Bacterial production of short-chain organic acids and trehalose from levulinic acid: a potential cellulose-derived building block as a feedstock for microbial production

Biotechnological valorization of levulinic acid as a non-sugar feedstock: New paradigm in biorefineries

Due to the severe climate crisis, biorefineries have been highlighted as replacements for fossil fuel-derived refineries. In traditional sugar-based biorefineries, levulinic acid (LA) is a byproduct. Nonetheless, in 2002, the US Department of Energy noted that LA is a significant building block obtained from biomass, and the biorefinery paradigm has shifted from being sugar-based to non-sugar-based. Accordingly, LA is of interest in this review since it can be converted into useful precursors and ultimately can broaden the product spectrum toward more valuable products (e.g., fuels, plastics, and pharmaceuticals), thereby enabling the construction of economically viable biorefineries. This study comprehensively reviews LA production techniques utilizing various bioresources. Recent progress in enzymatic and microbial routes for LA valorization and the LA-derived product spectrum and its versatility are discussed. Finally, challenges and future outlooks for LA-based non-sugar biorefineries are suggested.

Biochemical Methane Potential of a Biorefinery’s Process-Wastewater and its Components at Different Concentrations and Temperatures

A sustainable circular bioeconomy requires the side streams and byproducts of biorefineries to be assimilated into bioprocesses to produce value-added products. The present study endeavored to utilize such a byproduct generated during the synthesis of 5-hydroxymethylfurfural as a potential feedstock for biogas production. For this purpose, biochemical methane potential tests for the full process-wastewater, its components (5-hydroxymethylfurfural, furfural, levulinic acid, and glycolic acid), together with furfural’s metabolites (furfuryl alcohol and furoic acid), and phenols (syringaldehyde, vanillin, and phenol), were conducted at mesophilic and thermophilic temperatures to assess their biodegradability and gas production kinetics. 0.1, 0.2, 0.3, and 0.4 g COD of the test components were added separately into assays containing 35 mL of inoculum. At their lowest concentrations, the test components, other than the process-wastewater, exhibited a stimulatory effect on methane production at 37 °C, whereas their increased concentrations returned a lower mean specific methane yield at either temperature. For similar component loads, the mesophilic assays outperformed the thermophilic assays for the mean measured specific methane yields. Components that impaired the anaerobic process with their elevated concentrations were phenol, vanillin, and 5-hydroxymethylfurfural. Poor degradation of the process-wastewater was deduced to be linked to the considerable share of 5-hydroxymethylfurfural in the process-wastewater governing its overall characteristics. With excessive recalcitrant components, it is recommended to use such waste streams and byproducts as a substrate for biogas plants operating at moderate temperatures, but at low rates.

Microbial trehalose boosts the ecological fitness of biocontrol agents, the viability of probiotics during long-term storage and plants tolerance to environmental-driven abiotic stress

Despite the impressive gain in agricultural production and greater availability of food, a large portion of the world population is affected by food shortages and nutritional imbalance. This is due to abiotic stresses encountered by plants as a result of environmental-driven perturbations, loss of viability of starter cultures (probiotics) for functional foods during storage as well as the vulnerability of farm produce to postharvest pathogens. The use of compatible solutes (e.g., trehalose, proline, etc.) has been widely supported as a solution to these concerns. Trehalose is one of the widely reported microbial- or plant-derived metabolites that help microorganisms (e.g., biocontrol agents, probiotics and plant growth-promoting bacteria) and plants to tolerate harsh environmental conditions. Due to its recent categorization as generally regarded as safe (GRAS), trehalose is an essential tool for promoting nutrition-sensitive agriculture by replacing the overuse of chemical agents (e.g., pesticides, herbicides). Therefore, the current review evaluated the progress currently made in the application of trehalose in sustainable agriculture. The challenges, opportunities, and future of this biometabolite in food security were highlighted.

Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner-Doudoroff (ED), pentose-phosphate (PP), and lower Embden-Meyerhoff-Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

Emergent Approaches to Efficient and Sustainable Polyhydroxyalkanoate Production

Petroleum-derived plastics dominate currently used plastic materials. These plastics are derived from finite fossil carbon sources and were not designed for recycling or biodegradation. With the ever-increasing quantities of plastic wastes entering landfills and polluting our environment, there is an urgent need for fundamental change. One component to that change is developing cost-effective plastics derived from readily renewable resources that offer chemical or biological recycling and can be designed to have properties that not only allow the replacement of current plastics but also offer new application opportunities. Polyhydroxyalkanoates (PHAs) remain a promising candidate for commodity bioplastic production, despite the many decades of efforts by academicians and industrial scientists that have not yet achieved that goal. This article focuses on defining obstacles and solutions to overcome cost-performance metrics that are not sufficiently competitive with current commodity thermoplastics. To that end, this review describes various process innovations that build on fed-batch and semi-continuous modes of operation as well as methods that lead to high cell density cultivations. Also, we discuss work to move from costly to lower cost substrates such as lignocellulose-derived hydrolysates, metabolic engineering of organisms that provide higher substrate conversion rates, the potential of halophiles to provide low-cost platforms in non-sterile environments for PHA formation, and work that uses mixed culture strategies to overcome obstacles of using waste substrates. We also describe historical problems and potential solutions to downstream processing for PHA isolation that, along with feedstock costs, have been an Achilles heel towards the realization of cost-efficient processes. Finally, future directions for efficient PHA production and relevant structural variations are discussed.

Anaerobic Degradation of Individual Components from 5-Hydroxymethylfurfural Process-Wastewater in Continuously Operated Fixed Bed Reactors

Production of bio-based materials in biorefineries is coupled with the generation of organic-rich process-wastewater that requires further management. Anaerobic technologies can be employed as a tool for the rectification of such hazardous by-products. Therefore, 5-hydroxymethylfurfural process-wastewater and its components were investigated for their biodegradability in a continuous anaerobic process. The test components included 5-hydroxymethylfurfural, furfural, levulinic acid, and the full process-wastewater. Each component was injected individually into a continuously operating anaerobic filter at a concentration of 0.5 gCOD. On the basis of large discrepancies within the replicates for each component, we classified their degradation into the categories of “delayed”, “retarded”, and “inhibitory”. Inhibitory represented the replicates for all the test components that hampered the process. For the retarded degradation, their mean methane yield per 0.5 gCOD was between 21.31 ± 13.04 mL and 28.98 ± 25.38 mL. Delayed digestion was considered adequate for further assessments in which the order of conversion to methane according to specific methane yield for each component from highest to lowest was as follows: levulinic acid > furfural > 5-hydroxymethylfurfural > process-wastewater. Disparities and inconsistencies in the degradation of process-wastewater and its components can compromise process stability as a whole. Hence, the provision of energy with such feedstock is questionable.

Microbial and enzymatic conversion of levulinic acid, an alternative building block to fermentable sugars from cellulosic biomass

Levulinic acid (LA) is an important chemical building block listed among the top 12 value-added chemicals by the United States Department of Energy, and can be obtained through the hydrolysis of lignocellulosic biomass. Using the same approach as in the catalytic production of LA from biomass, catalytic methods to upgrade LA to higher value chemicals have been investigated. Since the discovery of the catabolic genes and enzymes in the LA metabolic pathway, bioconversion of LA into useful chemicals has attracted attention, and can potentially broaden the range of biochemical products derived from cellulosic biomass. With a brief introduction to the LA catabolic pathway in Pseudomonas spp., this review summarizes the current studies on the microbial conversion of LA into bioproducts, including the recent developments to achieve higher yields through genetic engineering of Escherichia coli cells. Three different types of reactions during the enzymatic conversion of LA are also discussed. KEY POINTS: • Levulinic acid is an alternative building block to sugars from cellulosic biomass. • Introduction of levulinic acid bioconversion with natural and engineered microbes. • Initial enzymatic conversion of levulinic acid proceeds via three different pathways. • 4-Hydroxyvalerate is one of the target chemicals for levulinic acid bioconversion.

