Study of the genes involved in Naphthenic acids (NAs) degradation by Rhodococcus spp.

Naphthenic acids (NAs) are an important group of organic pollutants mainly found in hydrocarbon deposits. Although these compounds are toxic, recalcitrant, and persistent in the environment, we are just learning the diversity of microbial communities involved in NAs- degradation and the mechanisms by which NAs are biodegraded. Studies have shown that naphthenic acids are susceptible to biodegradation, which decreases their concentration and reduces toxicity. Nevertheless, little is still known about their biodegradability. The present PhD Thesis’s work is aimed to study the biodegradation of simple model NAs using bacteria strains belonging to the Rhodococcus genus. In particular, Rh. sp. BCP1 and Rh. opacus R7 were able to utilize NAs such as cyclohexane carboxylic acid and cyclopentane carboxylic acid as the sole carbon and energy sources, even at concentrations up to 1000 mg/L. The presence of either substituents or longer carboxylic acid chains attached to the cyclohexane ring negatively affected the growth by pure bacterial cultures. Moreover, BCP1 and R7 cells incubated in the presence of CHCA or CPCA show a general increase of saturated and methyl-substituted fatty acids in their membrane, while the cis-mono-unsaturated ones decrease, as compared to glucose-grown cells. The observed lipid molecules modification during the growth in the presence of NAs is suggested as a possible mechanism to decrease the fluidity of the cell membrane to counteract NAs toxicity. In order to further evaluate this toxic effect on cell features, the morphological changes of BCP1 and R7 cells were also assessed through Transmission Electron Microscopy (TEM), revealing interesting ultrastructural changes. The induction of putative genes, and the construction of a random transposon mutagenesis library were also carried out to reveal the mechanisms by which these Rhodococcus strains can degrade toxic compounds such as NAs

Tunable photoluminescence properties of selenium nanoparticles: biogenic versus chemogenic synthesis

Various technological and biomedical applications rely on the ability of materials to emit light (photoluminescence [PL]), and, among them, metal nanoparticles (NPs) and semi-conductor Quantum Dots (QDs) represent ideal candidates as sensing probes and imaging tools, portraying better PL features than conventional organic dyes. However,theknowledgeofPLbehaviorofsemiconductorNPs – i.e., selenium; SeNPs – is still in its infancy, especially for those synthesized by microorganisms. Considering the essential role played by biogenic SeNPs as antimicrobial, anticancer, and antioxidant agents, or food supplements, their PL properties must be explored to take full advantage of them as eco-friendly and versatile tools. Here, PL features of SeNPs produced by the Se-tolerant Stenotrophomonasmaltophilia SeITE02 strain, compared with chemogenic ones, are investigated, highlighting the PL dependency on the NP size. Indeed, PL emission shifted from indigo-blue (emission wavelength λem 400–450 nm) to green-yellow (λem 480– 570 nm) and orange-red (λem 580–700 nm) for small (ca. 50 nm) and big (ca. 100 nm) SeNPs respectively, revealing the versatility of an environmental bacterial isolate to synthesize diverse PL probes. Besides, biogenic SeNPs show PL lifetime comparable to those of the most used fluorophores, supporting their potential application as markers for (bio)imaging

Influence of bacterial physiology on processing of selenite, biogenesis of nanomaterials and their thermodynamic stability

We explored how Ochrobactrum sp. MPV1 can convert up to 2.5 mM selenite within 120 h, surviving the challenge posed by high oxyanion concentrations. The data show that thiol-based biotic chemical reaction(s) occur upon bacterial exposure to low selenite concentrations, whereas enzymatic systems account for oxyanion removal when 2 mM oxyanion is exceeded. The selenite bioprocessing produces selenium nanomaterials, whose size and morphology depend on the bacterial physiology. Selenium nanoparticles were always produced by MPV1 cells, featuring an average diameter ranging between 90 and 140 nm, which we conclude constitutes the thermodynamic stability range for these nanostructures. Alternatively, selenium nanorods were observed for bacterial cells exposed to high selenite concentration or under controlled metabolism. Biogenic nanomaterials were enclosed by an organic material in part composed of amphiphilic biomolecules, which could form nanosized structures independently. Bacterial physiology influences the surface charge characterizing the organic material, suggesting its diverse biomolecular composition and its involvement in the tuning of the nanomaterial morphology. Finally, the organic material is in thermodynamic equilibrium with nanomaterials and responsible for their electrosteric stabilization, as changes in the temperature slightly influence the stability of biogenic compared to chemogenic nanomaterials

