A5024579365- Microbial Community Ecology and Physiology
- Wastewater Treatment and Nitrogen Removal
- Microbial Fuel Cells and Bioremediation
- Microbial Metabolic Engineering and Bioproduction
- Evolution and Genetic Dynamics
- Biofuel production and bioconversion
- Anaerobic Digestion and Biogas Production
- Evolutionary Game Theory and Cooperation
- Marine and coastal ecosystems
- Ammonia Synthesis and Nitrogen Reduction
- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- Electrochemical sensors and biosensors
- Bacterial biofilms and quorum sensing
- Chromium effects and bioremediation
- Algal biology and biofuel production
- Environmental DNA in Biodiversity Studies
- Antibiotic Resistance in Bacteria
- Plant Pathogens and Fungal Diseases
- Plant and fungal interactions
- Microbial Natural Products and Biosynthesis
- Fungal Biology and Applications
- Marine Biology and Ecology Research
- thermodynamics and calorimetric analyses
- Mathematical and Theoretical Epidemiology and Ecology Models
University of Washington
2018-2024
Institute for Systems Biology
2024
InSysBio (Russia)
2024
Montana State University
2011-2021
University of Minnesota
2010
Biotechnology Institute
2010
Cellular metabolism is a series of tightly linked oxidations and reductions that must be balanced. Recycling intracellular electron carriers during fermentation often requires substrate conversion to undesired products, while respiration demands constant addition acceptors. The use electrode-based acceptors balance biotransformations may overcome these constraints. To test this hypothesis, the metal-reducing bacterium Shewanella oneidensis was engineered stoichiometrically convert glycerol...
Ammonia oxidation to nitrite and its subsequent nitrate provides energy the two populations of nitrifying chemoautotrophs in energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools production new organic carbon (C) ocean. However, relationship flux C fluxes N steps remains unclear. Here, we show that, despite orders-of-magnitude difference cell abundances ammonia oxidizers oxidizers, sustain similar bulk N-oxidation rates throughout deep waters with...
ABSTRACT It is well established that respiratory organisms use proton motive force to produce ATP via F-type synthase aerobically and this process may reverse during anaerobiosis force. Here, we show Shewanella oneidensis strain MR-1, a nonfermentative, facultative anaerobe known respire exogenous electron acceptors, generates primarily from substrate-level phosphorylation under anaerobic conditions. Mutant strains lacking ackA (SO2915) pta (SO2916), genes required for acetate production...
Abstract Motivation: Elementary flux mode analysis (EFMA) decomposes complex metabolic network models into tractable biochemical pathways, which have been used for rational design and of regulatory networks. However, application EFMA has often limited to targeted or simplified representations due computational demands the method. Results: Division biological networks subnetworks enables complete enumeration elementary modes (EFMs) a broad range complexities, including genome-scale. Here, are...
A polyolefinic hydrocarbon was found in nonpolar extracts of Shewanella oneidensis MR-1 and identified as 3,6,9,12,15,19,22,25,28-hentriacontanonaene (compound I) by mass spectrometry, chemical modification, nuclear magnetic resonance spectroscopy. Compound I shown to be the product a head-to-head fatty acid condensation biosynthetic pathway dependent on genes denoted ole (for olefin biosynthesis). Four were present S. MR-1. Deletion entire oleABCD gene cluster led complete absence...
Computational representations of metabolism are increasingly common in medical, environmental, and bioprocess applications. Cellular growth is often an important output computational biology analyses, therefore, accurate measurement biomass constituents critical for relevant model predictions. There a distinct lack detailed macromolecular protocols, including comparisons to alternative assays methodologies, as well tools convert the experimental data into biochemical reactions Herein...
Abstract Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize classic diauxie phenotype, nor it follow common systems biology assumptions including preferential consumption of glucose with an ‘overflow’ metabolism. Despite these contradictions, P. competitive disparate environments underscoring knowledge gaps...
Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt changing environments. Here, we constructed quad-culture consisting of cellulolytic bacterium (Ruminiclostridium cellulolyticum), hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic (Methanosaeta concilii), sulfate-reducing (Desulfovibrio vulgaris). The four the cooperated via cross-feeding produce methane using cellulose as only carbon source electron donor....
Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated two general configurations; one-stage combine aerobic (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to (DNRA) compete for carbon nitrite can impact reactor performance because DNRA retains...
Abstract Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums monoculture properties, including >200% increase in cellobiose catabolism, >100% glycerol >800% ethanol production, and >120% biomass productivity. The consortium was to have primary secondary-resource specialist used crossfeeding with positive feedback mechanism, division labor, nutrient energy transfer via necromass catabolism. resource Clostridium...
Abstract Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is only identified Archaeal that can utilize acetate via kinase (Ack) phosphotransacetylase (Pta). Despite importance of ack as potential urkinase in ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for Bacteria , or Eukarya . Here we demonstrate ADP-Acs contain paralogous ATPase motifs previously Ack, which a novel relation between...
Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early improve cooperativity manifesting synergistic epistasis between genomes mutually species. Specifically, we have evolutionary trajectories syntrophic interactions Desulfovibrio vulgaris (Dv) with Methanococcus...
Summary Assimilatory and dissimilatory utilisation of autotroph biomass by heterotrophs is a fundamental mechanism for the transfer nutrients energy across trophic levels. Metagenome data from tractable, thermoacidophilic microbial community in Yellowstone National Park was used to build an silico model study heterotrophic using elementary flux mode analysis balance analysis. investigated 29 forms biomass‐derived dissolved organic carbon (DOC) including individual monomer pools,...
The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis oxide flux from observation wells proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape surface. To better understand controls emission at this site, we used combination isotopic, geochemical, molecular analyses show that chemodenitrification bacterial...
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at Oak Ridge Reservation (ORR). Previous studies examining microbial community composition removal ORR during biostimulation efforts reported increased abundances members genus concurrent with denitrification rates. Thus, we asked how genomic abiotic factors control biogeography site to understand these may influence transformation in an...
Abstract Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, soil may be exposed to oxygen (O 2 ) during droughts, or sulfate (SO 4 2- as a result of sea level rise. How these stressors – separately and together microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, stoichiometric modeling characterize elevated SO O levels on methane (CH dioxide (CO...
Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2–4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple communities are well-characterized geochemically. Consequently, these excellent model systems for studying the metabolic activity individual populations key interactions. The primary goals current study were integrate data collected...
Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is with high levels of nitric acid and multiple heavy metals. Amplicon sequencing 16S rRNA genes (V4 region) in sediment this area revealed an amplicon sequence variant (ASV) 100% identity to CPTF sequence. Notably, CPTF-matching ASV had highest relative abundance community survey, a median 3.77% comprised 20%-40% reads some samples. Pangenomic analysis...
Abstract Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between using microcalorimetry thermodynamic modeling. The constants derived from system were comparable those that have been reported meta‐analyses data chemostat studies. model accurately predicted temperature‐dependent biomass yield upper temperature limit Desulfovibrio...