Unique Carbon Source Research Articles

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii.

Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.

Phenotypic and genomic characterization of Methanothermobacter wolfeii strain BSEL, a CO2-capturing archaeon with minimal nutrient requirements.

A new variant of Methanothermobacter wolfeii was isolated from an anaerobic digester using enrichment cultivation in anaerobic conditions. The new isolate was taxonomically identified via 16S rRNA gene sequencing and tagged as M. wolfeii BSEL. The whole genome of the new variant was sequenced and de novo assembled. Genomic variations between the BSEL strain and the type strain were discovered, suggesting evolutionary adaptations of the BSEL strain that conferred advantages while growing under a low concentration of nutrients. M. wolfeii BSEL displayed the highest specific growth rate ever reported for the wolfeii species (0.27 ± 0.03 h-1) using carbon dioxide (CO2) as unique carbon source and hydrogen (H2) as electron donor. M. wolfeii BSEL grew at this rate in an environment with ammonium (NH4+) as sole nitrogen source. The minerals content required to cultivate the BSEL strain was relatively low and resembled the ionic background of tap water without mineral supplements. Optimum growth rate for the new isolate was observed at 64°C and pH 8.3. In this work, it was shown that wastewater from a wastewater treatment facility can be used as a low-cost alternative medium to cultivate M. wolfeii BSEL. Continuous gas fermentation fed with a synthetic biogas mimic along with H2 in a bubble column bioreactor using M. wolfeii BSEL as biocatalyst resulted in a CO2 conversion efficiency of 97% and a final methane (CH4) titer of 98.5%v, demonstrating the ability of the new strain for upgrading biogas to renewable natural gas.IMPORTANCEAs a methanogenic archaeon, Methanothermobacter wolfeii uses CO2 as electron acceptor, producing CH4 as final product. The metabolism of M. wolfeii can be harnessed to capture CO2 from industrial emissions, besides producing a drop-in renewable biofuel to substitute fossil natural gas. If used as biocatalyst in new-generation CO2 sequestration processes, M. wolfeii has the potential to accelerate the decarbonization of the energy generation sector, which is the biggest contributor of CO2 emissions worldwide. Nonetheless, the development of CO2 sequestration archaeal-based biotechnology is still limited by an uncertainty in the requirements to cultivate methanogenic archaea and the unknown longevity of archaeal cultures. In this study, we report the adaptation, isolation, and phenotypic characterization of a novel variant of M. wolfeii, which is capable of maximum growth with minimal nutrients input. Our findings demonstrate the potential of this variant for the production of renewable natural gas, paving the way for the development of more efficient and sustainable CO2 sequestration processes.

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.

Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico

Bacterial degradation of crude oil is a promising strategy for reducing the concentration of hydrocarbons in contaminated environments. In the first part of this study, we report the enrichment of two bacterial consortia from deep sediments of the Gulf of Mexico with crude oil as the sole carbon and energy source. We conducted a comparative analysis of the bacterial community in the original sediment, assessing its diversity, and compared it to the enrichment observed after exposure to crude oil in defined cultures. The consortium exhibiting the highest hydrocarbon degradation was predominantly enriched with Rhodococcus (75%). Bacterial community analysis revealed the presence of other hydrocarbonoclastic members in both consortia. In the second part, we report the isolation of the strain Rhodococcus sp. GOMB7 with crude oil as a unique carbon source under microaerobic conditions and its characterization. This strain demonstrated the ability to degrade long-chain alkanes, including eicosane, tetracosane, and octacosane. We named this new strain Rhodococcus qingshengii GOMB7. Genome analysis revealed the presence of several genes related to aromatic compound degradation, such as benA, benB, benC, catA, catB, and catC; and five alkB genes related to alkane degradation. Although members of the genus Rhodococcus are well known for their great metabolic versatility, including the aerobic degradation of recalcitrant organic compounds such as petroleum hydrocarbons, this is the first report of a novel strain of Rhodococcus capable of degrading long-chain alkanes under microaerobic conditions. The potential of R. qingshengii GOMB7 for applications in bioreactors or controlled systems with low oxygen levels offers an energy-efficient approach for treating crude oil-contaminated water and sediments.

