Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

Assessing the efficiency and potential for internally reusing nitrogen-containing effluent in the PHA accumulation stage under low C/N conditions in a mixed-culture process

Polyhydroxyalkanoates (PHAs) are biodegradable polyesters poised to replace plastics. Mixed culture (MC)-based three-stage processes are effective for carbon recovery from waste biomass, but the energy-intensive PHA synthesis is negatively affected by ammonia nitrogen, inhibiting PHA yield. This study aims to reuse ammonia nitrogen efficiently to mitigate its impact and prevent secondary pollution. PHA production assays under varying MC types, substrate types, feeding modes, and oxygen levels showed that the butyrate type substrate-enriched, high-load, low-oxygen mode (RBC(4)P(1)O(+)) achieved a PHA conversion ratio of 0.45 g COD/g COD, 1.8 times higher than RBC(2)P(5)O(++), with reduced energy consumption and CO2 emissions. Ammonia uptake was 0.06 g NH3-N/g PHA at a productivity of 4.54 g/L, showing improved nitrogen recycling. Direct recycling of ammonia nitrogen-containing effluent in the PHA-producing MC enrichment system was performed, and no significant decrease was observed in either the physical properties of the MC flocs or the metrics related to PHA synthesis capacity. These results highlight the feasibility of ammonia reuse and indicate that the soluble microbial products in the effluent have minimal impact on MC enrichment.

Innovations in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and nanocomposites for sustainable food packaging via biochemical biorefinery platforms: A comprehensive review

The substantial build-up of non-biodegradable plastic waste from packaging sector not only poses severe environmental threats but also hastens the depletion of natural petroleum-based resources. Presently, poly (3-hydroxybutyrate-co-3-hydroxy valerate) (PHBV), received enormous attention as ideal alternatives for such traditional petroleum-derived plastics based on their biocompatibility and superior mechanical properties. However, high cost of such copolymer, due to expensive nature of feedstock, inefficient microbial processes and unfavorable downstream processing strategies restricts its large-scale commercial feasibility in the packaging sector. This review explores merits and challenges associated with using potent agricultural and industrial waste biomasses as sustainable feedstocks alongside improved fermentation and downstream processing strategies for the biopolymer in terms of biorefinery concept. Despite PHBV's attractive properties, its inherent shortcomings like weak thermal stability, poor mechanical properties, processability difficulty, substantial hydrophobicity and comparatively higher water vapor permeability (WVP) demand the development of its composites based on the application. Based on this fact, the review assessed properties and potential applications of PHBV-based composite materials having natural raw materials, nanomaterials and synthetic biodegradable polymers. Besides, the review also enlightens sustainability, future prospects, and challenges associated with PHBV-based composites in the field of food packaging while considering insights about economic evaluation and life cycle assessment.

Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.

A review on microbes mediated resource recovery and bioplastic (polyhydroxyalkanoates) production from wastewater

BACKGROUND

Plastic is widely utilized in packaging, frameworks, and as coverings material. Its overconsumption and slow degradation, pose threats to ecosystems due to its toxic effects. While polyhydroxyalkanoates (PHA) offer a sustainable alternative to petroleum-based plastics, their production costs present significant obstacles to global adoption. On the other side, a multitude of household and industrial activities generate substantial volumes of wastewater containing both organic and inorganic contaminants. This not only poses a threat to ecosystems but also presents opportunities to get benefits from the circular economy. Production of bioplastics may be improved by using the nutrients and minerals in wastewater as a feedstock for microbial fermentation. Strategies like feast-famine culture, mixed-consortia culture, and integrated processes have been developed for PHA production from highly polluted wastewater with high organic loads. Various process parameters like organic loading rate, organic content (volatile fatty acids), dissolved oxygen, operating pH, and temperature also have critical roles in PHA accumulation in microbial biomass. Research advances are also going on in downstream and recovery of PHA utilizing a combination of physical and chemical (halogenated solvents, surfactants, green solvents) methods. This review highlights recent developments in upcycling wastewater resources into PHA, encompassing various production strategies, downstream processing methodologies, and techno-economic analyses.

SHORT CONCLUSION

Organic carbon and nitrogen present in wastewater offer a promising, cost-effective source for producing bioplastic. Previous attempts have focused on enhancing productivity through optimizing culture systems and growth conditions. However, despite technological progress, significant challenges persist, such as low productivity, intricate downstream processing, scalability issues, and the properties of resulting PHA.

