Sphingobium sp. FB3 degrades a mixture of polycyclic aromatic hydrocarbons

A soil sample collected underneath a sewage pipe of the west side of Yangpu refining factory in Haikou city, Hainan Province, China was inoculated in minimum medium supplemented with fluoranthene. After 8 enrichment cycles, a bacterial consortium (Y12) was obtained through water-silicone oil dual system in the laboratory. The consortium Y12 could degrade a mixture of polycyclic aromatic hydrocarbons (PAHs) including phenanthrene, anthracene, fluoranthene, pyrene and benzo[a]pyrene. The consortium Y12 was repeatedly cultured for more than 40 circles, from which a bacterial strain FB3 was isolated. This strain was identified as a Sphingobium sp. through the 16S rDNA sequence alignment. Strain FB3 could degrade 99 ± 0.4%, 67 ± 2%, 97 ± 3%, 72 ± 8%, and 6 ± 2% (uncorrected degradation percentages) of phenanthrene, anthracene, fluoranthene and pyrene each at level of 100 mg L⁻¹ and benzo[a]pyrene at 10 mg L⁻¹, respectively, in 10 days, which the five PAHs were the sole carbon source as a mixture in minimum medium. The degradation percentages of phenanthrene, anthracene, fluoranthene, pyrene (each at level of 100 mg L⁻¹) and benzo[a]pyrene (10 mg L⁻¹) by consortium Y12 were 99 ± 0.1%, 65 ± 3%, 99 ± 0.3%, 79 ± 1% and 7 ± 6%, respectively, in 10 days. Strain FB3 could degrade those PAHs under a range of pH 5–9, being optimum at pH 7.     

Simultaneous degradation of the pesticides methyl parathion and chlorpyrifos by an isolated bacterial consortium from a contaminated site

The simultaneous degradation of the pesticide methyl parathion and chlorpyrifos was tested using a bacterial consortium obtained by selective enrichment from highly contaminated soils in Moravia (Medellin, Colombia). Microorganisms identified in the consortium were Acinetobacter sp, Pseudomonas putida, Bacillus sp, Pseudomonas aeruginosa, Citrobacter freundii, Stenotrophomonas sp, Flavobacterium sp, Proteus vulgaris, Pseudomonas sp, Acinetobacter sp, Klebsiella sp and Proteus sp. In culture medium enriched with each of the pesticides, the consortium was able to degrade 150 mg l⁻¹ of methyl parathion and chlorpyrifos in 120 h. When a mixture of 150 mg l⁻¹ of both pesticides was used the percentage decreased to 72% for methyl parathion and 39% for chlorpyrifos. With the addition of glucose to the culture medium, the consortium simultaneously degraded 150 mg l⁻¹ of the pesticides in the mixture. 4 treatments were carried out in soil that included the addition of glucose with microorganisms, the addition of sugar cane with microorganisms, microorganisms without nutrient addition and without the addition of any item. In the treatment in which glucose was used, degradation percentages of methyl parathion and chlorpyrifos of 98% and 97% respectively were obtained in 120 h. This treatment also achieved the highest percentage of reduction in toxicity, monitored with Vibrio fischeri.     

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

The expression levels of sorbose/sorbosone dehydrogenase genes (sdh and sndh) and the synthesis genes (pqqABCDEN) of the adjoint cofactor pyrroloquinoline quinone (PQQ) were genetically manipulated in Ketogulonigenium vulgare to increase the production of 2-keto-l-gulonic acid (2-KLG), the precursor of vitamin C, in the consortium of K. vulgare and Bacillus cereus. We found that overexpression of sdh–sndh alone in K. vulgare could not significantly enhance the production of 2-KLG, revealing the cofactor PQQ was required for the biosynthesis of 2-KLG. Various expression levels of PQQ were achieved by differential expression of pqqA, pqqABCDE and pqqABCDEN, respectively. The combinatorial expression of sdh/sndh and pqqABCDEN in K. vulgare enabled a 20% increase in the production of 2-KLG (79.1±0.6 g l⁻¹) than that of the parental K. vulgare (65.9±0.4 g l⁻¹) in shaking flasks. Our results demonstrated the balanced co-expression of both the key enzymes and the related cofactors was an efficient strategy to increase chemicals' biosynthesis.     

