Microbial assimilation of hydrocarbons. I. The fine-structure of a hydrocarbon oxidizing Acinetobacter sp

Biological Process of Alkane Degradation by Gordonia sihwaniensis

With the development of the petroleum industry, oil pollution has become widespread. It is harmful to the digestive, immune, reproductive, and nervous systems of fishes, wild animals, and humans, causing severe threats to ecological safety and human health. Gordonia has increasingly attracted attention in the treatment of alkane pollution for its outstanding performance against hydrophobic refractory substances. However, the lack of knowledge about alkane uptake and degradation restricts the application of gordonia. In this paper, we studied the strain lys1-3 of Gordonia sihwaniensis isolated from coal chemical wastewater, which showed good alkane degradation performance by lys1-3. It is found that stimulated by an alkane, lys1-3 secreted biosurfactants, which emulsified large alkane particles to smaller particles. By active transport, unmodified alkane was transferred into cells and produced a large amount of acid, which was secreted out of the cells.

Composition and Corrosivity of Extracellular Polymeric Substances from the Hydrocarbon-Degrading Sulfate-Reducing Bacterium Desulfoglaeba alkanexedens ALDC

Sulfate-reducing bacteria (SRB) often exist as cell aggregates and in biofilms surrounded by a matrix of extracellular polymeric substances (EPSs). The chemical composition of EPSs may facilitate hydrophobic substrate biodegradation and promote microbial influenced corrosion (MIC). Although EPSs from non-hydrocarbon-degrading SRB have been studied; the chemical composition of EPSs from hydrocarbon-degrading SRBs has not been reported. The isolated EPSs from the sulfate-reducing alkane-degrading bacterium Desulfoglaeba alkanexedens ALDC was characterized with scanning and fluorescent microscopy, nuclear magnetic resonance spectroscopy (NMR), and by colorimetric chemical assays. Specific fluorescent staining and ¹H NMR spectroscopy revealed that the fundamental chemical structure of the EPS produced by D. alkanexedens is composed of pyranose polysaccharide and cyclopentanone in a 2:1 ratio. NMR analyses indicated that the pyranose ring structure is bonded by 1,4 connections with the cyclopentanone directly bonded to one pyranose ring. The presence of cyclopentanone presumably increases the hydrophobicity of the EPS that may facilitate the accessibility of hydrocarbon substrates to aggregating cells or cells in a biofilm. Weight loss and iron dissolution experiments demonstrated that the EPS did not contribute to the corrosivity of D. alkanexedens cells.

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.

Trans-membrane transport of n-octadecane by Pseudomonas sp. DG17

The trans-membrane transport of hydrocarbons is an important and complex aspect of the process of biodegradation of hydrocarbons by microorganisms. The mechanism of transport of (14)C n-octadecane by Pseudomonas sp. DG17, an alkane-degrading bacterium, was studied by the addition of ATP inhibitors and different substrate concentrations. When the concentration of n-octadecane was higher than 4.54 μmol/L, the transport of (14)C n-octadecane was driven by a facilitated passive mechanism following the intra/extra substrate concentration gradient. However, when the cells were grown with a low concentration of the substrate, the cellular accumulation of n-octadecane, an energy-dependent process, was dramatically decreased by the presence of ATP inhibitors, and n-octadecane accumulation continually increased against its concentration gradient. Furthermore, the presence of non-labeled alkanes blocked (14)C n-octadecane transport only in the induced cells, and the trans-membrane transport of n-octadecane was specific with an apparent dissociation constant K t of 11.27 μmol/L and V max of 0.96 μmol/min/mg protein. The results indicated that the trans-membrane transport of n-octadecane by Pseudomonas sp. DG17 was related to the substrate concentration and ATP.

Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain

The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.