Optimisation of the biological production of levulinic acid in a mixed microbial culture fed with synthetic grape pomace

Levulinic acid (LA) is a polymer with a vast industrial application range and can be co-produced as a minor by-product during the biological production of polyhydroxyalkanoates (PHA). However, the influence of key parameters as tools for favouring the production of LA over PHA is still unclear. In this study, we investigated how several critical operational conditions, i.e., carbon-nitrogen ratio (C/N), organic loading rate (OLR) and airflow, can be optimised to favour LA accumulation over PHA production by a mixed microbial culture (MMC), using synthetic grape pomace (GP) hydrolysate as the substrate. The results showed that it was possible to direct the MMC towards LA accumulation instead of PHA. The maximum LA yield was 2.7 ± 0.2 g LA/(L·d) using a C/N of 35, an airflow of 5 L/min and an OLR of 4 g sCOD/(L·d). The OLR and, to a lesser extent, the C/N ratio were the main factors significantly and positively correlated with the biological synthesis of LA.

Biodegradation of chloroethene compounds under microoxic conditions

The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.

Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments

The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.

Valorization of organic wastes using bioreactors for polyhydroxyalkanoate production: Recent advancement, sustainable approaches, challenges, and future perspectives

Microbial polyhydroxyalkanoates (PHA) are encouraging biodegradable polymers, which may ease the environmental problems caused by petroleum-derived plastics. However, there is a growing waste removal problem and the high price of pure feedstocks for PHA biosynthesis. This has directed to the forthcoming requirement to upgrade waste streams from various industries as feedstocks for PHA production. This review covers the state-of-the-art progress in utilizing low-cost carbon substrates, effective upstream and downstream processes, and waste stream recycling to sustain entire process circularity. This review also enlightens the use of various batch, fed-batch, continuous, and semi-continuous bioreactor systems with flexible results to enhance the productivity and simultaneously cost reduction. The life-cycle and techno-economic analyses, advanced tools and strategies for microbial PHA biosynthesis, and numerous factors affecting PHA commercialization were also covered. The review includes the ongoing and upcoming strategies viz. metabolic engineering, synthetic biology, morphology engineering, and automation to expand PHA diversity, diminish production costs, and improve PHA production with an objective of "zero-waste" and "circular bioeconomy" for a sustainable future.

Effect of composition of volatile fatty acids on yield of polyhydroxyalkanoates and mechanisms of bioconversion from activated sludge

Polyhydroxyalkanoates (PHA) is green biodegradable natural polymer. Here PHA production from volatile fatty acids (VFAs) was investigated in sequential batch reactors inoculated with activated sludge. Single or mixed VFAs ranging from acetate to valerate were evaluated, and the dominant VFA concentration was 2 times of that of the others in the tests. Results showed that mixed substrates achieved about 1.6 times higher yield of PHA production than single substrate. The butyrate-dominated substrates maximized PHA content at 72.08% of VSS, and the valerate-dominated substrates were followed with PHA content at 61.57%. Metabolic flux analysis showed the presence of valerate in the substrates caused a more robust PHA production. There was at least 20% of 3-hydroxyvalerate in the polymer. Hydrogenophaga and Comamonas were the main PHA producers. As VFAs could be produced in anaerobic digestion of organic wastes, the methods and data here could be referred for efficient green bioconversion of PHA.

Production of polyhydroxyalkanoates from renewable resources: a review on prospects, challenges and applications

Bioplastics replace synthetic plastics of petrochemical origin, which contributes challenge to both polymer quality and economics. Novel polyhydroxyalkanoates (PHA)-composite materials, with desirable product quality, could be developed, thus targeting the global plastics market, in the coming years. It is possible that PHA can be a greener substitute for their petroleum-based competitors since they are simply decomposed, which may lessen the pressure on municipal and industrial waste management systems. PHA production has proven to be the bottleneck in industrial application and commercialization because of the high price of carbon substrates and downstream processes required to achieve reliability. Bacterial PHA production by these municipal and industrial wastes, which act as a cheap, renewable carbon substrate, eliminates waste management hassles and acts as an efficient substitute for synthetic plastics. In the present review, challenges and opportunities related to the commercialization of polyhydroxyalkanoates are discussed and presented. Moreover, it discusses critical steps of their production process, feedstock evaluation, optimization strategies, and downstream processes. This information may provide us the complete utilization of bacterial PHA during possible applications in packaging, nutrition, medicine, and pharmaceuticals.

