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A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Industrial Fermentation".

Deadline for manuscript submissions: closed (10 December 2023) | Viewed by 34161

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Dr. Teresa Lopes Da Silva

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Bioenergy and Biorefineries Unit, National Laboratory of Energy and Geology, Estrada do Paço do Lumiar, 22, 1649-038 Lisbon, Portugal
Interests: microbial biorefineries; microbial fermentation; bioprocess monitoring; biofuels; intracellular lipids; high value-added products
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Dear Colleagues,

The increase in the world population has increased the energy demand in response to the population’s needs. Fossil fuels currently supply about 80% of the world's energy. However, this energy source is non-renewable, and the reserves are diminishing. Fossil fuel combustion increases the greenhouse gas emissions and other pollutants, which negatively affect the climate and human health. In addition, the geopolitical contexts concerning the main fossil fuel producers generate instability and uncertainty around the world.

Replacing fossil fuels with clean and renewable forms of energy is urgent and vital to ensure the sustainability, safety, and health of humankind’s future.

Biofuels derived from microorganisms have been considered an alternative to fossil fuels since their use is cleaner and emits fewer toxic chemicals than their fossil-fuel-derived counterparts.

However, so far, microbial biofuels are not economically competitive since their price is still higher than the price of fossil fuels.

A way to overcome this hindrance consists of using microorganisms to transform low-cost substrates, such as agriculture residues and industrial by-products and wastes into biofuels, simultaneously taking advantage of all the microbial biomass fractions, as well as the products produced by the microorganisms, as an integrated process. According to the International Energy Agency (IEA) Bioenergy Task 42, a biorefinery is “the sustainable processing of biomass into a spectrum of marketable products (food, feed, materials, chemicals) and energy (fuels, power, heat)”. Therefore, a holistic view of the production processes of microbial biofuels and bioproducts based on the biorefinery concept and circular economy principles is urgently needed to obtain sustainable biofuels and biocompounds derived from microorganisms. This approach will boost the value and profit obtained from the whole process, with a desired minimum environmental impact, producing sustainable biofuels and biocompounds.

The goal of this Special Issue is to publish recent and innovative research results as well as review papers on microbial biorefineries, emphasising feedstocks, processes, techniques, and products involved in this approach. If you would like to contribute a review paper, please contact one of the editors to discuss the topic’s relevance before submitting the manuscript.

Dr. Teresa Lopes Da Silva
Guest Editor

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Keywords

biorefinery
biofuels
microorganisms
bioproducts
bioprocesses
circular economy

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Published Papers (12 papers)

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Research

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14 pages, 2354 KiB

Open AccessArticle

Xylitol Production by Debaryomyces hansenii in Extracted Olive Pomace Dilute-Acid Hydrolysate

by Ana Rita C. Morais, Luís C. Duarte, Pedro Lourenço, Ivone Torrado, Teresa Brás, Luísa A. Neves and Florbela Carvalheiro

Fermentation 2023, 9(12), 1020; https://doi.org/10.3390/fermentation9121020 - 14 Dec 2023

Cited by 1 | Viewed by 1721

Abstract

The extracted olive pomace (EOP) is an industrial lignocellulosic by-product of olive pomace oil extraction, currently mainly used for energy production through combustion. In this work, the hemicellulosic fraction of EOP was selectively hydrolyzed by diluted acid hydrolysis to obtain pentose-rich hydrolysates that can potentially be upgraded by Debaryomyces hansenii, targeting xylitol production. The monosaccharides and degradation by-products released along the pre-treatment were quantified and several detoxification methods for the removal of potentially toxic compounds were evaluated, including pH adjustment to 5.5, the use of anion-exchange resins, adsorption into activated charcoal, concentration by evaporation, and membrane techniques, i.e., nanofiltration. The latter approach was shown to be the best method allowing the full removal of furfural, 41% of 5-hydroxymethylfurfural, 54% of acetic acid, and 67% of the phenolic compounds present in the hydrolysate. The effects of the supplementation of both non-detoxified and detoxified hydrolysates were also assessed. The non-detoxified hydrolysate, under aerobic conditions, supported the yeast growth and xylitol production at low levels. Supplementation with the low-cost corn steep liquor of the nanofiltration detoxified hydrolysate showed a higher xylitol yield (0.57 g/g) compared to the non-detoxified hydrolysate. The highest xylitol productivity was found in hydrolysate detoxified with anionic resins (0.30 g/L·h), which was 80% higher than in the non-detoxified culture medium. Overall, the results showed that EOP dilute acid hydrolysates can efficiently be used for xylitol production by D. hansenii if detoxification, and supplementation, even with low-cost supplements, are performed. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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14 pages, 1535 KiB

