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

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.

First application of the novel anaerobic/aerobic/anoxic (AOA) process for advanced nutrient removal in a wastewater treatment plant

The stringent effluent quality standards in wastewater treatment plants (WWTPs) can effectively mitigate environmental issues such as eutrophication by reducing the discharge of nutrients into water environments. However, the current wastewater treatment process often struggles to achieve advanced nutrient removal while also saving energy and reducing carbon consumption. The first full-scale anaerobic/aerobic/anoxic (AOA) system was established with a wastewater treatment scale of 40,000 m3/d. Over one year of operation, the average TN and TP concentration in the effluent of 7.53 ± 0.81 and 0.37 ± 0.05 mg/L was achieved in low TN/COD (C/N) ratio (average 5) wastewater treatment. The post-anoxic zones fully utilized the internal carbon source stored in pre-anaerobic zones, removing 41.29 % of TN and 36.25 % of TP. Intracellular glycogen (Gly) and proteins in extracellular polymeric substances (EPS) served as potential drivers for post-anoxic denitrification and phosphorus uptake. The sludge fermentation process was enhanced by the long anoxic hydraulic retention time (HRT) of the AOA system. The relative abundance of fermentative bacteria was 31.66 - 55.83 %, and their fermentation metabolites can provide additional substrates and energy for nutrient removal. The development and utilization of internal carbon sources in the AOA system benefited from reducing excess sludge production, energy conservation, and advanced nutrient removal under carbon-limited. The successful full-scale validation of the AOA process provided a potentially transformative technology with wide applicability to WWTPs.

Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability

The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.

Engineering of Yarrowia lipolytica as a platform strain for producing adipic acid from renewable resource

There is an increasing demand for bio-based dicarboxylic acids (DCA) as an eco-friendly alternatives to chemically synthesized DCA. Adipic acid, which is not naturally produced by microorganisms, is an essential DCA with significant industrial importance. This study aimed to develop a platform strain using Yarrowia lipolytica for efficient bioconversion of renewable resources into adipic acid. To prevent the complete oxidation of adipic acid, peroxisomal β-oxidation was engineered by selectively disrupting acyl-CoA oxidases. Furthermore, ω-oxidation activity was improved via introducing an additional copy of cytochrome P450 monooxygenase (ALK5) and reductase (CPR1) with fatty alcohol oxidase (FAO1). The production phase used SP92D medium in a two-stage bioconversion process, during which the engineered strain exhibited the highest production level, achieving a remarkable 9.7-fold increase compared to that of the parental strain. To our knowledge, this is the first report demonstrating that engineered Y. lipolytica can produce adipic acid from fatty acid methyl esters.

Polyhydroxyalkanoate production from fermentation of domestic sewage sludge monitoring greenhouse gas emissions: A pilot plant case study at the WRRF of Palermo University (Italy)

This paper presents a comprehensive study on polyhydroxyalkanoate (PHA) production from sewage sludge. Greenhouse gas (GHG) emissions were monitored for the first time to assess the impact of climate change and environmental sustainability. The pilot plant was composed of a fermenter with a membrane and two biological reactors (namely, selection and accumulation). Results showed that despite a low organic loading rate (namely, 0.06 kg BOD kg SS-1 day-1), a good PHA yield was obtained (namely, 0.37 g PHA/g volatile fatty acids), confirming that sewage sludge can be a suitable feedstock. GHG emissions were 3.85E-04 g CO2eq/g and 32.40 g CO2eq/g, direct and indirect, respectively. Results provided valuable insights in view of finding a trade-off between PHA production and GHG emissions to prove the PHA production process as an effective solution for biosolids disposal at a low carbon footprint.