Whole cell bioreporter application for rapid detection and evaluation of crude oil spill in seawater caused by Dalian oil tank explosion

Accidents involving the release of crude oil to seawater pose serious threat to human and animal health, fisheries and marine ecosystems. A whole cell bioreporter detection method, which has unique advantages for the rapid evaluation on toxicity and bioavailability, is a useful tool to provide environmental risk assessments at crude oil-contaminated sites. Acinetobacter baylyi ADPWH_alk and ADPWH_recA are chromosomally-based alkane and genotoxicity bioreporters which can be activated to express bioluminescence in the presence of alkanes and genotoxic compounds. In this study, we applied Acinetobacter ADPWH_alk and ADPWH_recA bioreporters to examine six seawater and six sediment samples around the Dalian Bay four weeks after an oil tank explosion in Dalian, China in 2010, and compared the results with samples from the same sites one year after. The results of bioreporter detection suggest that seawater and sediments from five sites (DB, NT, JSB, XHP and FJZ) four weeks after the oil-spill were contaminated by the crude oil with various extents of genotoxicity. Among these six sites, DB and NT had high oil contents and genotoxicity, and JSB had high oil content but low genotoxicity in comparison with an uncontaminated site LSF, which is located at other side of the peninsula. These three sites (DB, NT and JSB) with detectable genotoxicity are within 30 km away from the oil spill point. The far-away two sites XHP (38.1 km) and FJZ (31.1 km) were lightly contaminated with oil but no genotoxicity suggesting that they are around the contamination boundary. Bioreporter detection also indicates that all six sites were clean one year after the oil-spill as the alkane and genotoxicity were below detection limit. This study demonstrates that bioreporter detection can be used as a rapid method to estimate the scale of a crude oil spill accident and to evaluate bioavailability and genotoxicity of contaminated seawater and sediments, which are crucial to risk assessment and strategic decision-making for environmental management and clean-up.

Enigmatic reticulated filaments in subsurface granite

In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morphology, mode of formation and growth. A tentative microbial origin has been elusive since these filaments are found as hollow tubular sheaths and could not be affiliated to any known microorganism. We describe the presence of similar structures in a 16th century granite tunnel in Porto, Northwest Portugal. The reticulated filaments we identify exhibit fine geometry surface ornamentation formed by cross-linked Mn-rich nanofibres, surrounded by a large amount of extracellular polymeric substances. Within these Mn-rich filaments we report for the first time the occurrence of microbial cells.

In vitro microbial degradation of bituminous hydrocarbons and in situ colonization of bitumen surfaces within the athabasca oil sands deposit

Bituminous hydrocarbons extracted from the Athabasca oil sands of north-eastern Alberta were adsorbed onto filter supports and placed at sites in the Athabasca River and its tributaries where these rivers come in contact with the oil sands formation. Colonization of the hydrocarbon surfaces at summer and winter ambient temperatures was examined by scanning and transmission electron microscopy as well as by epifluorescence microscopy of acridine orange-stained cross sections. Ruthenium red and alkaline bismuth stains visualized an association of bacteria with the hydrocarbon surface which was mediated by bacterial polysaccharides. Bacteria apparently lacking a glycocalyx were also found closely associated with the surface of the hydrophobic substrate and in channels within the substrate. A solvent precipitation and column chromatographic fractionation of the bitumen was followed by cross-tests for growth on the fractions by various isolated sediment microorganisms, as determined by epifluorescence count. All fractions except the asphaltenes supported the growth of at least two of the isolates, although fractionation of degraded bitumen revealed that the saturate, aromatic, and first polar fractions were preferentially degraded.

Synthesis of rhamnolipid biosurfactant and mode of hexadecane uptake by Pseudomonas species

Background

Microorganisms have devised ways by which they increase the bioavailability of many water immiscible substrates whose degradation rates are limited by their low water solubility. Hexadecane is one such water immiscible hydrocarbon substrate which forms an important constituent of oil. One major mechanism employed by hydrocarbon degrading organisms to utilize such substrates is the production of biosurfactants. However, much of the overall mechanism by which such organisms utilize hydrocarbon substrate still remains a mystery.