Engineering Vibrio alginolyticus as a novel chassis for PHB production from starch

Vibrio alginolyticus LHF01 was engineered to efficiently produce poly-3-hydroxybutyrate (PHB) from starch in this study. Firstly, the ability of Vibrio alginolyticus LHF01 to directly accumulate PHB using soluble starch as the carbon source was explored, and the highest PHB titer of 2.06 g/L was obtained in 18 h shake flask cultivation. Then, with the analysis of genomic information of V. alginolyticus LHF01, the PHB synthesis operon and amylase genes were identified. Subsequently, the effects of overexpressing PHB synthesis operon and amylase on PHB production were studied. Especially, with the co-expression of PHB synthesis operon and amylase, the starch consumption rate was improved and the PHB titer was more than doubled. The addition of 20 g/L insoluble corn starch could be exhausted in 6-7 h cultivation, and the PHB titer was 4.32 g/L. To the best of our knowledge, V. alginolyticus was firstly engineered to produce PHB with the direct utilization of starch, and this stain can be considered as a novel host to produce PHB using starch as the raw material.

Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA)

Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments.

Graphical Abstract

Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-022-01008-5.

Finding of Novel Galactose Utilizing Halomonas sp. YK44 for Polyhydroxybutyrate (PHB) Production

Polyhydroxybutyrate (PHB) is a biodegradable bioplastic with potential applications as an alternative to petroleum-based plastics. However, efficient PHB production remains difficult. The main cost of PHB production is attributed to carbon sources; hence, finding inexpensive sources is important. Galactose is a possible substrate for polyhydroxyalkanoate production as it is abundant in marine environments. Marine bacteria that produce PHB from galactose could be an effective resource that can be used for efficient PHB production. In this study, to identify a galactose utilizing PHB producer, we examined 16 Halomonas strains. We demonstrated that Halomonas cerina (Halomonas sp. YK44) has the highest growth and PHB production using a culture media containing 2% galactose, final 4% NaCl, and 0.1% yeast extract. These culture conditions yielded 8.98 g/L PHB (78.1% PHB content (w/w)). When galactose-containing red algae (Eucheuma spinosum) hydrolysates were used as a carbon source, 5.2 g/L PHB was produced with 1.425% galactose after treatment with activated carbon. Since high salt conditions can be used to avoid sterilization, we examined whether Halomonas sp. YK44 could produce PHB in non-sterilized conditions. Culture media in these conditions yielded 72.41% PHB content. Thus, Halomonas sp. YK44 is robust against contamination, allowing for long-term culture and economical PHB production.

Characterization and Whole-Genome Analysis of a Zearalenone-Degrading Stappia sp. WLB 29

Zearalenone (ZEN) is a widely distributed mycotoxin that frequently contaminates crops and animal feed. Our previous studies showed that a new strain, Stappia sp. WLB 29 with a 97.47% of similarity to Stappia indica B106^T, isolated from the soil samples in the rhizosphere of the crops in Xinjiang, was capable of effectively degrading ZEN in minimal medium. In this study, we determined the complete genomic sequence of the Stappia sp. WLB 29 (Genbank accession number: JALBGD000000000; BioProject ID in GenBank is PRJNA814005). The total length of all sequences was 4,745,415 bp with a GC content of 67.08%. Moreover, the genome-wide analysis showed the presence of laccase- and peroxiredoxin-encoding genes in Stappia sp. WLB 29, which may be associated with ZEN degradation. The genome sequence of Stappia sp. WLB 29 reported here will serve as a reference for comparative genomic studies of ZEN degradation in the feed and food industry.

Halophyte biorefinery for polyhydroxyalkanoates production from Ulva sp. Hydrolysate with Haloferax mediterranei in pneumatically agitated bioreactors and ultrasound harvesting

The present study tested the outdoor cultivation of Haloferax mediterranei for PHA production from green macroalgae Ulva sp. in pneumatically agitated bioreactors and applied ultrasonic separation for enhanced settling of archaeal cells. Scaled-up cultivation (40 L) yielded maximum biomass productivity of 50.1 ± 0.11 mg·L^-1·h^-1 with a PHA productivity of 27 ± 0.01 mg·L^-1·h^-1 and conversion yield of 0.107 g PHA per gram Ulva_DW. The maximum mass fraction of PHA achieved in biomass was calculated to be 56% w/w. Ultrasonic harvesting of Hfx. mediterranei cells approached 30% removal at energy inputs around 7.8 kWh·m^-3, and indicated no significant aggregation enhancement by Ca²⁺ addition. Molecular weight analysis showed an increase in Polydispersity Index (PDI) when the corresponding air velocities were increased suggesting that the polymer was more homogeneous at lower mixing velocities. The current study demonstrated scalable processes for PHA production using Ulva sp. feedstock providing new technologies for halophilic biorefinery.

