Polyhydroxyalkanoate biosynthesis and simplified polymer recovery by a novel moderately halophilic bacterium isolated from hypersaline microbial mats

Advances in polyhydroxyalkanoate (PHA) production from renewable waste materials using halophilic microorganisms: A comprehensive review

Polyhydroxyalkanoates (PHAs) are biodegradable and biocompatible polymers that can replace conventional plastics in different sectors. However, PHA commercialization is hampered due to their high production cost resulting from the use of high purity substrates, their low conversion into PHAs by using conventional microbial chassis and the high downstream processing cost. Taking these challenges into account, researchers are focusing on the use of waste by-products as alternative low-cost feedstocks for fast-growing and contamination-resistant halophilic microorganisms (Bacteria, Archaea…). This is of great importance since these extremophiles can use low-cost substrates, produce high PHA content of copolymers or different PHA monomer compositions. They can present high potential for reducing the costs of PHA fermentation and recovery processes, making their use in commercial applications easier. However, little is known about the potential of halophiles in advancing the PHA production from renewable waste materials at lab-scale and their successful implementation at industrial-scale. This review presents actual advances in PHA production by halophilic pure/engineered species (e.g. Haloferax mediterranei, Halomonas spp.) and mixed microbial consortia (MMC) using organic waste streams. The development of optimal PHA production process involves robust genetic engineering strategies, advanced fermentation processes using mixed microbial consortia versus pure/engineered strains as well as algal biomass as feedstocks.

Isolation and characterization of a Halomonas species for non-axenic growth-associated production of bio-polyesters from sustainable feedstocks

Biodegradable plastics are urgently needed to replace petroleum-derived polymeric materials and prevent their accumulation in the environment. To this end, we isolated and characterized a halophilic and alkaliphilic bacterium from the Great Salt Lake in Utah. The isolate was identified as a Halomonas species and designated "CUBES01." Full-genome sequencing and genomic reconstruction revealed the unique genetic traits and metabolic capabilities of the strain, including the common polyhydroxyalkanoate (PHA) biosynthesis pathway. Fluorescence staining identified intracellular polyester granules that accumulated predominantly during the strain's exponential growth, a feature rarely found among natural PHA producers. CUBES01 was found to metabolize a range of renewable carbon feedstocks, including glucosamine and acetyl-glucosamine, as well as sucrose, glucose, fructose, and further glycerol, propionate, and acetate. Depending on the substrate, the strain accumulated up to ~60% of its biomass (dry wt/wt) in poly(3-hydroxybutyrate), while reaching a doubling time of 1.7 h at 30°C and an optimum osmolarity of 1 M sodium chloride and a pH of 8.8. The physiological preferences of the strain may not only enable long-term aseptic cultivation but also facilitate the release of intracellular products through osmolysis. The development of a minimal medium also allowed the estimation of maximum polyhydroxybutyrate production rates, which were projected to exceed 5 g/h. Finally, also, the genetic tractability of the strain was assessed in conjugation experiments: two orthogonal plasmid vectors were stable in the heterologous host, thereby opening the possibility of genetic engineering through the introduction of foreign genes.

IMPORTANCE

The urgent need for renewable replacements for synthetic materials may be addressed through microbial biotechnology. To simplify the large-scale implementation of such bio-processes, robust cell factories that can utilize sustainable and widely available feedstocks are pivotal. To this end, non-axenic growth-associated production could reduce operational costs and enhance biomass productivity, thereby improving commercial competitiveness. Another major cost factor is downstream processing, especially in the case of intracellular products, such as bio-polyesters. Simplified cell-lysis strategies could also further improve economic viability.

Reclamation of chromium-contaminated soil by native Cr(VI)-reducing and PHA-accumulating Bacillus aryabhattai CTSI-07

Reclamation of chromium-contaminated soil by bacteria is a big confront concerning to soil health restoration, food safety, and environmental protection. Herein, the chromium-resistant Bacillus aryabhattai CTSI-07 (MG757377) showed resistance to 1000 and 300 ppm of Cr(VI) in nutrient rich Luria Bertani (LB) and nutrient-deficient sucrose low phosphate (SLP) medium, respectively. It reduced 96.7% of Cr(VI) from contaminated soil in the presence of 100 ppm of Mg within 96 h under optimized conditions. Furthermore, Cr(VI) reduction by the bacteria was validated by Fourier transform infrared spectroscopic (FTIR) and X-ray diffraction (XRD) analysis. Besides Cr(VI) reduction, the bacterial strain also showed plant growth promoting traits like N2 fixation and indole acetic acid (IAA) production. On the other hand, transmission electron microscopy (TEM) imaging confirmed polyhydroxyalkanoates' (PHAs) granule accumulation and 0.5 g/l of PHAs was extracted from bacterial cell using SLP medium. Infra-red (IR) spectra and proton nuclear magnetic resonance (1H NMR) chemical shift patterns established the PHAs as polyhydroxybutyrate (PHB). Melting (Tm) and thermal degradation (Td) temperature of the PHB were 169 °C and 275 °C, respectively, as evident from thermogravimetry differential thermal analysis (TG-DTA). Atomic force microscopic (AFM) imaging depicted that the PHB film surface was rough and regular. Furthermore, the multi-metal-resistant, plant growth-promoting, and PHB-producing bacteria could reduce 99.82% of Cr(VI) from contaminated soil within 120 days in pot culture. Thus, it can be used for long-term reclamation of chromium-contaminated soil to restore soil health, provide food safety, and environmental protection.