Results

With an aim to gain more insight into hydrocarbon uptake mechanism, an efficient biosurfactant producing and n-hexadecane utilizing Pseudomonas sp was isolated from oil contaminated soil which was found to produce rhamnolipid type of biosurfactant containing a total of 13 congeners. Biosurfactant action brought about the dispersion of hexadecane to droplets smaller than 0.22 μm increasing the availability of the hydrocarbon to the degrading organism. Involvement of biosurfactant was further confirmed by electron microscopic studies. Biosurfactant formed an emulsion with hexadecane thereby facilitating increased contact between hydrocarbon and the degrading bacteria. Interestingly, it was observed that "internalization" of "biosurfactant layered hydrocarbon droplet" was taking place suggesting a mechanism similar in appearance to active pinocytosis, a fact not earlier visually reported in bacterial systems for hydrocarbon uptake.

Conclusion

This study throws more light on the uptake mechanism of hydrocarbon by Pseudomonas aeruginosa. We report here a new and exciting line of research for hydrocarbon uptake involving internalization of biosurfactant covered hydrocarbon inside cell for subsequent breakdown.

Two acyl-CoA dehydrogenases of Acinetobacter sp. strain M-1 that uses very long-chain n-alkanes

Two genes encoding acyl-CoA dehydrogenases, acdA and acdB, arranged in tandem, were found in the chromosomal DNA of Acinetobacter sp. strain M-1. AcdA was purified from the parental strain and AcdB was purified from an Escherichia coli strain expressing the cloned gene. The substrate specificities of the two enzymes suggest that AcdA is a medium-chain acyl-CoA dehydrogenase and that AcdB is a long-chain acyl-CoA dehydrogenase. Characterization of n-alkane metabolism in Acinetobacter sp. strain M-1 has revealed parallel pathways as well as enzymes with overlapping specificities in a single pathway. The two acyl-CoA dehydrogenases described here provide another example of the physiological complexity underlying n-alkane utilization.

Envelope glycosylation determined by lectins in microscopy sections of Acinetobacter venetianus induced by diesel fuel

It was suggested in a previous study that cells of Acinetobacter venetianus VE-C3 adhere to diesel fuel by synthesizing a capsular polysaccharide containing glucose and/or mannose. To study the fine structure of cells and localization of bacterial polysaccharide in the presence of diesel fuel, two lectins were used: ConA, an agglutinin from Canavalia ensiformis specific for mannose and/or glucose residues, and PNA, an agglutinin from Arachis hypogaea, for terminal galactose residues. The lectins were conjugated with electron dense ferritin for transmission electron microscopy (TEM) and with fluorescein isothiocyanate (FITC) for scanning confocal laser microscopy (SCLM). Samples were prepared by freeze substitution, which allows glycosylation to be determined in situ in thin sections of specimens. The distribution of glycosylation was imaged with and without treatment of specimens with their specific hapten (glucose and galactose). The glycosylation activity produced a polysaccharide capsule. Emulsified diesel fuel nanodroplets were observed at the cell envelope perimeter. Fine structure of vesicles consisted of polysaccharide and diesel fuel nanodroplets. Lectin blotting analysis showed ConA-positive glycoprotein with an apparent molecular mass of 22 kDa in the outer membrane. Its production was induced by diesel fuel. This glycoprotein was probably responsible for bioemulsifying activity at the cell envelope. Several other glycoproteins were positive for PNA lectin, the main constituent migrating with an apparent molecular weight of 17.8 kDa. However, they were all constitutive and probably involved in cell biofilm formation at the oil surface.

Selective transport and accumulation of alkanes by Rhodococcus erythropolis S+14He

Selective transport and accumulation of n-alkanes by Rhodococcus erythropolis S+14He was studied by growing cells on n-hexadecane, n-octadecane or the branched alkane pristane, and on mixtures of hydrocarbons. Ultrastructural analysis by transmission electron microscopy (TEM) revealed hydrocarbon inclusion bodies present in cells grown on the three alkanes, but not in cells grown on soluble media or exposed to nonmetabolized 2,2,4,4,6,8,8-heptamethylnonane (HMN). n-Hexadecane had the highest rates of accumulation within the cells and higher overall consumption rates relative to the other alkanes. These rates decreased when the molar concentration of n-hexadecane was decreased in hydrocarbon mixtures, but at the same time the accumulation of n-hexadecane in intracellular inclusions became increasingly selective. Sodium azide significantly inhibited the accumulation of n-hexadecane, consistent with an active transport mechanism for accumulation. These results indicate that R. erythropolis S+14He is able to selectively discriminate and preferentially transport n-hexadecane from mixtures of structurally similar alkanes into intracellular inclusions by an energy-driven transport system. This selective membrane transport of hydrocarbon isomers has potential application for separations, bioprocessing, and the development of novel biosensors.

