Effects of iron limitation on the degradation of toluene by Pseudomonas strains carrying the tol (pWWO) plasmid

Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis

The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.

Iron-Stimulated Production and Antimicrobial Potential of a Novel Biosurfactant Produced by a Drilling Waste-Degrading Pseudomonas citronellolis Strain

A Pseudomonas citronellolis strain was isolated from drilling waste (DW). This strain utilizes DW as the sole energy and carbon source to produce biosurfactants (BSs). The BS produced was thermally stable, amorphous and includes a peptide structure. FeSO4, FeCl3 and Fe(NO3)3 were supplemented at various concentration levels to assess possible enhancement of BS production and DW biodegradation. The limit concentration of Fe compounds between the increase in BS formation and microbial toxicity was 0.1 mM. FeCl3 enhanced DW biodegradation and more than doubled the BS formation yield, determining an optimization strategy for BS production. The BS was then partially purified and used against several Gram-negative and positive multi-drug resistant bacteria (such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli spp, Acinetobacter baumaniii, Enterococcus faecalis spp, Streptococcus pneumoniae, Staphylococcus aureus, Salmonella enterica). The minimum inhibitory concentration was defined at a range of 0.25 to 10 mg/mL. The antimicrobial properties of the partially purified BS established its effectiveness and suggested a down-stream processing cost reduction, as no additional purification steps were necessary. The study could lead to a sustainable low-cost bioprocess towards a circular bioeconomy because waste, a non-expensive substrate, is used; while the BS holds great potential as a novel compound with antibiotic and disinfectant-like action, following toxicity testing with human cells.

Recent developments in siderotyping: procedure and application

Siderophores are metal chelating secondary metabolites secreted by almost all organisms. Beside iron starvation, the ability to produce siderophores depends upon several other factors. Chemical structure of siderophore is very complex with vast structural diversity, thus the principle challenge involves its detection, quantification, purification and characterisation. Metal chelation is its most fascinating attribute. This metal chelation property is now forming the basis of its application as molecular markers, siderotyping tool for taxonomic clarification, biosensors and bioremediation agents. This has led researchers to develop and continuously modify previous techniques in order to provide accurate and reproducible methods of studying siderophores. Knowledge obtained via computational approaches provides a new horizon in the field of siderophore biosynthetic gene clusters and their interaction with various proteins/peptides. This review illustrates various techniques, bioinformatics tools and databases employed in siderophores' studies, the principle of analytical methods and their recent applications.

The Naphthalene Catabolic Genes of Pseudomonas putida BS3701: Additional Regulatory Control

Pseudomonas microorganisms are used for bioremediation of soils contaminated with petroleum hydrocarbons. The overall remediation efficiency is largely dependent on the presence of macro- and micronutrients. Widely varying concentrations of available nitrogen and iron (Fe) in soils were shown to affect residual hydrocarbons in the course of biodegradation. The regulatory mechanisms of expression of hydrocarbon catabolic genes in low nitrogen/low iron conditions remain unclear. The catabolism of naphthalene, a two-ring polycyclic aromatic hydrocarbon, has been well studied in pseudomonads in terms of the involvement of specific transcriptional activators, thus making it useful in revealing additional regulatory control of the adaptation of hydrocarbon destructors to a low level of the essential nutrients. The Pseudomonas putida strain BS3701 is a component of the "MicroBak" preparation for soil remediation. Previously, this strain was shown to contain genes encoding the key enzymes for naphthalene catabolism: naphthalene 1,2-dioxygenase, salicylate hydroxylase, catechol 2,3-dioxygenase, and catechol 1,2-dioxygenase. Our study aimed to clarify whether the naphthalene catabolic gene expression is dependent on the amount of nitrogen and iron in the growth culture medium, and if so, at exactly which stages the expression is regulated. We cultivated the strain in low nitrogen/low iron conditions with the concurrent evaluation of the activity of the key enzymes and the mRNA level of genes encoding these enzymes. We are the first to report that naphthalene catabolic genes are subject not only to transcriptional but also post-transcriptional regulation.

Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading

Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.

Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii

Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria

Marine microbes are an important control on the biogeochemical cycling of trace metals, but simultaneously, these metals can control the growth of microorganisms and the cycling of major nutrients like C and N. However, studies on the response/limitation of microorganisms to trace metals have traditionally focused on the response of autotrophic phytoplankton to Fe fertilization. Few reports are available on the response of heterotrophic prokaryotes to Fe, and even less to other biogeochemically relevant metals. We performed the first study coupling dark incubations with next generation sequencing to specifically target the functional and phylogenetic response of heterotrophic prokaryotes to Fe enrichment. Furthermore, we also studied their response to Co, Mn, Ni, Zn, Cu (individually and mixed), using surface and deep samples from either coastal or open-ocean waters. Heterotrophic prokaryotic activity was stimulated by Fe in surface open–ocean, as well as in coastal, and deep open-ocean waters (where Zn also stimulated). The most susceptible populations to trace metals additions were uncultured bacteria (e.g., SAR324, SAR406, NS9, and DEV007). Interestingly, hydrocarbon-degrading bacteria (e.g., Thalassolituus, Marinobacter, and Oleibacter) benefited the most from metal addition across all waters (regions/depths) revealing a predominant role in the cycling of metals and organic matter in the ocean.

Siderophores as molecular tools in medical and environmental applications

Almost all life forms depend on iron as an essential micronutrient that is needed for electron transport and metabolic processes. Siderophores are low-molecular-weight iron chelators that safeguard the supply of this important metal to bacteria, fungi and graminaceous plants. Although animals and the majority of plants do not utilise siderophores and have alternative means of iron acquisition, siderophores have found important clinical and agricultural applications. In this review, we will highlight the different uses of these iron-chelating molecules.

Functional redundancy in phenol and toluene degradation in Pseudomonas stutzeri strains isolated from the Baltic Sea

In the present study we describe functional redundancy of bacterial multicomponent monooxygenases (toluene monooxygenase (TMO) and toluene/xylene monooxygenase (XylAM) of TOL pathway) and cooperative genetic regulation at the expression of the respective catabolic operons by touR and xylR encoded regulatory circuits in five phenol- and toluene-degrading Pseudomonas stutzeri strains. In these strains both toluene degradation pathways (TMO and Xyl) are active and induced by toluene and phenol. The whole genome sequence of the representative strain 2A20 revealed the presence of complete TMO- and Xyl-upper pathway operons together with two sets of lower catechol meta pathway operons, as well as phenol-degrading operon in a single 292,430bp contig. The much lower GC content and analysis of the predicted ORFs refer to the plasmid origin of the approximately 130kb region of this contig, containing the xyl, phe and tou genes. The deduced amino acid sequences of the TMO, XylA and the large subunit of phenol monooxygenase (LmPH) show 98-100% identity with the respective gene products of the strain Pseudomonas sp. OX1. In both strains 2A20 and OX1 the meta-cleavage pathways for catechol degradation are coded by two redundant operons (phe and xyl). We show that in the strain 2A20 TouR and XylR are activated by different effector molecules, phenol and toluene, respectively, and they both control transcription of the xyl upper, tou (TMO) and phe catabolic operons. Although the growth parameters of redundant strains did not show advantage at toluene biodegradation, the functional redundancy could provide better flexibility to the bacteria in environmental conditions.

The positive relationship between ocean acidification and pollution

Ocean acidification and pollution coexist to exert combined effects on the functions and services of marine ecosystems. Ocean acidification can increase the biotoxicity of heavy metals by altering their speciation and bioavailability. Marine pollutants, such as heavy metals and oils, could decrease the photosynthesis rate and increase the respiration rate of marine organisms as a result of biotoxicity and eutrophication, facilitating ocean acidification to varying degrees. Here we review the complex interactions between ocean acidification and pollution in the context of linkage of multiple stressors to marine ecosystems. The synthesized information shows that pollution-affected respiration acidifies coastal oceans more than the uptake of anthropogenic carbon dioxide. Coastal regions are more vulnerable to the negative impact of ocean acidification due to large influxes of pollutants from terrestrial ecosystems. Ocean acidification and pollution facilitate each other, and thus coastal environmental protection from pollution has a large potential for mitigating acidification risk.