Recent Challenges and Trends of Polyhydroxyalkanoate Production by Extremophilic Bacteria Using Renewable Feedstocks

Polyhydroxyalkanoates (PHAs) are biodegradable polymers with immense potential in addressing the global plastic pollution crisis and advancing sustainable bioplastics production. Among the various microbes known for PHA production, extremophilic bacteria possess unique capabilities to thrive under extreme conditions, making them attractive candidates for PHA synthesis. Furthermore, the utilization of renewable feedstocks for PHA production aligns with the growing demand for sustainable bioplastic alternatives. A diverse range of extremophilic bacteria, especially halophiles and thermophiles, has provided cost-competitive platforms for producing customized PHA polymers. Extremophilic bacteria offer unique advantages over mesophiles due to their contamination resistance, high cell density growth, and unique culture conditions. The current status of Halomonas spp. as a chassis further allows exploration of metabolic engineering approaches to overcome the challenges associated with current industrial biotechnology. This article especially focuses on extremophilic bacteria and explores recent advances in utilizing renewable feedstocks such as lignocellulosic biomass, agro-industrial residues, and waste streams for PHA production. The integration of biorefinery concepts and circular economy principles in PHA manufacturing is also examined. This review is an attempt to provide an understanding of renewable substrates as feedstocks and emerging trends in PHA production by extremophilic bacteria. It underscores the pivotal role of extremophiles and sustainable feedstock sources in advancing the feasibility and eco-friendliness of PHAs as a promising biopolymer alternative.

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

BACKGROUND

Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis.

RESULTS

To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed.

CONCLUSIONS

Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.

Recent advances in polyhydroxyalkanoate production: Feedstocks, strains and process developments

Polyhydroxyalkanoates (PHAs) have been actively studied in academia and industry for their properties comparable to petroleum-derived plastics and high biocompatibility. However, the major limitation for commercialization is their high cost. Feedstock costs, especially carbon costs, account for the majority of the final cost. Finding cheap feedstocks for PHA production and associated process development are critical for a cost-effective PHA production. In this study, waste materials from different sources, particularly lignocellulosic biomass, were proposed as suitable feedstocks for PHA production. Strains involved in the conversion of these feedstocks into PHA were reviewed. Newly isolated strains were emphasized. Related process development, including the factors that affect PHA production, fermentation modes and downstream processing, was elaborated upon.

Production of Polyhydroxyalkanoates by Two Halophilic Archaeal Isolates from Chott El Jerid Using Inexpensive Carbon Sources

The large use of conventional plastics has resulted in serious environmental problems. Polyhydroxyalkanoates represent a potent replacement to synthetic plastics because of their biodegradable nature. This study aimed to screen bacteria and archaea isolated from an extreme environment, the salt lake Chott El Jerid for the accumulation of these inclusions. Among them, two archaeal strains showed positive results with phenotypic and genotypic methods. Phylogenetic analysis, based on the 16S rRNA gene, indicated that polyhydroxyalkanoate (PHA)-producing archaeal isolates CEJGTEA101 and CEJEA36 were related to Natrinema altunense and Haloterrigena jeotgali, respectively. Gas chromatography and UV-visible spectrophotometric analyses revealed that the PHA were identified as polyhydroxybutyrate and polyhydroxyvalerate, respectively. According to gas chromatography analysis, the strain CEJGTEA101 produced maximum yield of 7 wt % at 37 °C; pH 6.5; 20% NaCl and the strain CEJEA36 produced 3.6 wt % at 37 °C; pH 7; 25% NaCl in a medium supplemented with 2% glucose. Under nutritionally optimal cultivation conditions, polymers were extracted from these strains and were determined by gravimetric analysis yielding PHA production of 35% and 25% of cell dry weight. In conclusion, optimization of PHA production from inexpensive industrial wastes and carbon sources has considerable interest for reducing costs and obtaining high yield.

Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico

Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.

Fed-Batch Strategies for Production of PHA Using a Native Isolate of Halomonas venusta KT832796 Strain

In this study, polyhydroxyalkanoates (PHA) accumulation by Halomonas venusta KT832796, a moderate halophilic bacteria isolated from marine source was studied. Both nutritional requirements and process parameters for submerged cultivation of the organism in bioreactor have been standardized. From the shake flask studies, glucose and ammonium citrate as carbon and nitrogen source produced maximum PHA at a ratio 20 with 3.52 g/L of dry cell weight and 70.56% of PHA content. However, ammonium sulfate as the nitrogen source was found to be more suitable for fed-batch cultivation. Several feeding strategies including pH-based fed-batch and variants of pulse feeding were studied to improve the PHA levels. pH-based feeding, although improved PHA level to 26 g/L, most of the carbon flux was diverted towards biomass formation; hence, the percent PHA was only 39.15% of the dry cell weight. Maximum PHA of 33.4 g/L, which corresponded to 88.12% of the dry cell, was obtained from high concentration single pulse method. There was a net 8.65-fold increase in PHA using this feeding strategy when compared to batch studies. According to our knowledge, this is the highest amount of PHA reported for a Halomonas venusta strain.

Recent Advances and Challenges towards Sustainable Polyhydroxyalkanoate (PHA) Production

Sustainable biofuels, biomaterials, and fine chemicals production is a critical matter that research teams around the globe are focusing on nowadays. Polyhydroxyalkanoates represent one of the biomaterials of the future due to their physicochemical properties, biodegradability, and biocompatibility. Designing efficient and economic bioprocesses, combined with the respective social and environmental benefits, has brought together scientists from different backgrounds highlighting the multidisciplinary character of such a venture. In the current review, challenges and opportunities regarding polyhydroxyalkanoate production are presented and discussed, covering key steps of their overall production process by applying pure and mixed culture biotechnology, from raw bioprocess development to downstream processing.