Enhanced lindane removal from soil slurry by immobilized Streptomyces consortium

The aim of this work was to assess lindane removal from soil slurry by a Streptomyces consortium immobilized in cloth sachets, at different inoculum, lindane and slurry concentrations. In concentrated slurry (soil/water ratio of 2:3), the higher lindane removal (35.3 mg Kg⁻¹) was obtained with the medium inoculum (10⁷ CFU g⁻¹) and the highest lindane concentration tested, at 7 days of incubation. Although, lindane removal was also detected in abiotic controls, probably caused by pesticide adsorption to soil particles. Thus, these parameters were selected for evaluating the pesticide removal in diluted slurry (soil/water ratio of 1:4). After 14 days of incubation, 28.7 mg Kg⁻¹ of lindane were removed. Also, a phytotoxicity assay demonstrated that seeds growing on diluted slurries bioremediated during 7 and 14 days, showed an improvement in biological parameters, compared to those growing on non-bioremediated slurries. Thus, bioremediated slurries would not have toxic effects on lettuce seeds.     

Biodegradation potential of oily sludge by pure and mixed bacterial cultures

The biodegradation capacity of aliphatic and aromatic hydrocarbons of petrochemical oily sludge in liquid medium by a bacterial consortium and five pure bacterial cultures was analyzed. Three bacteria isolated from petrochemical oily sludge, identified as Stenotrophomonas acidaminiphila, Bacillus megaterium and Bacillus cibi, and two bacteria isolated from a soil contaminated by petrochemical waste, identified as Pseudomonas aeruginosa and Bacillus cereus demonstrated efficiency in oily sludge degradation when cultivated during 40 days. The bacterial consortium demonstrated an excellent oily sludge degradation capacity, reducing 90.7% of the aliphatic fraction and 51.8% of the aromatic fraction, as well as biosurfactant production capacity, achieving 39.4% reduction of surface tension of the culture medium and an emulsifying activity of 55.1%. The results indicated that the bacterial consortium has potential to be applied in bioremediation of petrochemical oily sludge contaminated environments, favoring the reduction of environmental passives and increasing industrial productivity.     

Relative quantitative PCR to assess bacterial community dynamics during biodegradation of diesel and biodiesel fuels under various aeration conditions

The degradation of diesel fuel, B20 blend and biodiesel in liquid cultures by a seven-member bacterial consortium was compared under conditions with full aeration or with limited aeration with nitrate added as main electron acceptor. Community dynamics was assessed employing real-time PCR and the ddCt method for relative quantification. Biodegradation rates increased with increasing biodiesel content, but were significantly reduced under conditions with nitrate. Despite large variations in biodegradation rates, magnitude changes in population numbers were typically observed only from zero to one order, regardless the type of fuel and electron acceptor. Only Comamonadaceae and Variovorax sp. distinctly preferred aerobic conditions, and during aerobic growth showed suppression as fuel contained more biodiesel. Thus, the consortium is relatively stable and most of the degraders can shift their metabolism from hydrocarbons to biodiesel. The stability of the consortium is of interest in the context of biodiesel-mediated biodegradation of petroleum hydrocarbons.     

Anaerobic degradation of benzoate to methane by a microbial consortium

A stabilized consortium of microbes which anaerobically degraded benzoate and produced CH₄ was established by inoculation of a benzoate-mineral salts medium with sewage sludge; the consortium was routinely subcultured anaerobically in this medium for 3 years. Acetate, formate, H₂ and CO₂ were identified as intermediates in the overall conversion of benzoate to CH₄ by the culture. Radioactivity was equally divided between the CH₄ and CO₂ from the degradation of uniformly ring-labeled [¹⁴C]benzoate. The methyl group of acetate was stoichiometrically converted to CH₄. Acetate, cyclohexanecarboxylate, 2-hydroxycyclohexanecarboxylate, o-hydroxybenzoic acid and pimelic acid were converted to CH₄ without a lag suggesting that benzoate was degraded by a reductive pathway. Addition of o-chlorobenzoate inhibited benzoate degradation but not acetate degradation or methane formation. Two methanogenic organisms were isolated from the mixed culture, neither organism was able to degrade benzoate, showing that the methanogenic bacteria served as terminal organisms of a metabolic food chain composed of several organisms. Removal of intermediates by the methanogenic bacteria provided thermodynamically favorable conditions for benzoate degradation.     