Propionic Acid: Method of Production, Current State and Perspectives

During the past years, there has been a growing interest in the bioproduction of propionic acid by Propionibacterium. One of the major limitations of the existing models lies in their low productivity yield. Hence, many strategies have been proposed in order to circumvent this obstacle. This article provides a comprehensive synthesis and review of important biotechnological aspects of propionic acid production as a common ingredient in food and biotechnology industries. We first discuss some of the most important production processes, mainly focusing on biological production. Then, we provide a summary of important propionic acid producers, including Propionibacterium freudenreichii and Propionibacterium acidipropionici, as well as a wide range of reported growth/production media. Furthermore, we describe bioprocess variables that can have impact on the production yield. Finally, we propose methods for the extraction and analysis of propionic acid and put forward strategies for overcoming the limitations of competitive microbial production from the economical point of view. Several factors influence the propionic acid concentration and productivity such as culture conditions, type and bioreactor scale; however, the pH value and temperature are the most important ones. Given that there are many reports about propionic acid production from glucose, whey permeate, glycerol, lactic acid, hemicelluloses, hydrolyzed corn meal, lactose, sugarcane molasses and enzymatically hydrolyzed whole wheat flour, only few review articles evaluate biotechnological aspects, i.e. bioprocess variables.

Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida

Levulinic acid (LA) is a building block alternative to fermentable sugars derived from cellulosic biomass. Among LA catabolic processes in Pseudomonas putida KT2440, ligation of coenzyme A (CoA) to LA by levulinyl-CoA synthetase (LvaE) is known to be an initial enzymatic step in LA metabolism. To identify the genes involved in the first step of LA metabolism in Pseudomonas citronellolis LA18T, RNA-seq-based comparative transcriptome analysis was carried out for LA18T cells during growth on LA and pyruvic acid. The two most highly upregulated genes with LA exhibited amino acid sequence homologies to cation acetate symporter and 5-aminolevulinic acid dehydratase from Pseudomonas spp. Potential LA metabolic genes (lva genes) in LA18T that clustered with these two genes and were homologous to lva genes in KT2440 were identified, including lvaE2 of LA18T, which exhibited 35% identity with lvaE of KT2440. Using Escherichia coli cells with the pCold™ expression system, LvaE2 was produced and investigated for its activity toward LA. High performance liquid chromatography analysis confirmed that crude extracts of E. coli cells expressing the lvaE2 gene could convert LA to levulinyl-CoA in the presence of both HS-CoA and ATP. Phylogenetic analysis revealed that LvaE2 and LvaE formed a cluster with medium-chain fatty acid CoA synthetase, but they fell on different branches. Superimposition of LvaE2 and LvaE homology-based model structures suggested that LvaE2 had a larger tunnel for accepting fatty acid substrates than LvaE. These results indicate that LvaE2 is a novel levulinyl-CoA synthetase.

Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.

Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid

Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T.

Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The draft genome sequence will aid the study of the LA catabolic pathway, which will allow for more applications of LA-utilizing bacteria.

A metabolic pathway for catabolizing levulinic acid in bacteria

Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. This discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.

Real-time ultrasensitive VUV-PIMS detection of representative endogenous volatile markers in cancers

BACKGROUND

Identifying endogenous volatile organic compounds (VOCs) as markers for different cancers currently requires time-consuming procedures and specialized operators.

OBJECTIVE

The objective of this study was to develop a rapid and simple method for measuring VOCs at trace levels.

METHODS

A simple vacuum ultraviolet photoionization mass spectrometer (VUV-PIMS) was used to detect trace levels of dimethyl trisulfide (DMTS), dimethyl sulfide (DMS), and 2-butanone, which correspond to volatile biomarker candidates present in the exhaled breath of patients with breast, liver, and lung cancers, respectively. The practicality of measuring endogenous VOCs using VUV-PIMS was confirmed by detecting them in cultured cell lines.

RESULTS

The abovementioned VOCs were detected with high sensitivity by VUV-PIMS. The limits of detection (LODs) for DMTS, DMS, and 2-butanone were 3.1, 3.9, and 23.2 pptv, respectively, under ambient conditions, which surpass the sensitivity of nearly all other MS-based techniques. Moreover, relatively high concentrations of 2-butanone and DMS were observed in VOCs emitted from the A549 lung cancer cell line and the HepG2 liver cancer cell line, respectively.