Open AccessArticle

Investigations for a Yarrowia-Based Biorefinery: In Vitro Proof-of-Concept for Manufacturing Sweetener, Cosmetic Ingredient, and Bioemulsifier

by Edina Eszterbauer and Áron Németh

Fermentation 2023, 9(9), 793; https://doi.org/10.3390/fermentation9090793 - 28 Aug 2023

Cited by 2 | Viewed by 1602

Abstract

Yarrowia lipolytica is a widely used microorganism in biotechnology since it is capable of producing a wide range of products (lipase, citric acid, polyols). A less-studied related strain is Y. divulgata, which is also capable of erythritol production in even higher concentration than most Y. lipolytica wild strains from glycerol as renewable feedstock. Thus, the aim of this work was to investigate Y. divulgata’s complex utilisation based on erythritol fermentation from glycerol to establish a Yarrowia-based biorefinery in which both the fermentation broth and separated cells are converted into high added-value products (erythritol, bioemulsifier, cosmetic ingredient, i.e., skin moisturizer). An important parameter of erythritol fermentation is an adequate oxygen level, so both the constant oxygen level and oxygen absorption rate were investigated regarding the three target products. DO (dissolved oxygen) = 10, 20, 30, 40% was examined in the bioreactor, and a KLa range of 18–655 h⁻¹ was investigated in both the bioreactor and in different types of shaking flasks, applying two different glycerol levels (100–150 g/L). The results showed that the Yarrowia divulagata NCAIM 1485 strain could produce one of the highest amounts of erythritol (44.14 ± 1 g/L) among wild-type yeasts from 150 g/L glycerol beside a K_La value of 655 h⁻¹. Cell-lysates skin hydrating activity was the highest (12%) when DO = 20% (K_La 26.4 h⁻¹) was applied. In all cases, the collected samples had an emulsification index above 69% which did not decrease below 54% after 24 h, showing good stability. Since Y. divulgata fermentations resulted in three high added-value products at the same time from a renewable raw material (glycerol), we concluded that it is suitable for complex utilisation in a microbial biorefinery, since the fermentation broth can be used for the isolation of a sweetener and bioemulsifier; meanwhile, the separated cells can be processed for cosmetic application as a skin moisturizer. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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12 pages, 1827 KiB

Open AccessArticle

Single-Cell Oil Production by Engineered Ashbya gossypii from Non-Detoxified Lignocellulosic Biomass Hydrolysate

by Miguel Francisco, Tatiana Q. Aguiar, Gabriel Abreu, Susana Marques, Francisco Gírio and Lucília Domingues

Fermentation 2023, 9(9), 791; https://doi.org/10.3390/fermentation9090791 - 27 Aug 2023

