrates tested. Therefore, cell cycling profiles of S. putrefaciens were found to mirror growth conditions.

The cytometric patterns were consistently detectable with exception of some biofilm types whose resolution remained challenging. Corresponding heat maps proved to be useful for clear visualization of growth behaviour under all tested conditions. Therefore, flow cytometry in combination with bioinformatic tools proved to be powerful means to determine various growth states of S. putrefaciens, even in constrained environments. The approach is universal and will also be applicable for other bacterial species.

Stable isotope composition of biogas allows early warning of complete process failure as a result of ammonia inhibition in anaerobic digesters

Four 15-L lab-scale continuous stirred tank reactors were operated under mesophilic conditions to investigate the effect of ammonia inhibition. Stable isotope fingerprinting of biogas was applied as a process monitoring tool. Ammonia inhibition was initiated by amendment of chicken manure to maize silage fed reactors. During the accumulation of ammonia, the concentration of volatile fatty acids increased while the biogas production and pH decreased. However, in one reactor, an inhibited steady state with stable gas production even at high ammonia levels was achieved, while the other reactor proceeded to complete process failure. A depletion of the δ(13)CH4 and δ(13)CO2 values preceded the process inhibition. Moreover, the stable isotope composition of biogas also forecasted the complete process failure earlier than other standard parameters. The stable isotope analyses of biogas have a potential for mechanistic insights in anaerobic processes, and may be used to pre-warn process failure under stress conditions.

Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer

Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.

Analysis of aging in lager brewing yeast during serial repitching

Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the same brewing yeast strain but different abiotic backgrounds and repitching regimes with varying numbers of reuses. Next to bud scar numbers the DNA content of the Saccharomyces pastorianus HEBRU cells was analyzed. Gene expression patterns were investigated using low-density microarrays with genes for aging, stress, storage compound metabolism and cell cycle. Two breweries showed a stable rejuvenation rate during serial repitching. In a third brewery the fraction of virgin cells varied, which could be explained with differing wort aeration rates. Furthermore, the number of bud scars per cell and cell size correlated in all 3 breweries throughout all runs. Transcriptome analyses revealed that from the 6th run on, mainly for the cells positive gene expression could be seen, for example up-regulation of trehalose and glycogen metabolism genes. Additionally, the cells' settling in the cone was dependent on cell size, with the lowest and the uppermost cone layers showing the highest amount of dead cells. In general, cells do not progressively age during extended serial repitching.

Diversity of protists and bacteria determines predation performance and stability

Predation influences prey diversity and productivity while it effectuates the flux and reallocation of organic nutrients into biomass at higher trophic levels. However, it is unknown how bacterivorous protists are influenced by the diversity of their bacterial prey. Using 456 microcosms, in which different bacterial mixtures with equal initial cell numbers were exposed to single or multiple predators (Tetrahymena sp., Poterioochromonas sp. and Acanthamoeba sp.), we showed that increasing prey richness enhanced production of single predators. The extent of the response depended, however, on predator identity. Bacterial prey richness had a stabilizing effect on predator performance in that it reduced variability in predator production. Further, prey richness tended to enhance predator evenness in the predation experiment including all three protists predators (multiple predation experiment). However, we also observed a negative relationship between prey richness and predator production in multiple predation experiments. Mathematical analysis of potential ecological mechanisms of positive predator diversity-functioning relationships revealed predator complementarity as a factor responsible for both enhanced predator production and prey reduction. We suggest that the diversity at both trophic levels interactively determines protistan performance and might have implications in microbial ecosystem processes and services.

Predicting post-stroke pneumonia: the PANTHERIS score

OBJECTIVES

Stroke-associated pneumonia (SAP) is a common complication with a known negative impact on neurological outcome. We developed a score to identify patients at highest risk of SAP in order to promote prophylactic measures.

MATERIALS AND METHODS

We conducted a cohort study on a neurological intensive care unit in patients suffering from acute ischemic MCA infarction. Association of predefined demographics, comorbidities, and clinical characteristics with SAP was investigated using logistic regression analysis.

