Bioconversion of dairy co-products to polyhydroxyalkanoates by halophilic microbes with salts and nutrients recycling

This study presented the cultivation of Haloferax mediterranei for polyhydroxyalkanoates (PHA) production from dairy co-products with spent salts recycling and provided the first insights of dissolved oxygen (DO) in regulating PHA biosynthesis by halophiles. PHA had yields up to 0.40 ± 0.02 g/g substrate from whey sugar and up to 0.17 ± 0.12 g/g substrate from delactosed permeate. A higher log-phase DO led to faster biosynthesis, but a lower final PHA production (2.0 ± 0.3 g/L) compared to lower DO levels (3.0 ± 0.1 g/L). This was later elucidated through mathematical modelling by the kinetic parameters and metabolic reaction rates. A novel approach was established to recycle up to 90 % salts and nutrients in the system and achieved consistent production and product quality. This study develops a sustainable biotechnology of converting dairy co-products to biomaterials, improve the economics of PHA and has the potential scalability for industrial applications.

Genetic algorithm-optimized artificial neural network for multi-objective optimization of biomass and exopolysaccharide production by Haloferax mediterranei

Microbial production of industrially important exopolysaccharide (EPS) from extremophiles has several advantages. In this study, key media components (i.e., sucrose, yeast extract, and urea) were optimized for biomass growth and extracellular EPS production in Haloferax mediterranei DSM 1411 using Box-Behnken design. In a multi-objective optimization framework, response surface methodology (RSM) and genetic algorithm (GA)-optimized artificial neural network (ANN) were used to minimize biomass growth while increasing EPS production. The performance of the selected ANN model for the prediction of biomass and EPS (R2: 0.964 and 0.975, respectively) was found to be better than that of the multiple regression model (R2: 0.818, 0.963, respectively). The main effect of sucrose and its interaction with urea appears to have a significant effect on both responses. The ANN model projects an increase in EPS production from 4.49 to 18.2 g l-1 while shifting the priority from biomass to biopolymer. The optimized condition predicted a maximum biomass and EPS production of 17.27 g l-1 and 17.80 g l-1, respectively, at concentrations of sucrose (19.98 g l-1), yeast extract (1.97 g l-1), and urea (1.99 g l-1). Based on multi-objective optimization, the GA-ANN model predicted an increase in the EPS to biomass ratio for increasing the EPS and associated biomass production. The extracted EPS, identified as Gellan gum through NMR spectroscopy, was further characterized for surface and elemental composition using SEM-EDX analysis.

Unlocking the potential of microbes: Concomitant production of polyhydroxyalkanoates and carotenoids

The escalating environmental concerns and depletion of crude oil resources have catalyzed interest in biologically derived polymers, particularly biodegradable ones such as polyhydroxyalkanoates. However, the high production costs associated with polyhydroxyalkanoates, driven by raw material expenses, stringent production conditions and low yields, hinder their widespread adoption. A potential strategy to mitigate these costs involves the production of PHAs and other high-value bioproducts, such as carotenoids simultaneously in microbial systems, utilizing shared metabolic pathways. Carotenoids, known for their antioxidant properties and applications in the food, cosmetics and pharmaceutical industries, offer substantial market potential. This review presents a comprehensive overview of the current progress in polyhydroxyalkanoate and carotenoid co-production, explores the co-synthesis pathways, addresses the challenges involved and explores the future prospects of this integrated bioprocess. By diversifying the product portfolio and optimizing microbial production systems, the co-production strategy could pave the way for more sustainable and economically viable bioplastics.

Long-term effects of cycle time and volume exchange ratio on poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production from food waste digestate by Haloferax mediterranei cultivated in sequencing batch reactors for 450 days

Food wastedigestatewas fed into a sequencing batch reactor (SBR) forHaloferax mediterranei(HM) to produce poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). This SBR was operated uninterruptedly for 450 days to test its stability, during which the cycle time and volume exchange ratiowere varied to understand their impacts on the PHBV fermentation performance under ranged organic loading rates (OLR). Results showed that 1) PHBV productivity was proportional to OLR of food wastedigestate; 2) substrate and product inhibitions were two limiting factors constraining substrate utilization and PHBV yields; 3) PHBV titer was dependent on the hydraulic retention time of the SBR while a volume exchange ratio lower than 0.5 is unfavorable due to the product inhibitor accumulation. This study for the first time demonstrated that the long-term stability of food waste-fed PHBV production byHMand revealed that inhibition effects could be barriers in SBR limiting the full-scale application of the technology.

