Advances in ethanol production

Microbial tolerance engineering for boosting lactic acid production from lignocellulose

Lignocellulosic biomass is an attractive non-food feedstock for lactic acid production via microbial conversion due to its abundance and low-price, which can alleviate the conflict with food supplies. However, a variety of inhibitors derived from the biomass pretreatment processes repress microbial growth, decrease feedstock conversion efficiency and increase lactic acid production costs. Microbial tolerance engineering strategies accelerate the conversion of carbohydrates by improving microbial tolerance to toxic inhibitors using pretreated lignocellulose hydrolysate as a feedstock. This review presents the recent significant progress in microbial tolerance engineering to develop robust microbial cell factories with inhibitor tolerance and their application for cellulosic lactic acid production. Moreover, microbial tolerance engineering crosslinking other efficient breeding tools and novel approaches are also deeply discussed, aiming to providing a practical guide for economically viable production of cellulosic lactic acid.

Strategy for efficiently utilizing Escherichia coli cells producing isobutanol by combining isobutanol and indigo production systems

Isobutanol is a potential biofuel, and its microbial production systems have demonstrated promising results. In a microbial system, the isobutanol produced is secreted into the media; however, the cells remaining after fermentation cannot be used efficiently during the isobutanol recovery process and are discarded as waste. To address this, we aimed to investigate the strategy of utilizing these remaining cells by combining the isobutanol production system with the indigo production system, wherein the product accumulates intracellularly. Accordingly, we constructed E. coli systems with genes, such as acetolactate synthase gene (alsS), ketol-acid reductoisomerase gene (ilvC), dihydroxyl-acid dehydratase (ilvD), and alpha-ketoisovalerate decarboxylase gene (kivD), for isobutanol production and genes, such as tryptophanase gene (tnaA) and flavin-containing monooxygenase gene (FMO), for indigo production. This system produced isobutanol and indigo simultaneously while accumulating indigo within cells. The production of isobutanol and indigo exhibited a strong linear correlation up to 72 h of production time; however, the pattern of isobutanol and indigo production varied. To our knowledge, this study is the first to simultaneously produce isobutanol and indigo and can potentially enhance the economy of biochemical production.

Water-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol production

BACKGROUND

Developing economically viable pathways to produce renewable energy has become an important research theme in recent years. Lignocellulosic biomass is a promising feedstock that can be converted into second-generation biofuels and bioproducts. Global warming has adversely affected climate change causing many environmental changes that have impacted earth surface temperature and rainfall patterns. Recent research has shown that environmental growth conditions altered the composition of drought-stressed switchgrass and directly influenced the extent of biomass conversion to fuels by completely inhibiting yeast growth during fermentation. Our goal in this project was to find a way to overcome the microbial inhibition and characterize specific compounds that led to this inhibition. Additionally, we also determined if these microbial inhibitors were plant-generated compounds, by-products of the pretreatment process, or a combination of both.

RESULTS

Switchgrass harvested in drought (2012) and non-drought (2010) years were pretreated using Ammonia Fiber Expansion (AFEX). Untreated and AFEX processed samples were then extracted using solvents (i.e., water, ethanol, and ethyl acetate) to selectively remove potential inhibitory compounds and determine whether pretreatment affects the inhibition. High solids loading enzymatic hydrolysis was performed on all samples, followed by fermentation using engineered Saccharomyces cerevisiae. Fermentation rate, cell growth, sugar consumption, and ethanol production were used to evaluate fermentation performance. We found that water extraction of drought-year switchgrass before AFEX pretreatment reduced the inhibition of yeast fermentation. The extracts were analyzed using liquid chromatography-mass spectrometry (LC-MS) to detect compounds enriched in the extracted fractions. Saponins, a class of plant-generated triterpene or steroidal glycosides, were found to be significantly more abundant in the water extracts from drought-year (inhibitory) switchgrass. The inhibitory nature of the saponins in switchgrass hydrolysate was validated by spiking commercially available saponin standard (protodioscin) in non-inhibitory switchgrass hydrolysate harvested in normal year.

CONCLUSIONS

Adding a water extraction step prior to AFEX-pretreatment of drought-stressed switchgrass effectively overcame inhibition of yeast growth during bioethanol production. Saponins appear to be generated by the plant as a response to drought as they were significantly more abundant in the drought-stressed switchgrass water extracts and may contribute toward yeast inhibition in drought-stressed switchgrass hydrolysates.