RESULTS

Between 2003 and 2010, a total of 335 patients were included in this analysis. Frequency of SAP was 31.3%. A 12-point scoring system was developed based on the following factors: Glasgow Coma Scale (GCS) [GCS < 9 = 5, GCS 9-12 = 2, GCS > 12 = 0], age [<60 = 0, 60-80 = 1, >80 = 2], increase in systolic arterial blood pressure >200 mmHg within the first 24 h after admission [no = 0, yes = 2], and white blood cell count >11.000/μl [no = 0, yes = 3]. The score revealed excellent discrimination (AUC = 0.85) and calibration (Nagelkerke's R² = 0.46) properties. Predictive properties were reproduced in an internal validation group.

CONCLUSIONS

The PANTHERIS score is a simple scoring system for the prediction of SAP based on easy-to-assess parameters. By identifying patients at high risk, it may guide intense monitoring or prophylactic measures. This score needs to be validated within external datasets.

Synthesis of the building block 2-hydroxyisobutyrate from fructose and butyrate by Cupriavidus necator H16

2-Hydroxyisobutyryl-coenzyme A mutase, originally discovered in the context of methyl tert-butyl ether degradation in Aquincola tertiaricarbonis L108, catalyzes the isomerization of 3-hydroxybutyryl-coenzyme A (3-HB-CoA) to 2-hydroxyisobutyryl-CoA. It thus constitutes the basis for a biotechnological route from practically any renewable carbon to 2-hydroxyisobutyrate (2-HIB) via the common metabolite 3-hydroxybutyrate. At first sight, recombinant Cupriavidus necator H16 expressing the mutase seems to be well suited for such a synthesis process, as a strong overflow metabolism via (R)-3-HB-CoA is easily induced in this bacterium possessing the poly-3-hydroxybutyrate metabolism. However, the recently established stereospecificity of the mutase, dominantly preferring the (S)-enantiomer of 3-HB-CoA, calls for a closer investigation of C. necator as potential 2-HIB production strain and raised the question about the strain's potential to yield 2-HIB from substrates directly providing (S)-3-HB-CoA. We compared two mutase-expressing C. necator H16 strains for their capability to synthesize 2-HIB from fructose and butyrate, delivering either (R)- or (S)-3-HB-CoA. Our results indicate that due to the enantiospecificity of the mutase, fructose is a weaker substrate for 2-HIB synthesis than butyrate. Production rates achieved with the PHB-negative strain H16 PHB(-)4 on butyrate were higher than on fructose. Using the wild-type did not significantly improve the production rates as the latter showed a 34-fold and a 5-fold lower 2-HIB synthesis rate compared to H16 PHB(-)4 on fructose and butyrate, respectively. Moreover, both strains showed concomitant excretion of undesired side products, such as pyruvate and 3-hydroxybutyrate, significantly decreasing the 2-HIB yield.

Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria

Mycelia have been recently shown to actively transport polycyclic aromatic hydrocarbons (PAH) in water-unsaturated soil over the range of centimeters, thereby efficiently mobilizing hydrophobic PAH beyond their purely diffusive transport in air and water. However, the question if mycelia-based PAH transport has an effect on PAH biodegradation was so far unsolved. To address this, we developed a laboratory model microcosm mimicking air-water interfaces in soil. Chemical analyses demonstrated transport of the PAH fluorene (FLU) by the mycelial oomycete Pythium ultimum that was grown along the air-water interfaces. Furthermore, degradation of mycelia-transported FLU by the bacterium Burkholderia sartisoli RP037-mChe was indicated. Since this organism expresses eGFP in response to a FLU flux to the cell, it was also as a bacterial reporter of FLU bioavailability in the vicinity of mycelia. Confocal laser scanning microscopy (CLSM) and image analyses revealed a significant increase of eGFP expression in the presence of P. ultimum compared to controls without mycelia or FLU. Hence, we could show that physically separated FLU becomes bioavailable to bacteria after transport by mycelia. Experiments with silicon coated glass fibers capturing mycelia-transported FLU guided us to propose a three-step mechanism of passive uptake, active transport and diffusion-driven release. These experiments were also used to evaluate the contributions of these individual steps to the overall mycelial FLU transport rate.

Evaluating the assignment of alkB terminal restriction fragments and sequence types to distinct bacterial taxa

Sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses revealed multiple alkB gene copies/cell in soil bacterial isolates and an apparently high genetic mobility among various phylogenetic groups. Identifying alkane degraders by alkB terminal restriction fragments (T-RFs) and sequences is strongly biased, as the phylogenetic trees based on 16S rRNA and alkB gene sequences were highly inconsistent.

