Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production

Sustainable production of biofuels from the algae-derived biomass

The worldwide fossil fuel reserves are rapidly and continually being depleted as a result of the rapid increase in global population and rising energy sector needs. Fossil fuels should not be used carelessly since they produce greenhouse gases, air pollution, and global warming, which leads to ecological imbalance and health risks. The study aims to discuss the alternative renewable energy source that is necessary to meet the needs of the global energy industry in the future. Both microalgae and macroalgae have great potential for several industrial applications. Algae-based biofuels can surmount the inadequacies presented by conventional fuels, thereby reducing the ‘food versus fuel’ debate. Cultivation of algae can be performed in all three systems; closed, open, and hybrid frameworks from which algal biomass is harvested, treated and converted into the desired biofuels. Among these, closed photobioreactors are considered the most efficient system for the cultivation of algae. Different types of closed systems can be employed for the cultivation of algae such as stirred tank photobioreactor, flat panel photobioreactor, vertical column photobioreactor, bubble column photobioreactor, and horizontal tubular photobioreactor. The type of cultivation system along with various factors, such as light, temperature, nutrients, carbon dioxide, and pH affect the yield of algal biomass and hence the biofuel production. Algae-based biofuels present numerous benefits in terms of economic growth. Developing a biofuel industry based on algal cultivation can provide us with a lot of socio-economic advantages contributing to a publicly maintainable result. This article outlines the third-generation biofuels, how they are cultivated in different systems, different influencing factors, and the technologies for the conversion of biomass. The benefits provided by these new generation biofuels are also discussed. The development of algae-based biofuel would not only change environmental pollution control but also benefit producers' economic and social advancement.

Graphical abstract

De novo biosynthesis of p-coumaric acid and caffeic acid from carboxymethyl-cellulose by microbial co-culture strategy

Background

Aromatic compounds, such as p-coumaric acid (p-CA) and caffeic acid, are secondary metabolites of various plants, and are widely used in diet and industry for their biological activities. In addition to expensive and unsustainable methods of plant extraction and chemical synthesis, the strategy for heterologous synthesis of aromatic compounds in microorganisms has received much attention. As the most abundant renewable resource in the world, lignocellulose is an economical and environmentally friendly alternative to edible, high-cost carbon sources such as glucose.

Results

In the present study, carboxymethyl-cellulose (CMC) was utilized as the sole carbon source, and a metabolically engineered Saccharomyces cerevisiae strain SK10-3 was co-cultured with other recombinant S. cerevisiae strains to achieve the bioconversion of value-added products from CMC. By optimizing the inoculation ratio, interval time, and carbon source content, the final titer of p-CA in 30 g/L CMC medium was increased to 71.71 mg/L, which was 155.9-fold higher than that achieved in mono-culture. The de novo biosynthesis of caffeic acid in the CMC medium was also achieved through a three-strain co-cultivation. Caffeic acid production was up to 16.91 mg/L after optimizing the inoculation ratio of these strains.

Conclusion

De novo biosynthesis of p-CA and caffeic acid from lignocellulose through a co-cultivation strategy was achieved for the first time. This study provides favorable support for the biosynthesis of more high value-added products from economical substrates. In addition, the multi-strain co-culture strategy can effectively improve the final titer of the target products, which has high application potential in the field of industrial production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01805-5.

Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630

Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.

Recent Progress on Chemical Production From Non-food Renewable Feedstocks Using Corynebacterium glutamicum

Due to the non-renewable nature of fossil fuels, microbial fermentation is considered a sustainable approach for chemical production using glucose, xylose, menthol, and other complex carbon sources represented by lignocellulosic biomass. Among these, xylose, methanol, arabinose, glycerol, and other alternative feedstocks have been identified as superior non-food sustainable carbon substrates that can be effectively developed for microbe-based bioproduction. Corynebacterium glutamicum is a model gram-positive bacterium that has been extensively engineered to produce amino acids and other chemicals. Recently, in order to reduce production costs and avoid competition for human food, C. glutamicum has also been engineered to broaden its substrate spectrum. Strengthening endogenous metabolic pathways or assembling heterologous ones enables C. glutamicum to rapidly catabolize a multitude of carbon sources. This review summarizes recent progress in metabolic engineering of C. glutamicum toward a broad substrate spectrum and diverse chemical production. In particularly, utilization of lignocellulosic biomass-derived complex hybrid carbon source represents the futural direction for non-food renewable feedstocks was discussed.