Beyond PHA: Stimulating intracellular accumulation of added-value compounds in mixed microbial cultures

This review compiled and analyzed the operational conditions (dissolved oxygen, feast and famine ratio, sequential batch reactor cycle length, organic loading rate (OLR), pH, C/N, and temperature) established during the feast and famine culture strategy for the mixed microbial cultures (MMC) selection to understand how these variables could affect the synthesis of polyhydroxyalkanoates, polyglucose, triacylglycerides, levulinic acid and adipic acid from non-fermented substrates. According to the reported information, the dissolved oxygen has a greater impact on the type and amount of produced compound. In a lesser extent, the OLR and the cycle length were identified to have an impact on the accumulation of polyhydroxyalkanoates, whose accumulation was favored at lower OLR and longer cycle lengths. Thereby, the information of this work will allow the design of future strategies for the simultaneous accumulation of compounds of interest other than the polyhydroxyalkanoates or understand the operational conditions that would optimize the polyhydroxyalkanoates production.

Carbon Source Applied in Enrichment Stage of Mixed Microbial Cultures Limits the Substrate Adaptability for PHA Fermentation Using the Renewable Carbon

Suitability of different substrates for enriched mixed microbial cultures (MMCs) is of importance to the polyhydroxyalkanoate (PHA) fermentation using renewable carbon. In this study, three enriched MMCs were evaluated for their fermentation features and kinetics with different carbon sources (sodium acetate, glucose, or starch). The results showed that the highly specific bacterial community composition was developed depending on the applied carbon source. Correspondence analysis suggested that the genus affiliated in Gammaproteobacteria_unclassified was related to 3-hydroxybutyrate (HB) synthesis in acetate-fed MMC (relative abundance of 38%) and glucose-fed MMC (relative abundance of 76.7%), whereas Vibrio genus was related to 3-hydroxyvalerate (HV) production in glucose-fed MMC (relative abundance of 0.4%) and starch-fed MMC (relative abundance of 94.6%). The acetate-fed MMC could not use glucose and starch as fermentation carbon sources, showing the limitation of microbial species developed with the specific metabolic substrate. Glucose-fed MMC produced the highest PHA cell content of 64.2% cell dry weight when using sodium acetate as the fermentation carbon. Glucose-fed MMC showed wide resilience and adaptation to various carbon sources. When actual landfill leachate was used for fermentation by glucose-fed MMC, maximum PHA cell content of 45.5% cell dry weight and the PHA volumetric productivity of 0.265 g PHA/(L·h) were obtained. This study suggested carbon sources applied in the MMC enrichment stage had a significant influence on utilization of carbon in the fermentation stage.

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.

Regulation of volatile fatty acid accumulation from waste: Effect of inoculum pretreatment

The study investigates the implications of waste feedstock, inoculum origin, and pretreatment on volatile fatty acids accumulation (VFA). The acidogenic fermentation of the feedstocks, rice mill effluent (RME), and brewery effluent (BE) was studied using untreated and pretreated (cyclic heat-acid shock) brewery anaerobic sludge as inoculum. The pretreatment was successful in refining and stabilizing VFA production from the feedstocks. The fermentation of RME with pretreated sludge had an enhanced acetate yield of 0.37 ± 0.02 mgCOD/mgCOD, even to odd ratio of 20.97 ± 0.08 mg/mg and the highest butyrate yield of 0.39 ± 0.01 mgCOD/mgCOD compared to untreated system. The pretreated system had stability in COD and pH profile, while VFA content depends on the origin of inoculum. Pretreatment inhibited the carbon sinks and augmented acetate-butyrate type metabolism with stable performance. The fermentation of RME by pretreated sludge produced a higher even-numbered VFAs and enhanced even to odd ratio in comparison with fermentation of BE, thereby affecting polymer composition and property. PRACTITIONER POINTS: The pretreated system had stable acidification, chemical oxygen demand, and pH profile. The pretreated system had higher acetate and butyrate yield compared to the untreated system. Rice mill effluent acidified with pretreated sludge had the highest even to odd ratio, 20.97 mg/mg. The even to odd ratio for acidification of brewery effluent was insignificant. Pretreatment, the origin of sludge, and the effluent had a regulatory effect on acidification.

Process optimization, metabolic engineering interventions and commercialization of microbial polyhydroxyalkanoates production - A state-of-the art review

Microbial polyhydroxyalkanoates (PHAs) produced using renewable resources could be the best alternative for conventional plastics. Despite their incredible potential, commercial production of PHAs remains very low. Nevertheless, sincere attempts have been made by researchers to improve the yield and economic viability of PHA production by utilizing low-cost agricultural or industrial wastes. In this context, the use of efficient microbial culture or consortia, adoption of experimental design to trace ideal growth conditions, nutritional requirements, and intervention of metabolic engineering tools have gained significant attention. This review has been structured to highlight the important microbial sources for PHA production, use of conventional and non-conventional substrates, product optimization using experimental design, metabolic engineering strategies, and global players in the commercialization of PHA in the past two decades. The challenges about PHA recovery and analysis have also been discussed which possess indirect hurdle while expanding the horizon of PHA-based bioplastics. Selection of appropriate microorganism and substrate plays a vital role in improving the productivity and characteristics of PHAs. Experimental design-based bioprocess, use of metabolic engineering tools, and optimal product recovery techniques are invaluable in this dimension. Optimization strategies, which are being explored in isolation, need to be logically integrated for the successful commercialization of microbial PHAs.

