Bioremediation of organic waste sites: A critical review of microbiological aspects

An overview is presented of the potential for bioremediation of a range of contaminated sites. Most of the compounds belong to groups that are widespread and are generally persistent or toxic. Although attention has been focused on microbiological aspects of their application, it is pointed out that a successful programme requires integrated input from geologists, engineers, chemists and microbiologists. It is emphasized that a protocol must be available for evaluating the success of the procedures that have been implemented. Attention is directed to critical issues, including partial degradation, formation of metabolites, and recalcitrance of specific components in complex mixtures. An attempt is made to discuss the basic aspects of the biodegradation of components specific to the various sites and to illustrate the outcome of experiments in bioremediation in laboratory-based, pilot-scale or full-scale field operations. Brief discussion is given of some less commonly perceived contaminants that may be present simultaneously.     

Initial steps in the degradation of benzene sulfonic acid, 4-toluene sulfonic acids,and orthanilic acid in Alcaligenes sp. strain O-1

Alcaligenes sp. strain O-1 grew with benzene sulfonate (BS) as sole carbon source for growth with either NH₄ ⁺ or NH₄ ⁺ plus orthanilate (2-aminobenzene sulfonate, OS) as the source(s) of nitrogen. The intracellular desulfonative enzyme did not degrade 3- or 4-aminobenzene sulfonates in the medium, although the enzyme in cell extracts degraded these compounds. We deduce the presence of a selective permeability barrier to sulfonates and conclude that the first step in sulfonate metabolism is transport into the cell. Cell-free desulfonation of BS in standard reaction mixtures required 2 mol of O₂ per mol. One mol of O₂ was required for a catechol 2,3-dioxygenase. When meta ring cleavage was inhibited with 3-chlorocatechol in desalted extracts, about 1 mol each of O₂ and of NAD(P)H per mol of BS were required for the reaction, and SO₃ ^2- and catechol were recovered in high yield. Catechol was shown to be formed by dioxygenation in an experiment involving ¹⁸O₂. 4-Toluene sulfonate was subject to NAD(P)H-dependent dioxygenation to yield SO₃ ^2- and 4-methylcatechol, which was subject to meta cleavage. OS also required 2 mol of O₂ per mol and NAD(P)H for degradation, and SO₃ ^2- and NH₄ ⁺ were recovered quantitatively. Inhibition of ring cleavage with 3-chrorocatechol reduced the oxygen requirement to 1 mol per mol of OS SO₃ ^2- (1 mol) and an unidentified organic intermediate, but no NH₄ ⁺, were observed.     

Transformations of Halogenated Aromatic Aldehydes by Metabolically Stable Anaerobic Enrichment Cultures

Metabolically stable enrichment cultures of anaerobic bacteria obtained by elective enrichment of sediment samples from the Baltic Sea and Gulf of Bothnia have been used to study the oxidation and reduction of the aldehyde group of various halogenated aromatic aldehydes. During the transformation of 5- and 6-chlorovanillin, 6-bromovanillin, 3-chloro-4-hydroxybenzaldehyde, 3,5-dichloro-4-hydroxybenzaldehyde, and 3,5-dibromo-4-hydroxybenzaldehyde, it was shown that synthesis of the corresponding carboxylic acids, which were the principal metabolites, was invariably accompanied by partial reduction of the aldehyde to a hydroxymethyl group in yields of between 3 and 30%. Complete reduction to a methyl group was observed with some of the halogenated vanillins, but to an extremely limited extent with the halogenated 4-hydroxybenzaldehydes. One consortium produced both the hydroxymethyl and methyl compounds from both 5- and 6-chlorovanillin: it was therefore assumed that the methyl compound was the ultimate reduction product. On the basis of the kinetics of formation of the metabolites, it was concluded that the oxidation and reduction reactions were mechanistically related. In addition to these oxidations and reductions, dehalogenation was observed with one of the consortia. In contrast to the transformations of 5- and 6-chlorovanillin, which produced chlorinated methylcatechols, the corresponding compounds were not observed with 5- and 6-bromovanillin: the former was debrominated, forming 4-methylcatechol, whereas the latter produced 6-bromovanillyl alcohol without demethylation. Similarly, although 3-chloro-4-hydroxybenzaldehyde formed the chlorinated carboxylic acid and the benzyl alcohol, the 3-bromo compound was debrominated with formation of 4-hydroxybenzoic acid and, ultimately, phenol. On prolonged incubation, the halogenated carboxylic acids were generally decarboxylated, so that the final products from these substrates were halogenated catechols or phenols. Reductive processes of the type revealed in this study might therefore plausibly occur in the environment during anaerobic transformation of halogenated aromatic aldehydes containing hydroxyl and/or methoxyl groups.     