Acidolysis as a biorefinery approach to producing advanced bioenergy from macroalgal biomass: A state-of-the-art review

Facing fossil fuels consumption and its accompanying environmental pollution, macroalgae, as a major part of the third-generation (3G) biomass, has great potential for bioenergy development due to its species-abundant, renewable and carbohydrate-rich properties. Diluted acid treatment is one of the most effective approaches to releasing fermentable sugars from macroalgal biomass in a short period, but the optimal conditions need to be explored to maximize the hydrolytic yield for the subsequent microbial conversion. Therefore, this review aims to summarize the latest advances in various acids and other auxiliary methods adopted to increase the hydrolytic efficiency of macroalgae. Following an overview of the strategies of different algal types, methods involved in the bioconversion of biofuels and microbial fuel cells (MFC) from algal hydrolysates are also described. For the 3G biorefinery development, the review further discusses key challenges and trends for future utilizing marine biomass to achieve the large-scale industrial production.

Butyric acid production from spent coffee grounds by engineered Clostridium tyrobutyricum overexpressing galactose catabolism genes

Clostridium tyrobutyricum cannot utilize galactose, which is abundant in lignocellulose and red algae, as a carbon source for butyric acid production. Hence, when using galactose-rich coffee ground hydrolysate as the substrate, the fermentation performance of C. tyrobutyricum is poor. In this work, a recombinant strain, C. tyrobutyricum ATCC 25755/ketp, overexpressing galactose catabolism genes (galK, galE, galT, and galP) from Clostridium acetobutylicum ATCC 824 was constructed for the co-utilization of glucose and galactose. Batch fermentation in the bioreactor showed that ATCC 25755/ketp could efficiently utilize galactose without glucose-induced carbon catabolite repression and consume nearly 100% of the galactose present in the spent coffee ground hydrolysate. Correspondingly, the butyric acid concentration and productivity of ATCC 25755/ketp reached 34.3 g/L and 0.36 g/L·h, respectively, an increase of 78.6% and 56.5% compared with the wild-type strain, indicating its potential for butyric acid production from hydrolysates of inexpensive and galactose-rich biomass.

Enhanced Fermentable Sugar Production from Enteromorpha Polysaccharides by the Crude Enzymes of Vibrio sp. H11

In recent years, large-scale outbreaks of the green alga Enteromorpha prolifera in China's offshore waters have posed a serious threat. This study aimed to improve Enteromorpha polysaccharide (EP) enzymatic sugar production using the hydrolase system of Vibrio sp. H11, an EP-utilizing microbial strain. Strain H11 was found to contain 711 carbohydrate-related genes, and 259 genes belong to glycoside hydrolases that have the potential to hydrolyze EP. To maximize the capability of strain H11 to hydrolyze EP, both the culture medium and the composition were optimized. Response surface methodology analysis showed that maximal enzymatic production from strain H11 was 8.43 U/mL after 26-h incubation. When 50 g/L of EP were treated with crude H11 enzyme, the concentration of fermentation sugars increased by 36.12%. Under these conditions, the hydrolysates were capable of generating 3,217 mL/L of biogas and 6.74 g/L of biosolvents, with increases of 28.17 and 7.29%, respectively, compared to controls. The combined application of the H11 enzymatic system and anaerobic fermentation has the potential to improve the comprehensive application of EP.

