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Application of Microbial Fermentation in Organic Matter Production

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A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 28665

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Dr. Alessandro Robertiello

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Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
Interests: microbiology; fermentation; microbial metabolism; bioreactors and fermenter; bacteria
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Dear Colleagues,

The compounds obtained from the fermentative metabolism of microorganisms have been intensively studied for their technological implications in the agri-food, pharmaceutical, and chemical industries. Microorganisms can be divided into:

Obligate anaerobes, with fermentation metabolism or anaerobic respiration;
Obligate aerobes, with aerobic respiration and part of fermentation metabolism;
Facultative anaerobes, with aerobic respiration and anaerobic pathways (anaerobic respiration or fermentation metabolism).

Furthermore, they may also be differentiated by their fermentation pathways, end-products, and for the substrate that can ferment. Fermentation begins with glycolysis in the same way as cellular respiration, but the formed pyruvate does not continue through the citric acid cycle. Two examples of typical metabolism in the fermentation process are lactic acid fermentation and ethanol fermentation.

In lactic acid fermentation, pyruvate accepts electrons from NADH and is reduced to lactic acid; in the homolactic fermentation, the end-product is only lactic acid, while the heterolactic fermentation contains a mixture of lactic acid, ethanol and/or acetic acid, and CO₂.

During ethanol fermentation, pyruvate is decarboxylated to acetaldehyde and CO_2, and then accepts electrons from NADH, reducing acetaldehyde to ethanol. Other common microbial fermentation pathways are:

Acetone–butanol–ethanol fermentation, with acetone, butanol, ethanol, and CO₂ as end-products;
Butanediol fermentation, with ethanol, formic and lactic acid, acetoin, 2,3 butanediol, CO₂, and hydrogen gas as end-products;
Butyric acid fermentation, with butyric acid, CO₂, and hydrogen gas as end-products;
Mixed acid fermentation, with acetic, formic, lactic, and succinic acids; and ethanol, CO₂, and hydrogen gas as end-products;
Propionic acid fermentation, with acetic acid, propionic acid, and CO₂ as end-products.

This Special Issue seeks but is not limited to original research articles or reviews; the impact of various microbial metabolisms on the fermentation process, highlighting the enzymes involved; natural and engineering metabolic pathway optimization; and the reduction of microbial stress conditions.

Dr. Alessandro Robertiello
Guest Editor

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Keywords

microbial metabolism
fermentation process
enzymes
metabolic engineering
microbial stress

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Published Papers (11 papers)

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Research

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14 pages, 2450 KiB

Open AccessArticle

Changes in the Concentration of Amino Acids and Bacterial Community in the Rumen When Feeding Artemisia absinthium and Cobalt Chloride

by Vitaly Ryazanov, Ekaterina Tarasova, Galimzhan Duskaev, Vladimir Kolpakov and Ivan Miroshnikov

Fermentation 2023, 9(8), 751; https://doi.org/10.3390/fermentation9080751 - 12 Aug 2023

Cited by 1 | Viewed by 1429

Abstract

The aim of the study was to analyze the effect of a plant feed additive based on Artemisia absinthium and the metal trace element CoCl₂ (cobalt chloride II) on the metabolism of amino acids closely related to the energy of feed and the bacterial community of the rumen of Kazakh white-headed bulls. Animals were divided into four groups: (A)—the control group of animals received the basic diet (BD), (B)—animals of the experimental group I were additionally given A. absinthium at a dose of 2.0 g/kg of dry matter (DM), (C)—II experimental group A. absinthium at a dose of 2.0 g/kg DM with additional CoCl₂ (1.5 mg/kg/DM), and (D)—III experimental group was given only CoCl₂ (1.5 mg/kg/DM) to study the rumen metabolism of amino acids and bacterial diversity of animals, rumen cannula were installed, the experiment was carried out using a 4 × 4 Latin square. It was found that additional feeding of A. absinthium, both separately and in combination with CoCl₂, led to a change in the indices of the alpha biodiversity of the bacterial community. Correlation analysis revealed a linear relationship between the concentration of amino acids and the rumen bacterial community (p ≤ 0.05). The relationship between the values of amino acid concentrations and certain OTUs was established, with a possible percentile probability of 95% for the genera unclassified Lachnospiraceae, unclassified Clostridiales, unclassified Bacteroidales, Fibrobacter, Ihubacter, Phocaeicola, Paludibacter, Akkermansia, Vampirovibrio, unclassified Ruminococcaceae, and Alistipes. Thus, the use of A. absinthium and CoCl₂ as feed additives, both in combination and without, leads to a change in the taxonomic structure affecting the concentration of amino acids. However, further research is needed to better understand the effectiveness and safety of these supplements. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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16 pages, 2328 KiB