Bioconversion of bread waste into high-quality proteins and biopolymers by fermentation of archaea Haloferax mediterranei

The valorization of bread waste into high-quality protein and biopolymers using the halophilic microorganism Haloferax mediterranei presents a sustainable approach to food waste management and resource optimization. This study successfully coproduced protein and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) biopolymer with a biomass content of 8.0 ± 0.1 g L-1 and a productivity of 11.1 mg L-1 h-1. The fermentation process employed 3.0% w/v of enzymatically hydrolyzed bread waste. The amino acid profile of the cell biomass revealed a total content of 358 g kg-1 of biomass dry weight (DW), including 147 g kg-1 DW of essential amino acids. The protein quality, assessed through in-vitro enzyme digestion, indicated a high-quality protein with a digestibility value of 0.91 and a protein digestibility-corrected amino acid score (PDCAAS) of 0.78. The PHBV biopolymer component (36.0 ± 6.3% w/w) consisted of a copolymer of 3-hydroxybutyrate and 3-hydroxyvalerate in a 91:9 mol% ratio. This bioconversion process not only mitigates food waste but also generates valuable biomaterials.

Effects of magnetic field exposure patterns on polyhydroxyalkanoates synthesis by Haloferax mediterranei at extreme hypersaline context: Carbon distribution and salt tolerance

The synthesis of polyhydroxyalkanoates (PHAs) by extremophiles presents a promising alternative to mitigate pollution originating from the use of petroleum-based plastics. This study focuses on the impact of different magnetic field (MF) exposure patterns on PHA production and carbon metabolism, aiming to enhance PHA productivity by Haloferax mediterranei within the extreme hypersaline environment and subsequently reducing production costs. Results indicated that under 300 g/L salinity, the highest PHA productivity (1.45 ± 0.06 g/(L d)) and PHA content (65.91 % PHA/cell dry weight) were achieved with 50 mT MF exposure throughout the fermentation period. Continuous exposure to 50 mT MF proved vital for maximizing cell biomass and PHA productivity. Continuous exposure to 50 mT MF enabled Haloferax mediterranei to channel acetyl-CoA towards the PHA synthesis pathway while maintaining growth and proliferation. Correlation analysis further proved the principal role of carbon flux on PHA accumulation. Due to the demand for balancing osmotic pressure, cellular substances were sacrificed to ensure PHA synthesis as anti-salinity substance. Meanwhile, the observed promotion of MF on PHA production, betaine aldehyde dehydrogenase activity, and K+ uptake contributed to sustaining cellular activity at 300 g/L salinity. This study provides a non-gene editing approach to enhance PHA productivity.

Bioplastic Production from Agri-Food Waste through the Use of Haloferax mediterranei: A Comprehensive Initial Overview

The research on bioplastics (both biobased and biodegradable) is steadily growing and discovering environmentally friendly substitutes for conventional plastic. This review highlights the significance of bioplastics, analyzing, for the first time, the state of the art concerning the use of agri-food waste as an alternative substrate for biopolymer generation using Haloferax mediterranei. H. mediterranei is a highly researched strain able to produce polyhydroxybutyrate (PHB) since it can grow and produce bioplastic in high-salinity environments without requiring sterilization. Extensive research has been conducted on the genes and pathways responsible for PHB production using H. mediterranei to find out how fermentation parameters can be regulated to enhance cell growth and increase PHB accumulation. This review focuses on the current advancements in utilizing food waste as a substitute for costly substrates to reduce feedstock expenses. Specifically, it examines the production of biomass and the recovery of PHB from agri-food waste. Furthermore, it emphasizes the characterization of PHB and the significance of hydroxyvalerate (HV) abundance in the formation of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) copolymer. The downstream processing options are described, and the crucial factors associated with industrial scale-up are assessed, including substrates, bioreactors, process parameters, and bioplastic extraction and purification. Additionally, the economic implications of various options are discussed.

Spatial separation of nitrifiers and denitrifiers promotes selection and enrichment of polyhydroxyalkanoates storing mixed cultures fed by crude glycerol and propionate wastewater

Polyhydroxyalkanoates (PHA) recovery from industrial wastewater has been highlighted as a promising strategy for a circular bioeconomy. However, the high and varying level of nitrogen in wastewater makes enrichment of mixed microbial culture (MMC) low efficiency. In this study, spatial separation of nitrifiers and denitrifiers was adopted by adding biocarriers in MMC and decreasing the sludge retention time (SRT) to accelerate the enrichment of PHA-storing MMC fed by mixed wastewater containing glycerol and propionate. Nitrifiers and denitrifiers were sustained on biocarriers, obtaining a high total inorganic nitrogen removal and allowing a more efficient selective pressure of a high carbon and nitrogen ratio (C/N) under low SRT conditions. The maximum PHA cell content and relative abundance of PHA-storing bacteria were increased to 60.51 % (SRT 6 d) and 49.62 % (SRT 6 d) with the decrease of SRT, respectively. This study demonstrates an efficient way to highly enrich PHA-storing MMC from crude glycerol, which provide a relevant technical support for high-efficiency enrichment of PHA-storing bacteria in low C/N wastewater.