Highways versus pipelines: contributions of two fungal transport mechanisms to efficient bioremediation

Based on experimental studies, two different fungus-mediated transport mechanisms have been suggested to facilitate the bacterial degradation of organic soil pollutants: bacteria may use liquid films around fungal hyphae for quick dispersal ('fungal highways'), and fungi may take up and translocate pollutants through their mycelial network ('fungal pipelines'). Both mechanisms are anticipated to enhance the bioavailability of pollutants to degrading bacteria. Using a microbial simulation model, we therefore investigated their respective efficiency in increasing biodegradation performance. We analysed networks that act either as bacterial dispersal vectors or as pollutant translocation vectors or as a combination of both. Our results suggest that each mechanism can improve biodegradation performance. The degree of improvement, however, varies distinctly depending on the environmental conditions, and is even negligible under certain conditions. Mycelial networks acting as 'highways' allow bacteria to overcome motility restrictions and reach remote areas, whereas networks acting as 'pipelines' may initiate degradation by bringing remote pollutants to bacteria. As a consequence, highest biodegradation improvements often emerge from the combination of both mechanisms. We conclude that 'fungal highways' as well as 'fungal pipelines' should be considered for developing novel bioremediation strategies based on fungus-mediated transport in soils.

Alkane-degrading bacteria at the soil-litter interface: comparing isolates with T-RFLP-based community profiles

Alkane-degrading bacteria were isolated from uncontaminated soil microcosms, which had been incubated with maize litter as natural alkane source. The isolates served to understand spatio-temporal community changes at the soil-litter interface, which had been detected using alkB as a functional marker gene for bacterial alkane degraders. To obtain a large spectrum of isolates, liquid subcultivation was combined with a matrix-assisted enrichment (Teflon membranes, litter). Elevated cell numbers of alkane degraders were detected by most probable number counting indicating enhanced alkane degradation potential in soil in response to litter treatment. Partial 16S rRNA gene sequencing of 395 isolates revealed forty different phylogenetic groups [operational taxonomic units (OTUs)] and spatio-temporal shifts in community composition. Ten OTUs comprised so far unknown alkane degraders, and five OTUs represented putative new bacterial genera. The combination of enrichment methods yielded a higher diversity of isolates than liquid subcultivation alone. Comparison of 16S rRNA gene T-RFLP profiles indicated that many alkane degraders present in the enrichments were not detectable in the DNA extracts from soil microcosms. These possibly rare specialists might represent a seed bank for the alkane degradation capacity in uncontaminated soil. This relevant ecosystem function can be fostered by the formation of the soil-litter interface.

Chip-calorimetric monitoring of biofilm eradication with antibiotics provides mechanistic information

Increased antibiotic resistance of pathogenic bacteria dwelling in biofilm structures has motivated the development of various monitoring tools specifically designed for biofilm investigations. In this study, the potential of the recently emerging chip calorimetry for this purpose was analysed. The activity of biofilms of Pseudomonas putida PaW340 was monitored chip-calorimetrically and compared with counts of colony forming units (CFU), bioluminescence-based ATP measurements, and quantitative confocal laser scanning microscopy (CLSM). The biofilms were treated with antibiotics differing in their mechanisms of action (bactericidal kanamycin vs. bacteriostatic tetracycline) and referenced to untreated biofilms. For untreated biofilms, all methods gave comparable results. Calorimetric killing curves, however, reflecting metabolic responses to biofilm eradication non-invasively in real time, differed from those obtained with the established methods. For instance, heat signals increased right after addition of the antibiotics. This transient increase of activity was not detected by the other methods, since only calorimetry delivers specific information about the catabolic part of the metabolism. In case of the bactericidal antibiotic, CFU misleadingly indicated successful biofilm eradication, whereas calorimetry revealed enduring activity. Our results show that calorimetry holds promise to provide valuable mechanistic information, thereby complementing other methods of biofilm analysis.

