Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms

Response mechanism of ethanol-tolerant Saccharomyces cerevisiae strain ES-42 to increased ethanol during continuous ethanol fermentation

BACKGROUND

Continuous fermentation offers advantages in improving production efficiency and reducing costs, making it highly competitive for industrial ethanol production. A key requirement for Saccharomyces cerevisiae strains used in this process is their tolerance to high ethanol concentrations, which enables them to adapt to continuous fermentation conditions. To explore how yeast cells respond to varying levels of ethanol stress during fermentation, a two-month continuous fermentation was conducted. Cells were collected at different ethanol concentrations (from 60 g/L to 100 g/L) for comparative transcriptomic analysis.

RESULTS

During continuous fermentation, as ethanol concentration increased, the expression of genes associated with cytoplasmic ribosomes, translation, and fatty acid biosynthesis progressively declined, while the expression of genes related to heat shock proteins (HSPs) and ubiquitin-mediated protein degradation gradually increased. Besides, cells exhibited distinct responses to varying ethanol concentrations. At lower ethanol concentrations (nearly 70 g/L), genes involved in mitochondrial ribosomes, oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, antioxidant enzymes, ergosterol synthesis, and glycerol biosynthesis were specifically upregulated compared to those at 60 g/L. This suggests that cells enhanced respiratory energy production, ROS scavenging capacity, and the synthesis of ergosterol and glycerol to counteract stress. At relatively higher ethanol concentrations (nearly 80 g/L), genes involved in respiration and ergosterol synthesis were inhibited, while those associated with glycolysis and glycerol biosynthesis were notably upregulated. This suggests a metabolic shift from respiration towards enhanced glycerol synthesis. Interestingly, the longevity-regulating pathway seemed to play a pivotal role in mediating the cellular adaptations to different ethanol concentrations. Upon reaching an ethanol concentration of 100 g/L, the aforementioned metabolic activities were largely inhibited. Cells primarily focused on enhancing the clearance of denatured proteins to preserve cellular viability.

CONCLUSIONS

This study elucidated the mechanisms by which an ethanol-tolerant S. cerevisiae strain adapts to increasing ethanol concentrations during continuous fermentation. The findings suggest that the longevity-regulating pathway may play a critical role in adapting to varying ethanol stress by regulating mitochondrial respiration, glycerol synthesis, ergosterol synthesis, antioxidant enzyme, and HSPs. This work provides a novel and valuable understanding of the mechanisms that govern ethanol tolerance during continuous fermentation.

Toxic Effects of Butanol in the Plane of the Cell Membrane

Solvent toxicity limits n-butanol fermentation titer, increasing the cost and energy consumption for subsequent separation processes and making biobased production more expensive and energy-intensive than petrochemical approaches. Amphiphilic solvents such as n-butanol partition into the cell membrane of fermenting microorganisms, thinning the transverse structure, and eventually causing a loss of membrane potential and cell death. In this work, we demonstrate the deleterious effects of n-butanol partitioning upon the lateral dimension of the membrane structure, called membrane domains or lipid rafts. Lipid rafts are regions of the cell membrane enriched with certain lipids, providing a reservoir of high melting temperature lipids and a platform for membrane protein partitioning and oligomerization. Neutron scattering experiments and molecular dynamics simulations revealed that n-butanol increased the size of the lipid domains in a model membrane system. The data showed that n-butanol partitions more into the disordered lipid regions than into the raft-like phase, leading to a differential thinning of these coexisting phases in the plane of the membrane and increasing the hydrophobic mismatch. The resulting increase in line tension at the interface favors domain coalescence to minimize the ratio of the interfacial length to domain area. A detailed computational investigation of the lipid domain interface identifies the boundary as a site of membrane disorder and thinning due to an accumulation of n-butanol. Solvent-induced changes to domain morphology and membrane instability at the domain interface are unrecognized modes of solvent-induced stress to fermenting microbes, representing targets for new solvent tolerance strategies to increase the n-butanol titer.

Biotechnological potential of salt tolerant and xerophilic species of Aspergillus

Xerophilic fungi occupy versatile environments owing to their rich arsenal helping them successfully adapt to water constraints as a result of low relative humidity, high-osmolarity, and high-salinity conditions. The general term xerophilic fungi relates to organisms that tolerate and/or require reduced water activity, while halophilic and osmophilic are applied to specialized groups that require high salt concentrations or increased osmotic pressure, respectively. Species belonging to the family Aspergillaceae, and especially those classified in Aspergillus subgenus Aspergillus (sections Restricti and Aspergillus) and Polypaecilum, are particularly enriched in the group of osmophilic and salt-tolerant filamentous fungi. They produce an unprecedently wide spectrum of salt tolerant enzymes including proteases, peptidases, glutaminases, γ-glutamyl transpeptidases, various glycosidases such as cellulose-decomposing and starch-degrading hydrolases, lipases, tannases, and oxidareductases. These extremophilic fungi also represent a huge untapped treasure chest of yet-to-be-discovered, highly valuable, biologically active secondary metabolites. Furthermore, these organisms are indispensable agents in decolorizing textile dyes, degrading xenobiotics and removing excess ions in high-salt environments. They could also play a role in fermentation processes at low water activity leading to the preparation of daqu, meju, and tea. Considering current and future agricultural applications, salt-tolerant and osmophilic Aspergilli may contribute to the biosolubilization of phosphate in soil and the amelioration salt stress in crops. Transgenes from halophile Aspergilli may find promising applications in the engineering of salt stress and drought-tolerant agricultural crops. Aspergilli may also spoil feed and food and raise mycotoxin concentrations above the permissible doses and, therefore, the development of novel feed and food preservation technologies against these Aspergillus spp. is also urgently needed. On the other hand, some xerophilic Aspergilli have been shown to be promising biological control agents against mites. KEY POINTS: • Salt tolerant and osmophilic Aspergilli can be found in versatile environments • These fungi are rich resources of valuable enzymes and secondary metabolites • Biotechnological and agricultural applications of these fungi are expanding.

