Hydrophobicity development, alkane oxidation, and crude-oil emulsification in a Rhodococcus species

Microbial metabolism regulation on the efficient degradation of aromatic compounds for biochemical treatment process of coal chemical wastewater in pilot scale

At present, the common problems of biochemical treatment systems of coal chemical wastewater were the poor system stability and the difficulty in reaching COD discharge standards. Aromatic compounds were the main contributors to COD value. The effective removal of aromatic compounds was an urgent problem in the biochemical treatment systems of coal chemical wastewater. In this study, the dominant microbial strains that could degrade phenol, quinoline, and phenanthrene were isolated respectively and inoculated into the pilot scale biochemical tank of coal chemical wastewater. The regulation effect and mechanism of microbial metabolism on the efficient degradation of aromatic compounds were studied. The results indicated that the various aromatic compounds were significantly removed under the regulation of microbial metabolism, the removal efficiencies of COD, TOC, phenols, benzenes, N-CHs, and PAHs were increased by about 25%, 20%, 33%, 25%, 42%, and 45%, respectively, and their biotoxicity was also drastically reduced. Moreover, the abundance and diversity of microbial community, and the microbial activity were obviously improved, as well as the various functional strains were selectively enriched, suggesting that the regulation system could resist environmental stresses with high substrate concentration and toxicity, which could lead to more enhanced performance for aromatic compounds removal. In addition, the microbial EPS content was significantly increased, implying the formation of microbial hydrophobic cell surfaces, which could improve the bioavailability of aromatic compounds. Furthermore, the enzymatic activity analysis revealed that the relative abundance and activity of key enzymes were all obviously improved. In conclusion, multiple lines of evidence were provided to clarify the regulation mechanism of microbial metabolism on the efficient degradation of aromatic compounds for biochemical treatment process of coal chemical wastewater in pilot scale. The results laid a good foundation for realizing the harmless treatment of coal chemical wastewater.

Metabolic fates and response strategies of microorganisms to aromatic compounds with different structures

In this study, the metabolic fates and response strategies of microorganisms to aromatic compounds with different structures (phenol, naphthalene, phenanthrene, and pyrene) were comparatively studied. The results indicated that the phenol (90.9%), naphthalene (68.4%), phenanthrene (69.5%), and pyrene (67.1%) could be mineralized, and the biotoxicity also has been drastically reduced. The degradation characteristics and toxic effects were closely related to their chemical structure. The microorganisms showed different response strategies to aromatic compounds with different structures. Phenol had a simple structure and low toxicity, the microbial community structure was simple, and the rapid expression of key enzymes enabled it to be rapidly degraded. For the hydrophobic and complex naphthalene, phenanthrene, and pyrene, the more complex the structure, the higher the microbial diversity, the EPS showed different response for the purpose of improving their bioavailability, and the activity of key enzymes was positively correlated with their structural complexity.

Biotechnology of Rhodococcus for the production of valuable compounds

Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. KEY POINTS: • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance. Graphical abstract.

Aerobic Growth of Rhodococcus aetherivorans BCP1 Using Selected Naphthenic Acids as the Sole Carbon and Energy Sources

Naphthenic acids (NAs) are an important group of toxic organic compounds naturally occurring in hydrocarbon deposits. This work shows that Rhodococcus aetherivorans BCP1 cells not only utilize a mixture of eight different NAs (8XNAs) for growth but they are also capable of marked degradation of two model NAs, cyclohexanecarboxylic acid (CHCA) and cyclopentanecarboxylic acid (CPCA) when supplied at concentrations from 50 to 500 mgL-1. The growth curves of BCP1 on 8XNAs, CHCA, and CPCA showed an initial lag phase not present in growth on glucose, which presumably was related to the toxic effects of NAs on the cell membrane permeability. BCP1 cell adaptation responses that allowed survival on NAs included changes in cell morphology, production of intracellular bodies and changes in fatty acid composition. Transmission electron microscopy (TEM) analysis of BCP1 cells grown on CHCA or CPCA showed a slight reduction in the cell size, the production of EPS-like material and intracellular electron-transparent and electron-dense inclusion bodies. The electron-transparent inclusions increased in the amount and size in NA-grown BCP1 cells under nitrogen limiting conditions and contained storage lipids as suggested by cell staining with the lipophilic Nile Blue A dye. Lipidomic analyses revealed significant changes with increases of methyl-branched (MBFA) and polyunsaturated fatty acids (PUFA) examining the fatty acid composition of NAs-growing BCP1 cells. PUFA biosynthesis is not usual in bacteria and, together with MBFA, can influence structural and functional processes with resulting effects on cell vitality. Finally, through the use of RT (Reverse Transcription)-qPCR, a gene cluster (chcpca) was found to be transcriptionally induced during the growth on CHCA and CPCA. Based on the expression and bioinformatics results, the predicted products of the chcpca gene cluster are proposed to be involved in aerobic NA degradation in R. aetherivorans BCP1. This study provides first insights into the genetic and metabolic mechanisms allowing a Rhodococcus strain to aerobically degrade NAs.

