The influence of nitrogen limitation on mcl-PHA synthesis by two newly isolated strains of Pseudomonas sp

Production of polyhydroxyalkanoates by the thermophile Cupriavidus cauae PHS1

Thermophilic production of polyhydroxyalkanoate is considered a very promising way to overcome the problems that may arise when using mesophilic strains. This study reports the first thermophilic polyhydroxybutyrate-producing Cupriavidus species, which are known as the best polyhydroxybutyrate-producing microorganisms. Cupriavidus cauae PHS1 harbors a phbCABR cluster with high similarity to the corresponding proteins of C. necator H16 (80, 93, 96, and 97 %). This strain can produce polyhydroxybutyrate from a range of substrates, including acetate (5 g/L) and phenol (1 g/L), yielding 7.6 % and 18.9 % polyhydroxybutyrate, respectively. Moreover, the strain produced polyhydroxybutyrate at temperatures ranging from 25 to 50 °C, with the highest polyhydroxybutyrate content (47 °C) observed at 45 °C from gluconate. Additionally, the strain could incorporate 3-hydroxyvalerate (12.5 mol. %) into the polyhydroxybutyrate polymer using levulinic acid as a precursor. Thus, Cupriavidus cauae PHS1 may be a promising polyhydroxybutyrate producer as alternative for mesophilic polyhydroxybutyrate-producing Cupriavidus species.

Two-Stage Bio-Hydrogen and Polyhydroxyalkanoate Production: Upcycling of Spent Coffee Grounds

Coffee waste is an abundant biomass that can be converted into high value chemical products, and is used in various renewable biological processes. In this study, oil was extracted from spent coffee grounds (SCGs) and used for polyhydroxyalkanoate (PHA) production through Pseudomonas resinovorans. The oil-extracted SCGs (OESCGs) were hydrolyzed and used for biohydrogen production through Clostridium butyricum DSM10702. The oil extraction yield through n-hexane was 14.4%, which accounted for 97% of the oil present in the SCGs. OESCG hydrolysate (OESCGH) had a sugar concentration of 32.26 g/L, which was 15.4% higher than that of the SCG hydrolysate (SCGH) (27.96 g/L). Hydrogen production using these substrates was 181.19 mL and 136.58 mL in OESCGH and SCGH media, respectively. The consumed sugar concentration was 6.77 g/L in OESCGH and 5.09 g/L in SCGH media. VFA production with OESCGH (3.58 g/L) increased by 40.9% compared with SCGH (2.54 g/L). In addition, in a fed-batch culture using the extracted oil, cell dry weight was 5.4 g/L, PHA was 1.6 g/L, and PHA contents were 29.5% at 24 h.

Optimized pulse-feeding fed-batch fermentation for enhanced lignin to polyhydroxyalkanoate transformation

With an anticipated growth of Bio-Circular-Green economy, the amount of lignin generated as by-product from biorefineries is increasing. Hence, lignin valorising strategies become a very interesting option to improve economic viability of the biorefineries. This study revealed the development of bioprocesses for upgrading lignin into bioplastic. Specifically, a novel strain of Pseudomonas fulva has been applied for microbial bioconversion of organosolv lignin to fermentative polyhydroxyalkanoate (PHA) production. Fed-batch fermentation of lignin-to-PHA with pulse-feeding approach was optimized using Design of Experiment. Effects of C:N ratio and feeding profiles on PHA accumulation in P. fulva were investigated to determine optimal operation. Under optimized fed-batch, the PHA concentration of 195.2 ± 6.6 mg/L could be reached and the PHA content was more than 2 folds enhancement compared to batch process. Type of PHA produced was also characterized for chemical composition via GC-MS analysis. The established lignin to PHA conversion could provide platform for developing integrated lignin bioprocessing to promote cost-effective biorefineries.

