Main Carbon Source Research Articles

Improvements of poly(3-hydroxybutyrate) production in an air-lift reactor using simple production media

BackgroundHalomonas boliviensis is a halophilic microorganism that accumulates poly(3-hydroxybutyrate) (PHB) using different carbons sources when nitrogen is depleted from the culture medium. This work presents an improved production of PHB using an air-lift reactor (ALR) that was fed with a concentrated solution of a carbon source, and was supplemented with an adequate airflow rate.ResultsSimple production media were used to study PHB production by H. boliviensis in an ALR. Glucose was first used as the main carbon source and was fed during the exponential phase of cell growth. The maximum CDW and PHB content were 31.7 g/L and 51 wt%, respectively, when the airflow rate entering the reactor varied between 0.5 and 1.2 L/min. Changing the air inflow to 0.5–0.9 L/min resulted in an improvement in PHB accumulation (62 wt%). A cultivation was performed by using the latter range of airflow rate and feeding glucose only when nitrogen was depleted from the medium; a considerable enhancement in PHB content (72 wt%) and CDW (27 g/L) was achieved under these conditions. Moreover, PHB was also produced using molasses as the main carbon source. Residual cell mass was about the same to that achieved with glucose, however the PHB content (52 wt%) was lower.ConclusionsPHB production by H. boliviensis in an ALR using a simple medium is possible. CDW and PHB content in H. boliviensis can be improved with respect to batch cultivations previously reported when a carbon source is fed to the reactor. The best strategy for the production of PHB consisted of starting the cultivation in a batch mode while glutamate was present in the medium; glucose should be fed when glutamate is depleted from the medium to keep an excess of the carbon source during the synthesis of PHB.

Isolation, screening and identification of potential cellulolytic and xylanolytic mold from oil palm waste

The objective of this research was to isolate, screen, and identify the cellulase and xylanase-producing mold from oil palm waste. There are thirty-two isolates from oil palm waste which are able to degrade and grow on media containing cellulose or xylan as a sole carbon source. Screening to determine cellulolytic and xylanolytic activity was performed by paper disc diffusion method using Congo Red as an indicator. All the thirty-two mold isolates showed cellulolytic and xylanolytic activity with relative enzyme activity (ratio of hydrolysed zone diameter and diameter of colony growth) ranging from 1.04 to 1.62. Based on the macro- and micromorphology characteristics, these isolates were identified as genus Trichoderma, Aspergillus, Rhizopus, Tallaromyces and Penicillium, with the number isolates in each genus was 22, 4, 3, 2, and 1 respectively. The highest cellulolytic and xylanolytic activity was achieved from the isolate namely OPT1(4) which was identified as Talaromyces pinophilus using morphological and molecular analysis. Under the optimum condition (30°C, 72 hours) in liquid medium containing carboxymethyl cellulose (CMC) and birch wood xylan as the main carbon source, Talaromyces pinophilus OPT1(4) presented glucanase and xylanase activity of 15.17 U/mL and 13.35 U/mL, respectively.

Production of Polyhydroxybutyrate (PHB) from Streptomyces Incanus and the Effect of Gamma Irradiation on its Production

Streptomyces incanus BK 128 isolated from the Rhizosphere of eggplant was employed for polyhydroxybutyrate (PHB) production from different agriculture waste wheat bran, rice bran, rice straw and from molasses as the main carbon sources. Some supplements such as (0.4 g) ammonium sulphate to optimize the PHB production medium. The maximum PHB production was achieved with wheat bran (1.9g/l). Different parameters including; initial pH of the medium, ammonium chloride concentration and inoculum size; were carried out under shaking flask conditions (150 rpm) at 30oC for 5 days of incubation to enhance the PHB production. The maximum PHB production (2.82gl-1) was achieved at pH 6.5, (2%) NH4CL and 5 ml inoculum size, respectively. The effect of gamma irradiation on the activity of Streptomyces incanus BK 128 towards PHB production showed that, at dose level 1.5 kGy the maximum PHB production obtained was 3.39 gl-1. Keywords: Biopolymer /PHB/ Streptomyces incanus / Wheat bran/ rice bran.

