Catalytic Cooperation between a Copper Oxide Electrocatalyst and a Microbial Community for Microbial Electrosynthesis.

Electrocatalytic metals and microorganisms can be combined for CO2 conversion in microbial electrosynthesis (MES). However, a systematic investigation on the nature of interactions between metals and MES is still lacking. To investigate this nature, we integrated a copper electrocatalyst, converting CO2 to formate, with microorganisms, converting CO2 to acetate. A co-catalytic (i. e. metabolic) relationship was evident, as up to 140 mg L-1 of formate was produced solely by copper oxide, while formate was also evidently produced by copper and consumed by microorganisms producing acetate. Due to non-metabolic interactions, current density decreased by over 4 times, though acetate yield increased by 3.3 times. Despite the antimicrobial role of copper, biofilm formation was possible on a pure copper surface. Overall, we show for the first time that a CO2 -reducing copper electrocatalyst can be combined with MES under biological conditions, resulting in metabolic and non-metabolic interactions.

Orange and Passion Fruit Wastes Characterization, Substrate Hydrolysis and Cell Growth of Cupriavidus necator, as Proposal to Converting of Residues in High Value Added Product.

Brazil is the world's largest producer of orange and passion fruit, which are destined mainly for industrialization, generating grand volumes of wastes. The solid portion of these residues is a rich source of pectin - composed mainly of galacturonic acid and neutral sugars, which through the hydrolysis process can be used in biological conversion processes, as the production of polyhydroxyalkanoates (PHAs). This way, we characterized these wastes, followed by the extraction and hydrolysis of pectin for employ as a substrate for the cell growth of Cupriavidus necator. The results confirmed the large portion of pectin (almost 40 g.100g-1) and soluble sugars, present in these wastes. The hydrolyzed extract showed as a good source of carbon for the cell growth of C. necator with YX/S 0.56 and 0.44, µMax 0.27 and 0.21 for orange and passion fruit wastes respectively, similar to other carbon sources. This way, the extraction and hydrolysis of orange and passion fruit wastes for the cellular growth of C. necator, can be a good alternative to converting of residues in high value added product.

Siderophore-Mediated Iron Acquisition Enhances Resistance to Oxidative and Aromatic Compound Stress in Cupriavidus necator JMP134.

Many bacteria secrete siderophores to enhance iron uptake under iron-restricted conditions. In this study, we found that Cupriavidus necator JMP134, a well-known aromatic pollutant-degrading bacterium, produces an unknown carboxylate-type siderophore named cupriabactin to overcome iron limitation. Using genome mining, targeted mutagenesis, and biochemical analysis, we discovered an operon containing six open reading frames (cubA-F) in the C. necator JMP134 genome that encodes proteins required for the biosynthesis and uptake of cupriabactin. As the dominant siderophore of C. necator JMP134, cupriabactin promotes the growth of C. necator JMP134 under iron-limited conditions via enhanced ferric iron uptake. Furthermore, we demonstrated that the iron concentration-dependent expression of the cub operon is mediated by the ferric uptake regulator (Fur). Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and resistance to oxidative and aromatic compound stress in C. necator JMP134. In conclusion, we identified a carboxylate-type siderophore named cupriabactin, which plays important roles in iron scavenging, bacterial motility, biofilm formation, and stress resistance.IMPORTANCE Since siderophores have been widely exploited for agricultural, environmental, and medical applications, the identification and characterization of new siderophores from different habitats and organisms will have great beneficial applications. Here, we identified a novel siderophore-producing gene cluster in C. necator JMP134. This gene cluster produces a previously unknown carboxylate siderophore, cupriabactin. Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and oxidative stress resistance. Most notably, this system also plays important roles in increasing the resistance of C. necator JMP134 to stress caused by aromatic compounds, which provide a promising strategy to engineer more efficient approaches to degrade aromatic pollutants.

Unraveling the predator-prey relationship of Cupriavidus necator and Bacillus subtilis.