Effect of short- and medium-chain fatty acid mixture on polyhydroxyalkanoate production by Pseudomonas strains grown under different culture conditions

Short- and medium-chain fatty acids (SMCFAs) derived from the acidogenic anaerobic mixed culture fermentation of acid whey obtained from a crude cheese production line and their synthetic mixture that simulates a real SMCFA-rich stream were evaluated for polyhydroxyalkanoate (PHA) production. Three individual Pseudomonas sp. strains showed different capabilities of growing and producing PHAs in the presence of a synthetic mixture of SMCFAs. Pseudomonas sp. GL06 exhibited the highest SMCFA tolerance and produced PHAs with the highest productivity (2.7 mg/L h). Based on these observations, this strain was selected for further investigations on PHA production in a fed-batch bioreactor with a SMCFA-rich stream extracted from the effluent. The results showed that PHA productivity reached up to 4.5 mg/L h at 24 h of fermentation together with the ammonium exhaustion in the growth medium. Moreover, the PHA monomeric composition varied with the bacterial strain and the type of the growth medium used. Furthermore, a differential scanning calorimetric and thermogravimetric analysis showed that a short- and medium-chain-length PHA copolymer made of 3-hydroxybutyric, -hexanoic, -octanoic, -decanoic, and -dodecanoic has promising properties. The ability of Pseudomonas sp. to produce tailored PHA copolymers together with the range of possible applications opens new perspectives in the development of PHA bioproduction as a part of an integrated valorization process of SMCFAs derived from waste streams.

Advances and trends in microbial production of polyhydroxyalkanoates and their building blocks

With the rapid development of synthetic biology, a variety of biopolymers can be obtained by recombinant microorganisms. Polyhydroxyalkanoates (PHA) is one of the most popular one with promising material properties, such as biodegradability and biocompatibility against the petrol-based plastics. This study reviews the recent studies focusing on the microbial synthesis of PHA, including chassis engineering, pathways engineering for various substrates utilization and PHA monomer synthesis, and PHA synthase modification. In particular, advances in metabolic engineering of dominant workhorses, for example Halomonas, Ralstonia eutropha, Escherichia coli and Pseudomonas, with outstanding PHA accumulation capability, were summarized and discussed, providing a full landscape of diverse PHA biosynthesis. Meanwhile, we also introduced the recent efforts focusing on structural analysis and mutagenesis of PHA synthase, which significantly determines the polymerization activity of varied monomer structures and PHA molecular weight. Besides, perspectives and solutions were thus proposed for achieving scale-up PHA of low cost with customized material property in the coming future.

Microplastics a Novel Substratum for Polyhydroxyalkanoate (PHA)-Producing Bacteria in Aquatic Environments

Polyhydroxyalkanoates (PHA) being biological polymers have attracted great attention. PHA have similar properties to that of synthetic plastic and are biodegradable. To discourage plastic pollution in the environment alternative solutions to the plastic pollution has to be readily available. High cost in production of PHA limits the production of these polymers at industrial scale. Bacteria are screened for PHA from diverse niches to meet the current requirements of cheap PHA production at industrial level. The microbial biofilm formed on the surface of microplastic could be a potential source in providing bacteria of economic importance. This paper is an attempt to search microplastic niche for potential PHA producers. PHA production variation was observed with different parameters such as type of carbon source, nitrogen source concentration and also time of incubation. Bacillus sp. CM27 showed maximum PHA yield up to 32.1% among other isolates at 48 h with 2% glucose as carbon source. Optimization of media leads to increase in PHA yield (37.69%) of CDW in Bacillus sp. CM27. Amino acid sequence of Bacillus sp.CM27 showed the presence of PhaC box with sequence, G-Y-C-M-G-G having cysteine in the middle of the box. The extracted polymer was confirmed by FTIR spectroscopy.

