Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

Background: The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results: Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63). For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual k-mers (k-19 to k-63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions: This study demonstrated that different k-mer choices result in various quantities of unique contigs per single k-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-k assemblies with redundancy removal. The complete extraction of biological information in de novo transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual k-mer assemblies but not in the CA

Electricity and catholyte production from ceramic MFCs treating urine

© 2016 The Authors The use of ceramics as low cost membrane materials for Microbial Fuel Cells (MFCs) has gained increasing interest, due to improved performance levels in terms of power and catholyte production. The catholyte production in ceramic MFCs can be attributed to a combination of water or hydrogen peroxide formation from the oxygen reduction reaction in the cathode, water diffusion and electroosmotic drag through the ion exchange membrane. This study aims to evaluate, for the first time, the effect of ceramic wall/membrane thickness, in terms of power, as well as catholyte production from MFCs using urine as a feedstock. Cylindrical MFCs were assembled with fine fire clay of different thicknesses (2.5, 5 and 10mm) as structural and membrane materials. The power generated increased when the membrane thickness decreased, reaching 2.1±0.19mW per single MFC (2.5mm), which was 50% higher than that from the MFCs with the thickest membrane (10mm). The amount of catholyte collected also decreased with the wall thickness, whereas the pH increased. Evidence shows that the catholyte composition varies with the wall thickness of the ceramic membrane. The possibility of producing different quality of catholyte from urine opens a new field of study in water reuse and resource recovery for practical implementation

Transcriptome analysis reveals the genetic foundation for the dynamics of starch and lipid production in Ettlia oleoabundans

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Comprehensive Study on Ceramic Membranes for Low-Cost Microbial Fuel Cells

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Microbial fuel cells (MFCs) made with different types of ceramic membranes were investigated to find a low-cost alternative to commercially available proton exchange membranes. The MFCs operated with fresh human urine as the fuel. Pyrophyllite and earthenware produced the best performance to reach power densities of 6.93 and 6.85 W m-3, respectively, whereas mullite and alumina achieved power densities of 4.98 and 2.60 Wm-3, respectively. The results indicate the dependence of bio-film growth and activity on the type of ceramic membrane applied. The most favourable conditions were created in earthenware MFCs. The performance of the ceramic membranes was related to their physical and chemical properties determined by environmental scanning electron microscopy and energy dispersive X-ray spectroscopy. The cost of mullite, earthenware, pyrophyllite and alumina was estimated to be 13.61, 4.14, 387.96 and 177.03 GBP m-2, respectively. The results indicate that earthenware and mullite are good substitutes for commercially available proton exchange membranes, which makes the MFC technology accessible in developing countries

Regeneration of the power performance of cathodes affected by biofouling

© 2016 The Authors. Air cathode microbial fuel cells (MFCs) were used in a cascade-system, to treat neat human urine as the fuel. Their long-term operation caused biodeterioration and biofouling of the cathodes. The cathodes were made from two graphite-painted layers, separated by a current collector. The initial performance of the MFCs was reaching average values of 105.5 ± 32.2 μW and current of 1164.5 ± 120.2 μA. After 3 months of operation the power performance decreased to 9.8 ± 3.5 μW, whilst current decreased to 461.2 ± 137.5 μA. Polarisation studies revealed significant transport losses accompanied by a biofilm formation on the cathodes. The alkaline lysis procedure was established to remove the biomass and chemical compounds adsorbed on the cathode's surface. As a result, the current increased from 378.6 ± 108.3 μA to 503.8 ± 95.6 μA. The additional step of replacing the outer layer of the cathode resulted in a further increase of current to 698.1 ± 130 μA. Similarly, the power performance of the MFCs was recovered to the original level reaching 105.3 ± 16.3 μW, which corresponds to 100% recovery. Monitoring bacterial cell number on the cathode's surface showed that biofilm formed during operation was successfully removed and composed mainly of dead bacterial cells after treatment. To the best of the authors' knowledge, this is the first time that the performance of deteriorating cathodes, has been successfully recovered for MFCs in-situ. Through this easy, fast and inexpensive procedure, designing multilayer cathodes may help enhance the range of operating conditions, if a biofilm forms on their surface

