The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme composed of two sepa- rately purifiable component proteins encoded by the structural genes nifH, nifD, and nifK. Deletion of the Azotobacter vine- landii nijS gene lowers the activities of both nitrogenase com- ponent proteins. Because both nitrogenase component proteins have metallocluster prosthetic groups that are composed of iron- and sulfur-containing cores, this result indicated that the nifS gene product could be involved in the mobilization of the iron or sulfur required for metallocluster formation. In the present work, it is shown that NIFS is a pyridoxal phosphate- containing homodimer that catalyzes the formation of L-alanine and elemental sulfur by using L-cysteine as substrate. NIFS activity is extremely sensitive to thiol-specific alkylating re- agents, which indicates the participation of a cysteinyl thiolate at the active site. Based on these results we propose that an enzyme-bound cysteinyl persulfide that requires the release of the sulfur from the substrate L-cysteine for its formation ultimately provides the inorganic sulfide required for nitroge- nase metallocluster formation. The recent discovery of nifS- like genes in non-nitrogen-fixing organisms also raises the possibility that the reaction catalyzed by NIFS represents a universal mechanism that involves pyridoxal phosphate chem- istry, in the mobilization of the sulfur required for metallo- cluster formation.

Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis (nitrogenase/FeS cores/pyridoxal phosphate/sulfur mobilization/cysteinyl persulfide)

Biofuel production: Challenges and opportunities

Geobacteracea are distinct for their ability to reduce insoluble oxidants including minerals and electrodes without apparent reliance on soluble extracellular electron transfer (ET) mediators. This property makes them important anode catalysts in new generation microbial fuel cells (MFCs) because it obviates the need to replenish ET mediators otherwise necessary to sustain power. Here we report cyclic voltammetry (CV) of biofilms of wild type (WT) and mutant G. sulfurreducens strains grown on graphite cloth anodes acting as electron acceptors with acetate as the electron donor. Our analysis indicates that WT biofilms contain a conductive network of bound ET mediators in which OmcZ (outer membrane c-type cytochrome Z) participates in homogeneous ET (through the biofilm bulk) while OmcB mediates heterogeneous ET (across the biofilm/electrode interface); that type IV pili are important in both reactions; that OmcS plays a secondary role in homogenous ET; that OmcE, important in Fe(III) oxide reduction, is not involved in either reaction; that catalytic current is limited overall by the rate of microbial uptake of acetate; that protons generated from acetate oxidation act as charge compensating ions in homogenous ET; and that homogenous ET, when accelerated by fast voltammetric scan rates, is limited by diffusion of protons within the biofilm. These results provide the first direct electrochemical evidence substantiating utilization of bound ET mediators by Geobacter biofilms and the distinct roles of OmcB and OmcZ in the extracellular ET properties of anode-reducing G. sulfurreducens.

sulfurreducens on fuel cell anodes indicates possible roles of OmcB, OmcZ, type IV pili, and protons in extracellular electron transfer†

Production of biohydrogen has the potential to be a renewable alternative to current technologies. There are varieties of technologies for biological hydrogen production mechanisms including biophotolysis, photo fermentation, dark fermentation and hybrid biohydrogen production by electrochemical processes. In these studies, a review on the recent developments of biohydrogen production is presented. First, the theoretical principles of biophotolysis by cyanobacteria and green micro algae, as well as direct and indirect of biophotolysis process on hydrogen production are described. Secondly, practical aspects and fundamental of biological hydrogen production processes by photo and dark fermentation are reviewed. This work also involved comparison of the maximum H2 yield, bacterial strains, operating condition, suitable substrates, and mathematical models for fermentative hydrogen production. A new hybrid biological hydrogen production processes by using the electrochemical process is then proposed. This study can also be used to improve the basic and current knowledge about the performance of the biophotolysis, fermentative and electrochemical process in producing hydrogen gas as the alternate fuel.

Development of biohydrogen production by photobiological, fermentation and electrochemical processes: A review

Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane. Long-term performance data, in conjunction with the 13C- and 57Fe-labelling batch experiments, demonstrated that AOM was coupled to Fe(III) reduction to Fe(II) in this bioreactor. Metagenomic analysis showed that this archaeon belongs to a novel genus within family Candidatus Methanoperedenaceae, and possesses genes encoding the “reverse methanogenesis” pathway, as well as multi-heme c-type cytochromes which are hypothesised to facilitate dissimilatory Fe(III) reduction. Metatranscriptomic analysis revealed upregulation of these genes, supporting that this archaeon can independently mediate AOM using Fe(III) as the terminal electron acceptor. We propose the name Candidatus “Methanoperedens ferrireducens” for this microorganism. The potential role of “M. ferrireducens” in linking the carbon and iron cycles in environments rich in methane and iron should be investigated in future research.

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A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

Achieving high-level nitrogen removal in mainstream by coupling anammox with denitrifying anaerobic methane oxidation in a membrane biofilm reactor.

Enhanced lipid accumulation of green microalga Scenedesmus sp. by metal ions and EDTA addition

Partial nitritation and Anammox processes are increasingly used for nitrogen removal from anaerobic sludge digestion liquor. However, their nitrogen removal efficiency is often limited due to the production of nitrate by the Anammox reaction and the sensitivity to the nitrite to ammonium ratio. This work develops and demonstrates an innovative process that achieves complete nitrogen removal from partially nitrified anaerobic sludge digestion liquor through the use of a membrane biofilm reactor (MBfR), with methane supplied through hollow fiber membranes. When steady state with a hydraulic retention time (HRT) of 1 day was reached, the process achieved complete nitrite and ammonium removal at rates of 560 mg N/L/d and 470 mg N/L/d, respectively, without any nitrate accumulation. The process is relatively insensitive to the nitrite to ammonium ratio, achieving complete nitrogen removal when their ratio in influent varied in the range of 1.125–1.32. Pyrosequencing and fluorescence in situ hybridization analy...

Complete Nitrogen Removal from Synthetic Anaerobic Sludge Digestion Liquor through Integrating Anammox and Denitrifying Anaerobic Methane Oxidation in a Membrane Biofilm Reactor

Guo-Jun Xie

Papers

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

Achieving high-level nitrogen removal in mainstream by coupling anammox with denitrifying anaerobic methane oxidation in a membrane biofilm reactor.

Enhanced lipid accumulation of green microalga Scenedesmus sp. by metal ions and EDTA addition

Complete Nitrogen Removal from Synthetic Anaerobic Sludge Digestion Liquor through Integrating Anammox and Denitrifying Anaerobic Methane Oxidation in a Membrane Biofilm Reactor

Hydrogen production from glucose by co-culture of Clostridium Butyricum and immobilized Rhodopseudomonas faecalis RLD-53