Protein as chemical cue: non-nutritional growth enhancement by exogenous protein in Pseudomonas putida KT2440

Research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. However, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. Here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of Pseudomonas putida KT2440, even when such proteins are not internalized by the cells. The growth enhancement is observed when the exogenous protein is not used as a source of carbon or nitrogen. The data show non-specific nature of the protein inducing growth; growth enhancement was observed irrespective of the protein type. It is shown that growth enhancement is mediated via increased siderophore secretion in response to the exogenous protein, leading to better iron uptake. We highlight the ecological significance of the observation and hypothesize that exogenous proteins serve as chemical cues in the case of P.putida and are perceived as indicator of the presence of competitors in the environment. It is argued that enhanced siderophore secretion in response to exogenous protein helps P.putida establish numerical superiority over competitors by way of enhanced iron assimilation and quicker utilization of aromatic substrates.

Alcanivorax borkumensis produces an extracellular siderophore in iron-limitation condition maintaining the hydrocarbon-degradation efficiency

Obligate marine hydrocarbonoclastic bacteria possess genetic and physiological features to use hydrocarbons as sole source of carbon and to compete for the uptake of nutrients in usually nutrient-depleted marine habitats. In the present work we have studied the siderophore-based iron uptake systems in Alcanivorax borkumensis SK2 and their functioning during biodegradation of an aliphatic hydrocarbon, tetradecane, under iron limitation conditions. The antiSMASH analysis of SK2 genome revealed the presence of two different putative operons of siderophore synthetases. Search for the predicted core structures indicated that one siderophore is clearly affiliated to the family of complex oligopeptidic siderophores possessing an Orn-Ser-Orn carboxyl motif whereas the second one is likely to belong to the family of SA (salicylic acid)-based siderophores. Analyzing the supernatant of SK2 culture, an extracellular siderophore was identified and its structure was resolved. Thus, along with the recently described membrane-associated amphiphilic tetrapeptidic siderophore amphibactin, strain SK2 additionally produces an extracellular type of iron-chelating molecule with structural similarity to pseudomonins. Comparative Q-PCR analysis of siderophore synthetases demonstrated their significant up-regulation in iron-depleted medium. Different expression patterns were recorded for two operons during the early and late exponential phases of growth, suggesting a different function of these two siderophores under iron-depleted conditions.

Pumping iron to keep fit: modulation of siderophore secretion helps efficient aromatic utilization in Pseudomonas putida KT2440

Studies of biotechnology applications of Pseudomonas putida KT2440 have been predominantly focused on regulation and expression of the toluene degradation (TOL) pathway. Unfortunately, there is limited information on the role of other physiological factors influencing aromatic utilization. In this report, we demonstrate that P. putida KT2440 increases its siderophore secretion in response to the availability of benzyl alcohol, a model aromatic substrate. It is argued that accelerated siderophore secretion in response to aromatic substrates provides an iron ‘boost’ which is required for the effective functioning of the iron-dependent oxygenases responsible for ring opening. Direct evidence for the cardinal role of siderophores in aromatic utilization is provided by evaluation of per capita siderophore secretion and comparative growth assessments of wild-type and siderophore-negative mutant strains grown on an alternative carbon source. Accelerated siderophore secretion can be viewed as a compensatory mechanism in P. putida in the context of its inability to secrete more than one type of siderophore (pyoverdine) or to utilize heterologous siderophores. Stimulated siderophore secretion might be a key factor in successful integration and proliferation of this organism as a bio-augmentation agent for aromatic degradation. It not only facilitates efficient aromatic utilization, but also provides better opportunities for iron assimilation amongst diverse microbial communities, thereby ensuring better survival and proliferation.

Perspective: what is known, and not known, about the connections between alkane oxidation and metal uptake in alkanotrophs in the marine environment

Should iron and copper be added to the environment to stimulate the natural bioremediation of marine oil spills? The key enzymes that catalyze the oxidation of alkanes require either iron or copper, and the concentration of these ions in seawater is vanishingly low. Nevertheless, the dependence of alkane oxidation activity on external metal concentrations remains unclear. This perspective will summarize what is known about the co-regulation of alkane oxidation and metal acquisition and pose a series of critical questions to which, for the most part, we do not yet have answers. The paucity of answers points to the need for additional studies to illuminate the cellular biology connecting microbial growth on alkanes to the acquisition of metal ions.

