Biodegradation and Fermentation in Biorefinery

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

Deadline for manuscript submissions: closed (21 December 2023) | Viewed by 20387

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Guest Editor
Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON M3J 1P3, Canada
Interests: green technology; environmental biotechnology; genetic engineering; enzyme technology; bioprocess development

Special Issue Information

Dear Colleagues,

The biorefinery concept is noticeably evolving to include the efficient conversion of diverse biomass feedstock into value-added products. The desire to replace fossil-based feedstock with renewable feedstock is leading to various technological innovations advancing biorefinery to become a suitable renewable equivalent to petroleum refinery. Biorefineries offer hope in organic waste valorization, the reduction of GHG emissions and the development of a circular bioeconomy.     

Microbial fermentation is one of the key components of a biorefinery platform, and harnesses the potential of microorganisms to convert diverse organic waste and biomass into biofuels and a spectrum of bio-based products. Fermentative bioconversion could produce a wide range of high-value and low-volume biochemicals, such as platform chemicals, pharmaceutical products, bioplastic building blocks, etc., as well as low-value and high-volume products such as biofuels. Nevertheless, there are several challenges associated with the fermentation process, especially in terms of economic process feasibility, scalability, and commercialization. Key challenges such as the quality of biomass, inhibitors, and the low conversion rate of complex biomass are actively being addressed to improve the fermentation process. The field is rapidly evolving, with various technological innovations and breakthrough research related to genetic engineering and strain improvement, as well as the optimization of process parameters to make the process more economical and sustainable.     

This Special Issue aims to reflect the significance and achievements of fermentation technology in biorefinery. The goal of this Issue is to publish original research, review, and short communication articles in the fields of bioprocesses, genetic engineering, microbial biodegradation, and their application in waste valorization, as well as the conversion of biomass into value-added products in energy, health, and bio-industrial sectors. 

Dr. Krishnamoorthy Hegde
Guest Editor

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Keywords

  • microbial fermentation
  • microbial biodegradation
  • genetic engineering
  • bioprocess engineering
  • biomass conversion
  • waste valorization
  • circular bioeconomy
  • bioproducts
  • biorefinery
  • biofuels

Published Papers (9 papers)

