A5091444590- Microbial Metabolic Engineering and Bioproduction
- Microbial Community Ecology and Physiology
- Chromium effects and bioremediation
- Biofuel production and bioconversion
- Microbial bioremediation and biosurfactants
- Wastewater Treatment and Nitrogen Removal
- Genomics and Phylogenetic Studies
- Groundwater flow and contamination studies
- Microbial Fuel Cells and Bioremediation
- Enzyme Catalysis and Immobilization
- Groundwater and Isotope Geochemistry
- Radioactive element chemistry and processing
- Metal Extraction and Bioleaching
- Hydrology and Watershed Management Studies
- Hydrocarbon exploration and reservoir analysis
- Environmental DNA in Biodiversity Studies
- Methane Hydrates and Related Phenomena
- Mine drainage and remediation techniques
- Environmental remediation with nanomaterials
- Enzyme Structure and Function
- Catalysis for Biomass Conversion
- Metabolomics and Mass Spectrometry Studies
- Anaerobic Digestion and Biogas Production
- Toxic Organic Pollutants Impact
- Atmospheric and Environmental Gas Dynamics
Lawrence Berkeley National Laboratory
2013-2024
University of Toronto
2005-2024
Joint BioEnergy Institute
2009-2019
Earth Island Institute
2016
Emery Oleochemicals (Malaysia)
2015
Lawrence Livermore National Laboratory
2000-2008
University of California, Davis
2008
Bellevue Hospital Center
1988-2005
University of Iowa
2002
Oregon State University
1985-2002
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled...
The capacity of some bacteria to metabolize hydrocarbons in the absence molecular oxygen was first recognized only about ten years ago. Since then, number hydrocarbon compounds shown be catabolized anaerobically by pure bacterial cultures has been steadily increasing. This review summarises current knowledge isolates capable anaerobic mineralization hydrocarbons, and biochemistry biology enzymes involved catabolic pathways these substrates. Several alkylbenzenes, alkanes or alkenes are...
ABSTRACT The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis 2,909,809-bp will facilitate our molecular and biochemical understanding unusual metabolic repertoire this bacterium, including its ability couple denitrification sulfur-compound oxidation, catalyze anaerobic, nitrate-dependent oxidation Fe(II) U(IV), oxidize mineral electron donors....
Core Ideas Development of a 300‐km 2 mountainous headwater testbed began in 2016 the East River. The can be used to explore how watershed changes impact downgradient water availability and quality. System‐of‐system, scale‐adaptive approaches potentially improve dynamics simulation. We have new monitor simulate partitioning system responses. River has been developed as “community” testbed. Extreme weather, fires, land use climate change are significantly reshaping interactions within...
We have developed a real-time polymerase chain reaction (PCR) method that can quantify hydrocarbon-degrading bacteria in sediment samples based on catabolic gene associated with the first step of anaerobic toluene and xylene degradation. The target gene, bssA, codes for α-subunit benzylsuccinate synthase. primer−probe set PCR was consensus regions bssA from four denitrifying bacterial strains; sequences two these strains were determined during this study. proved to be sensitive (detection...
A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% converted biomass nonvolatile metabolic by-products, primarily former. observed stoichiometric ratio moles sulfate consumed per mole consistent theoretical for coupled reduction hydrogen sulfide....
Anaerobic assays conducted with strain T, a denitrifying bacterium capable of mineralizing toluene to carbon dioxide, demonstrated that toluene-grown, permeabilized cells catalyzed the addition fumarate form benzylsuccinate. This reaction was not dependent on presence coenzyme A (CoA) or ATP. In CoA, formation E-phenylitaconate from benzylsuccinate also observed. Kinetic studies specific rate and in >30% consumption whole-cell suspensions nitrate; this observation suggests may be first...
Ralstonia eutropha is a facultatively chemolithoautotrophic bacterium able to grow with organic substrates or H2 and CO2 under aerobic conditions. Under conditions of nutrient imbalance, R. produces copious amounts poly[(R)-3-hydroxybutyrate] (PHB). Its ability utilize as sole carbon source renders it an interesting new candidate host for the production renewable liquid transportation fuels. We engineered fatty acid-derived, diesel-range methyl ketones. Modifications in included...
ABSTRACT We have engineered Escherichia coli to overproduce saturated and monounsaturated aliphatic methyl ketones in the C 11 15 (diesel) range; this group of includes 2-undecanone 2-tridecanone, which are importance flavor fragrance industry also favorable cetane numbers (as we report here). describe specific improvements that resulted a 700-fold enhancement ketone titer relative fatty acid-overproducing E. strain, including following: (i) overproduction β-ketoacyl coenzyme A (CoA)...