Towards efficient crude oil degradation by a mixed bacterial consortium

A laboratory study was undertaken to assess the optimal conditions for biodegradation of Bombay High (BH) crude oil. Among 130 oil degrading bacterial cultures isolated from oil contaminated soil samples, Micrococcus sp. GS2-22, Corynebacterium sp. GS5-66, Flavobacterium sp. DS5-73, Bacillus sp. DS6-86 and Pseudomonas sp. DS10-129 were selected for the study based on the efficiency of crude oil utilisation. A mixed bacterial consortium prepared using the above strains was also used. Individual bacterial cultures showed less growth and degradation than did the mixed bacterial consortium. At 1% crude oil concentration, the mixed bacterial consortium degraded a maximum of 78% of BH crude oil. This was followed by 66% by Pseudomonas sp. DS10-129, 59% by Bacillus sp. DS6-86, 49% by Micrococcus sp. GS2-22, 43% by Corynebacterium sp. GS5-66 and 41% by Flavobacterium sp. DS5-73. The percentage of degradation by the mixed bacterial consortium decreased from 78% to 52% as the concentration of crude oil was increased from 1% to 10%. Temperature of 30 degrees C and pH 7.5 were found to be optima for maximum biodegradation.

Ultrastructure of two oil-degrading bacteria isolated from the tropical soil environment

Two oil-degrading bacteria identified as Pseudomonas aeruginosa and Micrococcus luteus were isolated from crude-oil-polluted soils in Nigeria. The organisms were grown on n-hexadecane and sodium succinate and then examined for the presence of hydrocarbon inclusions. Inclusion bodies were found in n-hexadecane-grown cells and were absent in succinate-grown cells. Formation of hydrocarbon inclusion bodies appears to be a general phenomenon among hydrocarbon utilizers.

Gene structures and regulation of the alkane hydroxylase complex in Acinetobacter sp. strain M-1

In the long-chain n-alkane degrader Acinetobacter sp. strain M-1, two alkane hydroxylase complexes are switched by controlling the expression of two n-alkane hydroxylase-encoding genes in response to the chain length of n-alkanes, while rubredoxin and rubredoxin ruductase are encoded by a single gene and expressed constitutively.

Role of rhamnolipid biosurfactants in the uptake and mineralization of hexadecane in Pseudomonas aeruginosa

A study was undertaken to investigate the mechanisms for biosurfactant-enhanced hexadecane uptake into Pseudomonas aeruginosa. Two strains of Ps. aeruginosa were studied, one producing rhamnolipids (PG201) and the other rhamnolipid deficient (UO299). Rhamnolipids produced by PG201 acted to increase the solubility of n-hexadecane in the culture medium (from 1.84 to 22.76 microg l(-1). Rates of(l4)C-n-hexadecane uptake and mineralization were higher in PG201 than in UO299. However, the degree of difference was lower than expected. Additional studies were carried out on the cell surface properties of the two strains. During growth on n-hexadecane, the cell surface hydrophobicity of both PG201 (50.5%) and UO299 (33.7%) increased compared with that observed in water-soluble growth substrates (7-8%). Studies were also carried out to ascertain any energy requirements for the transport of n-hexadecane into Ps. aeruginosa cells. The addition of CCCP (an inhibitor of cytochrome oxidase which thereby blocks oxidative phosphorylation) at a range of concentrations caused a marked decrease in n-hexadecane uptake, indicating that n-hexadecane uptake in Ps. aeruginosa is an energy-dependent process. These studies support the hypothesis of alkane transport into microbial cells by direct contact with larger alkane droplets and by pseudosolubilization. Also, it appears that both mechanisms occur simultaneously.

