Increasing dissolved-oxygen disrupts iron homeostasis in production cultures of Escherichia coli

Quantitative proteomics reveals oxygen-induced adaptations in Caldalkalibacillus thermarum TA2.A1 microaerobic chemostat cultures

The thermoalkaliphile Caldalkalibacillus thermarum possesses a highly branched respiratory chain. These primarily facilitate growth at a wide range of dissolved oxygen levels. The aim of this study was to investigate the regulation of C. thermarum respiratory chain. C. thermarum was cultivated in chemostat bioreactors with a range of oxygen levels (0.25% O2-4.2% O2). Proteomic analysis unexpectedly showed that both the type I and the type II NADH dehydrogenase present are constitutive. The two terminal oxidases detected were the cytochrome c:oxygen aa 3 oxidase, whose abundance was highest at 4.2% O2. The cytochrome c:oxygen ba 3 oxidase was more abundant at most other O2 levels, but its abundance started to decline below 0.42% O2. We expected this would result in the emergence of the cytochrome c:oxygen bb 3 complex or the menaquinol:oxygen bd complex, the other two terminal oxidases of C. thermarum; but neither was detected. Furthermore, the sodium-proton antiporter complex Mrp was downregulated under the lower oxygen levels. Normally, in alkaliphiles, this enzyme is considered crucial for sodium homeostasis. We propose that the existence of a sodium:acetate exporter decreases the requirement for Mrp under strong oxygen limitation.

Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures while upregulating anaerobic respiratory chains

Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 μM) is characterized by lower biomass yield, higher acetate accumulation and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, previous studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. Here, the effect of iron availability on the energy metabolism of E. coli has been investigated. It was established that aerobic cultures growing under limiting iron conditions showed lower ATP yield per glucose, lower growth rate and lower TCA cycle activity and respiration, at the same time as increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independent of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiratory chain. In conditions of iron excess, some iron-requiring terminal reductases of the respiratory chain, that were thought to function only under anaerobiosis, were used by the E. coli, when in aerobic conditions, to maintain high respiratory activity. This allowed it to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase and catalase) and the iron-sulfur cluster repair systems.

Investigation of relationships between fecal contamination, cattle grazing, human recreation, and microbial source tracking markers in a mixed-land-use rangeland watershed

The United States National Forests are mixed-use lands that support human recreation and cattle grazing. Overuse by humans or cattle, however, can lead to the fecal contamination of local waterways. Until recently, the source of these contaminants was a subject of conjecture; however, microbial source tracking tools have become widely used and are proving to be a valid methodology to identify the contamination source. This study aims to analyze and model the quantity and sources of fecal contamination in the Mink Creek watershed in southeastern Idaho. The U.S. Forest Service Caribou-Targhee National Forest (USFS) manages this watershed. Previous research has indicated that some localities within the watershed exceed US EPA standards for coliform bacteria. In 2019, water samples were collected before livestock began grazing and throughout the spring, summer, and fall after livestock grazing had ended. Fourteen sites were sampled seven times during the field season, allowing the water to be analyzed for total coliforms and E. coli bacteria. Microbial source tracking techniques using Bacteroides bacteria, which are known to live in specific digestive tracks, were used to identify the source of E. coli at each sampling location. The analysis indicated that E. coli counts exceeded state regulatory limits 35% of the time. These exceedances were associated with DNA source tracking markers for humans (58.8%), cattle (5.9%), or both cattle and humans (5.9%). Unknown sources were responsible for the Bacteroides bacteria 29.4% of the time. A statistical model was developed to estimate E. coli using the datasets of microbial source tracking measures, the presence or absence of humans, cattle, the proximity of the sampling date to a holiday, and other seasonal factors. The resulting model showed good performance indices at all the 14 sites based on a K-fold cross-validation scheme (R² = 0.83 and NSE = 0.69). The results demonstrated that E. coli exceedances have a close association with human recreation and unknown sources and negatively influenced by dissolved oxygen.

Integrated Stirred-Tank Bioreactor with Internal Adsorption for the Removal of Ammonium to Enhance the Cultivation Performance of gdhA Derivative Pasteurella multocida B:2

Growth of mutant gdhA Pasteurella multocida B:2 was inhibited by the accumulation of a by-product, namely ammonium in the culture medium during fermentation. The removal of this by-product during the cultivation of mutant gdhA P. multocida B:2 in a 2 L stirred-tank bioreactor integrated with an internal column using cation-exchange adsorption resin for the improvement of cell viability was studied. Different types of bioreactor system (dispersed and internal) with resins were successfully used for ammonium removal at different agitation speeds. The cultivation in a bioreactor integrated with an internal column demonstrated a significant improvement in growth performance of mutant gdhA P. multocida B:2 (1.05 × 1011 cfu/mL), which was 1.6-fold and 8.4-fold as compared to cultivation with dispersed resin (7.2 × 1010 cfu/mL) and cultivation without resin (1.25 × 1010 cfu/mL), respectively. The accumulation of ammonium in culture medium without resin (801 mg/L) was 1.24-fold and 1.37-fold higher than culture with dispersed resin (642.50 mg/L) and culture in the bioreactor integrated with internal adsorption (586.50 mg/L), respectively. Results from this study demonstrated that cultivation in a bioreactor integrated with the internal adsorption column in order to remove ammonium could reduce the inhibitory effect of this by-product and improve the growth performance of mutant gdhA P. multocida B:2.

Effect of amino acids on transcription and translation of key genes in E. coli K and B grown at a steady state in minimal medium

Growing E. coli to high densities is a common strategy for biologicals production. The process is implemented by using complex or minimal media with different feeding strategies. To understand the effect of amino acids, E. coli B and K were grown at a steady state of 0.35 h^-1 in glucose minimal medium with and without amino acids, while their metabolism, protein abundance and gene expression were compared. The results showed that amino acids promoted higher acetate excretion, higher fatty acid biosynthesis (K strain), repressed glucose uptake rate, and decreased expression of proteins associated with the TCA cycle, glyoxylate shunt and amino acid biosynthesis. In presence of amino acids, E. coli K upregulated fatty acid biosynthesis and repressed more genes and proteins involved in amino acid biosynthesis than E. coli B. These findings are correlated with higher yield on glucose (Y_x/s) and high specific biomass production rate (q_x) in K strain in the presence of amino acids. In contrast, pre-formed precursor molecules such as amino acids did not affect fatty acid biosynthesis in E. coli B or Y_x/s and q_x, which were higher than those of E. coli K, suggesting that constitutive synthesis of energetically demanding precursors and higher fatty acid β-oxidation activity is key for high biomass-performer E. coli B. Both strains turned off unnecessary pathways and directed their metabolism to proteome efficient overflow metabolism likely to generate energy and provide protein to functions supporting higher growth rate.