Alessandro Presentato

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes

Rhodococcus sp. strain BCP1 was initially isolated for its ability to grow on gaseous n-alkanes, which act as inducers for the co-metabolic degradation of low-chlorinated compounds. Here, both molecular and metabolic features of BCP1 cells grown on gaseous and short-chain n-alkanes (up to n-heptane) were examined in detail. We show that propane metabolism generated terminal and sub-terminal oxidation products such as 1- and 2-propanol, whereas 1-butanol was the only terminal oxidation product detected from n-butane metabolism. Two gene clusters, prmABCD and smoABCD—coding for Soluble Di-Iron Monooxgenases (SDIMOs) involved in gaseous n-alkanes oxidation—were detected in the BCP1 genome. By means of Reverse Transcriptase-quantitative PCR (RT-qPCR) analysis, a set of substrates inducing the expression of the sdimo genes in BCP1 were assessed as well as their transcriptional repression in the presence of sugars, organic acids, or during the cell growth on rich medium (Luria–Bertani broth). The transcriptional start sites of both the sdimo gene clusters were identified by means of primer extension experiments. Finally, proteomic studies revealed changes in the protein pattern induced by growth on gaseous- (n-butane) and/or liquid (n-hexane) short-chain n-alkanes as compared to growth on succinate. Among the differently expressed protein spots, two chaperonins and an isocytrate lyase were identified along with oxidoreductases involved in oxidation reactions downstream of the initial monooxygenase reaction step.

Antimicrobial activity of biogenically produced spherical Se-nanomaterials embedded in organic material against Pseudomonas aeruginosa and Staphylococcus aureus strains on hydroxyapatite-coated surfaces.

In an effort to prevent the formation of pathogenic biofilms on hydroxyapatite (HA)‐based clinical devices and surfaces, we present a study evaluating the antimicrobial efficacy of Spherical biogenic Se‐Nanostructures Embedded in Organic material (Bio Se‐NEMO‐S) produced by Bacillus mycoides SelTE01 in comparison with two different chemical selenium nanoparticle (SeNP) classes. These nanomaterials have been studied as potential antimicrobials for eradication of established HA‐grown biofilms, for preventing biofilm formation on HA‐coated surfaces and for inhibition of planktonic cell growth of Pseudomonas aeruginosa NCTC 12934 and Staphylococcus aureus ATCC 25923. Bio Se‐NEMO resulted more efficacious than those chemically produced in all tested scenarios. Bio Se‐NEMO produced by B. mycoides SelTE01 after 6 or 24 h of Na2SeO3 exposure show the same effective antibiofilm activity towards both P. aeruginosa and S. aureus strains at 0.078 mg ml−1 (Bio Se‐NEMO6) and 0.3125 mg ml−1 (Bio Se‐NEMO24). Meanwhile, chemically synthesized SeNPs at the highest tested concentration (2.5 mg ml−1) have moderate antimicrobial activity. The confocal laser scanning micrographs demonstrate that the majority of the P. aeruginosa and S. aureus cells exposed to biogenic SeNPs within the biofilm are killed or eradicated. Bio Se‐NEMO therefore displayed good antimicrobial activity towards HA‐grown biofilms and planktonic cells, becoming possible candidates as new antimicrobials.

Biosynthesis of selenium-nanoparticles and -nanorods as a product of selenite bioconversion by the aerobic bacterium Rhodococcus aetherivorans BCP1

The wide anthropogenic use of selenium compounds represents the major source of selenium pollution worldwide, causing environmental issues and health concerns. Microbe-based strategies for metal removal/recovery have received increasing interest thanks to the association of the microbial ability to detoxify toxic metal/metalloid polluted environments with the production of nanomaterials. This study investigates the tolerance and the bioconversion of selenite (SeO32-) by the aerobically grown Actinomycete Rhodococcus aetherivorans BCP1 in association with its ability to produce selenium nanoparticles and nanorods (SeNPs and SeNRs). The BCP1 strain showed high tolerance towards SeO32- with a Minimal Inhibitory Concentration (MIC) of 500mM. The bioconversion of SeO32- was evaluated considering two different physiological states of the BCP1 strain, i.e. unconditioned and/or conditioned cells, which correspond to cells exposed for the first time or after re-inoculation in fresh medium to either 0.5 or 2mM of Na2SeO3, respectively. SeO32- bioconversion was higher for conditioned grown cells compared to the unconditioned ones. Selenium nanostructures appeared polydisperse and not aggregated, as detected by electron microscopy, being embedded in an organic coating likely responsible for their stability, as suggested by the physical-chemical characterization. The production of smaller and/or larger SeNPs was influenced by the initial concentration of provided precursor, which resulted in the growth of longer and/or shorter SeNRs, respectively. The strong ability to tolerate high SeO32- concentrations coupled with SeNP and SeNR biosynthesis highlights promising new applications of Rhodococcus aetherivorans BCP1 as cell factory to produce stable Se-nanostructures, whose suitability might be exploited for biotechnology purposes.

Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds

ABSTRACT Rhodococcus sp. strain BCP1 cometabolizes chlorinated compounds and mineralizes a broad range of alkanes, as it is highly tolerant to them. The high-quality draft genome sequence of Rhodococcus sp. strain BCP1, consisting of 6,231,823 bp, with a G+C content of 70.4%, 5,902 protein-coding genes, and 58 RNA genes, is presented here.