Feast/famine ratio regulates the succession of heterotrophic nitrification-aerobic denitrification and autotrophic ammonia oxidizing bacteria in halophilic aerobic granular sludge treating saline wastewater

Heterotrophic nitrification-aerobic denitrification (HN-AD) shows innovation potential of wastewater treatment process in a single tank. However, how to enrich HN-AD bacteria in activated sludge to enhance their contribution remained unknown. This study explored the impact of the feast/famine (F/F) ratio on the succession of autotrophic ammonia oxidizing bacteria (AOB) and HN-AD bacteria in a halophilic aerobic granular sludge (HAGS) system. As the F/F ratio decreased from 1/9 to 1/15, the total inorganic nitrogen (TIN) removal performance significantly decreased. The proportion of heterotrophic bacteria was dropped from 79.0 % to 33 %. Accordingly, the relative abundance of Paracoccus decreased from 70.8 % to 25.4 %, and the copy number of the napA gene was reduced from 2.2 × 1010 copies/g HAGS to 8.1 × 109 copies/g HAGS. It found the F/F ratio regulated the population succession of autotrophic AOB and HN-AD bacteria, thereby providing a solution to achieve the enrichment of HN-AD bacteria in HAGS.

Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress

Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.

Polyhydroxyalkanoates and exopolysaccharides: An alternative for valuation of the co-production of microbial biopolymers

Polyhydroxyalkanoates (PHAs) and exopolysaccharides (EPSs) belong to a class of abundant biopolymers produced by various fermenting microorganisms. These biocompounds have high value-added potential and can be produced concurrently. Co-production of PHAs and EPSs is a strategy employed by researchers to reduce costs associated with large-scale production. EPSs and PHAs are non-toxic, biocompatible, and biodegradable, making them suitable for various industrial sectors, including packaging and the medical and pharmaceutical industries. These biopolymers can be derived from agro-industrial residues, thus contributing to the bioeconomy by producing high-value-added products. This review investigates approaches for simultaneously synthesizing PHAs and EPSs using different carbon sources and microorganisms.

Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography

Haloalkane dehalogenase (HLD) enzymes employ an SN 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but the mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and x-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeAΔGG ) that provided diffraction-quality crystals. The 3.3 Å crystal structure reveals that DhmeAΔGG forms a ring-like 20-mer structure with outer and inner diameter of ~200 and ~80 Å, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization, and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates.

Effect of transient organic load and aeration changes to pollutant removal and extracellular polymeric substances

Transient organic load shocks have an important influence on the removal of pollutants and the content and composition of extracellular polymeric substances (EPS). This study was based on a micro-pressure reactor (MPR) with the influent COD concentration as the variable, while different operating conditions were controlled by adjusting the aeration rate. The effect of single-cycle transient organic loading shocks on EPS and pollutant removal and the correlation between their changes were investigated. The results showed that COD removal was unaffected under the shock, and the effect of nitrogen and phosphorus removal decreased. As the incoming carbon source increased, the EPS content at shock increased, with the polysaccharide (PS) content being the most affected. As aeration increased, the effect of organic load shock on EPS and pollutant removal decreased. Under different aeration conditions, PS contributed to denitrification and anaerobic phosphorus release during transient organic load shocks, and protein (PN) contributed to aerobic phosphorus uptake. The reduction in PS and PN relative to the pre-shock caused by the shock resulted in the EPS exhibiting a favourable effect on COD removal and an inhibitory effect on the effectiveness of nitrogen and phosphorus removal.

Online Omics Platform Expedites Industrial Application of Halomonas bluephagenesis TD1.0

Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics. Here we introduce a user-friendly, interactive website hosting multi-omics data. Importantly, this new platform allows non-experts to explore questions in an industrially important chassis whose cellular dynamics are still largely unknown. The web platform contains a complete KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis derived from principal components analysis, an interactive bio-cluster heatmap analysis of genes, and the Halomonas TD1.0 genome-scale metabolic (GEM) model. As a case study of the effectiveness of this platform, we applied unsupervised machine learning to determine key differences between Halomonas bluephagenesis TD1.0 cultivated under varied conditions. Specifically, cell motility and flagella apparatus are identified to drive energy expenditure usage at different osmolarities, and predictions were verified experimentally using microscopy and fluorescence labelled flagella staining. As more omics projects are completed, this landing page will facilitate exploration and targeted engineering efforts of the robust, industrial chassis H bluephagenesis for researchers without extensive bioinformatics background.

Potential interactive effect on biomass and bio-polymeric substances of microalgal-bacterial aerobic granular sludge as a valuable resource for sustainable development

The algal/bacterial biomass and extracellular polymeric substances (EPSs) existing in microalgal-bacterial aerobic granular sludge (MB-AGS) offer a promising bioresource. The current review-based paper presents a systematic overview of the compositions and interactions (gene transfer, signal transduction, and nutrient exchange) of microalgal and bacteria consortia, the role of cooperative or competitive partnerships of MB-AGS in the treatment of wastewater and recovery of resource, and the environmental/operational factors affecting their interactions and EPS production. Moreover, a brief notes is given on the opportunities and major challenges of utilizing the microalgal-bacterial biomass and EPS for phosphorus and polysaccharides chemical recovery, renewable energy (i.e. biodiesel, hydrogen, electricity) production. Overall, this compact review will pave the way for developing MB-AGS future biotechnology.