Development of a model for the ethanol concentration limit as a function of temperature and initial substrate concentration using the yeast Saccharomyces cerevisiae

In this study, a model was developed to simulate the effect of temperature (T $T$ ) and initial substrate concentration (S 0 ${S}_{0}$ ) on the ethanol concentration limit (P max ${P}_{\max }$ ) using the yeast Saccharomyces cerevisiae. To achieve this, regressions were performed using data provided by other authors forP max ${P}_{\max }$ to establish a model dependent onT $T$ andS 0 ${S}_{0}$ capable of predicting results with statistical significance. After constructing the model, a response surface was generated to determine the conditions whereP max ${P}_{\max }$ reaches higher values: temperatures between 28°C and 32°C and an initial substrate concentration around 200 g/L. Thus, the proposed model is consistent with the observations that increasing temperatures decrease the ethanol concentration obtained, and substrate concentrations above 200 g/L lead to a reduction in ethanol concentration even at low temperatures such as 28°C.

Construction of a Novel Vanillin-Induced Autoregulating Bidirectional Transport System in a Vanillin-Producing E. coli Cell Factory

Vanillin is one of the world's most extensively used flavoring agents with high application value. However, the yield of vanillin biosynthesis remains limited due to the low efficiency of substrate uptake and the inhibitory effect on cell growth caused by vanillin. Here, we screened high-efficiency ferulic acid importer TodX and vanillin exporters PP_0178 and PP_0179 by overexpressing genes encoding candidate transporters in a vanillin-producing engineered Escherichia coli strain VA and further constructed an autoregulatory bidirectional transport system by coexpressing TodX and PP_0178/PP_0179 with a vanillin self-inducible promoter ADH7. Compared with strain VA, strain VA-TodX-PP_0179 can efficiently transport ferulic acid across the cell membrane and convert it to vanillin, which significantly increases the substrate utilization rate efficiency (14.86%) and vanillin titer (51.07%). This study demonstrated that the autoregulatory bidirectional transport system significantly enhances the substrate uptake efficiency while alleviating the vanillin toxicity issue, providing a promising viable route for vanillin biosynthesis.

Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida

Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO2 has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding experiments under various conditions to identify the key limiting factors in shinorine production. The study combines meta-analysis of 13C-metabolic flux analysis, GEMs, synthetic biology, CRISPRi-mediated gene downregulation, and omics analysis to improve shinorine production, demonstrating the potential of Pseudomonas putida KT2440 as platform for shinorine production.

Polyextremophile engineering: a review of organisms that push the limits of life

Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.

The Concept of Life on Venus Informs the Concept of Habitability

An enduring question in astrobiology is how we assess extraterrestrial environments as being suitable for life. We suggest that the most reliable assessments of the habitability of extraterrestrial environments are made with respect to the empirically determined limits to known life. We discuss qualitatively distinct categories of habitability: empirical habitability that is constrained by the observed limits to biological activity; habitability sensu stricto, which is defined with reference to the known or unknown limits to the activity of all known organisms; and habitability sensu lato (habitability in the broadest sense), which is circumscribed by the limit of all possible life in the universe, which is the most difficult (and perhaps impossible) to determine. We use the cloud deck of Venus, which is temperate but incompatible with known life, as an example to elaborate and hypothesize on these limits.

Artificial Biosynthetic Pathway for Efficient Synthesis of Vanillin, a Feruloyl-CoA-Derived Natural Product from Eugenol

Eugenol, the main component of essential oil from the Syzygium aromaticum clove tree, has great potential as an alternative bioresource feedstock for biosynthesis purposes. Although eugenol degradation to ferulic acid was investigated, an efficient method for directly converting eugenol to targeted natural products has not been established. Herein we identified the inherent inhibitions by simply combining the previously reported ferulic acid biosynthetic pathway and vanillin biosynthetic pathway. To overcome this, we developed a novel biosynthetic pathway for converting eugenol into vanillin, by introducing cinnamoyl-CoA reductase (CCR), which catalyzes conversion of coniferyl aldehyde to feruloyl-CoA. This approach bypasses the need for two catalysts, namely coniferyl aldehyde dehydrogenase and feruloyl-CoA synthetase, thereby eliminating inhibition while simplifying the pathway. To further improve efficiency, we enhanced CCR catalytic efficiency via directed evolution and leveraged an artificialvanillin biosensor for high-throughput screening. Switching the cofactor preference of CCR from NADP+ to NAD+ significantly improved pathway efficiency. This newly designed pathway provides an alternative strategy for efficiently biosynthesizing feruloyl-CoA-derived natural products using eugenol.

Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans

Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1  h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.

Insights into the chaotropic tolerance of the desert cyanobacterium Chroococcidiopsis sp. 029 (Chroococcidiopsales, Cyanobacteria)

The mechanism of perchlorate resistance of the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated by assessing whether the pathways associated with its desiccation tolerance might play a role against the destabilizing effects of this chaotropic agent. During 3 weeks of growth in the presence of 2.4 mM perchlorate, an upregulation of trehalose and sucrose biosynthetic pathways was detected. This suggested that in response to the water stress triggered by perchlorate salts, these two compatible solutes play a role in the stabilization of macromolecules and membranes as they do in response to dehydration. During the perchlorate exposure, the production of oxidizing species was observed by using an oxidant-sensing fluorochrome and determining the expression of the antioxidant defense genes, namely superoxide dismutases and catalases, while the presence of oxidative DNA damage was highlighted by the over-expression of genes of the base excision repair. The involvement of desiccation-tolerance mechanisms in the perchlorate resistance of this desert cyanobacterium is interesting since, so far, chaotropic-tolerant bacteria have been identified among halophiles. Hence, it is anticipated that desert microorganisms might possess an unrevealed capability of adapting to perchlorate concentrations exceeding those naturally occurring in dry environments. Furthermore, in the endeavor of supporting future human outposts on Mars, the identified mechanisms might contribute to enhance the perchlorate resistance of microorganisms relevant for biologically driven utilization of the perchlorate-rich soil of the red planet.

Emerging nonmodel eukaryotes for biofuel production

Microbial synthesis of biofuels offers a promising solution to the global environmental and energy concerns. However, the main challenge of microbial cell factories is their high fermentation costs. Model hosts, such as Escherichia coli and Saccharomyces cerevisiae, are typically used for proof-of-concept studies of producing different types of biofuels, however, they have a limited potential for biofuel production at an industrially relevant scale due to the weak stability/robustness and narrow substrate scope. With the advancements of synthetic biology and metabolic engineering, nonmodel eukaryotes, with naturally favorable phenotypic and metabolic features, have been emerging as promising biofuel producers. Here, we introduce the emerging nonmodel eukaryotes for the biofuel production and discuss their specific advantages, especially those with the capacity of producing cellulosic ethanol, higher alcohols, and fatty acid-/terpene-derived biofuel molecules. We also propose the challenges and prospects for developing nonmodel eukaryotic as the ideal hosts for future biofuel production.

Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars

Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.

The waterbodies of the halo-volcanic Dallol complex: earth analogs to guide us, where to look for life in the universe

Microbes are the Earth life forms that have the highest degree of adaptability to survive, live, or even proliferate in very hostile environments. It is even stated that microbes can cope with any extreme physico-chemical condition and are, therefore, omnipresent all over the Earth: on all the continents, inside its crust and in all its waterbodies. However, our study suggests that there exists areas and even water rich environments on Earth where no life is possible. To support the fact that water rich environments can be lifeless, we performed an extensive survey of 10 different hyper extreme waterbodies of the halo-volcanic Dallol complex (Danakil depression, Ethiopia, Horn of Africa). In our study, we combined physico-chemical analyses, mineralogical investigations, XRD and SEM-EDX analyses, ATP measurements, 16S rDNA microbial community determinations, and microbial culturing techniques. According to our findings, we suggest that the individual physico-chemical parameters, water activity, and kosmo-chaotropicity, are the two most important factors that determine whether an environment is lifeless or capable of hosting specific extreme lifeforms. Besides, waterbodies that contained saturated levels of sodium chloride but at the same time possessed extreme low pH values, appeared to be poly-extreme environments in which no life could be detected. However, we clearly discovered a low diversity microbial community in waterbodies that were fully saturated with sodium chloride and only mildly acidic. Our results can be beneficial to more precisely classify whole or certain areas of planetary bodies, including water rich environments, as either potentially habitable or factual uninhabitable environments.

Designing glucose utilization "highway" for recombinant biosynthesis

cAMP receptor protein (CRP) is known as a global regulatory factor mainly mediating carbon source catabolism. Herein, we successfully engineered CRP to develop microbial chassis cells with improved recombinant biosynthetic capability in minimal medium with glucose as single carbon source. The obtained best-performing cAMP-independent CRPmu9 mutant conferred both faster cell growth and a 133-fold improvement in expression level of lac promoter in presence of 2% glucose, compared with strain under regulation of CRPwild-type. Promoters free from "glucose repression" are advantageous for recombinant expression, as glucose is a frequently used inexpensive carbon source in high-cell-density fermentations. Transcriptome analysis demonstrated that the CRP mutant globally rewired cell metabolism, displaying elevated tricarboxylic acid cycle activity; reduced acetate formation; increased nucleotide biosynthesis; and improved ATP synthesis, tolerance, and stress-resistance activity. Metabolites analysis confirmed the enhancement of glucose utilization with the upregulation of glycolysis and glyoxylate-tricarboxylic acid cycle. As expected, an elevated biosynthetic capability was demonstrated with vanillin, naringenin and caffeic acid biosynthesis in strains regulated by CRPmu9. This study has expanded the significance of CRP optimization into glucose utilization and recombinant biosynthesis, beyond the conventionally designated carbon source utilization other than glucose. The Escherichiacoli cell regulated by CRPmu9 can be potentially used as a beneficial chassis for recombinant biosynthesis.

Extremely chaotolerant and kosmotolerant Aspergillus atacamensis - a metabolically versatile fungus suitable for recalcitrant biosolid treatment

Obligate halophily is extremely rare in fungi. Nevertheless, Aspergillus atacamensis (strain EXF-6660), isolated from a salt water-exposed cave in the Coastal Range hills of the hyperarid Atacama Desert in Chile, is an obligate halophile, with a broad optimum range from 1.5 to 3.4 M of NaCl. When we tested its ability to grow at varied concentrations of both kosmotropic (NaCl, KCl, and sorbitol) and chaotropic (MgCl2, LiCl, CaCl2, and glycerol) solutes, stereoscopy and laser scanning microscopy revealed the formation of phialides and conidia. A. atacamensis EXF-6660 grew up to saturating levels of NaCl and at 2.0 M concentration of the chaotropic salt MgCl2. Our findings confirmed that A. atacamensis is an obligate halophile that can grow at substantially higher MgCl2 concentrations than 1.26 M, previously considered as the maximum limit supporting prokaryotic life. To assess the fungus' metabolic versatility, we used the phenotype microarray technology Biolog FF MicroPlates. In the presence of 2.0 M NaCl concentration, strain EXF-6660 metabolism was highly versatile. A vast repertoire of organic molecules (~95% of the substrates present in Biolog FF MicroPlates) was metabolized when supplied as sole carbon sources, including numerous polycyclic aromatic hydrocarbons, benzene derivatives, dyes, and several carbohydrates. Finally, the biotechnological potential of A. atacamensis for xenobiotic degradation and biosolid treatment was investigated. Interestingly, it could remove biphenyls, diphenyl ethers, different pharmaceuticals, phenols, and polyaromatic hydrocarbons. Our combined findings show that A. atacamensis EXF-6660 is a highly chaotolerant, kosmotolerant, and xerotolerant fungus, potentially useful for xenobiotic and biosolid treatments.

Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors

Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.

A Membrane Biophysics Perspective on the Mechanism of Alcohol Toxicity

Motivations for understanding the underlying mechanisms of alcohol toxicity range from economical to toxicological and clinical. On the one hand, acute alcohol toxicity limits biofuel yields, and on the other hand, acute alcohol toxicity provides a vital defense mechanism to prevent the spread of disease. Herein the role that stored curvature elastic energy (SCE) in biological membranes might play in alcohol toxicity is discussed, for both short and long-chain alcohols. Structure-toxicity relationships for alcohols ranging from methanol to hexadecanol are collated, and estimates of alcohol toxicity per alcohol molecule in the cell membrane are made. The latter reveal a minimum toxicity value per molecule around butanol before alcohol toxicity per molecule increases to a maximum around decanol and subsequently decreases again. The impact of alcohol molecules on the lamellar to inverse hexagonal phase transition temperature (T_H) is then presented and used as a metric to assess the impact of alcohol molecules on SCE. This approach suggests the nonmonotonic relationship between alcohol toxicity and chain length is consistent with SCE being a target of alcohol toxicity. Finally, in vivo evidence for SCE-driven adaptations to alcohol toxicity in the literature are discussed.