Assembly, growth and conductive properties of tellurium nanorods produced by Rhodococcus aetherivorans BCP1

Tellurite (TeO32−) is a hazardous and toxic oxyanion for living organisms. However, several microorganisms can bioconvert TeO32− into the less toxic form of elemental tellurium (Te0). Here, Rhodococcus aetherivorans BCP1 resting (non-growing) cells showed the proficiency to produce tellurium-based nanoparticles (NPs) and nanorods (NRs) through the bioconversion of TeO32−, depending on the oxyanion initial concentration and time of cellular incubation. Te-nanostructures initially appeared in the cytoplasm of BCP1 cells as spherical NPs, which, as the exposure time increased, were converted into NRs. This observation suggested the existence of an intracellular mechanism of TeNRs assembly and growth that resembled the chemical surfactant-assisted process for NRs synthesis. The TeNRs produced by the BCP1 strain showed an average length (>700 nm) almost doubled compared to those observed in other studies. Further, the biogenic TeNRs displayed a regular single-crystalline structure typically obtained for those chemically synthesized. The chemical-physical characterization of the biogenic TeNRs reflected their thermodynamic stability that is likely derived from amphiphilic biomolecules present in the organic layer surrounding the NRs. Finally, the biogenic TeNRs extract showed good electrical conductivity. Thus, these findings support the suitability of this strain as eco-friendly biocatalyst to produce high quality tellurium-based nanomaterials exploitable for technological purposes.

Selenium and tellurium nanomaterials

Abstract Over the last 40 years, the rapid and exponential growth of nanotechnology led to the development of various synthesis methodologies to generate nanomaterials different in size, shape and composition to be applied in various fields. In particular, nanostructures composed of Selenium (Se) or Tellurium (Te) have attracted increasing interest, due to their intermediate nature between metallic and non-metallic elements, being defined as metalloids. Indeed, this key shared feature of Se and Te allows us the use of their compounds in a variety of applications fields, such as for manufacturing photocells, photographic exposure meters, piezoelectric devices, and thermoelectric materials, to name a few. Considering also that the chemical-physical properties of elements result to be much more emphasized when they are assembled at the nanoscale range, huge efforts have been made to develop highly effective synthesis methods to generate Se- or Te-nanomaterials. In this context, the present book chapter will explore the most used chemical and/or physical methods exploited to generate different morphologies of metalloid-nanostructures, focusing also the attention on the major advantages, drawbacks as well as the safety related to these synthetic procedures. Graphical Abstract: Overview of the chemical and physical methods commonly used to produce various Se- and/or Te-based nanomaterials.

Stability of biogenic metal(loid) nanomaterials related to the colloidal stabilization theory of chemical nanostructures

Abstract In the last 15 years, the exploitation of biological systems (i.e. plants, bacteria, mycelial fungi, yeasts, and algae) to produce metal(loid) (Me)-based nanomaterials has been evaluated as eco-friendly and a cost-effective alternative to the chemical synthesis processes. Although the biological mechanisms of biogenic Me-nanomaterial (Bio-Me-nanomaterials) production are not yet completely elucidated, a key advantage of such bio-nanostructures over those chemically synthesized is related to their natural thermodynamic stability, with several studies ascribed to the presence of an organic layer surrounding these Bio-Me-nanostructures. Different macromolecules (e.g. proteins, peptides, lipids, DNA, and polysaccharides) or secondary metabolites (e.g. flavonoids, terpenoids, glycosides, organic acids, and alkaloids) naturally produced by organisms have been indicated as main contributors to the stabilization of Bio-Me-nanostructures. Nevertheless, the chemical–physical mechanisms behind the ability of these molecules in providing stability to Bio-Me-nanomaterials are unknown. In this context, transposing the stabilization theory of chemically synthesized Me-nanomaterials (Ch-Me-nanomaterials) to biogenic materials can be used towards a better comprehension of macromolecules and secondary metabolites role as stabilizing agents of Bio-Me-nanomaterials. According to this theory, nanomaterials are generally featured by high thermodynamic instability in suspension, due to their high surface area and surface energy. This feature leads to the necessity to stabilize chemical nanostructures, even during or directly after their synthesis, through the development of (i) electrostatic, (ii) steric, or (iii) electrosteric interactions occurring between molecules and nanomaterials in suspension. Based on these three mechanisms, this review is focused on parallels between the stabilization of biogenic or chemical nanomaterials, suggesting which chemical–physical mechanisms may be involved in the natural stability of Bio-Me-nanomaterials. As a result, macromolecules such as DNA, polyphosphates and proteins may electrostatically interact with Bio-Me-nanomaterials in suspension through their charged moieties, showing the same properties of counterions in Ch-Me-nanostructure suspensions. Since several biomolecules (e.g. neutral lipids, nonionic biosurfactants, polysaccharides, and secondary metabolites) produced by metal(loid)-grown organisms can develop similar steric hindrance as compared to nonionic amphiphilic surfactants and block co-polymers generally used to sterically stabilize Ch-Me-nanomaterials. These biomolecules, most likely, are involved in the development of steric stabilization, because of their bulky structures. Finally, charged lipids and polysaccharides, ionic biosurfactants or proteins with amphiphilic properties can exert a dual effect (i.e. electrostatic and steric repulsion interactions) in the contest of Bio-Me-nanomaterials, leading to the high degree of stability observed.