In-silico analysis of a halophilic bacterial isolate-Bacillus pseudomycoides SAS-B1 and its polyhydroxybutyrate production through fed-batch approach under differential salt conditions

Polyhydroxybutyrate (PHB) is a natural biopolymer and a viable substitute for petroleum-derived polymers that possess immense potential for diverse applications. In the present study, PHB was produced by a halophilic bacteria identified as Bacillus pseudomycoides SAS-B1 by 16S rRNA gene sequencing. The bacterial genome was evaluated through complete genome sequencing, which elucidated a 5,338,308 bp genome with 34.88 % of G + C content and 5660 genes. Other genome attributes were analyzed such as functional profiling, gene ontology, and metabolic pathways. Genes involved in PHB biochemical pathway were identified such as phaA, phaB, and phaC. Furthermore, sodium-dependent transporters and other ATP-binding genes were identified in the genome that may be involved in sodium uptake during saline conditions. The PHB production by B. pseudomycoides SAS-B1 was examined under differential salt conditions. The PHB yield was increased from 3.14 ± 0.02 g/L to 6.12 ± 0.04 g/L when salinity was increased upto 20 g/L with intermittent feeding of glucose and corn steep liquor. FTIR, NMR, and GC-MS studies elucidated the presence of desired functional groups, molecular structure, and monomeric compositions of PHB respectively. Further, TGA revealed the thermal stability of the recovered PHB upto (220-230) °C and has a crystallinity index of upto 33 ± 0.5 % as confirmed by XRD analysis.

Exploitation of wasted bread as substrate for polyhydroxyalkanoates production through the use of Haloferax mediterranei and seawater

The use of the halophile microorganism Haloferax mediterranei, able to synthesize poly(hydroxybutyrate-hydroxyvalerate) (PHBV), is considered as a promising tool for the industrial production of bioplastic through bioprocessing. A consistent supplementation of the growth substrate in carbohydrates and minerals is overall necessary to allow its PHBV production. In this work, wasted bread was used as substrate for bioplastic production by microbial fermentation. Instead of the consistent and expensive minerals supplement required for Hfx. mediterranei DSM1411 growth, microfiltered seawater was added to the wasted bread-derived substrate. The suitable ratio of wasted bread homogenate and seawater, corresponding to 40:60, was selected. The addition of proteases and amylase to the bread homogenate promoted the microbial growth but it did not correspond to the increase of bioplastic production by the microorganism, that reach, under the experimental conditions, 1.53 g/L. An extraction procedure of the PHBV from cells, based on repeated washing with water, followed or not by a purification through ethanol precipitation, was applied instead of the conventional extraction with chloroform. Yield of PHBV obtained using the different extraction methods were 21.6 ± 3.6 (standard extraction/purification procedure with CHCl3:H2O mixture), 24.8 ± 3.0 (water-based extraction), and 19.8 ± 3.3 mg PHAs/g of wasted bread (water-based extraction followed by ethanol purification). Slightly higher hydroxyvalerate content (12.95 vs 10.78%, w/w) was found in PHBV obtained through the water-based extraction compared to the conventional one, moreover, the former was characterized by purity of 100% (w/w). Results demonstrated the suitability of wasted bread, supplemented with seawater, to be used as substrate for bioplastic production through fermentation. Results moreover demonstrated that a solvent-free extraction, exclusively based on osmotic shock, could be used to recover the bioplastic from cells.

Bioconversion of Plastic Waste Based on Mass Full Carbon Backbone Polymeric Materials to Value-Added Polyhydroxyalkanoates (PHAs)

This review article will discuss the ways in which various polymeric materials, such as polyethylene (PE), polypropylene (PP), polystyrene (PS), and poly(ethylene terephthalate) (PET) can potentially be used to produce bioplastics, such as polyhydroxyalkanoates (PHAs) through microbial cultivation. We will present up-to-date information regarding notable microbial strains that are actively used in the biodegradation of polyolefins. We will also review some of the metabolic pathways involved in the process of plastic depolymerization and discuss challenges relevant to the valorization of plastic waste. The aim of this review is also to showcase the importance of methods, including oxidative degradation and microbial-based processes, that are currently being used in the fields of microbiology and biotechnology to limit the environmental burden of waste plastics. It is our hope that this article will contribute to the concept of bio-upcycling plastic waste to value-added products via microbial routes for a more sustainable future.

