Demonstrating the suitability of genetic algorithms for driving microbial ecosystems in desirable directions

The functioning of natural microbial ecosystems is determined by biotic interactions, which are in turn influenced by abiotic environmental conditions. Direct experimental manipulation of such conditions can be used to purposefully drive ecosystems toward exhibiting desirable functions. When a set of environmental conditions can be manipulated to be present at a discrete number of levels, finding the right combination of conditions to obtain the optimal desired effect becomes a typical combinatorial optimisation problem. Genetic algorithms are a class of robust and flexible search and optimisation techniques from the field of computer science that may be very suitable for such a task. To verify this idea, datasets containing growth levels of the total microbial community of four different natural microbial ecosystems in response to all possible combinations of a set of five chemical supplements were obtained. Subsequently, the ability of a genetic algorithm to search this parameter space for combinations of supplements driving the microbial communities to high levels of growth was compared to that of a random search, a local search, and a hill-climbing algorithm, three intuitive alternative optimisation approaches. The results indicate that a genetic algorithm is very suitable for driving microbial ecosystems in desirable directions, which opens opportunities for both fundamental ecological research and industrial applications.     

A Mycobacterium Strain with Extended Capacities for Degradation of Gasoline Hydrocarbons

A bacterial strain (strain IFP 2173) was selected from a gasoline-polluted aquifer on the basis of its capacity to use 2,2,4-trimethylpentane (isooctane) as a sole carbon and energy source. This isolate, the first isolate with this capacity to be characterized, was identified by 16S ribosomal DNA analysis, and 100% sequence identity with a reference strain of Mycobacterium austroafricanum was found. Mycobacterium sp. strain IFP 2173 used an unusually wide spectrum of hydrocarbons as growth substrates, including n-alkanes and multimethyl-substituted isoalkanes with chains ranging from 5 to 16 carbon atoms long, as well as substituted monoaromatic hydrocarbons. It also attacked ethers, such as methyl t-butyl ether. During growth on gasoline, it degraded 86% of the substrate. Our results indicated that strain IFP 2173 was capable of degrading 3-methyl groups, possibly by a carboxylation and deacetylation mechanism. Evidence that it attacked the quaternary carbon atom structure by an as-yet-undefined mechanism during growth on 2,2,4-trimethylpentane and 2,2-dimethylpentane was also obtained.     

Biosurfactants,an help in the biodegradation of hexadecane? The case of <Emphasis Type="Italic">Rhodococcus</Emphasis> and <Emphasis Type="Italic">Pseudomonas</Emphasis> strains

The roles of the extracellular biosurfactants produced by two bacterial strains, Pseudomonas aeruginosa GL1 and Rhodococcus equi Ou2, in hexadecane uptake and biodegradation were compared. For this purpose, cell hydrophobicity and production of glycolipidic biosurfactants were evaluated during bacterial growth on hexadecane, as well the effects of these biosurfactants on culture supernatants properties i.e., surface and interfacial tensions, and emulsification and pseudosolubilization capacities. The results showed that the role of biosurfactants was different in these two strains and was directly related to the hydrophobicity of the bacterial cells concerned. Extracellular biosurfactants produced by strain R. equi Ou2 had only a minor role in hexadecane degradation. Direct interfacial accession appeared to be the main mechanism for hexadecane uptake by the hydrophobic cells of strain R. equi Ou2. On the contrary, the biosurfactants produced by P. aeruginosa GL1 were required for growth on hexadecane, and their pseudosolubilization capacity rather than their emulsification capacity was involved in substrate degradation, allowing uptake from hexadecane micelles by the hydrophilic cells of this bacterium. The roles of biosurfactants thus differ widely among bacteria degrading hydrophobic compounds. J.-P. Vandecasteele—in retirement     

Recombinant expression of the voltage-dependent anion channel enhances the transfer of Ca2+ microdomains to mitochondria