Extracellular polymeric substances govern the development of biofilm and mass transfer of polycyclic aromatic hydrocarbons for improved biodegradation

The hypothesis that extracellular polymeric substances (EPS) affect the formation of biofilms for subsequent enhanced biodegradation of polycyclic aromatic hydrocarbons was tested. Controlled formation of biofilms on humin particles and biodegradation of phenanthrene and pyrene were performed with bacteria and EPS-extracted bacteria of Micrococcus sp. PHE9 and Mycobacterium sp. NJS-P. Bacteria without EPS extraction developed biofilms on humin, in contrast the EPS-extracted bacteria could not attach to humin particles. In the subsequent biodegradation of phenanthrene and pyrene, the biodegradation rates by biofilms were significantly higher than those of EPS-extracted bacteria. Although, both the biofilms and EPS-extracted bacteria showed increases in EPS contents, only the EPS contents in biofilms displayed significant correlations with the biodegradation efficiencies of phenanthrene and pyrene. It is proposed that the bacterial-produced EPS was a key factor to mediate bacterial attachment to other surfaces and develop biofilms, thereby increasing the bioavailability of poorly soluble PAH for enhanced biodegradation.

Production and characterization of a trehalolipid biosurfactant produced by the novel marine bacterium Rhodococcus sp., strain PML026

AIMS

The aim of this study was to evaluate biosurfactant production by a novel marine Rhodococcus sp., strain PML026 and characterize the chemical nature and properties of the biosurfactant.

METHODS AND RESULTS

A novel marine bacterium (Rhodococcus species; strain PML026) was shown to produce biosurfactant in the presence of hydrophobic substrate (sunflower oil). Biosurfactant production (identified as a trehalolipid) was monitored in whole-batch cultures (oil layer and aqueous phase), aqueous phase (no oil layer) and filtered (0·2 μm) aqueous phase (no oil or cells; extracellular) and was shown to be closely associated with growth/biomass production. Extracellular trehalolipid levels increased postonset of stationary growth phase. Purified trehalolipid was able to reduce the surface tension of water to 29 mN m(-1) at Critical Micellar Concentration (CMC) of c. 250 mg l(-1) and produced emulsions that were stable to a wide range of conditions (pH 2-10, temperatures of 20-100°C and NaCl concentrations of 5-25% w/v). Separate chemical analyses of the intact trehalolipid and its constituents demonstrated the compound was in fact a mixture of homologues (>1180 MW) consisting of a trehalose moiety esterified to a series of straight chain and hydroxylated fatty acids.

CONCLUSIONS

The trehalolipid biosurfactant produced by the novel marine strain Rhodococcus sp. PML026 was characterized and exhibited high surfactant activity under a wide range of conditions.

SIGNIFICANCE AND IMPACT OF STUDY

Strain PML026 of Rhodococcus sp. is a potential candidate for bioremediation or biosurfactant production for various applications.

Deciphering the traits associated with PAH degradation by a novel Serratia marcesencs L-11 strain

Polycyclic aromatic hydrocarbons (PAHs) are wide spread industrial pollutants that are released into the environment from burning of coal, distillation of wood, operation of gas works, oil refineries, vehicular emission, and combustion process. In this study a lipolytic bacterium was isolated from mixed stover compost of Saccharum munja and Brassica campestris. This strain was identified by both classical and 16S ribosomal DNA sequencing method and designated as Serratia marcesencs L-11. HPLC-based quantitation revealed 39- 100% degradation of PAH compounds within seven days. Further its ability to produce catechol 1, 2-dioxygenase (1.118 μM mL(-1) h(-1)) and biosurfactants (0.88 g L(-1)) during growth in PAH containing medium may be responsible for its PAH-degradation potential. This novel bacterium with an ability to produce lipases, biosurfactant and ring cleavage enzyme can prove to be useful for in-situ degradation of PAH compounds.