Preparation and Application of Directed Vat Set Indigenous Freeze-Drying Lentilactobacillus hilgardii Q19 Starter in Winemaking

In order to prepare a better direct vat set for malolactic fermentation (MLF) in high ethanol and low pH wines, the high-ethanol- and low-temperature-tolerant strain Lentilactobacillus hilgardii Q19, which was isolated from the eastern foothill of the Helan Mountain wine region in China, was used to prepare a direct vat set by vacuum freeze-drying. A superior freeze-dried lyoprotectant was obtained to create the starting culture by selecting, combining, and optimizing numerous lyoprotectants with higher protection for Q19 by using a single-factor experiment and response surface approach. Finally, the Lentilactobacillus hilgardii Q19 direct vat set was inoculated in Cabernet Sauvignon wine to carry out MLF on a pilot scale, with commercial starter culture Oeno1 as control. The volatile compounds, biogenic amines, and ethyl carbamate content were analyzed. The results showed that a combination of 8.5 g/100 mL skimmed milk powder, 14.5 g/100 mL yeast extract powder, and 6.0 g/100 mL sodium hydrogen glutamate offered better protection; with this lyoprotectant, there were (4.36 ± 0.34) × 10¹¹ CFU/g cells after freeze-drying, and it showed an excellent ability to degrade L-malic acid and could successfully finish MLF. In addition, in terms of aroma and wine safety, compared with Oeno1, the quantity and complexity of volatile compounds were increased after MLF, and biogenic amines and ethyl carbamate were produced less during MLF. We conclude that the Lentilactobacillus hilgardii Q19 direct vat set could be applied as a new MLF starter culture in high-ethanol wines.

Influence of Biotreatment on Hordeum vulgare L. Cereal Wholemeal Contamination and Enzymatic Activities

Crop contamination with mycotoxins is a global problem with a negative impact on human and animal health as well as causing economical losses in food and feed chains. This study was focused on the evaluation of the effect of lactic acid bacteria (LAB) strain (Levilactobacillus brevis-LUHS173, Liquorilactobacillus uvarum-LUHS245, Lactiplantibacillus plantarum-LUHS135, Lacticaseibacillus paracasei-LUHS244 and Lacticaseibacillus casei-LUHS210) fermentation on the changes in the level of deoxynivalenol (DON) and its conjugates in Fusarium spp.-contaminated barley wholemeal (BWP). Samples, with different contamination of DON and its conjugates, were treated separately (for 48 h). In addition to mycotoxin content, enzymatic activities (amylolytic, xylanolytic, and proteolytic) of BWP (before and after fermentation) were evaluated. It was established that the effect of decontamination depends on the LAB strain used, and a significant reduction in DON and the concentration of its conjugates in Lc. casei fermented samples was achieved: the amount of DON decreased on average by 47%, and the amount of D3G, 15-ADON and 3-ADON decreased by 82.4, 46.1, and 55.0%, respectively. Lc. casei also showed viability in the contaminated fermentation medium and an effective production of organic acids was obtained. Additionally, it was found that enzymes are involved to the detoxification mechanism of DON and its conjugates in BWP. These findings indicate that fermentation with selected LAB strains could be applied for contaminated barley treatment in order to significantly reduce Fusarium spp. mycotoxin levels in BWP and improve the sustainability of grain production.

Ethanol tolerance of Clostridium thermocellum: the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity

BACKGROUND

Clostridium thermocellum is a promising candidate for consolidated bioprocessing of lignocellulosic biomass to ethanol. The low ethanol tolerance of this microorganism is one of the remaining obstacles to industrial implementation. Ethanol inhibition can be caused by end-product inhibition and/or chaotropic-induced stress resulting in increased membrane fluidization and disruption of macromolecules. The highly reversible glycolysis of C. thermocellum might be especially sensitive to end-product inhibition. The chaotropic effect of ethanol is known to increase with temperature. This study explores the relative contributions of these two aspects to investigate and possibly mitigate ethanol-induced stress in growing and non-growing C. thermocellum cultures.

RESULTS

To separate chaotropic from thermodynamic effects of ethanol toxicity, a non-ethanol producing strain AVM062 (P_{clo1313_2638}::ldh* ∆adhE) was constructed by deleting the bifunctional acetaldehyde/alcohol dehydrogenase gene, adhE, in a lactate-overproducing strain. Exogenously added ethanol lowered the growth rate of both wild-type and the non-ethanol producing mutant. The mutant strain grew quicker than the wild-type at 50 and 55 °C for ethanol concentrations ≥ 10 g L^-1 and was able to reach higher maximum OD₆₀₀ at all ethanol concentrations and temperatures. For the wild-type, the maximum OD₆₀₀ and relative growth rates were higher at 45 and 50 °C, compared to 55 °C, for ethanol concentrations ≥ 15 g L^-1. For the mutant strain, no positive effect on growth was observed at lower temperatures. Growth-arrested cells of the wild-type demonstrated improved fermentative capacity over time in the presence of ethanol concentrations up to 40 g L^-1 at 45 and 50 °C compared to 55 °C.

CONCLUSION

Positive effects of temperature on ethanol tolerance were limited to wild-type C. thermocellum and are likely related to mechanisms involved in the ethanol-formation pathway and redox cofactor balancing. Lowering the cultivation temperature provides an attractive strategy to improve growth and fermentative capacity at high ethanol titres in high-cellulose loading batch cultivations. Finally, non-ethanol producing strains are useful platform strains to study the effects of chaotropicity and thermodynamics related to ethanol toxicity and allow for deeper understanding of growth and/or fermentation cessation under industrially relevant conditions.

