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28 pages, 3411 KB

Open AccessArticle

Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia

by Eylem Atak, Petra Tavčar Verdev, Marko Petek, Anna Coll, Daniel Bosch, Marko Dolinar, Viktoriia Komarysta, Neli Glavaš and Ana Rotter

Mar. Drugs 2026, 24(1), 26; https://doi.org/10.3390/md24010026 - 8 Jan 2026

Viewed by 2808

Abstract

Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising [...] Read more.

Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats. Full article

(This article belongs to the Special Issue Bioactive Molecules from Extreme Environments III)

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24 pages, 2102 KB

Open AccessReview

Unraveling the Potentials of Extremophiles in Bioextraction of Valuable Metals from Industrial Solid Wastes: An Overview

by Adegoke Isiaka Adetunji and Mariana Erasmus

Minerals 2024, 14(9), 861; https://doi.org/10.3390/min14090861 - 24 Aug 2024

Cited by 6 | Viewed by 4543

Abstract

The continuous dumping of industrial solid wastes into the immediate environment is incommodious since these waste materials cause pollution and serious hazards to human health. In addition, these solid wastes are complex and consist of toxic chemical substances, heavy metals, and valuable metals, [...] Read more.

The continuous dumping of industrial solid wastes into the immediate environment is incommodious since these waste materials cause pollution and serious hazards to human health. In addition, these solid wastes are complex and consist of toxic chemical substances, heavy metals, and valuable metals, hence warranting treatment before disposal. Bioleaching is a green and sustainable technology for the solubilization and mobilization of metals from solid matrices. The leaching efficacy is contingent on the types and physiology of the organisms, the elemental content of the solid wastes, and the presence of appropriate bioprocess parameters at optimum conditions. Extremophilic microbes, including thermophiles, acidophiles, alkaliphiles, and halophiles, are recognized as excellent biological agents for the efficient bioextraction of metals from industrial solid wastes due to their aptitude for survival under harsh bioleaching conditions. Therefore, this review provides insights into the employability of extremophilic microorganisms as a biofactory for the recovery of valuable metals from various industrial solid wastes. More so, it discusses the sustainability of the bioleaching technique in terms of its life cycle assessment (LCA) and techno-economic analysis. Full article

(This article belongs to the Special Issue Bioleaching of Metals from Waste/Wastewater)

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18 pages, 2200 KB

Open AccessArticle

Optimized Operating Conditions for a Biological Treatment Process of Industrial Residual Process Brine Using a Halophilic Mixed Culture

by Thomas Mainka, Christoph Herwig and Stefan Pflügl

Fermentation 2022, 8(6), 246; https://doi.org/10.3390/fermentation8060246 - 25 May 2022

Cited by 2 | Viewed by 4116

Abstract

Residual process brine is a sustainable raw material for chlor-alkali electrolysis processes. This study investigates the influence of critical process parameters on the performance of a continuous treatment process for residual process brine using halophilic microorganisms. The goal of the bioprocess is an [...] Read more.

Residual process brine is a sustainable raw material for chlor-alkali electrolysis processes. This study investigates the influence of critical process parameters on the performance of a continuous treatment process for residual process brine using halophilic microorganisms. The goal of the bioprocess is an efficient degradation of the organic impurities formate, aniline, phenol, and 4,4′-methylenedianline from this residual stream. It was shown that formate could be degraded with high efficiencies (89–98%) during the treatment process. It was observed that formate degradation was influenced by the co-substrate glycerol. The lowest residual formate concentrations were achieved with specific glycerol uptake rates of 8.0–16.0 × 10⁻³ g L⁻¹ h⁻¹ OD₆₀₀⁻¹. Moreover, a triple-nutrient limitation for glycerol, ammonium, and phosphate was successfully applied for continuous cultivations. Furthermore, it was shown that all aromatic impurities were degraded with an efficiency of 100%. Ultimately, this study proposed optimized operating conditions, allowing the efficient degradation of organics in the residual process brine under various process conditions. Future optimization steps will require a strategy to prevent the accumulation of potential intermediate degradation products formed at high aniline feed concentrations and increase the liquid dilution rates of the system to achieve a higher throughput of brines. Full article