Emergent Approaches to Efficient and Sustainable Polyhydroxyalkanoate Production

Petroleum-derived plastics dominate currently used plastic materials. These plastics are derived from finite fossil carbon sources and were not designed for recycling or biodegradation. With the ever-increasing quantities of plastic wastes entering landfills and polluting our environment, there is an urgent need for fundamental change. One component to that change is developing cost-effective plastics derived from readily renewable resources that offer chemical or biological recycling and can be designed to have properties that not only allow the replacement of current plastics but also offer new application opportunities. Polyhydroxyalkanoates (PHAs) remain a promising candidate for commodity bioplastic production, despite the many decades of efforts by academicians and industrial scientists that have not yet achieved that goal. This article focuses on defining obstacles and solutions to overcome cost-performance metrics that are not sufficiently competitive with current commodity thermoplastics. To that end, this review describes various process innovations that build on fed-batch and semi-continuous modes of operation as well as methods that lead to high cell density cultivations. Also, we discuss work to move from costly to lower cost substrates such as lignocellulose-derived hydrolysates, metabolic engineering of organisms that provide higher substrate conversion rates, the potential of halophiles to provide low-cost platforms in non-sterile environments for PHA formation, and work that uses mixed culture strategies to overcome obstacles of using waste substrates. We also describe historical problems and potential solutions to downstream processing for PHA isolation that, along with feedstock costs, have been an Achilles heel towards the realization of cost-efficient processes. Finally, future directions for efficient PHA production and relevant structural variations are discussed.

Biowaste-to-bioplastic (polyhydroxyalkanoates): Conversion technologies, strategies, challenges, and perspective

Biowaste management is a challenging job as it is high in nutrient content and its disposal in open may cause a serious environmental and health risk. Traditional technologies such as landfill, bio-composting, and incineration are used for biowaste management. To gain revenue from biowaste researchers around the world focusing on the integration of biowaste management with other commercial products such as volatile fatty acids (VFA), biohydrogen, and bioplastic (polyhydroxyalkanoates (PHA)), etc. PHA production from various biowastes such as lignocellulosic biomass, municipal waste, waste cooking oils, biodiesel industry waste, and syngas has been reported successfully. Various nutrient factors i.e., carbon and nitrogen source concentration and availability of dissolved oxygen are crucial factors for PHA production. This review is an attempt to summarize the recent advancements in PHA production from various biowaste, its downstream processing, and other challenges that need to overcome making bioplastic an alternate for synthetic plastic.

Effect of increasing salinity and low C/N ratio on the performance and microbial community of a sequencing batch reactor

The purpose of this study was to investigate the effects of increasing salinity on the performance and microbial community structure in a sequencing batch reactor (SBR) treating low C/N ratio wastewater. The SBR was subjected to a gradual increased salinity from 0 wt% to3.0 wt% under low Chemical Oxygen Demand (COD)/N ratio, operating for 80 days. The study results indicated that high salinity decreased the removal efficiency of ammonium (NH4+-N) from 77.09% (1.0 wt%) to 45.7% (3.0wt%). The organic matter removal are not significantly affected by the high salinity. Non-metric Multi-Dimensional Scaling (NMDS) analysis showed that the gradual increased salinity altered the overall bacterial community structure, and low salinity (1wt%) promoted the bacterial diversity, while high salinity (2 and 3 wt%) significantly decreased the bacterial diversity in low C/N ratio activated sludge system. Further analysis revealed that two genera related to nitrification process (unclassified-Nitrosomonadales and g-Nitrospira) were inhibited, while a genus related to organic removal (Piscicoccus) and three genera related to denitrification (Rodobacteraceae, Denitromonas and Hyphomicrobium) increased significantly at a salinity of 3 wt%. This study provides insights of shifts in the bacteria community under the stress of high salinity in low C/N ratio of activated sludge systems.

Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.