Cited by 4 | Viewed by 1608

Abstract

In this work, microbial lipid production from non-detoxified Eucalyptus bark hydrolysate (EBH) with oleaginous xylose-utilizing Ashbya gossypii strains was explored. The best producing strain from a set of engineered strains was identified in synthetic media mimicking the composition of the non-detoxified EBH (SM), the lipid profile was characterized, and yeast extract and corn steep liquor (CSL) were pinpointed as supplements enabling a good balance between lipid accumulation, biomass production, and autolysis by A. gossypii. The potential of the engineered A. gossypii A877 strain to produce lipids was further validated and optimized with minimally processed inhibitor-containing hydrolysate and high sugar concentration, and scaled up in a 2 L bioreactor. Lipid production from non-detoxified EBH supplemented with CSL reached a lipid titer of 1.42 g/L, paving the way for sustainable single-cell oil production within the concept of circular economy and placing lipids as an alternative by-product within microbial biorefineries. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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14 pages, 2551 KiB

Open AccessArticle

Single-Cell Protein Production from Industrial Off-Gas through Acetate: Techno-Economic Analysis for a Coupled Fermentation Approach

by Elodie Vlaeminck, Evelien Uitterhaegen, Koen Quataert, Tom Delmulle, Stoilas-Stylianos Kontovas, Nikiforos Misailidis, Rafael G. Ferreira, Demetri Petrides, Karel De Winter and Wim K. Soetaert

Fermentation 2023, 9(8), 771; https://doi.org/10.3390/fermentation9080771 - 18 Aug 2023

Cited by 7 | Viewed by 4573

Abstract

Third-generation (3G) biorefineries harnessing industrial off-gases have received significant attention in the transition towards a sustainable circular economy. However, uncertainties surrounding their techno-economic feasibility are hampering widespread commercialization to date. This study investigates the production of single-cell protein (SCP), a sustainable alternative food and feed protein, from steel mill off-gas through an efficient coupled fermentation approach utilizing acetate as an intermediate. A comprehensive model that comprises both the gas-to-acetate and the acetate-to-SCP fermentation processes, as well as gas pretreatment and downstream processing (DSP) operations, was developed and used to perform a techno-economic analysis (TEA). Sensitivity analyses demonstrated that significant cost reductions can be achieved by the process intensification of the gas-to-acetate fermentation. As such, an increase in the acetate concentration to 45 g/L and productivity to 4 g/L/h could lead to a potential cost reduction from 4.15 to 2.78 USD/kg. In addition, the influence of the production scale and other economic considerations towards the commercialization of off-gas-based SCPs are discussed. Conclusively, this research sheds light on the practical viability of a coupled fermentation process for SCP production by identifying key cost-influencing factors and providing targets for further optimization of the acetate platform, fostering sustainable and economically feasible bio-based innovations. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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12 pages, 2034 KiB

Open AccessArticle

Optimization of Esterase Production in Solid-State Fermentation of Agricultural Digestate

by Daniela Bulgari, Stefano Renzetti, Saida Messgo-Moumene, Eugenio Monti and Emanuela Gobbi

Fermentation 2023, 9(6), 524; https://doi.org/10.3390/fermentation9060524 - 29 May 2023

Cited by 8 | Viewed by 2066

Abstract

The continuous increase in biogas production poses the need for innovative applications for its by-products. Solid-state fermentation (SSF) has regained attention in the development of several products because of the possibility to use low-cost and easily available substrates, such as organic wastes. SSF represents a valuable process for agricultural digestate valorization in terms of enzyme production. In the present study, cellulase and esterase were produced by Trichoderma asperellum R on a digestate-based substrate in SSF, with esterase as the highest obtained activity. After assessing the effect of light on it, the esterase production in SSF was optimized using response surface methodology. The influence of substrate composition, temperature and humidity on the enzyme production was evaluated on two sets of data generated based on digestate concentration (50% and 70% w/w). The statistical analyses revealed that these parameters affected esterase production only when Trichoderma asperellum grew on substrate containing 50% w/w of digestate. The best esterase activity (264.6 mU/mg total protein) was achieved with the following optimized SSF parameters: 50% digestate, 50% fruits, 10% sawdust, 30 °C. The current finding of esterase production on digestate-based substrates makes the SSF method presented here a sustainable and completely circular technology. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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18 pages, 3692 KiB