Although the physiological relevance of mitochondrial Ca2+ homeostasis is widely accepted, no information is yet available on the molecular identity of the proteins involved in this process. Here we analyzed the role of the voltage-dependent anion channel (VDAC) of the outer mitochondrial membrane in the transmission of Ca2+ signals between the ER and mitochondria by measuring cytosolic and organelle [Ca2+] with targeted aequorins and Ca2+-sensitive GFPs. In HeLa cells and skeletal myotubes, the transient expression of VDAC enhanced the amplitude of the agonist-dependent increases in mitochondrial matrix Ca2+ concentration by allowing the fast diffusion of Ca2+ from ER release sites to the inner mitochondrial membrane. Indeed, high speed imaging of mitochondrial and cytosolic [Ca2+] changes showed that the delay between the rises occurring in the two compartments is significantly shorter in VDAC-overexpressing cells. As to the functional consequences, VDAC-overexpressing cells are more susceptible to ceramide-induced cell death, thus confirming that mitochondrial Ca2+ uptake plays a key role in the process of apoptosis. These results reveal a novel function for the widely expressed VDAC channel, identifying it as a molecular component of the routes for Ca2+ transport across the mitochondrial membranes.     

Effects of low chronic doses of ionizing radiation on antioxidant enzymes and G6PDH activities in Stipa capillata (Poaceae)

Stipa capillata (Poaceae) seeds were harvested from a control area (displaying a gamma dose rate of 0.23 micro Sv h(-1)) (C plants) and from two contaminated areas (5.4 and 25 micro Sv h(-1)) on the Semipalatinsk nuclear test site (SNTS) in Kazakhstan. The plants were grown for 124 d in a greenhouse under controlled conditions and exposed to three different treatments: (0) control; (E) external gamma irradiation delivered by a sealed 137Cs source with a dose rate of 66 micro Sv h(-1); (E+I) E treatment combined with internal beta irradiation due to contamination by 134Cs and 85Sr via root uptake from the soil. The root uptake led to a contamination of 100 Bq g(-1) for 85Sr and 5 Bq g(-1) for 134Cs (of plant dry weight) as measured at harvest. The activity of SOD, APX, GR, POD, CAT, G6PDH, and MDHAR enzymes was measured in leaves. Under (0) treatment, all enzymes showed similar activities, except POD, which had higher activity in plants originating from contaminated areas. Treatment (E) induced an enhancement of POD, CAT, GR, SOD, and G6PDH activities in plants originating from contaminated areas. Only control plants showed any stimulation of APX activity. Treatment (E+I) had no significant effect on APX, GR, CAT, and POD activities, but MDHAR activity was significantly reduced while SOD and G6PDH activities were significantly increased. The increase occurred in plants from all origins for SOD, with a greater magnitude as a function of their origin, and it occurred only in plants from the more contaminated populations for G6PDH. This suggests that exposure to a low dose rate of ionizing radiation for almost a half century in the original environment of Stipa has led to natural selection of the most adapted genotypes characterized by an efficient induction of anti-oxidant enzyme activities, especially SOD and G6PDH, involved in plant protection against reactive oxygen species.     

A chlorophyll a fluorescence-based Lemna minor bioassay to monitor microbial degradation of nanomolar to micromolar concentrations of linuron

A plant-microbial bioassay, based on the aquatic macrophyte Lemna minor L. (duckweed), was used to monitor biodegradation of nano- and micromolar concentrations of the phenylurea herbicide linuron. After 7 days of exposure to linuron, log-logistic-based dose-response analysis revealed significant growth inhibition on the total frond area of L. minor when linuron concentrations > or = 80 nM were added to the bioassay. A plant-protective effect was obtained for all concentrations > 80 nM by inoculation with either a bacterial consortium or Variovorax paradoxus WDL1, which is probably the main actor in this consortium. The outcome of the plant-microbe-toxicant interaction was also assessed using pulse amplitude-modulated chlorophyll a fluorescence and chlorophyll a fluorescence imaging. Linuron toxicity to L. minor became apparent as a significant decrease in the effective quantum yield (Delta F/Fm') within 90 min after exposure of the plants to linuron concentrations > or = 160 nM. Inoculation of the bioassay with the linuron-degrading bacteria neutralized the effect on the effective quantum yield at concentrations > or = 160 nM, indicating microbial degradation of these concentrations. The chlorophyll a fluorescence-based Lemna bioassay described here offers a sensitive, fast and cost-effective approach to study the potential of biodegrading microorganisms to break down minute concentrations of photosynthesis-inhibiting xenobiotics.     

