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)

Heterogeneous catalysis involves solid-state catalysts, among which metal nanoparticles occupy an important position. Unfortunately, no two nanoparticles from conventional synthesis are the same at the atomic level, though such regular nanoparticles can be highly uniform at the nanometer level (e.g., size distribution ∼5%). In the long pursuit of well-defined nanocatalysts, a recent success is the synthesis of atomically precise metal nanoclusters protected by ligands in the size range from tens to hundreds of metal atoms (equivalently 1-3 nm in core diameter). More importantly, such nanoclusters have been crystallographically characterized, just like the protein structures in enzyme catalysis. Such atomically precise metal nanoclusters merge the features of well-defined homogeneous catalysts (e.g., ligand-protected metal centers) and enzymes (e.g., protein-encapsulated metal clusters of a few atoms bridged by ligands). The well-defined nanoclusters with their total structures available constitute a new class of model catalysts and hold great promise in fundamental catalysis research, including the atomically precise size dependent activity, control of catalytic selectivity by metal structure and surface ligands, structure-property relationships at the atomic-level, insights into molecular activation and catalytic mechanisms, and the identification of active sites on nanocatalysts. This Review summarizes the progress in the utilization of atomically precise metal nanoclusters for catalysis. These nanocluster-based model catalysts have enabled heterogeneous catalysis research at the single-atom and single-electron levels. Future efforts are expected to achieve more exciting progress in fundamental understanding of the catalytic mechanisms, the tailoring of active sites at the atomic level, and the design of new catalysts with high selectivity and activity under mild conditions.

Toward Active-Site Tailoring in Heterogeneous Catalysis by Atomically Precise Metal Nanoclusters with Crystallographic Structures.

Trichloroethylene (TCE) was metabolized by the natural microflora of three different environmental water samples when stimulated by the addition of either toluene or phenol. Two different strains of Pseudomonas putida that degrade toluene by a pathway containing a toluene dioxygenase also metabolized TCE. A mutant of one of these strains lacking an active toluene dioxygenase could not degrade TCE, but spontaneous revertants for toluene degradation also regained TCE-degradative ability. The results implicate toluene dioxygenase in TCE metabolism.

Trichloroethylene metabolism by microorganisms that degrade aromatic compounds. [Pseudomonas putida]

Enhanced photocatalytic degradation of methyl orange by porous graphene/ZnO nanocomposite.

In situ preparation of p-n BiOI@Bi5O7I heterojunction for enhanced PFOA photocatalytic degradation under simulated solar light irradiation

Supported gold clusters as effective and reusable photocatalysts for the abatement of endocrine-disrupting chemicals under visible light

Photodegradation of fluorotelomer carboxylic 5:3 acid and perfluorooctanoic acid using zinc oxide.

While bioremediation technologies for trichloroethene (TCE), a suspected carcinogen, have been successfully demonstrated in neutral pH aquifers, these technologies are often ineffective for remediating TCE contamination in acidic aquifers (i.e., pH < 5.5). Acidophilic methanotrophs have been detected in several low pH environments, but their presence and potential role in TCE degradation in acidic aquifers is unknown. This study applied a stable isotope probing-based technique to identify active methanotrophs that are capable of degrading TCE in microcosms prepared from two low pH aquifers. A total of thirty-five clones of methanotrophs were derived from low pH microcosms in which methane and TCE degradation had been observed, with 29 clustered in γ-Proteobacteria and 6 clustered in α-Proteobacteria. None of the clones has a high similarity to known acidophilic methanotrophs from other environments. The presence and diversity of particulate MMO and soluble MMO were also investigated. The pmoA gene was detected predominantly at one site, and the presence of a specific form of mmoX in numerous samples suggested that Methylocella spp. may be common in acidic aquifers. Finally, a methane-grown culture at pH 4 was enriched from an acidic aquifer and its ability to biodegrade various chlorinated ethenes was tested. Interestingly, the mixed culture rapidly degraded TCE and vinyl chloride, but not cis-dichloroethene after growth on methane. The data suggest that aerobic biodegradation of TCE and other chlorinated solvents in low pH groundwater may be facilitated by methanotrophic bacteria, and that there are potentially a wide variety of different strains that inhabit acidic aquifers.