Extrapolation of design strategies for lignocellulosic biomass conversion to the challenge of plastic waste

The goal of cost-effective production of fuels and chemicals from biomass has been a substantial driver of the development of the field of Metabolic Engineering. The resulting design principles and procedures provide a guide for the development of cost-effective methods for degradation, and possibly even valorization, of plastic wastes. Here we highlight these parallels, using the creative work of Lonnie O'Neal (Neal) Ingram in enabling production of fuels and chemicals from lignocellulosic biomass, with a focus on ethanol production as an exemplar process.

Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview

Endophytic bacteria colonize plants and live inside them for part of or throughout their life without causing any harm or disease to their hosts. The symbiotic relationship improves the physiology, fitness, and metabolite profile of the plants, while the plants provide food and shelter for the bacteria. The bacteria-induced alterations of the plants offer many possibilities for biotechnological, medicinal, and agricultural applications. The endophytes promote plant growth and fitness through the production of phytohormones or biofertilizers, or by alleviating abiotic and biotic stress tolerance. Strengthening of the plant immune system and suppression of disease are associated with the production of novel antibiotics, secondary metabolites, siderophores, and fertilizers such as nitrogenous or other industrially interesting chemical compounds. Endophytic bacteria can be used for phytoremediation of environmental pollutants or the control of fungal diseases by the production of lytic enzymes such as chitinases and cellulases, and their huge host range allows a broad spectrum of applications to agriculturally and pharmaceutically interesting plant species. More recently, endophytic bacteria have also been used to produce nanoparticles for medical and industrial applications. This review highlights the biotechnological possibilities for bacterial endophyte applications and proposes future goals for their application.

Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms

Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.

Steam Explosion Pretreatment of Beechwood. Part 2: Quantification of Cellulase Inhibitors and Their Effect on Avicel Hydrolysis

Biomass pretreatment is a mandatory step for the biochemical conversion of lignocellulose to chemicals. During pretreatment, soluble compounds are released into the prehydrolyzate that inhibit the enzymatic hydrolysis step. In this work, we investigated how the reaction conditions in steam explosion pretreatment of beechwood (severity: 3.0–5.25; temperature: 160–230 °C) influence the resulting amounts of different inhibitors. Furthermore, we quantified the extent of enzyme inhibition during enzymatic hydrolysis of Avicel in the presence of the prehydrolyzates. The amounts of phenolics, HMF, acetic acid and formic acid increased with increasing pretreatment severities and maximal quantities of 21.6, 8.3, 43.7 and 10.9 mg/gbeechwood, respectively, were measured at the highest severity. In contrast, the furfural concentration peaked at a temperature of 200 °C and a severity of 4.75. The presence of the prehydrolyzates in enzymatic hydrolysis of Avicel lowered the glucose yields by 5–26%. Mainly, the amount of phenolics and xylose and xylooligomers contributed to the reduced yield. As the maximal amounts of these two inhibitors can be found at different conditions, a wide range of pretreatment severities led to severely inhibiting prehydrolyzates. This study may provide guidelines when choosing optimal pretreatment conditions for whole slurry enzymatic hydrolysis.

Steam Explosion Pretreatment of Beechwood. Part 1: Comparison of the Enzymatic Hydrolysis of Washed Solids and Whole Pretreatment Slurry at Different Solid Loadings

Steam explosion is a well-known process to pretreat lignocellulosic biomass in order to enhance sugar yields in enzymatic hydrolysis, but pretreatment conditions have to be optimized individually for each material. In this study, we investigated how the results of a pretreatment optimization procedure are influenced by the chosen reaction conditions in the enzymatic hydrolysis. Beechwood was pretreated by steam explosion and the resulting biomass was subjected to enzymatic hydrolysis at glucan loadings of 1% and 5% employing either washed solids or the whole pretreatment slurry. For enzymatic hydrolysis in both reaction modes at a glucan loading of 1%, the glucose yields markedly increased with increasing severity and with increasing pretreatment temperature at identical severities and maximal values were reached at a pretreatment temperature of 230 °C. However, the optimal severity was 5.0 for washed solids enzymatic hydrolysis, but only 4.75 for whole slurry enzymatic hydrolysis. When the glucan loading was increased to 5%, glucose yields hardly increased for pretreatment temperatures between 210 and 230 °C at a given severity, and a pretreatment temperature of 220 °C was sufficient under these conditions. Consequently, it is important to precisely choose the desired conditions of the enzymatic hydrolysis reaction, when aiming to optimize the pretreatment conditions for a certain biomass.