Microbial detoxification of lignocellulosic biomass hydrolysates: Biochemical and molecular aspects, challenges, exploits and future perspectives

Valorization of lignocellulosic biomass (LB) has the potential to secure sustainable energy production without impacting food insecurity, whist relieving over reliance on finite fossil fuels. Agro-derived lignocellulosic residues such as wheat straw, switchgrass, rice bran, and miscanthus have gained relevance as feedstocks for the production of biofuels and chemicals. However, the microorganisms employed in fermentative conversion of carbohydrates to fuels and chemicals are unable to efficiently utilize the sugars derived from LB due to co-production of lignocellulose-derived microbial inhibitory compounds (LDMICs) during LB pretreatment. LDMICs impact microbial growth by inhibition of specific enzymes, cause DNA and cell membrane damage, and elicit cellular redox imbalance. Over the past decade, success has been achieved with the removal of LDMICs prior to fermentation. However, LDMICs removal by chemical processes is often accompanied by sugar losses, which negatively impacts the overall production cost. Hence, in situ removal of LDMICs by fermentative organisms during the fermentation process has garnered considerable attention as the "go-to" approach for economical LDMICs detoxification and bio-chemicals production. In situ removal of LDMICs has been pursued by either engineering more robust biocatalysts or isolating novel microbial strains with the inherent capacity to mineralize or detoxify LDMICs to less toxic compounds. While some success has been made along this line, efficient detoxification and robust production of target bio-chemicals in lignocellulosic hydrolysates (LHs) under largely anaerobic fermentative conditions remains a lingering challenge. Consequently, LB remains an underutilized substrate for bio-chemicals production. In this review, the impact of microbial LH detoxification on overall target molecule production is discussed. Further, the biochemical pathways and mechanisms employed for in situ microbial detoxification of furanic LDMICs [e.g., furfural and 5-hydroxymethylfurfural (HMF)] and phenolic LDMICs (e.g., syringaldehyde, p-coumaric acid, 4-hydroxybenzaldehyde, vanillin, and ferulic acid) are discussed. More importantly, metabolic engineering strategies for the development of LDMIC-tolerant and bio-chemicals overproducing strains and processes are highlighted.

Photoantimicrobials in agriculture

Classical approaches for controlling plant pathogens may be impaired by the development of pathogen resistance to chemical pesticides and by limited availability of effective antimicrobial agents. Recent increases in consumer awareness of and/or legislation regarding environmental and human health, and the urgent need to improve food security, are driving increased demand for safer antimicrobial strategies. Therefore, there is a need for a step change in the approaches used for controlling pre- and post-harvest diseases and foodborne human pathogens. The use of light-activated antimicrobial substances for the so-called antimicrobial photodynamic treatment is known to be effective not only in a clinical context, but also for use in agriculture to control plant-pathogenic fungi and bacteria, and to eliminate foodborne human pathogens from seeds, sprouted seeds, fruits, and vegetables. Here, we take a holistic approach to review and re-evaluate recent findings on: (i) the ecology of naturally-occurring photoantimicrobials, (ii) photodynamic processes including the light-activated antimicrobial activities of some plant metabolites, and (iii) fungus-induced photosensitization of plants. The inhibitory mechanisms of both natural and synthetic light-activated substances, known as photosensitizers, are discussed in the contexts of microbial stress biology and agricultural biotechnology. Their modes-of-antimicrobial action make them neither stressors nor toxins/toxicants (with specific modes of poisonous activity), but a hybrid/combination of both. We highlight the use of photoantimicrobials for the control of plant-pathogenic fungi and quantify their potential contribution to global food security.

Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines

If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO₄ -induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters. This article is protected by copyright. All rights reserved.

Glycerol Utilization as a Sole Carbon Source Disrupts the Membrane Architecture and Solventogenesis in Clostridium beijerinckii NCIMB 8052

Efficient bioconversion of abundant waste glycerol to value-added chemicals calls for a wider range of fermentative workhorses that can catabolize glycerol. In this study, we used quantitative gene expression and solvent profiling, qualitative metabolite analysis, and enzyme activity assays to investigate the factors that limit glycerol utilization as a sole carbon source by Clostridium beijerinckii NCIMB 8052. C. beijerinckii NCIMB 8052 did not produce acetate, acetone and butanol on glycerol. Congruently, the genes encoding the coenzyme A transferase subunits (ctfAB) and bifunctional acetaldehyde-CoA/alcohol dehydrogenase (adhE) were down-regulated up to 135- and 21-fold, respectively, at 12 h in glycerol-grown cells compared to glucose-grown cells. Conversely, NADH-dependent butanol dehydrogenase A (bdhA) was upregulated 2-fold. Glycerol dehydrogenase (gldA) and dihydroxyacetone kinase (subunit dhaK) were upregulated up to 5- and 881-fold, respectively. Glyceraldehyde-3-phosphate dehydrogenase (gapdh) showed mostly similar expression profiles at 12 h on glucose and glycerol. At 24 h, gapdh was downregulated 1.5-fold, while NADP+-dependent gapdh was upregulated up to 1.9-fold. Glycerol-grown cells showed higher or similar activity profiles for all solventogenic enzymes studied, compared to glucose-grown cells. Butyraldehyde (3 g/L) supplementation led to the production of ~0.1 g/L butanol, whilst butyrate (3.5 g/L) supplementation produced 0.7 and 0.5 g/L acetone and butanol, respectively, with glycerol. Further, the long chain saturated fatty acids cyclopentaneundecanoic acid, methyl ester and hexadecanoic acid, butyl ester were detected in glucose- but not in glycerol-grown cells. Collectively, growth on glycerol appears to disrupt synthesis of saturated long chain fatty acids, as well as solventogenesis in C. beijerinckii NCIMB 8052.

Comparative Proteomic Analysis of Psychrophilic vs. Mesophilic Bacterial Species Reveals Different Strategies to Achieve Temperature Adaptation

The old debate of nature (genes) vs. nurture (environmental variables) is once again topical concerning the effect of climate change on environmental microorganisms. Specifically, the Polar Regions are experiencing a drastic increase in temperature caused by the rise in greenhouse gas emissions. This study, in an attempt to mimic the molecular adaptation of polar microorganisms, combines proteomic approaches with a classical microbiological analysis in three bacterial species Shewanella oneidensis, Shewanella frigidimarina, and Psychrobacter frigidicola. Both shewanellas are members of the same genus but they live in different environments. On the other hand, Shewanella frigidimarina and Psychrobacter frigidicola share the same natural environment but belong to a different genus. The comparison of the strategies employed by each bacterial species estimates the contribution of genome vs. environmental variables in the adaptation to temperature. The results show a greater versatility of acclimatization for the genus Shewanella with respect to Psychrobacter. Besides, S. frigidimarina was the best-adapted species to thermal variations in the temperature range 4–30°C and displayed several adaptation mechanisms common with the other two species. Regarding the molecular machinery used by these bacteria to face the consequences of temperature changes, chaperones have a pivoting role. They form complexes with other proteins in the response to the environment, establishing cooperation with transmembrane proteins, elongation factors, and proteins for protection against oxidative damage.

Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence

The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.

Active Microbial Airborne Dispersal and Biomorphs as Confounding Factors for Life Detection in the Cell-Degrading Brines of the Polyextreme Dallol Geothermal Field

Determining the precise limits of life in polyextreme environments is challenging. Studies along gradients of polyextreme conditions in the Dallol proto-volcano area (Danakil salt desert, Ethiopia) showed the occurrence of archaea-dominated communities (up to 99%) in several hypersaline systems but strongly suggested that life did not thrive in the hyperacidic (pH ∼0), hypersaline (∼35% [wt/vol],) and sometimes hot (up to 108°C) ponds of the Dallol dome. However, it was recently claimed that archaea flourish in these brines based on the detection of one Nanohaloarchaeotas 16S rRNA gene and fluorescent in situ hybridization (FISH) experiments with archaea-specific probes. Here, we characterized the diversity of microorganisms in aerosols over Dallol, and we show that, in addition to typical bacteria from soil/dust, they transport halophilic archaea likely originating from neighboring hypersaline ecosystems. We also show that cells and DNA from cultures and natural local halophilic communities are rapidly destroyed upon contact with Dallol brine. Furthermore, we confirm the widespread occurrence of mineral particles, including silica-based biomorphs, in Dallol brines. FISH experiments using appropriate controls show that DNA fluorescent probes and dyes unspecifically bind to mineral precipitates in Dallol brines; cellular morphologies were unambiguously observed only in nearby hypersaline ecosystems. Our results show that airborne cell dispersal and unspecific binding of fluorescent probes are confounding factors likely affecting previous inferences of archaea thriving in Dallol. They highlight the need for controls and the consideration of alternative abiotic explanations before safely drawing conclusions about the presence of life in polyextreme terrestrial or extraterrestrial systems.

Antimicrobial Activity of Zymomonas mobilis Is Related to Its Aerobic Catabolism and Acid Resistance

Zymomonas mobilis is an ethanologenic, facultatively anaerobic alpha-proteobacterium, known for its inhibitory effect on the growth of a wide variety of microorganisms. This property might be interesting for the design of novel antimicrobials, yet it has negative implications for biotechnology, as it hinders the use of Z. mobilis as a producer microorganism in cocultivation. So far, the chemical nature of its inhibitory compound(s) has not been established. In the present study, we demonstrate that the putative inhibitor is a low-molecular-weight (below 3 kDa), thermostable compound, resistant to protease treatment, which is synthesized under aerobic conditions in Z. mobilis strains via the active respiratory chain. It is also synthesized by aerated nongrowing, glucose-consuming cells in the presence of chloramphenicol, thus ruling out its bacteriocin-like peptide nature. The inhibitory activity is pH-dependent and strongly correlated with the accumulation of propionate and acetate in the culture medium. Although, in Z. mobilis, the synthesis pathways of these acids still need to be identified, the acid production depends on respiration, and is much less pronounced in the non-respiring mutant strain, which shows low inhibitory activity. We conclude that propionate and acetate play a central role in the antimicrobial effects of Z. mobilis, which itself is known to bear high resistance to organic acids.

Alkane-priming of Beauveria bassiana strains to improve biocontrol of the redbanded stink bug Piezodorus guildinii and the bronze bug Thaumastocoris peregrinus

Insect epicuticle hydrocarbons (CHC) are known to be important determinants in the susceptibility degree of insects to fungal entomopathogens. Five Beauveria bassiana (Balsamo) Vuillemin (Hypocreales; Clavicipitaceae) strains were phenotypically analyzed regarding their response to CHC nutrition and their pathogenicity and virulence towards high fungal-susceptible Thaumastocoris peregrinus (Carpintero and Dellapé) (Heteroptera: Thaumastocoridae) and low fungal-susceptible Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), which are important hemipteran pests in eucalyptus and soybean plantations, respectively. Two of these strains, which were the most (ILB308) and the least (ILB299) virulent to P. guildinii, were also evaluated at gene expression level after growth on n-pentadecane, a P. guildinii epicuticular hydrocarbon. Beauveria bassiana hypervirulent strain ILB308 showed the lowest growth on most evaluated CHC media. However, this strain distinctively induced most of the analyzed genes involved in CHC assimilation, cuticle degradation and stress tolerance. Virulence towards low susceptibility P. guildinii was enhanced in both hypervirulent ILB308 and hypovirulent ILB299 strains after growth on n-pentadecane as the sole carbon source, whereas virulence enhancement towards high susceptibility T. peregrinus was only observed in the hypervirulent strain. Virulence enhancement towards P. guildinii could be mostly explained by a priming effect produced by CHC on the induction of some genes related to hydrocarbon assimilation in ILB299 and ILB308, such as cytochrome P450 genes (BbCyp52g11 and BbCyp52x1), together with adhesion and stress tolerance genes, such as hydrophobin (Bbhyd2) and catalase (Bbcatc) and glutathione peroxidase (Bbgpx), respectively.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

Photobiology of the keystone genus Metarhizium

Metarhizium fungi are soil-inhabiting ascomycetes which are saprotrophs, symbionts of plants, pathogens of insects, and participate in other trophic/ecological interactions, thereby performing multiple essential ecosystem services. Metarhizium species are used to control insect pests of crop plants and insects that act as vectors of human and animal diseases. To fulfil their functions in the environment and as biocontrol agents, these fungi must endure cellular stresses imposed by the environment, one of the most potent of which is solar ultraviolet (UV) radiation. Here, we examine the cellular stress biology of Metarhizium species in context of their photobiology, showing how photobiology facilitates key aspects of their ecology as keystone microbes and as mycoinsectides. The biophysical basis of UV-induced damage to Metarhizium, and mechanistic basis of molecular and cellular responses to effect damage repair, are discussed and interpreted in relation to the solar radiation received on Earth. We analyse the interplay between UV and visible light and how the latter increases cellular tolerance to the former via expression of a photolyase gene. By integrating current knowledge, we propose the mechanism through which Metarhizium species use the visible fraction of (low-UV) early-morning light to mitigate potentially lethal damage from intense UV radiation later in the day. We also show how this mechanism could increase Metarhizium environmental persistence and improve its bioinsecticide performance. We discuss the finding that visible light modulates stress biology in the context of further work needed on Metarhizium ecology in natural and agricultural ecosystems, and as keystone microbes that provide essential services within Earth's biosphere.