Cupriavidus necator is a non-obligate bacterial predator of Gram-negative and Gram-positive bacteria. In this study, we set out to determine the conditions, which are necessary to observe predatory behavior of C. necator. Using Bacillus subtilis as a prey organism, we confirmed that the predatory performance of C. necator is correlated with the available copper level, and that the killing is mediated, at least in part, by secreted extracellular factors. The predatory activity depends on the nutrition status of C. necator, but does not require a quorum of predator cells. This suggests that C. necator is no group predator. Further analyses revealed that sporulation enables B. subtilis to avoid predation by C. necator. In contrast to the interaction with predatory myxobacteria, however, an intact spore coat is not required for resistance. Instead resistance is possibly mediated by quiescence.

Metabolic engineering of Cupriavidus necator for heterotrophic and autotrophic alka(e)ne production.

Alkanes of defined carbon chain lengths can serve as alternatives to petroleum-based fuels. Recently, microbial pathways of alkane biosynthesis have been identified and enabled the production of alkanes in non-native producing microorganisms using metabolic engineering strategies. The chemoautotrophic bacterium Cupriavidus necator has great potential for producing chemicals from CO2: it is known to have one of the highest growth rate among natural autotrophic bacteria and under nutrient imbalance it directs most of its carbon flux to the synthesis of the acetyl-CoA derived polymer, polyhydroxybutyrate (PHB), (up to 80% of intracellular content). Alkane synthesis pathway from Synechococcus elongatus (2 genes coding an acyl-ACP reductase and an aldehyde deformylating oxygenase) was heterologously expressed in a C. necator mutant strain deficient in the PHB synthesis pathway. Under heterotrophic condition on fructose we showed that under nitrogen limitation, in presence of an organic phase (decane), the strain produced up to 670mg/L total hydrocarbons containing 435mg/l of alkanes consisting of 286mg/l of pentadecane, 131mg/l of heptadecene, 18mg/l of heptadecane, and 236mg/l of hexadecanal. We report here the highest level of alka(e)nes production by an engineered C. necator to date. We also demonstrated the first reported alka(e)nes production by a non-native alkane producer from CO2 as the sole carbon source.

Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha.

Autotrophic fixation of carbon dioxide into cellular carbon occurs via several pathways but quantitatively, the Calvin-Benson-Bassham cycle is the most important. CbbR regulates the expression of the cbb genes involved in CO2 fixation via the Calvin-Benson-Bassham cycle in a number of autotrophic bacteria. A gene potentially encoding CbbR (cbbR(AF)) has been predicted in the genome of the chemolithoautotrophic, extreme acidophile Acidithiobacillus ferrooxidans. However, this microorganism is recalcitrant to genetic manipulation impeding the experimental validation of bioinformatic predictions. Two novel functional assays were devised to advance our understanding of cbbR(AF) function using the mutated facultative autotroph Ralstonia eutropha H14 ΔcbbR as a surrogate host to test gene function: (i) cbbR(AF) was expressed in R. eutropha and was able to complement ΔcbbR; and (ii) CbbR(AF) was able to regulate the in vivo activity of four A. ferrooxidans cbb operon promoters in R. eutropha. These results open up the use of R. eutropha as a surrogate host to explore cbbR(AF) activity.

Green synthesis and structural characterization of selenium nanoparticles and assessment of their antimicrobial property.

In the present study, selenium nanoparticles were biologically synthesized by non-pathogenic, economic and easy to handle bacterium Ralstonia eutropha. The selenium oxo anion was reduced to selenium nanoparticles in the presence of the bacterium. The bacterium was grown aerobically in the reaction mixture. An extracellular, stable, uniform, spherical selenium nanoparticle was biosynthesized. The TEM analysis revealed that the biosynthesized selenium nanoparticles were spherical in shape with size range of 40-120 nm. XRD and SAED analysis showed that nanocrystalline selenium of pure hexagonal phase was synthesized. The formation of actinomorphic trigonal selenium nanorods was also observed. A mechanism of biosynthesis of selenium nanoparticles by R. eutropha was proposed. The biosynthesized selenium nanoparticles were investigated for their antimicrobial activity against potential pathogens. Selenium nanoparticles showed excellent antimicrobial activity. The 100, 100, 250 and 100 µg/ml selenium nanoparticles were found to inhibit 99 % growth of Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and Streptococcus pyogenes, respectively. Similarly, the 500 µg/ml of selenium nanoparticles was found to inhibit the growth of pathogenic fungi Aspergillus clavatus. The antimicrobial efficacy of selenium nanoparticle was comparable with commercially available antibiotic drug Ampicillin.

Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system.

Photovoltaic cells have considerable potential to satisfy future renewable-energy needs, but efficient and scalable methods of storing the intermittent electricity they produce are required for the large-scale implementation of solar energy. Current solar-to-fuels storage cycles based on water splitting produce hydrogen and oxygen, which are attractive fuels in principle but confront practical limitations from the current energy infrastructure that is based on liquid fuels. In this work, we report the development of a scalable, integrated bioelectrochemical system in which the bacterium Ralstonia eutropha is used to efficiently convert CO2, along with H2 and O2 produced from water splitting, into biomass and fusel alcohols. Water-splitting catalysis was performed using catalysts that are made of earth-abundant metals and enable low overpotential water splitting. In this integrated setup, equivalent solar-to-biomass yields of up to 3.2% of the thermodynamic maximum exceed that of most terrestrial plants. Moreover, engineering of R. eutropha enabled production of the fusel alcohol isopropanol at up to 216 mg/L, the highest bioelectrochemical fuel yield yet reported by >300%. This work demonstrates that catalysts of biotic and abiotic origin can be interfaced to achieve challenging chemical energy-to-fuels transformations.

Coping with anoxia: a comprehensive proteomic and transcriptomic survey of denitrification.

Ralstonia eutropha H16 is a denitrifying microorganism able to use nitrate and nitrite as terminal electron acceptors under oxygen deprivation. To identify proteins showing an altered expression pattern in response to oxygen supply, R. eutropha cells grown aerobically and anaerobically were compared in a comprehensive proteome and transcriptome approach. Nearly 700 proteins involved in several processes including respiration, formation of cell appendages, and DNA and cofactor biosynthesis were found to be differentially expressed. A combination of 1D gel-LC and conventional 2D gel analysis of six consecutive sample points covering the entire denitrification sequence revealed a detailed view on the shifting abundance of the key proteins of denitrification. Denitrification- or anaerobiosis-induced alterations of the respiratory chain included a distinct expression pattern for multiple terminal oxidases. Alterations in the central carbon metabolism were restricted to a few key functions including the isoenzymes for aconitase and isocitrate dehydrogenase. Although R. eutropha is a strictly respiratory bacterium, the abundance of certain fermentation enzymes was increased. This work represents a comprehensive survey of denitrification on the proteomic and transcriptomic levels and provides unique insight into how R. eutropha adapts its metabolism to low oxygen conditions.

Leguminous plants nodulated by selected strains of Cupriavidus necator grow in heavy metal contaminated soils amended with calcium silicate.

Increasing concern regarding mining area environmental contamination with heavy metals has resulted in an emphasis of current research on phytoremediation. The aim of the present study was to assess the efficiency of symbiotic Cupriavidus necator strains on different leguminous plants in soil contaminated with heavy metals following the application of inorganic materials. The application of limestone and calcium silicate induced a significant increase in soil pH, with reductions in zinc and cadmium availability of 99 and 94 %, respectively. In addition, improved nodulation of Mimosa caesalpiniaefolia, Leucaena leucocephala and Mimosa pudica in soil with different levels of contamination was observed. Significant increases in the nitrogen content of the aerial parts of the plant were observed upon nodulation of the root system of Leucaena leucocephala and Mimosa pudica by strain UFLA01-659 (36 and 40 g kg(-1)) and by strain UFLA02-71 in Mimosa caesalpiniaefolia (39 g kg(-1)). The alleviating effect of calcium silicate resulted in higher production of dry matter from the aerial part of the plant, an increase in nodule number and an increase in the nitrogen fixation rate. The results of the present study demonstrate that the combination of rhizobia, leguminous plants and calcium silicate may represent a key factor in the remediation of areas contaminated by heavy metals.

Influence of pH on the molecular weight of poly-3-hydroxybutyric acid (P3HB) produced by recombinant Escherichia coli.