Degradation of diclofop-methyl by pure cultures of bacteria isolated from Manitoban soils

Pure cultures of Chryseomonas luteola and Sphingomonas paucimobilis isolated from Manitoban soils were able to utilize diclofop-methyl (methyl-2-[4-(2,4-dichlorophenoxy)phenoxy] propanoate) as the sole source of carbon and energy. An actively growing culture of C. luteola completely degraded 1.5 micrograms diclofop-methyl.mL-1 to diclofop acid and 4-(2,4-dichlorophenoxy)phenol within 71 h, as determined by gas chromatographic analysis. The accumulation of these metabolites in the growth medium resulted in the cessation of growth, indicating the organism's inability to degrade phenoxyphenol in the presence of diclofop acid. Sphingomonas paucimobilis mineralized 1.5 micrograms diclofop-methyl.mL-1 to diclofop acid within 54 h. A biphasic growth pattern indicated that this organism was capable of degrading diclofop acid to 4-(2,4-dichlorophenoxy)phenol and 2,4-dichlorophenol and (or) phenol. Neither of the organisms was able to utilize 2,4-dichlorophenol as the sole source of carbon and energy.

Basic and applied aspects of microbial adhesion at the hydrocarbon:water interface

Microbial hydrophobicity has been studied since 1924. During the last decade, various techniques have become available for measuring hydrophobic surface properties of microbial cells. This has led to a surge in investigations suggesting a role for hydrophobicity in adhesion of bacteria to an array of surfaces (oral surfaces, mineral particles, fatty meat, epithelial cells, phagocytes, biomaterials), partitioning at interfaces, as well as gliding mobility. The present manuscript comprises a critical, chronological look at the origins of microbial hydrophobicity research, its development, origins, and applications. Emphasis is placed on microbial adhesion to hydrocarbons, a technique with which the author has the most experience and research interest.

Metabolism of n-alkanes by Aspergillus japonicus

Cells of Aspergillus japonicus could degrade n-alkanes as a sole source of carbon. One of the pathways operative during the degradative process was the terminal pathway. Electron micrographs showed that the hydrocarbons were present in the cells as microdroplets.

Ultracytochemical localization of aldehyde dehydrogenase in Acinetobacter calcoaceticus

A membrane-bound aldehyde dehydrogenase is induced in Acinetobacter calcoaceticus grown on aliphatic hydrocarbons as sole carbon source. This enzyme is NADP-dependent and is able to oxidize medium- and long-chain aliphatic aldehydes to their corresponding fatty acids. Electron micrographs of sectioned alkane-adapted bacteria showed hydrocarbon inclusions in the cytoplasmic matrix. The cytochemical phenazine methosulphate-tetranitro tetrazolium blue capture reaction allowed to localize the activity of the aldehyde dehydrogenase near the surface of these inclusions. At the same location we also found a NADPH tetrazolium-reducing activity.

Growth of Acinetobacter sp. strain HO1-N on n-hexadecanol: physiological and ultrastructural characteristics

The growth of Acinetobacter sp. strain HO1-N on hexadecanol results in the formation of intracytoplasmic membranes and intracellular rectangular inclusions containing one of the end products of hexadecanol metabolism, hexadecyl palmitate. The intracellular inclusions were purified and characterized as "wax ester inclusions" consisting of 85.6% hexadecyl palmitate, 4.8% hexadecanol, and 9.6% phospholipid, with a phospholipid-to-protein ratio of 0.42 mumol of lipid phosphate per mg of inclusion protein. The cellular lipids consisted of 69.8% hexadecyl palmitate, 22.8% phospholipid, 1.9% triglyceride, 4.7% mono- and diglyceride, 0.1% free fatty acid, and 0.8% hexadecanol, as compared with 98% hexadecyl palmitate and 1.9% triglyceride, which comprised the extracellular lipids. Cell-associated hexadecanol represented 0.05% of the exogenously supplied hexadecanol, with hexadecyl palmitate accounting for 14.7% of the total cellular dry weight. Acinetobacter sp. strain HO1-N possesses a mechanism for the intracellular packaging of hexadecyl palmitate in wax ester inclusions, which differ in structure and chemical composition from "hydrocarbon inclusions" isolated from hexadecane-grown cells.