Fast-stimulating bioremediation of macro crude oil in soils using matching Fenton pre-oxidation

This study aims at exploring the mechanism of fast-stimulating bioremediation of macro crude oil using matching Fenton pre-oxidation. The 80-day biodegradation experiment for soil S1 and S2, containing macro crude oil: C19–C29 and C17–C29 respectively, was conducted after Fenton pre-oxidation with three concentrations of H2O2 (225 mM, 450 mM, and 900 mM). Experimental results indicated that the bioremediation efficiency of macro crude oil was up to 57.1% (8853 mg/kg, S1) and 64.4% (11,719 mg/kg, S2) for 80-day fast-stimulating bioremediation using matching Fenton pre-oxidation (450 mM H2O2), which was 1.8–2.6 times that (S1: 22.2–37.1%; S2: 36.1–39.6%) for slow-stimulating bioremediation using un-matching Fenton pre-oxidation. Furthermore, the high-throughput analysis revealed that genera Sedimentibacter, Caenispirillum, and Brevundimonas became the dominant bacteria after matching Fenton pre-oxidation. Meanwhile, the highest logarithmic growth rate of indigenous hydrocarbon degraders (IHD) was obtained (S1: 64% and S2: 60%) for fast-stimulating bioremediation. And the consumption of NH4+-N was up to 90% and 94% in S1 and S2 within 60 days for fast-stimulating bioremediation, approximately 1.4 and 2.2 times that (S1: 65% and 62%; S2: 47% and 41%) for slow-stimulating remediation. The results showed that the macro crude oil became the main carbon source for IHD for the fast-stimulating bioremediation, resulting in the rapid growth of IHD. Thus, this study provides a fast and efficient remediation technology for bioremediation of macro crude oil-contaminated soils.

Transcriptome analysis of metabolic pathways associated with oil accumulation in developing seed kernels of Styrax tonkinensis, a woody biodiesel species

BackgroundStyrax tonkinensis (Pierre) Craib ex Hartwich has great potential as a woody biodiesel species having seed kernels with high oil content, excellent fatty acid composition and good fuel properties. However, no transcriptome information is available on the molecular regulatory mechanism of oil accumulation in developing S. tonkinensis kernels.ResultsThe dynamic patterns of oil content and fatty acid composition at 11 time points from 50 to 150 days after flowering (DAF) were analyzed. The percent oil content showed an up-down-up pattern, with yield and degree of unsaturation peaking on or after 140 DAF. Four time points (50, 70, 100, and 130 DAF) were selected for Illumina transcriptome sequencing. Approximately 73 million high quality clean reads were generated, and then assembled into 168,207 unigenes with a mean length of 854 bp. There were 5916 genes that were differentially expressed between different time points. These differentially expressed genes were grouped into 9 clusters based on their expression patterns. Expression patterns of a subset of 12 unigenes were confirmed by qRT-PCR. Based on their functional annotation through the Basic Local Alignment Search Tool and publicly available protein databases, specific unigenes encoding key enzymes, transmembrane transporters, and transcription factors associated with oil accumulation were determined. Three main patterns of expression were evident. Most unigenes peaked at 70 DAF, coincident with a rapid increase in oil content during kernel development. Unigenes with high expression at 50 DAF were associated with plastid formation and earlier stages of oil synthesis, including pyruvate and acetyl-CoA formation. Unigenes associated with triacylglycerol biosynthesis and oil body development peaked at 100 or 130 DAF.ConclusionsTranscriptome changes during oil accumulation show a distinct temporal trend with few abrupt transitions. Expression profiles suggest that acetyl-CoA formation for oil biosynthesis is both directly from pyruvate and indirectly via acetaldehyde, and indicate that the main carbon source for fatty acid biosynthesis is triosephosphate originating from phosphohexose outside the plastid. Different sn-glycerol-3-phosphate acyltransferases are implicated in diacylglycerol biosynthesis at early versus late stages of oil accumulation. Triacylglycerol biosynthesis may be accomplished by both diacylglycerol and by phospholipid:diacylglycerol acyltransferases.