Ethanol extract of propolis prevents high-fat diet-induced insulin resistance and obesity in association with modulation of gut microbiota in mice

Propolis has beneficial effects anti-inflammatory, anti-diabetes and anti-obesity in human or murine models, but its mechanism has not been fully elucidated. This study was to investigate the effects of ethanol extract of propolis (EEP) on the gut microbiota, and to analyze the associations between these alterations of gut microbiota and insulin resistance and obesity in high fat diet (HFD)-fed mice. Male C57BL/6J mice were fed with chow diet, high-fat diet, and high-fat diet supplemented with 1% EEP or 2%EEP. EEP supplementation reduced HFD-induced weight gain and liver fat accumulation, proinflammatory cytokines and insulin resistance, and improved glucose tolerance and lipid profile. Meanwhile, EEP supplementation in HFD-fed mice increased anti-obesity and anti-inflammatory bacteria such as genera Roseburia and Intestinimonas and species Parabacteroides goldsteinii and Parabacteroides distasonis, and reduced pro-inflammatory bacteria such as genera Faecalibaculum and Prevotella and species Bacteroides vulgatus. These dominant bacterial taxa altered by EEP were significantly associated with the metabolic parameters of insulin resistance and obesityin HFD-fed mice. The results in this study indicated that EEP reduced HFD-induced obesity and insulin resistant, which may be mediated by modulating the composition and function of gut microbiota.

Clostridium sp. as Bio-Catalyst for Fuels and Chemicals Production in a Biorefinery Context

Clostridium sp. is a genus of anaerobic bacteria capable of metabolizing several substrates (monoglycerides, diglycerides, glycerol, carbon monoxide, cellulose, and more), into valuable products. Biofuels, such as ethanol and butanol, and several chemicals, such as acetone, 1,3-propanediol, and butyric acid, can be produced by these organisms through fermentation processes. Among the most well-known species, Clostridium carboxidivorans, C. ragsdalei, and C. ljungdahlii can be highlighted for their ability to use gaseous feedstocks (as syngas), obtained from the gasification or pyrolysis of waste material, to produce ethanol and butanol. C. beijerinckii is an important species for the production of isopropanol and butanol, with the advantage of using hydrolysate lignocellulosic material, which is produced in large amounts by first-generation ethanol industries. High yields of 1,3 propanediol by C. butyricum are reported with the use of another by-product from fuel industries, glycerol. In this context, several Clostridium wild species are good candidates to be used as biocatalysts in biochemical or hybrid processes. In this review, literature data showing the technical viability of these processes are presented, evidencing the opportunity to investigate them in a biorefinery context.

Ultrasonic treatment enhances sludge disintegration and degradation in a photosynthetic bacteria-bioelectrochemical system

Excess sludge contains a large amount of organic matter, most of which is present in the form of bacteria and extracellular polymeric substances. In this study, a photosynthetic bioelectrochemical system (BES) combined with ultrasonic treatment (UT) was investigated to mineralize sludge. The sludge was disintegrated by the UT, and the supernatant separated from the treated sludge was further degraded through a bioelectrochemical system containing photosynthetic bacteria (PSB-BES). The UT efficiency was enhanced by supernatant separation. The PSB-BES method effectively improved the degradation of the soluble chemical oxygen demand (SCOD) from the supernatant. The SCOD and protein removal were increased 1.4 and 1.5 times, respectively, compared to BES without PSB. In addition, the effects of several key operating factors including illumination, voltage, and temperature were systematically investigated. This study provides a basis for further development of sludge mineralization processes. PRACTITIONER POINTS: The sludge was disintegrated by the ultrasound treatment. The supernatant separated from treated sludge was further degraded by a bioelectrochemical system combined with photosynthetic bacteria. The ultrasonic treatment efficiency was enhanced by supernatant separation. The PSB-BES method effectively improved the soluble chemical oxygen demand (SCOD) degradation from the supernatant. The effects of several key operating factors including light (dark-photo), voltage, and temperature were systematically investigated.

Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems

Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.

Enhanced bioconversion of hemicellulosic biomass by microbial consortium for biobutanol production with bioaugmentation strategy

As a renewable and sustainable source for next-generation biofuel production, lignocellulosic biomass can be effectively utilized in environmentally friendly manner. In this study, a stable, xylan-utilizing, anaerobic microbial consortium MC1 enriched from mangrove sediments was established, and it was taxonomically identified that the genera Ruminococcus and Clostridium from this community played a crucial role in the substrate utilization. In addition, a butanol-producing Clostridium sp. strain WST was introduced via the bioaugmentation process, which resulted in the conversion of xylan to biobutanol up to 10.8 g/L, significantly improving the butanol yield up to 0.54 g/g by 98-fold. When this system was further applied to other xylan-rich biomass, 1.09 g/L of butanol could be achieved from 20 g/L of corn cob. These results provide another new method to efficiently convert xylan, the main hemicellulose from lignocellulosic biomass into biofuels through a low-cost and eco-friendly manner.