Coupling Magnetic Field and Salinity Upshock To Improve Polyhydroxyalkanoate Productivity by Haloferax mediterranei Feeding on Molasses Wastewater

Low polyhydroxyalkanoate (PHA) volumetric productivity from wastewater limits low-cost PHA production. To resolve this problem, an external magnetic field (MF) coupled with upshock salinity was applied to PHA production by Haloferax mediterranei (family Halobacteriaceae). Elevating the fermentation salinity over the optimal growth salinity (200 g/L) increased the PHA cell content while inhibiting cell proliferation, decreasing volumetric productivity. When a MF of 50 mT in 300 g/L salinity was applied, H. mediterranei proliferation and PHA cell content were promoted, leading to a 7.95% increase in PHA volumetric productivity in synthetic molasses wastewater and a 13.82% increase in glucose feeding compared with those in 200 g/L salinity. Under the MF, osmotic pressure regulation was activated by accumulating K⁺ and increasing betaine synthesis. The maximum betaine content increased by 74.33% in 300 g/L salinity with a 50-mT MF compared with that in 200 g/L salinity. When a 50-mT MF in 300 g/L salinity was applied, the malondialdehyde (MDA) content decreased by 32.66% and the activity of superoxide dismutase (SOD) increased by 46.89%, which reduced the oxidative damage. This study provides a new solution to enhance PHA volumetric productivity by MF and an insight into the magnetic effects of H. mediterranei. IMPORTANCE The obstacle to replacing petroplastics with PHA is its high production cost. To increase the fermentation economy, a novel strategy of coupling a MF with salinity upshock was applied, which enhanced the PHA volumetric productivity of H. mediterranei in fermenting molasses wastewater. The magnetic effect of H. mediterranei was found at a MF of 50 mT, which improved the salt tolerance of H. mediterranei and reduced the oxidative damage induced by the elevated salinity, thereby promoting proliferation and PHA cell content. This is the first time a technical method for enhancing PHA volumetric productivity by means of a MF has been proposed. Such a strategy can advance the utilization of H. mediterranei for the industrial production of PHA using organic wastewater.

Membrane Fouling Mitigation in MBR via the Feast–Famine Strategy to Enhance PHA Production by Activated Sludge

Fouling is considered one of the main drawbacks of membrane bioreactor (MBR) technology. Among the main fouling agents, extracellular polymeric substances (EPS) are considered one of the most impactful since they cause the decrease of sludge filterability and decline of membrane flux in the long term. The present study investigated a biological strategy to reduce the membrane-fouling tendency in MBR systems. This consisted of seeding the reactor with activated sludge enriched in microorganisms with polyhydroxyalkanoate (PHA) storage ability and by imposing proper operating conditions to drive the carbon toward intracellular (PHA) rather than extracellular (EPS) accumulation. For that purpose, an MBR lab-scale plant was operated for 175 days, divided into four periods (1–4) according to different food to microorganisms’ ratios (F/M) (0.80 kg COD kg TSS⁻¹ d⁻¹ (Period 1), 0.13 kg COD kg TSS⁻¹ d⁻¹ (Period 2), 0.28 kg COD kg TSS⁻¹ d⁻¹ (Period 3), and 0.38 kg COD kg TSS⁻¹ d⁻¹ (Period 4)). The application of the feast/famine strategy favored the accumulation of intracellular polymers by bacteria. The increase of the PHA accumulation inside the cells corresponded to the decrease of EPS and an F/M of 0.40–0.50 kg COD kg TSS⁻¹ d⁻¹ was found as optimum to maximize the PHA production, while minimizing EPS. The lowest EPS content in the sludge (18% of total suspended solids) that corresponded to the maximum content of PHA (9.3%) was found in Period 4 and determined significant mitigation of the fouling rate, whose value was close to 0.10 × 10¹¹ m⁻¹ h⁻¹. Thus, by imposing proper operating conditions, it was possible to drive the organic matter toward PHA accumulation. Moreover, a lower EPS content corresponded to a decrease in the irreversible fouling mechanism, which would imply a lower frequency of the extraordinary cleaning operations. This study highlighted the possibility of obtaining a double benefit by applying an MBR system in the frame of wastewater valorization: minimizing the fouling tendency of the membrane and recovery precursors of bioplastics from wastewater in line with the circular economy model.

Inorganic carbon stimulates the metabolic routes related to the polyhdroxybutyrate production in a Synechocystis sp. strain (cyanobacteria) isolated from wastewater

Cyanobacteria are capable of transforming CO₂ into polyhydroxybutyrate (PHB). In this study, different inorganic carbon concentrations (0-2 gC L^-1) were evaluated for a Synechocystis sp. strain isolated from wastewater. Quantitative RT-qPCR was also performed to decipher the links between inorganic carbon and PHB and glycogen metabolism. 2 gC L^-1 of bicarbonate stimulated cell growth, nutrients consumption and production of PHB. Using this concentration, a 14%_dcw of PHB and an average productivity of 2.45 mgPHB L^-1 d^-1 were obtained. Gene expression analysis revelated that these conditions caused the overexpression of genes related to glycogen and PHB synthesis. Moreover, a positive correlation between the genes codifying for the glycogen phosphorylase, the acetyl-CoA reductase and the poly(3-hydroxyalkanoate) polymerase was found, meaning that PHB synthesis and glycogen catabolism are strongly related. These results provide an exhaustive evaluation of the effect of carbon on the PHB production and cyanobacterial metabolism.