Open AccessArticle

Fermentation of the Brown Seaweed Alaria esculenta by a Lactic Acid Bacteria Consortium Able to Utilize Mannitol and Laminari-Oligosaccharides

by Leila Allahgholi, Madeleine Jönsson, Monica Daugbjerg Christensen, Andrius Jasilionis, Mehrnaz Nouri, Shahram Lavasani, Javier A. Linares-Pastén, Guðmundur Óli Hreggviðsson and Eva Nordberg Karlsson

Fermentation 2023, 9(6), 499; https://doi.org/10.3390/fermentation9060499 - 23 May 2023

Cited by 1 | Viewed by 2765

Abstract

The brown seaweed Alaria esculenta is the second most cultivated species in Europe, and it is therefore of interest to expand its application by developing food products. In this study, a lactic acid bacteria consortium (LAB consortium) consisting of three Lactiplantibacillus plantarum strains (relative abundance ~94%) and a minor amount of a Levilactobacillus brevis strain (relative abundance ~6%) was investigated for its ability to ferment carbohydrates available in brown seaweed. The consortium demonstrated the ability to ferment glucose, mannitol, galactose, mannose, and xylose, of which glucose and mannitol were the most favored substrates. No growth was observed on fucose, mannuronic and guluronic acid. The consortium used different pathways for carbohydrate utilization and produced lactic acid as the main metabolite. In glucose fermentation, only lactic acid was produced, but using mannitol as a carbohydrate source resulted in the co-production of lactic acid, ethanol, and succinate. Xylose fermentation resulted in acetate production. The consortium was also able to utilize laminari-oligosaccharides (DP2-4), obtained after enzymatic hydrolysis of laminarin, and produced lactic acid as a metabolite. The consortium could grow directly on A. esculenta, resulting in a pH decrease to 3.8 after 7 days of fermentation. Incubation of the same seaweed in corresponding conditions without inoculation resulted in spoilage of the seaweed by endogenous bacteria. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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10 pages, 1190 KiB

Open AccessCommunication

Pyruvic Acid Production from Sucrose by Escherichia coli Pyruvate Dehydrogenase Variants

by W. Chris Moxley and Mark A. Eiteman

Fermentation 2023, 9(5), 478; https://doi.org/10.3390/fermentation9050478 - 16 May 2023

Viewed by 2826

Abstract

Sucrose is an abundant, cheap, and renewable carbohydrate which makes it an attractive feedstock for the biotechnological production of chemicals. Escherichia coli W, one of the few safe E. coli strains able to metabolize sucrose, was examined for the production of pyruvate. The repressor for the csc regulon was deleted in E. coli W strains expressing a variant E1 component of the pyruvate dehydrogenase complex, and these strains were screened in a shake flask culture for pyruvate formation from sucrose. The pyruvate accumulated at yields of 0.23–0.57 g pyruvate/g sucrose, and the conversion also was accompanied by the accumulation of some fructose and/or glucose. Selected strains were examined in 1.25 L controlled batch processes with 40 g/L sucrose to obtain time–course formation of pyruvate and monosaccharides. Pyruvate re-assimilation was observed in several strains, which demonstrates a difference in the metabolic capabilities of glucose- and sucrose-grown E. coli cultures. An engineered strain expressing AceE[H106M;E401A] generated 50.6 g/L pyruvate at an overall volumetric productivity of 1.6 g pyruvate/L·h and yield of 0.68 g pyruvate/g sucrose. The results demonstrate that pyruvate production from sucrose is feasible with comparable volumetric productivity and yield to glucose-based processes. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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12 pages, 1227 KiB

Open AccessArticle

Isolation and Cultivation of Penicillium citrinum for Biological Control of Spodoptera litura and Plutella xylostella

by Hoang Chinh Nguyen, Kuan-Hung Lin, Thanh Phong Nguyen, Hong Son Le, Kim Ngan Ngo, Dinh Chuong Pham, Tuyet Nhung Tran, Chia-Hung Su and Colin J. Barrow