Iron based catalysts from novel low-cost organic precursors for enhanced oxygen reduction reaction in neutral media microbial fuel cells

© 2016 The Royal Society of Chemistry. Two iron-based platinum group metal-free catalysts for the oxygen reduction reaction (ORR) were synthesized from novel and low cost organic precursors named niclosamide and ricobendazole. These catalysts have been characterized, incorporated in a gas diffusional electrode and tested in "clean" conditions as well as in operating microbial fuel cell (MFC) for 32 days. Both catalysts demonstrated unprecedented performance yielding a power density 25% higher than that of platinum (Pt) and roughly 100% higher than activated carbon (AC) used as a control. Durability tests were performed and showed that Pt-based cathodes lost their activity within the first week of operation, reaching the level of the supporting AC-based electrode. Fe-ricobendazole, however, demonstrated the highest performance during the long-term study with a power density of 195 ± 7 μW cm-2 (day 2) that slightly decreased to 186 ± 9 μW cm-2 at day 29. Fe-niclosamide also outperformed Pt and AC but the power density roughly decreased with 20% for the 32 days of the study. Accelerated poisoning test using S2- as pollutant showed high losses in activity for Pt. Fe-niclosamide suffered higher losses compared to Fe-ricobendazole. Importantly, Fe-ricobendazole represents a 55-fold cost reduction compared to platinum

Biocatalytic electrode improvement strategies in microbial fuel cell systems

Microbial fuel cells (MFCs) produce electricity as a result of the microbial metabolism of organic substrates, hence they represent a sustainable approach for energy production and waste treatment. If the technology is to be implemented in industry, low cost and sustainable bioelectrodes must be developed to increase power output, increase waste treatment capacity, and improve service intervals. Although the current application of abiotic electrode catalysts, such as platinum and electrode binders such as Nafion leads to greater MFC performance, their use cost prohibitive. Novel bioelectrodes which use cost effective and sustainable materials are being developed. These electrodes are developed with the intention to reduce start‐up time, reduce costs, extend life‐span and improve core MFC performance metrics (ie. power density, current density, chemical oxygen demand (COD) reduction and Coulombic efficiency (CE)). Comparison of different MFC systems is not an easy task. This is due to variations in MFC design, construction, operation, and different inocula (in the case of mixed‐culture MFCs). This high intra system variability should be considered when assessing MFC data, operation and performance. In this review article, we examine the major issues surrounding bioanode and biocathode improvement in different MFC systems, with the ultimate goal of streamlining and standardising improvement processes

A family of Fe-N-C oxygen reduction electrocatalysts for microbial fuel cell (MFC) application: Relationships between surface chemistry and performances

© 2016 The Author(s) Different iron-based cathode catalysts have been studied for oxygen reduction reaction (ORR) in neutral media and then applied into microbial fuel cells (MFC). The catalysts have been synthesized using sacrificial support method (SSM) using eight different organic precursors named Niclosamide, Ricobendazole, Guanosine, Succinylsulfathiazole, Sulfacetamide, Quinine, Sulfadiazine and Pyrazinamide. Linear Sweep Voltammetry (LSV) curves were obtained for the catalysts using a O2 saturated in 0.1M potassium phosphate buffer and 0.1M KCl solution and a Rotating Ring Disk Electrode (RRDE) setup in order to study the ORR characteristics. Additionally, we analyze the peroxide yield obtained for each catalyst which helps us determine the reaction kinetics. Those catalysts have been mixed with activated carbon (AC), carbon black (CB) and PTFE and pressed on a metallic mesh forming a pellet-like gas diffusion electrode (GDE). Results showed that Fe-Ricobendazole, Fe-Niclosamide and Fe-Pyrazinamide had the highest cathode polarization curves and highest power densities output that was above 200μWcm−2. Fe-Ricobendazole, Fe-Niclosamide, Fe-Pyrazinamide, Fe-Guanosine Fe-Succinylsulfathiazole and Fe-Sulfacetamide outperformed compared to Pt cathode. Fe-Sulfadiazene and Fe-Quinine performed better than AC used as control but less than Pt. Correlation of surface composition with performance showed that power density achieved is directly related to the total amount of nitrogen, and in particularly, N coordinated to metal and pyridinic and pyrrolic types while larger amounts of graphitic nitrogen result in worse performance