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Research

23 pages, 2377 KiB  
Article
Process Sustainability Analysis of Biorefineries to Produce Biofertilizers and Bioenergy from Biodegradable Residues
by Johana Marisol Burbano-Cuasapud, Juan Camilo Solarte-Toro, Daissy Lorena Restrepo-Serna and Carlos Ariel Cardona Alzate
Fermentation 2023, 9(9), 788; https://doi.org/10.3390/fermentation9090788 - 25 Aug 2023
Viewed by 1367
Abstract
The use of chemical fertilizers is essential for agricultural development when soils do not have the nutritional balance required for plants. The continuous use of chemical fertilizers has changed the soil physicochemical and biological properties. Biofertilizer production has been considered as an alternative [...] Read more.
The use of chemical fertilizers is essential for agricultural development when soils do not have the nutritional balance required for plants. The continuous use of chemical fertilizers has changed the soil physicochemical and biological properties. Biofertilizer production has been considered as an alternative to reduce chemical fertilizers dependence and the environmental impact. The aim of this study is the evaluation of three technologies for the production of biofertilizers and bioenergy at technical, economic, environmental, and social levels. Ammonium sulfate and digestate-based biofertilizers were obtained via anaerobic digestion; biochar was produced via gasification; and amino acids as plants biostimulants were obtained via protein hydrolysis. Different indicators were calculated for elucidating the sustainability of the processes. Technical, economic, environmental, and social analysis is performed for each of the biorefineries processing stage (complex and stand-alone) without considering the agronomic stage or other value chain links. Scenario 1 presented a positive impact on the economic, environmental, and social aspects since this process has a payback period of 10 years, a carbon footprint of 0.67 kg CO2-eq/kg product, and a potential to generate nine jobs in the Colombian context due to the products portfolio, in contrast with scenario 2 and 3. As conclusion, the integration of biofertilizers and bioenergy in biorefineries have the potential to expand the range of bioproducts and to increase the process sustainability. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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22 pages, 2508 KiB  
Article
Joint Multi-Optimization of an Extremophilic Microbial Bioanode for Mitigation of Mixed Hazardous Azo Dyes in Textile Synthetic Wastewater
by Sirine Saadaoui, Benjamin Erable, Luc Etchevery, Ameur Cherif and Habib Chouchane
Fermentation 2023, 9(9), 782; https://doi.org/10.3390/fermentation9090782 - 24 Aug 2023
Viewed by 5487
Abstract
Bioelectrochemical systems (BESs), rather than physicochemical processes, are used for wastewater remediation, electricity production, and zero carbon dioxide emission. Textile effluents contain organic and inorganic compounds that can fuel BESs. The main goal of this study was to understand the interplay between the [...] Read more.
Bioelectrochemical systems (BESs), rather than physicochemical processes, are used for wastewater remediation, electricity production, and zero carbon dioxide emission. Textile effluents contain organic and inorganic compounds that can fuel BESs. The main goal of this study was to understand the interplay between the anode material, its surface area, the potential applied to the working electrode (WE), and the concentration of the co-substrate, and how these factors lead to the formation of highly efficient thermohalophilic bioanodes (THB) retrieved from Chott El Djerid (SCD) hypersaline sediment for the treatment of synthetic textile wastewater. To this end, twenty-seven bioanode formation experiments were designed using a Box-Behnken matrix and response surface methodology to understand concomitant interactions. All experiments were conducted in electrochemical reactors of final volume 750 mL inoculated with 80% of enrichment medium containing three azo dyes at a concentration of 300 ppm and 20% of biocatalyst microbial SCD source, at 45 °C. The optimal levels were predicted using NemrodW software as carbon felt (CF) anode material, 6 cm2 anode surface, 7 g/L glucose concentration, and −0.1 V applied potential. These theoretical results were experimentally validated, using maximum current output of 5.23 ± 0.30 A/m2, decolorization rate of 100%, and a chemical oxygen demand (COD) removal rate of 96 ± 1%. Illumina Miseq results revealed that bacterial community harbored the bioanode was dominated at phylum level by Firmicutes (67.1%). At the species level, the biofilm was mainly colonized by Orenia metallireducens species (59.5%). Obtained findings show a promising application of THB in the degradation of recalcitrant molecules as well as for the energy recovery. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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14 pages, 2525 KiB  
Article
Exploration and Biorefinery Antimicrobial Agent through Solid State Fermentation from Indonesia’s Marine Actinomycetes
by Aspita Laila, Fendi Setiawan, Widyastuti Widyastuti, Muhammad Rizky Fadhilah, Andi Setiawan, Ni Luh Gede Ratna Juliasih, Wawan Abdullah Setiawan, Ety Apriliana, Peni Ahmadi, Masayoshi Arai and John Hendri
Fermentation 2023, 9(4), 334; https://doi.org/10.3390/fermentation9040334 - 28 Mar 2023
Viewed by 1977
Abstract