Mechanism of K-catalyzed transformation of solid carbon structure into carbon nanotubes in coal

In this paper, the changes in solid-phase carbon structure and the formation of carbon nanotubes in the process of K-catalyzed pyrolysis of bituminous coal were investigated. The results showed that the content of carbon nanotubes in K-catalyzed coal pyrolysis products increased with the extension of residence time. When the residence times were 0, 30 and 90 min, the yields of carbon nanotubes in the coal pyrolysis products were 1.98 wt%, 6.85 wt% and 10.16 wt%, respectively. It was found that the aromatic carbon CC, CH and ether carbon C-O-C structures in coal were the main carbon sources for the growth of carbon nanotubes. The probable growth mechanism of carbon nanotubes in the process of K-catalyzed coal pyrolysis was proposed to be as follows: aromatic CC and CH structures in coal convert K components such as K2CO3 and K2O into metal K, and then metal K converts carbon atoms in the ether bond C-O-C structure into carbon atoms or clusters, which generate carbon nanotubes under the action of Fe catalyst particles in coal. This method provides a new strategy for the simultaneous high-value utilization of coal resources and macroscopic, low-cost preparation of carbon nanotubes.

The importance of Calanus glacialis for the feeding success of young polar cod: a circumpolar synthesis

Understanding the feeding ecology of polar cod (Boreogadus saida) during its first year of life is crucial to forecasting its response to the ongoing borealization of Arctic seas. We investigated the relationships between diet composition and feeding success in 1797 polar cod larvae and juveniles 4.5–55.6 mm standard length (SL) collected in five Arctic seas from 1993 to 2009. Prey were identified to species and developmental stages when possible, measured, and their carbon content was estimated using taxon-specific allometric equations. Feeding success was defined as the ratio of ingested carbon to fish weight. Carbon uptake in polar cod larvae < 15 mm was sourced primarily from calanoid copepods eggs and nauplii which were positively selected from the plankton. With increasing length, carbon sources shifted from eggs and nauplii to the copepodites of Calanus glacialis, Calanus hyperboreus and Pseudocalanus spp. Calanus glacialis copepodites were the main carbon source in polar cod > 25 mm and the only copepodite positively selected for. Pseudocalanus spp. copepodites became important replacement prey when C. glacialis left the epipelagic layer at the end of summer. Calanus glacialis was the preferred prey of polar cod, contributing from 23 to 84% of carbon uptake at any stage in the early development. Feeding success was determined by the number of prey captured in larvae < 15 mm and by the size of prey in juveniles > 30 mm. As Arctic seas warm, the progressive displacement of C. glacialis by the smaller Calanus finmarchicus could accelerate the replacement of polar cod, the dominant Arctic forage fish, by boreal species.

Efficient bioproduction of 5-aminolevulinic acid, a promising biostimulant and nutrient, from renewable bioresources by engineered Corynebacterium glutamicum

