Flow cytometry for quantitation of polyhydroxybutyrate production by Cupriavidus necator using alkaline pretreated liquor from corn stover

CnRed: Efficient, Marker-free Genome Engineering of Cupriavidus necator H16 by Adapted Lambda Red Recombineering

Due to its ability to utilize carbon dioxide, native intracellular accumulation of bioplastic precursors, and a high protein content, the bacterium Cupriavidus necator offers potential solutions for social problems tackled by modern biotechnology. Yet, engineering of high-performing chemolithotrophic production strains has so far been hindered by the lack of adequate genome editing methods. In this work we present the establishment of a lambda Red recombineering system for use in Cupriavidus necator H16. In combination with electroporation as DNA delivery system, it enables an efficient and fast gene deletion methodology utilizing either suicide plasmids or, for the first time, linear PCR product. The novel lambda Red system was validated for the modification of three different genomic loci and, as a proof-of-concept, ultimately utilized for stable genomic integration of Escherichia coli phytase gene appA into the phaC1 locus. A Cre/loxP system further enabled efficient marker recycling. The combination of a minimal transformation protocol with lambda Red recombineering and a Cre/loxP system offers a robust, freedom-to-operate synthetic biology tool in an increasingly important bacterial production host. This approach simplifies and accelerates genome engineering in C. necator and is expected to significantly enhance future strain development efforts.

Valorization of biodiesel-derived crude glycerol for simultaneous biosynthesis of biodegradable polyhydroxybutyrate and exopolysaccharide by the newly isolated Burkholderia sp. SCN-KJ

This study demonstrated that Burkholderia sp. SCN-KJ is a promising novel species for the biovalorization of crude glycerol to polyhydroxybutyrate (PHB) and galactose-rich heteroexopolysaccharide (EPS). Whole-genome and genetic evolution analyses revealed separation of the different clades according to the ANIb and dDDH analyses, which confirmed that Burkholderia sp. SCN-KJ is a novel species. The highest PHB production from crude glycerol was 12.9 ± 0.4 g/L (72.9 ± 2.1 % w/w), with a productivity of 0.46 g/L/h and YP/S of 0.3 g/g at 28 h in a 10 L fermenter. The galactose-rich hetero-EPS began to be produced after nitrogen depletion, resulting in a concentration of 22.4 ± 0.2 g/L at 38 h. Examination of the carbon-to‑nitrogen ratio (C/N) showed that nitrogen-rich condition (C/N 20) was optimal for PHB production, whereas nitrogen-depleted condition promoted EPS production, showing two different extrema. The findings showed that Burkholderia sp. SCN-KJ has the potential to transform the landscape of biovalorization for sustainable production.

Impact of the environmental parameters on single cell protein production and composition by Cupriavidus necator

Due to the rapid increase in the world's population, many developing countries are facing malnutrition problems, including famine and food insecurity. Particularly, the deficiency of protein sources becomes a serious problem for human and animal nutrition. In this context, Single Cell Proteins, could be exploited as an alternative source of unconventional proteins. The aim of the study was to investigate SCP production and composition by Cupriavidus necator under various environmental conditions, temperature and pH values. A mono-factorial approach was implemented using batch bioreactor cultures under well-controlled conditions. Results were compared in terms of bacterial growth and SCP composition (proteins, nucleic acids, amino acids and elemental formula). Complementary analyses were performed by flow cytometry to study cell morphology, membrane permeability and the presence of Poly(3-hydroxybutyrate) (PHB) production. Our data confirmed the ability of C. necator to produce high amount of proteins (69 %DW at 30 °C and pH7). The results showed that temperature and pH independently impact SCP production and composition. This impact was particularly observed at the highest temperature (40 °C) and also the lowest pH value (pH5) providing lower growth rates, cell elongation, changes in granularity and lower amounts of proteins (down to 44 %DW at pH5) and nucleic acids. These low percentages were related to the production of PHB production (up to 44 %DW at 40 °C) which is the first report of a PHB accumulation in C. necator under nutrient unlimited conditions.

Monitoring Phenotype Heterogeneity at the Single-Cell Level within Bacillus Populations Producing Poly-3-hydroxybutyrate by Label-Free Super-resolution Infrared Imaging

