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Journal: AMB Express


The contaminant concentrations over which type strains of the species Dehalogenimonas alkenigignens and Dehalogenimonas lykanthroporepellens were able to reductively dechlorinate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were evaluated. Although initially isolated from an environment with much lower halogenated solvent concentrations, D. alkenigignens IP3-3T was found to reductively dehalogenate chlorinated alkanes at concentrations comparable to D. lykanthroporepellens BL-DC-9T. Both species dechlorinated 1,2-DCA, 1,2-DCP, and 1,1,2-TCA present at initial concentrations at least as high as 8.7, 4.0, and 3.5 mM, respectively. The ability of Dehalogenimonas spp. to carry out anaerobic reductive dechlorination even in the presence of high concentrations of chlorinated aliphatic alkanes has important implications for remediation of contaminated soil and groundwater.

Concepts: Ethanol, Water pollution, Benzene, Environmental remediation, Solution, Hexane, Environmental chemistry, Pentane


Agro-industrial wastes are generated during the industrial processing of agricultural products. These wastes are generated in large amounts throughout the year, and are the most abundant renewable resources on earth. Due to the large availability and composition rich in compounds that could be used in other processes, there is a great interest on the reuse of these wastes, both from economical and environmental view points. The economic aspect is based on the fact that such wastes may be used as low-cost raw materials for the production of other value-added compounds, with the expectancy of reducing the production costs. The environmental concern is because most of the agro-industrial wastes contain phenolic compounds and/or other compounds of toxic potential; which may cause deterioration of the environment when the waste is discharged to the nature. Although the production of bioethanol offers many benefits, more research is needed in the aspects like feedstock preparation, fermentation technology modification, etc., to make bioethanol more economically viable.

Concepts: Environment, Natural environment, Natural resource, Material, Recycling, Habitat conservation, Environmentalism, Ethanol fuel


Agricultural sustainability may represent the greatest encumbrance to increasing food production. On the other hand, as a component of sustainability, replacement of chemical fertilizers by bio-fertilizers has the potential to lower costs for farmers, to increase yields, and to mitigate greenhouse-gas emissions and pollution of water and soil. Rhizobia and plant-growth-promoting rhizobacteria (PGPR) have been broadly used in agriculture, and advances in our understanding of plant-bacteria interactions have been achieved; however, the use of signaling molecules to enhance crop performance is still modest. In this study, we evaluated the effects of concentrated metabolites (CM) from two strains of rhizobia—Bradyrhizobium diazoefficiens USDA 110T (BD1) and Rhizobium tropici CIAT 899T (RT1)—at two concentrations of active compounds (10–8 and 10–9 M)—on the performances of two major plant-microbe interactions, of Bradyrhizobium spp.-soybean (Glycine max (L.) Merr.) and Azospirillum brasilense-maize (Zea mays L.). For soybean, one greenhouse and two field experiments were performed and effects of addition of CM from the homologous and heterologous strains, and of the flavonoid genistein were investigated. For maize, three field experiments were performed to examine the effects of CM from RT1. For soybean, compared to the treatment inoculated exclusively with Bradyrhizobium, benefits were achieved with the addition of CM-BD1; at 10–9 M, grain yield was increased by an average of 4.8%. For maize, the best result was obtained with the addition of CM-RT1, also at 10–9 M, increasing grain yield by an average of 11.4%. These benefits might be related to a combination of effects attributed to secondary compounds produced by the rhizobial strains, including exopolysaccharides (EPSs), plant hormones and lipo-chitooligosaccharides (LCOs). The results emphasize the biotechnological potential of using secondary metabolites of rhizobia together with inoculants containing both rhizobia and PGPR to improve the growth and yield of grain crops.

Concepts: Agriculture, Wheat, Poaceae, Soybean, Cereal, Maize, Rice, Staple food


The term cellulase refers to any component of the enzymatic complex produced by some fungi, bacteria and protozoans which act serially or synergistically to catalyze the cleavage of cellulosic materials. Cellulases have been widely used in many industrial applications ranging from food industry to the production of second generation ethanol. In an effort to develop new strategies to minimize the costs of enzyme production we describe the development of a Pichia pastoris strain able to coproduce two different cellulases. For that purpose the eglII (endoglucanase II) and cbhII (cellobiohydrolase II) genes from Trichoderma reesei were fused in-frame separated by the self-processing 2A peptide sequence from the foot-and-mouth disease virus. The protein fusion construct was placed under the control of the strong inducible AOX1 promoter. Analysis of culture supernatants from methanol-induced yeast transformants showed that the protein fusion was effectively processed. Enzymatic assay showed that the processed enzymes were fully functional with the same catalytic properties of the individual enzymes produced separately. Furthermore, when combined both enzymes acted synergistically on filter paper to produce cellobiose as the main end-product. Based on these results we propose that P. pastoris should be considered as an alternative platform for the production of cellulases at competitive costs.