A Review on Enhancing Cupriavidus necator Fermentation for Poly(3-hydroxybutyrate) (PHB) Production From Low-Cost Carbon Sources

In the context of a circular economy, bioplastic production using biodegradable materials such as poly(3-hydroxybutyrate) (PHB) has been proposed as a promising solution to fundamentally solve the disposal issue of plastic waste. PHB production techniques through fermentation of PHB-accumulating microbes such as Cupriavidus necator have been revolutionized over the past several years with the development of new strategies such as metabolic engineering. This review comprehensively summarizes the latest PHB production technologies via Cupriavidus necator fermentation. The mechanism of the biosynthesis pathway for PHB production was first assessed. PHB production efficiencies of common carbon sources, including food waste, lignocellulosic materials, glycerol, and carbon dioxide, were then summarized and critically analyzed. The key findings in enhancing strategies for PHB production in recent years, including pre-treatment methods, nutrient limitations, feeding optimization strategies, and metabolism engineering strategies, were summarized. Furthermore, technical challenges and future prospects of strategies for enhanced production efficiencies of PHB were also highlighted. Based on the overview of the current enhancing technologies, more pilot-scale and larger-scale tests are essential for future implementation of enhancing strategies in full-scale biogas plants. Critical analyses of various enhancing strategies would facilitate the establishment of more sustainable microbial fermentation systems for better waste management and greater efficiency of PHB production.

Insightful Advancement and Opportunities for Microbial Bioplastic Production

Impetuous urbanization and population growth are driving increased demand for plastics to formulate impeccable industrial and biomedical commodities. The everlasting nature and excruciating waste management of petroleum-based plastics have catered to numerous challenges for the environment. However, just implementing various end-of-life management techniques for assimilation and recycling plastics is not a comprehensive remedy; instead, the extensive reliance on finite resources needs to be reduced for sustainable production and plastic product utilization. Microorganisms, such as bacteria and algae, are explored substantially for their bioplastic production repertoire, thus replacing fossil-based plastics sooner or later. Nevertheless, the utilization of pure microbial cultures has led to various operational and economical complications, opening the ventures for the usage of mixed microbial cultures (MMCs) consisting of bacteria and algae for sustainable production of bioplastic. The current review is primarily focuses on elaborating the bioplastic production capabilities of different bacterial and algal strains, followed by discussing the quintessence of MMCs. The present state-of-the-art of bioplastic, different types of bacterial bioplastic, microalgal biocomposites, operational factors influencing the quality and quantity of bioplastic precursors, embracing the potential of bacteria-algae consortia, and the current global status quo of bioplastic production has been summarized extensively.

What Is New in the Field of Industrial Wastes Conversion into Polyhydroxyalkanoates by Bacteria?

The rising global consumption and industrialization has resulted in increased food processing demand. Food industry generates a tremendous amount of waste which causes serious environmental issues. These problems have forced us to create strategies that will help to reduce the volume of waste and the contamination to the environment. Waste from food industries has great potential as substrates for value-added bioproducts. Among them, polyhydroxyalkanaotes (PHAs) have received considerable attention in recent years due to their comparable characteristics to common plastics. These biodegradable polyesters are produced by microorganisms during fermentation processes utilizing various carbon sources. Scale-up of PHA production is limited due to the cost of the carbon source metabolized by the microorganisms. Therefore, there is a growing need for the development of novel microbial processes using inexpensive carbon sources. Such substrates could be waste generated by the food industry and food service. The use of industrial waste streams for PHAs biosynthesis could transform PHA production into cheaper and more environmentally friendly bioprocess. This review collates in detail recent developments in the biosynthesis of various types of PHAs produced using waste derived from agrofood industries. Challenges associated with this production bioprocess were described, and new ways to overcome them were proposed.

Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation

Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma⁵⁴-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.

Biosynthesis of Polyhydroxyalkanoates (PHAs) by the Valorization of Biomass and Synthetic Waste