Phenotypic heterogeneity is commonly found among bacterial cells within microbial populations due to intrinsic factors as well as equipping the organisms to respond to external perturbations. The emergence of phenotypic heterogeneity in bacterial populations, particularly in the context of using these bacteria as microbial cell factories, is a major concern for industrial bioprocessing applications. This is due to the potential impact on overall productivity by allowing the growth of subpopulations consisting of inefficient producer cells. Monitoring the spread of phenotypes across bacterial cells within the same population at the single-cell level is key to the development of robust, high-yield bioprocesses. Here, we discuss the novel development of optical photothermal infrared (O-PTIR) spectroscopy to probe phenotypic heterogeneity within Bacillus strains by monitoring the production of the bioplastic poly-3-hydroxybutyrate (PHB) at the single-cell level. Measurements obtained on single-point and in imaging mode show significant variability in the PHB content within bacterial cells, ranging from whether or not a cell produces PHB to variations in the intragranular biochemistry of PHB within bacterial cells. Our results show the ability of O-PTIR spectroscopy to probe PHB production at the single-cell level in a rapid, label-free, and semiquantitative manner. These findings highlight the potential of O-PTIR spectroscopy in single-cell microbial metabolomics as a whole-organism fingerprinting tool that can be used to monitor the dynamic of bacterial populations as well as for understanding their mechanisms for dealing with environmental stress, which is crucial for metabolic engineering research.

Use of Flavin-Related Cellular Autofluorescence to Monitor Processes in Microbial Biotechnology

Cellular autofluorescence is usually considered to be a negative phenomenon because it can affect the sensitivity of fluorescence microscopic or flow cytometric assays by interfering with the signal of various fluorescent probes. Nevertheless, in our work, we adopted a different approach, and green autofluorescence induced by flavins was used as a tool to monitor fermentation employing the bacterium Cupriavidus necator. The autofluorescence was used to distinguish microbial cells from abiotic particles in flow cytometry assays, and it was also used for the determination of viability or metabolic characteristics of the microbial cells. The analyses using two complementary techniques, namely fluorescence microscopy and flow cytometry, are simple and do not require labor sample preparation. Flavins and their autofluorescence can also be used in a combination with other fluorophores when the need for multi-parametrical analyses arises, but it is wise to use dyes that do not emit a green light in order to not interfere with flavins' emission band (500-550 nm).

Enhanced co-production of medium-chain-length polyhydroxyalkanoates and phenazines from crude glycerol by high cell density cultivation of Pseudomonas chlororaphis in membrane bioreactor

Enhanced co-production of medium-chain-length polyhydroxyalkanoates (mcl-PHA) and extracellular phenazines was assessed through a high cell density cultivation of Pseudomonas chlororaphis subsp. aurantiaca (DSM 19603) in a membrane bioreactor using crude glycerol as a fermentative substrate. A maximum dry cell weight (DCW) of 59.25 ± 0.31 g/L was achieved at 90 h of cultivation with a maximum mcl-PHA and extracellular phenazines concentrations of respectively 19.05 ± 0.04 g/L (32.16% of DCW) and 79.42 ± 0.35 mg/L. mcl-PHA concentration achieved through cell retention culture was 28.43-folds higher than that obtained by batch culture. Fourier transform infrared spectroscopy, gas chromatography-mass spectrometry, and ¹H nuclear magnetic resonance analysis identified the produced PHA as a mcl-PHA copolymer of 3-hydroxyhexanoate (0.68%), 3-hydroxyoctanoate (7.76%), 3-hydroxydecanoate (49.18%), 3-hydroxydodecanoate (4.89%), and 3-hydroxytetradecanoate (37.50%). The mcl-PHA exhibited a highly amorphous structure with low crystallinity index (4.19%) and high thermal stability. This is the first report on the enhanced co-production of mcl-PHA and phenazines in a membrane bioreactor.

In vivo quantification of polyhydroxybutyrate (PHB) in the alphaproteobacterial methanotroph, Methylocystis sp. Rockwell

Methane is a common industrial by-product that can be used as feedstock for production of the biopolymer polyhydroxybutyrate (PHB) by alphaproteobacterial methanotrophs. In vivo assessment of PHB production would shed light on the biosynthesis process and guide design of improved production strategies, but it is currently difficult to perform efficiently. In this study, the alphaproteobacterial methanotroph Methylocystis sp. Rockwell was grown on methane with three different nitrogen sources (ammonium, nitrate, and atmospheric nitrogen), and biomass samples were harvested at defined time points during lag, exponential, and stationary growth phases. PHB cell content was analyzed at these sampling points via a standard gas chromatography-flame ionization detector method, which requires hydrolysis of PHB and esterification of the resulting monomer under acidic conditions, and a novel, rapid, cost-effective approach based on fixation and staining of bacterial cells via Nile Blue A fluorescent dye enabling differential staining of cell membranes and intracellular PHB granules for single-cell analysis through fluorescence microscopy. Overall, the two PHB quantification approaches were in agreement at all stages of growth and in all three growing conditions tested. The PHB cell content was greatest with atmospheric nitrogen as a nitrogen source, followed by ammonium and nitrate. Under atmospheric nitrogen and ammonium conditions, PHB cell content decreased with growth progression, while under nitrate conditions PHB cell content remained unchanged in all growth phases. In addition to presenting a rapid, efficient method enabling in vivo quantification of PHB production, the present study highlights the impact of nitrogen source on PHB production by Methylocystis sp. Rockwell. KEY POINTS: • A novel fluorescence microscopy method to quantify PHB in single cells was developed • The microscopy method was validated by the derivation/gas chromatography method • Methylocystis sp. Rockwell synthesizes PHB granules without nutrient stress.

