Identification and structural characterisation of novel trehalose dinocardiomycolates from n-alkane-grown Rhodococcus opacus 1CP

Biosurfactant is a powerful tool for the bioremediation of heavy metals from contaminated soils

Heavy metal toxicity has become a pressing ecological problem that affects the ecosystems through bioaccumulation, representing a serious public health hazard. Many conventional strategies have been developed and applied to decontaminate and restore metal-contaminated areas. However, these conventional approaches are not very suitable and environmentally safe for heavy metal remediation because of their high operational costs, high energy requirements, post-waste disposal problems, and secondary pollutant generation. Thus, biosurfactant-based bioremediation of heavy metals is a sustainable and promising approach because of its biodegradation capability, economic effectiveness, and ecofriendly nature. Pseudomonas sp., Bacillus sp., Citrobacter freundii, and Candida tropicalis have been isolated as potential sources of biosurfactants and produce compounds such as surfactin, rhamnolipids, and sophorolipids. Owing to the severity of heavy metal pollution in certain parts of the environment, biosurfactants have garnered great interest and attention as an emerging multi-functional technology of the new century for successful removal of heavy metal pollutants. The present study describes the role of biosurfactants in the bioremediation of heavy metals from contaminated environments. Moreover, the interaction mechanism underlying biosurfactant-metal complexation and metal remediation are discussed. Based on the review of the literature, further research is warranted to elucidate the mechanistic roles and explore the structural characterization and gene regulation of biosurfactants to improve their productivity and expand their applicability in bioremediation.

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.

Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence

The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.

Cell Walls and Membranes of Actinobacteria

Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.

Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium

Biosurfactants are amphipathic molecules with relevance in biotechnology due to their structural diversity, low toxicity and biodegradability. The genus Rhodococcus has extensively been studied because of its capacity to produce trehalose-containing surfactants as well as trehalose lipids as potential pathogenic factor. Here we present the draft genome sequence of Rhodococcus erythropolis B7g isolated with toluene from fuel-contaminated soil. The genome comprises 7,175,690 bp in 121 contigs, a G + C content of 62,4% and 7,153 coding DNA sequences (CDSs), and it contains genes for trehalose biosynthesis and surfactant production. Additionally, genes for the production of trehalose-tetraester biosurfactant were identified, whose function was experimentally verified making the strain B7g a potential candidate for use in bioremediation applications or in biosurfactant exploration.

Response of Rhodococcus erythropolis strain IBBPo1 to toxic organic solvents

Recently, there has been a lot of interest in the utilization of rhodococci in the bioremediation of petroleum contaminated environments. This study investigates the response of Rhodococcus erythropolis IBB_Po1 cells to 1% organic solvents (alkanes, aromatics). A combination of microbiology, biochemical, and molecular approaches were used to examine cell adaptation mechanisms likely to be pursued by this strain after 1% organic solvent exposure. R. erythropolis IBB_Po1 was found to utilize 1% alkanes (cyclohexane, n-hexane, n-decane) and aromatics (toluene, styrene, ethylbenzene) as the sole carbon source. Modifications in cell viability, cell morphology, membrane permeability, lipid profile, carotenoid pigments profile and 16S rRNA gene were revealed in R. erythropolis IBB_Po1 cells grown 1 and 24 h on minimal medium in the presence of 1% alkanes (cyclohexane, n-hexane, n-decane) and aromatics (toluene, styrene, ethylbenzene). Due to its environmental origin and its metabolic potential, R. erythropolis IBB_Po1 is an excellent candidate for the bioremediation of soils contaminated with crude oils and other toxic compounds. Moreover, the carotenoid pigments produced by this nonpathogenic Gram-positive bacterium have a variety of other potential applications.

Glycolipid biosurfactants: Potential related biomedical and biotechnological applications

Glycolipids, consisting of a carbohydrate moiety linked to fatty acids, are microbial surface active compounds produced by various microorganisms. They are characterized by highly structural diversity and have the ability to decrease the surface and interfacial tension at the surface and interface respectively. Rhamnolipids, trehalolipids, mannosylerythritol-lipids and cellobiose lipids are among the most popular glycolipids. Moreover, their ability to form pores and destabilize biological membrane permits their use in biomedicine as antibacterial, antifungal and hemolytic agents. Their antiviral and antitumor effects enable their use in pharmaceutic as therapeutic agents. Also, glycolipids can inhibit the bioadhesion of pathogenic bacteria enabling their use as anti-adhesive agents and for disruption of biofilm formation and can be used in cosmetic industry. Moreover, they have great potential application in industry as detergents, wetting agents and for flotation. Furthermore, glycolipids can act at the surface and can modulate enzyme activity permitting the enhancement or the inhibition of the activity of certain enzymes.