Interactive effects of global climate change and pollution on marine microbes: the way ahead

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Effect of the metals iron, copper and silver on fluorobenzene biodegradation by Labrys portucalensis

Organic and metallic pollutants are ubiquitous in the environment. Many metals are reported to be toxic to microorganisms and to inhibit biodegradation. The effect of the metals iron, copper and silver on the metabolism of Labrys portucalensis F11 and on fluorobenzene (FB) biodegradation was examined. The results indicate that the addition of 1 mM of Fe(2+) to the culture medium has a positive effect on bacterial growth and has no impact in the biodegradation of 1 and 2 mM of FB. The presence of 1 mM of Cu(2+) was found to strongly inhibit the growth of F11 cultures and to reduce the biodegradation of 1 and 2 mM of FB to ca. 50 %, with 80 % of stoichiometrically expected fluoride released. In the experiments with resting cells, the FB degraded (from 2 mM supplied) was reduced ca. 20 % whereas the fluoride released was reduced to 45 % of that stoichiometrically expected. Ag(+) was the most potent inhibitor of FB degradation. In experiments with growing cells, the addition of 1 mM of Ag(+) to the culture medium containing 1 and 2 mM of FB resulted in no fluoride release, whereas FB degradation was only one third of that observed in control cultures. In the experiments with resting cells, the addition of Ag(+) resulted in 25 % reduction in substrate degradation and fluoride release was only 20 % of that stoichiometrically expected. The accumulation of catechol and 4-fluorocatechol in cultures supplemented with Cu(2+) or Ag(+) suggest inhibition of the key enzyme of FB metabolism-catechol 1,2-dioxygenase.

Siderophore-producing bacteria from a sand dune ecosystem and the effect of sodium benzoate on siderophore production by a potential isolate

Bioremediation in natural ecosystems is dependent upon the availability of micronutrients and cofactors, of which iron is one of the essential elements. Under aerobic and alkaline conditions, iron oxidizes to Fe(+3) creating iron deficiency. To acquire this essential growth-limiting nutrient, bacteria produce low-molecular-weight, high-affinity iron chelators termed siderophores. In this study, siderophore-producing bacteria from rhizosphere and nonrhizosphere areas of coastal sand dunes were isolated using a culture-dependent approach and were assigned to 8 different genera with the predominance of Bacillus sp. Studies on the ability of these isolates to grow on sodium benzoate revealed that a pigmented bacterial culture TMR2.13 identified as Pseudomonas aeruginosa showed growth on mineral salts medium (MSM) with 2% of sodium benzoate and produced a yellowish fluorescent siderophore identified as pyoverdine. This was inhibited above 54 μM of added iron in MSM with glucose without affecting growth, while, in presence of sodium benzoate, siderophore was produced even up to the presence of 108 μM of added iron. Increase in the requirement of iron for metabolism of aromatic compounds in ecosystems where the nutrient deficiencies occur naturally would be one of the regulating factors for the bioremediation process.

Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations

Gas chromatography-isotope ratio mass spectrometry (GC-IRMS) has made it possible to analyze natural stable isotope ratios (e.g., (13)C/(12)C, (15)N/(14)N, (2)H/(1)H) of individual organic contaminants in environmental samples. They may be used as fingerprints to infer contamination sources, and may demonstrate, and even quantify, the occurrence of natural contaminant transformation by the enrichment of heavy isotopes that arises from degradation-induced isotope fractionation. This review highlights an additional powerful feature of stable isotope fractionation: the study of environmental transformation mechanisms. Isotope effects reflect the energy difference of isotopologues (i.e., molecules carrying a light versus a heavy isotope in a particular molecular position) when moving from reactant to transition state. Measuring isotope fractionation, therefore, essentially allows a glimpse at transition states! It is shown how such position-specific isotope effects are "diluted out" in the compound average measured by GC-IRMS, and how a careful evaluation in mechanistic scenarios and by dual isotope plots can recover the underlying mechanistic information. The mathematical framework for multistep isotope fractionation in environmental transformations is reviewed. Case studies demonstrate how isotope fractionation changes in the presence of mass transfer, enzymatic commitment to catalysis, multiple chemical reaction steps or limited bioavailability, and how this gives information about the individual process steps. Finally, it is discussed how isotope ratios of individual products evolve in sequential or parallel transformations, and what mechanistic insight they contain. A concluding session gives an outlook on current developments, future research directions and the potential for bridging the gap between laboratory and real world systems.