This study aimed to obtain novel bioactive compounds derived from actinomycetes associated with marine biota from the coast of Indonesia. Actinomycetes have been identified as a potential source of bioactive compounds through enzymatic fermentation. In order to obtain bioactive compounds from the results [...] Read more.
This study aimed to obtain novel bioactive compounds derived from actinomycetes associated with marine biota from the coast of Indonesia. Actinomycetes have been identified as a potential source of bioactive compounds through enzymatic fermentation. In order to obtain bioactive compounds from the results of the biorefinery process, cultivation was performed by solid state fermentation (SSF) on shrimp shell waste medium. The inhibitory activity against pathogenic microorganisms was measured based on the optical density of samples from Gorontalo and Buleleng, Bali, Indonesia. Six isolates had a clear zone as an indicator of the chitinase activity of chitinase enzymes. The SSF extract, obtained after 14 days of incubation, was assayed for its antimicrobial activity by the 96-well plate microtiter method. Among the six isolates, isolate 19B19A1 had antibacterial and antifungal activity against Staphylococcus aureus and Malassezia globosa, respectively. DNA analysis indicated that the 19B19A1 isolate was Streptomyces tritolerans 19B19A1 and that its extract contained an alkaloid component that played a role in antimicrobial activity. These results indicate that shrimp shells can be used as a nutrient-rich alternative culture medium for actinomycetes. This study is expected to become a source of information related to biorefinery, especially in the exploration of bioactive compounds produced by actinomycetes. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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20 pages, 7955 KiB  
Article
Roles of Process Parameters on the Ricinoleic Acid Production from Castor Oil by Aspergillus flavus BU22S
by Shikha Singh, Sumit Sharma, Saurabh Jyoti Sarma and Satinder Kaur Brar
Fermentation 2023, 9(4), 318; https://doi.org/10.3390/fermentation9040318 - 23 Mar 2023
Cited by 1 | Viewed by 1922
Abstract
Ricinoleic acid is a biobased green chemical industrially produced from castor oil. Microbial conversion is a cleaner and greener approach to ricinoleic acid production from castor oil. These processes should be further optimized for a better yield of the product. Aspergillus flavus BU22S [...] Read more.
Ricinoleic acid is a biobased green chemical industrially produced from castor oil. Microbial conversion is a cleaner and greener approach to ricinoleic acid production from castor oil. These processes should be further optimized for a better yield of the product. Aspergillus flavus BU22S was used to convert castor oil into ricinoleic acid. The strain was isolated and identified by molecular biological techniques. It was found to be effective in the biotransformation of castor oil. The ricinoleic acid production and dry cell weight of the fungus were studied as functions of time. In this study, to increase the yield of ricinoleic acid and decrease the oil loss, which microorganisms utilizes in biomass production, response surface methodology (RSM) has been used for process optimization. The central composite design was used to optimize the predictor variables such as oil concentration (% w/v), glucose concentration (% w/v), and calcium chloride concentration (% w/v) to increase the overall yield of ricinoleic acid. A quadratic model was found to be the best fit to predict the responses of the experimental results. The model suggested that the concentrations of oil, glucose, and calcium chloride should be lower in order to increase the ricinoleic acid yield and minimize the oil loss. The bench scale studies of optimized conditions from RSM were also conducted. The yield of ricinoleic acid in batch and fed-batch culture studies was also compared. The yield of the ricinoleic acid in batch culture was 21.67 g/kg of total oil. The yield of ricinoleic acid in fed-batch culture in the absence of an external air supply was 46.77 g/kg of total oil. In this case, the oil loss was also reduced to only 12%. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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12 pages, 1430 KiB  
Article
Evaluating the Potential of Newly Developed Energy Cane Clones for First- and Second-Generation Ethanol Production
by Sutticha Na-Ranong Thammasittirong, Prasert Chatwachirawong, Kedwarin Khemdee and Anon Thammasittirong
Fermentation 2023, 9(3), 267; https://doi.org/10.3390/fermentation9030267 - 08 Mar 2023
Cited by 2 | Viewed by 1347
Abstract
The rapid increases in fuel ethanol demand and food security concerns have driven the need for diverse feedstocks in the ethanol production process. Energy cane is an energy crop that is an ideal sustainable biofuel feedstock. The present study evaluated ethanol production of [...] Read more.