Monitoring functions in managed microbial systems by cytometric bar coding

Cytometric monitoring of microbial community dynamics can be used to estimate stability of technical microbial processes like biogas production by analysis of segregated cell abundance changes. In this study, structure variations of a biogas community were cytometrically recorded over 9 months and found to be of diagnostic value for process details. The reactor regime was intentionally disturbed with regard to substrate overload or H(2)S accumulation. A single-cell based approach called cytometric bar coding (CyBar) for fast identification of reactive subcommunities was used. Functionality of specific subcommunities was uncovered by processing CyBar data with abiotic reactor parameters using Spearman's correlation coefficient. Twenty subcommunities showed a discrete and divergent behavior. For example, a 4-fold substrate overload increased the cell number of two acidogenic index subcommunities to 176 and 193% within three days. Supplementary analyses were done using DNA fingerprinting, cloning, and sequencing. Bioreactor perturbations were shown to create cell abundance changes in subcommunities rather than variations in their phylogenetic composition. The used workflow and macros are ready-to-use tools and allow on-site monitoring and interpretation of variation in microbial community functions within a few hours.

Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments

Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.

Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium

Benzene is a major contaminant in various environments, but the mechanisms behind its biodegradation under strictly anoxic conditions are not yet entirely clear. Here we analyzed a benzene-degrading, sulfate-reducing enrichment culture originating from a benzene-contaminated aquifer by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). The time-resolved, quantitative analysis of carbon fluxes within the community supplied with either (13)C-labeled benzene or (13)C-labeled carbonate yielded different functional groups of organisms, with their peptides showing specific time dependencies of (13)C relative isotope abundance indicating different carbon utilization. Through a detailed analysis of the mass spectrometric (MS) data, it was possible to quantify the utilization of the initial carbon source and the metabolic intermediates. The functional groups were affiliated to Clostridiales, Deltaproteobacteria and Bacteroidetes/Chlorobi. The Clostridiales-related organisms were involved in benzene degradation, putatively by fermentation, and additionally used significant amounts of carbonate as a carbon source. The other groups of organisms were found to perform diverse functions, with Deltaproteobacteria degrading fermentation products and Bacteroidetes/Chlorobi being putative scavengers feeding on dead cells. A functional classification of identified proteins supported this allocation and gave further insights into the metabolic pathways and the interactions between the community members. This example shows how protein-SIP can be applied to obtain temporal and phylogenetic information about functional interdependencies within microbial communities.

Mycelia promote active transport and spatial dispersion of polycyclic aromatic hydrocarbons

To cope with heterogeneous subsurface environments mycelial microorganisms have developed a unique ramified growth form. By extending hyphae, they can obtain nutrients from remote places and transport them even through air gaps and in small pore spaces, repectively. To date, studies have been focusing on the role that networks play in the distribution of nutrients. Here, we investigated the role of mycelia for the translocation of nonessential substances, using polycyclic aromatic hydrocarbons (PAHs) as model compounds. We show that the hyphae of the mycelial soil oomycete Pythium ultimum function as active translocation vectors for a wide range of PAHs. Visualization by two-photon excitation microscopy (TPEM) demonstrated the uptake and accumulation of phenanthrene (PHE) in lipid vesicles and its active transport by cytoplasmic streaming of the hyphae ('hyphal pipelines'). In mycelial networks, contaminants were translocated over larger distances than by diffusion. Given their transport capacity and ubiquity, hyphae may substantially distribute remote hydrophobic contaminants in soil, thereby improving their bioavailability to bacterial degradation. Hyphal contaminant dispersal may provide an untapped potential for future bioremediation approaches.

Field testing of arsenic in groundwater samples of Bangladesh using a test kit based on lyophilized bioreporter bacteria

A test kit based on living, lyophilized bacterial bioreporters emitting bioluminescence as a response to arsenite and arsenate was applied during a field campaign in six villages across Bangladesh. Bioreporter field measurements of arsenic in groundwater from tube wells were in satisfying agreement with the results of spectroscopic analyses of the same samples conducted in the lab. The practicability of the bioreporter test in terms of logistics and material requirements, suitability for high sample throughput, and waste disposal was much better than that of two commercial chemical test kits that were included as references. The campaigns furthermore demonstrated large local heterogeneity of arsenic in groundwater, underscoring the use of well switching as an effective remedy to avoid high arsenic exposure.

Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA

Coenzyme B(12)-dependent acyl-CoA mutases are radical enzymes catalyzing reversible carbon skeleton rearrangements in carboxylic acids. Here, we describe 2-hydroxyisobutyryl-CoA mutase (HCM) found in the bacterium Aquincola tertiaricarbonis as a novel member of the mutase family. HCM specifically catalyzes the interconversion of 2-hydroxyisobutyryl- and (S)-3-hydroxybutyryl-CoA. Like isobutyryl-CoA mutase, HCM consists of a large substrate- and a small B(12)-binding subunit, HcmA and HcmB, respectively. However, it is thus far the only acyl-CoA mutase showing substrate specificity for hydroxylated carboxylic acids. Complete loss of 2-hydroxyisobutyric acid degradation capacity in hcmA and hcmB knock-out mutants established the central role of HCM in A. tertiaricarbonis for degrading substrates bearing a tert-butyl moiety, such as the fuel oxygenate methyl tert-butyl ether (MTBE) and its metabolites. Sequence analysis revealed several HCM-like enzymes in other bacterial strains not related to MTBE degradation, indicating that HCM may also be involved in other pathways. In all strains, hcmA and hcmB are associated with genes encoding for a putative acyl-CoA synthetase and a MeaB-like chaperone. Activity and substrate specificity of wild-type enzyme and active site mutants HcmA I90V, I90F, and I90Y clearly demonstrated that HCM belongs to a new subfamily of B(12)-dependent acyl-CoA mutases.

Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples

Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II.

The relevance of conditional dispersal for bacterial colony growth and biodegradation

Bacterial degradation is an ecosystem service that offers a promising method for the remediation of contaminated soils. To assess the dynamics and efficiency of bacterial degradation, reliable microbial simulation models, along with the relevant processes, are required. We present an approach aimed at improving reliability by studying the relevance and implications of an important concept from theoretical ecology in the context of a bacterial system: conditional dispersal denoting that the dispersal strategy depends on environmental conditions. Different dispersal strategies, which either incorporate or neglect this concept, are implemented in a bacterial model and results are compared to data obtained from laboratory experiments with Pseudomonas putida colonies growing on glucose agar. Our results show that, with respect to the condition of resource uptake, the model's correspondence to experimental data is significantly higher for conditional than for unconditional bacterial dispersal. In particular, these results support the hypothesis that bacteria disperse less when resources are abundant. We also show that the dispersal strategy has a considerable impact on model predictions for bacterial degradation of resources: disregarding conditional bacterial dispersal can lead to overestimations when assessing the performance of this ecosystem service.

Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment

Wastewater treatment often suffers from instabilities and the failure of specific functions such as biological phosphorus removal by polyphosphate accumulating organisms. Since most of the microorganisms involved in water clarification are unknown it is challenging to operate the process accounting for the permanent varying abiotic parameters and the complex composition and unrevealed metabolic capacity of a wastewater microbial community. Fulfilling the demands for water quality irrespective of substrate inflow conditions may emit severe problems if the limited management resources of municipal wastewater treatment plants are regarded. We used flow cytometric analyses of cellular DNA and polyphosphate to create patterns mirroring dynamics in community structure. These patterns were resolved in up to 15 subclusters, the presence and abundances of which correlated with abiotic data. The study used biostatistics to determine the kind and strength of the correlation. Samples investigated were obtained from a primary clarifier and two activated sludge basins. The stability of microbial community structure was found to be high in the basins and low in the primary clarifier. Despite major abiotic changes certain subcommunities were dominantly present (up to 80% stability), whereas others emerged only sporadically (down to 3% stability, both according to equivalence testing). Additionally, subcommunities of diagnostic value were detected showing positive correlation with substrate influxes. For instance blackwater (r(s) = 0.5) and brewery inflow (both r(s) = 0.6) were mirrored by increases in cell abundances in subclusters 1 and 6 as well as 4 and 8, respectively. Phosphate accumulation was obviously positively correlated with nitrate (r(s) = 0.4) and the presence of denitrifying organisms (Rhodacyclaceae). Various other correlations between community structure and abiotic parameters were apparent. The bacterial composition of certain subcommunities was determined by cell sorting and phylogenetic tools like T-RFLP. In essence, we developed a monitoring tool which is quick, cheap and causal in its interpretation. It will make laborious PCR based technique less obligatory as it allows reliable process monitoring and control in wastewater treatment plants.