The draft genome sequence of Clostridium sp. strain CT7, an isolate capable of producing butanol but not acetone and 1,3-propanediol from crude glycerol

A solventogenic Clostridium sp. strain CT7 which could utilize glycerol directly to produce high yields of butanol was isolated. In the presence of crude glycerol, strain CT7 synthesized butanol through a unique butanol-ethanol (BE) fermentation pathway in which acetone and 1,3-propanediol (1,3-PDO) were not produced. The genome of strain CT7 which has a G + C content of 30.3% was estimated to be 5.99 Mb and contained 4319 putative Open Reading Frames (ORF). The putative annotated genes, which play major roles in BE production from crude glycerol, included glycerol dehydrogenase gene (gdh), acetoacetyl-CoA transferase gene (ctfA/B), and bifunctional alcohol and aldehyde dehydrogenase gene (adhE). In addition, non-typical BE production is not coupled to 1,3-propanediol formation, which may due to the defect of 1, 3-PDO dehydrogenase gene (dhaT).

Enhanced performance and microbial community analysis of bioelectrochemical system integrated with bio-contact oxidation reactor for treatment of wastewater containing azo dye

Feasibility and superiority of the bioelectrochemical system integrated with biocontact oxidation (BES-BCO) for degradation and/or mineralization of azo dyes have been confirmed. In this study, the effects of hydraulic retention time (HRT), applied voltage, and dissolved oxygen (DO) concentration at the bioanode on the performance of BES-BCO and traditional BES were investigated. Using the response surface methodology, the optimum values of HRT, applied voltage, and DO concentration at the bioanode of BES-BCO were investigated to obtain the maximum decolouration and COD removal efficiency and minimum specific energy consumption (SEC). The microbial community structure in BES-BCO was studied for analyzing the change following the introduction of oxygen. The optimised solution was an applied voltage of 0.59V, HRT of 12h, and DO concentration of 0.96mg/L at the bioanode. Under such conditions, the DE, COD removal efficiency, and SEC values were 94.62±0.63%, 89.12±0. 32%, and 687.57±3.86J/g, respectively. In addition, after changing from BES to BES-BCO, the bacterial community structure of the bioanode underwent significant changes. Several aerobic aniline-degrading bacteria and anode-respiration bacteria (ARB) were found to dominate the community of the anode biofilm. The results showed that the removal of azo dye degradation by-products was closely correlated with the o-bioanode and the BCO bacterial community structure.

The Draft Genome Sequence of Clostridium sp. Strain NJ4, a Bacterium Capable of Producing Butanol from Inulin Through Consolidated Bioprocessing

A novel butanogenic Clostridium sp. NJ4 was successfully isolated and characterized, which could directly produce relatively high titer of butanol from inulin through consolidated bioprocessing (CBP). The assembled draft genome of strain NJ4 is 4.09 Mp, containing 3891 encoded protein sequences with G+C content of 30.73%. Among these annotated genes, a levanase, a hypothetical inulinase, and two bifunctional alcohol/aldehyde dehydrogenases (AdhE) were found to play key roles in the achievement of ABE production from inulin through CBP.

Consolidated processing of biobutanol production from food wastes by solventogenic Clostridium sp. strain HN4

In this study, biobutanol production from glucose, starch and food waste by newly identified Clostridium sp. strain HN4 was comprehensively investigated, which is capable of secreting amylase indigenously for the following acetone-butanol-ethanol fermentation. With pH adjustment, strain HN4 could produce 5.23 g/L of butanol from 60 g/L of starch with secretion of 1.95 U/mL amylase through consolidated bioprocessing. Further supplementation of 3 g/L of CaCO₃ and 0.5% non-ionic surfactant of Tween 80 could stimulate both amylase activities and the final butanol titer, leading to 17.64 g/L of butanol with yield of 0.15 g/g. Fed batch fermentation integrated with in situ removal could further improve the butanol titer to 35.63 g/L with yield of , representing the highest butanol production and yield from food waste. These unique features of Clostridium sp. strain HN4 could open the door to the possibility of cost-effective biobutanol production from food waste on a large scale.