Fermentation 2023, 9(5), 438; https://doi.org/10.3390/fermentation9050438 - 2 May 2023

Cited by 1 | Viewed by 3761

Abstract

Biological control agents are a promising substitute for chemical pesticides in agricultural pest management. In this study, Penicillium sp. with high pathogenicity to the agricultural pests oriental leafworm moth (Spodoptera litura) and diamondback moth (Plutella xylostella) were isolated from naturally infected insects and grown on different agricultural residues as an inexpensive substrate for their sporulation. Ten strains of Penicillium (P.01~P.10) were identified as P. citrinum based on morphological features and molecular studies, with sequence analysis using an internal transcribed spacer region. Different fungal isolates exhibited a varying degree of pathogenicity against S. litura and Pl. xylostella, and strains P.04 and P.09 showed the highest pathogenicity to S. litura, with a mortality rate of 92.13% after 7 days of treatments, while strain P.06 resulted in the highest mortality of Pl. xylostella (100%) after 6 days of treatment. Moreover, among ten isolates infected with both S. litura and P. xylostella, P.06 showed potential virulence against S. litura and Pl. xylostella, with lethal time for 50% mortality (LT₅₀) values of 4.5 days and 3.0 days, respectively. The ten isolates showed higher virulence to Pl. xylostella than to S. litura. The agro-industrial-based medium showed efficiency for the cultivation of isolates for sporulation on an industrial scale, suggesting that the newly isolated P. citrinum is a potential biological control agent for controlling insect pests and could be further developed for microbial pesticide production. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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Review

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28 pages, 5267 KiB

Open AccessReview

Oleaginous Yeast Biorefinery: Feedstocks, Processes, Techniques, Bioproducts

by Teresa Lopes da Silva, Afonso Fontes, Alberto Reis, Carla Siva and Francisco Gírio

Fermentation 2023, 9(12), 1013; https://doi.org/10.3390/fermentation9121013 - 12 Dec 2023

Viewed by 3890

Abstract

The world climate crisis has triggered the search for renewable energy sources. Oleaginous yeasts are a potential renewable source of biofuels. However, the yeast-derived biofuels cost is still non-competitive with the fossil fuel prices. To improve the sustainability of yeast-derived biofuels, it is necessary to valorize all yeast biomass fractions, an approach based on the biorefinery concept. This review describes the present situation of the oleaginous yeast biorefinery research, emphasizing the feedstock, processes and techniques involved in this concept, as well as on potential bioproducts that can be obtained from oleaginous yeast biomass. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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26 pages, 2384 KiB

Open AccessReview

A Review of Liquid and Gaseous Biofuels from Advanced Microbial Fermentation Processes

by Sonil Nanda, Falguni Pattnaik, Biswa R. Patra, Kang Kang and Ajay K. Dalai

Fermentation 2023, 9(9), 813; https://doi.org/10.3390/fermentation9090813 - 6 Sep 2023

Cited by 9 | Viewed by 4039

Abstract

Biofuels are the sustainable counterparts of fossil fuels to meet the increasing energy demands of the current and future generations. Biofuels are produced from waste organic residues with the application of mechanical, thermochemical and biological methods and processes. While mechanical and thermochemical conversion processes involve the use of heat, pressure, catalysts and other physicochemical attributes for the direct conversion of biomass, biological conversion requires microorganisms and their enzymes as biocatalysts to degrade the fermentable substrates into biofuels and biochemicals. This article highlights the advances and opportunities in biological conversion technologies for the development of a closed-loop biorefinery approach. This review highlights the distinction between biological and thermochemical conversion technologies, including a discussion on the pros and cons of the pathways. Different categories of biological conversion processes, such as enzymatic saccharification, submerged fermentation, solid-state fermentation and simultaneous saccharification and fermentation are also discussed in this article. The main essence of this article is the description of different fermentative technologies to produce next-generation biofuels, such as bioethanol, biobutanol, biomethane, biohydrogen and biodiesel. This article provides a state-of-the-art review of the literature and a technical perspective on the bioproduction of bioethanol, acetone–ethanol–butanol fermentation, anaerobic digestion, photo/dark fermentation, and the transesterification of lignocellulosic substrates to produce the above-mentioned biofuels. In addition, recommendations for improving bioprocessing efficiency and biofuel yields are provided in this comprehensive article. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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21 pages, 3640 KiB