The production of ultrahigh molecular weight poly-3-hydroxybutyric acid (P3HB) from carbohydrates by recombinant Escherichia coli harboring genes from Ralstonia eutropha was evaluated. In shaken-flask experiments, E. coli XL1 Blue harboring plasmid pSK::phaCAB produced P3HB corresponding to 40 and 27% of cell dry weight from glucose and xylose, respectively. Cultures in bioreactor using glucose as the sole carbon source at variable pH values (6.0, 6.5, or 7.0) allowed the production of P3HB with molecular weight varying between 2.0 and 2.5 MDa. These figures are significantly higher than the values often obtained by natural bacterial strains (0.5-1.0 MDa). Contrary to reports of other authors, no influence of pH was observed on the molecular weight of the polymer produced. Using xylose, P3HB with high molecular weight was also produced, indicating the possibility to produce these polymers from lignocellulosic materials.

Cupriavidus necator isolates are able to fix nitrogen in symbiosis with different legume species.

The aim of the present study was to identify a collection of 35 Cupriavidus isolates at the species level and to examine their capacity to nodulate and fix N(2). These isolates were previously obtained from the root nodules of two promiscuous trap species, Phaseolus vulgaris and Leucaena leucocephala, inoculated with soil samples collected near Sesbania virgata plants growing in Minas Gerais (Brazil) pastures. Phenotypic and genotypic methods applied for this study were SDS-PAGE of whole-cell proteins, and 16S rRNA and gyrB gene sequencing. To confirm the ability to nodulate and fix N(2), the presence of the nodC and nifH genes was also determined, and an experiment was carried out with two representative isolates in order to authenticate them as legume nodule symbionts. All 35 isolates belonged to the betaproteobacterium Cupriavidus necator, they possessed the nodC and nifH genes, and two representative isolates were able to nodulate five different promiscuous legume species: Mimosa caesalpiniaefolia, L. leucocephala, Macroptilium atropurpureum, P. vulgaris and Vigna unguiculata. This is the first study to demonstrate that C. necator can nodulate legume species.

Analyses of soluble and membrane proteomes of Ralstonia eutropha H16 reveal major changes in the protein complement in adaptation to lithoautotrophy.

The soil-dwelling lithoautotrophic bacterium Ralstonia eutropha H16 utilizes hydrogen as the key source of energy during aerobic growth on hydrogen and carbon dioxide. We examined the soluble and membrane protein complements of lithoautotrophically grown cells and compared them to the protein complements of cells grown organoheterotrophically on succinate. (14)N/(15)N-based inverse metabolic labeling in combination with GeLC-MS led to the identification of 1452 proteins, 1174 of which could be quantitated. Far more proteins were found to be more abundant in the lithoautotrophically than in the organoheterotrophically grown cells. In addition to the induction of the key enzymes of hydrogen oxidation and carbon dioxide fixation, we observed several characteristic alterations in the proteome correlated with lithoautotrophic growth. (I) Genes for three terminal oxidases were upregulated. (II) NAD(P) transhydrogenase and enzymes for the accumulation of poly(3-hydroxybutyrate) (PHB) showed increased protein abundance. (III) Lithoautotrophically grown cells were equipped with an enhanced inventory of transport systems. (IV) The expression of cell surface appendages involved in cell movement was markedly increased, while proteins involved in cell adhesion were decreased. Our data show that the hydrogen-based lifestyle of R. eutropha H16 relies on an extensive protein repertoire adapting the organism to the alternative energy and carbon sources.

Use of controlled exogenous stress for improvement of poly(3-hydroxybutyrate) production in Cupriavidus necator.

The PHB production by Cupriavidus necator H16 depends on the type and concentration of stress factors and on the time of stress application. Hydrogen peroxide and ethanol significantly enhanced PHB accumulation in C. necator cells. Improved yields (10.9 g/L PHB) were observed after exposure of bacterial culture to 0.5 mmol/L H2O2 at the beginning of cultivation and to additional peroxide stress (5 mmol/L H2O2) after 60 h of cultivation (beginning of the stationary phase). Production was then approximately 28 % higher than in control (8.50 g/L PHB). The highest yields (11.2 g/L PHB) were observed when ethanol (0.5 %) was applied at the beginning of stationary phase. An application of exogenous stress could thus be used as a simple strategy for a significant improvement of PHB production in C. necator.