Quantification of Neoagaro-Oligosaccharide Production through Enzymatic Hydrolysis and Its Anti-Oxidant Activities

Neoagaro-oligosaccharides (NAOS) have health benefits that are related to their amount and degree of polymerization (DP). However, the current methods that are used to quantify enzymatically released NAOS are un-specific and time-consuming. Agar has been extracted from Gelidium amansii and has been degraded by AgaXa (a recombinant β-agarase). Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) has been adapted in order to quantify NAOS. In addition, the anti-oxidant activity of the degraded samples has been assessed. We have found that the PACE method provided sensitive, precise, and accurate quantification for each of the six NAOS samples. PACE has revealed that the DP of the enzymatic products from the AgaXa digestion were mainly neoagaro-octaose and neoagaro-decaose. The degraded samples exhibited increased radical-scavenging activity towards 2,2-diphenyl-1-picrylhydrazyl and 2,2-azino-bis(3-ethylbenzothiazoline sulfonic acid) radicals. While the anti-oxidant activity may have been from NAOS activity and contributions from neoagaro-octaose and neoagaro-decaose. The adapted PACE method that has been presented here is promising for large sample analysis during quality control and for characterizing novel β-agarase degradation mechanisms.

High-efficient production of biobutanol by a novel Clostridium sp. strain WST with uncontrolled pH strategy

A novel Clostridium sp. strain WST isolated from mangrove sediments demonstrated its unique characteristics of producing high titer of biobutanol from low concentration of substrates via anaerobic fermentation. The strain is able to convert glucose and galactose to high amount of biobutanol up to 16.62 and 12.11 g/L, respectively, and the yields of 0.54 and 0.55 g/g were determined to be much higher than those from the previous reports on Clostridial batch fermentation. Moreover, the inherent strong regulatory system of strain WST also prompts itself to perform the fermentation process without any requirement of pH control. In addition to tolerance of high butanol concentration and negligible production of by-products (e.g., ethanol or acids), this strain has immense potential for the sustainable industry-scale production of biobutanol.

The Draft Genome Sequence of a Novel High-Efficient Butanol-Producing Bacterium Clostridium Diolis Strain WST

A wild-type solventogenic strain Clostridium diolis WST, isolated from mangrove sediments, was characterized to produce high amount of butanol and acetone with negligible level of ethanol and acids from glucose via a unique acetone-butanol (AB) fermentation pathway. Through the genomic sequencing, the assembled draft genome of strain WST is calculated to be 5.85 Mb with a GC content of 29.69% and contains 5263 genes that contribute to the annotation of 5049 protein-coding sequences. Within these annotated genes, the butanol dehydrogenase gene (bdh) was determined to be in a higher amount from strain WST compared to other Clostridial strains, which is positively related to its high-efficient production of butanol. Therefore, we present a draft genome sequence analysis of strain WST in this article that should facilitate to further understand the solventogenic mechanism of this special microorganism.

Exploitation of novel wild type solventogenic strains for butanol production

Butanol has been regarded as an important bulk chemical and advanced biofuel; however, large scaling butanol production by solventogenic Clostridium sp. is still not economically feasible due to the high cost of substrates, low butanol titer and yield caused by the toxicity of butanol and formation of by-products. Renewed interests in biobutanol as biofuel and rapid development in genetic tools have spurred technological advances to strain modifications. Comprehensive reviews regarding these aspects have been reported elsewhere in detail. Meanwhile, more wild type butanol producers with unique properties were also isolated and characterized. However, few reviews addressed these discoveries of novel wild type solventogenic Clostridium sp. strains. Accordingly, this review aims to comprehensively summarize the most recent advances on wild type butanol producers in terms of fermentation patterns, substrate utilization et al. Future perspectives using these native ones as chassis for genetic modification were also discussed.