No description available.

No description available.

No description available.

No description available.

No description available.

Vicibactin is a small, high-affinity iron chelator produced by Rhizobium leguminosarum ATCC 14479. Previous work has shown that vicibactin is produced and secreted from the cell to sequester ferric iron from the environment during iron-deplete conditions. This ferric iron is then transported into the cell to be converted into ferrous iron. This study uses UV-Vis spectroscopy as well as ion trap-time of flight mass spectroscopy to determine that vicibactin does form a complex with copper(II) ions, however, at a much lower affinity than for iron(III). Stability tests have shown that the copper(II)-vicibactin complex is stable over time. The results of this study show that vicibactin could be used in order to remove copper(II) ions from the soil or other media if they are present in toxic amounts. It also suggests that vicibactin’s purpose for the rhizobia could be expanded to include both copper sequestering and to reduce extracellular copper concentrations to prevent toxicity.

No description available.

Tidal freshwater wetland soils contain large amounts of organic carbon, some of which is mineralized to carbon dioxide (CO2) and methane (CH4) by a diverse consortium of anaerobic microorganisms that includes fermenters, syntrophs, and methanogens (MG). These microbial groups are tightly linked and often rely on cooperative interspecies metabolisms (i.e., syntrophy) to survive. Environmental perturbations can disrupt these interactions and thus alter the rates and pathways of carbon cycling. One environmental change of particular concern in coastal wetlands is sea level rise, which can result in increased episodic saltwater intrusion events into these ecosystems. These events cause an influx of sulfate (SO4-2) to the soils and may stimulate sulfate-reducing bacteria (SRB), which can directly compete with syntrophs for energy sources (e.g., fermentation products such as butyrate). Since syntroph metabolism generates byproducts that serve as the energy source for many MG, this competition can have indirect negative effects on methanogenesis. In addition, SRB can directly compete with MG for these byproducts, particularly formate, H2, and/or acetate. The goal of this study was to understand how both MG and syntroph-MG consortia respond to and recover from SRB competition during an episodic saltwater intrusion event. To achieve this, microcosms containing soil slurry from a freshwater wetland were subjected to simulated saltwater intrusion, and metabolic inhibitors were used to isolate the activity of the various functional groups. This study focused on the breakdown of butyrate, which is a key energy source in syntroph‑MG consortia metabolisms. The observed changes in butyrate breakdown rates and byproduct accumulation during butyrate degradation assays confirmed that butyrate breakdown was mediated through syntroph-MG consortia, and that formate, rather than H2, was likely used as an electron carrier during syntrophic activity. Additions of SO4‑2 (as Na2SO4) to the freshwater microcosms stimulated SRB activity and shifted the MG community to favor acetoclastic members. These changes were accompanied by a 24% increase in CO2 production and an 80% decrease in CH4 production. Interestingly, when NaCl was added to achieve similar ionic strength, CH4 production decreased by ~32%, suggesting SRB competition is not the only factor affecting methanogenesis. Butyrate degradation rates demonstrated that while SRB were strong competitors for butyrate, concurrent syntrophic metabolism was possible. Further, data show that SRB were poor competitors for acetate, which could explain the increase in acetoclastic MG. Following removal of SRB competition, CH4 production recovered but only by ~50% after 28 days, which suggests that some MG communities in tidal freshwater wetlands may not be resilient to saltwater intrusion events. Over this same time, rates of syntrophic butyrate breakdown largely recovered, but butyrate breakdown resulted in the production of less CH4 and acetate and more CO2 and formate, indicating saltwater intrusion events may lead to persistent changes in the byproducts and pathways of carbon breakdown in tidal freshwater wetlands.

Use of an induced blanket reactor (IBR) to break down organic matter into methane is a financially attractive method to reduce the environmental impact of animal or industrial waste. In order to better understand the biological processes involved with the conversion of waste to biogas by an IBR, it is necessary to gain a better understanding of the microorganisms and their roles in the reactor. Molecular techniques based on the isolation of 16S rDNA were used in order to avoid the limitations posed by conventional culture-based techniques. Total DNA was extracted and amplified using universal primers specific to eubacteria and archaea with the purpose of identifying the dominant microorganisms in the IBR. The amplified DNA was separated based on its sequence composition by denaturing gradient gel electrophoresis (DGGE). Several bands were then excised, cloned, and sequenced, in order to characterize the phylogenetic affiliation of many of the microorganisms and create a useful molecular fingerprint. By using this approach, close relatives of several microorganisms that are typical in anaerobic digestion have been identified, including species of Clostridium, Flavobacterium, Bacteroides, Spirochaeta, Methanobrevibacter, and Methanosarcina. Several species were also identified whose role in the reactor is not completely understood, consisting of relatives of Dehalococcoides, Planctomyces, Aequorivita, and Sedimentibacter species. The information obtained in this project may enable refinements that promote desirable reactions and enhance reactor efficiency.

Bacterial microcompartments, or BMCs, are 80-200nm, enzyme-encompassing organelles composed of interlocking proteins that form cyclical hexamers with a small central pore. Clostridium phytofermentans or Cphy, is a Gram-positive, rod shaped, anaerobic soil microbe that has the ability to not only break down multiple polysaccharides simultaneously but also proceeds to ferment them into biofuels. The genome of Cphy contains 3 BMC loci. During growth on fucose and rhamnose, one of these loci is highly expressed and microcompartments can be viewed using TEM. Under these growth conditions, three products, ethanol, propanol and propionate, which could potentially be highly useful in the biofuel and bioproducts industries, are produced. Gene expression microarrays have revealed that the genes for the fucose/rhamnose-related microcompartment are also highly expressed on D-arabinose. The role of BMCs during growth on D-arabinose has not been reported in any organism. My goal is to determine the role of BMCs in D-arabinose metabolism in C. phytofermentans.