Background5-Aminolevulinic acid (5-ALA) is a promising biostimulant, feed nutrient, and photodynamic drug with wide applications in modern agriculture and therapy. Considering the complexity and low yield of chemical synthesis methods, bioproduction of 5-ALA has drawn intensive attention recently. However, the present bioproduction processes use refined glucose as the main carbon source and the production level still needs further enhancement.ResultsTo lay a solid technological foundation for large-scale commercialized bioproduction of 5-ALA, an industrial workhorse Corynebacterium glutamicum was metabolically engineered for high-level 5-ALA biosynthesis from cheap renewable bioresources. After evaluation of 5-ALA synthetases from different sources, the 5-ALA biosynthetic pathway and anaplerotic pathway were rebalanced by regulating intracellular activities of 5-ALA synthetase and phosphoenolpyruvate carboxylase. The engineered biocatalyst produced 5.5 g/L 5-ALA in shake flasks and 16.3 g/L in 5-L bioreactors with a one-step fermentation process from glucose. To lower the cost of feedstock, cheap raw materials were used to replace glucose. Enzymatically hydrolyzed cassava bagasse was proven to be a perfect alternative to refined sugars since the final 5-ALA titer further increased to 18.5 g/L. Use of corn starch hydrolysate resulted in a similar 5-ALA production level (16.0 g/L) with glucose, whereas use of beet molasses caused seriously inhibition. The results obtained here represent a new record of 5-ALA bioproduction. It is estimated that replacing glucose with cassava bagasse will reduce the carbon source cost by 90.1%.ConclusionsThe high-level biosynthesis of 5-ALA from cheap bioresources will brighten the prospects for industrialization of this sustainable and environment-friendly process. The strategy for balancing metabolic flux developed in this study can also be used for improving the bioproduction of other value-added chemicals.

Contrast in soil microbial metabolic functional diversity to fertilization and crop rotation under rhizosphere and non-rhizosphere in the coal gangue landfill reclamation area of Loess Hills.

Very poor reclaimed soil quality and weak microbial activity occur in the reclamation area of a coal gangue landfill in the Loess Hills. The fourth and fifth years after farmland soil was reclaimed were studied, and the changes in and carbon source utilization characteristics of rhizosphere (R) and non-rhizosphere (S) soil microorganisms under organic and inorganic (OF), inorganic (F), and organic (O) fertilizer application and a control treatment (CK) in soybean (S) and maize (M) rotation systems were compared and analysed in Guljiao Tunlan, Shanxi Province, China. Biolog-EcoPlate technology was used to analyse the mechanism of soil characteristic change from the perspective of soil microbial metabolism function to provide a theoretical basis for reclamation and ecological reconstruction in this area. The average well colour development (AWCD) absorption and Shannon-Wiener index values of soybean and maize rhizosphere microorganisms were higher than those of non-rhizosphere microorganisms, and the mean value of the fertilizer treatment was higher than that for CK. Principal component analysis shows the main carbon sources that impact the functional diversity of the soybean rhizosphere and non-rhizosphere soil communities are a-cyclodextrin, a-D-lactose, ß-methyl D-glucoside, and glucose-1-phosphate and L-phenylalanine, while those for the maize rhizosphere and non-rhizosphere soil communities are D-cellobiose, glucose-1-phosphate, ß-methyl D-glucoside, methyl pyruvate, D-galactosate gamma lactone, D-mannitol, N-acetyl-D-glucosamine, D-galactosalonic acid, and L-serine. The comprehensive utilization score of the non-rhizosphere soil carbon source in the maize season increased with respect to that in the soybean season, and the maximum increase was 1.09 under the OF treatment. Redundancy analysis showed that the soil nutrient factors driving the changes in the metabolic function diversity index values of the rhizosphere and non-rhizosphere soil microbial communities in the different crop seasons in the reclamation area differed, but they were all related to the soil organic matter and available phosphorus. This may explain why OF treatment is the most beneficial to soil fertility under the rotation system in mining reclamation areas.

Mutagenesis of echinocandin B overproducing Aspergillus nidulans capable of using starch as main carbon source

Echinocandin B, a kind of antimycotic with cyclic lipo-hexapeptides, was produced by fermentation with Aspergillus nidulans using fructose as main carbon source. The objective of this study was to screen a high-yield mutant capable of using cheap starch as main carbon source by atmospheric and room temperature plasma (ARTP) treatment in order to decrease the production cost of echinocandin B. A stable mutant A. nidulans ZJB19033, which can use starch as optimal carbon source instead of expensive fructose, was selected from two thousands isolates after several cycles of ARTP mutagenesis. To further increase the production of echinocandin B, the optimization of fermentation medium was performed by response surface methodology (RSM), employing Plackett-Burman design (PBD) followed by Box-Behnken design (BBD). The optimized fermentation medium provided the optimal yield of echinocandin B, 2425.9 ± 43.8 mg/L, 1.3-fold compared to unoptimized medium. The results indicated that the mutant could achieve high echinocandin B production using cheap starch as main carbon source, and the cost of carbon sources in fermentation medium reduced dramatically by about 45%.