Engineering transport systems for microbial production

The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.

A Case of Auto-brewery Syndrome Treated with Micafungin

Auto-brewery syndrome is caused by alcohol brewing inside the human body; it is a rare clinical condition where the patient becomes inebriated without exogenous alcohol use. Yeast is responsible, and treatment requires an appropriate antifungal agent. If undiagnosed, the patient's life becomes a misery. We present a case of a 45-year-old male who suffered from this condition for over three years with two arrests for driving under the influence prior to being diagnosed. The patient stated that he felt the episodes were related to his meal intakes; therefore, he would skip most meals of the day. The patient visited several centers where he was told there was not much they could offer him and he was left without a diagnosis. A carbohydrate challenge test in a monitored setting showed elevated blood alcohol levels. He was treated with antifungals and a low carbohydrate diet which resulted in the resolution of his symptoms. Hence the importance of awareness among physicians is necessary along with a high index of suspicion.

Cloning of novel bacterial xylanases from lignocellulose-enriched compost metagenomic libraries

Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.

Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A

BACKGROUND

The model yeast, Saccharomyces cerevisiae, is not known to be oleaginous. However, an industrial wild-type strain, D5A, was shown to accumulate over 20% storage lipids from glucose when growth is nitrogen-limited compared to no more than 7% lipid accumulation without nitrogen stress.

METHODS AND RESULTS

To elucidate the mechanisms of S. cerevisiae D5A oleaginicity, we compared physiological and metabolic changes; as well as the transcriptional profiles of the oleaginous industrial strain, D5A, and a non-oleaginous laboratory strain, BY4741, under normal and nitrogen-limited conditions using analytic techniques and next-generation sequencing-based RNA-Seq transcriptomics. Transcriptional levels for genes associated with fatty acid biosynthesis, nitrogen metabolism, amino acid catabolism, as well as the pentose phosphate pathway and ethanol oxidation in central carbon (C) metabolism, were up-regulated in D5A during nitrogen deprivation. Despite increased carbon flux to lipids, most gene-encoding enzymes involved in triacylglycerol (TAG) assembly were expressed at similar levels regardless of the varying nitrogen concentrations in the growth media and strain backgrounds. Phospholipid turnover also contributed to TAG accumulation through increased precursor production with the down-regulation of subsequent phospholipid synthesis steps. Our results also demonstrated that nitrogen assimilation via the glutamate-glutamine pathway and amino acid metabolism, as well as the fluxes of carbon and reductants from central C metabolism, are integral to the general oleaginicity of D5A, which resulted in the enhanced lipid storage during nitrogen deprivation.

CONCLUSION

This work demonstrated the disequilibrium and rebalance of carbon and nitrogen contribution to the accumulation of lipids in the oleaginous yeast S. cerevisiae D5A. Rather than TAG assembly from acyl groups, the major switches for the enhanced lipid accumulation of D5A (i.e., fatty acid biosynthesis) are the increases of cytosolic pools of acetyl-CoA and NADPH, as well as alternative nitrogen assimilation.

SELECTION OF THE COMPLEX OF ENZYME PREPARATIONS FOR THE HYDROLYSIS OF GRAIN CONSTITUENTS DURING THE FERMENTATION OF THE WORT OF HIGH CONCENTRATION

In this paper, an optimal complex is selected of enzyme preparations for hydrolysis of the components of grain raw materials during fermentation of high concentration wort. When selecting enzyme systems, their effect on the technical and chemical parameters of the fermented wash during the fermentation of wort is investigated. For the research, maize grain with a starch content of 69.0 % was used. Fermentation was carried out with 18–30% of dry matters (DM) in the wort, using the osmophilic yeast strain Saccharomyces cerevisiae DO-16.The recommended concentration of the enzyme preparation Amylex 4 T (the source of the α-amylase enzyme) – 0.4–0.6 units of α-amylase ability/g of starch – is optimal for the concentration 18–27% of DS in the wort. For 30 % of DS, it is practical to use 0.6 units of α-amylase ability/g of starch. With the use of the enzyme preparation Diazyme TGA (the source of the enzyme glucoamylase), the value is 7.5 units of glucoamylase ability/g of starch, alcohol accumulation in fermented washes was 10.51, 13.35, 15.78% vol., according to the wort concentrations 18, 27, 30 %, respectively. It has been established that with the application of the cytolytic enzyme Laminex 750, the concentrations of dissolved carbohydrates and non-dissolved starch have a tendency to decrease. In the samples where the proteolytic enzyme preparation Alphalase AFP was added at a concentration of 0.05 units of proteolytic ability/g of raw materials, there was an increase in the accumulation of yeast cells by 6.5% compared with the reference sample. The recommended concentration of Deltazyme VR XL (the source of β-glucanase and xylanase) is 0.05 units β-glucose/g of raw materials. The addition of a cytolytic and proteolytic enzyme preparation in combination with β-glucanase and xylanase contributed to an increase in the accumulation of ethanol in the washes by 1.7 % compared with the reference sample, and to an almost 33 % decrease in the concentration of dissolved carbohydrates and non-dissolved starch. On the basis of experimental studies, it has been found that using a complex of enzyme preparations – amylolytic (Amylex 4T), saccharifying (Diazyme TGA), proteolytic (Alphalase AFP), cytolytic (Laminex 750), and complex AF β-glucanase and xylanase (Deltazyme VR XL), in various combinations of their concentrations, – contributed to the intensification of the fermentation process of the wort and increased accumulation of the target product, ethanol, by 0.8–1.4 %, depending on the wort concentration. The highest amount of ethanol accumulated at the maximum dosage of additional enzyme preparations.

