Steven Singer

Culturing compost-derived microbial communities on biofuel feedstocks under industrial conditions is a technique to enrich for organisms and lignocellulolytic enzymes for bioenergy feedstock deconstruction. In this study, microbial communities from green waste compost (GWC) and grape pomace compost (GPC) were cultured on switchgrass and eucalyptus to observe the impact of inoculation on feedstock decomposition and microbial community structure. Respiration was monitored as a measure of microbial activity, and 16S ribosomal RNA gene sequencing was used to characterize microbial community structure. The enriched community structure and respiration were influenced by the choice of feedstock, compost type, and application of thermophilic, high-solids conditions. However, the effect of compost source was significantly less than the effects of the other culture variables. Although there are subtle differences in potentially lignocellulolytic taxa between GPC- and GWC-derived communities, ...

Microorganisms from extreme environments are often very difficult to cultivate, precluding detailed study by biochemical and physiological techniques. Recent advances in genomic sequencing and proteomic measurements of samples obtained from natural communities have allowed new access to these uncultivated extremophiles and identified abundant proteins that can be isolated directly from natural samples. Here we report the isolation of two abundant heme proteins from low-diversity biofilm microbial communities that thrive in very acidic (pH ~ 1), metal-rich water in a subsurface mine. Purification and detailed characterization of these proteins has afforded new insight into the possible mechanism of Fe(II) oxidation by Leptospirillum Group II, the dominant population in most of these biofilms, and demonstrated that the abundance and posttranslational modifications of one of these proteins is dependent on the lifecycle of the biofilm.

Upon exposure to CO during anaerobic growth, the purple phototrophic bacterium Rhodospirillum rubrum expresses a CO-oxidizing H(2) evolving enzymatic system. The CO-oxidizing enzyme, carbon monoxide dehydrogenase (CODH), has been purified and extensively characterized. However the electron transfer pathway from CODH to the CO-induced hydrogenase that evolves H(2) is not well understood. CooF is an Fe-S protein that is the proposed mediator of electron transfer between CODH and the CO-induced hydrogenase. Here we present the spectroscopic and biochemical properties of the CODH:CooF complex. The characteristic EPR signals observed for CODH are largely insensitive to CooF complexation. Metal analysis and EPR spectroscopy show that CooF contains 2 Fe(4)S(4) clusters. The observation of 2 Fe(4)S(4) clusters for CooF contradicts the prediction of 4 Fe(4)S(4) clusters based on analysis of the amino acid sequence of CooF and structural studies of CooF homologs. Comparison of in vivo and in ...

Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Mediu...

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. ...

The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.

The ruthenium hydride of (Ar(4)CpOH)Ru(CO)(2)H exchanges cleanly and rapidly with D(2) at room temperature to generate the ruthenium deuteride. A chain mechanism is proposed to explain the much more rapid exchange of RuH/D(2) than RuCO exchange with (13)CO.

ABSTRACT Addition of excess HCO2H to {2,5-Ph2-3,4-Tol2(η5-C4CO)]Ru(CO)2}2 (6) at -20°C led to the formation of [2,5-Ph2-3,4-Tol2(η5-C4COH)]Ru(CO)2(η1-OCHO) (5), a proposed intermediate in catalytic transfer hydrogenations developed by Shvo. Hydroxycyclopentadienyl formate 5 undergoes rapid reversible dissociation of HCO2H at –20°C, and undergoes decarboxylation at 1°C to form a 1:10 mixture of {[2,5-Ph2-3,4-Tol2(η5-C4CO)]2H}Ru2(CO)4(µ-H) (3):[2,5-Ph2-3,4-Tol2(η5-C4COH)Ru(CO)2H] (4). 5 does not reduce PhCHO below the temperature at which 5 is converted to hydride 4. The catalytic production of benzyl alcohol from 5 and PhCHO in the presence of excess HCO2H is not accelerated by higher concentrations of PhCHO, indicating that 5 does not directly reduce PhCHO. Formate complex 5 is the precursor of hydride 4 which transfers hydrogen to PhCHO. A crucial role for the CpOH proton in the decarboxylation of 5 was indicated by the much slower decarboxylation of the methoxycyclopentadienyl analog [2,5-Ph2-3,4-Tol2(η5-C4COCH3)]Ru(CO)2(η1-OCHO) (7). A mechanism for decarboxylation of 5 is proposed which involves reversible dissociation of formic acid to form the unsaturated dienone dicarbonyl ruthenium intermediate C, followed by simultaneous transfer of hydride to ruthenium from the formic acid carbon and of proton to the carbonyl of C from the formic acid OH group.Key words: Shvo catalyst, ruthenium formate, decarboxylation.

