Aromatic hydrocarbon biodegradation activates neutral lipid biosynthesis in oleaginous yeast

Enhanced remediation of polyaromatic hydrocarbon using agro-industrial waste for biofuel production and environmental pollution mitigation

In the present study, attention has been paid to the development of economically feasible strategies for enhanced remediation of anthracene and its conversion into biofuels. The strategies developed (B1, B2, B3, and B4) include bagasse and lipid-producing strain Rhodotorula mucilagenosa IIPL32 synthesizing surface active metabolites. The results indicate the highest production of surface-active metabolites in strategies B2, B3, and B4 along with a maximum biodegradation rate. GC-MS analysis affirmed the conversion of anthracene into phthalic acid in all the strategies. Biofuel quality of the lipid produced by the strain showed higher cetane number and improved cold flow property indicating the efficiency of the developed strategies for the production of commercial grade biodiesel. Furthermore, the phytotoxicity study of the spent wash revealed that 50% and 75% diluted spent wash were non-toxic and can be employed for ferti-irrigation. Thus, the study signifies the development of an economically feasible process that can be commercially employed in biofuel industries.

Yarrowia lipolytica growth, lipids, and protease production in medium with higher alkanes and alkenes

Two strains of Yarrowia lipolytica (CBS 2075 and DSM 8218) were first studied in bioreactor batch cultures, under different controlled dissolved oxygen concentrations (DOC), to assess their ability to assimilate aliphatic hydrocarbons (HC) as a carbon source in a mixture containing 2 g·L-1 of each alkane (dodecane and hexadecane), and 2 g·L-1 hexadecene. Both strains grew in the HC mixture without a lag phase, and for both strains, 30 % DOC was sufficient to reach the maximum values of biomass and lipids. To enhance lipid-rich biomass and enzyme production, a pulse fed-batch strategy was tested, for the first time, with the addition of one or three pulses of concentrated HC medium. The addition of three pulses of the HC mixture (total of 24 g·L-1 HC) did not hinder cell proliferation, and high protease (> 3000 U·L-1) and lipids concentrations of 3.4 g·L-1 and 4.3 g·L-1 were achieved in Y. lipolytica CBS 2075 and DSM 8218 cultures, respectively. Lipids from the CBS 2075 strain are rich in C16:0 and C18:1, resembling the composition of palm oil, considered suitable for the biodiesel industry. Lipids from the DSM 8218 strain were predominantly composed of C16:0 and C16:1, the latter being a valuable monounsaturated fatty acid used in the pharmaceutical industry. Y. lipolytica cells exhibited high intrinsic surface hydrophobicity (> 69 %), which increased in the presence of HC. A reduction in surface tension was observed in both Y. lipolytica cultures, suggesting the production of extracellular biosurfactants, even at low amounts. This study marks a significant advancement in the valorization of HC for producing high-value products by exploring the hydrophobic compounds metabolism of Y. lipolytica.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Influence of Borassus flabellifer Endocarps Hydrolysate on Fungal Biomass and Fatty Acids Production by the Marine Fungus Aspergillus sp

Polyunsaturated Fatty Acids (PUFAs) are important nutrients for human health. We aimed to evaluate the efficiency of marine water fungus Aspergillus sp. (Accession no: MZ505709) for lipid biosynthesis. The Yeast Extract Glucose (YEG) medium was supplemented with different concentration of Borassus flabellifer Endocarps Hydrolysate (BFEH; 1-5%) to evaluate the fungal biomass and its lipid accumulation. The combination of glucose and BFEH as carbon source increased the fresh weight (25.43 ± 0.33 g/L), dry weight (21.39 ± 0.77 g/L) and lipid yield (3.14 ± 0.09 g/L) of fungal biomass. The lipid content of dried fungal biomass has shown 91.08 ± 5.07 mg cod liver oil equivalents/g and 125.98 ± 5.96 mg groundnut oil equivalents/g biomass. GC-MS and NMR spectrometry analysis revealed the compounds involved in fatty acid metabolism and lipid signaling pathways along with the presence of linolenic acid. Interestingly, fungus grown in BFEH enriched medium has recorded the maximum amount of lipids with major fatty acid derivatives. Increase in the growth rate of Artemia franciscana was observed, when the extracted fungal lipid was supplemented as a food supplement. Therefore, this study suggests that marine fungal lipid may serve as potential natural compound as nutraceuticals and aquafeeds.

Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs

A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L-1 pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.