Engineering and Evolution of Saccharomyces cerevisiae to Produce Biofuels and Chemicals

To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology. Together, these innovations have resulted in rapid and efficient manipulation of S. cerevisiae to expand fermentable substrates and diversify value-added products. Here, we discuss recent and major advances in rational (relying on prior experimentally-derived knowledge) and combinatorial (relying on high-throughput screening and genomics) approaches to engineer S. cerevisiae for producing ethanol, butanol, 2,3-butanediol, fatty acid ethyl esters, isoprenoids, organic acids, rare sugars, antioxidants, and sugar alcohols from glucose, xylose, cellobiose, galactose, acetate, alginate, mannitol, arabinose, and lactose.

Endophytic bacteria: a new source of bioactive compounds

In recent years, bioactive compounds are in high demand in the pharmaceuticals and naturopathy, due to their health benefits to human and plants. Microorganisms synthesize these compounds and some enzymes either alone or in association with plants. Microbes residing inside the plant tissues, known as endophytes, also produce an array of these compounds. Endophytic actinomycetes act as a promising resource of biotechnologically valuable bioactive compounds and secondary metabolites. Endophytic Streptomyces sp. produced some novel antibiotics which are effective against multi-drug-resistant bacteria Antimicrobial agents produced by endophytes are eco-friendly, toxic to pathogens and do not harm the human. Endophytic inoculation of the plants modulates the synthesis of bioactive compounds with high pharmaceutical properties besides promoting growth of the plants. Hydrolases, the extracellular enzymes, produced by endophytic bacteria, help the plants to establish systemic resistance against pathogens invasion. Phytohormones produced by endophytes play an essential role in plant development and drought resistance management. The high diversity of endophytes and their adaptation to various environmental stresses seem to be an untapped source of new secondary metabolites. The present review summarizes the role of endophytic bacteria in synthesis and modulation of bioactive compounds.

Fed-batch hydrolysate addition and cell separation by settling in high cell density lignocellulosic ethanol fermentations on AFEX™ corn stover in the Rapid Bioconversion with Integrated recycling Technology process

The Rapid Bioconversion with Integrated recycling Technology (RaBIT) process uses enzyme and yeast recycling to improve cellulosic ethanol production economics. The previous versions of the RaBIT process exhibited decreased xylose consumption using cell recycle for a variety of different micro-organisms. Process changes were tested in an attempt to eliminate the xylose consumption decrease. Three different RaBIT process changes were evaluated in this work including (1) shortening the fermentation time, (2) fed-batch hydrolysate addition, and (3) selective cell recycling using a settling method. Shorting the RaBIT fermentation process to 11 h and introducing fed-batch hydrolysate addition eliminated any xylose consumption decrease over ten fermentation cycles; otherwise, decreased xylose consumption was apparent by the third cell recycle event. However, partial removal of yeast cells during recycle was not economical when compared to recycling all yeast cells.

Equilibrium, kinetic and thermodynamic studies of acid soluble lignin adsorption from rice straw hydrolysate by a self-synthesized macro/mesoporous resin

A self-synthesized HQ-8 resin was prepared using a O/W suspension polymerization technique and employed as a potential adsorbent for the removal of acid soluble lignin (ASL) from rice straw hydrolysate (RSH).