Recovery of Polyhydroxyalkanoates from Cooked Mussel Processing Wastewater at High Salinity and Acidic Conditions

Polyhydroxyalkanoates (PHA) are biodegradable polymers that can be intracellularly produced by microorganisms valorizing organic-rich wastes. In the present study, a PHA production system was fed with mussel cooker wastewater after acidogenic fermentation. Besides low pH (4.0 ± 0.3) and high salt (21.7 ± 2.9 g NaCl/L) concentrations, this wastewater also contained nitrogen concentrations (0.8 ± 0.1 g N/L), which were previously reported to be a challenge to the PHA accumulating bacteria enrichment. Bacteria with a PHA storage capacity were selected in an enrichment sequencing batch reactor (SBR) after 60 days of operation. The enriched mixed microbial culture (MMC) was mainly formed by microorganisms from phylum Bacteroidetes, and genera Azoarcus, Comamonas and Thauera from phylum Proteobacteria. The MMC was able to accumulate up to 25 wt% of PHA that was mainly limited by the wastewater nitrogen content, which promoted biomass growth instead of PHA accumulation. Indeed, when the presence of nutrient was limited, PHA stored in the accumulation reactor increased to up to 40.9 wt%. This work demonstrated the feasibility of the enrichment of a MMC with a PHA storage ability valorizing the fish-canning industrial wastewater at low pH, which is generally difficult to treat in wastewater treatment plants.

Influence of inoculum variation and nutrient availability on polyhydroxybutyrate production from activated sludge

Carbon recovery through polyhydroxybutyrate (PHB) production can create a value-added waste management system. Activated sludge as inoculum enables PHB production using cheap and renewable carbons source, bringing PHB at par to conventional plastics. The PHB accumulating potential of activated sludge needs to be improved to realize the objective. The interaction between the origin of activated sludge, petroleum refinery sludge and brewery sludge, and nitrogen availability was explored to effect culture enrichment, improve PHB accumulation, and polymer characteristics through aerobic dynamic feeding. Consequently, nitrogen excess and limitation enrichment of both sludges produced mix microbial culture with adequate PHB storage of 7.8 ± 0.05%, 14.4 ± 0.04%, 14.4 ± 0.04%, 13.4 ± 0.02% respectively. Batch accumulation revealed higher PHB accumulation of 76.1 ± 0.03% and 71.7 ± 0.05% under nitrogen limitation for PRS and BS enriched under nitrogen excess condition compared to any other combination. The higher decomposition temperature of 285 °C, 293 °C, and a lower melting point of 168 °C, 165 °C with a higher molecular weight of 4.3x10⁵g/mol and semi-crystalline arrangement indicates the potential applications for extracted PHB. PHB production enhanced under nitrogen limited conditions with culture enriched under nitrogen excess condition. However, similar PHB storage, physiochemical property, and overlapping microbial community show an insignificant effect of sludge origin on PHB production.

Substrate strategy optimization for polyhydroxyalkanoates producing culture enrichment from crude glycerol

Crude glycerol is by-product produced from biodiesel industry and can be converted directly by mixed microbial culture (MMC) into polyhydroxyalkanoates (PHAs). This study investigated the effects of the reverse (SBR_A) and positive (SBR_B) glycerol gradient substrate strategy on PHA-accumulating culture enrichment and the maximum PHA accumulating stability under substrates with different glycerol and volatile fatty acid (VFA) proportion. The results showed that crude glycerol was mainly used for PHA production rather than biomass growth in SBR_A. The maximum q_PHA was 0.65 g COD/g X^-1·h^-1 under sole crude glycerol condition in SBR_A, which was 2.41 times higher than that of SBR_B. Moreover, the PHA accumulating ability of the biomass from SBR_A was more stable than SBR_B. Saccharibacteria_genera_incertae_sedis was for the first time found to be the dominant genus using crude glycerol for PHA production. This research provides an insight into enrichment strategy to effectively enrich PHA-accumulating culture from crude glycerol.

Response and Adaptation of Microbial Community in a CANON Reactor Exposed to an Extreme Alkaline Shock

Responses of a microbial community in the completely autotrophic nitrogen removal over nitrite (CANON) process, which was shocked by a pH of 11.0 for 12 h, were investigated. During the recovery phase, the performance, anaerobic ammonia oxidation (anammox) activity, microbial community, and correlation of bacteria as well as the influencing factors were evaluated synchronously. The performance of the CANON process deteriorated rapidly with a nitrogen removal rate (NRR) of 0.13 kg·m^-3·d^-1, and Firmicutes, spore-forming bacteria, were the dominant phyla after alkaline shock. However, it could self-restore within 107 days after undergoing four stages, at which Planctomycetes became dominant with a relative abundance of 64.62%. Network analysis showed that anammox bacteria (Candidatus Jettenia, Kuenenia, and Brocadia) were positively related to some functional bacteria such as Nitrosomonas, SM1A02, and Calorithrix. Canonical correspondence analysis presented a strong correlation between the microbial community and influencing factors during the recovery phase. With the increase of nitrogen loading rate, the decrease of free nitrous acid and the synergistic effects, heme c content, specific anammox activity (SAA), NRR, and the abundance of dominant genus increased correspondingly. The increase of heme c content regulates the quorum sensing system, promotes the secretion of extracellular polymeric substances, and further improves SAA, NRR, and the relative abundance of the dominant genus. This study highlights some implications for the recovery of the CANON reactor after being exposed to an alkaline shock.