Reaction of Vanadyl with Hydrogen Peroxide. An ESR and Spin Trapping Study

Vanadyl reacts with hydrogen peroxide forming hydroxyl radicals in a Fenton-like reaction. The hydroxyl radicals were spin trapped and identified using 5.5-dimethyl-I-pyrroline-N-oxide (DMPO). The quantity of hydroxyl radicals spin trapped during the reaction between vanadyl and hydrogen peroxide are equal to half of the hydroxyl radicals spin trapped during the reaction between ferrous ions and hydrogen peroxide. Experiments in the presence of formate show that this hydroxyl radical scavenger effectively competes with DMPO preventing the formation of the DMPO-OH adduct. However. in experiments using ethanol as the hydroxyl radical scavenger it was not possible to completely prevent the formation of DMPO-OH. The formation of this additional DMPO-OH in the presence of ethanol does not depend on the concentration of dissolved oxygen, but does depend on the concentration of hydrogen peroxide added to the vanadyl solution. The results suggest that the additional DMPO-OH formed in the presence of ethanol originates from a vanadium (V) intermediate. This intermediate may oxidize DMPO leading to the formation of DMPO-0; which rapidly decomposes forming DMPO-OH.     

Energetic constraints and foraging efficiency

Previous research considers foraging options that differ interms of their gross rate of gain b and rate of energy expenditurec. This research argues that maximizing efficiency b/c willmaximize net energetic gain when there is an upper limit onthe amount of energy that can be assimilated. This analysisdoes not include the expenditure during the time for which theanimal is unable to forage because of this constraint. Whenthis expenditure is included, maximizing efficiency is no longeroptimal. Instead the best feeding option is the one with thehighest value of b/(c – c₁), where c, is the metabolicrate when the animal is not foraging.     

Avian daily foraging patterns: Effects of digestive constraints and variability

Summary Birds show a typical daily pattern of heavy morning and secondary afternoon feeding. We investigate the pattern of foraging by a bird that results in the lowest long-term rate of mortality. We assume the following: mortality is the sum of starvation and predation. The bird is characterized by two state variables, its energy reserves and the amount of food in its stomach. Starvation occurs during the day if the bird's reserves fall to zero. The bird starves during the night if the total energy stored in reserves and the stomach is less than a critical amount. The probability that the bird is killed by a predator is higher if the bird is foraging than if it is resting. Furthermore, the predation risk while foraging increases with the bird's mass. From these assumptions, we use dynamic programming techniques to find the daily foraging routine that minimizes mortality. The principal results are (1) Variability in food finding leads to routines with feeding concentrated early in the day, (2) digestive constraints cause feeding to be spread more evenly through the day, (3) even under fairly severe digestive constraints, the stomach is generally not full and (4) optimal fat reserve levels are higher in more variable environments and under digestive constraints. This model suggests that the characteristic daily feeding pattern of small birds is not due to digestive constraints but is greatly influenced by environmental variability.     