Carbon Source Applied in Enrichment Stage of Mixed Microbial Cultures Limits the Substrate Adaptability for PHA Fermentation Using the Renewable Carbon

Suitability of different substrates for enriched mixed microbial cultures (MMCs) is of importance to the polyhydroxyalkanoate (PHA) fermentation using renewable carbon. In this study, three enriched MMCs were evaluated for their fermentation features and kinetics with different carbon sources (sodium acetate, glucose, or starch). The results showed that the highly specific bacterial community composition was developed depending on the applied carbon source. Correspondence analysis suggested that the genus affiliated in Gammaproteobacteria_unclassified was related to 3-hydroxybutyrate (HB) synthesis in acetate-fed MMC (relative abundance of 38%) and glucose-fed MMC (relative abundance of 76.7%), whereas Vibrio genus was related to 3-hydroxyvalerate (HV) production in glucose-fed MMC (relative abundance of 0.4%) and starch-fed MMC (relative abundance of 94.6%). The acetate-fed MMC could not use glucose and starch as fermentation carbon sources, showing the limitation of microbial species developed with the specific metabolic substrate. Glucose-fed MMC produced the highest PHA cell content of 64.2% cell dry weight when using sodium acetate as the fermentation carbon. Glucose-fed MMC showed wide resilience and adaptation to various carbon sources. When actual landfill leachate was used for fermentation by glucose-fed MMC, maximum PHA cell content of 45.5% cell dry weight and the PHA volumetric productivity of 0.265 g PHA/(L·h) were obtained. This study suggested carbon sources applied in the MMC enrichment stage had a significant influence on utilization of carbon in the fermentation stage.

Metabolic potential of the moderate halophile Yangia sp. ND199 for co-production of polyhydroxyalkanoates and exopolysaccharides

Yangia sp. ND199 is a moderately halophilic bacterium isolated from mangrove samples in Northern Vietnam, which was earlier reported to grow on several sugars and glycerol to accumulate poly(hydroxyalkanoates) (PHA). In this study, the potential of the bacterium for co‐production of exopolysaccharides (EPS) and PHA was investigated. Genome sequence analysis of the closely related Yangia sp. CCB‐M3 isolated from mangroves in Malaysia revealed genes encoding enzymes participating in different EPS biosynthetic pathways. The effects of various cultivation parameters on the production of EPS and PHA were studied. The highest level of EPS (288 mg/L) was achieved using sucrose and yeast extract with 5% NaCl and 120 mM phosphate salts but with modest PHA accumulation (32% of cell dry weight, 1.3 g/L). Growth on fructose yielded the highest PHA concentration (85% of CDW, 3.3 g/L) at 90 mM phosphate and higher molecular weight EPS at 251 mg/L yield at 120 mM phosphate concentration. Analysis of EPS showed a predominance of glucose, followed by fructose and galactose, and minor amounts of acidic sugars.

Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes

The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.

Polyhydroxyalkanoates from extremophiles: A review

Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.

A review of extracellular polysaccharides from extreme niches: An emerging natural source for the biotechnology. From the adverse to diverse!

Every year, new organisms that survive and colonize adverse environments are discovered and isolated. Those organisms, called extremophiles, are distributed throughout the world, both in aquatic and terrestrial environments, such as sulfurous marsh waters, hydrothermal springs, deep waters, volcanos, terrestrial hot springs, marine saltern, salt lakes, among others. According to the ecosystem inhabiting, extremophiles are categorized as thermophiles, psychrophiles, halophiles, acidophiles, alkalophilic, piezophiles, saccharophiles, metallophiles and polyextremophiles. They have developed chemical adaptation strategies that allow them to maintain their cellular integrity, altering physiology or improving repair capabilities; one of them is the biosynthesis of extracellular polysaccharides (EPS), which constitute a slime and hydrated matrix that keep the cells embedded, protecting from environmental stress (desiccation, salinity, temperature, radiation). EPS have gained interest; they are explored by their unique properties such as structural complexity, biodegradability, biological activities, and biocompatibility. Here, we present a review concerning the biosynthesis, characterization, and potential EPS applications produced by extremophile microorganisms, namely, thermophiles, halophiles, and psychrophiles. A bibliometric analysis was conducted, considering research articles published within the last two decades. Besides, an overview of the culture conditions used for extremophiles, the main properties and multiple potential applications of their EPS is also presented.

Archaea Biotechnology

Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.

The metabolic pathways of polyhydroxyalkanoates and exopolysaccharides synthesized by Haloferax mediterranei in response to elevated salinity