Biological Materials: The Next Frontier for Cell-Free Synthetic Biology

Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.

Optimization of an enriched mixed culture to increase PHA accumulation using industrial saline complex wastewater as a substrate

Polyhydroxyalkanoates (PHA) appear as good candidates to substitute conventional petroleum-based plastics since they have similar properties but with the advantage of being biodegradable. Wastewater streams with high organic content are feasible substrates for PHA production resulting in an opportunity for waste recovery. One of the main challenges is the optimization of the selection of microorganisms with high PHA storage capacity. This microbial selection is performed in sequencing batch reactors (SBR) operated under an aerobic feast/famine (F/F) regime. In the present study, a settling stage was added at the end of the feast phase of the enrichment cycle of a SBR fed with pre-acidified cooked mussel processing wastewater (containing up to 12 g NaCl/L). Settling and subsequent supernatant discharge favoured the wash-out of non-accumulating microorganisms as well as the removal of substances that enhanced their undesired development (proteins and carbohydrates). Microbial analysis performed by fluorescence in situ hybridization (FISH) technique showed shifts in the microbial community; the presence of genus Paracoccus increased whereas genera Comamonas decreased. Moreover, the process efficiency was improved with the increase of the PHA production yield (Y_PHA) and the maximum PHA storage capacity (max. PHA) from 0.48 to 0.72 Cmmol_PHA/Cmmol_VFA and from 40 to 60 wt%, respectively. The polymer composition also changed, its HB:HV ratio varied from 83:17 to 70:30. Results obtained in the present study showed that settling after the feast phase promoted the removal of carbon sources that did not contribute to PHA production and the washout of non-storing bacteria, which favoured the culture enrichment.

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.

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.

Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics

The polyhydroxyalkanoates (PHAs) are microbially-produced biopolymers that could potentially be used as sustainable alternatives to oil-derived plastics. However, PHAs are currently more expensive to produce than oil-derived plastics. Therefore, more efficient production processes would be desirable. Cell-free metabolic engineering strategies have already been used to optimize several biosynthetic pathways and we envisioned that cell-free strategies could be used for optimizing PHAs biosynthetic pathways. To this end, we developed several Escherichia coli cell-free systems for in vitro prototyping PHAs biosynthetic operons, and also for screening relevant metabolite recycling enzymes. Furthermore, we customized our cell-free reactions through the addition of whey permeate, an industrial waste that has been previously used to optimize in vivo PHAs production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by approximately 50%. In cell-free transcription-translation prototyping reactions, gas chromatography-mass spectrometry quantification of cell-free 3-hydroxybutyrate (3HB) production revealed differences between the activities of the Native ΔPhaC_C319A (1.18 ± 0.39 µM), C104 ΔPhaC_C319A (4.62 ± 1.31 µM) and C101 ΔPhaC_C319A (2.65 ± 1.27 µM) phaCAB operons that were tested. Interestingly, the most active operon, C104 produced higher levels of PHAs (or PHAs monomers) than the Native phaCAB operon in both in vitro and in vivo assays. Coupled cell-free biotransformation/transcription-translation reactions produced greater yields of 3HB (32.87 ± 6.58 µM), and these reactions were also used to characterize a Clostridium propionicum Acetyl-CoA recycling enzyme. Together, these data demonstrate that cell-free approaches complement in vivo workflows for identifying additional strategies for optimizing PHAs production.

Mixed culture polyhydroxyalkanoate (PHA) synthesis from nutrient rich wet oxidation liquors

Organic waste residues can be hydrothermally treated to produce organic acid rich liquors. These hydrothermal liquors are a potential feedstock for polyhydroxyalkanoate (PHA) production. We investigated the effect of dissolved oxygen concentration and substrate feeding regimes on PHA accumulation and yield using two hydrothermal liquors derived from a mixture of primary and secondary municipal wastewater treatment sludge and food waste. The enriched culture accumulated a maximum of 41% PHA of cell dry weight within 7 h; which is among the highest reported for N and P rich hydrothermal liquors. Recovered PHA was 77% polyhydroxybutyrate and 23% polyhydroxyvalerate by mass. The families Rhodocyclaceae (84%) and Saprospiraceae (20.5%) were the dominant Proteobacteria (73%) in the enriched culture. The third most abundant bacterial genus, Bdellovibrio, includes species of known predators of PHA producers which may lead to suboptimal PHA accumulation. The PHA yield was directly proportional to DO concentration for ammonia stripped liquor (ASL) and inversely proportional to DO concentration for low strength liquor (LSL). The highest yield of 0.50 Cmol PHA/Cmol substrate was obtained for ASL at 25% DO saturation. A progressively increasing substrate feeding regime resulted in increased PHA yields. These findings demonstrate that substrate feeding regime and oxygen concentration can be used to control the PHA yield and accumulation rate thereby enhancing PHA production viability from nutrient rich biomass streams.