The use of ionic liquids (ILs) to disrupt the recalcitrant structure of lignocellulose and make polysaccharides accessible to hydrolytic enzymes is an emerging technology for biomass pretreatment in lignocellulosic biofuel production. Despite efforts to reclaim and recycle IL from pretreated biomass, residual IL can be inhibitory to microorganisms used for downstream fermentation. As a result, pathways for IL tolerance are needed to improve the activity of fermentative organisms in the presence of IL. In this study, microbial communities from compost were cultured under high-solids and thermophilic conditions in the presence of 1-ethyl-3-methylimidazolium-based ILs to enrich for IL-tolerant microorganisms. A strain of Bacillus coagulans isolated from an IL-tolerant community was grown in liquid and solid-state culture in the presence of the ILs 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) or 1-ethyl-3-methylimidazolium chloride ([C2mim][Cl]) to gauge IL tolerance. Viability and respiration varied with the concentration of IL applied and the type of IL used. B. coagulans maintained growth and respiration in the presence of 4 wt% IL, a concentration similar to that present on IL-pretreated biomass. In the presence of both [C2mim][OAc] and [C2mim][Cl] in liquid culture, B. coagulans grew at a rate approximately half that observed in the absence of IL. However, in solid-state culture, the bacteria were significantly more tolerant to [C2mim][Cl] compared with [C2mim][OAc]. B. coagulans tolerance to IL under industrially relevant conditions makes it a promising bacterium for understanding mechanisms of IL tolerance and discovering IL tolerance pathways for use in other microorganisms, particularly those used in bioconversion of IL-pretreated plant biomass.

ABSTRACT We are developing an integrated Microbial-ElectroCatalytic (MEC) ­system consisting of Ralstonia eutropha as a chemolithoautotrophic host for metabolic engineering coupled to a small-molecule electrocatalyst for the production of biofuels from CO2 and H2. R. eutropha is an aerobic bacterium that grows with CO2 as the carbon source and H2 as electron donor while producing copious amounts of polyhydroxybutyrate. Metabolic flux from existing R. eutropha pathways is being diverted into engineered pathways that produce biofuels. Novel molybdenum electrocatalysts that can convert water to hydrogen in neutral aqueous media will act as chemical mediators to generate H2 from electrodes in the presence of engineered strains of R. eutropha. To increase the local concentration of H2, we are engineering R. eutropha’s outer-membrane proteins to tether the electrocatalysts to the bacterial surface. The integrated MEC system will provide a transformational new source of renewable liquid transportation fuels that extends beyond biomass-derived substrates.

The characterization of natural microbial communities at a systems biology level can be addressed in significant detail with a technology platform based on high performance mass spectrometry interfaced closely with computational approaches for mining the raw MS data, compiling protein results, and finally integrating with physiological and genomic information. To this end, we have focused on a model environmental microbial

Ionic liquids (ILs) are emerging as superior solvents for numerous industrial applications, including the pretreatment of biomass for the microbial production of biofuels. However, some of the most effective ILs used to solubilize cellulose inhibit microbial growth, decreasing efficiency in the overall process. Here we identify an IL-resistance mechanism consisting of two adjacent genes from Enterobacter lignolyticus, a rain forest soil bacterium that is tolerant to an imidazolium-based IL. These genes retain their full functionality when transferred to an Escherichia coli biofuel host, with IL resistance established by an inner membrane transporter, regulated by an IL-inducible repressor. Expression of the transporter is dynamically adjusted in direct response to IL, enabling growth and biofuel production at levels of IL that are toxic to native strains. This natural auto-regulatory system provides the basis for engineering IL-tolerant microbes, which should accelerate progress tow...

NanoSIMS is a powerful analytical technique for investigating element distributions at the nanometer scale, but quantifying elemental abundances requires appropriate standards, which are not readily available for biological materials. Standards for trace element analyses have been extensively developed for secondary ion mass spectrometry (SIMS) in the semiconductor industry and in the geological sciences. The three primary approaches for generating standards

Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of varying compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX- and IL-pretreatment enhanced the deconstruction of the SG biomass by approximately 2-fold. 2D-NMR experiments and acetyl bromide-reactive lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during mi...