Involvement of several transcriptional regulators in the differential expression of tfd genes in Cupriavidus necator JMP134.

Cupriavidus necator JMP134 has been extensively studied because of its ability to degrade chloroaromatic compounds, including the herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoic acid (3-CB), which is achieved through the pJP4-encoded chlorocatechol degradation gene clusters: tfdCIDIEIFI and tfdDIICIIEIIFII. The present work describes a different tfd-genes expression profile depending on whether C. necator cells were induced with 2,4-D or 3-CB. By contrast, in vitro binding assays of the purified transcriptional activator TfdR showed similar binding to both tfd intergenic regions; these results were confirmed by in vivo studies of the expression of transcriptional lacZ fusions for these intergenic regions. Experiments aimed at investigating whether other pJP4 plasmid or chromosomal regulatory proteins could contribute to the differences in the response of both tfd promoters to induction by 2,4-D and 3-CB showed that the transcriptional regulators from the benzoate degradation pathway, CatR1 and CatR2, affected 3-CB- and 2,4-D-related growth capabilities. It was also determined that the ISJP4-interrupted protein TfdT decreased growth on 3-CB. In addition, an ORF with 34% amino acid identity to IclR-type transcriptional regulator members and located near the tfdII gene cluster module was shown to modulate the 2,4-D growth capability. Taken together, these results suggest that tfd transcriptional regulation in C. necator JMP134 is far more complex than previously thought and that it involves proteins from different transcriptional regulator families.

Essential role of the hprK gene in Ralstonia eutropha H16.

Ralstonia eutropha H16 possesses an incomplete phosphoenolpyruvate (PEP):sugar phosphotransferase system (PTS) composed of EI, HPr, EIIA(Ntr) (PtsN) and EIIA(Man) (PtsM). We could show that in vitro the incomplete PTS phosphorylation cascade is partially functional. HPr becomes phosphorylated by PEP and EI, and transfers the phosphoryl group to EIIA(Ntr), but only extremely slowly to EIIA(Man). Components of this system have previously been shown to regulate the metabolism of polyhydroxybutyrate. Downstream from ptsN this organism contains an hprK gene, which codes for a homologue of HPr kinase/phosphorylase. We show that this enzyme phosphorylates HPr using ATP as phosphoryl donor. Interestingly, hprK appeared to be essential in R. eutropha because this gene could not be deleted in the wild-type strain, but could be deleted in mutants lacking ptsH or ptsI. This suggests that an increase in the HPr and/or P approximate His-HPr concentrations might be responsible for the growth defect. To test this hypothesis, various ptsH alleles were introduced into the ptsH hprK double mutant. Complementation of this mutant was possible only with the ptsH(His15Ala) allele, but not with the wild-type or ptsH(Ser46Ala) alleles. We conclude that elevated amounts of His-15-phosphorylated HPr, formed in the hprK mutant, are responsible for its growth defect.

On-line characterization of physiological state in poly(beta-hydroxybutyrate) production by Wautersia eutropha.

Culture fluorescence measurement technique has the potential for on-line characterization of metabolic status of fermentation processes. Many fluorophores present inside the living cells such as NADH + H+, tryptophan, pyridoxine, and riboflavin fluoresce at specific excitation and emission wavelength combinations. Since these key intracellular metabolites are involved in cell growth and metabolism, their concentration change at any time inside the cell could reflect the changes in cell metabolic activity. NADH + H+ spectrofluorometry was used for on-line characterization of physiological state during batch cultivation of poly-beta-hydroxybutyric acid (PHB) production by Wautersia eutropha. The culture fluorescence increased with an increase in the biomass concentration with time. A linear correlation between cell mass concentration and net NADH + H+ fluorescence was established during active growth phase (13 to 38 h) of batch cultivation. The rate of change of culture fluorescence (dF/dt) exhibited a gradual increase during the predominantly growth phase of batch cultivation (till 20 h). Thereafter, a sudden drop in the dF/dt rate and its leveling was recorded indicating major changes in culture metabolism status which synchronized with the start-up of accumulation of PHB. After 48 h, yet another decrease in the rate of change of fluorescence (dF/dt) was observed primarily due to severe substrate limitation in the reactor. On-line NADH + H+ fluorescence signal and its rate (dF/dt) could therefore be used to distinguish the growth, product formation, and nutrient depletion stage (the metabolic state marker) during the batch cultivation of W. eutropha.

