Identification of Inhibitors in Lignocellulosic Slurries and Determination of Their Effect on Hydrocarbon-Producing Microorganisms

Recent Advances in Food Waste Transformations into Essential Bioplastic Materials

Lignocellulose is a major biopolymer in plant biomass with a complex structure and composition. It consists of a significant amount of high molecular aromatic compounds, particularly vanillin, syringeal, ferulic acid, and muconic acid, that could be converted into intracellular metabolites such as polyhydroxyalkanoates (PHA) and hydroxybutyrate (PHB), a key component of bioplastic production. Several pre-treatment methods were utilized to release monosaccharides, which are the precursors of the relevant pathway. The consolidated bioprocessing of lignocellulose-capable microbes for biomass depolymerization was discussed in this study. Carbon can be stored in a variety of forms, including PHAs, PHBs, wax esters, and triacylglycerides. From a biotechnology standpoint, these compounds are quite adaptable due to their precursors' utilization of hydrogen energy. This study lays the groundwork for the idea of lignocellulose valorization into value-added products through several significant dominant pathways.

Improved xylitol production by the novel inhibitor-tolerant yeast Candida tropicalis K2

Production of potential value-added products from different lignocellulosic biomass is becoming more common due to the availability of the feedstocks in abundance and the environment- friendly nature of the microbial production process. Due to the large array of its applications in the pharmaceutical and food sectors, xylitol is considered as potential value-added compound for production. In this study, organic waste samples were collected from various habitats and screened for potential yeast isolates for xylitol production. Among 124 tested isolates, Candida tropicalis K2 showed the highest potential for xylitol production as well as inhibitors tolerance (Furfural, 5-hydroxymethyl furfural and acetic acid) phenotypes. C. tropicalis K2 produced 90 g/L of xylitol in batch fermentation (100 g/L xylose supplemented with 20 g/L of glycerol as co-substrate) with the yield and productivity of 0.90 g/g and 1.5 g/L.h, respectively, at pH 5.5 and 30°C temperature. Together, >10% higher xylitol yield was achieved when glycerol was used as a co-substrate with pure xylose. Moreover, with non-detoxified corncob and Albizia pod hydrolysates, C. tropicalis K2 isolate produced 0.62 and 0.69 g/g of xylitol yields and 1.04 and 0.75 g/L.h xylitol productivities, respectively. Thus, C. tropicalis K2 isolate could be considered as promising candidate for xylitol production from different lignocellulosic biomass.HIGHLIGHTS Candia tropicalis K2 isolate was screened from natural sites of biomass degradation and characterized for xylitol production.Non-detoxified Albizia pod and corncob hydrolysates were explored for xylitol production using selected C. tropicalis K2 isolate.A maximum of 0.90 g/g yield and 1.07 g/L.h xylitol productivity was achieved with pure xylose.A >10% increase in xylitol yield was achieved using glycerol as a co-substrate.

Removal of phenolic inhibitors from lignocellulose hydrolysates using laccases for the production of fuels and chemicals

Lignocellulose is the most abundant biopolymer in the biosphere. It is inexpensive and therefore considered an attractive feedstock to produce biofuels and other biochemicals. Thermochemical and/or enzymatic pretreatment is used to release fermentable monomeric sugars. However, a variety of inhibitory by-products such as weak acids, furans, and phenolics that inhibit cell growth and fermentation are also released. Phenolic compounds are among the most toxic components in lignocellulosic hydrolysates and slurries derived from lignin decomposition, affecting overall fermentation processes and production yields and productivity. Ligninolytic enzymes have been shown to lower inhibitor concentrations in these hydrolysates, thereby enhancing their fermentability into valuable products. Among them, laccases, which are capable of oxidizing lignin and a variety of phenolic compounds in an environmentally benign manner, have been used for biomass delignification and detoxification of lignocellulose hydrolysates with promising results. This review discusses the state of the art of different enzymatic approaches to hydrolysate detoxification. In particular, laccases are used in separate or in situ detoxification steps, namely in free enzyme processes or immobilized by cell surface display technology to improve the efficiency of the fermentative process and consequently the production of second-generation biofuels and bio-based chemicals.