High-pressure carbon dioxide/water pre-treatment of sugarcane bagasse and elephant grass: Assessment of the effect of biomass composition on process efficiency

The performance of two lignocellulosic biomasses was studied in high-pressure carbon dioxide/water pre-treatment. Sugarcane bagasse and elephant grass were used to produce C₅-sugars from hemicellulose and, simultaneously, to promote cellulose digestibility for enzymatic saccharification. Different pre-treatment conditions, with combined severity factor ranging from -1.17 to -0.04, were evaluated and maximal total xylan to xylose yields of 59.2wt.% (34.4wt.% xylooligomers) and 46.4wt.% (34.9wt.% xylooligomers) were attained for sugarcane bagasse and elephant grass, respectively. Furthermore, pre-treated biomasses were highly digestible, with glucan to glucose yields of 77.2mol% and 72.4mol% for sugarcane bagasse and elephant grass, respectively. High-pressure carbon dioxide/water pre-treatment provides high total C₅-sugars and glucose recovery from both lignocellulosic biomasses; however it is highly influenced by composition and intrinsic features of each biomass. The obtained results confirm this approach as an effective and greener alternative to conventional pre-treatment processes.

Influence of Linker Length Variations on the Biomass-Degrading Performance of Heat-Active Enzyme Chimeras

Plant cell walls are composed of complex polysaccharides such as cellulose and hemicellulose. In order to efficiently hydrolyze cellulose, the synergistic action of several cellulases is required. Some anaerobic cellulolytic bacteria form multienzyme complexes, namely cellulosomes, while other microorganisms produce a portfolio of diverse enzymes that work in synergistic fashion. Molecular biological methods can mimic such effects through the generation of artificial bi- or multifunctional fusion enzymes. Endoglucanase and β-glucosidase from extremely thermophilic anaerobic bacteria Fervidobacterium gondwanense and Fervidobacterium islandicum, respectively, were fused end-to-end in an approach to optimize polysaccharide degradation. Both enzymes are optimally active at 90 °C and pH 6.0-7.0 representing excellent candidates for fusion experiments. The direct linkage of both enzymes led to an increased activity toward the substrate specific for β-glucosidase, but to a decreased activity of endoglucanase. However, these enzyme chimeras were superior over 1:1 mixtures of individual enzymes, because combined activities resulted in a higher final product yield. Therefore, such fusion enzymes exhibit promising features for application in industrial bioethanol production processes.

Recent trends in bioethanol production from food processing byproducts

The widespread use of corn starch and sugarcane as sources of sugar for the production of ethanol via fermentation may negatively impact the use of farmland for production of food. Thus, alternative sources of fermentable sugars, particularly from lignocellulosic sources, have been extensively investigated. Another source of fermentable sugars with substantial potential for ethanol production is the waste from the food growing and processing industry. Reviewed here is the use of waste from potato processing, molasses from processing of sugar beets into sugar, whey from cheese production, byproducts of rice and coffee bean processing, and other food processing wastes as sugar sources for fermentation to ethanol. Specific topics discussed include the organisms used for fermentation, strategies, such as co-culturing and cell immobilization, used to improve the fermentation process, and the use of genetic engineering to improve the performance of ethanol producing fermenters.

Delignification of miscanthus using ethylenediamine (EDA) with or without ammonia and subsequent enzymatic hydrolysis to sugars

Pretreatment of miscanthus is essential for efficient enzymatic production of cellulosic ethanol. This study reports a possible pretreatment method for miscanthus using aqueous ethylenediamine (EDA) for 30 min at 180 °C with or without ammonia. The mass ratio of miscanthus to EDA was varied from 1:3, 1:1, and 1:0.5, keeping the mass ratio of miscanthus to liquid (EDA + Water) constant at 1:8. The ammonia-to-miscanthus ratio was 1:0.25. After pretreatment with a ratio of 1:3 miscanthus to EDA, about 75 % of the lignin was removed from the raw miscanthus with 90 % retention of cellulose and 50 % of hemicellulose in the recovered solid. Enzymatic hydrolysis of the recovered solid miscanthus gave 63 % glucose and 62 % xylose conversion after 72 h. EDA provides an effective pretreatment for miscanthus, achieving good delignification and enhanced sugar yield by enzyme hydrolysis. Results using aqueous EDA with or without ammonia are much better than those using hot water and compare favorably with those using aqueous ammonia. The delignification efficiency of EDA pretreatment is high compared to that for hot-water pretreatment and is nearly as efficient as that obtained for aqueous-ammonia pretreatment.