Evaluation of methanotrophic bacterial communities capable of biodegrading trichloroethene (TCE) in acidic aquifers

Poly(3-hydroxybutyrate) (PHB)-a renewable and biodegradable polymer-is a promising alternative to nonbiodegradable synthetic plastics that are derived from petrochemicals. The methods currently employed for PHB production are costly, in part, due to the expensive cultivation feedstocks and the need to sterilize the culture medium, which is energy-intensive. This study investigates the feasibility of nonsterile PHB production from several saline organic wastes using a salt-tolerant strain, Zobellella denitrificans ZD1 (referred to as strain ZD1). Factors such as the pH, salinity, carbon/nitrogen (C/N) ratio, nitrogen source, and electron acceptor that might affect the growth of strain ZD1 and its PHB production were determined. Our results showed successful nonsterile PHB production by growing the strain ZD1 on nonsterile synthetic crude glycerol, high-strength saline wastewater, and real municipal wastewater-activated sludge under saline conditions. The PHB production was significantly enhanced when the levels of salts and nitrate-nitrogen in the culture medium were increased. This study suggested a promising low-cost nonsterile PHB production strategy from organic wastes using strain ZD1.

From Organic Wastes to Bioplastics: Feasibility of Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella denitrificans ZD1

We have developed a 3D dry lift-off process to localize multiple types of nitrifying bacteria in polyethylene glycol diacrylate (PEGDA) cubes for enhanced nitrification, a two-step biological process that converts ammonium to nitrite and then to nitrate. Ammonia-oxidizing bacteria (AOB) is responsible for converting ammonia into nitrite, and nitrite-oxidizing bacteria (NOB) is responsible for converting nitrite to nitrate. Successful nitrification is often challenging to accomplish, in part because AOB and NOB are slow growers and highly susceptible to many organic and inorganic chemicals in wastewater. Most importantly, the transportation of chemicals among scattered bacteria is extremely inefficient and can be problematic. For example, nitrite, produced from ammonia oxidation, is toxic to AOB and can lead to the failure of nitrification. To address these challenges, we closely localize AOB and NOB in PEGDA cubes as microenvironment modules to promote synergetic interactions. The AOB is first localized in the vicinity of the surface of the PEGDA cubes that enable AOB to efficiently uptake ammonia from a liquid medium and convert it into nitrite. The produced nitrite is then efficiently transported to the NOB localized at the center of the PEGDA particle and converted into non-toxic nitrate. Additionally, the nanoscale PEGDA fibrous structures offer a protective environment for these strains, defending them from sudden toxic chemical shocks and immobilize in cubes. This engineered microenvironment cube significantly enhances nitrification and improves the overall ammonia removal rate per single AOB cell. This approach—encapsulation of multiple strains at close range in cube in order to control their interactions—not only offers a new strategy for enhancing nitrification, but also can be adapted to improve the production of fermentation products and biofuel, because microbial processes require synergetic reactions among multiple species.

/pdf/fabrication-of-bacteria-environment-cubes-with-dry-lift-off-bnfk2z2pqz.pdf

Yiru Shao

Papers

Supported gold clusters as effective and reusable photocatalysts for the abatement of endocrine-disrupting chemicals under visible light

Photodegradation of fluorotelomer carboxylic 5:3 acid and perfluorooctanoic acid using zinc oxide.

Evaluation of methanotrophic bacterial communities capable of biodegrading trichloroethene (TCE) in acidic aquifers

From Organic Wastes to Bioplastics: Feasibility of Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella denitrificans ZD1

Fabrication of Bacteria Environment Cubes with Dry Lift-Off Fabrication Process for Enhanced Nitrification