A sequential aerobic/microaerophilic decolorization of sulfonated mono azo dye Golden Yellow HER by microbial consortium GG-BL

This study is a part of efforts to develop new batch method with the help of prepared consortium GG-BL using two microbial cultures viz. Galactomyces geotrichum MTCC 1360 and Brevibacillus laterosporus NCIM 2298, varying oxidation conditions for the bio-treatment processes to produce reusable water by decolorization of Golden Yellow HER (GYHER) to less toxic metabolites. Consortium was found to be much faster for decolorization and degradation of GYHER as compared to the individual strains. The intensive metabolic activity of these strains led to 100% decolorization of GYHER (50 mg l⁻¹) within 24 h with significant reduction in chemical oxygen demand (84%) and total organic carbon (63%). The presence of veratryl alcohol oxidase, NADH-DCIP reductase and induction in laccase, tyrosinase, azo reductase and riboflavin reductase during decolorization suggests their role in decolorization process. Substrate staining of nondenaturing polyacrylamide electrophoresis gel (PAGE) also confirms induction of oxidative enzymes during GYHER degradation. The degradation of the GYHER into different metabolites by individual organism and in consortium was confirmed using High Performance Thin Layer Chromatography (HPTLC), High Performance Liquid Chromatography (HPLC), Fourier Transform Infra Red Spectroscopy (FTIR), Gas Chromatography Mass Spectroscopy (GC–MS) analysis. Phytotoxicity studies revealed nontoxic nature of the metabolites of GYHER.     

Removal of sulphate, COD and Cr(VI) in simulated and real wastewater by sulphate reducing bacteria enrichment in small bioreactor and FTIR study

The present study was conducted to investigate the chromium(VI), COD and sulphate removal efficiency from aqueous solution and treatment of real effluent (CETP) in a small scale bioreactor using sulphate reducing bacteria consortium. Effect of different hydraulic retention times (HRTs), initial metal concentrations, various carbon sources and temperatures were studied on removal of chromium(VI), COD and sulphate. Maximum chromium(VI) and sulphate removal was found to be 96.0% and 82.0%, respectively, at initial concentration of 50 mg l⁻¹ using lactate as carbon source. However, highest COD removal was 36.2% in medium containing fructose as the carbon source and electron donor. NADH dependent chromate reductase activity was not observed which indicated the anaerobic consortium. Initially consortium medium with a strong negative oxidation reduction potential indicated the reducing activity. The FTIR spectrum of the sulphate reducing bacteria consortium clearly shows the existence of the sulphate ions and signifies that sulfate reducing bacteria have used sulfate during the growth phase.     

Chronic metformin intake and gastric cancer: A pooled analysis within the Stomach cancer Pooling (StoP) Project

IntroductionThe association between chronic use of metformin and risk of gastric cancer (GC) has been investigated with contradicting results. We aimed to study the association between chronic use of metformin and GC by using data from the Stomach cancer Pooling (StoP) Project, an epidemiological consortium of case-control studies on GC.MethodsData from three studies of the StoP Project with available information on metformin intake were analyzed.Multivariable logistic regression models were used to estimate study-specific odds ratios (ORs) and 95% confidence intervals (CIs) for the association between chronic use of metformin and GC risk. Analyses were adjusted for sex, age, socioeconomic status, body mass index, smoking status, alcohol drinking status, and history of diabetes. Study-specific ORs and 95% CIs were then pooled with a random-effects model.The dose-response relationship between the duration of metformin intake and GC was assessed with a one-stage logistic model, and the duration of intake was modelled using second-order fractional polynomials.ResultsThe OR of GC in metformin users versus non-users was 1.01 (95% CI=0.61, 1.67). The association between metformin and GC did not change among different strata of study participants’ characteristics or when restricting the analyses to those with a history of diabetes.The dose-response analysis showed a slightly reducing trend in the OR of GC and a borderline significant association with increasing duration of metformin intake.ConclusionsThe results of our study do not clearly support an association between chronic use of metformin and GC, warranting further research.     

Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii

We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The structure, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four-stranded beta-sheet with a classic Greek-key topology and an oligonucleotide/oligosaccharide beta-barrel (OB) fold. The electrostatic surface of S28E exhibits positive and negative patches on opposite sides, the former constituting a putative binding site for RNA. The 13 C-terminal residues of the protein contain a consensus sequence motif constituting the signature of the S28E protein family. Surprisingly, this C-terminal segment is unstructured in solution.     

