Thermophilic production of polyhydroxyalkanoates by a novel Aneurinibacillus strain isolated from Gudao oilfield, China

The Undeniable Potential of Thermophiles in Industrial Processes

Extremophilic microorganisms play a key role in understanding how life on Earth originated and evolved over centuries. Their ability to thrive in harsh environments relies on a plethora of mechanisms developed to survive at extreme temperatures, pressures, salinity, and pH values. From a biotechnological point of view, thermophiles are considered a robust tool for synthetic biology as well as a reliable starting material for the development of sustainable bioprocesses. This review discusses the current progress in the biomanufacturing of high-added bioproducts from thermophilic microorganisms and their industrial applications.

Microbial PolyHydroxyAlkanoate (PHA) Biopolymers-Intrinsically Natural

Global pollution from fossil plastics is one of the top environmental threats of our time. At their end-of-life phase, fossil plastics, through recycling, incineration, and disposal result in microplastic formation, elevated atmospheric CO₂ levels, and the pollution of terrestrial and aquatic environments. Current regional, national, and global regulations are centered around banning plastic production and use and/or increasing recycling while ignoring efforts to rapidly replace fossil plastics through the use of alternatives, including those that occur in nature. In particular, this review demonstrates how microbial polyhydroxyalkanoates (PHAs), a class of intrinsically natural polymers, can successfully remedy the fossil and persistent plastic dilemma. PHAs are bio-based, biosynthesized, biocompatible, and biodegradable, and thus, domestically and industrially compostable. Therefore, they are an ideal replacement for the fossil plastics pollution dilemma, providing us with the benefits of fossil plastics and meeting all the requirements of a truly circular economy. PHA biopolyesters are natural and green materials in all stages of their life cycle. This review elaborates how the production, consumption, and end-of-life profile of PHAs are embedded in the current and topical, 12 Principles of Green Chemistry, which constitute the basis for sustainable product manufacturing. The time is right for a paradigm shift in plastic manufacturing, use, and disposal. Humankind needs alternatives to fossil plastics, which, as recalcitrant xenobiotics, contribute to the increasing deterioration of our planet. Natural PHA biopolyesters represent that paradigm shift.

The Role of Bacterial Polyhydroalkanoate (PHA) in a Sustainable Future: A Review on the Biological Diversity

Environmental challenges related to the mismanagement of plastic waste became even more evident during the COVID-19 pandemic. The need for new solutions regarding the use of plastics came to the forefront again. Polyhydroxyalkanoates (PHA) have demonstrated their ability to replace conventional plastics, especially in packaging. Its biodegradability and biocompatibility makes this material a sustainable solution. The cost of PHA production and some weak physical properties compared to synthetic polymers remain as the main barriers to its implementation in the industry. The scientific community has been trying to solve these disadvantages associated with PHA. This review seeks to frame the role of PHA and bioplastics as substitutes for conventional plastics for a more sustainable future. It is focused on the bacterial production of PHA, highlighting the current limitations of the production process and, consequently, its implementation in the industry, as well as reviewing the alternatives to turn the production of bioplastics into a sustainable and circular economy.

Biosynthesis of versatile PHA copolymers by thermophilic members of the genus Aneurinibacillus

Thermophilic members of the genus Aneurinibacillus constitute a remarkable group of microorganisms that exhibit extraordinary flexibility in terms of polyhydroxyalkanoates (PHA) synthesis. In this study, we demonstrate that these Gram-positive bacteria are capable of the utilization of selected lactones, namely, γ-valerolactone (GVL), γ-hexalactone (GHL), and δ-valerolactone (DVL) as the structural precursors of related PHA monomers. In the presence of GVL, a PHA copolymer consisting of 3-hydroxybutyrate, 3-hydroxyvalerate, and also 4-hydroxyvalerate was synthesized, with a 4 HV fraction as high as 53.1 mol%. Similarly, the application of GHL resulted in the synthesis of PHA copolymer containing 4-hydroxyhexanaote (4HHx) (4HHx fraction reached up to 11.5 mol%) and DVL was incorporated into PHA in form of 5-hydroxyvalerate (5 HV) (maximal 5 HV content was 44.2 mol%). The produced materials were characterized by thermoanalytical and spectroscopic methods; the results confirmed extremely appealing material properties of produced copolymers. Further, due to their unique metabolic features and capability of incorporating various PHA monomers into the PHA chain, thermophilic Aneurinibacillus spp. can be considered not only promising chassis for PHA production but also potential donors of PHA-relevant genes to improve PHA production in other thermophiles by using approaches of synthetic biology.