Trends and challenges in the valorization of kitchen waste to polyhydroxyalkanoates

Kitchen waste (KW) is frequently available for free or with a negative cost due to its huge production. It contains a large proportion of organic substances, especially fermentable sugars, which can be used for bioplastic (polyhydroxyalkanoates or PHA) synthesis. Nevertheless, due to the difficulties in processing, various pre-treatments of KW are being investigated to enhance the concentration of simple sugars released during its hydrolysis. The effective use of KW will help in minimizing the issues of its inappropriate disposal. However, the review on KW to bioplastic synthesis is rarely reported in the literature. Hence, this particular review provides a comprehensive summary of the updated research developments in KW valorization and its potency as a feedstock for PHAs synthesis. Additionally, the impacts of KW, its availability, the necessary pre-treatments for the biopolymerization process, as well as the prospects and challenges for industrially generating sustainable PHAs, are critically discussed.

A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor

Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.

Transcriptomic analysis of formic acid stress response in Saccharomyces cerevisiae

Formic acid is a representative small molecule acid in lignocellulosic hydrolysate that can inhibit the growth of Saccharomyces cerevisiae cells during alcohol fermentation. However, the mechanism of formic acid cytotoxicity remains largely unknown. In this study, RNA-Seq technology was used to study the response of S. cerevisiae to formic acid stress at the transcriptional level. Scanning electron microscopy and Fourier transform infrared spectroscopy were conducted to observe the surface morphology of yeast cells. A total of 1504 genes were identified as being differentially expressed, with 797 upregulated and 707 downregulated genes. Transcriptomic analysis showed that most genes related to glycolysis, glycogen synthesis, protein degradation, the cell cycle, the MAPK signaling pathway, and redox regulation were significantly induced under formic acid stress and were involved in protein translation and synthesis amino acid synthesis genes were significantly suppressed. Formic acid stress can induce oxidative stress, inhibit protein biosynthesis, cause cells to undergo autophagy, and activate the intracellular metabolic pathways of energy production. The increase of glycogen and the decrease of energy consumption metabolism may be important in the adaptation of S. cerevisiae to formic acid. In addition, formic acid can also induce sexual reproduction and spore formation. This study through transcriptome analysis has preliminarily reveal the molecular response mechanism of S. cerevisiae to formic acid stress and has provided a basis for further research on methods used to improve the tolerance to cell inhibitors in lignocellulose hydrolysate.

Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development

The model ethanologenic bacterium Zymomonas mobilis has many advantages for diverse biochemical production. Although the impact of temperature especially high temperature on the growth and ethanol production of Z. mobilis has been reported, the transcriptional profiles of Z. mobilis grown at different temperatures have not been systematically investigated. In this study, Z. mobilis wild-type strain ZM4 was used to study the effect of a broad range of temperatures of 24, 30, 36, 40, and 45 °C on cell growth and morphology, glucose utilization and ethanol production, as well as the corresponding global gene expression profiles using RNA-Seq-based transcriptomics. In addition, a recombinant Z. mobilis strain expressing reporter gene EGFP (ZM4_EGFP) was constructed to study the effect of temperature on heterologous protein expression at different temperatures. Our result demonstrated that the effect of temperature on the growth and morphology of ZM4 and ZM4_EGFP were similar. The biomass of these two strains decreased along with the temperature increase, and an optimal temperature range is needed for efficient glucose utilization and ethanol production. Temperatures lower or higher than normal temperature investigated in this work was not favorable for the glucose utilization and ethanol production as well as the expression of exogenous protein EGFP based on the results of flow cytometry and Western blot. Temperature also affected the transcriptional profiles of Z. mobilis especially under high temperature. Compared with ZM4 cultured at 30 °C, 478 genes were up-regulated and 481 genes were down-regulated at 45 °C. The number of differentially expressed genes of ZM4 cultured at other temperatures (24, 36 or 40 °C) was relatively small though compared with those at 30 °C. Since temperature usually increases during the fermentation process, and heat tolerance is one of the important robustness traits of industrial strains, candidate genes related to heat resistance based on our RNA-Seq result and literature report were then selected for genetics study using the strategies of plasmid overexpression of candidate gene or replacement of the native promoter of candidate gene by an inducible Ptet promoter. The genetics studies indicated that ZMO0236, ZMO1335, ZMO0994, operon groESL, and cspL, which encodes Mrp family chromosome partitioning ATPase, flavoprotein WrbA, an uncharacterized protein, chaperonin Cpn10 and GroEL, and an exogenous cold shock protein, respectively, were associated with heat tolerance, and recombinant strains over-expressing these genes can improve their heat tolerance. Our work thus not only explored the effects of temperature on the expression of exogenous gene EGFP and endogenous genes, but also selected and confirmed several genes associated with heat tolerance in Z. mobilis, which provided a guidance on identifying candidate genes associated with phenotypic improvement through systems biology strategy and genetics studies for other microorganisms.