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

DNA methylation is an epigenetic modification detected in both prokaryotic and eukaryotic genomic DNAs. In bacteria, the importance of 5-methylcytosine (m5C) in gene expression has been less investigated than in eukaryotic systems. Through dot-blot analysis employing m5C antibodies against chromosomal DNA, we have previously demonstrated that m5C influences the differentiation of Streptomyces coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media. Here, we mapped the methylated cytosines of the M145 strain growing in the defined Maltose Glutamate (MG) liquid medium. Sequencing of the M145 genome after bisulfite treatment (BS-sequencing) evidenced 3360 methylated cytosines and the two methylation motifs, GGCmCGG and GCCmCG, in the upstream regions of 321 genes. Besides, the role of cytosine methylation was investigated using the hypo-methylating agent 5'-aza-2'-deoxycytidine (5-aza-dC) in S. coelicolor cultures, demonstrating that m5C affects both growth and antibiotic biosynthesis. Finally, quantitative reverse-transcription polymerase-chain-reaction (RT-qPCR) analysis of genes containing the methylation motifs in the upstream regions showed that 5-aza-dC treatment influenced their transcriptional levels and those of the regulatory genes for two antibiotics. To the best of our knowledge, this is the first study that reports the cytosine methylome of S. coelicolor M145, supporting the crucial role ascribed to cytosine methylation in controlling bacterial gene expression

Microbial-Based Bioremediation of Selenium and Tellurium Compounds

The chalcogens selenium (Se) and tellurium (Te) are rare earth elements, which are mainly present in the environment as toxic oxyanions, due to the anthropogenic activities. Thus, the increased presence of these chalcogen-species in the environment and the contamination of wastewaters nearby processing facilities led to the necessity in developing remediation strategies aimed to detoxify waters, soils and sediments. Among the different decontamination approaches, those based on the ability of microorganisms to bioaccumulate, biomethylate or bioconvert Se- and/or Te-oxyanions are considered the leading strategy for achieving a safe and eco-friendly bioremediation of polluted sites. Recently, several technologies based on the use of bacterial pure cultures, bacterial biofilms or microbial consortia grown in reactors with different configurations have been explored for Se- and Te-decontamination purposes. Further, the majority of microorganisms able to process chalcogen-oxyanions have been described to generate valuable Se- and/or Te-nanomaterials as end-products of their bioconversion, whose potential applications in biomedicine, optoelectronics and environmental engineering are still under investigation. Here, the occurrence, the use and the toxicity of Se- and Te-compounds will be briefly overviewed, while the microbial mechanisms of chalcogen-oxyanions bioprocessing, as well as the microbial-based strategies used for bioremediation approaches will be extensively described

Chemogenic versus biogenic synthesis of Selenium nanoparticles: a structural characterization

Among the plethora of available metal- and metalloid-based nanomaterials (NMs), selenium nanostructures (SeNSs) are one of the most interesting from an applicative perspective due to their intermediate properties between metals and non-metals, as well as their high biocompatibility. In this regard, the capability of microorganisms to biotransform toxic Se-oxyanions – i.e., selenite (SeO32-) and selenate (SeO42-) – into their less bioavailable elemental forms [Se(0)], mostly generating Se nanoparticles (SeNPs), represents as a useful and green alternative over chemogenic synthesis allowing to obtain highly thermodynamically stable NMs. However, their structural characterization, in terms of biomolecules and interactions stabilizing the biogenic colloidal solution, is still a black hole in the microbial nanotechnology field, impairing the exploitation of biogenic SeNP full potential. Here, a parallel characterization between biogenic and chemogenic SeNPs was carried out through Fourier Transform Infrared spectroscopy in Attenuated Total Reflectance (ATR-FTIR) mode, Nuclear Magnetic Resonance (NMR) spectroscopy, and Density Functional Theory (DFT) calculations, to better understand which functional groups, hence biomolecules, contribute the most to the stabilization of biogenic SeNPs