ABSTRACT Aliphatic hydrocarbons are highly appealing targets for advanced cellulosic biofuels, as they already predominant components of petroleum-based gasoline and diesel fuels. We have studied alkene biosynthesis in Micrococcus luteus ATCC 4698, a close relative Sarcina lutea (now Kocuria rhizophila ), which 4 decades ago was reported to biosynthesize iso - anteiso -branched, long-chain alkenes. The underlying biochemistry genetics were not elucidated those studies. show here that...
Abstract Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment perennially suboxic aquifer Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive diverse chemolithoautotrophic bacterial activity relevant C, S, N Fe cycling. Before injection, anaerobic ammonia-oxidizing (anammox) bacteria...
The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work been done develop genetic part libraries enable such endeavors. We report the development of a toolbox metabolic engineering H16. have constructed set broad-host-range plasmids bearing variety origins replication, promoters, 5' mRNA...
The Design–Build–Test–Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts biofuels biobased products. Here, we report on implementation of two DBTL cycles optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. first cycle employed simple strategy...
Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published newly generated data, is used to better understand the interplay of hydrology, geochemistry, biology controlling cycling carbon, nitrogen, oxygen, iron, sulfur, uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved...
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families ∼2.3 million genome contigs. find that small genomes are approximately 3-fold more prevalent than host prokaryotic Our enriches for translated microbiomes, suggesting the identified coding. More 9,000 encode potentially secreted or transmembrane proteins, 5,000 predicted anti-CRISPR and 500 antimicrobial proteins. By...
Toluene degradation occurred concomitantly with sulfate reduction in anaerobic microcosms inoculated contaminated subsurface soil from an aviation fuel storage facility near the Patuxent River (Md.). Similar results were obtained for enrichment cultures which toluene was sole carbon source. Several lines of evidence suggest that directly coupled to and cultures: (i) two processes synchronous highly correlated, (ii) observed stoichiometric ratios moles consumed per mole consistent theoretical...
ABSTRACT Under anaerobic conditions and at circumneutral pH, cells of the widely distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: oxidation required presence nitrate was strongly correlated with consumption. This is first report by an autotrophic bacterium.
The mechanism for anaerobic metabolism of benzene remains unknown. To date, there have been only a few studies reporting metabolites biodegradation, in part because benzene-degrading enrichment cultures are not very common and two isolates characterized to date. Phenol benzoate, consistent with hydroxylation or carboxylation, identified previously mixed cultures, more recently methylation toluene has proposed as another possible degradation. In this study, 13C6-benzene was added...
Hexavalent chromium, Cr(VI), is a widespread and toxic groundwater contaminant. Reductive immobilization to Cr(III) treatment option, but its success depends on the long-term potential for reduced chromium precipitates remain immobilized under oxidizing conditions. In this unique study, aquifer sediments subjected reductive Cr(VI) different biogeochemical regimes were tested their susceptibility reoxidation. After 1 year, exposed oxygenated conditions another 2 years in flow-through,...
Tropical forests absorb large amounts of atmospheric CO2 through photosynthesis but elevated temperatures suppress this absorption and promote monoterpene emissions. Using 13 labeling, here we show that emissions from tropical leaves derive recent demonstrate distinct temperature optima for five groups (Groups 1-5), potentially corresponding to different enzymatic temperature-dependent reaction mechanisms within β-ocimene synthases. As diurnal seasonal leaf increased during the Amazonian...
ABSTRACT The initial enzymatic steps in anaerobic m -xylene oxidation were studied Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing via 3-methylbenzoate. Permeabilized cells -xylene-grown T catalyzed the addition to fumarate form (3-methylbenzyl)succinate. In presence succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized E -(3-methylphenyl)itaconate (or closely related isomer) Kinetic studies conducted with permeabilized whole-cell suspensions...
Permeabilized cells of toluene-mineralizing, sulfate-reducing strain PRTOL1 catalyzed the addition toluene to fumarate form benzylsuccinate under anaerobic conditions. Recent in vitro studies with two denitrifying bacteria demonstrated same reaction and indicated that it may be first step degradation. This study shows activation by occurs as disparate species (members delta beta subclasses Proteobacteria, respectively).
ABSTRACT Recent studies of anaerobic toluene catabolism have demonstrated a novel reaction for hydrocarbon activation: the addition methyl carbon to fumarate form benzylsuccinate. In vitro benzylsuccinate synthase indicate that H atom abstracted from group during is retained in succinyl moiety Based on structural formed anaerobic, assays with denitrifying, toluene-mineralizing strain T, we now report following characteristics reaction: (i) it highly stereospecific, resulting >95%...