Optimization of cultivation medium and cyclic fed-batch fermentation strategy for enhanced polyhydroxyalkanoate production by Bacillus thuringiensis using a glucose-rich hydrolyzate

The accumulation of petrochemical plastic waste is detrimental to the environment. Polyhydroxyalkanoates (PHAs) are bacterial-derived polymers utilized for the production of bioplastics. PHA-plastics exhibit mechanical and thermal properties similar to conventional plastics. However, high production cost and obtaining high PHA yield and productivity impedes the widespread use of bioplastics. This study demonstrates the concept of cyclic fed-batch fermentation (CFBF) for enhanced PHA productivity by Bacillus thuringiensis using a glucose-rich hydrolyzate as the sole carbon source. The statistically optimized fermentation conditions used to obtain high cell density biomass (OD600 of 2.4175) were: 8.77 g L-1 yeast extract; 66.63% hydrolyzate (v/v); a fermentation pH of 7.18; and an incubation time of 27.22 h. The CFBF comprised three cycles of 29 h, 52 h, and 65 h, respectively. After the third cyclic event, cell biomass of 20.99 g L-1, PHA concentration of 14.28 g L-1, PHA yield of 68.03%, and PHA productivity of 0.219 g L-1 h-1 was achieved. This cyclic strategy yielded an almost threefold increase in biomass concentration and a fourfold increase in PHA concentration compared with batch fermentation. FTIR spectra of the extracted PHAs display prominent peaks at the wavelengths unique to PHAs. A copolymer was elucidated after the first cyclic event, whereas, after cycles CFBF 2-4, a terpolymer was noted. The PHAs obtained after CFBF cycle 3 have a slightly higher thermal stability compared with commercial PHB. The cyclic events decreased the melting temperature and degree of crystallinity of the PHAs. The approach used in this study demonstrates the possibility of coupling fermentation strategies with hydrolyzate derived from lignocellulosic waste as an alternative feedstock to obtain high cell density biomass and enhanced PHA productivity.

The Magnesium Concentration in Yeast Extracts Is a Major Determinant Affecting Ethanol Fermentation Performance of Zymomonas mobilis

Zymomonas mobilis is a model ethanologenic bacterium for diverse biochemical production. Rich medium (RM) is a complex medium that is routinely used to cultivate Z. mobilis, which contains carbon sources such as glucose, nitrogen sources such as yeast extract (YE), and KH2PO4. Glucose consumption and cell growth of Z. mobilis is usually coupled during ethanol fermentation. However, sometimes glucose was not consumed during the exponential growth phase, and it took extended time for cells to consume glucose and produce ethanol, which eventually reduced the ethanol productivity. In this study, the effects of different nitrogen sources, as well as the supplementation of an additional nitrogen source into RM and minimal medium (MM), on cell growth and glucose consumption of Z. mobilis were investigated to understand the uncoupled cell growth and glucose consumption. Our results indicated that nitrogen sources such as YE from different companies affected cell growth, glucose utilization, and ethanol production. We also quantified the concentrations of major ion elements in different nitrogen sources using the quantitative analytic approach of Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES), and demonstrated that magnesium ion in the media affected cell growth, glucose consumption, and ethanol production. The effect of magnesium on gene expression was further investigated using RNA-Seq transcriptomics. Our results indicated that the lack of Mg2+ triggered stress responses, and the expression of genes involved in energy metabolism was reduced. Our work thus demonstrated that Mg2+concentration in nitrogen sources is essential for vigorous cell growth and ethanol fermentation, and the difference of Mg2+concentration in different YE is one of the major factors affecting the coupled cell growth, glucose consumption and ethanol fermentation in Z. mobilis. We also revealed that genes responsive for Mg2+ deficiency in the medium were majorly related to stress responses and energy conservation. The importance of magnesium on cell growth and ethanol fermentation suggests that metal ions should become one of the parameters for monitoring the quality of commercial nitrogen sources and optimizing microbial culture medium.