SACARIFICACIÓN ENZIMÁTICA DE BAGAZO DE CAÑA DE AZÚCAR PRETRATADO CON PEROXIDO DE HIDROGENO PARA LA PRODUCCIÓN DE BIOETANOL

<p><strong>Background.</strong> Sugarcane (<em>Saccharum officinarum</em> L.) is one of the main crops in Mexico; during the harvest 2021-2022, 54.6 million tons of raw milled sugarcane were industrialized, ranking sixth in production worldwide. However, during processing, several products and co-products are generated, including sugarcane bagasse, that is used to produce electricity by combustion, converting nearly 25% of its weight into greenhouse gases and generating environmental problems. For this reason, it is necessary to design processes aligned with the axes of sustainable development (environmental, social and economic) to promote valorization and diversification. <strong>Objective</strong>. To determine the effect of two pretreatments on the enzymatic saccharification of sugarcane bagasse for its subsequent conversion to bioethanol. <strong>Methodology.</strong> The production of enzymatic extracts by solid state fermentation (SSF) was carried out using sugarcane bagasse as support-substrate and autochthonous fungal strains as inoculum. For the enzymatic saccharification the sugarcane bagasse was pretreated with hydrogen peroxide and microwaves, for the hydrogen peroxide pretreatment the variables time (1, 3 and 6 h), ratio mL of peroxide per gram of bagasse (16. 6:1, 33.3:1 and 100:1), temperature (26, 50 and 70°C) and peroxide concentration (1, 3 and 5%); and for microwave pretreatment the variables microwave power (p30, p50 and p80) and time (5 and 10 min) were evaluated. For the enzymatic saccharification, enzymatic extracts produced by SSF and bagasse pretreated with hydrogen peroxide were used. Finally, fermentable sugars obtained from the enzymatic saccharification of sugarcane bagasse were used as a unique carbon source in alcoholic fermentation system. <strong>Results.</strong> The SSF results showed the presence of cellulase (2 U/g) and xylanase (61 U/g) activity. On the other hand, the results of pretreatment of sugarcane bagasse with hydrogen peroxide indicated that the best conditions were 100 mL of 3% hydrogen peroxide per gram of sugarcane bagasse at 50°C, while the best conditions of microwave pretreatment were 50p for 5 minutes. The enzymatic saccharification of sugarcane bagasse showed a maximum yield of reducing sugars when the sugarcane bagasse was pretreated with hydrogen peroxide, obtaining 0.41 g/g. Finally, the maximum ethanol concentration (4.32 g/L) was obtained after 48 hours of fermentation with commercial <em>Saccharomyces cerevisae</em>. <strong>Implications.</strong> The sugar agroindustry in Mexico is limited to the production of sucrose and ethanol, being necessary a sustainable productive diversification. <strong>Conclusions.</strong> The isolation of autochthonous fungal strains allowed the production of cellulases and xylanases by solid fermentation with adequate specificity to hydrolyze/saccharify pretreated sugarcane bagasse and its subsequent conversion to ethanol.</p>

In vivo bioluminescence imaging of natural bacteria within deep tissues via ATP-binding cassette sugar transporter

Most existing bioluminescence imaging methods can only visualize the location of engineered bacteria in vivo, generally precluding the imaging of natural bacteria. Herein, we leverage bacteria-specific ATP-binding cassette sugar transporters to internalize luciferase and luciferin by hitchhiking them on the unique carbon source of bacteria. Typically, the synthesized bioluminescent probes are made of glucose polymer (GP), luciferase, Cy5 and ICG-modified silicon nanoparticles and their substrates are made of GP and D-luciferin-modified silicon nanoparticles. Compared with bacteria with mutations in transporters, which hardly internalize the probes in vitro (i.e., ~2% of uptake rate), various bacteria could robustly engulf the probes with a high uptake rate of around 50%. Notably, the developed strategy enables ex vivo bioluminescence imaging of human vitreous containing ten species of pathogens collected from patients with bacterial endophthalmitis. By using this platform, we further differentiate bacterial and non-bacterial nephritis and colitis in mice, while their chemiluminescent counterparts are unable to distinguish them.

Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86T

A soil bacterium, strain CSV86T isolated from a petrol station in Bangalore, India displays a unique carbon source utilization hierarchy with preferential utilization of various genotoxic aromatic compounds over glucose. Cells were Gram-negative, motile rods, oxidase- and catalase-positive. Strain CSV86T possess a 6.79 Mb genome with 62.72 G + C mol%. 16S rRNA gene phylogeny relates strain CSV86T to the genus Pseudomonas, with highest similarity to Pseudomonas japonica WLT (99.38%). Multi-locus sequence analyses of gyrB-rpoB-rpoD-recA and 33 ribosomal proteins (rps) displayed overall low similarities to its phylogenetic relatives with poor similarity score (6%). Average nucleotide identity (ANI) and in-silico DNA-DNA hybridization (DDH) showed poor (87.11% and 33.2%, respectively) genomic relatedness of strain CSV86T to its closest relatives, indicating genomic distinctiveness. The major cellular fatty acids were 16:0, 17:0cyclo, summed-feature-3 (16:1ω7c/16:1ω6c) and −8 (18:1ω7c). Further, differential abundance of 12:0, 10:0 3-OH and 12:0 3-OH and phenotypic differences distinguished strain CSV86T from closest relatives, hence designated as Pseudomonas bharatica. The unique aromatic degradation ability, resistance to heavy metals, efficient nitrogen-sulfur assimilation, beneficial eco-physiological traits (production of indole acetic acid, siderophore and fusaric acid efflux) and plasmid-free genome suggest strain CSV86T to be a model organism for bioremediation and ideal host for metabolic engineering.

Selection of Biodegrading Phytosterol Strains.

The phytosterol-biotransforming strains can be selected from Mycobacterium sp. using a high concentration of β-sitosterol. The selection is made by culturing the strains in a medium enriched with 14g/L of β-sitosterol as the unique source of carbon. During 2months, the bacterial cultures are transferred successively. The extraction of the biotransformation products is made with methanol and ethyl acetate. The qualitative and quantitative analyses are made by means of thin-layer chromatography, gas-liquid chromatography (GLC), and GLC-mass spectrometry. Under these conditions, it is observed that after seven transfers, the strains Mycobacterium sp. MB-3683 and Mycobacterium fortuitum B-11045 increase their biotransformation capacity from 20% to 64% and from 34% to 55%, respectively. The products in the highest proportion identified for each trial are androstenedione and androstadienedione. The results suggest that the high substrate concentration could be a selective mechanism to obtain strains more efficient in the biotransformation of β-sitosterol into steroidal bases.

Green synthesis of multi-doped carbon dots from Prickly Pear in the presence of nitrogen, phosphorus, and nitrogen-phosphorus solutions

Carbon dots (CDs) have gained popularity in research due to their desirable characteristics in electrical, catalytic, and optical applications. The exploration of unique carbon sources with complex chemical compositions can open avenues for the straightforward production of multi-doped nanomaterials. In particular, prickly pear has distinctive properties and a mineral-rich composition, and high production yields under low water usage conditions. In this work, prickly pears were used to prepare fluorescent green multi-doped CDs through a carbonization technique in the presence of nitrogen, phosphorus, and nitrogen-phosphorus solutions at 180°C for 7 hours. Results from different characterization techniques such as Fourier Transform Infrared (FTIR), X-ray diffraction (XRD), UV-vis, and Potential demonstrated the functionalization of the surface, semi-crystalline structures, a broad absorbance at the UV range with a strong peak at 275 nm, stability in water, and negative surface charge of nitrogen-doped carbon dots (NCDs), phosphorus-doped carbon dots (PCDs), and nitrogen-phosphorus doped carbon dots (NPCDs). Overall, the prickly pear was demonstrated to be a suitable source for synthesizing multi-doped CDs while maintaining nano-synthesis towards sustainable and eco-friendly directions.

