What Are the Multi-Omics Mechanisms for Adaptation by Microorganisms to High Alkalinity? A Transcriptomic and Proteomic Study of a Bacillus Strain with Industrial Potential.

Alkaliphilic organisms are among an industrially important class of extremophile microorganisms with the ability to thrive at pH 10-11.5. Microorganisms that exhibit alkaliphilic characteristics are sources of alkali-tolerant enzymes such as proteases, starch degrading enzymes, cellulases, and metabolites such as antibiotics, enzyme inhibitors, siderophores, organic acids, and cholic acid derivatives, which have found various applications in industry for human and environmental health. Yet, multi-omics mechanisms governing adaptation to high alkalinity have been poorly studied. We undertook the present work to understand, as a case study, the alkaliphilic adaptation strategy of the novel microorganism, Bacillus marmarensis DSM 21297, to alkaline conditions using a multi-omics approach that employed transcriptomics and proteomics. As alkalinity increased, bacteria remodeled the peptidoglycan layer by changing peptide moieties along with the peptidoglycan constituents and altered the cell membrane to reduce lipid motility and proton leakiness to adjust intracellular pH. Different transporters also contributed to the maintenance of this pH homeostasis. However, unlike in most well-known alkaliphiles, not only sodium ions but also potassium ions were involved in this process. Interestingly, increased pH has triggered the expression of neither general stress proteins nor gene encoding proteins associated with heat, salt, and nutrient stresses. Only an increase in the expression of oxidative stress related genes was evident. Endospore formation, also a phenomenon closely linked to stress, was unclear. This questioned if high pH was a real stress for B. marmarensis. These new findings, corroborated using the multi-omics approach of the present case study, broaden the knowledge on the mechanisms of alkaliphilic adaptation and might also potentially offer useful departure points for further industrial applications with other microorganisms.

Assessment of hazelnut husk as a lignocellulosic feedstock for the production of fermentable sugars and lignocellulolytic enzymes.

The present work focuses firstly on the evaluation of the effect of laccase on enzymatic hydrolysis of hazelnut husk which is one of the most abundant lignocellulosic agricultural residues generated in Turkey. In this respect, the co-enzymatic treatment of hazelnut husk by cellulase and laccase, without a conventional pretreatment step is evaluated. Using 2.75 FPU/g substrate (40 g/L substrate) and a ratio of 131 laccase U/FPU achieved the highest reducing sugars concentration. Gas chromatography mass spectrometry confirmed that the hydrolysate was composed of glucose, xylose, mannose, arabinose and galactose. The inclusion of laccase in the enzyme mixture [carboxymethyl cellulase (CMCase) and ß-glucosidase] increased the final glucose content of the reducing sugars from 20 to 50%. Therefore, a very significant increase in glucose content of the final reducing sugars concentration was obtained by laccase addition. Furthermore, the production of cellulases and laccase by Pycnoporus sanguineus DSM 3024 using hazelnut husk as substrate was also investigated. Among the hazelnut husk concentrations tested (1.5, 6, 12, 18 g/L), the highest CMCase concentration was obtained using 12 g/L husk concentration on the 10th day of fermentation. Besides CMCase, P. sanguineus DSM 3024 produced ß-glucosidase and laccase using hazelnut husk as carbon source. In addition to CMCase and ß-glucosidase, the highest laccase activity measured was 2240 ± 98 U/L (8.89 ± 0.39 U/mg). To the best of our knowledge, this is the first study to report hazelnut husk hydrolysis in the absence of pretreatment procedures.

A sigmoidal model for biosorption of heavy metal cations from aqueous media.

A novel multi-input single output (MISO) black-box sigmoid model is developed to simulate the biosorption of heavy metal cations by the fission yeast from aqueous medium. Validation and verification of the model is done through statistical chi-squared hypothesis tests and the model is evaluated by uncertainty and sensitivity analyses. The simulated results are in agreement with the data of the studied system in which Schizosaccharomyces pombe biosorbs Ni(II) cations at various process conditions. Experimental data is obtained originally for this work using dead cells of an adapted variant of S. Pombe and represented by Freundlich isotherms. A process optimization scheme is proposed using the present model to build a novel application of a cost-merit objective function which would be useful to predict optimal operation conditions.