Biodegradation of diphenylarsinic acid to arsenic acid by novel soil bacteria isolated from contaminated soil

Microorganisms capable of degrading diphenylarsinic acid (DPAA) were enriched from contaminated soil using the soil-charcoal perfusion method. Two novel bacterial strains, L2406 and L2413, that can degrade DPAA in a mineral salt medium supplemented with DPAA as the sole carbon source were isolated. Based on comparative morphology, physiology, and comparison of the 16S rRNA gene sequences, both were presumed to be species closely related to Ensifer adhaerens. As the metabolites, phenylarsonic acid (PAA) was determined by liquid chromatography-mass spectrometry analysis as well as three unknown peaks all of whose molecular weights were estimated to be 278. The increase of m/z = 16 from DPAA in the unknowns suggests monohydroxylation of DPAA at the 2-, 3- and 4-positions. The ability of strains L2406 and L2413 to degrade DPAA was suppressed in iron insufficient conditions, e.g. less than 7.2 muM iron in the culture medium. These facts strongly suggest the following hypothesis: Monooxygenase works at the initial degradation step of DPAA degradation by the isolates; and direct hydrolysis from DPAA to PAA is not likely to occur. In addition, release of arsenic acid from PAA by strain L2406 was confirmed by liquid chromatography-inductively coupled plasma mass spectrometry. From these results, strain L2406 was considered to be capable of degrading DPAA to arsenic acid via PAA when DPAA was supplied as the sole carbon source.

Fate of the nitrilotriacetic acid-Fe(III) complex during photodegradation and biodegradation by Rhodococcus rhodochrous

Aminopolycarboxylic acids are ubiquitous in natural waters and wastewaters. They have the ability to form very stable water-soluble complexes with many metallic di- or trivalent ions. The iron complex nitrilotriacetic acid-Fe(III) (FeNTA) has been previously shown to increase drastically the rate of photo- and biodegradation of 2-aminobenzothiazole, an organic pollutant, by Rhodococcus rhodochrous. For this paper, the fate of FeNTA was investigated during these degradation processes. First, it was shown, using in situ (1)H nuclear magnetic resonance, that the complex FeNTA was biodegraded by Rhodococcus rhodochrous cells, but the ligand (NTA) alone was not. This result indicates that FeNTA was transported and biotransformed inside the cell. The same products, including iminodiacetic acid, glycine, and formate, were obtained during the photo- and biodegradation processes of FeNTA, likely because they both involve oxidoreduction mechanisms. When the results of the different experiments are compared, the soluble iron, measured by spectrophotometry, was decreasing when microbial cells were present. About 20% of the initial iron was found inside the cells. These results allowed us to propose detailed mechanistic schemes for FeNTA degradation by solar light and by R. rhodochrous.

Biodegradation of sodium benzoate by a Gram-negative consortium in a laboratory-scale fluidized bed bioreactor

Gram-negative bacteria with the potential to metabolize n-alkanes and cyclic hydrocarbons were isolated from local soils and identified using 16S rDNA sequence analysis. Three isolates (CS1CO, GL1CO, GCI1CO) were identified as strains of Pseudomonas (P.) aeruginosa and a further strain (DSS2) as P. putida. Isolates were co-cultured in a laboratory-scale fluidized bed biofilm bioreactor (FBBR) utilizing sodium benzoate as the sole carbon source, under two batch and/or one continuous growth conditions. Biofilm and planktonic bacterial growth dynamics were monitored by plate counts, and optical density measurements (230 nm) determined benzoate biodegradation. Overall higher attached and planktonic bacterial counts, and benzoate depletion, were determined under batch compared to continuous conditions, and the bioreactor performed better during the second batch phase when compared to the first batch phase. It thus appeared that both the planktonic and biofilm components of the system were necessary for the most successful sodium benzoate degradation in this system.