Isolation and functional analysis of a glycolipid producing Rhodococcus sp. strain IITR03 with potential for degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT)

A 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degrading bacterium strain IITR03 producing trehalolipid was isolated and characterized from a pesticides contaminated soil. The strain IITR03 was identified as a member of the genus Rhodococcus based on polyphasic studies. Under aqueous culture conditions, the strain IITR03 degraded 282 μM of DDT and could also utilize 10mM concentration each of 4-chlorobenzoic acid, 3-chlorobenzoic acid and benzoic acid as sole carbon and energy source. The catechol 1,2-dioxygenase enzyme activity resulted in conversion of catechol to form cis,cis-muconic acid. Cloning and sequencing of partial nucleotide sequence of catechol 1,2-dioxygenase gene (cat) from strain IITR03 revealed its similarity to catA gene present in Rhodococcus sp. strain Lin-2 (97% identity) and Rhodococcus strain AN22 (96% identity) degrading benzoate and aniline, respectively. The results suggest that the strain IITR03 could be useful for field bioremediation studies of DDT-residues and chlorinated aromatic compounds present in contaminated sites.

Deep-sea Rhodococcus sp. BS-15, lacking the phytopathogenic fas genes, produces a novel glucotriose lipid biosurfactant

Glycolipid biosurfactant-producing bacteria were isolated from deep-sea sediment collected from the Okinawa Trough. Isolate BS15 produced the largest amount of the glycolipid, generating up to 6.31 ± 1.15 g l(-1) after 4 days at 20 °C. Glucose was identified in the hydrolysate of the purified major component of the biosurfactant glycolipid. According to gas chromatography/mass spectrometry analysis, the hydrophobic moieties in the major component were hexadecanoate, octadecanoate, 3-hydroxyhexadecanoate, 2-hydroxyoctanoate, and succinate. The molecular weight of the purified major glycolipid was calculated to be 1,211, while (1)H and (13)C nuclear magnetic resonance spectra confirmed that the major component consisted of 2 mol of α-glucoside and 1 mol of β-glucoside. The molecular structure was assigned as novel trisaccharide-type glycolipid biosurfactant, glucotriose lipids. The critical micelle concentration of the purified major glycolipid was 2.3 × 10(-6) M, with a surface tension of 29.5 mN m(-1). Phylogenetic analysis showed isolate BS15 was closely related to a Rhodococcus strains isolated from Antarctica, and to Rhodococcus fascians, a phytopathogen. PCR analysis showed that the fasA, fasB, fasC, fasD, fasE, and fasF genes, which are involved in phytohormone-like cytokinin production, were not present in the genome of BS15; however, analysis of a draft genome sequence of BS15 (5.5 Mb) identified regions with 31 %, 53 %, 46 %, 30 %, and 31 % DNA sequence identity to the fasA, fasB, fasC, and fasD genes, respectively.

Bacteria induced degradation of fluoranthene in minimal salt medium mediated by catabolic enzymes in vitro condition

Fluoranthene is highly toxic and ubiquitous in the environment. A study on degradation of 200 ppm of fluoranthene in MSM by two bacterial strains Pseudomonas aeruginosa PSA5, Rhodococcus sp. NJ2 and their consortium revealed that fluoranthene was degraded 74% by Rhodococcus sp. NJ2, 61% by Pseudomonas sp. PSA5 and 97% by their consortium. Higher degradation in the consortium may be attributed to synergistic action between two bacteria. It was also observed that several degradative enzymes catechol 1,2 dioxygenase, catechol 2,3 dioxygenase, protocatechuate 2,3 dioxygenase, protocatechuate 3,4 dioxygenase, protocatechuate 4,5 dioxygenase, salicylate hydroxylase and 2-carboxybenzaldehyde dehydrogenase were differentially induced at different stages of fluoranthene degradation. Biodegradation kinetics indicated half life period of fluoranthene degradation. Besides, glycolipid, as a biosurfactant, was induced to facilitate the degradation process. Hence, both the bacteria may be used individually or in combination for effective decontamination of oil and sludge contaminated soil.

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.