Microbial degradation and fate in the environment of methyl tert-butyl ether and related fuel oxygenates

Oxygenates, mainly methyl tert-butyl ether (MTBE), are commonly added to gasoline to enhance octane index and improve combustion efficiency. Other oxygenates used as gasoline additives are ethers such as ethyl tert-butyl ether (ETBE), tert-amyl methyl ether (TAME), and alcohols such as tert-butyl alcohol (TBA). As a result of its wide use, MTBE has been detected, mainly in the USA, in groundwater and surface waters, and is a cause of concern because of its possible health effects and other undesirable consequences. MTBE is a water-soluble and mobile compound that generates long pollution plumes in aquifers impacted by gasoline releases from leaking tanks. Field observations concur in estimating that, because of recalcitrance to biodegradation, natural attenuation is slow (half-life of at least 2 years). However, quite significant advances have been made in recent years concerning the microbiology of the degradation of MTBE and other oxygenated gasoline additives. The recalcitrance of these compounds results from the presence in their structure of an ether bond and of a tertiary carbon structure. For the most part, only aerobic microbial degradation systems have been reported so far. Consortia capable of mineralizing MTBE have been selected. Multiple instances of the cometabolism of MTBE with pure strains or with microflorae, growing on n-alkanes, isoalkanes, cyclohexane or ethers (diethyl ether, ETBE), have been described. MTBE was converted into TBA in all cases and was sometimes further degraded, but it was not used as a carbon source by the pure strains. However, mineralization of MTBE and TBA by several pure bacterial strains using these compounds as sole carbon and energy source has recently been reported. The pathways of metabolism of MTBE involve the initial attack by a monooxygenase. In several cases, the enzyme was characterized as a cytochrome P-450. After oxygenation, the release of a C -unit as formaldehyde or formate leads to the production of TBA, which can be converted to 2-hydroxyisobutyric acid and further metabolized. Developments in microbiology make biological treatment of water contaminated with MTBE and other oxygenates an attractive possibility. Work concerning ex situ treatment in biofilters by consortia and by pure strains, and involving or not cometabolism, is under way. Furthermore, the development of in situ treatment processes is a promisinggoal.     

Degradation of isooctane by Mycobacterium austroafricanum IFP 2173: growth and catabolic pathway

AIMS: Isooctane (2,2,4-trimethylpentane), a major component of gasoline formulations, is recalcitrant to biodegradation probably because of the quaternary carbon group it contains. Information on the biodegradability of this hydrocarbon is essential to evaluate its fate in the environment. For these reasons, the degradation kinetics and the catabolic pathway of isooctane were investigated in Mycobacterium austroafricanum IFP 2173, the only strain characterized to use it as sole carbon and energy source. METHODS AND RESULTS: The selected strain exhibited a rather moderate maximum growth rate (micromax = 0.053 h(-1)) but degraded isooctane up to 99% with a mineralization yield of 45%, indicating attack of the quaternary carbon group. The GC/MS identification of metabolites, 2,4,4-trimethylpentanoic and dimethylpropanoic (pivalic) acids, which transiently accumulated in the cultures indicated that degradation started from the isopropyl extremity of the molecule and subsequently proceeded by catabolism of the tert-butyl moiety. The degradation of putative metabolic intermediates was investigated. The initial isooctane oxidation system was tentatively characterized. CONCLUSIONS: The isooctane-degrading strain harboured two candidate systems for initial alkane oxidation. Although a cytochrome P450 was induced by isooctane degradation, the functional oxidation system was probably a nonheme alkane monooxygenase as indicated by PCR amplification and RT-PCR expression of an alkB gene. SIGNIFICANCE AND IMPACT OF THE STUDY: Isooctane is a recalcitrant branched alkane. A plausible pathway of its degradation by Myco. austroafricanum was put forward.