Gas Fermentation-A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks

There is an immediate need to drastically reduce the emissions associated with global fossil fuel consumption in order to limit climate change. However, carbon-based materials, chemicals, and transportation fuels are predominantly made from fossil sources and currently there is no alternative source available to adequately displace them. Gas-fermenting microorganisms that fix carbon dioxide (CO2) and carbon monoxide (CO) can break this dependence as they are capable of converting gaseous carbon to fuels and chemicals. As such, the technology can utilize a wide range of feedstocks including gasified organic matter of any sort (e.g., municipal solid waste, industrial waste, biomass, and agricultural waste residues) or industrial off-gases (e.g., from steel mills or processing plants). Gas fermentation has matured to the point that large-scale production of ethanol from gas has been demonstrated by two companies. This review gives an overview of the gas fermentation process, focusing specifically on anaerobic acetogens. Applications of synthetic biology and coupling gas fermentation to additional processes are discussed in detail. Both of these strategies, demonstrated at bench-scale, have abundant potential to rapidly expand the commercial product spectrum of gas fermentation and further improve efficiencies and yields.

Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis

Contamination susceptibility, water usage, and inability to utilize 5-carbon sugars and disaccharides are among the major obstacles in industrialization of sustainable biorefining. Extremophilic thermophiles and acidophiles are being researched to combat these problems, but organisms which answer all the above problems have yet to emerge. Here, we present engineering of the unexplored, extreme alkaliphile Bacillus marmarensis as a platform for new bioprocesses which meet all these challenges. With a newly developed transformation protocol and genetic tools, along with optimized RBSs and antisense RNA, we engineered B. marmarensis to produce ethanol at titers of 38 g/l and 65% yields from glucose in unsterilized media. Furthermore, ethanol titers and yields of 12 g/l and 50%, respectively, were produced from cellobiose and xylose in unsterilized seawater and algal-contaminated wastewater. As such, B. marmarensis presents a promising approach for the contamination-resistant biorefining of a wide range of carbohydrates in unsterilized, non-potable seawater.

Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1

BACKGROUND

Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status.

RESULTS

Among the genes that exhibited significant differences between the hepA deletion strain (ΔhepA) and the wild type (WT), most (95.0 %) were upregulated in ΔhepA compared with WT. The expression of the key transcription factor for cellulolytic enzyme gene (e.g., repressor CreA and activator ClrB) increased significantly. However, the deletion of hepA led to downregulation of prominent extracellular cellulolytic enzyme genes. Among the top 10 extracellular glycoside hydrolases (Amy15A, Amy13A, Cel7A/CBHI, Cel61A, Chi18A, Cel3A/BGLI, Xyn10A, Cel7B/EGI, Cel5B/EGII, and Cel6A/CBHII), in which secretion amount is from the highest to the tenth in P. oxalicum secretome, eight genes, including two amylase genes (amy15A and amy13A), all five cellulase genes (cel7A/cbh1, cel6A/cbh2, cel7B/eg1, cel5B/eg2, and cel3A/bgl1), and the cellulose-active LPMO gene (cel61A) expression were downregulated. Results of chromatin accessibility real-time PCR (CHART-PCR) showed that the chromatin of all three tested upstream regions opened specifically because of the deletion of hepA in the case of two prominent cellulase genes cel7A/cbh1 and cel7B/eg1. However, the open chromatin status did not occur along with the activation of cellulolytic enzyme gene expression. The overexpression of hepA upregulated the cellulolytic enzyme gene expression without chromatin modification. The overexpression of hepA remarkably activated the cellulolytic enzyme synthesis, not only in WT (~150 % filter paper activity (FPA) increase), but also in the industry strain RE-10 (~20-30 % FPA increase).

CONCLUSIONS

HepA is required for chromatin condensation of prominent cellulase genes. However, the opening of chromatin mediated by the deletion of hepA was not positively correlated with cellulolytic enzyme gene activation. HepA is actually a positive regulator for cellulolytic enzyme gene expression and could be a promising target for genetic modification to improve cellulolytic enzyme synthesis.