Engineering a defined culture medium to grow Piscirickettsia salmonis for its use in vaccine formulations

Piscirickettsia salmonis is a facultative Gram-negative intracellular bacterium that produces piscirickettsiosis, disease that causes a high negative impact in salmonid cultures. The so-far-unidentified nutritional requirements have hindered its axenic culture at laboratory and industrial scales for the formulation of vaccines. The present study describes the development of a defined culture medium for P. salmonis. The culture medium was formulated through rational design involving auxotrophy test and statistical designs of experiments, considering the genome-scale metabolic reconstruction of P. salmonis reported by our group. The whole optimization process allowed for a twofold increase in biomass and a reduction of about 50% of the amino acids added to the culture medium. The final culture medium contains twelve amino acids, where glutamic acid, threonine and arginine were the main carbon and energy sources, supporting 1.65g/L of biomass using 6.5g/L of amino acids in the formulation. These results will contribute significantly to the development of new operational strategies to culture this bacterium for the production of vaccines.

Low carbon containing Al2O3-C refractories with nanocarbon as the sole carbon source

The functional refractories used in the continuous casting process of steel are mostly made up of alumina (Al2O3) - carbon (C) system. Graphite is used as the main carbon source because of the properties it offered. Generally, these refractories contain about 30% residual carbon after coking. But the use of high carbon content leads to several disadvantages like carbon pickup by steel, high heat loss and generation of higher extent of COx gases, etc. Hence, the development of low carbon Al2O3-C refractories without conceding any beneficial properties is the challenge to the refractory technologists. Such a challenge is intended in current study with the use of nanocarbon as a complete alternative for graphite. The variation in physical, mechanical and thermo-mechanical properties with variation in amount of nanocarbon in the composition is studied. Phase analysis and microstructural developments are also evaluated along with the oxidation resistance at different temperatures. Because of its high reactivity, nanocarbon helps to form in-situ ceramic phases at much lower temperatures thereby enhances strength and other properties. But the increase in amount of nanocarbon above 2% found to deteriorate the properties.

Spent mushroom substrates affect soil humus composition, microbial biomass and functional diversity in paddy fields

Spent mushroom substrate (SMS) is the residue after mushroom production. The aims of this work were to analyze the effects of continuous application of SMS for nearly 10 years on soil organic carbon (SOC), soil humus composition, microbial biomass and functional diversity in paddy fields and to provide a theoretical basis for scientific application of SMS. A continuous application of SMS from Agaricus bisporus experiment was established in paddy field of southeastern China in 2007. Soils were collected from 6 treatments in 2016. The results showed that application of SMS could significantly increase the contents of SOC, soil total alkali-soluble humic carbon (HEC), humic acid carbon (HAC), especially the treatment of with high quantity of SMS, but not significantly increase the content of fulvic acid carbon (FAC). The microbial biomass carbon and nitrogen contents of MR3 (the amounts of SMS were 9574.5 kg hm−2, converted to pure nitrogen were 180 kg hm−2) were the largest, it illustrated that the amount of SMS was not the more the better. The average well color development (AWCD), the Shannon index, Simpson index and McIntosh index of MR3 treatment were the highest. Microorganisms of MR3 treatment could make better use of carbon sources. Carboxylic acids, carbohydrates and polymers were the main carbon source types. Sufficient but not excessive application of SMS was beneficial to the carbon source utilization of fast-growing microorganisms and was considered to be a good way to improve the productivity of paddy soil.