Cell Factories for Industrial Production Processes: Current Issues and Emerging Solutions

Despite all the progresses made by metabolic engineering, still only a few biotechnological processes are running at an industrial level. In order to boost the biotechnological sector, integration strategies as well as long-term views are needed. The aim of the present review is to identify the main drawbacks in biotechnological processes, and to propose possible solutions to overcome the issues in question. Novel cell factories and bioreactor design are discussed as possible solutions. In particular, the following microorganisms: Yarrowia lipolytica, Trichosporon oleaginosus, Ustilago cynodontis, Debaryomyces hansenii along with sequential bioreactor configurations are presented as possible cell factories and bioreactor design solutions, respectively.

Review on pulp and paper activated sludge pretreatment, inhibitory effects and detoxification strategies for biovalorization

Biovalorization of pulp and paper activated sludge to value-added products could be an effective alternative to traditional sludge management methods, which tend to pose serious environmental issues. Since pulp and paper activated sludge consists of microbial biomass, cellulose, hemicellulose and lignin and thus, could be subjected to different hydrolysis methods to solubilize sludge solids and release simple sugars to form value-added products by the microbial fermentation process. Hence, different sludge hydrolysis methods have been summarized in this review paper. However, hydrolysis of lignocellulosic materials generates variety of toxic compounds during hydrolysis and causes detrimental effects. Therefore, different toxic compounds and their impact on microorganisms, cellulolytic enzymes and fermentation process have been discussed in detail and recent strategies to counteract the problems of inhibitors have also been briefly explained.

Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions

Zymomonas mobilis 8b is an ethanologenic bacterium engineered to utilize both glucose and xylose. The impacts of lignocellulosic hydrolyzate inhibitors on the growth of Zymomonas mobilis 8b have been investigated. However, the molecular responses of these inhibitors have not been completely elucidated yet. In this study, molecular responses to furfural were investigated using transcriptomic approaches of both chip-based microarray and a directional mRNA-Seq. Furfural acute shock time-course experiment with 3 g/L furfural supplemented when cells reached exponential phase and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the physiological and transcriptional profiles of short-term and long-term effects of furfural on 8b. Furfural negatively affected 8b growth in terms of final biomass and the fermentation time. Transcriptomic studies indicated that the response of 8b to furfural was dynamic and complex, and differences existed between short-term shock and long-term stress responses. However, the gene function categories were similar with most down-regulated genes related to translation and biosynthesis, while the furfural up-regulated genes were mostly related to general stress responses. Several gene candidates have been identified and genetic studies indicated that expression of ZMO0465 and cysteine synthase operon ZMO0003-0006 driven by its native promoter in a shuttle vector enhanced the furfural tolerance of 8b. In addition, the relationship between microarray and mRNA-Seq was compared with good correlations. The directional mRNA-Seq data not only provided the gene expression profiling, but also can be applied for transcriptional architecture improvement to identify and confirm operons, novel transcripts, hypothetical gene functions, transcriptional start sites, and promoters with different strength.

Development and characterization of acidic-pH-tolerant mutants of Zymomonas mobilis through adaptation and next-generation sequencing-based genome resequencing and RNA-Seq

BACKGROUND

Acid pretreatment is a common strategy used to break down the hemicellulose component of the lignocellulosic biomass to release pentoses, and a subsequent enzymatic hydrolysis step is usually applied to release hexoses from the cellulose. The hydrolysate after pretreatment and enzymatic hydrolysis containing both hexoses and pentoses can then be used as substrates for biochemical production. However, the acid-pretreated liquor can also be directly used as the substrate for microbial fermentation, which has an acidic pH and contains inhibitory compounds generated during pretreatment. Although the natural ethanologenic bacterium Zymomonas mobilis can grow in a broad range of pH 3.5 ~ 7.5, cell growth and ethanol fermentation are still affected under acidic-pH conditions below pH 4.0.