Polyhydroxyalkanoate production from rice straw hydrolysate: Insights into feast-famine dynamics and microbial community shifts

Activated sludge contains a versatile microbiome capable of converting wastes into valuable chemicals like polyhydroxyalkanoates (PHA). This study investigated the influence of repeated feast and famine phases on PHA production as well as the corresponding microbial population dynamics using waste activated sludge (WAS) as inoculum. Hydrolysate derived from rice straw was employed as a substrate for PHA production. The 16sRNA analysis results revealed that Corynebacteriaceae (40%), Bacillaceae (23%), and Pseudomonas (5%) were the primary contributors to PHA synthesis. Notably, Bacillaceae and Pseudomonas thrived in all the feast and famine phases. The achieved PHA concentration was 3.5 ± 0.2 g/L, and its structure and composition were assessed using Fourier Transform Infrared Spectroscopy (FTIR) and Nuclear Magnetic Resonance (NMR). The analysis revealed that the PHA consists of a copolymer of hydroxybutyrate (HB) and hydroxyvalerate (HV), specifically identified as Poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV).

Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge

Obtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of specific kits. However, the evaluation of the performance of commercial kits for sludge DNA extraction is scarce and optimization of these methods to obtain a high quantity and quality of DNA is necessary, especially for downstream genomic sequencing. Sequential batch reactors (SBRs) loaded with lignocellulosic biomass are used for the synthesis of renewable resources such as levulinic acid (LA), adipic acid (AA), and polyhydroxyalkanoates (PHAs), and the biochemical synthesis of these compounds is conducted through the inoculation of microbes present in the residual activated sludge (AS) obtained from a municipal wastewater treatment plant. To characterize these microbes, the extraction of DNA from residual sewage sludge was conducted with three different commercial kits: Nucleospin® Soil from Macherey-Nagel, DNEasy® PowerSoil® from Qiagen, and E.Z.N.A.® Plant DNA Kit from Omega BIO-TEK. Nevertheless, to obtain the highest load and quality of DNA for next-generation sequencing (NGS) analysis, different pretreatments and different combinations of these pretreatments were used. The pretreatments considered were an ultrasonic bath and a temperature of 80 °C, together and separately with different incubation time periods of 30, 60, and 90 min. The results obtained suggest a significant improvement in the efficiency and quality of DNA extraction with the three commercial extraction kits when used together with the ultrasonic bath and 80 °C for 60 min. Here, we were able to prove that physical pretreatments are a viable alternative to chemical lysis for DNA extraction from complex samples such as sludge.

Toward the use of mixed microbial cultures for the biological production of adipic and levulinic acid

Biological synthesis of high added-value compounds like adipic acid (AA), levulinic acid (LA), or polyhydroxybutyrate (PHB) using pure culture has been separately reported. However, pure culture requires sterile conditions and the use of specific carbon sources resulting in high operating costs. Different alternatives based on the use of mixed microbial cultures (MMC) have been explored to resolve this problem. MMC have been widely reported for the production of PHB, but scarcely reported for LA production and never for AA synthesis. This work presents a novel strategy for the co-production of AA LA, and PHB using MMC. The strategy consists in selecting an MMC producer of AA, LA and PHB from an inoculum obtained from a wastewater treatment plant, which is then subjected to the feast and famine culture strategy in a sequential batch reactor, coupled with a batch reactor step to enhance the accumulation of AA and LA. The results showed that the MMC could produce a 16 ± 2, 23 ± 1 and 5 ± %1 (g compound/g volatile solids) of AA, LA and PHB, respectively, using a non-fermented residual biomass rich in pentose, namely synthetic hemicellulose hydrolysate (SHH) as the carbon source. These results contribute to generating future research to better understand and optimise the biosynthesis of these compounds by MMC.

Screening potential polyhydroxyalkanoate-producing bacteria from wastewater sludge

We applied fluorescence staining of Nile red, polymerase chain reaction (PCR), and carbon substrate utilization and pressure tolerance analysis to execute three-stage screening for potential polyhydroxyalkanoate (PHA) producers in the sludge samples of 21 large-scale wastewater treatment plants of city and industrial parks in Taiwan area. Total 35,429 colonies were grown on 196 plates, the screened 30 strains were subjected to 16S rRNA analysis, and 18 identified genera belonged to Proteobacteria (67%), Firmicutes (17%), and Actinomycetota (16%). The PHA accumulation results revealed that nine genera (50% of 18 screened) produced PHAs by limiting the nitrogen source and excess single carbon sources of glucose in an aerobic status. The PHA accumulation percentage was 1.44-58.77% at dry cell weight, and the theoretical yield from glucose was 0.52-58.76%. Our results indicate that our triple-screening method is promising for identifying a high biodiversity of PHA-accumulating bacteria from activated sludge for future industrial applications.