Chip-calorimetry provides real time insights into the inactivation of biofilms by predatory bacteria

Control or removal of undesired biofilms has frequently been found to be quite difficult. In addition to biocidal or antibiotic chemicals or materials designed to prevent biofouling, biological control agents appear to be promising. Reports of bacterial predators eradicating biofilms or eliminating pathogens motivate a more systematic screening of biofilm-eliminating bacterial predators. Unfortunately, the analysis of the eradication process is demanding. In the present study, chip-calorimetry was applied to monitor the elimination of Pseudomonas sp. biofilms by Bdellovibrio bacteriovorus. The method uses metabolic heat as a real-time parameter for biofilm activity. The method is non-invasive, fast and convenient due to real-time data acquisition. In addition, heat-production data can reveal information about the energetics of the predator-prey interaction. The calorimetric results were validated by confocal laser scanning microscopy. The approach described may be useful for the screening of biofilm susceptibility to different predators.

Use of mycelia as paths for the isolation of contaminant-degrading bacteria from soil

Mycelia of fungi and soil oomycetes have recently been found to act as effective paths boosting bacterial mobility and bioaccessibility of contaminants in vadose environments. In this study, we demonstrate that mycelia can be used for targeted separation and isolation of contaminant‐degrading bacteria from soil. In a ‘proof of concept’ study we developed a novel approach to isolate bacteria from contaminated soil using mycelia of the soil oomycete Pythium ultimum as translocation networks for bacteria and the polycyclic aromatic hydrocarbon naphthalene (NAPH) as selective carbon source. NAPH‐degrading bacterial isolates were affiliated with the genera Xanthomonas, Rhodococcus and Pseudomonas. Except for Rhodococcus the NAPH‐degrading isolates exhibited significant motility as observed in standard swarming and swimming motility assays. All steps of the isolation procedures were followed by cultivation‐independent terminal 16S rRNA gene terminal fragment length polymorphism (T‐RFLP) analysis. Interestingly, a high similarity (63%) between both the cultivable NAPH‐degrading migrant and the cultivable parent soil bacterial community profiles was observed. This suggests that mycelial networks generally confer mobility to native, contaminant‐degrading soil bacteria. Targeted, mycelia‐based dispersal hence may have high potential for the isolation of bacteria with biotechnologically useful properties.

Dissolved organic carbon enhances the mass transfer of hydrophobic organic compounds from nonaqueous phase liquids (NAPLs) into the aqueous phase

The hypothesis that dissolved organic carbon (DOC) enhances the mass transfer of hydrophobic organic compounds from nonaqueous phase liquids (NAPLs) into the aqueous phase above that attributable to dissolved molecular diffusion alone was tested. In controlled experiments, mass transfer rates of five NAPL-phase PAHs (log K(OW) 4.15-5.39) into the aqueous phase containing different concentrations of DOC were measured. Mass transfer rates were increased by up to a factor of 4 in the presence of DOC, with the greatest enhancement being observed for more hydrophobic compounds and highest DOC concentrations. These increases could not be explained by dissolved molecular diffusion alone, and point to a parallel DOC-mediated diffusive pathway. The nature of the DOC-mediated diffusion pathway as a function of the DOC concentration and PAH sorption behavior to the DOC was investigated using diffusion-based models. The DOC-enhanced mass transfer of NAPL-phase hydrophobic compounds into the aqueous phase has important implications for their bioremediation as well as bioconcentration and toxicity.

Dispersal networks for enhancing bacterial degradation in heterogeneous environments

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils.

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.

Numerical approach to speciation and estimation of parameters used in modeling trace metal bioavailability

Speciation affects trace metal bioavailability. One model used to describe the importance of speciation is the biotic ligand model (BLM), wherein the competition of inorganic and organic ligands with a biotic ligand for free-ion trace metal determines the ultimate metal availability to biota. This and similar models require natural ligand concentrations and conditional stability constants as input parameters. In concept, the BLM is itself an analogue of some analytical approaches to the determination of trace metal speciation. A notable example is competitive ligand equilibration/cathodic stripping voltammetry, which employs an artificial ligand for comparative assessment of natural ligand concentrations and discrete conditional stability constants (i.e., BLM parameters) in a natural sample. Here, we report a new numerical approach to voltammetric speciation and parameter estimation that employs multiple analytical windows and a two-step optimization process, simultaneously generating both parameters and a complete suite of corresponding species concentrations. This approach is more powerful, systematic, and flexible than those previously reported.