Glucose-6-Phosphate Dehydrogenase, ZwfA, a Dual Cofactor-Specific Isozyme Is Predominantly Involved in the Glucose Metabolism of Pseudomonas bharatica CSV86T.

Glucose-6-phosphate dehydrogenase (Zwf) is an important enzyme in glucose metabolism via the Entner-Doudoroff pathway and the first enzyme in the oxidative pentose-phosphate pathway. It generates NAD(P)H during the conversion of glucose-6-phosphate (G6P) to 6-phosphogluconolactone, thus aiding in anabolic processes, energy yield, and oxidative stress responses. Pseudomonas bharatica CSV86T preferentially utilized aromatic compounds over glucose and exhibited a significantly lower growth rate on glucose (0.24 h-1) with a prolonged lag phase (~10 h). In strain CSV86T, glucose was metabolized via the intracellular phosphorylative route only because it lacked an oxidative (gluconate and 2-ketogluconate) route. The genome harbored three genes zwfA, zwfB, and zwfC encoding three Zwf isozymes. The present study aimed to understand gene arrangement, gene expression profiling, and molecular and kinetic properties of the purified enzymes to unveil their physiological significance in the strain CSV86T. The zwfA was found to be a part of the zwfA-pgl-eda operon, which was proximal to other glucose transport and metabolic clusters. The zwfB was found to be arranged as a gnd-zwfB operon, while zwfC was present independently. Among the three, zwfA was transcribed maximally, and the purified ZwfA displayed the highest catalytic efficiency, cooperativity with respect to G6P, and dual cofactor specificity. Isozymes ZwfB and ZwfC were NADP+-preferring and NADP+-specific, respectively. Among other functionally characterized Zwfs, ZwfA from strain CSV86T displayed poor catalytic efficiency and the further absence of oxidative routes of glucose metabolism reflected its lower growth rate on glucose compared to P. putida KT2440 and could be probable reasons for the unique carbon source utilization hierarchy. IMPORTANCE Pseudomonas bharatica CSV86T metabolizes glucose exclusively via the intracellular phosphorylative Entner-Doudoroff pathway leading the entire glucose flux through Zwf as the strain lacks oxidative routes. This may lead to limiting the concentration of downstream metabolic intermediates. The strain CSV86T possesses three isoforms of glucose-6-phosphate dehydrogenase, ZwfA, ZwfB, and ZwfC. The expression profile and kinetic properties of purified enzymes will help to understand glucose metabolism. Isozyme ZwfA dominated in terms of expression and displayed cooperativity with dual cofactor specificity. ZwfB preferred NADP+, and ZwfC was NADP+ specific, which may aid in redox cofactor balance. Such beneficial metabolic flexibility facilitated the regulation of metabolic pathways giving survival/fitness advantages in dynamic environments. Additionally, multiple genes allowed the distribution of function among these isoforms where the primary function was allocated to one of the isoforms.

Depolymerization of lignin by extracellular activity of Pycnoporus cinnabarinus, to obtain cellulose