TaSTP13 contributes to wheat susceptibility to stripe rust possibly by increasing cytoplasmic hexose concentration

BackgroundBiotrophic fungi make intimate contact with host cells to access nutrients. Sugar is considered as the main carbon sources absorbed from host cells by pathogens. Partition, exchanges and competition for sugar at plant-pathogen interfaces are controlled by sugar transporters. Previous studies have indicated that the leaf rust resistance (Lr) gene Lr67, a natural mutation of TaSTP13 encoding a wheat sugar transport protein, confers partial resistance to all three wheat rust species and powdery mildew possibly due to weakened sugar transport activity of TaSTP13 by heterodimerization. However, one major problem that remains unresolved concerns whether TaSTP13 participates in wheat susceptibility to rust and mildew.ResultsIn this study, expression of TaSTP13 was highly induced in wheat leaves challenged by Puccinia striiformis f. sp. tritici (Pst) and certain abiotic treatments. TaSTP13 was localized in the plasma membrane and functioned as homooligomers. In addition, a functional domain for its transport activity was identified in yeast. Suppression of TaSTP13 reduced wheat susceptibility to Pst by barley stripe mosaic virus-induced gene silencing (VIGS). While overexpression of TaSTP13 promoted Arabidopsis susceptibility to powdery mildew and led to increased glucose accumulation in the leaves.ConclusionsThese results indicate that TaSTP13 is transcriptionally induced and contributes to wheat susceptibility to stripe rust, possibly by promoting cytoplasmic hexose accumulation for fungal sugar acquisition in wheat-Pst interactions.

Efficient production of ulvan lyase from Ulva prolifera by Catenovulum sp. LP based on stage-controlled fermentation strategy

Ulvan lyase, specifically depolymerizing ulvan to unsaturated sulfated oligosaccharides with diverse biological activities, is becoming more and more popular. To provide an economical fermentative strategy, Catenovulum sp. LP cultured in low-cost medium that directly used Ulva prolifera as the main carbon source was used to produce ulvan lyase. The fermentation conditions were established in a shake flask containing 5% (w/v) U. prolifera powder, 0.2% K2HPO4, 0.4% NH4Cl, 0.5% NaCl, and 0.05% MgSO4. In a 5-L fermentor, series of strategies were used to systematically discuss the fermentation process. The enzyme with the best activity was obtained by the condition of a two-stage temperature (28–32 °C), initial pH 7.0, 1.5 vvm and two-stage agitation (200–400 rpm). The fermentation kinetic model of substrate consumption indicated that a shorter culture time may improve the ulvan lyase activity. Moreover, 10.09% improvement in enzyme activity was observed in a 30-L fermentor by shortening the fermentation time to 20 h. This fermentation method offers a promising prospect to enlarge the production of ulvan lyase and also provides a potential possibility to mildly prepare bioactive unsaturated oligosaccharides.

Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach

Clostridium cellulovorans is among the most promising candidates for consolidated bioprocessing (CBP) of cellulosic biomass to liquid biofuels (ethanol, butanol). C. cellulovorans metabolizes all the main plant polysaccharides and mainly produces butyrate. Since most butyrate and butanol biosynthetic reactions from acetyl-CoA are common, introduction of single heterologous alcohol/aldehyde dehydrogenase can divert the branching-point intermediate (butyryl-CoA) towards butanol production in this strain. However, engineering C. cellulovorans metabolic pathways towards industrial utilization requires better understanding of its metabolism. The present study aimed at improving comprehension of cellulose metabolism in C. cellulovorans by comparing growth kinetics, substrate consumption/product accumulation and whole-cell soluble proteome (data available via ProteomeXchange, identifier PXD015487) with those of the same strain grown on a soluble carbohydrate, glucose, as the main carbon source. Growth substrate-dependent modulations of the central metabolism were detected, including regulation of several glycolytic enzymes, fermentation pathways (e.g. hydrogenase, pyruvate formate lyase, phosphate transacetylase) and nitrogen assimilation (e.g. glutamate dehydrogenase). Overexpression of hydrogenase and increased ethanol production by glucose-grown bacteria suggest a more reduced redox state. Higher energy expenditure seems to occur in cellulose-grown C. cellulovorans (likely related to overexpression and secretion of (hemi-)cellulases), which induces up-regulation of ATP synthetic pathways, e.g. acetate production and ATP synthase. SignificanceC. cellulovorans can metabolize all the main plant polysaccharides (cellulose, hemicelluloses and pectins) and, unlike other well established cellulolytic microorganisms, can produce butyrate. C. cellulovorans is therefore among the most attractive candidates for direct fermentation of lignocellulose to high-value chemicals and, especially, n-butanol, i.e. one of the most promising liquid biofuels for the future. Recent studies aimed at engineering n-butanol production in C. cellulovorans represent milestones towards production of biofuels through one-step fermentation of lignocellulose but also indicated that more detailed understanding of the C. cellulovorans central carbon metabolism is essential to refine metabolic engineering strategies towards improved n-butanol production in this strain. The present study helped identifying key genes associated with specific catabolic reactions and indicated modulations of central carbon metabolism (including redox and energy balance) associated with cellulose consumption. This information will be useful to determine key enzymes and possible metabolic bottlenecks to be addressed towards improved metabolic engineering of this strain.