The rapid increases in fuel ethanol demand and food security concerns have driven the need for diverse feedstocks in the ethanol production process. Energy cane is an energy crop that is an ideal sustainable biofuel feedstock. The present study evaluated ethanol production of the juice and bagasse of two newly developed energy cane clones, TByEFC08-0035 and TByEFC10-0004. The results of the chemical composition analyses of the juice and bagasse samples revealed that the two energy cane clones contained high contents of both sucrose (15.36–17.95%) and fiber (13.44–24.16%). The maximum ethanol concentrations from the juice on a laboratory scale (87.10 g/L) and on an agronomic scale (1211.76 kg/ha) were recorded for TByEFC10-0004 fermented with a new isolate Kluyveromyces marxianus SJT83, whereas the maximum ethanol concentrations from bagasse on a laboratory scale (9.81 g/L) and on an agronomic scale (790.68 kg/ha) were reached with TByEFC08-0035 fermented with Scheffersomyces shehatae TTC79. The total ethanol yields from the juice and bagasse samples per cultivation area of both energy cane clones were in the range 1294.23–1469.14 kg/ha, being 1.70–1.93 and 1.08–1.23 times higher than the control energy cane Biotec2 variety and the commercial sugar cane Khon Kaen3 variety, respectively. This study revealed the potential of the energy cane clones TByEFC08-0035 and TByEFC10-0004 currently being developed as sugar and lignocellulose substrates for first- and second-generation ethanol industry applications. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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20 pages, 3116 KiB  
Article
Geranyl Diphosphate Synthase (CrtE) Inhibition Using Alendronate Enhances Isoprene Production in Recombinant Synechococcus elongatus UTEX 2973: A Step towards Isoprene Biorefinery
by Indrajeet Yadav, Akhil Rautela, Agendra Gangwar, Vigya Kesari, Aditya K. Padhi and Sanjay Kumar
Fermentation 2023, 9(3), 217; https://doi.org/10.3390/fermentation9030217 - 24 Feb 2023
Cited by 6 | Viewed by 1982
Abstract
A hemiterpene, isoprene, is commercially produced from crude oil refining processes. As a result of fossil fuel depletion, isoprene production process development is gaining attention from recombinant cyanobacteria and other microbial systems for its industrial and biofuel applications. In the present study, a [...] Read more.
A hemiterpene, isoprene, is commercially produced from crude oil refining processes. As a result of fossil fuel depletion, isoprene production process development is gaining attention from recombinant cyanobacteria and other microbial systems for its industrial and biofuel applications. In the present study, a fast-growing and CO2-tolerant cyanobacteria, Synechococcus elongatus UTEX 2973, is engineered with Pueraria montana isoprene synthase (IspS) at neutral site I (NSI) in the genome of S. elongatus UTEX 2973. Furthermore, to enhance isoprene production a key enzyme (isopentenyl diphosphate isomerase, IDI) of the methyl-D-erythritol 4-phosphate (MEP) pathway is also overexpressed at neutral site III (NSIII). Wild-type and recombinant strains of S. elongatus UTEX 2973 (UTEX IspS and UTEX IspS.IDI) are studied for growth and isoprene production in the presence of an inducer (IPTG) and/or inhibitor (alendronate). Alendronate is used for the inhibition of geranyl diphosphate synthase (CrtE), downstream of the MEP pathway that catalyzes dimethylallyl diphosphate/isopentenyl pyrophosphate (DMAPP/IPP) condensation in the recombinant UTEX 2973 strains. The docking studies on SeCrtE (CrtE of Synechcoccus elongatus PCC 7942) and alendronate as an inhibitor have revealed that alendronate binds more tightly than IPP in the cavity of SeCrtE, with a higher number of intermolecular interactions and energy. The UTEX IspS strain has shown isoprene production below the limit of detection in the presence of an inducer and/or inhibitor; however, production studies using UTEX IspS.IDI showed a maximum production of 79.97 and 411.51 µg/g dry cell weight (DCW) in a single day in the presence of an inducer only and an inducer along with an inhibitor, respectively. The UTEX IspS.IDI strain produced 0.41 mg/g DCW of cumulative isoprene in the presence of an inducer and 1.92 mg/g DCW in the presence of an inducer as well as an inhibitor during six days of production. The yield improvement of isoprene is observed as being 4.7-fold by using the inhibition strategy, which is used for the first time in the recombinant cyanobacterial system. The average productivities of isoprene obtained from UTEX IspS.IDI are observed to be 2.8 μg/g DCW/h in the presence of an inducer and 13.35 μg/g DCW/h in the presence of an inducer as well as an inhibitor. This study provides a basis for the process development and yield improvement in isoprene production using a novel inhibition strategy in fast-growing recombinant cyanobacteria. Recombinant strains and metabolic pathway inhibition studies can be used in future attempts to photosynthetically produce hemiterpenes. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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11 pages, 1286 KiB  
Article
Crabtree Effect on Rhodosporidium toruloides Using Wood Hydrolysate as a Culture Media
by Carlos S. Osorio-González, Rahul Saini, Krishnamoorthy Hegde, Satinder Kaur Brar, Alain Lefebvre and Antonio Avalos Ramírez
Fermentation 2023, 9(1), 11; https://doi.org/10.3390/fermentation9010011 - 23 Dec 2022
Cited by 2 | Viewed by 1612
Abstract
The interest in microorganisms to produce microbial lipids at large-scale processes has increased during the last decades. Rhodosporidium toruloides-1588 could be an efficient option for its ability to simultaneously utilize five- and six-carbon sugars. Nevertheless, one of the most important characteristics that [...] Read more.