Abstract Cellulose can be used to produce biofuels and many other products like pharmaceutical goods, food supplements, cosmetics, bio-plastics, etc. Lignocellulosic materials, like O. ficus indica residuals, are a heterogeneous biopolymer formed mainly by lignin, hemicellulose and cellulose. Lignin provides protection to the plants against chemical and microbial degradation, but it can be degraded by white rot fungi species, like Pycnoporus cinnabarinus. Since cellulose molecules are arranged in regular bundles enveloped by hemicellulose and lignin molecules, it is necessary to brake lignin and hemicellulose molecules to recover cellulose for its use in bioprocess. In this work, a biotechnological process for cellulose recovery from cactus waste through depolymerization of lignin by P. cinnabarinus, is presented. The delignification is carried out by aerobic culture in batch stirred bioreactors, with a liquid culture medium enriched with nutrients and minerals with O. ficus indica residuals as the unique carbon source, during eight-day span under continuous feeding of oxygen. A factorial design of experiments (DOE) for eight sets of factor values was selected for this study. The factors were: particle size, pH level, and process temperature. For each experiment, biomass, total reducing carbohydrates (TRC) and dissolved oxygen (DO) concentrations were measured every 24 h. At the end of each experiment, the percentage of delignification, and cellulose recovery was measured by Infrared (IR) spectroscopy. Up to 67% of delignification and 22% of cellulose recovery were obtained by the process. These results were analyzed by a factorial DOE in order to maximize each response individually and to optimize both responses together. The delignification of Opuntia ficus indica thorns has not been previously reported to our knowledge.

CO2 enrichment in greenhouse production: Towards a sustainable approach.

As the unique source of carbon in the atmosphere, carbon dioxide (CO2) exerts a strong impact on crop yield and quality. However, CO2 deficiency in greenhouses during the daytime often limits crop productivity. Crucially, climate warming, caused by increased atmospheric CO2, urges global efforts to implement carbon reduction and neutrality, which also bring challenges to current CO2 enrichment systems applied in greenhouses. Thus, there is a timely need to develop cost-effective and environmentally friendly CO2 enrichment technologies as a sustainable approach to promoting agricultural production and alleviating environmental burdens simultaneously. Here we review several common technologies of CO2 enrichment in greenhouse production, and their characteristics and limitations. Some control strategies of CO2 enrichment in distribution, period, and concentration are also discussed. We further introduce promising directions for future CO2 enrichment including 1) agro-industrial symbiosis system (AIS); 2) interdisciplinary application of carbon capture and utilization (CCU); and 3) optimization of CO2 assimilation in C3 crops via biotechnologies. This review aims to provide perspectives on efficient CO2 utilization in greenhouse production.

Corynebacterium sp. 2-TD Mediated Toxicity of 2-Tridecanone to Helicoverpa armigera.

Cotton bollworm (Helicoverpa armigera) is a Lepidopteran noctuid pest with a global distribution. It has a wide range of host plants and can harm cotton, tomato, tobacco, and corn, as well as other crops. H. armigera larvae damage the flower buds, flowers, and fruits of tomato and cause serious losses to tomato production. Tomato uses the allelochemical 2-tridecanone to defend against this damage. So far, there have been no reports on whether the adaptation of H. armigera to 2-tridecanone is related to its symbiotic microorganisms. Our study found that Corynebacterium sp. 2-TD, symbiotic bacteria in H. armigera, mediates the toxicity of the 2-tridecanone to H. armigera. Corynebacterium sp. 2-TD, which was identified by 16S rDNA gene sequence analysis, was screened out using a basal salt medium containing a unique carbon source of 2-tridecanone. Then, Corynebacterium sp. 2-TD was confirmed to be distributed in the gut of H. armigera by quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH). The survival rate of H. armigera increased by 38.3% under 2-tridecanone stress after inoculation with Corynebacterium sp. 2-TD. The degradation effect of Corynebacterium sp. 2-TD on 2-tridecanone was verified by ultra-high-performance liquid chromatography (UPLC). Our study is the first to report the isolation of gut bacteria that degrade 2-tridecanone from the important agricultural pest H. armigera and to confirm bacterial involvement in host adaptation to 2-tridecanone, which provides new insights into the adaptive mechanism of agricultural pests to host plants.

Cell adaptation of the extremophilic red microalga Galdieria sulphuraria to the availability of carbon sources.