How polymer synthesis is mobilized or activated as a biological response of Haloferax mediterranei against hypertonic conditions remains largely unexplored. This study investigated the protein expression of H. mediterranei in response to high salinity by using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. The microbes were harvested at end of fermentation at the NaCl salinity of 75 and 250 g L^-1. Among the identified 2123 proteins, 170 proteins were differentially expressed. Gene ontology annotation revealed that the highest number of proteins was annotated in biological process category, which was responsible for metabolic process, cellular component and catalytic activity. Differentially expressed proteins were belonged to the class of response to stimulus as well as catalytic activity and binding. Under high salinity conditions, three pathways were established as key responses of PHA and EPS production to hypertonic pressure. Two overexpressed proteins, beta-ketoacyl-ACP reductase and 3-hydroxyacyl-CoA dehydrogenase, enhanced the synthesis of PHAs. The serine-pyruvate transaminase and serine-glyoxylate transaminase were upregulated, thereby increasing the conversion of glucose to PHA. Downregulated levels of sulfate-adenylyl transferase and adenylyl-sulfate kinase could cause diminished EPS synthesis. This study could contribute to better understanding of the proteomic mechanisms of the synthesized polymers in defending against salt stress. SIGNIFICANCE: Haloferax mediterranei, a family member of halophilic archaea, is well known for its fermentative production of poly-β-hydroxyalkanoates (PHAs). PHAs are natural polymers that exhibit great potential in a wide range of applications such as a good alternative to petroleum-based plastics and the biocompatible material. For decades, the functional role of PHAs synthesized by H. mediterranei is deemed to be carbon and energy reservations. The finding proved that differential production of PHA and EPS in H. mediterranei exposed to elevated salinity was caused by differential protein expression. This is the first report on how PHA and EPS synthesized by H. mediterranei is mobilized as the response of increased salinity, contributing to the understanding of halophilic archaea's response to hypertonic stress and the precise control of fermentation production. Despite its advantages as a PHA cell factory, H. mediterranei synthesized EPS simultaneously, thereby lowering the maximum yield of PHA production. Overall, salinity can be used as a vital microbial fermentation parameter to obtain the highest harvest of PHA, as well as the lowest EPS synthesis in industrial fermentation.

Production and characterization of a bioactive extracellular homopolysaccharide produced by Haloferax sp. BKW301

The production of extracellular polysaccharides (EPS) by haloarchaeal members, with novel and unusual physicochemical properties, is of special importance and has the potential for extensive biotechnological exploitation. An extremely halophilic archaeon, Haloferax sp. BKW301 (GenBank Accession No. KT240044) isolated from a solar saltern of Baksal, West Bengal, India has been optimized for the production of EPS under batch culture. It produced a considerable amount (5.95 g/L) of EPS in the medium for halophiles with 15% NaCl, 3% glucose, 0.5% yeast extract, and 6% inoculum under shake flask culture at 120 rpm. The purified EPS, a homopolymer of galactose as revealed by chromatographic methods and Fourier-transform infrared spectroscopy, is noncrystalline (CI_xrd , 0.82), amorphous, and could emulsify hydrocarbons like kerosene, petrol, xylene, and so forth. Moreover, the polymer is highly thermostable (up to 420°C) and displayed pseudoplastic rheology. Biologically, the EPS was able to scavenge DPPH (2,2-diphenyl-1-picrylhydrazyl) radical efficiently and inhibit the proliferation of the Huh-7 cell line at an IC₅₀ value of 6.25 µg/ml with a Hill coefficient of 0.844. Large-scale production of this thermostable, pseudoplastic homopolysaccharide, therefore, could find suitable applications in industry and biotechnology.

Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy

Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.

From Organic Wastes to Bioplastics: Feasibility of Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella denitrificans ZD1

Poly(3-hydroxybutyrate) (PHB)—a renewable and biodegradable polymer—is a promising alternative to nonbiodegradable synthetic plastics that are derived from petrochemicals. The methods currently employed for PHB production are costly, in part, due to the expensive cultivation feedstocks and the need to sterilize the culture medium, which is energy-intensive. This study investigates the feasibility of nonsterile PHB production from several saline organic wastes using a salt-tolerant strain, Zobellella denitrificans ZD1 (referred to as strain ZD1). Factors such as the pH, salinity, carbon/nitrogen (C/N) ratio, nitrogen source, and electron acceptor that might affect the growth of strain ZD1 and its PHB production were determined. Our results showed successful nonsterile PHB production by growing the strain ZD1 on nonsterile synthetic crude glycerol, high-strength saline wastewater, and real municipal wastewater-activated sludge under saline conditions. The PHB production was significantly enhanced when the levels of salts and nitrate-nitrogen in the culture medium were increased. This study suggested a promising low-cost nonsterile PHB production strategy from organic wastes using strain ZD1.

Bioplastic (poly-3-hydroxybutyrate) production by the marine bacterium Pseudodonghicola xiamenensis through date syrup valorization and structural assessment of the biopolymer

Biobased degradable plastics have received significant attention owing to their potential application as a green alternative to synthetic plastics. A dye-based procedure was used to screen poly-3-hydroxybutyrate (PHB)-producing marine bacteria isolated from the Red Sea, Saudi Arabia. Among the 56 bacterial isolates, Pseudodonghicola xiamenensis, identified using 16S rRNA gene analyses, accumulated the highest amount of PHB. The highest PHB production by P. xiamenensis was achieved after 96 h of incubation at pH 7.5 and 35 °C in the presence of 4% NaCl, and peptone was the preferred nitrogen source. The use of date syrup at 4% (w/v) resulted in a PHB concentration of 15.54 g/L and a PHB yield of 38.85% of the date syrup, with a productivity rate of 0.162 g/L/h, which could substantially improve the production cost. Structural assessment of the bioplastic by Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy revealed the presence of methyl, hydroxyl, methine, methylene, and ester carbonyl groups in the extracted polymer. The derivative products of butanoic acid estimated by gas chromatography-mass spectrometry [butanoic acid, 2-amino-4-(methylseleno), hexanoic acid, 4-methyl-, methyl ester, and hexanedioic acid, monomethyl ester] confirmed the structure of PHB. The present results are the first report on the production of a bioplastic by P. xiamenensis, suggesting that Red Sea habitats are a potential biological reservoir for novel bioplastic-producing bacteria.