(This article belongs to the Special Issue Process Intensification in Microbial Biotechnology)

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11 pages, 993 KB

Open AccessArticle

Optimization of Lipopeptide Biosurfactant Production by Salibacterium sp. 4CTb in Batch Stirred-Tank Bioreactors

by José Martín Márquez-Villa, Juan Carlos Mateos-Díaz, Jorge Alberto Rodríguez-González and Rosa María Camacho-Ruíz

Microorganisms 2022, 10(5), 983; https://doi.org/10.3390/microorganisms10050983 - 8 May 2022

Cited by 10 | Viewed by 3139

Abstract

Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) [...] Read more.

Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) and a response surface methodology (RSM) tailored and taken from the literature, the present work focuses on the evaluation of a composite central design (CCD) under batch cultures in stirred-tank bioreactors with the halophilic bacteria Salibacterium sp. 4CTb in order to determine the operative conditions that favor mass transfer and optimize the production of a lipopeptide. The results obtained showed profiles highlighting the most favorable culture conditions, which lead to an emulsification index (E₂₄%) higher than 70%. Moreover, through the behavior of dissolved oxygen (DO), it was possible to experimentally evaluate the higher volumetric coefficient of mass transfer in the presence of lipopeptide (k_La = 31 1/h) as a key criterion for the synthesis of the biosurfactant on further cell expansion. Full article

(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)

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12 pages, 2331 KB

Open AccessFeature PaperArticle

l-Fucose Synthesis Using a Halo- and Thermophilic l-Fucose Isomerase from Polyextremophilic Halothermothrix orenii

by In Jung Kim and Kyoung Heon Kim

Appl. Sci. 2022, 12(8), 4029; https://doi.org/10.3390/app12084029 - 15 Apr 2022

Cited by 7 | Viewed by 3586

Abstract

l-Fucose isomerase (l-FucI)-mediated isomerization is a promising biotechnological approach for synthesizing various rare sugars of industrial significance, including l-fucose. Extremozymes that can retain their functional conformation under extreme conditions, such as high temperature and salinity, offer favorable applications in [...] Read more.

l-Fucose isomerase (l-FucI)-mediated isomerization is a promising biotechnological approach for synthesizing various rare sugars of industrial significance, including l-fucose. Extremozymes that can retain their functional conformation under extreme conditions, such as high temperature and salinity, offer favorable applications in bioprocesses that accompany harsh conditions. To date, only one thermophilic l-FucI has been characterized for l-fucose synthesis. Here, we report l-FucI from Halothermothrix orenii (HoFucI) which exhibits both halophilic and thermophilic properties. When evaluated under various biochemical conditions, HoFucI exhibited optimal activities at 50–60 °C and pH 7 with 0.5–1 M NaCl in the presence of 1 mM Mn²⁺ as a cofactor. The results obtained here show a unique feature of HoFucI as a polyextremozyme, which facilitates the biotechnological production of l-fucose using this enzyme. Full article

(This article belongs to the Special Issue Enzyme Catalysis: Advances, Techniques, and Outlooks)

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16 pages, 2973 KB

Open AccessArticle

Techno-Economic Analysis on an Industrial-Scale Production System of Polyhydroxyalkanoates (PHA) from Cheese By-Products by Halophiles

by Ke Wang, Alex Michael Hobby, Yike Chen, Allan Chio, Bryan Martin Jenkins and Ruihong Zhang

Processes 2022, 10(1), 17; https://doi.org/10.3390/pr10010017 - 23 Dec 2021

Cited by 57 | Viewed by 11056

Abstract

Polyhydroxyalkanoates (PHA) are a family of biodegradable plastics used as an ecofriendly alternative for conventional plastics in various applications. In this study, an industrial-scale PHA production system was designed and analyzed for the material flows and economics with the use of SuperPro Designer. [...] Read more.