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in microbial fuel cell: A promising process for saline water treatment

In this study, Microbial Fuel Cell (MFC) capable of treating saline starch water was developed. Sodium chloride (NaCl) concentrations ranging from 500 mM to 3000 mM were tested at the anode. Nitrate was used as an electron acceptor at the biocathode. The halophilic bacteria were isolated from Sambhar Lake, India. Results indicated successful removal of starch (1.83 kg/m³-d) and nitrate (0.13 kg/m³-d NO₃^--N) with concomitant power output of 207.05 mW/m² at 1000 mM NaCl concentration. An increase in power density from 71.06 mW/m² to 207.05 mW/m² (2.92 folds) was observed when NaCl concentration was increased from 500 mM to 1000 mM. A decline in power density was observed when the salt concentrations >1000 mM were used. Concentration of 3000 mM supported power output as well as the highest starch degradation (3.2 kg/m³-d) and amylase activity of 2.26 IU/ml. The halophilic exoelectrogens were isolated and identified. The present study demonstrates the utility of MFC for degrading starch in saline water.

Overall process of using a valerate-dominant sludge hydrolysate to produce high-quality polyhydroxyalkanoates (PHA) in a mixed culture

The overall process of polyhydroxyalkanoates (PHA) production in a mixed culture fed by thermophilic fermented valerate-dominant sludge hydrolysate with high-level soluble organics (proteins and carbohydrates) and nutrients (nitrogen and phosphorus) was investigated in this study. The valerate-dominant hydrolysate was fed to enrich a PHA culture with an increasing concentration, and the enriched culture displayed a strong PHA-producing capacity under feast-famine conditions. Valerate in the feedstock was preferentially utilized over acetate and butyrate, and its uptake correlated with the production of 3-hydroxyvalerate (3HV) and 3-hydroxy-2-methylvalerate (3H2MV). The maximum PHA content (42.31%) was highest to date in a mixed culture with complex feedstock, and the PHA consisted of 3-hydroxybutyrate (3HB), 3HV, 3H2MV at 68.4, 23.7, 7.9 mmol C%. PHA production was inhibited when the nutrients exceeded a certain limit. Microbial analysis revealed that valerate-dominant feedstock caused Delftia (53%) to become the prevailing group over other PHA-producing bacteria. For long-term operation, 75% of the biomass at the end of feast phase was collected for PHA recovery, and the entire process exhibited a potential to produce 5 g PHA from 1 kg sludge. These findings indicate that the complex valerate-dominant sludge hydrolysate can be used to stably produce PHA containing high 3HV and 3H2MV.

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.

Detection of Viable Bacteria during Sludge Ozonation by the Combination of ATP Assay with PMA-Miseq Sequencing

Using sludge obtained from municipal sewage treatment plants, the response of viable bacterial populations during the sludge ozonation process was investigated by a combination of adenosine triphosphate (ATP) assay and propidium monoazide (PMA)-Miseq sequencing. The ATP assay was first optimized for application on sludge samples by adjusting the sludge solid contents and reaction time. PMA-modified polymerase chain reaction (PCR) was also optimized by choosing the suitable final PMA concentration. The quantity and composition of viable bacterial populations during sludge ozonation were further elucidated using the optimized ATP and PMA-modified PCR methods. The results indicated that after the sludge was exposed to ozone (O3) at 135 mg·O3/g total suspended solids (TSS), the viable biomass displayed a substantial decrease, with a reduction rate reaching 70.89%. The composition of viable bacterial communities showed a faster succession, showing that an ozone dosage of 114 mg·O3/g TSS is enough to significantly change the viable bacterial population structure. Floc-forming genera, such as Zoogloea, Ferruginibacter, Thauera and Turneriella, are sensitive to ozonation, while the relative abundances of some functional bacterial genera, including SM1A02, Nitrospira and Candidatus Accumulibacter, remained constant or increased in the viable bacterial population during sludge ozonation, indicating that they are more resistant to ozonation.

Salinity effect on production of PHA and EPS byHaloferax mediterranei

Salinity effect on production of PHA and EPS byHaloferax mediterranei.