Synthetic pollutants are a looming threat to the entire ecosystem, including wildlife, the environment, and human health. Polyhydroxyalkanoates (PHAs) are natural biodegradable microbial polymers with a promising potential to replace synthetic plastics. This research is focused on devising a sustainable approach to produce PHAs by a new microbial strain using untreated synthetic plastics and lignocellulosic biomass. For experiments, 47 soil samples and 18 effluent samples were collected from various areas of Punjab, Pakistan. The samples were primarily screened for PHA detection on agar medium containing Nile blue A stain. The PHA positive bacterial isolates showed prominent orange-yellow fluorescence on irradiation with UV light. They were further screened for PHA estimation by submerged fermentation in the culture broth. Bacterial isolate 16a produced maximum PHA and was identified by 16S rRNA sequencing. It was identified as Stenotrophomonas maltophilia HA-16 (MN240936), reported first time for PHA production. Basic fermentation parameters, such as incubation time, temperature, and pH were optimized for PHA production. Wood chips, cardboard cutouts, plastic bottle cutouts, shredded polystyrene cups, and plastic bags were optimized as alternative sustainable carbon sources for the production of PHAs. A vital finding of this study was the yield obtained by using plastic bags, i.e., 68.24 ± 0.27%. The effective use of plastic and lignocellulosic waste in the cultivation medium for the microbial production of PHA by a novel bacterial strain is discussed in the current study.

Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems

The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and—among nitrifiers—unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.

The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.

Mutagenesis of PhaR, a Regulator Gene of Polyhydroxyalkanoate Biosynthesis of Xanthomonas oryzae pv. oryzae Caused Pleiotropic Phenotype Changes

Polyhydroxyalkanoates (PHAs) are intracellular carbon and energy storage materials produced in various microorganisms under nutrient-limited conditions. PhaR is a regulatory protein involved in PHA synthesis. Xanthomonas oryzae pv. oryzae (Xoo) is one of the most important bacterial pathogens in rice and has PHA biosynthesis genes in its genome, but the biological function of phaR in Xoo is unknown. In this study, we investigated the effects of the mutagenesis of phaR gene in Xoo strain PXO99A. Compared to the wildtype, the PhaR gene knock-out mutant PXO99ΔphaR was hypermotile and showed decreased growth rates in both rich and limited nutrient media. PXO99ΔphaR also showed almost 75% decrease in extracellular polysaccharide (EPS) production. When inoculated in rice leaves by leaf-clipping method, PXO99ΔphaR displayed reduced virulence in terms of lesion length and bacterial multiplication compared with the wildtype strain. PXO99ΔphaR also showed enhanced hypersensitive response (HR) induction in the leaves of non-host Nicotiana benthamiana with elevated hpa1 gene expression. Introduction of a cosmid containing the phaR coding sequence restored the phenotypes of the mutant to those of the wildtype strain. These results suggest that PhaR gene is an important gene that affects multiple bacterial characteristics, including EPS production, growth rate, defense response induced harpin production and motility, related to its virulence in plant.

Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress

Bacterial response to environmental stimuli is essential for survival. In response to fluctuating environmental conditions, the physiological status of bacteria can change due to the actions of transcriptional regulatory machinery. The synthesis and accumulation of polyhydroxyalkanoates (PHAs) are one of the survival strategies in harsh environments. In this study, we used transcriptome analysis of Pseudomonas putida KT2440 to gain a genome-wide view of the mechanisms of environmental-friendly biopolymers accumulation under nitrogen-limiting conditions during conversion of metabolically different carbon sources (sodium gluconate and oleic acid). Transcriptomic data revealed that phaG expression is associated with medium-chain-length-PHAs' synthesis not only on sodium gluconate but also on oleic acid, suggesting that PhaG may play a role in this process, as well. Moreover, genes involved in the β-oxidation pathway were induced in the PHAs production phase when sodium gluconate was supplied as the only carbon and energy source. The transition from exponential growth to stationary phase caused a significant expression of genes involved in nitrogen metabolism, energy supply, and transport system. In this study, several molecular mechanisms, which drive mcl-PHAs synthesis, have been investigated. The identified genes may provide valuable information to improve the efficiency of this bioprocess and make it more economically feasible.

Effect of famine-phase reduced aeration on polyhydroxyalkanoate accumulation in aerobic granules

The effects of variable aeration in the famine period on polyhydroxyalkanoate (PHA) accumulation in aerobic granules were investigated. Results showed that regardless of the aeration rates used during famine period, all aerobic granules achieved a similar chemical oxygen demand removal and PHA content. The decrease in famine-period aeration rates accelerated the maximum PHA accumulation together with increase in granular size and settling ability. The PHA-accumulating microorganisms were found to have shifted closer to the surface of the granules when the aeration rate was reduced. Moreover, PHA compositional changes occurred, where the hydroxyvalerate content had increased with the reduction in aeration rate. Ultimately, the results indicate that the requirement of aeration for PHA accumulation in aerobic granules is highly insignificant in the famine phase. PHA production in aerobic granules under zero aeration in the famine period may result in an energy input reduction of up to 74%.