Biosynthesis of platform chemical 3-hydroxypropionic acid (3-HP) directly from CO2 in cyanobacterium Synechocystis sp. PCC 6803

3-hydroxypropionic acid (3-HP) is an important platform chemical with a wide range of applications. So far large-scale production of 3-HP has been mainly through petroleum-based chemical processes, whose sustainability and environmental issues have attracted widespread attention. With the ability to fix CO2 directly, cyanobacteria have been engineered as an autotrophic microbial cell factory to produce fuels and chemicals. In this study, we constructed the biosynthetic pathway of 3-HP in cyanobacterium Synechocystis sp. PCC 6803, and then optimized the system through the following approaches: i) increasing expression of malonyl-CoA reductase (MCR) gene using different promoters and cultivation conditions; ii) enhancing supply of the precursor malonyl-CoA by overexpressing acetyl-CoA carboxylase and biotinilase; iii) improving NADPH supply by overexpressing the NAD(P) transhydrogenase gene; iv) directing more carbon flux into 3-HP by inactivating the competing pathways of PHA and acetate biosynthesis. Together, the efforts led to a production of 837.18 mg L(-1) (348.8 mg/g dry cell weight) 3-HP directly from CO2 in Synechocystis after 6 days cultivation, demonstrating the feasibility photosynthetic production of 3-HP directly from sunlight and CO2 in cyanobacteria. In addition, the results showed that overexpression of the ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) gene from Anabaena sp. PCC 7120 and Synechococcus sp. PCC 7942 led to no increase of 3-HP production, suggesting CO2 fixation may not be a rate-limiting step for 3-HP biosynthesis in Synechocystis.

Converting Sugars to Biofuels: Ethanol and Beyond

To date, the most significant sources of biofuels are starch- or sugarcane-based ethanol, which have been industrially produced in large quantities in the USA and Brazil, respectively. However, the ultimate goal of biofuel production is to produce fuels from lignocellulosic biomass-derived sugars with optimal fuel properties and compatibility with the existing fuel distribution infrastructure. To achieve this goal, metabolic pathways have been constructed to produce various fuel molecules that are categorized into fermentative alcohols (butanol and isobutanol), non-fermentative alcohols from 2-keto acid pathways, fatty acids-derived fuels and isoprenoid-derived fuels. This review will focus on current metabolic engineering efforts to improve the productivity and the yield of several key biofuel molecules. Strategies used in these metabolic engineering efforts can be summarized as follows: (1) identification of better enzymes; (2) flux control of intermediates and precursors; (3) elimination of competing pathways; (4) redox balance and cofactor regeneration; and (5) bypassing regulatory mechanisms. In addition to metabolic engineering approaches, host strains are optimized by improving sugar uptake and utilization, and increasing tolerance to toxic hydrolysates, metabolic intermediates and/or biofuel products.

Assessment of holocellulose for the production of bioethanol by conserving Pinus radiata cones as renewable feedstock

Renewable and green energy sources are much sought. Bioethanol is an environmentally friendly transportation fuel. Pine cones from Pinus radiata were shown to be a potential feedstock for the production of bioethanol. Alkaline (NaOH) pretreatment was carried out to delignify the lignocellulosic material and generate holocellulose (72 wt. % yield). The pretreated biomass was hydrolysed using HCl as catalyst under microwave irradiation and hydrothermal conditions. Microwave irradiation was found to be better than the hydrothermal process. Microwave irradiation accelerated the hydrolysis of biomass (42 wt. % conversion) with the reaction conditions being 3 M HCl and 5 min of irradiation time. Interestingly, even the xylose, which is the major component of the hydrolyzate was found to be metabolized to ethanol using Baker's yeast (Saccharomyces cerevisiae) under the experimental conditions. 5.7 g of ethanol could be produced from 100 g of raw pine cones.

An overview of key pretreatment processes for biological conversion of lignocellulosic biomass to bioethanol

Second-generation bioethanol can be produced from various lignocellulosic biomasses such as wood, agricultural or forest residues. Lignocellulosic biomass is inexpensive, renewable and abundant source for bioethanol production. The conversion of lignocellulosic biomass to bioethanol could be a promising technology though the process has several challenges and limitations such as biomass transport and handling, and efficient pretreatment methods for total delignification of lignocellulosics. Proper pretreatment methods can increase concentrations of fermentable sugars after enzymatic saccharification, thereby improving the efficiency of the whole process. Conversion of glucose as well as xylose to bioethanol needs some new fermentation technologies to make the whole process inexpensive. The main goal of pretreatment is to increase the digestibility of maximum available sugars. Each pretreatment process has a specific effect on the cellulose, hemicellulose and lignin fraction; thus, different pretreatment methods and conditions should be chosen according to the process configuration selected for the subsequent hydrolysis and fermentation steps. The cost of ethanol production from lignocellulosic biomass in current technologies is relatively high. Additionally, low yield still remains as one of the main challenges. This paper reviews the various technologies for maximum conversion of cellulose and hemicelluloses fraction to ethanol, and it point outs several key properties that should be targeted for low cost and maximum yield.