Open AccessReview

Research Progress of Lytic Chitin Monooxygenase and Its Utilization in Chitin Resource Fermentation Transformation

by Delong Pan, Jinze Liu, Peiyao Xiao, Yukun Xie, Xiuling Zhou and Yang Zhang

Fermentation 2023, 9(8), 754; https://doi.org/10.3390/fermentation9080754 - 13 Aug 2023

Cited by 3 | Viewed by 1640

Abstract

Every year, seafood waste produced globally contains about 10 million tons of wasted crab, shrimp and lobster shells, which are rich in chitin resources. The exploitation and utilization of chitin resources are of great significance to environmental protection, economic development and sustainable development. Lytic polysaccharide monooxygenases (LPMOs) can catalyze polysaccharides by oxidative breakage of glycosidic bonds and have catalytic activity for chitin and cellulose, so they play an important role in the transformation of refractory polysaccharides into biomass. Although there have been many studies related to LPMOs, the research related to lytic chitin monooxygenases (LCMs) is still very limited. The specific catalytic mechanism of LCMs has not been fully elucidated, which poses a challenge to their application in industrial biomass conversion. This review introduces the present situation of resource development and utilization in chitin, the origin and classification of different LCMs families, the structural characteristics of LCMs and the relationship between structure and function. The research results related to activity detection, screening, preparation and transformation of LCMs were summarized and discussed. Finally, the synergistic effect of LCMs and chitin enzyme on biomass degradation was reviewed, and the existing problems and future research directions were pointed out. This is the first review focusing on Chitin-Active LPMOs in recent years, intending to provide a reference for applying chitin degradation enzymes system in the industry. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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23 pages, 1535 KiB

Open AccessReview

Creating Value from Acidogenic Biohydrogen Fermentation Effluents: An Innovative Approach for a Circular Bioeconomy That Is Acquired via a Microbial Biorefinery-Based Framework

by Patrick T. Sekoai, Viren Chunilall and Obinna Ezeokoli

Fermentation 2023, 9(7), 602; https://doi.org/10.3390/fermentation9070602 - 27 Jun 2023

Cited by 4 | Viewed by 2199

Abstract

As a response to the environmental and societal issues that emanate from the high reliance on fossil fuels, the world is now transitioning toward a circular bioeconomy. Acidogenic biohydrogen production is envisaged as a clean fuel of the future due to its non-polluting features and affordability. The major encumbrance for the industrialization of this process is due to the accumulation of metabolic inhibitors (volatile fatty acids (VFAs)), which lower the H₂ yields. This review discusses novel methods that can be adopted to valorize the acidogenic VFAs via a “cascade microbial biorefinery-based” approach that enables this process to be economically feasible as it leads to the concomitant production of diverse high-value-added products. The work also elucidates the key setpoint parameters governing the recovery of VFAs during the acidogenic H₂ process. It further explores the recent advances in the use of VFAs in microbial biorefineries. Finally, the paper provides some recommendations that might help develop acidogenic microbial biorefineries in the future. Studies focusing on microbial biorefineries tailored towards the valorization/beneficiation of acidogenic VFAs are very scarce in the literature. This work aims to provide new insights into microbial biorefinery-based processes involving the use of acidogenic VFAs as substrates. Full article

(This article belongs to the Special Issue Microbial Biorefineries)

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