Production of Bioethanol—A Review of Factors Affecting Ethanol Yield

Fossil fuels are a major contributor to climate change, and as the demand for energy production increases, alternative sources (e.g., renewables) are becoming more attractive. Biofuels such as bioethanol reduce reliance on fossil fuels and can be compatible with the existing fleet of internal combustion engines. Incorporation of biofuels can reduce internal combustion engine (ICE) fleet carbon dioxide emissions. Bioethanol is typically produced via microbial fermentation of fermentable sugars, such as glucose, to ethanol. Traditional feedstocks (e.g., first-generation feedstock) include cereal grains, sugar cane, and sugar beets. However, due to concerns regarding food sustainability, lignocellulosic (second-generation) and algal biomass (third-generation) feedstocks have been investigated. Ethanol yield from fermentation is dependent on a multitude of factors. This review compares bioethanol production from a range of feedstocks, and elaborates on available technologies, including fermentation practices. The importance of maintaining nutrient homeostasis of yeast is also examined. The purpose of this review is to provide industrial producers and policy makers insight into available technologies, yields of bioethanol achieved by current manufacturing practices, and goals for future innovation.

Advances in developing metabolically engineered microbial platforms to produce fourth-generation biofuels and high-value biochemicals

Producing bio-based chemicals is imperative to establish an eco-friendly circular bioeconomy. However, the compromised titer of these biochemicals hampers their commercial implementation. Advances in genetic engineering tools have enabled researchers to develop robust strains producing desired titers of the next-generation biofuels and biochemicals. The native and non-native pathways have been extensively engineered in various host strains via pathway reconstruction and metabolic flux redirection of lipid metabolism and central carbon metabolism to produce myriad biomolecules including alcohols, isoprenoids, hydrocarbons, fatty-acids, and their derivatives. This review has briefly covered the research efforts made during the previous decade to produce advanced biofuels and biochemicals through engineered microbial platforms along with the engineering approaches employed. The efficiency of the various techniques along with their shortcomings is also covered to provide a comprehensive overview of the progress and future directions to achieve higher titer of fourth-generation biofuels and biochemicals while keeping environmental sustainability intact.

Enhancement of lysine biosynthesis confers high-temperature stress tolerance to Escherichia coli cells

Abstract

Lysine, a nutritionally important amino acid, is involved in adaptation and tolerance to environmental stresses in various organisms. Previous studies reported that lysine accumulation occurs in response to stress and that lysine supplementation enhances stress tolerance; however, the effect of lysine biosynthesis enhancement on stress tolerance has yet to be elucidated. In this study, we confirmed that lysine supplementation to the culture medium increased intracellular lysine content and improved cell growth of Escherichia coli at high temperature (42.5 °C). Lysine-overproducing strains were then isolated from the lysine analogue S-adenosylmethionine-resistant mutants by conventional mutagenesis and exhibited higher tolerance to high-temperature stress than the wild-type strain. We identified novel amino acid substitutions Gly474Asp and Cys554Tyr on ThrA, a bifunctional aspartate kinase/homoserine dehydrogenase (AK/HSDH), in the lysine-overproducing mutants. Interestingly, the Gly474Asp and Cys554Tyr variants of ThrA induced lysine accumulation and conferred high-temperature stress tolerance to E. coli cells. Enzymatic analysis revealed that the Gly474Asp substitution in ThrA reduced HSDH activity, suggesting that the intracellular level of aspartate semialdehyde, which is a substrate for HSDH and an intermediate for lysine biosynthesis, is elevated by the loss of HSDH activity and converted to lysine in E. coli. The present study demonstrated that both lysine supplementation and lysine biosynthesis enhancement improved the high-temperature stress tolerance of E. coli cells. Our findings suggest that lysine-overproducing strains have the potential as stress-tolerant microorganisms and can be applied to robust host cells for microbial production of useful compounds.

Key points

• Lysine supplementation improved the growth of E. coli cells at high temperature.

• The G474D and C554Y variant ThrA increased lysine productivity in E. coli cells.

• The G474D substitution in ThrA reduced homoserine dehydrogenase activity.

• E. coli cells that overproduce lysine exhibited high-temperature stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11519-0.

Increased xerotolerance of Saccharomyces cerevisiae during an osmotic pressure ramp over several generations

Although mechanisms involved in response of Saccharomyces cerevisiae to osmotic challenge are well described for low and sudden stresses, little is known about how cells respond to a gradual increase of the osmotic pressure (reduced water activity; aw ) over several generations as it could encounter during drying in nature or in food processes. Using glycerol as a stressor, we propagated S. cerevisiae through a ramp of the osmotic pressure (up to high molar concentrations to achieve testing-to-destruction) at the rate of 1.5 MPa day-1 from 1.38 to 58.5 MPa (0.990-0.635 aw ). Cultivability (measured at 1.38 MPa and at the harvest osmotic pressure) and glucose consumption compared with the corresponding sudden stress showed that yeasts were able to grow until about 10.5 MPa (0.926 aw ) and to survive until about 58.5 MPa, whereas glucose consumption occurred until 13.5 MPa (about 0.915 aw ). Nevertheless, the ramp conferred an advantage since yeasts harvested at 10.5 and 34.5 MPa (0.778 aw ) showed a greater cultivability than glycerol-shocked cells after a subsequent shock at 200 MPa (0.234 aw ) for 2 days. FTIR analysis revealed structural changes in wall and proteins in the range 1.38-10.5 MPa, which would be likely to be involved in the resistance at extreme osmotic pressure.

