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)

Advances in direct interspecies electron transfer and conductive materials: Electron flux, organic degradation and microbial interaction.

Sparking Anaerobic Digestion: Promoting Direct Interspecies Electron Transfer to Enhance Methane Production

Improving anaerobic digestion via direct interspecies electron transfer requires development of suitable characterization methods.

Remediation of nitrate contamination by membrane hydrogenotrophic denitrifying biofilm integrated in microbial electrolysis cell.

Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors.

A stand-alone down-flow hanging sponge (DHS) system with a two-stage configuration was operated for 700 days to treat synthetic soft drink wastewater at 3000 mg/L chemical oxygen demand (COD). Throughout the operation, >90% COD and total organic carbon (TOC) removal efficiency was obtained by the first stage, and a final effluent of COD 80% than that at <50%. Specifically, operational taxonomic units closely related to Tolumonas auensis and Rivicola pingtungensis were identified as important populations that were responsible for degrading the major substrate in the soft drink wastewater toward to the end of the reactor operation. In addition, high abundance of Bacteroidetes in the reactor was speculated to be responsible for the VFA accumulation in the effluent. This study demonstrated that stand-alone DHS reactor could be used in treating high-strength wastewater efficiently.

Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics

Method for treating effluent waste from a cation-exchange column regeneration cycle, including backwashing the column; regenerating the column using rinse water and a regenerant brine having a temperature warmer than room temperature, thereby forming a waste effluent containing divalent cations; precipitating the divalent cations in a precipitation reactor at a temperature warmer than room temperature; filtering the precipitation effluent; optionally, adjusting the filtered precipitation effluent pH; concentrating the filtered precipitation effluent via membrane-based water recovery, thereby forming separated concentrated salt and pure rinse water; and recirculating the separated concentrated salt and pure rinse water back to the column for a subsequent regeneration cycle. Also, a system including an exhausted cation-exchange column; a chemical precipitation reactor; a filtration unit; an optional pH adjustment unit; and a membrane-based water recovery unit, wherein the system is a closed-loop through which salt and rinse water having a temperature warmer than room temperature recirculate.

Jimmy Yu

Papers

Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors.

Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics

Ion Exchange Regeneration Process Utilizing Membrane Distillation