The interest in microorganisms to produce microbial lipids at large-scale processes has increased during the last decades. Rhodosporidium toruloides-1588 could be an efficient option for its ability to simultaneously utilize five- and six-carbon sugars. Nevertheless, one of the most important characteristics that any strain needs to be considered or used at an industrial scale is its capacity to grow in substrates with high sugar concentrations. In this study, the effect of high sugar concentrations and the effect of ammonium sulfate were tested on R. toruloides-1588 and its capacity to grow and accumulate lipids using undetoxified wood hydrolysates. Batch fermentations showed a catabolic repression effect on R. toruloides-1588 growth at sugar concentrations of 120 g/L. The maximum lipid accumulation was 8.2 g/L with palmitic, stearic, oleic, linoleic, and lignoceric acids as predominant fatty acids in the produced lipids. Furthermore, R. toruloides-1588 was able to utilize up to 80% of the total xylose content. Additionally, this study is the first to report the effect of using high xylose concentrations on the growth, sugar utilization, and lipid accumulation by R. toruloides-1588. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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14 pages, 2537 KiB  
Article
Overexpression of LAS21 in Cellulase-Displaying Saccharomyces cerevisiae for High-Yield Ethanol Production from Pretreated Sugarcane Bagasse
by Jantima Arnthong, Piyada Bussadee, Apisan Phienluphon, Pacharawan Deenarn, Kan Tulsook, Sa-ngapong Plupjeen, Chatuphon Siamphan, Chakrit Tachaapaikoon, Verawat Champreda and Surisa Suwannarangsee
Fermentation 2022, 8(11), 652; https://doi.org/10.3390/fermentation8110652 - 18 Nov 2022
Cited by 5 | Viewed by 1560
Abstract
The valorization of lignocellulosic feedstocks into biofuels and biochemicals has received much attention due to its environmental friendliness and sustainability. However, engineering an ideal microorganism that can both produce sufficient cellulases and ferment ethanol is highly challenging. In this study, we have tested [...] Read more.
The valorization of lignocellulosic feedstocks into biofuels and biochemicals has received much attention due to its environmental friendliness and sustainability. However, engineering an ideal microorganism that can both produce sufficient cellulases and ferment ethanol is highly challenging. In this study, we have tested seven different genes that are involved in glycosylphosphatidylinositol (GPI) biosynthesis and remodeling for the improvement of cellulase activity tethered on the S. cerevisiae cell surface. It was found that the overexpression of LAS21 can improve β-glucosidase activity by 48.8% compared to the original strain. Then, the three cellulase genes (cellobiohydrolase, endoglucanase, and β-glucosidase) and the LAS21 gene were co-introduced into a diploid thermotolerant S. cerevisiae strain by a multiple-round transformation approach, resulting in the cellulolytic ECBLCCE5 strain. Further optimization of the bioprocess parameters was found to enhance the ethanol yield of the ECBLCCE5 strain. Scaling up the valorization of pretreated sugarcane bagasses in a 1 L bioreactor resulted in a maximum ethanol concentration of 28.0 g/L (86.5% of theoretical yield). Our study provides a promising way to improve the economic viability of second-generation ethanol production. Moreover, the engineering of genes involved in GPI biosynthesis and remodeling can be applied to other yeast cell surface display applications. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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21 pages, 2186 KiB  
Article
Production, Physicochemical and Structural Characterization of a Bioemulsifier Produced in a Culture Medium Composed of Sugarcane Bagasse Hemicellulosic Hydrolysate and Soybean Oil in the Context of Biorefineries
by Fernanda Gonçalves Barbosa, Paulo Ricardo Franco Marcelino, Talita Martins Lacerda, Rafael Rodrigues Philippini, Emma Teresa Giancaterino, Marcos Campos Mancebo, Júlio Cesar dos Santos and Silvio Silvério da Silva
Fermentation 2022, 8(11), 618; https://doi.org/10.3390/fermentation8110618 - 09 Nov 2022
Cited by 8 | Viewed by 1804
Abstract
Biosurfactants are amphipathic molecules, biodegradable, with reduced toxicity. They can be synthesized by fermentative processes from oleaginous compounds and agro-industrial by-products. In this context, the present study describes the production and the physical, chemical, and structural characterization of the bioemulsifier secreted by the [...] Read more.
Biosurfactants are amphipathic molecules, biodegradable, with reduced toxicity. They can be synthesized by fermentative processes from oleaginous compounds and agro-industrial by-products. In this context, the present study describes the production and the physical, chemical, and structural characterization of the bioemulsifier secreted by the yeast Scheffersomyces shehatae 16-BR6-2AI in a medium containing hemicellulosic sugarcane bagasse hydrolysate combined with soybean oil. The bioemulsifier was produced in Erlenmeyer flasks and isolated; then, the physicochemical and structural characterization of the formed molecule was carried out. The following fermentation parameters were obtained: YX/S = 0.45, YP/S = 0.083, and productivity of 0.076 g/L/h. The bioemulsifier was found to be a polymer containing 53% of carbohydrates, 40.92% of proteins, and 6.08% of lipids, respectively. The FTIR spectrum confirmed the presence of functional groups such as amides, amines, and carbonyls. The bioemulsifier was stable over a range of temperature (−20 °C to 120 °C), salinity (1–15%), and pH (2–12). It was observed that the biomolecule has a better emulsifying action in organic solvents with a non-polar character. Therefore, this biomolecule is a potential substitute for synthetic surfactants and can be used in different applications. Full article
(This article belongs to the Special Issue Biodegradation and Fermentation in Biorefinery)
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