Alteration in cell surface properties of Burkholderia spp. during surfactant-aided biodegradation of petroleum hydrocarbons

Chemical surfactants may impact microbial cell surface properties, i.e., cell surface hydrophobicity (CSH) and cell surface charge, and may thus affect the uptake of components from non-aqueous phase liquids (NAPLs). This work explored the impact of Triton X-100, Igepal CA 630, and Tween 80 (at twice the critical micelle concentration, CMC) on the cell surface characteristics of Burkholderia cultures, Burkholderia cepacia (ES1, aliphatic degrader) and Burkholderia multivorans (NG1, aromatic degrader), when grown on a six-component model NAPL. In the presence of Triton X-100, NAPL biodegradation was enhanced from 21% to 60% in B. cepacia and from 18% to 53% in B. multivorans. CSH based on water contact angle (50-52°) was in the same range for both strains while zeta potential at neutral pH was -38 and -31 mV for B. cepacia and B. multivorans, respectively. In the presence of Triton X-100, their CSH increased to greater than 75° and the zeta potential decreased. This induced a change in the mode of uptake and initiated aliphatic hydrocarbon degradation by B. multivorans and increased the rate of aliphatic hydrocarbon degradation in B. cepacia. Igepal CA 630 and Tween 80 also altered the cell surface properties. For B. cepacia grown in the presence of Triton X-100 at two and five times its CMC, CSH increased significantly in the log growth phase. Growth in the presence of the chemical surfactants also affected the abundance of chemical functional groups on the cell surface. Cell surface changes had maximum impact on NAPL degradation in the presence of emulsifying surfactants, Triton X-100 and Igepal CA630.

Alkane-degrading properties of Dietzia sp. H0B, a key player in the Prestige oil spill biodegradation (NW Spain)

AIMS

Investigation of the alkane-degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill.

METHODS AND RESULTS

Using molecular and chemical analyses, the alkane-degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n-alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8-Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane-degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR-amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation.

CONCLUSIONS

The results from this study suggest novel alkane-degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil-degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.

Biodegradation of kerosene by Aspergillus ochraceus NCIM-1146

The filamentous fungus Aspergillus ochraceus NCIM-1146 was found to degrade kerosene, when previously grown mycelium (96 h) was incubated in the broth containing kerosene. Higher levels of NADPH-DCIP reductase, aminopyrine N-demethylase and kerosene biodegradation activities were found to be present after the growth in potato dextrose broth for 96 h, when compared with the activities at different time intervals during the growth phase. NADPH was the preferred cofactor for enzyme activity, which was inhibited by CO, indicating cytochrome P450 mediated reactions. A significant increase in all the enzyme activities was observed when mycelium incubated for 18 h in mineral salts medium, containing cholesterol, camphor, naphthalene, 1,2-dimethoxybenzene, phenobarbital, n-hexane, kerosene or saffola oil as inducers. Acetaldehyde produced by alcohol dehydrogenase could be used as an indicator for the kerosene biodegradation.

Hexadecane and Tween 80 stimulate lipase production in Burkholderia glumae by different mechanisms

Burkholderia glumae strain PG1 produces a lipase of biotechnological relevance. Lipase production by this strain and its derivative LU8093, which was obtained through classical strain improvement, was investigated under different conditions. When 10% hexadecane was included in the growth medium, lipolytic activity in both strains could be increased approximately 7-fold after 24 h of growth. Hexadecane also stimulated lipase production in a strain containing the lipase gene fused to the tac promoter, indicating that hexadecane did not affect lipase gene expression at the transcriptional level, which was confirmed using lipA-gfp reporter constructs. Instead, hexadecane appeared to enhance lipase secretion, since the amounts of lipase in the culture supernatant increased in the presence of hexadecane, with a concomitant decrease in the cells, even when protein synthesis was inhibited with chloramphenicol. In the presence of olive oil as a carbon source, nonionic detergents, such as Tween 80, increased extracellular lipase activity twofold. Like hexadecane, Tween 80 appeared to stimulate lipase secretion, although in a more disruptive manner, since other, normally nonsecreted proteins were found in the culture supernatant. Additionally, like olive oil, Tween 80 was found to induce lipase gene expression in strain PG1 in medium containing sucrose as a carbon source but not in glucose-containing medium, suggesting that lipase gene expression is prone to catabolite repression. In contrast, lipase production in the lipase-overproducing strain LU8093 was independent of the presence of an inducer and was not inhibited by glucose. In conclusion, hexadecane and Tween 80 enhance lipase production in B. glumae, and they act via different mechanisms.