The Value of a hoard: not just energy

We present a stochastic dynamic programming model of the contributionof stored food to winter survival. Using the acorn woodpecker(Melanerpes formtcivorus) as a model organism, we demonstratethat a hoard of small energetic value can impart considerableimprovement in the probability of surviving the winter and soimprove fitness. With this model we hope to resolve Koenig andMumme's paradox, that acorn woodpeckers expend much time andeffort to create and maintain hoards of acorns which provideno more that 16% of their energetic needs over the period inwhich they are used. We further demonstrate that the contributionof hoarded acorns to survival depends on the variability inforaging outcome, independently of the energetic value of thehoard in absolute terms. We point out that the results applyin principle to all hoarding animals and suggest a number offurther elaborations of the model.     

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd.

Interactions of divalent metal cations (Mg2+, Ca2+, Ba2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) with DNA have been investigated by laser Raman spectroscopy. Both genomic calf-thymus DNA (> 23 kilobase pairs) and mononucleosomal fragments (160 base pairs) were employed as targets of metal interaction in solutions containing 5 weight-% DNA and metal:phosphate molar ratios of 0.6:1. Raman difference spectra reveal that transition metal cations (Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) induce the greatest structural changes in B-DNA. The Raman (vibrational) band differences are extensive and indicate partial disordering of the B-form backbone, reduction in base stacking, reduction in base pairing, and specific metal interaction with acceptor sites on the purine (N7) and pyrimidine (N3) rings. Many of the observed spectral changes parallel those accompanying thermal denaturation of B-DNA and suggest that the metals link the bases of denatured DNA. While exocyclic carbonyls of dT, dG, and dC may stabilize metal ligation, correlation plots show that perturbations of the carbonyls are mainly a consequence of metal-induced denaturation of the double helix. Transition metal interactions with the DNA phosphates are weak in comparison to interactions with the bases, except in the case of Cu2+, which strongly perturbs both base and phosphate group vibrations. On the other hand, the Raman signature of B-DNA is largely unperturbed by Mg2+, Ca2+, Sr2+, and Ba2+, suggesting much weaker interactions of the alkaline earth metals with both base and phosphate sites. A notable exception is a moderate perturbation by alkaline earths of purine N7 sites in 160-base pair DNA, with Ca2+ causing the greatest effect. Correlation plots demonstrate a strong interrelationship between perturbations of Raman bands assigned to ring vibrations of the bases and those of bands assigned to exocyclic carbonyls and backbone phosphodiester groups. However, strong correlations do not occur between the Raman phosphodioxy band (centered near 1092 cm-1) and other Raman bands, suggesting that the former is not highly sensitive to the structural changes induced by divalent metal cations. The structural perturbations induced by divalent cations are much greater for > 23-kilobase pair DNA than for 160-base pair DNA, as evidenced by both the Raman difference spectra and the tendency toward the formation of insoluble aggregates. In the presence of transition metals, aggregation of high-molecular-weight DNA is evident at temperatures as low as 11 degrees C.(ABSTRACT TRUNCATED AT 400 WORDS)     

Aggregation of melted DNA by divalent metal ion-mediated cross-linking.

In an accompanying paper we reported the use of differential scanning calorimetry and optical densitometry to characterize the melting and aggregation of 160 bp fragments of calf thymus DNA during heating in the presence of divalent metal cations. Aggregation is observed as thermal denaturation begins and becomes more extensive with increasing temperature until the melting temperature Tm is reached, after which the aggregates dissolve extensively. The order of effectiveness of the metals in inducing aggregation is generally consistent with their ability to induce melting: Cd > Ni > Co > Mn approximately Ca > Mg. Under our experimental conditions (50 mg/ml DNA, 100 mM MCl2, [metal]/[DNA phosphate] approximately 0.6), no measurable aggregates were observed for BaDNA or SrDNA. In this paper we show that the Shibata-Schurr theory of aggregation in the thermal denaturation region provides a good model for our observations. Free energies of cross-linking, induced by the divalent cations, are estimated to be between 34% and 38% of the free energies of base stacking. The ability of a divalent metal cation to induce DNA aggregation can be attributed to its ability to disrupt DNA base pairing and simultaneously to link two different DNA sites.