Schizosaccharomyces pombe and its Ni(II)-insensitive mutant GA1 in Ni(II) uptake from aqueous solutions: a biodynamic model.

In the present study, Ni(II) uptake from aqueous solution by living cells of the Schizosaccharomyces pombe haploid 972 with h (-) mating type and a Ni(II)-insensitive mutant GA1 derived from 972 was investigated at various initial glucose and Ni(II) concentrations. A biodynamic model was developed to predict the unsteady and steady-state phases of the uptake process. Gompertz growth and uptake process parameters were optimized to predict the maximum growth rate µ m and the process metric C r, the remaining Ni(II) content in the aqueous solution. The simulated overall metal uptake values were found to be in acceptable agreement with experimental results. The model validation was done through regression statistics and uncertainty and sensitivity analyses. To gain insight into the phenomenon of Ni(II) uptake by wild-type and mutant S. pombe, probable active and passive metal transport mechanisms in yeast cells were discussed in view of the simulation results. The present work revealed the potential of mutant GA1 to remove Ni(II) cations from aqueous media. The results obtained provided new insights for understanding the combined effect of biosorption and bioaccumulation processes for metal removal and offered a possibility for the use of growing mutant S. pombe cell in bioremediation.

The performance of BALISTIKA 2010 system for 9 mm × 19 mm and 7.65 mm × 17 mm cartridge case correlation.

The firearm identification has two examination phases; the first phase is "one by one" cartridge case or bullet identification. The second phase is "Open Case File (OCF)" examination. Due to the size of the OCF archive, the OCF examination with only comparison microscopes takes a long time and is an unfeasible process. The Computerized Ballistic Identification Systems (CBIS) has become an essential tool for archive examination by correlation and preliminary eliminations. In this study, two objectives were pursued; the first is measuring the performance of the BALISTIKA 2010 system on cartridge case acquisition of handguns, correlation and examination. The second objective is the examination of the performance on the correlation according to brand and models of firearms. Detailed experimental results are demonstrated for about 2000 cartridge cases.

Biosorption of Ni (II) by Schizosaccharomyces pombe: kinetic and thermodynamic studies.

The potential of the dried yeast, wild-type Schizosaccharomyces pombe, to remove Ni(II) ion was investigated in batch mode under varying experimental conditions including pH, temperature, initial metal ion concentration and biosorbent dose. Optimum pH for biosorption was determined as 5.0. The highest equilibrium uptake of Ni(II) on S. pombe, q (e), was obtained at 25 °C as 33.8 mg g(-1). It decreased with increasing temperature within a range of 25-50 °C denoting an exothermic behaviour. Increasing initial Ni(II) concentration up to 400 mg L(-1) also elevated equilibrium uptake. No more adsorption took place beyond 400 mg L(-1). Equilibrium data fitted better to Langmuir model rather than Freundlich model. Sips, Redlich-Peterson, and Kahn isotherm equations modelled the investigated system with a performance not better than Langmuir. Kinetic model evaluations showed that Ni(II) biosorption process followed the pseudo-second order rate model while rate constants decreased with increasing temperature. Gibbs free energy changes (ΔG°) of the system at 25, 30, 35 and 50 °C were found as -1.47E + 4, -1.49E + 4, -1.51E + 4, and -1.58E + 4 J mol(-1), respectively. Enthalpy change (ΔH°) was determined as -2.57E + 3 J mol(-1) which also supports the observed exothermic behaviour of the biosorption process. Entropy change (ΔS°) had a positive value (40.75 J mol(-1) K(-1)) indicating an increase in randomness during biosorption process. Consequently, S. pombe was found to be a potential low-cost agent for Ni(II) in slightly acidic aqueous medium. In parallel, it has been assumed to act as a separating agent for Ni(II) recovery from its aqueous solution.