Internal arsenite bioassay calibration using multiple bioreporter cell lines

Bioassays with bioreporter bacteria are usually calibrated with analyte solutions of known concentrations that are analysed along with the samples of interest. This is done as bioreporter output (the intensity of light, fluorescence or colour) does not only depend on the target concentration, but also on the incubation time and physiological activity of the cells in the assay. Comparing the bioreporter output with standardized colour tables in the field seems rather difficult and error‐prone. A new approach to control assay variations and improve application ease could be an internal calibration based on the use of multiple bioreporter cell lines with drastically different reporter protein outputs at a given analyte concentration. To test this concept, different Escherichia coli‐based bioreporter strains expressing either cytochrome c peroxidase (CCP, or CCP mutants) or β‐galactosidase upon induction with arsenite were constructed. The reporter strains differed either in the catalytic activity of the reporter protein (for CCP) or in the rates of reporter protein synthesis (for β‐galactosidase), which, indeed, resulted in output signals with different intensities at the same arsenite concentration. Hence, it was possible to use combinations of these cell lines to define arsenite concentration ranges at which none, one or more cell lines gave qualitative (yes/no) visible signals that were relatively independent of incubation time or bioreporter activity. The discriminated concentration ranges would fit very well with the current permissive (e.g. World Health Organization) levels of arsenite in drinking water (10 µg l⁻¹).

Activity and viability of polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LB126 in a DC-electrical field typical for electrobioremediation measures

There has been growing interest in employing electro‐bioremediation, a hybrid technology of bioremediation and electrokinetics for the treatment of contaminated soil. Knowledge however on the effect of weak electrokinetic conditions on the activity and viability of pollutant‐degrading microorganisms is scarce. Here we present data about the influence of direct current (DC) on the membrane integrity, adenosine triphosphate (ATP) pools, physico‐chemical cell surface properties, degradation kinetics and culturability of fluorene‐degrading Sphingomonas sp. LB126. Flow cytometry was applied to quantify the uptake of propidium iodide (PI) and the membrane potential‐related fluorescence intensities (MPRFI) of individual cells within a population. Adenosine tri‐phosphate contents and fluorene biodegradation rates of bulk cultures were determined and expressed on a per cell basis. The cells' surface hydrophobicity and electric charge were assessed by contact angle and zeta potential measurements respectively. Relative to the control, DC‐exposed cells exhibited up to 60% elevated intracellular ATP levels and yet remained unaffected on all other levels of cellular integrity and functionality tested. Our data suggest that direct current (X = 1 V cm⁻¹; J = 10.2 mA cm⁻²) as typically used for electrobioremediation measures has no negative effect on the activity of the polycyclic aromatic hydrocarbon (PAH)‐degrading soil microorganism, thereby filling a serious gap of the current knowledge of the electrobioremediation methodology.

Microbial growth with vapor-phase substrate

Limited information exists on influences of the diffusive transport of volatile organic contaminants (VOC) on bacterial activity in the unsaturated zone of the terrestrial subsurface. Diffusion of VOC in the vapor-phase is much more efficient than in water and results in effective VOC transport and high bioavailability despite restricted mobility of bacteria in the vadose zone. Since many bacteria tend to accumulate at solid-water, solid-air and air-water interfaces, such phase boundaries are of a special interest for VOC-biodegradation. In an attempt to evaluate microbial activity toward air-borne substrates, this study investigated the spatio-temporal interplay between growth of Pseudomonas putida (NAH7) on vapor-phase naphthalene (NAPH) and its repercussion on vapor-phase NAPH concentrations. Our data demonstrate that growth rates of strain PpG7 were inversely correlated to the distance from the source of vapor-phase NAPH. Despite the high gas phase diffusivity of NAPH, microbial growth was absent at distances above 5 cm from the source when sufficient biomass was located in between. This indicates a high efficiency of suspended bacteria to acquire vapor-phase compounds and influence headspace concentration gradients at the centimeter-scale. It further suggests a crucial role of microorganisms as biofilters for gas-phase VOC emanating from contaminated groundwater or soil.