Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them

Microbial production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), from lab to the shelf: A review

Polyhydroxyalkanoates (PHAs) are natural biopolyesters produced by microorganisms that represent one of the most promising candidates for the replacement of conventional plastics due to their complete biodegradability and advantageous material properties which can be modulated by varying their monomer composition. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] has received particular research attention because it can be synthesized based on the same microbial platform developed for poly(3-hydroxybutyrate) [P(3HB)] without much modification, with as high productivity as P(3HB). It also offers more useful mechanical and thermal properties than P(3HB), which broaden its application as a biocompatible and biodegradable polyester. However, a significant commercial disadvantage of P(3HB-co-3HV) is its rather high production cost, thus many studies have investigated the economical synthesis of P(3HB-co-3HV) from structurally related and unrelated carbon sources in both wild-type and recombinant microbial strains. A large number of metabolic engineering strategies have also been proposed to tune the monomer composition of P(3HB-co-3HV) and thus its material properties. In this review, recent metabolic engineering strategies designed for enhanced production of P(3HB-co-3HV) are discussed, along with their current status, limitations, and future perspectives.

Estuarine mangrove niches select cultivable heterotrophic diazotrophs with diverse metabolic potentials-a prospective cross-dialog for functional diazotrophy

Introduction

Biological nitrogen fixation (BNF), an unparalleled metabolic novelty among living microorganisms on earth, globally contributes ~88-101 Tg N year-1 to natural ecosystems, ~56% sourced from symbiotic BNF while ~22-45% derived from free-living nitrogen fixers (FLNF). The success of symbiotic BNF is largely dependent on its interaction with host-plant, however ubiquitous environmental heterotrophic FLNFs face many limitations in their immediate ecological niches to sustain unhindered BNF. The autotrophic FLNFs like cyanobacteria and oceanic heterotrophic diazotrophs have been well studied about their contrivances acclimated/adapted by these organisms to outwit the environmental constraints for functional diazotrophy. However, FLNF heterotrophs face more adversity in executing BNF under stressful estuarine/marine/aquatic habitats.

Methods

In this study a large-scale cultivation-dependent investigation was accomplished with 190 NCBI accessioned and 45 non-accessioned heterotrophic FLNF cultivable bacterial isolates (total 235) from halophilic estuarine intertidal mangrove niches of Indian Sundarbans, a Ramsar site and UNESCO proclaimed World Heritage Site. Assuming ~1% culturability of the microbial community, the respective niches were also studied for representing actual bacterial diversity via cultivation-independent next-generation sequencing of V3-V4 rRNA regions.

Results

Both the studies revealed a higher abundance of culturable Gammaproteobacteria followed by Firmicutes, the majority of 235 FLNFs studied belonging to these two classes. The FLNFs displayed comparable selection potential in media for free nitrogen fixers and iron-oxidizing bacteria, linking diazotrophy with iron oxidation, siderophore production, phosphorus solubilization, phosphorus uptake and accumulation as well as denitrification.

Discussion

This observation validated the hypothesis that under extreme estuarine mangrove niches, diazotrophs are naturally selected as a specialized multidimensional entity, to expedite BNF and survive. Earlier metagenome data from mangrove niches demonstrated a microbial metabolic coupling among C, N, P, S, and Fe cycling in mangrove sediments, as an adaptive trait, evident with the co-abundant respective functional genes, which corroborates our findings in cultivation mode for multiple interrelated metabolic potential facilitating BNF in a challenging intertidal mangrove environment.