Polyhydroxyalkanoates (PHA) are a family of biodegradable plastics used as an ecofriendly alternative for conventional plastics in various applications. In this study, an industrial-scale PHA production system was designed and analyzed for the material flows and economics with the use of SuperPro Designer. Haloferax mediterranei was utilized to produce poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Byproduct streams from a local cheese plant, with an input of 168.7 metric ton/day (MT/day) lactose, were used as the feedstock. Three scenarios with different processes for the treatments of used enzyme and spent medium were investigated and the major factors that influence the overall economics were identified. The simulated system produces 9700 MT/year PHBV with a yield of 0.2 g PHBV/g lactose and an overall process efficiency of 87%. The breakeven price was found to be more sensitive to the lactose price than enzyme price. The scenario with enzyme reuse and spent medium recycling achieved the lowest breakeven price among others, which can be less than 4 $/kg PHA based on the delactosed permeate (DLP) unit price. The study suggests utilizing dairy derived feedstocks has the potential to make PHA competitive in the bioplastic market, which could be beneficial to both dairy and bioplastic industries. Full article

(This article belongs to the Special Issue Advances in Bioprocess Technology)

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17 pages, 2657 KB

Open AccessArticle

Statistical Based Bioprocess Design for Improved Production of Amylase from Halophilic Bacillus sp. H7 Isolated from Marine Water

by J. N. Bandal, V. A. Tile, R. Z. Sayyed, H. P. Jadhav, N. I. Wan Azelee, Subhan Danish and Rahul Datta

Molecules 2021, 26(10), 2833; https://doi.org/10.3390/molecules26102833 - 11 May 2021

Cited by 26 | Viewed by 6466

Abstract

Amylase (EC 3.2.1.1) enzyme has gained tremendous demand in various industries, including wastewater treatment, bioremediation and nano-biotechnology. This compels the availability of enzyme in greater yields that can be achieved by employing potential amylase-producing cultures and statistical optimization. The use of Plackett–Burman design [...] Read more.

Amylase (EC 3.2.1.1) enzyme has gained tremendous demand in various industries, including wastewater treatment, bioremediation and nano-biotechnology. This compels the availability of enzyme in greater yields that can be achieved by employing potential amylase-producing cultures and statistical optimization. The use of Plackett–Burman design (PBD) that evaluates various medium components and having two-level factorial designs help to determine the factor and its level to increase the yield of product. In the present work, we are reporting the screening of amylase-producing marine bacterial strain identified as Bacillus sp. H7 by 16S rRNA. The use of two-stage statistical optimization, i.e., PBD and response surface methodology (RSM), using central composite design (CCD) further improved the production of amylase. A 1.31-fold increase in amylase production was evident using a 5.0 L laboratory-scale bioreactor. Statistical optimization gives the exact idea of variables that influence the production of enzymes, and hence, the statistical approach offers the best way to optimize the bioprocess. The high catalytic efficiency (kcat/Km) of amylase from Bacillus sp. H7 on soluble starch was estimated to be 13.73 mL/s/mg. Full article

(This article belongs to the Special Issue Food Proteins and Peptides Focused on Functional and Bioactive Properties)

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14 pages, 2621 KB

Open AccessArticle

Soft Sensor-Based Monitoring and Efficient Control Strategies of Biomass Concentration for Continuous Cultures of Haloferax mediterranei and Their Application to an Industrial Production Chain

by Thomas Mainka, Nicole Mahler, Christoph Herwig and Stefan Pflügl

Microorganisms 2019, 7(12), 648; https://doi.org/10.3390/microorganisms7120648 - 4 Dec 2019

Cited by 15 | Viewed by 3916

Abstract

Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was [...] Read more.

Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was to implement a control and online monitoring strategy for biomass in continuous cultures. For the first time, a feedforward cultivation strategy in a membrane-based cell retention system allowed to control the biomass concentration of the extreme halophilic Haloferax mediterranei at defined levels. Moreover, soft sensor-based biomass estimation allowed reliable monitoring of biomass online. Application of the combined monitoring and control strategy using industrial process water containing formate, phenol, aniline and 4,4′-methylenedianiline could for the first time demonstrate high throughput degradation in this extremophilic bioremediation process, obtaining degradation efficiencies of up to 100%. This process demonstrates the usefulness of continuous halophilic cultures in a circular economy application. Full article

(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)

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18 pages, 2879 KB

Open AccessArticle

Utilization of Sugarcane Bagasse by Halogeometricum borinquense Strain E3 for Biosynthesis of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)

by Bhakti B. Salgaonkar and Judith M. Bragança

Bioengineering 2017, 4(2), 50; https://doi.org/10.3390/bioengineering4020050 - 25 May 2017

Cited by 109 | Viewed by 11779

Abstract

Sugarcane bagasse (SCB), one of the major lignocellulosic agro-industrial waste products, was used as a substrate for biosynthesis of polyhydroxyalkanoates (PHA) by halophilic archaea. Among the various wild-type halophilic archaeal strains screened, Halogeometricum borinquense strain E3 showed better growth and PHA accumulation as [...] Read more.

Sugarcane bagasse (SCB), one of the major lignocellulosic agro-industrial waste products, was used as a substrate for biosynthesis of polyhydroxyalkanoates (PHA) by halophilic archaea. Among the various wild-type halophilic archaeal strains screened, Halogeometricum borinquense strain E3 showed better growth and PHA accumulation as compared to Haloferaxvolcanii strain BBK2, Haloarcula japonica strain BS2, and Halococcus salifodinae strain BK6. Growth kinetics and bioprocess parameters revealed the maximum PHA accumulated by strain E3 to be 50.4 ± 0.1 and 45.7 ± 0.19 (%) with specific productivity (qp) of 3.0 and 2.7 (mg/g/h) using NaCl synthetic medium supplemented with 25% and 50% SCB hydrolysate, respectively. PHAs synthesized by strain E3 were recovered in chloroform using a Soxhlet apparatus. Characterization of the polymer using crotonic acid assay, X-ray diffraction (XRD), differential scanning calorimeter (DSC), Fourier transform infrared (FT-IR), and proton nuclear magnetic resonance (¹H-NMR) spectroscopy analysis revealed the polymer obtained from SCB hydrolysate to be a co-polymer of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] comprising of 13.29 mol % 3HV units. Full article

(This article belongs to the Special Issue Advances in Polyhydroxyalkanoate (PHA) Production)

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17 pages, 833 KB

Open AccessArticle

Dynamic Experiments for Bioprocess Parameter Optimization with Extreme Halophilic Archaea

by Bettina Lorantfy, Bernhard Seyer and Christoph Herwig

Bioengineering 2014, 1(1), 1-17; https://doi.org/10.3390/bioengineering1010001 - 7 Nov 2013

Cited by 3 | Viewed by 6231

Abstract

The to-date studies on extreme halophiles were focused on shake flask cultivations. Bioreactor technology with quantitative approaches can offer a wide variety of biotechnological applications to exploit the special biochemical features of halophiles. Enabling industrial use of Haloferax mediterranei, finding the optima [...] Read more.

The to-date studies on extreme halophiles were focused on shake flask cultivations. Bioreactor technology with quantitative approaches can offer a wide variety of biotechnological applications to exploit the special biochemical features of halophiles. Enabling industrial use of Haloferax mediterranei, finding the optima of cultivation parameters is of high interest. In general, process parameter optimizations were mainly carried out with laborious and time-consuming chemostat cultures. This work offers a faster alternative for process parameter optimization by applying temperature ramps and pH shifts on a halophilic continuous bioreactor culture. Although the hydraulic equilibrium in continuous culture is not reached along the ramps, the main effects on the activity from the dynamic studies can still be concluded. The results revealed that the optimal temperature range may be limited at the lower end by the activity of the primary metabolism pathways. At the higher end, the mass transfer of oxygen between the gaseous and the liquid phase can be limiting for microbial growth. pH was also shown to be a key parameter for avoiding overflow metabolism. The obtained experimental data were evaluated by clustering with multivariate data analyses. Showing the feasibility on a halophilic example, the presented dynamic methodology offers a tool for accelerating bioprocess development. Full article

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