Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor

Pseudomonas putida KT2440 is an emerging biomanufacturing host amenable for use with renewable carbon streams including aromatics such as para-coumarate. We used a pooled transposon library disrupting nearly all (4,778) non-essential genes to characterize this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays. Assessing differential fitness values by monitoring changes in mutant strain abundance identified 33 gene mutants with improved fitness across multiple stirred-tank bioreactor formats. Twenty-one deletion strains from this subset were reconstructed, including GacA, a regulator, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Thirteen deletion strains with roles in varying cellular functions were evaluated for conversion of para-coumarate, to a heterologous bioproduct, indigoidine. Several mutants, such as the ΔgacA strain improved fitness in a bioreactor by 35 fold and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/g, 23% of maximum theoretical yield) from para-coumarate as the carbon source.

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).

Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro

In the search for molecular machinery for custom biosynthesis of valuable compounds, the modular type I polyketide synthases (PKSs) offer great potential. In this study, we investigate the flexibility of BorM5, the iterative fifth module of the borrelidin synthase, with a panel of non-native priming substrates in vitro. BorM5 differentially extends various aliphatic and substituted substrates. Depending on substrate size and substitution BorM5 can exceed the three iterations it natively performs. To probe the effect of methyl branching on chain length regulation, we engineered a BorM5 variant capable of incorporating methylmalonyl- and malonyl-CoA into its intermediates. Intermediate methylation did not affect overall chain length, indicating that the enzyme does not to count methyl branches to specify the number of iterations. In addition to providing regulatory insight about BorM5, we produced dozens of novel methylated intermediates that might be used for production of various hydrocarbons or pharmaceuticals. These findings enable rational engineering and recombination of BorM5 and inform the study of other iterative modules.

Effects of key operational parameters on biohydrogen production via anaerobic fermentation in a sequencing batch reactor

In this study, a series of tests were conducted in a 6L anaerobic sequencing batch reactor (ASBR) to investigate the effect of pH, hydraulic retention time (HRT) and organic loading rate on biohydrogen production at 28°C. Sucrose was used as the main substrate to mimic carbohydrate-rich wastewater and inoculum was prepared from anaerobic digested sludge without pretreatment. The reactor was operated initially with nitrogen sparging to form anaerobic condition. Results showed that methanogens were effectively suppressed. The optimum pH value would vary depending on the HRT. Maximum hydrogen production rate and yield of 3.04 L H(2)/L reactor d and 2.16 mol H(2)/mol hexose respectively were achieved at pH 4.5, HRT 30 h, and OLR 11.0 kg/m(3)d. Two relationships involving the propionic acid/acetic acid ratio and ethanol/acetic acid ratio were derived from the analysis of the metabolites of fermentation. Ethanol/acetic acid ratio of 1.25 was found to be a threshold value for higher hydrogen production.

Permeability of wood pellets in the presence of fines

Broken pellets and fines are produced when pellets are handled. The resistance to air flow was measured for clean pellets and for pellets mixed with 1-20% broken pellets (fines). A pellet diameter was 6mm. The lengths ranged from 6 to 12 mm. Clean pellets were defined as particles that remained on a 4mm screen. A typical sieve analysis showed 30% of the mass of particles that passed through the 4mm screen was smaller than 1mm. The airflow rates used in the experiment ranged from 0.004 to 0.357 ms(-1). The corresponding pressure drop ranged from 1.9 to 271 Pam(-1) for clean pellets, from 4.8 to 1100 Pam(-1) for 10% fines content, and from 7.9 to 1800 Pam(-1) for 20% fines content. Coefficients of Hukill and Ives' equation were estimated for clean pellets and a multiplier was defined to calculate pressure drop for pellets mixed with fines.

Degradation of greenhouse twines derived from natural fibers and biodegradable polymer during composting

Commercial composting operations generally do not accept organic wastes with plastic twines from the greenhouse vegetable industry and the bulk of the waste materials ends up in landfills. The objectives of this paper are to identify environmentally compatible substitutes that could replace the current use of petrochemically derived plastic twines in greenhouse vegetable production, thus diverting them from landfills, and to assess the extent of their degradation via composting. Physical properties of the twines, including linear density, percent weight loss and tensile strength were monitored for the biodegradation tests. A pilot-scale composting trial was conducted in an in-vessel composting system. Results showed that the three biodegradable twine materials (cotton, jute and EcoPLA) could degrade readily in a composting environment within a reasonable time frame. Specifically, at the end of 105 days of composting, 85.3%, 84.8% and 81.1% of weight loss was observed for cotton, jute and EcoPLA, respectively. Furthermore, EcoPLA exhibited a slower decline in tensile strength with time, when compared to jute and cotton.

Development and performance of an alternative biofilter system

Step tracer tests were carried out on lab-scale biofilters to determine the residence time distributions (RTDs) of gases passing through two types of biofilters: a standard biofilter with vertical gas flow and a modified biofilter with horizontal gas flow. Results were used to define the flow patterns in the reactors. "Non-ideal flow" indicates that the flow reactors did not behave like either type of ideal reactor: the perfectly stirred reactor [often called a "continuously stirred tank reactor" (CSTR)] or the plug-flow reactor. The horizontal biofilter with back-mixing was able to accommodate a shorter residence time without the usual requirement of greater biofilter surface area for increased biofiltration efficiency. Experimental results indicated that the first bed of the modified biofilter behaved like two CSTRs in series, while the second bed may be represented by two or three CSTRs in series. Because of the flow baffles used in the horizontal biofilter system, its performance was more similar to completely mixed systems, and hence, it could not be modeled as a plug-flow reactor. For the standard biofilter, the number of CSTRs was found to be between 2 and 9 depending on the airflow rate. In terms of NH3 removal efficiency and elimination capacity, the standard biofilter was not as good as the modified system; moreover, the second bed of the modified biofilter exhibited greater removal efficiency than the first bed. The elimination rate increased as biofilter load increased. An opposite trend was exhibited with respect to removal efficiency.

Ultrafiltration tests for the reutilization of greenhouse wastewater

A lab-scale experiment was performed using two different pore-size ultrafiltration membranes to investigate the removal efficiency of Tomato Mosaic Virus (ToMV), retainability of pollutant and nutrients, and flow characteristics. From the experiment, it may be concluded that ultrafiltration can be used effectively to eliminate ToMV. Tests with a 30K pore-size ultrafiltration membrane achieved 99% virus removal efficiency and a 5K membrane practically removed 100% of the virus in greenhouse wastewater. Nutrient analysis indicated that all the essential nutrients could be retained and re-utilized.

Bone metastases in pheochromocytoma. Optimal timing of I-123 MIBG scintigraphy

The optimal timing of I-123 MIBG scintigraphy in the evaluation of pheochromocytoma is unknown. Although some centers perform early imaging, many delay imaging until 24 hours after injection. The authors describe the case of a bony metastasis in the left femur that was detected 5 hours after injection, but which was not visualized at 24 hours.