Concepts: Protein, Metabolism, Enzyme, Catalysis, Cellulose, Hydrolysis, Enzyme assay, Cellulosic ethanol


The ability to solubilize fixed inorganic phosphorus (P) for plant growth is important for increasing crop yield. More P can be released by inoculating soil with inorganic-phosphate-solubilizing bacteria (iPSBs). We used 96-well microplates instead of traditional 200-mm petri dishes to rapidly screen iPSB strains for their solubilizing ability. We simultaneously obtained 76 iPSB isolates from 576 wells containing two agricultural soils. This method conveniently identified positive iPSB strains and effectively prevented fungal cross-contamination. Maximum-likelihood phylogenetic trees of the isolated strains showed that Bacillus megaterium was the most dominant iPSB, and strains Y99, Y95, Y924 and Y1412 were selected as representatives for the analysis of P solubilization. Succinic acid was the main organic acid of B. megaterium for releasing P. It was strongly correlated with the increase in soluble P concentration during 168 h of incubation of these four strains. pH was negatively exponentially correlated with the amount of soluble P in the medium, and the amount of succinic acid was strongly linearly correlated with the amount of P released (P < 0.001), suggesting that organic acid may mobilize microbial P. Our study provides an efficient and effective method for identifying and analyzing the growth of iPSB strains able to solubilize inorganic P and gives a better understanding of the mechanism of P solubilization.

Concepts: Oxygen, Bacteria, Agriculture, Acid, Soil, Bacillus, Phosphorus, Bacillus megaterium


To improve the biodegradation of biodegradable plastic (BP) mulch films, 1227 fungal strains were isolated from plant surface (phylloplane) and evaluated for BP-degrading ability. Among them, B47-9 a strain isolated from the leaf surface of barley showed the strongest ability to degrade poly-(butylene succinate-co-butylene adipate) (PBSA) and poly-(butylene succinate) (PBS) films. The strain grew on the surface of soil-mounted BP films, produced breaks along the direction of hyphal growth indicated that it secreted a BP-degrading enzyme, and has directly contributing to accelerating the degradation of film. Treatment with the culture filtrate decomposed 91.2 wt%, 23.7 wt%, and 14.6 wt% of PBSA, PBS, and commercially available BP polymer blended mulch film, respectively, on unsterlized soil within 6 days. The PCR-DGGE analysis of the transition of soil microbial community during film degradation revealed that the process was accompanied with drastic changes in the population of soil fungi and Acantamoeba spp., as well as the growth of inoculated strain B47-9. It has a potential for application in the development of an effective method for accelerating degradation of used plastics under actual field conditions.

Concepts: Microbiology, Plant, Fungus, Hypha, Plastic, Biodegradation, Bioplastic, Biodegradable plastic


Isopropanol represents a widely-used commercial alcohol which is currently produced from petroleum. In nature, isopropanol is excreted by some strains of Clostridium beijerinckii, simultaneously with butanol and ethanol during the isopropanol butanol ethanol (IBE) fermentation. In order to increase isopropanol production, the gene encoding the secondary-alcohol dehydrogenase enzyme from C. beijerinckii NRRL B593 (adh), which catalyzes the reduction of acetone to isopropanol, was cloned into the acetone, butanol and ethanol (ABE)-producing strain C. acetobutylicum ATCC 824. The transformants showed high capacity for conversion of acetone into isopropanol (> 95 %). To increase isopropanol production levels in ATCC 824, polycistronic transcription units containing, in addition to the adh gene, homologous genes of the acetoacetate decarboxylase (adc), and/or the acetoacetyl-CoA:acetate/butyrate:CoA transferase subunits A and B (ctfA and ctfB)) were constructed and introduced into the wild-type strain. Combined overexpression of the ctfA and ctfB genes resulted in enhanced solvent production. In non-pH-controlled batch cultures, the total solvents excreted by the transformant overexpressing the adh, ctfA, ctfB and adc were 24.4 g/L IBE (including 8.8 g/L isopropanol), while the control strain harbouring an empty plasmid produced only 20.2 g/L ABE (including 7.6 g/L acetone). The overexpression of the adc gene had limited effect on IBE production. Interestingly, all transformants with the adh gene converted acetoin (a minor fermentation product) into 2,3-butanediol, highlighting the wide metabolic versatility of solvent-producing Clostridia.