Potential assessment and kinetic modeling of carboxylic acids production using dairy wastewater as substrate

Carboxylic acids (CA) are high added-value compounds that can be produced via anaerobic fermentation by using agroindustrial residues as substrates. However, different compounds in wastewater impose uncontrolled metabolic pathways, in which the acidogenic fermentation kinetics need to be elucidated. This work aimed to assess the potential production of CA from dairy wastewater (DW) and to perform the kinetic modeling of the process. The experiments were conducted in quadruplicate batch reactors (250 mL of working volume) with inoculum from a brewery UASB at 0.61 ± 0.04 gCOD gVSS−1. To inhibit methanogenesis, 0.05 % (v/v) chloroform was added to the reactors. The tests showed that DW is a readily fermentable substrate to acidogenic microorganisms because it presents high rates of short-chain CA formation in the first two days of the experiment. The low concentrations of medium-chain CA found indicate that fats and proteins did not function as the main carbon source for DW fermentation. The yield obtained was 0.66 mgCA mgCODA−1, which corresponds to 0.83 mgCODCA mgCODA−1. Kinetic modeling studies have shown that mathematical models that can describe an exponential phase, such as First-order and Fitzhugh models, are suitable for simulating the production of carboxylic acids. Finally, DW seems to be a promising substrate to be investigated in the carboxylic platform.

Characterization and genomic function analysis of phenanthrene-degrading bacterium Pseudomonas sp. Lphe-2

A stain of Pseudomonas sp. Lphe-2, which could degrade phenanthrene as the main carbon and energy source, was isolated from the aerobic sludge of a coking plant. Then its biodegradation characteristics, whole genome sequence and biodegradation pathway were examined. The Lphe-2 strain exhibited broad-spectrum degradation activities for various polycyclic aromatic hydrocarbons (PAHs), including naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR). Under the optimal conditions, the degradation efficiency of phenanthrene (100 mg/L) is 92.76% on the 7th day, and 2-carboxybenzaldehyde and 1-hydroxy-2-naphthoic acid are the major metabolites found in phenanthrene metabolism. Genomic analysis of Pseudomonas sp. Lphe-2 showed that a total of 3879 genes from the Lphe-2 strain were annotated based on the COG classification, and the genomic information was annotated to 185 metabolic pathways. Based on the intermediate metabolites detected by Gas Chromatography-Mass Spectrometer (GC-MS) and all potential phenanthrene-degrading genes identified by BLAST search, a phenanthrene biodegradation pathway of Lphe-2 strain was proposed. These results suggested that Lphe-2 strain has a good prospect in the bioremediation of PAHs pollution.

Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms.

RuBisCO-catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2 -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2 /O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

Origin of CO2 as the main carbon source in syngas-to-methanol process over Cu: theoretical evidence from a combined DFT and microkinetic modeling study

A theoretical study combining DFT and microkinetic modeling provides evidence that CO2 is the main carbon source in methanol synthesis from syngas (CO, CO2 and H2) over Cu.