Microbial cultures were evaluated for organic acid production and their potential utility for leaching of rare earth elements (REE) from retorted phosphor powder (RPP) and spent fluid catalytic cracking (FCC) catalyst. Two bacterial and one fungal strain were isolated from environmental and industrial materials known to contain REE and compared to the industrially important bacterium Gluconobacter oxydans. Gluconic acid was the predominant organic acid product identified in all of the cultures. Maximum REE leaching (49% of the total REE) from the FCC material was observed using cell-free culture supernatants of G. oxydans, with preferential recovery of lanthanum over cerium. The phosphor powder was more difficult to leach; only about 2% of the total REE was leached with G. oxydans. Leaching experiments with the RPP material indicated that the extent of REE solubilization was similar whether whole cell cultures or cell-free supernatants were used. Abiotic control experiments showed that increasing gluconic acid concentrations increased leaching efficiency; for example, total REE leaching from FCC catalyst increased from 24% to 45% when gluconic acid was increased from 10 mM to 90 mM. However, G. oxydans cell-free culture supernatants containing 10-15 mM gluconic acid were more effective than abiotically prepared leaching solutions with higher gluconic acid concentrations, suggesting that other exudate components were important too. Our results indicate that microorganisms producing gluconic and other organic acids can induce effective leaching of REE from waste materials, and that increasing organic acid production will improve recovery.

The success of lignocellulosic biofuels and biochemical industries depends on an economic and reliable supply of high-quality biomass. However, research and development efforts have been historically focused on the utilization of agriculturally derived cellulosic feedstocks, without considerations of their low energy density, high variations in compositions and potential supply risks in terms of availability and affordability. This chapter demonstrated a strategy of feedstock blending and densification to address the supply chain challenges. Blending takes advantage of low-cost feedstock to avoid the prohibitive costs incurred through reliance on a single feedstock resource, while densification produces feedstocks with increased bulk density and desirable feed handling properties, as well as reduced transportation cost. We also review recent research on the blending and densification dealing with various types of feedstocks with a focus on the impacts of these preprocessing steps on biochemical conversion, that is, various thermochemical pretreatment chemistries and enzymatic hydrolysis, into fermentable sugars for biofuel production.

The enzyme hydroxyquinol 1,2-dioxygenase, which catalyzes ortho cleavage of hydroxyquinol (1,2,4-trihydroxybenzene) to produce maleylacetate, was purified from Escherichia coli cells containing the tftH gene from Burkholderia cepacia AC1100. Reduction of the double bond in maleylacetate is catalyzed by the enzyme maleylacetate reductase, which was also purified from E. coli cells, these cells containing the tftE gene from B. cepacia AC1100. The two enzymes together catalyzed the conversion of hydroxyquinol to 3-oxoadipate. The purified hydroxyquinol 1,2-dioxygenase was specific for hydroxyquinol and was not able to use catechol, tetrahydroxybenzene, 6-chlorohydroxyquinol, or 5-chlorohydroxyquinol as its substrate. The native molecular mass of hydroxyquinol 1,2-dioxygenase was 68 kDa, and the subunit size of the protein was 36 kDa, suggesting a dimeric protein of identical subunits.

Burkholderia cepacia AC1100 utilizes 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a sole source of carbon and energy. PT88 is a chromosomal deletion mutant of B. cepacia AC1100 and is unable to grow on 2,4,5-T. The nucleotide sequence of a 5.5-kb chromosomal fragment from B. cepacia AC1100 which complemented PT88 for growth on 2,4,5-T was determined. The sequence revealed the presence of six open reading frames, designated ORF1 to ORF6. Five polypeptides were produced when this DNA region was under control of the T7 promoter in Escherichia coli; however, no polypeptide was produced from the fourth open reading frame, ORF4. Homology searches of protein sequence databases were performed to determine if the proteins involved in 2,4,5-T metabolism were similar to other biodegradative enzymes. In addition, complementation studies were used to determine which genes were essential for the metabolism of 2,4,5-T. The first gene of the cluster, ORF1, encoded a 37-kDa polypeptide which was essential for complementation of PT88 and showed significant homology to putative trans-chlorodienelactone isomerases. The next gene, ORF2, was necessary for complementation and encoded a 47-kDa protein which showed homology to glutathione reductases. ORF3 was not essential for complementation; however, both the 23-kDa protein encoded by ORF3 and the predicted amino acid sequence of ORF4 showed homology to glutathione S-transferases. ORF5, which encoded an 11-kDa polypeptide, was essential for growth on 2,4,5-T, but the amino acid sequence did not show homology to those of any known proteins. The last gene of the cluster, ORF6, was necessary for complementation of PT88, and the 32-kDa protein encoded by this gene showed homology to catechol and chlorocatechol-1,2-dioxygenases.

A high-throughput mass spectrometry assay to measure the catalytic activity of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase, LpxC, is described. This reaction is essential in the biosynthesis of lipopolysaccharide (LPS) of gram-negative bacteria and is an attractive target for the development of new antibacterial agents. The assay uses the RapidFire mass spectrometry platform to measure the native LpxC substrate and the reaction product and thereby generates a ratiometric readout with minimal artifacts due to detection interference. The assay was robust in a high-throughput screen of a library of more than 700,000 compounds arrayed as orthogonal mixtures, with a median Z' factor of 0.74. Selected novel inhibitors from the screening campaign were confirmed as binding to LpxC by biophysical measurements using a thermal stability shift assay. Some inhibitors showed whole-cell antimicrobial activity against a sensitive strain of Escherichia coli with reduced LpxC activity (strain D22; minimum inhibitory concentrations ranging from 0.625-20 microg/mL). The results show that mass spectrometry-based screening is a valuable high-throughput screening tool for detecting inhibitors of enzymatic targets involving difficult to detect reactions.