Open AccessArticle

The Production of Bioaroma by Auriporia aurulenta Using Agroindustrial Waste as a Substrate in Submerged Cultures

by Rafael Donizete Dutra Sandes, Mônica Silva De Jesus, Hannah Caroline Santos Araujo, Raquel Anne Ribeiro Dos Santos, Juliete Pedreira Nogueira, Maria Terezinha Santos Leite Neta and Narendra Narain

Fermentation 2023, 9(7), 593; https://doi.org/10.3390/fermentation9070593 - 25 Jun 2023

Cited by 2 | Viewed by 1451

Abstract

The present study was carried out to investigate the potential of the basidiomycete Auriporia aurulenta to metabolize residues remaining from the processing of umbu, cajá, plum, and persimmon fruits for the production of natural aroma compounds using submerged fermentation. The volatile compounds obtained from the fermentation of A. aurulenta cultivated in these residues were extracted via stir bar sorptive extraction (SBSE) and analyzed using a gas chromatography-mass spectrometry (GC-MS) system. Esters and alcohols were the main compounds produced, with emphasis on the compounds 2-phenethyl acetate and 2-phenylethanol, which were mainly produced from umbu residue. The acid medium favored the production of 2-phenethyl acetate, reaching its maximum value (11.38 mg/L) on day 3.5, while higher concentrations of 2-phenylethanol were found in the basic medium, with optimal production (2.27 mg/L) on the 7th day. By varying the concentrations of pre-inoculum and residue in the optimization of this fermentation process, it was possible to double the production (24.47 mg/L) of 2-phenethyl acetate and obtain a seven times higher concentration (15.56 mg/L) of 2-phenylethanol. The diversity and expressive production of these aromatic compounds found in the fermentation media using these agroindustrial residues indicate that their use as substrates is an economical and environmentally viable alternative. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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15 pages, 1134 KiB

Open AccessArticle

Enhancing Succinic Acid Production by Sequential Adaptation of Selected Basfia succiniciproducens Strains to Arundo donax Hydrolysate

by Alessandro Robertiello, Ida Romano, Valeria Ventorino, Vincenza Faraco and Olimpia Pepe

Fermentation 2023, 9(6), 573; https://doi.org/10.3390/fermentation9060573 - 16 Jun 2023

Cited by 2 | Viewed by 1619

Abstract

Promising green technologies that can overcome the challenges associated with the use of fossil fuels require microorganisms that can effectively ferment lignocellulosic hydrolysate for biochemical production with reduced sensitivity to toxic chemicals derived from the pretreatment process. In this study, a sequential adaptation approach was developed to obtain new bacterial lines from Basfia (B.) succiniciproducens strains, which are adapted to inhibitory compounds of the Arundo (A.) donax hydrolysate or those that accumulate during the fermentation process. The early adaptation stages resulted in newly adapted B. succiniciproducens bacterial lines that can tolerate fermentation end-products such as acetic, lactic, and succinic acids, as well as toxic compounds such as furfural and hydroxymethylfurfural. These adapted bacterial lines were further investigated to assess their ability to produce succinic acid in an MHM medium supplemented with a filtrate of A. donax hydrolysate. Batch growth tests on a small laboratory scale showed that bacterial lines 2E and 4D produced 5.80 ± 0.56 g L⁻¹ and 5.81 ± 0.39 g L⁻¹ of succinic acid, respectively, after 24 h of fermentation. Based also on its growth rate, the adapted bacterial line B. succiniciproducens 4D was selected for tests in a lab-scale fermenter, where it was able to synthesize up to 17.24 ± 0.39 g L⁻¹ of succinate (corresponding to YSA/gluc 0.96 ± 0.02 g g⁻¹ and to YSA/(G + X) 0.48 ± 0.01 g g⁻¹) from MHM medium added with A. donax hydrolysate. Experiments showed an increase of ~17% compared to the control strain. The overall results demonstrate the potential of adapted bacterial lines for succinate production from A. donax hydrolysate and the development of improved technologies for bio-based succinic acid production. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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14 pages, 3567 KiB

Open AccessArticle

Adaptive Laboratory Evolution of Bacillus subtilis 168 for Efficient Production of Surfactin Using NH₄Cl as a Nitrogen Source

by Jie Li, Weiyi Tao, Shenghui Yue, Zhangzhong Yuan and Shuang Li

Fermentation 2023, 9(6), 525; https://doi.org/10.3390/fermentation9060525 - 29 May 2023