Sugarcane bagasse as support for immobilization of Bacillus pumilus HZ-2 and its use in bioremediation of mesotrione-contaminated soils

The degrading microorganisms isolated from environment usually fail to degrade pollutants when used for bioremediation of contaminated soils; thus, additional treatments are needed to enhance biodegradation. In the present study, the potential of sugarcane bagasse as bacteria-immobilizing support was investigated in mesotrione biodegradation. A novel isolate Bacillus pumilus HZ-2 was applied in bacterial immobilization, which was capable of degrading over 95 % of mesotrione at initial concentrations ranging from 25 to 200 mg L(-1) within 4 days in flask-shaking tests. Scanning electron microscope (SEM) images showed that the bacterial cells were strongly absorbed and fully dispersed on bagasse surface after immobilization. Specially, 86.5 and 82.9 % of mesotrione was eliminated by bacteria immobilized on bagasse of 100 and 60 mesh, respectively, which indicated that this immobilization was able to maintain a high degrading activity of the bacteria. Analysis of the degradation products determined 2-amino-4-methylsulfonylbenzoic acid (AMBA) and 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) as the main metabolites in the biodegradation pathway of mesotrione. In the sterile soil, approximately 90 % of mesotrione was degraded after supplementing 5.0 % of molasses in bacteria-bagasse composite, which greatly enhanced microbial adaptability and growth in the soil environment. In the field tests, over 75 % of mesotrione in soil was degraded within 14 days. The immobilized preparation demonstrated that mesotrione could be degraded at a wide range of pH values (5.0-8.0) and temperatures (25-35 °C), especially at low concentrations of mesotrione (5 to 20 mg kg(-1)). These results showed that sugarcane bagasse might be a good candidate as bacteria-immobilizing support to enhance mesotrione degradation by Bacillus p. HZ-2 in contaminated soils.

Cell surface engineering of industrial microorganisms for biorefining applications

In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.

Production by Tobacco Transplastomic Plants of Recombinant Fungal and Bacterial Cell-Wall Degrading Enzymes to Be Used for Cellulosic Biomass Saccharification

Biofuels from renewable plant biomass are gaining momentum due to climate change related to atmospheric CO2 increase. However, the production cost of enzymes required for cellulosic biomass saccharification is a major limiting step in this process. Low-cost production of large amounts of recombinant enzymes by transgenic plants was proposed as an alternative to the conventional microbial based fermentation. A number of studies have shown that chloroplast-based gene expression offers several advantages over nuclear transformation due to efficient transcription and translation systems and high copy number of the transgene. In this study, we expressed in tobacco chloroplasts microbial genes encoding five cellulases and a polygalacturonase. Leaf extracts containing the recombinant enzymes showed the ability to degrade various cell-wall components under different conditions, singly and in combinations. In addition, our group also tested a previously described thermostable xylanase in combination with a cellulase and a polygalacturonase to study the cumulative effect on the depolymerization of a complex plant substrate. Our results demonstrate the feasibility of using transplastomic tobacco leaf extracts to convert cell-wall polysaccharides into reducing sugars, fulfilling a major prerequisite of large scale availability of a variety of cell-wall degrading enzymes for biofuel industry.

Engineered biochar from biofuel residue: characterization and its silver removal potential

A novel approach was used to prepare engineered biochar from biofuel residue (stillage from bagasse ethanol production) through slow pyrolysis. The obtained biochar was characterized for its physicochemical properties as well as silver sorption ability. Sorption experimental data showed that engineered biochar quickly and efficiently removed silver ion (Ag(+)) from aqueous solutions with a Langmuir maximum capacity of 90.06 mg/g. The high sorption of Ag(+) onto the biochar was attributed to both reduction and surface adsorption mechanisms. The reduction of Ag(+) by the biochar was confirmed with scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy analyses of the postsorption biochar, which clearly showed the presence of metallic silver nanoparticles on the surface of the carbon matrix. An antimicrobial ability test indicated that silver-laden biochar effectively inhibited the growth of Escherichia coli, while the original biochar without silver nanoparticles promoted growth. Thus, biochar, prepared from biofuel residue materials, could be potentially applied not only to remove Ag(+) from aqueous solutions but also to produce a new value-added nanocomposite with antibacterial ability.