RESULTS

In this study, adaptive laboratory evolution (ALE) strategy was applied to adapt Z. mobilis under acidic-pH conditions. Two mutant strains named 3.6M and 3.5M with enhanced acidic pH tolerance were selected and confirmed, of which 3.5M grew better than ZM4 but worse than 3.6M in acidic-pH conditions that is served as a reference strain between 3.6M and ZM4 to help unravel the acidic-pH tolerance mechanism. Mutant strains 3.5M and 3.6M exhibited 50 ~ 130% enhancement on growth rate, 4 ~ 9 h reduction on fermentation time to consume glucose, and 20 ~ 63% improvement on ethanol productivity than wild-type ZM4 at pH 3.8. Next-generation sequencing (NGS)-based whole-genome resequencing (WGR) and RNA-Seq technologies were applied to unravel the acidic-pH tolerance mechanism of mutant strains. WGR result indicated that compared to wild-type ZM4, 3.5M and 3.6M have seven and five single nucleotide polymorphisms (SNPs), respectively, among which four are shared in common. Additionally, RNA-Seq result showed that the upregulation of genes involved in glycolysis and the downregulation of flagellar and mobility related genes would help generate and redistribute cellular energy to resist acidic pH while keeping normal biological processes in Z. mobilis. Moreover, genes involved in RND efflux pump, ATP-binding cassette (ABC) transporter, proton consumption, and alkaline metabolite production were significantly upregulated in mutants under the acidic-pH condition compared with ZM4, which could help maintain the pH homeostasis in mutant strains for acidic-pH resistance. Furthermore, our results demonstrated that in mutant 3.6M, genes encoding F₁F₀ ATPase to pump excess protons out of cells were upregulated under pH 3.8 compared to pH 6.2. This difference might help mutant 3.6M manage acidic conditions better than ZM4 and 3.5M. A few gene targets were then selected for genetics study to explore their role in acidic pH tolerance, and our results demonstrated that the expression of two operons in the shuttle plasmids, ZMO0956-ZMO0958 encoding cytochrome bc1 complex and ZMO1428-ZMO1432 encoding RND efflux pump, could help Z. mobilis tolerate acidic-pH conditions.

CONCLUSION

An acidic-pH-tolerant mutant 3.6M obtained through this study can be used for commercial bioethanol production under acidic fermentation conditions. In addition, the molecular mechanism of acidic pH tolerance of Z. mobilis was further proposed, which can facilitate future research on rational design of synthetic microorganisms with enhanced tolerance against acidic-pH conditions. Moreover, the strategy developed in this study combining approaches of ALE, genome resequencing, RNA-Seq, and classical genetics study for mutant evolution and characterization can be applied in other industrial microorganisms.

Physiological mechanism of improved tolerance of Saccharomyces cerevisiae to lignin-derived phenolic acids in lignocellulosic ethanol fermentation by short-term adaptation

BACKGROUND

Phenolic acids are lignin-derived fermentation inhibitors formed during many pretreatment processes of lignocellulosic biomass. In this study, vanillic, p-hydroxybenzoic, and syringic acids were selected as the model compounds of phenolic acids, and the effect of short-term adaptation strategies on the tolerance of S. cerevisiae to phenolic acids was investigated. The mechanism of phenolic acids tolerance in the adapted yeast strains was studied at the morphological and physiological levels.

RESULTS

The multiple phenolic acids exerted the synergistic inhibitory effect on the yeast cell growth. In particular, a significant interaction between vanillic and hydroxybenzoic acids was found. The optimal short-term adaptation strategies could efficiently improve the growth and fermentation performance of the yeast strain not only in the synthetic media with phenolic acids, but also in the simultaneous saccharification and ethanol fermentation of corncob residue. Morphological analysis showed that phenolic acids caused the parental strain to generate many cytoplasmic membrane invaginations with crack at the top of these sites and some mitochondria gathered around. The adapted strain presented the thicker cell wall and membrane and smaller cell size than those of the parental strain. In particular, the cytoplasmic membrane generated many little protrusions with regular shape. The cytoplasmic membrane integrity was analyzed by testing the relative electrical conductivity, leakage of intracellular substance, and permeation of fluorescent probe. The results indicated that the short-term adaptation improved the membrane integrity of yeast cell.

CONCLUSION

The inhibition mechanism of phenolic acid might be attributed to the combined effect of the cytoplasmic membrane damage and the intracellular acidification. The short-term adaptation strategy with varied stressors levels and adaptive processes accelerated the stress response of yeast cell structure to tolerate phenolic acids. This strategy will contribute to the development of robust microbials for biofuel production from lignocellulosic biomass.

Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds

The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.