Cited by 3 | Viewed by 2876

Abstract

Bacillus subtilis strain 168 is commonly used as a host to produce recombinant proteins and as a chassis for bio-based chemicals production. However, its preferred nitrogen source is organic nitrogen, which greatly increases production costs. In this study, adaptive laboratory evolution (ALE) was used to improve B. subtilis 168 growth using NH₄Cl as the sole nitrogen source. The cell density (OD₆₀₀) of a mutant strain LJ-3 was 208.7% higher than that of the original strain. We also optimized the metal ions in the medium and this resulted in a further increase in growth rate by 151.3%. Reintroduction of the sfp+ gene into strain LJ-3 led to the LJ-31 clone, which restored LJ-3’s ability to synthesize surfactin. The fermentation system was optimized (C/N, aeration, pH) in a 5 L bioreactor. Dry cell weight of 7.4 g/L and surfactin concentration of 4.1 g/L were achieved using the optimized mineral salt medium after 22 h of batch fermentation with a Y_P/S value of 0.082 g/g and a Y_P/X of 0.55 g/g. HPLC analysis identified the surfactin isoforms produced by strain LJ-31 in the synthetic medium as C₁₃-surfactin 13.3%, C₁₄-surfactin 44.02%, and C₁₅-surfactin 32.79%. Hence, the variant LJ-3 isolated by ALE is a promising engineering chassis for efficient and cost-effective production of a variety of metabolites. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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15 pages, 3541 KiB

Open AccessArticle

Dynamic Responses of Streptomyces albulus QLU58 and Its Acid-Tolerant Derivatives to the Autoacidification in ε-Poly-l-Lysine Production

by Xidong Ren, Yan Chen, Yangzi Guo, Kunpeng Li, Chenying Wang and Xinli Liu

Fermentation 2023, 9(5), 459; https://doi.org/10.3390/fermentation9050459 - 10 May 2023

Cited by 1 | Viewed by 1594

Abstract

Streptomyces albulus is a kind of safety bacteria that is used to produce a natural food preservative named ε-poly-l-lysine (ε-PL). Environmental autoacidification (the pH declined from 6.8 to approximately 3.0) inevitably occurred in ε-PL biosynthesis by S. albulus. In this study, the dynamic responses of S. albulus QLU58 and its acid-tolerant mutants to autoacidification were investigated at the physiological and transcriptional levels. The results showed that cell growth, ε-PL production, cell respiratory activity, and intracellular pH (pH_i) homeostasis were disturbed by autoacidification. In the initial autoacidification stage (before 24 h), the acid tolerance of S. albulus was effectively improved by increasing the intracellular ATP and related amino acids contents and the H⁺-ATPase activity, regulating the membrane fatty acids composition, and maintaining the pH_i at about 7.7. However, as the autoacidification degree deepened (after 24 h), the metabolic activities decreased and negative cell growth appeared, which weakened the acid tolerance and caused the pH_i to decline to about 6.5. Additionally, the acid-tolerant mutants exhibited better performances during autoacidification, which was also confirmed by the related genes’ improved transcription levels. These results provide references for the analysis of progressive environmental modification in ε-PL production. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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19 pages, 2526 KiB

Open AccessArticle

The Profile of Exopolysaccharides Produced by Various Lactobacillus Species from Silage during Not-Fat Milk Fermentation

by Elena Nikitina, Tatyana Petrova, Alya Sungatullina, Oxana Bondar, Maria Kharina, Polina Mikshina, Elizaveta Gavrilova and Airat Kayumov

Fermentation 2023, 9(2), 197; https://doi.org/10.3390/fermentation9020197 - 20 Feb 2023

Cited by 9 | Viewed by 2570

Abstract

The exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) and released into fermented milk play a protective role from stress factors as well as improve emulsifying and thickening properties of the product, reduce syneresis, and increase elasticity. Here we report the relationship between the properties, composition, and microstructure of EPS produced by six different strains of lactobacilli (L. bulgaricus and five strains isolated from silage). The presence of fructose together with negative-charged uronic acid was found to play a significant role in changing the EPS properties. Thus, the increased fraction of rhamnose and arabinose and a decrease in xylose leads to compaction of the EPS, decreased porosity and increased both OH- and superoxide scavenging and Fe-chelating activities. By contrast, increased xylose and low rhamnose and arabinose apparently leads to loss of large aggregates and high DPPH activity and FRAP. The high content of glucose, however, provides the formation of large pores. The increased fructan fraction (69.9 mol%) with a high fraction of galacturonic (18.2 mol%) and glucuronic acids (6.7 mol%) apparently determines the highly porous spongy-folded EPS microstructure. Taken together, our results indicate that both the quantitative characteristics of the individual components of the fraction and the structural features of EPS are important for the antioxidant potential of fermented milk and depend on the strain used for milk fermentation, suggesting the advantage of a multicomponent starter to achieve the optimal beneficial properties of fermented milk. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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18 pages, 307 KiB