On-Line Control of Feast/Famine Cycles to Improve PHB Accumulation during Cultivation of Mixed Microbial Cultures in Sequential Batch Reactors

Production of polyhydroxyalkanoates (PHA) has generated great interest as building blocks for bioplastic production. Their production using mixed microbial cultures represents an interesting alternative, since it enables the use of organic wastes as a carbon source. Feast/famine strategy is a common way to promote selection of microorganisms with PHA accumulation capacity. However, when using waste sources, changes in substrate concentration are expected, that may affect performance and efficiency of the process. This study showed how the dissolved oxygen level can be used for online control of the cycle time, ensuring that the desired feast/famine ratio is effectively applied. An operation strategy is presented and validated, using sequential batch reactors fed with acetate as the carbon source. Production of polyhydroxybutyrate (PHB) was studied, which is the expected type of PHA to be synthetized when using acetate as substrate. Two reactors were operated by applying the proposed control strategy, to provide F/F ratios of 0.2 and 0.6, respectively. A third reactor was operated with a fixed cycle time, for comparison purposes. Results showed that the reactor that operated at an F/F ratio of 0.6 promoted higher biomass productivity and PHB content, as a result of a better use of available time, preventing unnecessary long famine times. The application of the tested strategy is a simple a reliable way to promote a better performance of feast/famine-based bioreactors involving mixed microbial cultures for PHB production.

Rapid start-up strategy of partial denitrification and microbially driven mechanism of nitrite accumulation mediated by dissolved organic matter

The rapid start-up of Partial denitrification (PD; nitrate to nitrite) was investigated based on the analysis of microbially driven mechanism of nitrite accumulation mediated by Dissolved organic matter (DOM) in this study. The nitrate to Nitrite transformation ratio (NTR) > 90% and effluent nitrate < 5 mg/L were achieved in 17 days by feeding with lower nitrate of ~ 35 mg/L and removing the idling period. And the enhanced nitrite accumulation when applying the above strategy is related to the decreased utilization of the aliphatic DOM during nitrite reduction process. Additionally, the rapid enriched Thauera and OLB13 (37.21%) and inhibited norank_f__Blastocatellaceae (2.86%), and the increased disparity (2.0-fold) between the genes involved in nitrite generation (e.g., narH) and for nitrite reduction (e.g., nirK) jointly contributed to PD start-up. While the genes (e.g., DLD) related to producing electrons from aliphatic DOM also up-regulated by 0.1-fold, which led to the increased nitrate removal and NTR.

Burkholderia sacchari (synonym Paraburkholderia sacchari): An industrial and versatile bacterial chassis for sustainable biosynthesis of polyhydroxyalkanoates and other bioproducts

This is the first review presenting and discussing Burkholderia sacchari as a bacterial chassis. B. sacchari is a distinguished polyhydroxyalkanoates producer strain, with low biological risk, reaching high biopolymer yields from sucrose (0.29 g/g), and xylose (0.38 g/g). It has great potential for integration into a biorefinery using residues from biomass, achieving 146 g/L cell dry weight containing 72% polyhydroxyalkanoates. Xylitol (about 70 g/L) and xylonic acid [about 390 g/L, productivity 7.7 g/(L.h)] are produced by the wild-type B. sacchari. Recombinants were constructed to allow the production and monomer composition control of diverse tailor-made polyhydroxyalkanoates, and some applications have been tested. 3-hydroxyvalerate and 3-hydroxyhexanoate yields from substrate reached 80% and 50%, respectively. The genome-scale reconstruction of its metabolic network, associated with the improvement of tools for genetic modification, and metabolic fluxes understanding by future research, will consolidate its potential as a bioproduction chassis.