Concepts: Gene, Alcohol, Acetone, Ethanol, Clostridium acetobutylicum, Solvent, Clostridium, Clostridiaceae


The composition and function of the intestinal microbiota play important roles in digestion and degradation of herbal medicines (HMs). However, few studies have examined the relationship between the fecal microbiota and HMs. In this study the effect of unfermented Astragalus (UA) and fermented Astragalus (FA) on growth performance, serum biochemical parameters, and fecal microbiota was evaluated in broiler chickens. In total, 180 one-day-old broiler chickens (Avian breeds) were randomly assigned to a control © group fed a basal diet, an unfermented (U) group fed a basal diet containing 0.5% UA, or a fermented (F) group fed a basal diet containing 0.5% FA, for 42 days. The F/G ratio was lower in F and U groups than in C group from 22 to 42 days (P < 0.05). Glutathione superoxide dismutase, antioxidant capacity, and total superoxide dismutase were higher, whereas malondialdehyde was lower in F group than in C and U groups from 1 to 21 days and from 22 to 42 days (P < 0.05). Fecal microbiota were profiled on an Illumina MiSeq platform following PCR amplification of the V4 region of the 16S rRNA gene. At the genus level Lactobacillus was the most abundant genus on day 7 in F group. Importantly, a potentially pathogenic genus, Enterococcus, was less abundant in the U and F groups than in the C group on day 35 (P < 0.05). These results indicate that dietary supplementation with 0.5% FA has beneficial effects on growth performance, serum biochemical parameters and fecal microbiota of broiler chickens.


Sortases are enzymes mostly found in Gram-positive bacteria which cleave proteins site-specifically. This feature makes them a promising tool in molecular biology and biotechnology. In this study, using bacterial surface display of recombinant proteins and ability of sortase A in site-specifically cleavage of the amino acid sequences, a novel method for one-step purification of recombinant proteins was developed. Using computational program tools, a chimeric protein containing a metallothionein (mt) and chitin binding domain (ChBD) was attached to the C-terminal domain of the truncated outer membrane protein A (Lpp'-ompA) using sortase recognition site (amino acid residues: LPQTG) as a separator. The structure of the chimeric protein was simulated using molecular dynamics to determine if the LPQTG motif is accessible to the sortase active site. The designed chimeric protein was expressed and purified. The purified chimeric protein was also displayed on the surface of E. coli cells. Both purified chimeric protein and the E. coli cells displaying Lpp'-ompA-mt-ChBD carrier protein were then treated with sortase to evaluate the efficiency of sortase-mediated cleavage of purified chimeric protein as well as surface displayed-chimeric protein. It is shown that mt-ChBD protein was successfully cleaved and dissociated from Lpp'-ompA carrier and released into the medium after treatment with sortase in both recombinant protein and surface displayed-chimeric protein. The experimental results confirmed the molecular dynamics analysis results. The presented method could be regarded as a novel strategy for one step expression and purification of recombinant proteins.


Brewers' spent grain (BSG) is a by-product generated from the beer manufacturing industry, which is extremely rich in protein and fiber. Here we use low cost BSG as the raw material for the production of a novel growth media, through a bioconversion process utilizing a food grade fungi to hydrolyze BSG. The novel fermentation media was tested on the yeast Rhodosporidium toruloides, a natural yeast producing carotenoid. The yeast growth was analysed using the growth curve and the production of intracellular fatty acids and carotenoids. Untargeted GCMS based metabolomics was used to analyse the constituents of the different growth media, followed by multivariate data analysis. Growth media prepared using fermented BSG was found to be able to support the growth in R. toruloides (21.4 mg/ml) in comparable levels to YPD media (24.7 mg/ml). Therefore, the fermented BSG media was able to fulfill the requirement as a nitrogen source for R. toruloides growth. This media was able to sustain normal metabolomics activity in yeast, as indicated by the level of fatty acid and carotenoid production. This can be explained by the fact that, in the fermented BSG media metabolites and amino acids were found to be higher than in the unfermented media, and close to the levels in YPD media. Taken together, our study provided evidence of a growth media for yeast using BSG. This should have potential in replacing components in the current yeast culture media in a sustainable and cost effective manner.

Concepts: Protein, Bacteria, Metabolism, Nutrition, Yeast, Fermentation