Physical–chemical properties of biogenic selenium nanostructures produced by Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1

Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1 were isolated from the rhizosphere soil of the selenium-hyperaccumulator legume Astragalus bisulcatus and waste material from a dumping site for roasted pyrites, respectively. Here, these bacterial strains were studied as cell factories to generate selenium-nanostructures (SeNS) under metabolically controlled growth conditions. Thus, a defined medium (DM) containing either glucose or pyruvate as carbon and energy source along with selenite (www.frontiersin.org) was tested to evaluate bacterial growth, oxyanion bioconversion and changes occurring in SeNS features with respect to those generated by these strains grown on rich media. Transmission electron microscopy (TEM) images show extra- or intra-cellular emergence of SeNS in SeITE02 or MPV1 respectively, revealing the presence of two distinct biological routes of SeNS biogenesis. Indeed, the stress exerted by www.frontiersin.org upon SeITE02 cells triggered the production of membrane vesicles (MVs), which surrounded Se-nanoparticles (SeNPsSeITE02-G_e and SeNPsSeITE02-P_e with average diameter of 179 ± 56 and 208 ± 60 nm, respectively), as highlighted by TEM and scanning electron microscopy (SEM), strongly suggesting that MVs might play a crucial role in the excreting mechanism of the SeNPs in the extracellular environment. On the other hand, MPV1 strain biosynthesized intracellular inclusions likely containing hydrophobic storage compounds and SeNPs (123 ± 32 nm) under pyruvate conditioning, while the growth on glucose as the only source of carbon and energy led to the production of a mixed population of intracellular SeNPs (118 ± 36 nm) and nanorods (SeNRs; average length of 324 ± 89). SEM, fluorescence spectroscopy, and confocal laser scanning microscopy (CLSM) revealed that the biogenic SeNS were enclosed in an organic material containing proteins and amphiphilic molecules, possibly responsible for the high thermodynamic stability of these nanomaterials. Finally, the biogenic SeNS extracts were photoluminescent upon excitation ranging from 380 to 530 nm, whose degree of fluorescence emission (λem = 416–640 nm) was comparable to that from chemically synthesized SeNPs with L-cysteine (L-cys SeNPs). This study offers novel insights into the formation, localization, and release of biogenic SeNS generated by two different Gram-negative bacterial strains under aerobic and metabolically controlled growth conditions. The work strengthens the possibility of using these bacterial isolates as eco-friendly biocatalysts to produce high quality SeNS targeted to possible biomedical applications and other biotechnological purposes

New Synthetic Nitro-Pyrrolomycins as Promising Antibacterial and Anticancer Agents

Pyrrolomycins (PMs) are polyhalogenated antibiotics known as powerful biologically active compounds, yet featuring high cytotoxicity. The present study reports the antibacterial and antitumoral properties of new chemically synthesized PMs, where the three positions of the pyrrolic nucleus were replaced by nitro groups, aiming to reduce their cytotoxicity while maintaining or even enhancing the biological activity. Indeed, the presence of the nitro substituent in diverse positions of the pyrrole determined an improvement of the minimal bactericidal concentration (MBC) against Gram-positive (i.e., Staphylococcus aureus) or -negative (i.e., Pseudomonas aeruginosa) pathogen strains as compared to the natural PM-C. Moreover, some new nitro-PMs were as active as or more than PM-C in inhibiting the proliferation of colon (HCT116) and breast (MCF 7) cancer cell lines and were less toxic towards normal epithelial (hTERT RPE-1) cells. Altogether, our findings contribute to increase the knowledge of the mode of action of these promising molecules and provide a basis for their rationale chemical or biological manipulation

The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion

The effects of oxyanions selenite (SeO32−) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized

Superior Antibacterial Activity of Integral Lemon Pectin Extracted via Hydrodynamic Cavitation

Pectin extracted via hydrodynamic cavitation in water only from waste lemon peel and further isolated via freeze drying displays significant antibacterial activity against Staphylococcus aureus, a Gram positive pathogen which easily contaminates food. The antibacterial effect of the new IntegroPectin is largely superior to that of commercial citrus pectin, opening the way to advanced applications of a new bioproduct now obtainable in large amounts and at low cost from citrus juice industry's waste