CONCLUSIONS

Our results show that VUV-PIMS may serve as a reliable method for real-time measurement of endogenous volatile cancer biomarkers.

Efficient performance and the microbial community changes of submerged anaerobic membrane bioreactor in treatment of sewage containing cellulose suspended solid at 25°C

Influence of cellulose as suspended solid (SS) on the performance of submerged anaerobic membrane bioreactor (SAnMBR) was evaluated at 25°C using two types of synthetic sewage (SS contained or not). During the 110days operation, COD and BOD removal, CH4 gas recovery and cellulose accumulation were investigated in detail. The influence of cellulose as SS in sewage on the SAnMBR performance was not significant at HRT longer than12h and 65-72% of the influent COD was recovered as methane gas at HRT of 12h. At HRT of 6h, the quality of effluent got worse and the accumulation of cellulose was found in reactor. 16S rRNA analysis revealed that the microbial diversity distribution including Archaea and Bacteria changed due to the addition of SS in sewage and specific microbe for cellulose degradation such as Proteobacteria was detected. Sludge in SAnMBR could acclimate to characteristics of sewage by self-adaptation.

Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate

Burkholderia stabilis LA20W produces trehalose using levulinic acid (LA) as a substrate. Here, we report the 7.97-Mb draft genome sequence of B. stabilis LA20W, which will be useful in investigations of the enzymes involved in LA metabolism and the mechanism of LA-induced trehalose production.

Cold stress promoting a psychrotolerant bacterium Pseudomonas fragi P121 producing trehaloase

A newly isolated Pseudomonas fragi P121 strain in a soil sample taken from the Arctic Circle is able to produce trehalose. The P121 strain was able to grow at temperatures ranging from 4 to 25 °C, had an optimum pH of 6.5, and an optimum salt concentration of 2 %. The P121 strain had a survival rate of 29.1 % after being repeatedly frozen and thawed five times, and a survival rate of 78.9 % when placed in physiological saline for 15 days at 20 °C after cold shock, which is far higher than the type strain Pseudomonas fragi ATCC 4973. The P121 strain could produce 2.89 g/L trehalose, which was 18.6 % of dry cell weight within 52 h in a 25 L fermention tank using the malt extract prepared from barley as medium at 15 °C, while only 11.8 % of dry cell weight at 20 °C. These results suggested that cold stress promoted the strain producing trehalose. It is the first reported cold-tolerant bacterium that produces trehalose, which may protect cells against the cold environment.

Biocatalytic Production of Trehalose from Maltose by Using Whole Cells of Permeabilized Recombinant Escherichia coli

Trehalose is a non-reducing disaccharide, which can protect proteins, lipid membranes, and cells from desiccation, refrigeration, dehydration, and other harsh environments. Trehalose can be produced by different pathways and trehalose synthase pathway is a convenient, practical, and low-cost pathway for the industrial production of trehalose. In this study, 3 candidate treS genes were screened from genomic databases of Pseudomonas and expressed in Escherichia coli. One of them from P. stutzeri A1501 exhibited the best transformation ability from maltose into trehalose and the least byproduct. Thus, whole cells of this recombinant E. coli were used as biocatalyst for trehalose production. In order to improve the conversion rate of maltose to trehalose, optimization of the permeabilization and biotransformation were carried out. Under optimal conditions, 92.2 g/l trehalose was produced with a high productivity of 23.1 g/(l h). No increase of glucose was detected during the whole course. The biocatalytic process developed in this study might serve as a candidate for the large scale production of trehalose.

Isolation and characterization of bacterial strains with the ability to utilize high concentrations of levulinic acid, a platform chemical from inedible biomass

Nineteen levulinic acid (LA)-utilizing bacteria were isolated from environmental samples. Following examination of the use of 80 g/L LA by some isolated strains, Brevibacterium epidermidis LA39–2 consumed 62.6 g/L LA following 8 days incubation. The strain also utilized both 90 and 100 g/L LA, with consumption ratio of 84.3 and 53.3%, respectively, after 10 days incubation.