Global energy demand and fossil fuels impact on climate can be partially managed by an increase in the use of biofuels for transports and industries. Biodiesel production is generally preceded by a transesterification process of the green biomass triacylglycerols that generates large amounts of glycerol as a by-product. In this study, the extremophilic red microalga Galdieria sulphuraria 074W was cultivated in heterotrophy. The microalgal growth parameters and biomass composition were compared when grown on an equivalent molar concentration of carbon of either glucose or glycerol as unique carbon source. The maximal biomass reached in these two conditions was not significantly different (∼2.5 g.L–1). Fatty acid profile, protein and storage carbohydrate contents were also statistically similar, irrespectively of the metabolized carbon source. We also observed that the pigment content of G. sulphuraria cells decreased during heterotrophic growth compared to photoautotrophic cultivated cells, and that this diminution was more important in the presence of glucose than glycerol: cells were yellowish in the presence of glucose and green in the presence of glycerol. The pigmentation was restored when glucose was totally consumed in the medium, suggesting that the presence of glucose repressed pigment synthesis. Based on this observation, a transcriptome analysis was performed in order to better understand the mechanisms involved in the loss of color mediated by darkness and by glucose in G. sulphuraria. Three conditions were analyzed: heterotrophy with glycerol or glucose and phototrophy. This allowed us to understand the transcriptional response of cells to light and dark environments both at the nuclear and chloroplast levels, and to show that transcription of gene families, acquired by horizontal gene transfer, such as sugar, amino acid, or acetate transporters, were involved in the response to the availability of different (in)organic sources.

A unique global metabolic trait of Pseudomonas bharatica CSV86T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids.

Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.

Degradation of Exogenous Fatty Acids in Escherichia coli.

Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.

Characterization of a novel Vibrio parahaemolyticus host-phage pair and antibacterial effect against the host.

Vibrio parahaemolyticus is a widely recognized pathogen that has caused numerous outbreaks and is prevalent in the marine environment. In this study, we investigated the characteristics of the novel V. parahaemolyticus strain BTXS2 and its associated phage, VB_VpP_BT-1011, isolated from the Bohai Coast (Tianjin, China). Strain BTXS2 is a short coryneform bacterium with a terminal flagellum and is able to utilize and metabolize a wide variety of organic matter because of its unique carbon source utilization and enzyme activity. It grows well in medium between pH 5.0 and 9.0 and salinities of simulated freshwater, estuary water, and seawater (NaCl 0.5%-3%). Multiple antibiotic resistance genes and virulence genes that endanger human health were found in the BTXS2 genome. Phage VB_VpP_BT-1011, which infects BTXS2, is a 40,065-bp double-stranded DNA virus of the family Myoviridae with a latent time of 30 min and burst size of 24 PFU/cell. Like its host, the phage tolerates a broad range of environmental conditions (salinity, 0-3% NaCl; pH 5.0-9.0; temperature, 4-37°C). A host range test showed that the phage only infected and inhibited isolate BTXS2. In summary, we investigated a novel V. parahaemolyticus host-phage pair and the antibacterial effect of the phage on V. parahaemolyticus, providing insights into marine microbial ecology and risks.

Bioremediation potential of glyphosate-degrading microorganisms in eutrophicated Ecuadorian water bodies

Phosphonate compounds are the basis of many xenobiotic pollutants, such as Glyphosate (N-(phosphonomethyl-glycine). Only procaryotic microorganisms and the lower eukaryotes are capable of phosphonate biodegradation through C–P lyase pathways. Thus, the aim of this study was to determine the presence of C–P lyase genes in Ecuadorian freshwater systems as a first step towards assessing the presence of putative glyphosate degraders. To that end, two Nested PCR assays were designed to target the gene that codifies for the subunit J (phnJ), which breaks the C-P bond that is critical for glyphosate mineralization. The assays designed in this study led to the detection of phnJ genes in 7 out of 8 tested water bodies. The amplified fragments presented 85–100% sequence similarity with phnJ genes that belong to glyphosate-degrading microorganisms. Nine sequences were not reported previously in the GenBank. The presence of phosphonate degraders was confirmed by isolating three strains able to grow using glyphosate as a unique carbon source. According to the 16S sequence, these strains belong to the Pantoea, Pseudomonas, and Klebsiella genera. Performing a Nested PCR amplification of phnJ genes isolated from eutrophicated water bodies, prior to isolation, may be a cost-effective strategy for the bioprospection of new species and/or genes that might have new properties for biotech industries, laying the groundwork for additional research.