Quantifying the surface characteristics and flocculability of Ralstonia eutropha.

The microbial surface and flocculability were qualitatively characterized through the combination of the surface thermodynamic and the extended DLVO approaches, with Ralstonia eutropha, a polyhydroxybutyrate-producing bacterium, as an example. The negativity of the zeta potential of R. eutropha decreased from the initial -19.5 to -11 mV in its cultivation with the consumption of glucose. The total interfacial free energy (DeltaGadh) was changed from -80 to 28.5 mJ m(-2) in its entire growth process. This suggests that the bacterial surface changed from hydrophobic into hydrophilic, resulting in an alteration of its surface characteristics and flocculability in its different growth phases. As a result, the stability ratio of suspensions increased with the increasing cultivation time, indicating that the cell particles became more repulsive with each other and led to a more stable suspension of R. eutropha in its cultivation. The obtained information in this work might be useful for better understanding the surface characteristics and the flocculability and even manipulating its flocculability in the microbial growth process.

Formation of a dinitrosyl iron complex by NorA, a nitric oxide-binding di-iron protein from Ralstonia eutropha H16.

In Ralstonia eutropha H16, two genes, norA and norB, form a dicistronic operon that is controlled by the NO-responsive transcriptional regulator NorR. NorB has been identified as a membrane-bound NO reductase, but the physiological function of NorA is unknown. We found that, in a NorA deletion mutant, the promoter activity of the norAB operon was increased 3-fold, indicating that NorA attenuates activation of NorR. NorA shows limited sequence similarity to the oxygen carrier hemerythrin, which contains a di-iron center. Indeed, optical and EPR spectroscopy of purified NorA revealed the presence of a di-iron center, which binds oxygen in a similar way as hemerythrin. Diferrous NorA binds two molecules of NO maximally. Unexpectedly, binding of NO to the diferrous NorA required an external reductant. Two different NorA-NO species could be resolved. A minor species (up to 20%) showed an S = (1/2) EPR signal with g( perpendicular) = 2.041, and g( parallel) = 2.018, typical of a paramagnetic dinitrosyl iron complex. The major species was EPR-silent, showing characteristic signals at 420 nm and 750 nm in the optical spectrum. This species is proposed to represent a novel dinitrosyl iron complex of the form Fe(2+)-[NO](2)(2-), i.e. NO is bound as NO(-). The NO binding capacity of NorA in conjunction with its high cytoplasmic concentration (20 mum) suggests that NorA regulates transcription by lowering the free cytoplasmic concentration of NO.

Characterization of the signaling domain of the NO-responsive regulator NorR from Ralstonia eutropha H16 by site-directed mutagenesis.

In Ralstonia eutropha H16, the nitric oxide (NO)-responsive transcriptional activator NorR controls the expression of a dicistronic operon that encodes a membrane-bound NO reductase, NorB, and a protein of unknown function, NorA. The N-terminal domain (NTD) of NorR is responsible for perception of the signal molecule, nitric oxide. Thirteen out of 29 conserved residues of the NTD were exchanged by site-directed mutagenesis. Replacement of R63, R72, D93, D96, C112, D130, or F137 strongly decreased NorR-dependent promoter activation, while the exchange of Y95 or H110 led to an increase in promoter activity compared to that of the wild type. A purified truncated NorR comprising only the NTD (NorR-NTD) contained one iron atom per molecule and was able to bind NO in the as-isolated state. Based on the iron content of NorR-NTD proteins with single amino acid replacements, residues R72, D93, D96, C112, and D130 are likely candidates for iron ligands. Residues R63, Y95, and H110 appear not to be involved in NO binding but may take part in subsequent steps of the signal transduction mechanism of NorR.