Medium-chain-length polyhydroxyalkanoates synthesis by Pseudomonas putida KT2440 relA/spoT mutant: bioprocess characterization and transcriptome analysis

Pseudomonas putida KT2440 is a model bacteria used commonly for medium-chain-length polyhydroxyalkanoates (mcl-PHAs) production using various substrates. However, despite many studies conducted on P. putida KT2440 strain, the molecular mechanisms of leading to mcl-PHAs synthesis in reaction to environmental stimuli are still not clear. The rearrangement of the metabolism in response to environmental stress could be controlled by stringent response that modulates the transcription of many genes in order to promote survival under nutritional deprivation conditions. Therefore, in this work we investigated the relation between mcl-PHAs synthesis and stringent response. For this study, a relA/spoT mutant of P. putida KT2440, unable to induce the stringent response, was used. Additionally, the transcriptome of this mutant was analyzed using RNA-seq in order to examine rearrangements of the metabolism during cultivation. The results show that the relA/spoT mutant of P. putida KT2440 is able to accumulate mcl-PHAs in both optimal and nitrogen limiting conditions. Nitrogen starvation did not change the efficiency of mcl-PHAs synthesis in this mutant. The transition from exponential growth to stationary phase caused significant upregulation of genes involved in transport system and nitrogen metabolism. Transcriptional regulators, including rpoS, rpoN and rpoD, did not show changes in transcript abundance when entering the stationary phase, suggesting their limited role in mcl-PHAs accumulation during stationary phase.

Bacterial polyhydroxyalkanoates: Still fabulous?

Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed.

The diversity of bacteria isolated from antarctic freshwater reservoirs possessing the ability to produce polyhydroxyalkanoates

The diversity of polyhydroxyalkanoates-producing bacteria in freshwater reservoirs in the Ecology Glacier foreland, Antarctica, was examined by a cultivation-dependent method. Isolated strains were analyzed phylogenetically by 16S rRNA gene sequencing, and classified as members of Alpha-, Beta-, or Gammaproteobacteria classes. Polymerase chain reaction was used to detect PHA synthase genes. Potential polyhydroxyalkanoates (PHAs) producers belonging mainly to Pseudomonas sp., and Janthinobacterium sp. were isolated from all five sampling sites, suggesting that PHA synthesis is a common bacterial feature at pioneer sites. All Pseudomonas strains had the genetic potential to synthesize medium-chain-length PHAs, whereas some isolated Janthinobacterium strains might produce short-chain-length PHAs or medium-chain-length PHAs. It is the first report revealing that Janthinobacterium species could have the potential to produce medium-chain-length PHAs.

Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha

(R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha H16 (RePhaB) is an enzyme that catalyzes the NADPH-dependent reduction of acetoacetyl-CoA, an intermediate of polyhydroxyalkanoates (PHA) synthetic pathways. Polymeric PHA is used to make bioplastics, implant biomaterials, and biofuels. Here, we report the crystal structures of RePhaB apoenzyme and in complex with either NADP(+) or acetoacetyl-CoA, which provide the catalytic mechanism of the protein. RePhaB contains a Rossmann fold and a Clamp domain for binding of NADP(+) and acetoacetyl-CoA, respectively. The NADP(+)-bound form of RePhaB structure reveals that the protein has a unique cofactor binding mode. Interestingly, in the RePhaB structure in complex with acetoacetyl-CoA, the conformation of the Clamp domain, especially the Clamp-lid, undergoes a large structural change about 4.6 Å leading to formation of the substrate pocket. These structural observations, along with the biochemical experiments, suggest that movement of the Clamp-lid enables the substrate binding and ensures the acetoacetyl moiety is located near to the nicotinamide ring of NADP(+).