Discovery of a new polyhydroxyalkanoate synthase from limestone soil through metagenomic approach

Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products

Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.

Complete Genome Sequence of a Novel Polyhydroxyalkanoate (PHA) Producer, Jeongeupia sp. USM3 (JCM 19920) and Characterization of Its PHA Synthases

A novel polyhydroxyalkanoate (PHA)-producing bacterium, Jeongeupia sp. USM3 (JCM 19920) was isolated from the limestone soil at Gua Tempurung, Perak, Malaysia. This is the first report on the complete genome sequence for the genus Jeongeupia. This genome consists of a circular chromosome with a size of 3,788,814 bp and contains 3557 genes. Two PHA synthase (phaC) genes encoding for the key enzyme in the polymerization of PHA monomers and other PHA-associated genes were identified from the genome. Phylogenetic analysis of the PhaC protein sequences has revealed that both PhaC1 and PhaC2 of Jeongeupia sp. USM3 are categorized as Class I PHA synthases with 56% similarity to each other. Both of the PHA synthase genes of this isolate were cloned and heterologously expressed in a PHA mutant strain Cupriavidus necator PHB^-4. The ability of the transformants to accumulate PHA showed that both PhaC1 and PhaC2 were functional.

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.

A review on the conversion of volatile fatty acids to polyhydroxyalkanoates using dark fermentative effluents from hydrogen production

The production of bio/microbial-based polymers, polyhydroxyalkanoates (PHAs) from volatile fatty acids (VFAs) of dark fermentative effluents in the bio-H₂ reactor is being paid attention, owing to their commercial demand, applications and as carbon as well as energy storage source. Since, they are the cheap precursors for such valuable renewable biopolymers which all possess the properties; those are analogous to the petro-derived plastics. Several studies were stated, related to the consumption of both individual and mixed VFAs for the potential PHAs production. Their biodegradability nature makes them extremely desirable alternative to fossil-derived synthetic polymers. In this regard, this review summarizes the use of bio-based PHAs production via both microbial and biochemical pathways using dark fermentative bio-H₂ production from waste streams as feedstock. Furthermore, this review deals the characteristics, synthesis and production of the bio-based PHAs along with their co-polymers and applications to give an outlook on future research.

Challenges of scaling-up PHA production from waste streams. A review

The search for new materials that replace fossil fuel-based plastics has been focused on biopolymers with similar physicochemical properties to fossil fuel-based plastics, such as Polyhydroxyalkanoates (PHA). The present paper reviews the challenges of scaling-up PHA production from waste streams during the period from 2014 to 2016, focusing on the feasibility of the alternatives and the most promising alternatives to its scaling-up. The reviewed research studies mainly focus on reducing costs or obtaining more valuable polymers. In the future, the integration of PHA production into processes such as wastewater treatment plants, hydrogen production or biodiesel factories could enhance its implementation at industrial scale.

Molecular Diagnostic for Prospecting Polyhydroxyalkanoate-Producing Bacteria

The use of molecular diagnostic techniques for bioprospecting and microbial diversity study purposes has gained more attention thanks to their functionality, low cost and quick results. In this context, ten degenerate primers were designed for the amplification of polyhydroxyalkanoate synthase (phaC) gene, which is involved in the production of polyhydroxyalkanoate (PHA)—a biodegradable, renewable biopolymer. Primers were designed based on multiple alignments of phaC gene sequences from 218 species that have their genomes already analyzed and deposited at Biocyc databank. The combination of oligos phaCF3/phaCR1 allowed the amplification of the expected product (PHA synthases families types I and IV) from reference organisms used as positive control (PHA producer). The method was also tested in a multiplex system with two combinations of initiators, using 16 colonies of marine bacteria (pre-characterized for PHA production) as a DNA template. All amplicon positive organisms (n = 9) were also PHA producers, thus no false positives were observed. Amplified DNA was sequenced (n = 4), allowing for the confirmation of the phaC gene identity as well its diversity among marine bacteria. Primers were also tested for screening purposes using 37 colonies from six different environments. Almost 30% of the organisms presented the target amplicon. Thus, the proposed primers are an efficient tool for screening bacteria with potential for the production of PHA as well to study PHA genetic diversity.

Novel polyhydroxyalkanoate copolymers produced in Pseudomonas putida by metagenomic polyhydroxyalkanoate synthases

Bacterially produced biodegradable polyhydroxyalkanoates (PHAs) with versatile properties can be achieved using different PHA synthases (PhaCs). This work aims to expand the diversity of known PhaCs via functional metagenomics and demonstrates the use of these novel enzymes in PHA production. Complementation of a PHA synthesis-deficient Pseudomonas putida strain with a soil metagenomic cosmid library retrieved 27 clones expressing either class I, class II, or unclassified PHA synthases, and many did not have close sequence matches to known PhaCs. The composition of PHA produced by these clones was dependent on both the supplied growth substrates and the nature of the PHA synthase, with various combinations of short-chain-length (SCL) and medium-chain-length (MCL) PHA. These data demonstrate the ability to isolate diverse genes for PHA synthesis by functional metagenomics and their use for the production of a variety of PHA polymer and copolymer mixtures.