Bacteria for Bioplastics: Progress, Applications, and Challenges

Bioplastics are one of the answers that can point society toward a sustainable future. Under this premise, the synthesis of polymers with competitive properties using low-cost starting materials is a highly desired factor in the industry. Also, tackling environmental issues such as nonbiodegradable waste generation, high carbon footprint, and consumption of nonrenewable resources are some of the current concerns worldwide. The scientific community has been placing efforts into the biosynthesis of polymers using bacteria and other microbes. These microorganisms can be convenient reactors to consume food and agricultural wastes and convert them into biopolymers with inherently attractive properties such as biodegradability, biocompatibility, and appreciable mechanical and chemical properties. Such biopolymers can be applied to several fields such as packing, cosmetics, pharmaceutical, medical, biomedical, and agricultural. Thus, intending to elucidate the science of microbes to produce polymers, this review starts with a brief introduction to bioplastics by describing their importance and the methods for their production. The second section dives into the importance of bacteria regarding the biochemical routes for the synthesis of polymers along with their advantages and disadvantages. The third section covers some of the main parameters that influence biopolymers' production. Some of the main applications of biopolymers along with a comparison between the polymers obtained from microorganisms and the petrochemical-based ones are presented. Finally, some discussion about the future aspects and main challenges in this field is provided to elucidate the main issues that should be tackled for the wide application of microorganisms for the preparation of bioplastics.

Comparative computational study to augment UbiA prenyltransferases inherent in purple photosynthetic bacteria cultured from mangrove microbial mats in Qatar for coenzyme Q10 biosynthesis

Coenzyme Q10 (CoQ10) is a powerful antioxidant with a myriad of applications in healthcare and cosmetic industries. The most effective route of CoQ10 production is microbial biosynthesis. In this study, four CoQ10 biosynthesizing purple photosynthetic bacteria: Rhodobacter blasticus, Rhodovulum adriaticum, Afifella pfennigii and Rhodovulum marinum, were identified using 16S rRNA sequencing of enriched microbial mat samples obtained from Purple Island mangroves (Qatar). The membrane bound enzyme 4-hydroxybenzoate octaprenyltransferase (UbiA) is pivotal for bacterial biosynthesis of CoQ10. The identified bacteria could be inducted as efficient industrial bio-synthesizers of CoQ10 by engineering their UbiA enzymes. Therefore, the mutation sites and substitution residues for potential functional enhancement were determined by comparative computational study. Two mutation sites were identified within the two conserved Asp-rich motifs, and the effect of proposed mutations in substrate binding affinity of the UbiA enzymes was assessed using multiple ligand simultaneous docking (MLSD) studies, as a groundwork for experimental studies.

Analysis of Polyhydroxyalkanoates Granules in Haloferax mediterranei by Double-Fluorescence Staining with Nile Red and SYBR Green by Confocal Fluorescence Microscopy

Haloferaxmediterranei is a haloarchaeon of high interest in biotechnology because it produces and mobilizes intracellular polyhydroxyalkanoate (PHA) granules during growth under stress conditions (limitation of phosphorous in the culture media), among other interesting metabolites (enzymes, carotenoids, etc.). The capability of PHA production by microbes can be monitored with the use of staining-based methods. However, the staining of haloarchaea cells is a challenging task; firstly, due to the high ionic strength of the medium, which is inappropriate for most of dyes, and secondly, due to the low permeability of the haloarchaea S-layer to macromolecules. In this work, Haloferax mediterranei is used as a halophilic archaeon model to describe an optimized protocol for the visualization and analysis of intracellular PHA granules in living cells. The method is based on double-fluorescence staining using Nile red and SYBR Green by confocal fluorescence microscopy. Thanks to this method, the capability of PHA production by new haloarchaea isolates could be easily monitored.

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.

Characterization of the promising poly(3-hydroxybutyrate) producing halophilic bacterium Halomonas halophila

This work explores molecular, morphological as well as biotechnological features of the highly promising polyhydroxyalkanoates (PHA) producer Halomonas halophila. Unlike many other halophiles, this bacterium does not require expensive complex media components and it is capable to accumulate high intracellular poly(3-hydroxybutyrate) (PHB) fractions up to 82% of cell dry mass. Most remarkably, regulating the concentration of NaCl apart from PHB yields influences also the polymer's molecular mass and polydispersity. The bacterium metabolizes various carbohydrates including sugars predominant in lignocelluloses and other inexpensive substrates. Therefore, the bacterium was employed for PHB production on hydrolysates of cheese whey, spent coffee grounds, sawdust and corn stover, which were hydrolyzed by HCl; required salinity of cultivation media was set up during neutralization by NaOH. The bacterium was capable to use all the tested hydrolysates as well as sugar beet molasses for PHB biosynthesis, indicating its potential for industrial PHB production.