Biodegradation of phenanthrene and analysis of degrading cultures in the presence of a model organo-mineral matrix and of a simulated NAPL phase

Two mixed bacterial cultures (C(B-BT) and C(I-AT)) degraded phenanthrene when it was: (i) in the presence of either hexadecane as a non aqueous phase liquid or a montmorillonite-Al(OH)x-humic acid complex as a model organo-mineral matrix; (ii) sorbed to the complex, either alone or in the presence of hexadecane. The cultures had different kinetic behaviours towards phenanthrene with or without hexadecane. The degradation of Phe alone as well as that of Phe in hexadecane ended in 8 and 15 days with C(B-BT) and C(I-AT) cultures, respectively. Hexadecane increased Phe bioavailability for C(I-AT) bacteria which degraded Phe according to first-order kinetics. The same effect was observed for C(B-BT) bacteria, but with an initial 2 days lag phase and in accordance with zero-order kinetics. The presence of hexadecane did not affect the degradation of phenanthrene sorbed and aged on the complex by C(I-AT )culture. This capability was exhibited also after experimental aging of 30 days. The dynamics of the bacterial community composition was investigated through PCR-DGGE (denaturing gradient gel electrophoresis) of 16S rRNA gene fragments. Individual bands changed their intensity during the incubation time, implying that particular microbe's relative abundance changed according to the culture conditions. Isolation of phenanthrene and/or hexadecane degraders was in accord with cultivation-independent data. Growth-dependent changes in the cell surface hydrophobicity of the two cultures and of the isolates suggested that modulation of cell surface hydrophobicity probably played an important role for an efficient phenanthrene assimilation/uptake.

Interaction of metabolites with R. rhodochrous during the biodegradation of di-ester plasticizers

The commonly used plasticizers di-ethylhexyl phthalate (DEHP) and di-ethylhexyl adipate (DEHA) are known to partially degrade in the presence of soil microorganisms, such as Rhodococcus rhodochrous, releasing persistent and toxic metabolites. The metabolites adipic acid and 2-ethylhexanol were both shown to inhibit growth of the degrading microbe. 2-Ethylhexanol enhanced the activity of ethanol dehydrogenase - an enzyme involved in its metabolism - but the activity of this enzyme was inhibited by adipic acid. The metabolite usually seen in the highest concentrations - 2-ethylhexanoic acid - did not exhibit any evidence of inhibition. It was shown that the high concentration of this metabolite was due to the inability of R. rhodochrous to degrade it. Comparisons with other small carboxylic acids supported the argument that the ethyl branch was the reason for the resistance of 2-ethylhexanoic acid to degradation. The hydrophobicity of the cell surface was shown to be a factor in plasticizer degradation. The primary carbon source could be either water-soluble or hydrophobic and a hydrophobic substrate led to a cell surface that attracted the plasticizer and facilitated degradation. The most hydrophobic of the plasticizers, DEHP, was particularly sensitive to this effect.

Surface properties of Yarrowia lipolytica and their relevance to ?-decalactone formation from methyl ricinoleate

The surface of the lipid-degrading yeast, Yarrowia lipolytica, was characterized by contact angle and zeta potential (zeta) measurements. The cells were mainly hydrophilic with a negative charge that was only affected from pH 2 to 4. To study the effects of the surface charges on the biotransformation of methyl ricinoleate into the aroma compound, gamma-decalactone, the zeta values of the substrate droplets were modified by adding a cationic surfactant into the medium at concentrations that did not diminish cell viability: the adhesion of the lipid substrate to the cells was increased but not the overall performance of the process, therefore the adhesion is not the rate limiting here. Our methodology offers interesting perspectives for further applications.

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.

Carbon source-induced modifications in the mycolic acid content and cell wall permeability of Rhodococcus erythropolis E1

The influence of the carbon source on cell wall properties was analyzed in an efficient alkane-degrading strain of Rhodococcus erythropolis (strain E1), with particular focus on the mycolic acid content. A clear correlation was observed between the carbon source and the mycolic acid profiles as estimated by high-performance liquid chromatography and mass spectrometry. Two types of mycolic acid patterns were observed after growth either on saturated linear alkanes or on short-chain alkanoates. One type of pattern was characterized by the lack of odd-numbered carbon chains and resulted from growth on linear alkanes with even numbers of carbon atoms. The second type of pattern was characterized by mycolic acids with both even- and odd-numbered carbon chains and resulted from growth on compounds with odd-numbered carbon chains, on branched alkanes, or on mixtures of different compounds. Cellular short-chain fatty acids were twice as abundant during growth on a branched alkane (pristane) as during growth on acetate, while equal amounts of mycolic acids were found under both conditions. More hydrocarbon-like compounds and less polysaccharide were exposed at the cell wall surface during growth on alkanes. Whatever the substrate, the cells had the same affinity for aqueous-nonaqueous solvent interfaces. By contrast, bacteria displayed completely opposite susceptibilities to hydrophilic and hydrophobic antibiotics and were found to be strongly stained by hydrophobic dyes after growth on pristane but not after growth on acetate. Taken together, these data show that the cell wall composition of R. erythropolis E1 is influenced by the nutritional regimen and that the most marked effect is a radical change in cell wall permeability.