Optimization of nitrogen source supply for enhanced biosynthesis and quality of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by extremely halophilic archaeon Haloferax mediterranei

The extreme halophilic archaeon, Haloferax mediterranei can accumulate polyhydroxyalkanoate (PHA) from different renewable resources. To enhance the biosynthesis and quality of PHA, H. mediterranei cultivation media was optimized at different C/N ratios using glucose as the main carbon source. Three sets of media (yeast extract [YE], NH₄ Cl and combination of YE and NH₄ Cl) were prepared at different nitrogen concentrations to achieve C/N ratios of 9, 20, and 35, respectively. The media containing YE (organic nitrogen source) produced a higher growth rate of H. mediterranei than NH₄ Cl (inorganic source) at all tested C/N ratios. The highest PHA accumulation (18.4% PHA/cell dry mass) was achieved in a media that combined YE with NH₄ Cl at a C/N ratio of 20. Analysis of the produced polymers revealed the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBHV) with different 3-hydroxyvalerate (3HV) content. The polymers produced from YE and the combined media have greater 3HV content (10 mol%) than those polymers recovered from NH₄ Cl (1.5 mol%). Resultingly, PHBHV from YE and the combined media displayed reduced melting points at 144°C. The nitrogen type/concentration was found to also have an impact on the molecular weights and polydispersity indices of the produced biopolymers. Furthermore, the tensile strengths were found to vary with the best tensile strength (14.4 MPa) being recorded for the polymer recovered from YE at C/N = 9. Interestingly, the tensile strength of PHBHV was significantly higher than petroleum-based polyethylene (13.5 MPa), making it a much more suitable bioplastic for industrial application.

Current developments on polyhydroxyalkanoates synthesis by using halophiles as a promising cell factory

Plastic pollution is a severe threat to our environment which necessitates implementation of bioplastics to realize sustainable development for a green world. Polyhydroxyalkanoates (PHA) represent one of the potential candidates for these bioplastics. However, a major challenge faced by PHA is the high production cost which limits its commercial application. Halophiles are considered to be a promising cell factory for PHA synthesis due to its several unique characteristics including high salinity requirement preventing microbial contamination, high intracellular osmotic pressure allowing easy cell lysis for PHA recovery, and capability to utilize wide spectrum of low-cost substrates. Optimization of fermentation parameters has made it plausible to achieve large-scale production at low cost by using halophiles. Further deeper insights into halophiles have revealed the existence of diversified and even novel PHA synthetic pathways within different halophilic species that greatly affects PHA type. Thus, precise metabolic engineering of halophiles with the help of advanced tools and strategies have led to more efficient microbial cell factory for PHA production. This review is an endeavour to summarize the various research achievements in these areas which will help the readers to understand the current developments as well as the future efforts in PHA research.

Polyhydroxyalkanoate Biosynthesis at the Edge of Water Activitiy-Haloarchaea as Biopolyester Factories

Haloarchaea, the extremely halophilic branch of the Archaea domain, encompass a steadily increasing number of genera and associated species which accumulate polyhydroxyalkanoate biopolyesters in their cytoplasm. Such ancient organisms, which thrive in highly challenging, often hostile habitats characterized by salinities between 100 and 300 g/L NaCl, have the potential to outperform established polyhydroxyalkanoate production strains. As detailed in the review, this optimization presents due to multifarious reasons, including: cultivation setups at extreme salinities can be performed at minimized sterility precautions by excluding the growth of microbial contaminants; the high inner-osmotic pressure in haloarchaea cells facilitates the recovery of intracellular biopolyester granules by cell disintegration in hypo-osmotic media; many haloarchaea utilize carbon-rich waste streams as main substrates for growth and polyhydroxyalkanoate biosynthesis, which allows coupling polyhydroxyalkanoate production with bio-economic waste management; finally, in many cases, haloarchaea are reported to produce copolyesters from structurally unrelated inexpensive substrates, and polyhydroxyalkanoate biosynthesis often occurs in parallel to the production of additional marketable bio-products like pigments or polysaccharides. This review summarizes the current knowledge about polyhydroxyalkanoate production by diverse haloarchaea; this covers the detection of new haloarchaea producing polyhydroxyalkanoates, understanding the genetic and enzymatic particularities of such organisms, kinetic aspects, material characterization, upscaling and techno-economic and life cycle assessment.