Trehalose phosphate synthases OtsA1 and OtsA2 of Rhodococcus opacus 1CP

Rhodococcus opacus 1CP produces trehalose dinocardiomycolates during growth on long-chained n-alkanes. Trehalose and trehalose-6-phosphate, which are synthesized via the OtsAB pathway, are probable intermediates in the biosynthesis of these biosurfactants. By molecular genetic screening for trehalose-6-phosphate synthases (TPSs and OtsAs), two chromosomal fragments of strain 1CP were obtained. Each contained an ORF whose amino acid sequence showed high similarity to TPSs. To prove the activity of the otsA1 and otsA2 gene product and to detect catalytic differences, both were expressed as His-tagged fusion proteins. Enzyme kinetics of the enriched proteins using several potential glucosyl acceptors showed an exclusive preference for glucose-6-phosphate. In contrast, both enzymes were shown to differ significantly from each other in their activity with different glucosyl nucleotides as glucosyl donors. OtsA1-His10 showed highest activity with ADP-glucose and UDP-glucose, whereas OtsA2-His10 preferred UDP-glucose. In addition, the wild-type OtsA activity of R. opacus 1CP was investigated and compared with recombinant enzymes. Results indicate that OstA2 mainly contributes to the trehalose pool of strain 1CP. OtsA1 seems to be involved in the overproduction of trehalose lipids. For the first time, a physiological role of two different OtsAs obtained of a single Rhodococcus strain was presumed.

Diversion of phagosome trafficking by pathogenic Rhodococcus equi depends on mycolic acid chain length

Rhodococcus equi is a close relative of Mycobacterium spp. and a facultative intracellular pathogen which arrests phagosome maturation in macrophages before the late endocytic stage. We have screened a transposon mutant library of R. equi for mutants with decreased capability to prevent phagolysosome formation. This screen yielded a mutant in the gene for β-ketoacyl-(acyl carrier protein)-synthase A (KasA), a key enzyme of the long-chain mycolic acid synthesizing FAS-II system. The longest kasA mutant mycolic acid chains were 10 carbon units shorter than those of wild-type bacteria. Coating of non-pathogenic E. coli with purified wild-type trehalose dimycolate reduced phagolysosome formation substantially which was not the case with shorter kasA mutant-derived trehalose dimycolate. The mutant was moderately attenuated in macrophages and in a mouse infection model, but was fully cytotoxic.Whereas loss of KasA is lethal in mycobacteria, R. equi kasA mutant multiplication in broth was normal proving that long-chain mycolic acid compounds are not necessarily required for cellular integrity and viability of the bacteria that typically produce them. This study demonstrates a central role of mycolic acid chain length in diversion of trafficking by R. equi.

Nocardia brasiliensis cell wall lipids modulate macrophage and dendritic responses that favor development of experimental actinomycetoma in BALB/c mice

Nocardia brasiliensis is a Gram-positive facultative intracellular bacterium frequently isolated from human actinomycetoma. However, the pathogenesis of this infection remains unknown. Here, we used a model of bacterial delipidation with benzine to investigate the role of N. brasiliensis cell wall-associated lipids in experimental actinomycetoma. Delipidation of N. brasiliensis with benzine resulted in complete abolition of actinomycetoma without affecting bacterial viability. Chemical analyses revealed that trehalose dimycolate and an unidentified hydrophobic compound were the principal compounds extracted from N. brasiliensis with benzine. By electron microscopy, the extracted lipids were found to be located in the outermost membrane layer of the N. brasiliensis cell wall. They also appeared to confer acid-fastness. In vitro, the extractable lipids from the N. brasiliensis cell wall induced the production of the proinflammatory cytokines interleukin-1β (IL-1β), IL-6, and CCL-2 in macrophages. The N. brasiliensis cell wall extractable lipids inhibited important macrophage microbicidal effects, such as tumor necrosis factor alpha (TNF-α) and nitric oxide (NO) production, phagocytosis, bacterial killing, and major histocompatibility complex class II (MHC-II) expression in response to gamma interferon (IFN-γ). In dendritic cells (DCs), N. brasiliensis cell wall-associated extractable lipids suppressed MHC-II, CD80, and CD40 expression while inducing tumor growth factor β (TGF-β) production. Immunization with delipidated N. brasiliensis induced partial protection preventing actinomycetoma. These findings suggest that N. brasiliensis cell wall-associated lipids are important for actinomycetoma development by inducing inflammation and modulating the responses of macrophages and DCs to N. brasiliensis.

Structural studies of cord factors from Mycobacterium simiae related to the capacity for tumour necrosis factor alpha (α-TNF) induction

The structure of cord factor was studied in several strains of Mycobacterium simiae, including 'habana' TMC 5135, considered as highly immunogenic in experimental tuberculosis and leprosy. The mycolic acids liberated from cord factor were identified in all cases as α'-, α- and keto-mycolates. According to the general NMR and MS data, α'-mycolates were mono-unsaturated and contained from 64 to 68 carbon atoms, whereas α-mycolates mainly presented two 2,3-disubstituted cyclopropane rings and a chain length of 80-91 carbon atoms; keto-mycolates mostly contained one cyclopropane ring and 85-91 carbon atoms. Taking into account the (1)H-NMR results, strains varied in the ratio of the different mycolates, and the high levels of keto-mycolates found in the cord factors of TMC 5135 and ATCC 25275(T) stood out. Notably, MS revealed that the odd carbon number series of α-mycolates (C87-C89) predominated in the cord factor of TMC 5135, in contrast to the remaining studied strains, in which the even (C84-C86) and odd carbon number series appeared more equal. The fine structural differences detected among the cord factors studied did not seem to be relevant to the general capacity of these molecules to induce the secretion of tumour necrosis factor alpha, as the cord factors from several strains of M. simiae (TMC 5135, IPK-342 and ATCC 25275(T)) induced similar amounts of this cytokine in RAW 264.7 cells.