Bacterial communities in home-made Doushen with and without chili pepper

Doushen is a traditional Chinese fermented soybean product prepared with sterilizated soybeans under open conditions. However, little is known on the bacterial community and their influence on the flavor of Doushen. In the present study, Doushen samples with and without chili pepper were collected to reveal the bacterial community and assess a correlation between bacterial community and VFCs in the two kinds of Doushen samples. We identified four phyla and 97 bacterial genera in the two kinds of Doushen samples. In addition, a total of 17 significantly different OTUs were detected by LEfSe (Line Discriminant Analysis (LDA) Effect Size). Results of Principal coordinates analysis (PCoA), unweighted pair-group method (UPGMA) and functional and phenotypes prediction showed that bacterial communities in the two kinds of Doushen were significantly different. Spearman correlation analysis showed that all the dominant genera, except Clostridium Sensu stricto 1, were significantly correlated with the characteristic VFCs. This study provides a theoretical basis for improving the flavour quality of traditional homemade Doushen.

A review on production of polyhydroxyalkanoate (PHA) biopolyesters by thermophilic microbes using waste feedstocks

Polyhydroxyalkanoates (PHAs) are produced by numerous microbes as a subcellular energy source. Despite of their diverse applications, exorbitant production cost limits their commercial synthesis. Apart from various cost determining factors such as cost-effective feedstocks or economic recovery methods, the use of appropriate bacteria holds the key to reduce the fermentation economics. Extremophiles, especially thermophilic PHA producers, could make the bioprocess economically viable by reducing the production cost in several aspects. Using variety of waste feedstocks as carbon substrates could open the way for the valorisation of industrial waste streams and cost-effective PHA production. Therefore, the article critically reviews the current knowledge of the synthesis of PHA polyesters in thermophilic conditions. Additionally, it summarises several studies on thermophilic PHA producing bacteria grown on various waste substrates. To conclude, the paper focuses on screening and recovery methods as well as technical challenges in thermophilic PHA production.

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.

Improving the thermostability of trehalose synthase from Thermomonospora curvata by covalent cyclization using peptide tags and investigation of the underlying molecular mechanism

One of the most desirable properties for industrial enzymes is high thermotolerance, which can reduce the amount of biocatalyst used and lower the production cost. Aiming to improve the thermotolerance of trehalose synthase (TreS, EC 5.4.99.16) from Thermomonospora curvata, four mutants (G78D, V289L, G322A, I323L) and four cyclized TreS variants fused using different Tag/Catcher pairs (SpyTag-TreS-SpyCatcher, SpyTag-TreS-KTag, SnoopTag-TreS-SnoopCatcher, SnoopTagJR-TreS-DogTag) were constructed. The results showed that cyclization led to a much larger increase of thermostability than that achieved via site-directed mutagenesis. The t_1/2 of all four cyclized TreS variants at 55 °C increased 2- to 3- fold, while the analysis of kinetic and thermodynamic stability indicated that the T₅₀ of the different cyclized TreS variants increased by between 7.5 °C and 15.5 °C. Molecular dynamics simulations showed that the Rg values of cyclized TreS decreased significantly, indicating that the protein maintained a tight tertiary structure at high temperatures, avoiding exposure of the hydrophobic core to the solvent. Cyclization using a Tag/Catcher pair is a simple and effective method for improving the thermotolerance of enzymes.

Introducing the Newly Isolated Bacterium Aneurinibacillus sp. H1 as an Auspicious Thermophilic Producer of Various Polyhydroxyalkanoates (PHA) Copolymers-1. Isolation and Characterization of the Bacterium

Extremophilic microorganisms are considered being very promising candidates for biotechnological production of various products including polyhydroxyalkanoates (PHA). The aim of this work was to evaluate the PHA production potential of a novel PHA-producing thermophilic Gram-positive isolate Aneurinibacillus sp. H1. This organism was capable of efficient conversion of glycerol into poly(3-hydroxybutyrate) (P3HB), the homopolyester of 3-hydroxybutyrate (3HB). In flasks experiment, under optimal cultivation temperature of 45 °C, the P3HB content in biomass and P3HB titers reached 55.31% of cell dry mass and 2.03 g/L, respectively. Further, the isolate was capable of biosynthesis of PHA copolymers and terpolymers containing high molar fractions of 3-hydroxyvalerate (3HV) and 4-hydroxybutyrate (4HB). Especially 4HB contents in PHA were very high (up to 91 mol %) when 1,4-butanediol was used as a substrate. Based on these results, it can be stated that Aneurinibacillus sp. H1 is a very promising candidate for production of PHA with tailored material properties.

Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica

The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) through whole-genome sequence analysis. The Pseudomonas isolates were found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively. On the other hand, the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis was detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment showed that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. PHA biosynthesis and in vitro PhaC enzymatic assay results showed that this uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional. This report adds new knowledge to the PHA synthase database as we describe scarce information of PHA synthase genes and PHA-associated gene clusters from the antarctic bacterial isolates (extreme and geographically isolated environment) and comparing with those from non-antarctic PHA-producing bacteria.

Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges

Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.

Thermophilic production of poly(3-hydroxybutyrate-co-3-hydrovalerate) by a mixed methane-utilizing culture

The production of polyhydroxyalkanoates (PHAs) from methane is limited to mesophiles and thus suffers from high energy requirements for cooling. To address this issue, the use of thermophilic processes is gaining interest, as this strategy may deliver improved economic feasibility for PHA production. This study reports the first thermophilic PHA-producing culture grown on methane at 55 °C in fill-and-draw batch reactors. Harvested cells were incubated with various combinations of methane, propionic acid and valeric acid to assess their capacity for the synthesis of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Only PHB was produced when fed with methane alone. The addition of odd-carbon-number fatty acids resulted in higher PHA content with 3 HV fractions in the range of 15-99 mol%, depending on the types of fatty acids added. Acetic acid addition enhanced the synthesis of 3HB monomer, but not of 3 HV. On increasing the temperature to 58 °C, PHA productivity was not significantly affected.

Engineering Bacillus megaterium for production of functional intracellular materials

BACKGROUND

Over the last 10-15 years, a technology has been developed to engineer bacterial poly(3-hydroxybutyrate) (PHB) inclusions as functionalized beads, for applications such as vaccines, diagnostics and enzyme immobilization. This has been achieved by translational fusion of foreign proteins to the PHB synthase (PhaC). The respective fusion protein mediates self-assembly of PHB inclusions displaying the desired protein function. So far, beads have mainly been produced in recombinant Escherichia coli, which is problematic for some applications as the lipopolysaccharides (LPS) co-purified with such inclusions are toxic to humans and animals.

RESULTS

In this study, we have bioengineered the formation of functional PHB inclusions in the Gram-positive bacterium Bacillus megaterium, an LPS-free and established industrial production host. As B. megaterium is a natural PHB producer, the PHB-negative strain PHA05 was used to avoid any background PHB production. Plasmid-mediated T7 promoter-driven expression of the genes encoding β-ketothiolase (phaA), acetoacetyl-CoA-reductase (phaB) and PHB synthase (phaC) enabled PHB production in B. megaterium PHA05. To produce functionalized PHB inclusions, the N- and C-terminus of PhaC was fused to four and two IgG binding Z-domains from Staphylococcus aureus, respectively. The ZZ-domain PhaC fusion protein was strongly overproduced at the surface of the PHB inclusions and the corresponding isolated ZZ-domain displaying PHB beads were found to purify IgG with a binding capacity of 40-50 mg IgG/g beads. As B. megaterium has the ability to sporulate and respective endospores could co-purify with cellular inclusions, a sporulation negative production strain was generated by disrupting the spoIIE gene in PHA05. This strain did not produce spores when tested under sporulation inducing conditions and it was still able to synthesize ZZ-domain displaying PHB beads.

CONCLUSIONS

This study provides proof of concept for the successful genetic engineering of B. megaterium as a host for the production of functionalized PHB beads. Disruption of the spoIIE gene rendered B. megaterium incapable of sporulation but particularly suitable for production of functionalized PHB beads. This sporulation-negative mutant represents an improved industrial production strain for biotechnological processes otherwise impaired by the possibility of endospore formation.