Five hundred and twenty‐eight microsatellite markers for ecological genomic investigations using Daphnia

Until recently, an enormous effort was needed to apply genomic tools to ecological investigations, especially when striving to uncover the functional mechanisms of phenotypic plasticity and the genetic basis of evolutionary adaptation within natural populations. This present study aimed to develop a genomic resource for an organism ideally suited for functional ecology and evolutionary research. Over 760 unique DNA fragments containing microsatellite loci were isolated and characterized from Daphnia to provide more than 500 molecular markers for constructing a genetic map and for localizing chromosomal regions containing genes of ecological importance via quantitative trait locus analyses. Although primarily developed to genotype members of the Daphnia pulex species complex, a significant fraction of these markers is potentially valuable for population genetics and recombination mapping of distantly related species. Over 60% of markers tested in cross‐specific amplifications are possibly conserved within the subgenus Daphnia, whereas 48 and 18% of tested primers are found to amplify subgenus Hyalodaphnia and subgenus Ctenodaphnia DNA, which represents ～140 and 200 million years of evolutionary preservation.     

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.     

CFHR3 is a potential novel biomarker for hepatocellular carcinoma

Complement factor H-related 3 (CFHR3) is a protein-coding gene acting in various diseases. However, its prognostic values of CFHR3 in hepatocellular carcinoma (HCC) are not understandable. Therefore, we present a further study on CFHR3 in HCC. CFHR3 expression data were acquired from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). We compared the differential expression of CFHR3 between the low-stage (stage I and II) and high-stage (stage III and IV) patients with HCC in the TCGA and ICGC cohorts. Furthermore, we assessed the CFHR3 expression as a prognostic marker using the Kaplan-Meier survival analysis, univariate, and multivariate analysis. The Kaplan-Meier analysis declared that CFHR3 overexpression was correlated with a good prognosis for HCC patients. Multivariate analysis proved the prognostic significance of CFHR3 expression levels (P < .001 and .003 for TCGA and ICGC, respectively). Immune-related scores in low-risk cohorts were higher than high-risk cohorts. Gene set enrichment analysis implied that the low CFHR3 expression phenotype was significantly enriched in critical biological functions and pathways and was associated with tumorigenesis, such as regulation of cell activation cycle, and the WNT and NOTCH signal pathway. Above all, CFHR3 could be a novel prognostic biomarker and therapeutic target for HCC.     

Biodegradation of Reactive Blue 59 by isolated bacterial consortium PMB11

Morphologically different, three bacterial strains, capable of decolorizing Reactive Blue 59 were isolated from dye effluent contaminated soil sample, collected from Ichalkaranji, India. The individual bacterial strains viz. Bacillus odysseyi SUK3, Morganella morganii SUK5 and Proteus sp. SUK7 decolorized Reactive Blue 59 (50 mg l(-1)) completely within 60, 30, 24 h, respectively, while the bacterial consortium PMB11 of these strains required 3 h for the complete decolorization. The decolorization was confirmed by UV-Vis spectroscopy. Further, the biodegradation of Reactive Blue 59 in to different metabolites was confirmed by High performance liquid chromatography and Fourier transform infrared spectroscopy analysis. Significant increase in the activity of aminopyrine N-demethylase (AND) in the individual as well consortium cells, obtained after decolorization showed involvement of AND in the decolorization process. Phytotoxicity studies, revealed the nontoxic nature of the degraded metabolites of Reactive Blue 59 indicating effectiveness of bacterial consortium PMB11 for the treatment of textile effluent containing Reactive Blue 59.     

Achieving yield gains in wheat

Wheat provides 20% of calories and protein consumed by humans. Recent genetic gains are <1% per annum (p.a.), insufficient to meet future demand. The Wheat Yield Consortium brings expertise in photosynthesis, crop adaptation and genetics to a common breeding platform. Theory suggest radiation use efficiency (RUE) of wheat could be increased ～50%; strategies include modifying specificity, catalytic rate and regulation of Rubisco, up-regulating Calvin cycle enzymes, introducing chloroplast CO(2) concentrating mechanisms, optimizing light and N distribution of canopies while minimizing photoinhibition, and increasing spike photosynthesis. Maximum yield expression will also require dynamic optimization of source: sink so that dry matter partitioning to reproductive structures is not at the cost of the roots, stems and leaves needed to maintain physiological and structural integrity. Crop development should favour spike fertility to maximize harvest index so phenology must be tailored to different photoperiods, and sensitivity to unpredictable weather must be modulated to reduce conservative responses that reduce harvest index. Strategic crossing of complementary physiological traits will be augmented with wide crossing, while genome-wide selection and high throughput phenotyping and genotyping will increase efficiency of progeny screening. To ensure investment in breeding achieves agronomic impact, sustainable crop management must also be promoted through crop improvement networks.