The Potential of Tufa as a Tool for Paleoenvironmental Research—A Study of Tufa from the Zrmanja River Canyon, Croatia

Tufa is a fresh-water surface calcium carbonate deposit precipitated at or near ambient temperature, and commonly contains the remains of macro- and microphytes. Many Holocene tufas are found along the Zrmanja River, Dalmatian karst, Croatia. In this work we present radiocarbon dating results of older tufa that was found for the first time at the Zrmanja River near the Village of Sanaderi. Tufa outcrops were observed at different levels, between the river bed and up to 26 m above its present level. Radiocarbon dating of the carbonate fraction revealed ages from modern, at the river bed, up to 40 kBP ~20 m above its present level. These ages fit well with the hypothesis that the Zrmanja River had a previous surface connection with the Krka River, and changed its flow direction toward the Novigrad Sea approximately 40 kBP (Marine Isotope Stage 3). Radiocarbon AMS dating of tufa organic residue yielded a maximum conventional age of 17 kBP for the highest outcrop position indicating probable penetration of younger organic material to hollow tufa structures, as confirmed by radiocarbon analyses of humin extracted from the samples. Stable carbon isotope composition (δ13C) of the carbonate fraction of (−10.4 ± 0.6)‰ and (−9.7 ± 0.8)‰ for the Holocene and the older samples, respectively, indicate the autochthonous origin of the carbonate. The δ13C values of (−30.5 ± 0.3)‰ and (−29.6 ± 0.6)‰ for organic residue, having ages <500 BP and >5000 BP, respectively, suggest a unique carbon source for photosynthesis, mainly atmospheric CO2, with an indication of the Suess effect in δ13C during last centuries. The oxygen isotopic composition (δ18O) agrees well with deposition of tufa samples in two stages, the Holocene (−8.02 ± 0.72‰) and “old” (mainly MIS 3 and the beginning of MIS 2) (−6.89 ± 0.34‰), suggesting a ~4 °C lower temperature in MIS 3 compared to the current one.

Valorization of date juice by the production of lipopeptide biosurfactants by a Bacillus mojavensis BI2 strain: bioprocess optimization by response surface methodology and study of surface activities.

Lipopeptides biosurfactants (BioS)are natural surface-active compounds produced by a variety of microorganisms. They have great interest in environmental, biomedical and agro-industrial fields. However their large-scale application and production is limited by the cost of culture media and the low yield of production. Therefore, the improvement of the production yields and the development of efficient and cost-effective bioprocess became of a great interest. In this aim, we applied the response surface method to optimize an economic BioSproduction by a newly isolated strain Bacillus mojavensis BI2 on date Juice called "Luegmi" as unique carbon and nitrogen source. Using a Box-Bhenken design, we studied the effect of three independent variables on lipopeptide production; Leugmi concentration, Na2HPO4 and incubation time. The results of this study showed that Leugmi concentration at 25%, Na2HPO4 at 0.1% and incubation time of 24h were optimal conditions for BioS production, with a maximum Surface Tension (ST) decreasing capacity of 55% corresponding to 27 mN/m and an Oil Dispersing Activity (ODA) of 30 cm2 corresponding to a diameter of 6cm. Preliminary characterization of the BioSproduced on Luegmi by UV-Spectra and Thin Layer Chromatography showed its lipopeptide nature. Physic-chemical characterization of the produced lipopeptide on Leugmi showed its great surface activities and stabilities at different pH, temperature and salts concentration. The results of this study suggested that Leugmi, an agricultural byproducts can be used as a low-cost substrate to enhance the yield of lipopeptide BioS with great surface activities for potential environmental application.