Open AccessArticle

Two-Stage Fermented Feather Meal Enhances Growth Performance and Amino Acid Digestibility in Broilers

by Ruei-Han Yeh, Chia-Wen Hsieh and Kuo-Lung Chen

Fermentation 2023, 9(2), 128; https://doi.org/10.3390/fermentation9020128 - 29 Jan 2023

Cited by 3 | Viewed by 2638

Abstract

The study aimed to investigate the dose tolerance of enzymatically degraded feather meal (EFM) in the diet, and the effect of the two-stage fermented feather meal on the growth performance and amino acid digestibility of broilers. In trial 1, 160 one-day-old broilers were randomly assigned into 0, 10, 15, and 20% EFM groups. In trial 2, 160 one-day-old broilers were randomly assigned into control, 10% EFM, Bacillus subtilis var. natto N21 + B. coagulans L12 fermented EFM (BBEFM), and B. subtilis var. natto N21 + Saccharomyces cerevisiae Y10 fermented EFM (BSEFM) groups. Trial 3 involved 32 twenty-one-day-old male broilers randomly assigned into nitrogen-free diet, highly digestible protein, EFM, and BSEFM groups for a 7-day metabolic trial. During all of the feeding periods, increasing the EFM dosage in the diet linearly and quadratically inhibited weight gain (WG), feed intake, and feed conversion ratio (FCR) (p < 0.05), except the FCR at 22–35 days (p > 0.05). Dietary inclusion of more than 15% resulted in a negative impact on growth performance over days 1–35 (p < 0.05). Therefore, the EFM dose tolerance in the broiler diet is 10%. The WG, FCR, and production efficiency factor of the BSEFM group were better than those of the control group in days 1–35 (p < 0.05). The apparent and standardized ideal amino acid digestibility of BSEFM was higher than EFM in trial 3, except for Met, Cys, and Trp (p < 0.05). In conclusion, the EFM dose tolerance for the broiler diet is 10%. Bacillius subtilis var. natto N21 + S. cerevisiae Y10 fermentation can improve the amino acid digestibility of EFM and enhance broiler growth performance. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

12 pages, 2072 KiB

Open AccessArticle

Exogenous Indole-3-Acetic Acid Production and Phosphate Solubilization by Chlorella vulgaris Beijerinck in Heterotrophic Conditions

by Rafaela Leticia Brito Bispo, Sandra Regina Ceccato-Antonini, Marco Aurélio Takita and Marcia Maria Rosa-Magri

Fermentation 2023, 9(2), 116; https://doi.org/10.3390/fermentation9020116 - 25 Jan 2023

Cited by 4 | Viewed by 2402

Abstract

The role of soil-borne microalgae in the edaphic ecosystem is barely known, especially concerning their plant-growth-promoting traits, although they are used as biofertilizers. In this study, a microalgal strain isolated from soil cultivated with maize was evaluated as an exogenous producer of indole-3-acetic acid (IAA) in potato dextrose broth—PD—and sugarcane molasses, with or without tryptophan, and phosphate solubilizer (in ‘National Botanical Research Institute’s phosphate’—NBRIP—medium with tricalcium phosphate)with plant-growth-promoting traits, under heterotrophic conditions. The species of microalga was identified, by sequencing the ITS region in the rDNA and the morphological characteristics, as Chlorella vulgaris. Its growth was significantly higher in the PD medium, with slower growth in molasses. The addition of tryptophan did not influence the growth of C. vulgaris in either medium, but it increased the production of IAA, mainly in the PD medium, to 265 µg mL⁻¹. The microalga grew in the medium with insoluble phosphate, releasing phosphorus into the medium (30 mg L⁻¹ after 72 h). This is the first study on the application of C. vulgaris as a phosphate solubilizer. More studies should be performed on C. vulgaris as a prospective plant-growth-promoting microorganism, besides its ability to produce exogenous IAA, and further investigations should be conducted on developing inexpensive culture media. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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12 pages, 4126 KiB