Novel Polyoxyethylene-Containing Glycolipids Are Synthesized in Corynebacterium matruchotii and Mycobacterium smegmatis Cultured in the Presence of Tween 80

The addition of polyoxyethylene sorbitan monooleate (Tween 80) to a culture of mycobacteria greatly influences cell permeability and sensitivity to antibiotics but very little is known regarding the underlying mechanism. Here we show that Corynebacterium matruchotii (surrogate of mycobacteria) converts Tween 80 to a structural series of polyoxyethylenic acids which are then used to form novel series-2A and series-2B glycolipids. Minor series-3 glycolipids were also synthesized. The polyoxyethylenic acids replaced corynomycolic acids in the cell wall. Correspondingly the trehalose dicorynomycolate content was reduced. MALDI mass spectrometry, MS-MS, ¹H-NMR, and ¹³C-NMR were used to characterize the series-2 glycolipids. Series-2A glycolipid is trehalose 6-C_36:2-corynomycolate-6′-polyoxyethylenate and series-2B glycolipid is trehalose 6-C_36:2-corynomycolate-6′-furan ring-containing polyoxyethylenate. Mycobacterium smegmatis grown in the presence of Tween 80 also synthesizes series-2 type glycolipids. The synthesis of these novel glycolipids in corynebacteria and mycobacteria should result in gross changes in the cell wall permeability and drug sensitivity.

Oil spill remediation by using the remediation agent JE1058BS that contains a biosurfactant produced by Gordonia sp. strain JE-1058

A remediation agent containing a biosurfactant was prepared by spray drying the sterilized culture broth of Gordonia sp. strain JE-1058, and the agent was designated as JE1058BS. On subjection to the baffled flask test developed by the United States Environmental Protection Agency, JE1058BS showed a strong potential to be applied as an oil spill dispersant even in the absence of a solvent. It also proved to be an effective bioremediation agent for the remediation of oil spills at sea. The addition of JE1058BS to seawater stimulated the degradation of weathered crude oil (ANS 521) via the activity of the indigenous marine bacteria. Its addition also stimulated the removal of crude oil from the surface of contaminated sea sand. These results indicate that biosurfactant-containing JE1058BS has a strong potential to be applied as a remediation agent for the clean-up of oil spills at sea and on shorelines.

Efficient purification of the biosurfactant viscosin from Pseudomonas libanensis strain M9-3 and its physicochemical and biological properties

Viscosin (1), an effective surface-active cyclic lipopeptide, was efficiently recovered from Pseudomonas libanensis M9-3 with a simple purification protocol. A major pigment also obtained during this process was identified as phenazine-1-carboxylic acid. The critical micelle concentration (cmc) of viscosin was determined to be 54 mg L (-1), and the minimum surface tension between air and water at the cmc was 28 mN m (-1). Viscosin forms stable emulsions even at low concentrations (7.5 mg L (-1)), and the conditional stability constant for a cadmium-viscosin complex was determined to be 5.87. The physicochemical properties measured for viscosin are similar to other well-studied biosurfactants such as rhamnolipid and surfactin. Viscosin inhibited migration of the metastatic prostate cancer cell line, PC-3M, without visible toxicity. These properties suggest the potential of viscosin in environmental and biomedical applications.

Stabilization of water-in-oil emulsion by Rhodococcus opacus B-4 and its application to biotransformation

Rhodococcus opacus B-4, which has recently been isolated as an organic solvent-tolerant bacterium, stabilized water-in-oil (w/o) emulsions by inhibition of droplet coalescence when the cells were dispersed in 90% (v/v) organic solvents. Confocal microscopy revealed that many bacterial cells assembled at the interface between oil and water droplets, though free cells were also detectable at the inside of water droplets. Bacterial cells in the w/o emulsion were capable of utilizing both a water-soluble (glucose) and an oil-soluble substrate (oleic acid) as an energy source. Availability of the w/o emulsion as an immobilized cell system in organic solvents was demonstrated using production of indigo from indole and production of o-cresol from toluene as model conversions. When glucose and oleic acid were simultaneously supplied as energy sources, the w/o emulsion culture of R. opacus B-4 produced indigo and o-cresol at levels of 0.217 and 2.12 mg ml(-1), respectively, by 12 h.