Valorization of agro-wastes for the biosynthesis and characterization of polyhydroxybutyrate by Bacillus sp. isolated from rice bran dumping yard

Investigations have been made to determine the usage of inexpensive agro-waste products as an alternative carbon source for the production of degradable bacterial polyester. Among 33 bacterial isolates, a gram-positive bacterium PPECLRB-16 isolated from rice bran dumping yard was found to accumulate a relatively higher quantity of PHB and identified as Bacillus sp. through 16S rRNA gene sequence analysis. The higher PHB producing bacterial isolate was grown with different inexpensive agro-wastes to determine the suitable carbon source for its growth and PHB production. The one-factor-at-a-time approach comparatively enhanced PHB yield (5.64 g/L) when grown for 48 h with 1.5% (w/v) of defatted oil cake at a pH of 7.0. The bacterially accumulated PHB was isolated from the cells, purified, and characterized using solid-state ¹³C NMR, FT-IR, Powder XRD, TGA, GPC, Tensile and HR-SEM analyses. The hydrophobicity and printing accessibility of recovered PHB were demonstrated using contact angle measurement by coating on different surfaces. The results obtained in the present investigation have thrown light on the potential usage of agro-waste by-products, mainly oil cake, as an appropriate carbon source for the commercial production of PHB by Bacillus sp. in a cost-effective way.

Production and high throughput quantification of fucoxanthin and lipids in Tisochrysis lutea using single-cell fluorescence

This work aimed to investigate the accumulation of fucoxanthin and lipids in Tisochrysis lutea during growth (N+) and nitrogen-starvation (N-) and to correlate these products with single-cell emissions using fluorescence-activated cell sorting (FACS). Fucoxanthin content decreased 52.94% from N+ to N- in batch cultivation; increased 40.53% as dilution rate changed from 0.16 to 0.55 d^-1 in continuous cultivation. Total lipids (N-) were constant (~250 mg/g), but the abundance of neutral lipids increased from 4.87% to 40.63%. Nile red can stain both polar and neutral lipids. However, in vivo, this differentiation is limited due to an overlapping of signals between 600 and 660 nm, caused by neutral lipids concentrations above 3.48% (W/W). Chlorophyll autofluorescence (720 nm) was reported for the first time as a proxy for fucoxanthin (R² = 0.90) and polar lipids (R² = 0.98). FACS can be used in high throughput quantification of pigments and lipids and to select and sort cells with high-fucoxanthin/lipids.

Fed-batch polyhydroxybutyrate production by Paraburkholderia sacchari from a ternary mixture of glucose, xylose and arabinose

Polyhydroxybutyrate (PHB) is a biodegradable bioplastic that is comparable with many petroleum-based plastics in terms of mechanical properties and is highly biocompatible. Lignocellulosic biomass conversion into PHB can increase profit and add sustainability. Glucose, xylose and arabinose are the main monomer sugars derived from upstream lignocellulosic biomass processing. The sugar mixture ratios may vary greatly depending on the pretreatment and enzymatic hydrolysis conditions. Paraburkholderia sacchari DSM 17165 is a bacterium strain that can convert all three sugars into PHB. In this study, fed-batch mode was applied to produce PHB on three sugar mixtures (glucose:xylose:arabinose = 4:2:1, 2:2:1, 1:2:1). The highest PHB concentration produced was 67 g/L for 4:2:1 mixture at 41 h corresponding to an accumulation of 77% of cell dry weight as PHB. Corresponding sugar conversion efficiency and productivity were 0.33 g PHB/g sugar consumed and 1.6 g/L/h, respectively. The results provide references for process control to maximize PHB production from real sugar streams derived from corn fibre.

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.

Fed-batch cultivation and adding supplements to increase yields of polyhydroxybutyrate production by Cupriavidus necator from corn stover alkaline pretreatment liquor

The aim of this study was to evaluate polyhydroxybutyrate (PHB) production and productivity with supplements under fed-batch cultivation at bioreactor scale (1.3 L). In this study, multiple supplements including oxidative enzyme, mediators, surfactants and silicon nanoparticles were added to Cupriavidus necator culture growing on alkaline pretreatment liquor (APL). At 1.3 L bioreactor scale, PHB production reached 3.3 g/L. To further enhance PHB production, fed-batch cultivation with two different feeding strategies were applied. Under single pulse feeding of 300 mL medium, PHB production reached 4.0 g/L. Under 4 pulses feeding of 75 mL medium each time, PHB production reached 4.5 g/L. This is the highest PHB production from lignin that the authors are aware of in literature.