Open AccessArticle

Isolation of Lactococcus sp. X1 from Termite Gut, and Its Application in Lactic Acid Production

by Nana Li, Alei Geng, Zhuowei Tu, Yanan Fan, Rongrong Xie, Xia Li and Jianzhong Sun

Fermentation 2023, 9(2), 85; https://doi.org/10.3390/fermentation9020085 - 18 Jan 2023

Cited by 4 | Viewed by 2581

Abstract

The production of lactic acid (LA) from lignocellulosic biomass is an important route for the exploitation of renewable resources; nevertheless, effective LA production from this feedstock is challenged by several limitations, such as pentose and oligosaccharide utilization. In this study, a new strain, Lactococcus sp. X1, which is capable of fermenting glucose, xylose, and several disaccharides to produce L-lactic acid, was isolated from the gut of a wood-feeding termite, Coptotermes formosanus. Compared to conventional lactic acid bacteria, Lactococcus sp. X1 requires less complex nitrogen sources, which might in turn reduce the cost of LA production. In addition, Lactococcus sp. X1 was able to completely ferment 50 g/L of glucose within 3 days, giving a high LA yield of 99.9%, and its LA yield from 50 g/L of pretreated corncob reached up to 0.34 g/g substrates in the presence of a commercial cellulase. Strain X1 was also capable of excreting two kinds of nutritional factors, namely biotin and vitamin C, indicating its crucial role in the nourishment of the termite. In conclusion, Lactococcus sp. X1 is a new lactic acid bacterium, which may hold promise for application in cost-effective LA production as well as in the field of food additives. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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13 pages, 2133 KiB

Open AccessArticle

Production of Butyric Acid from Hydrolysate of Rice Husk Treated by Alkali and Enzymes in Immobilized Fermentation by Clostridium tyrobutyricum CtΔpta

by Yueying Lin, Wanjing Sun, Geng Wang, Haohan Chen, Xun Pei, Yuyue Jin, Shang-Tian Yang and Minqi Wang

Fermentation 2022, 8(10), 531; https://doi.org/10.3390/fermentation8100531 - 11 Oct 2022

Viewed by 2115

Abstract

Rice husk, as a cellulose-rich by-product in agriculture, has been considered as a low-cost substrate for the production of bioethanol and chemicals. In this study, rice husk was pretreated with an alkali, followed by cellulose and β-glucosidase hydrolysis optimized by an orthogonal experiment and response surface methodology (RSM), respectively. Under the optimal treatment conditions, a hydrolysate containing a high reducing sugar yield (77.85%) was obtained from the rice husk. Then, the hydrolysate was used as a carbon substrate for butyric acid production through Clostridium tyrobutyricum Δpta fermentation. Compared to free-cell fermentation, higher concentrations of butyric acid (50.01 g/L vs. 40.8 g/L and 49.03 g/L vs. 27.49 g/L) were observed in immobilized-cell fermentation for the carbon source of glucose and hydrolysate, respectively. A final butyric acid concentration of 16.91 g/L, a yield of 0.31 g/g, and an overall productivity of 0.35 g/L/h from rice husk hydrolysate were obtained in the repeated-fed-batch mode. Taken together, rice husk hydrolysate can be effectively utilized for the bioproduction of butyrate with immobilized-cell fermentation. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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Review

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15 pages, 1798 KiB

Open AccessReview

Current Status, Challenges, and Prospects for the Biological Production of Vanillin

by Wankui Jiang, Xiaoyue Chen, Yifan Feng, Jingxiang Sun, Yujia Jiang, Wenming Zhang, Fengxue Xin and Min Jiang

Fermentation 2023, 9(4), 389; https://doi.org/10.3390/fermentation9040389 - 17 Apr 2023

Cited by 13 | Viewed by 6120

Abstract

Vanillin has been widely used as a flavoring agent in the food industry and as a precursor in the medicine and polymer industries. However, the use of chemically synthesized vanillin is prohibited in food and some other industries. Additionally, the harsh conditions and toxic substrates in chemically synthesized vanillin lead to some environmental challenges and energy waste. With the rapid development of synthetic biology, the biological production of vanillin from renewable resources through microbial fermentation has gained great attention owing to its high selectivity and environmentally friendly properties. Accordingly, this article will discuss the vanillin biosynthesis technology from the aspects of chassis cell types and substrate types. The key enzymes involved in metabolic pathways are also discussed. Then, we summarize some improvements in the process of vanillin production to increase its production and reduce the toxicity of vanillin in microorganisms, and the possible future directions for vanillin biosynthesis will also be outlined. Full article

(This article belongs to the Special Issue Application of Microbial Fermentation in Organic Matter Production)

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