Anthracene biodegradation and surface activity by an iron-stimulated Pseudomonas sp

Iron may enhance polycyclic aromatic hydrocarbons (PAHs) degradation directly by increasing the activity of the enzymes involved in the aerobic biodegradation pathways for hydrocarbons, and indirectly by increasing the PAHs bioavailability due to the stimulation of biosurfactant production. In the present work, the PAH anthracene was used in order to study the effect of different forms and concentrations of iron on its biodegradation and surfactant production by Pseudomonas spp. isolates from a 14-years old petrochemical sludge landfarm site. Among the iron forms, iron nitrate was chosen based on its high solubility and effect on the increase in the growth of the isolate. Iron concentration of 0.1mM was selected as the limit between deficiency and toxicity for isolates growth and anthracene degradation. After 48 days Pseudomonas citronellolis isolate 222A degraded 72% of anthracene related to iron stimulation and surface tension decrease, indicating surfactant production. Pseudomonas aeruginosa isolate 332C was iron-stimulated but did not reduce surface tension while P. aeruginosa isolate 312A exhibited a noniron and surfactant dependence to degrade 72% of anthracene. Isolate 222A showed a direct dependence on iron to stimulate surfactant activity, which probably increased anthracene bioavailability. To our knowledge, this is the first report about the iron effect on anthracene degradation and surfactant production by a Pseudomonas sp. Based on the iron requirement and surfactant activity, the Pseudomonas isolates may be useful for bioremediation of PAHs.

Fluorogenic surrogate substrates for toluene-degrading bacteria—Are they useful for activity analysis?

Cultivated bacterial toluene degraders use one or several of four described pathways for the aerobic degradation of this priority groundwater contaminant. To be able to identify un-cultivated toluene-degrading bacteria within enriched or natural consortia, we attempted to develop a set of staining techniques that invariably label toluene-degrading bacteria while differentiating between the different degradation pathways. In the literature, we found suggestions for pathway-specific labels of individual cells that rely on the conversion of toluene surrogates into specific colored and fluorescent products. These surrogate substrates were phenylacetylene (PA), cinnamonitrile, 3-hydroxyphenylacetylene (3-HPA), and indole. We were able to confirm that the chromogenic reactions reliably verified the pathway-specific reactions of well-characterized toluene-degrading bacterial species. However, it was most surprising to find out that three (PA, 3-HPA and cinnamonitrile) of the four supplied surrogate substrates did not lead to any product fluorescence above the cultures' autofluorescence, neither inside of cells nor in supernatants. More disturbingly, the original surrogate compound 3-HPA was inherently fluorescent and found to stain cells at intensities that depended on their states in the cell cycle. Indoxyl originating from the surrogate substrate indole was the only fluorescent product that was formed. It was detected intracellularly when the cells were sealed with para-formaldehyde, but its appearance was unrelated to the presence of expressed toluene degradation pathways. These findings were scrutinized by fluorescence spectroscopy, fluorescence microscopy, and flow cytometry. Activity and growth of the test bacteria were determined by analyzing chromosome numbers and membrane integrity. Our results contradict literature reports that propose the surrogate fluorogenic substrates for the identification of toluene degraders and the identification of specific pathways used by them.

Bioremediation of crystal violet using air bubble bioreactor packed with Pseudomonas aeruginosa

Seven water and sediment samples were collected and tested for decolorizing crystal violet. Pseudomonas aeruginosa was the most effective isolate for dye decolorization. The LC50 of the crystal violet (115 mg/l) was measured using Artemia salina as a biomarker. The effect of different heavy metals on crystal violet decolorization was investigated. Cd2+ and Fe3+ ions showed marginal enhancement of the decolorization process, the rate was 1.35 mg/l/h compared to (1.25 mg/l/h) for the control. Phenol and m-cresol showed no effect on crystal violet decolorization, meanwhile p-cresol and p-nitrophenol reduced the decolorization rate to 1.07 and 0.01 mg/l/h, respectively. P. aeruginosa cells were immobilized by entrapment in agar-alginate beads. The beads were cultivated and reused in Erlenmeyer flask and in an air bubble column bioreactor and they enhanced the crystal violet decolorization rate to 3.33 and 7.5 mg/l/h, respectively.

Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture

Clostridium thermocellum is a thermophilic, anaerobic, cellulolytic bacterium that produces ethanol and acetic acid as major fermentation end products. The effect of growth conditions on gene expression in C. thermocellum ATCC 27405 was studied using cells grown in continuous culture under cellobiose or cellulose limitation over a approximately 10-fold range of dilution rates (0.013 to 0.16 h(-1)). Fermentation product distribution displayed similar patterns in cellobiose- or cellulose-grown cultures, including substantial shifts in the proportion of ethanol and acetic acid with changes in growth rate. Expression of 17 genes involved or potentially involved in cellulose degradation, intracellular phosphorylation, catabolite repression, and fermentation end product formation was quantified by real-time PCR, with normalization to two calibrator genes (recA and the 16S rRNA gene) to determine relative expression. Thirteen genes displayed modest (fivefold or less) differences in expression with growth rate or substrate type: sdbA (cellulosomal scaffoldin-dockerin binding protein), cdp (cellodextrin phosphorylase), cbp (cellobiose phosphorylase), hydA (hydrogenase), ldh (lactate dehydrogenase), ack (acetate kinase), one putative type IV alcohol dehydrogenase, two putative cyclic AMP binding proteins, three putative Hpr-like proteins, and a putative Hpr serine kinase. By contrast, four genes displayed >10-fold-reduced levels of expression when grown on cellobiose at dilution rates of >0.05 h(-1): cipA (cellulosomal scaffolding protein), celS (exoglucanase), manA (mannanase), and a second type IV alcohol dehydrogenase. The data suggest that at least some cellulosomal components are transcriptionally regulated but that differences in expression with growth rate or among substrates do not directly account for observed changes in fermentation end product distribution.

Bioremediation of crystal violet using air bubble bioreactor packed with Pseudomonas aeruginosa

Seven water and sediment samples were collected and tested for decolorizing crystal violet. Pseudomonas aeruginosa was the most effective isolate for dye decolorization. The LC(50) of the crystal violet (115 mg/l) was measured using Artemia salina as a biomarker. The effect of different heavy metals on crystal violet decolorization was investigated. Cd(2+) and Fe(3+) ions showed marginal enhancement of the decolorization process, the rate was 1.35 mg/l/h compared to 1.25 mg/l/h for the control. Phenol and m-cresol showed no effect on crystal violet decolorization, meanwhile p-cresol and p-nitrophenol reduced the decolorization rate to 1.07 and 0.01 mg/l/h, respectively. P. aeruginosa cells were immobilized by entrapment in agar-alginate beads. The beads were cultivated and reused in Erlenmeyer flask and in an air bubble column bioreactor and they enhanced the crystal violet decolorization rate to 3.33 and 7.5 mg/l/h, respectively.

Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase

The genome sequence of Pseudomonas putida strain KT2440, a nutritionally versatile, saprophytic and plant root-colonizing Gram-negative soil bacterium, was recently determined by K. E. Nelson et al. (2002, Environ Microbiol 4: 799-808). Here, we present a two-dimensional gel protein reference map of KT2440 cells grown in mineral salts medium with glucose as carbon source. Proteins were identified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) analysis, in conjunction with an in-house database developed from the genome sequence of KT2440, and approximately 200 two-dimensional gel spots were assigned. The map was used to assess the genomic response of KT2440 to iron limitation stress and to compare this response with that of the closely related facultative human pathogen Pseudomonas aeruginosa strain PAO1. The synthesis of about 25 proteins was affected in both strains, including four prominent upregulated ferric uptake regulator (Fur) protein-dependent proteins, but there were also striking differences in their proteome responses, for example in the expression of superoxide dismutases (Sod), which may indicate important roles of iron-responsive functions in the adaptation of these two bacteria to different lifestyles. The Sod enzyme of KT2440 was shown to be a novel heterodimer of the SodA and SodB polypeptides.