Plant metabolite 5-pentadecyl resorcinol is produced by the Amazonian fungus Penicillium sclerotiorum LM 5679

Since the classic studies of Alexander Flemming, Penicillium strains have been known as a rich source of antimicrobial substances. Recent studies have identified novel metabolites produced by Penicillium sclerotiorum that have antibacterial, antifouling and pharmaceutical activities. Here, we report the isolation of a P. sclerotiorum (LM 5679) from Amazonian soil and carry out a culture-based study to determine whether it can produce any novel secondary metabolite(s) that are not thus-far reported for this genus. Using a submerged culture system, secondary metabolites were recovered by solvent extract followed by thin-layer chromatography, nuclear magnetic resonance, and mass spectroscopy. One novel secondary metabolite was isolated from P. sclerotiorum (LM 5679); the phenolic compound 5-pentadecyl resorcinol widely known as an antifungal, that is produced by diverse plant species. This metabolite was not reported previously in any Penicillium species and was only found once before in fungi (that time, in a Fusarium). Here, we discuss the known activities of 5-pentadecyl resorcinol in the context of its mode-of-action as a hydrophobic (chaotropicity-mediated) stressor.

Astrobiology of life on Earth

Astrobiology is mistakenly regarded by some as a field confined to studies of life beyond Earth. Here, we consider life on Earth through an astrobiological lens. Whereas classical studies of microbiology historically focused on various anthropocentric sub-fields (such as fermented foods or commensals and pathogens of crop plants, livestock and humans), addressing key biological questions via astrobiological approaches can further our understanding of all life on Earth. We highlight potential implications of this approach through the articles in this Environmental Microbiology special issue 'Ecophysiology of Extremophiles'. They report on the microbiology of places/processes including low-temperature environments and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism in hypersaline lakes, dysoxic marine waters, and thermal acidic springs; biology of extremophile viruses; the survival of terrestrial extremophiles on the surface of Mars; biological soils crusts and rock-associated microbes of deserts; subsurface and deep biosphere, including a salticle formed within Triassic halite; and interactions of microbes with igneous and sedimentary rocks. These studies, some of which we highlight here, contribute to our understanding of the spatiotemporal reach of Earth'sfunctional biosphere, and the tenacity of terrestrial life. Their findings will help set the stage for future work focused on the constraints for life, and how organisms adapt and evolve to circumvent these constraints.

Subsurface and surface halophile communities of the chaotropic Salar de Uyuni

Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl₂ , LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.

OSIP1 is a self-assembling DUF3129 protein required to protect fungal cells from toxins and stressors

Secreted proteins are key players in fungal physiology and cell protection against external stressing agents and antifungals. Oak stress-induced protein 1 (OSIP1) is a fungal-specific protein with unknown function. By using Podospora anserina and Phanerochaete chrysosporium as models, we combined both in vivo functional approaches and biophysical characterization of OSIP1 recombinant protein. The P. anserina OSIP1^Δ mutant showed an increased sensitivity to the antifungal caspofungin compared to the wild type. This correlated with the production of a weakened extracellular exopolysaccharide/protein matrix (ECM). Since the recombinant OSIP1 from P. chrysosporium self-assembled as fibers and was capable of gelation, it is likely that OSIP1 is linked to ECM formation that acts as a physical barrier preventing drug toxicity. Moreover, compared to the wild type, the OSIP1^Δ mutant was more sensitive to oak extractives including chaotropic phenols and benzenes. It exhibited a strongly modified secretome pattern and an increased production of proteins associated to the cell-wall integrity signalling pathway, when grown on oak sawdust. This demonstrates that OSIP1 has also an important role in fungal resistance to extractive-induced stress.

The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life

The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.

Electrochemical Impedance Spectroscopy of Anion-Exchange Membrane AMX-Sb Fouled by Red Wine Components

The broad possibilities of electrochemical impedance spectroscopy for assessing the capacitance of interphase boundaries; the resistance and thickness of the foulant layer were shown by the example of AMX-Sb membrane contacted with red wine from one side and 0.02 M sodium chloride solution from the other side. This enabled us to determine to what extent foulants affect the electrical resistance of ion-exchange membranes, the ohmic resistance and the thickness of diffusion layers, the intensity of water splitting, and the electroconvection in under- and over-limiting current modes. It was established that short-term (10 h) contact of the AMX-Sb membrane with wine reduces the water-splitting due to the screening of fixed groups on the membrane surface by wine components. On the contrary, biofouling, which develops upon a longer membrane operation, enhances water splitting, due to the formation of a bipolar structure on the AMX-Sb surface. This bipolar structure is composed of a positively charged surface of anion-exchange membrane and negatively charged outer membranes of microorganisms. Using optical microscopy and microbiological analysis, it was found that more intense biofouling is observed on the AMX-Sb surface, that has not been in contacted with wine.

Collagen Peptide Provides Saccharomyces cerevisiae with Robust Stress Tolerance for Enhanced Bioethanol Production

Efficient production of bioethanol is desirable for bioenergy large-scale applications, but it is severely challenged by ethanol and sugar stresses. Here, collagen peptide (CP), as a renewable nitrogen-containing biomass, remarkably enhanced the stress resistance of Saccharomyces cerevisiae SLL-510 against ethanol challenge, based on its unique amino acid composition. Transcriptome analysis showed that the energy, lipid, cofactor, and vitamin metabolism may involve in stress tolerance provided by CP. When CP was added into the media containing 249.99 mg/mL glucose, the bioethanol yield increased from 8.03 to 12.25% (v/v) and 11.35 to 12.29% (v/v) at 43 and 120 h, respectively. Moreover, at 286.79 mg/mL glucose, the highest yield reached 14.48% (v/v), with 99.58% glucose utilization rate. The protection and promotion effects of CP were also shown by four other industrial S. cerevisiae strains. These results coupled with the advantages of abundant reserves, cleanliness, and renewability revealed that CP is a promising economically viable and industrially scalable enhancer for bioethanol fermentation.

Yeast Cellular Stress: Impacts on Bioethanol Production

Bioethanol is the largest biotechnology product and the most dominant biofuel globally. Saccharomyces cerevisiae is the most favored microorganism employed for its industrial production. However, obtaining maximum yields from an ethanol fermentation remains a technical challenge, since cellular stresses detrimentally impact on the efficiency of yeast cell growth and metabolism. Ethanol fermentation stresses potentially include osmotic, chaotropic, oxidative, and heat stress, as well as shifts in pH. Well-developed stress responses and tolerance mechanisms make S. cerevisiae industrious, with bioprocessing techniques also being deployed at industrial scale for the optimization of fermentation parameters and the effective management of inhibition issues. Overlap exists between yeast responses to different forms of stress. This review outlines yeast fermentation stresses and known mechanisms conferring stress tolerance, with their further elucidation and improvement possessing the potential to improve fermentation efficiency.