Biosurfactant Production from the Biodegradation of n-Paraffins, Isoprenoids and Aromatic Hydrocarbons from Crude Petroleum by Yarrowia lipolytica IMUFRJ 50682

Yarrowia lipolytica is a unique, strictly aerobic yeast with the ability to degrade efficiently hydrophobic substrates. In the present work, we evaluated the degrading potential of Yarrowia lipolytica IMUFRJ 50682, isolated from tropical estuarine water in Rio de Janeiro (Brazil), and the possible biomolecules produced during this process. To investigate which crude oil compounds are degraded by Y. lipolytica IMUFRJ 50682, this microorganism was grown in a medium containing Marlim petroleum (19 °API, American Petroleum Institute gravity) at 28 °C and 160 rpm for 5 days. The residual petroleum was submitted to gas chromatograph-mass spectrometric analysis (GC-MS). The chromatographic fingerprints of the residual petroleum were compared with the abiotic control test incubated in the same conditions. Y. lipolytica assimilates high molecular weight hydrocarbons, such as n-alkanes (C11-C19), isoprenoids (pristane and phytane), aromatics with two or three aromatics rings (naphthalene, methylnaphthalenes, dimethylnaphthalenes, trimethylnaphthalenes, phenanthrene, methylphenanthrenes, dimethylphenanthrenes, anthracene). This strain was also capable of consuming more complex hydrocarbons, such as tricyclic terpanes. During this biodegradation, the emulsification index of the culture medium increased significantly, showing that biosurfactant molecules can be produced from this process. Therefore, Y. lipolytica IMUFRJ 50682 showed to be a potential crude oil degrading yeast, which can be used for bioremediation processes and simultaneously produce bioproducts of commercial interest.

Valorization of phenol contaminated wastewater for lipid production by Rhodosporidium toruloides 9564T

Phenol is one of the most common hazardous organic compound presents in several industrial effluents which directly affects the aquatic environment. The present study envisaged the phenol biodegradation and simultaneous lipid production along with its underlying mechanism by oleaginous yeast Rhodosporidium toruloides 9564^T. Experiments were designed using simulated wastewater by varying phenol concentration in the range of 0.25-1.5 g/L and inoculum size of 1, 5, and 10% with and without glucose. The oleaginous yeast was found to completely degrade up to 0.75 g/L phenol with lipid accumulation of 26.3%. Phenol at > 0.5 g/L severely inhibited the growth of R. toruloides 9564^T at 1% and 5% inoculum size. Phenol toxicity up to 0.75 g/L can be overcome by increasing inoculum size to 10%. The maximum specific growth rate (μ_max) and phenol degradation rate (q_max) were found to be 0.0717 h^-1 and 0.01523 h^-1, respectively. The enzymatic pathway study suggested that R. toruloides 9564^T follows an ortho cleavage pathway for phenol degradation and lipid accumulation. Phytotoxicty and cytotoxicity tests for treated and untreated samples clearly demonstrated a decline in toxicity of the treated wastewater. R. toruloides brought about an important paradigm shift toward a circular economy in which industrial wastewater is considered a valuable resource for bioenergy production.

Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network

Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.

Enhanced biodiesel and β-carotene production in Rhodotorula pacifica INDKK using sugarcane bagasse and molasses by an integrated biorefinery framework

Dependency on fossil fuels raises an economic and ecological concern that has urged to look for alternative sources of energy. Bio-refinery concept is one of the alternate frameworks for the biomass conversion into biofuel and other value-added by-products. The present work illustrates importance of an oleaginous yeast Rhodotorula pacifica INDKK in an integrated bio-refinery field by utilizing renewable sugars generated from lignocellulosic biomass. The maximum 11.8 g/L lipid titer, 210.4 mg/L β-carotene and 7.1 g animal feed were produced by R. pacifica INDKK in bioreactor containing 5% (v/v) molasses supplemented with enzymatically hydrolyzed and alkali-pretreated sugarcane bagasse hydrolysate (35% v/v). Furthermore, xylooligosaccharides (20.6 g/L), a beneficial prebiotics were also produced from the hemicellulosic fraction separated after alkali pretreatment of bagasse. This novel concept of integrated yeast bio-refinery for concomitant production of biodiesel and multiple value-added products with minimum waste generation is proposed as a sustainable and profitable process.

A review on contemporary approaches in enhancing the innate lipid content of yeast cell

For the past few decades, industrialization has made a huge environmental hazard to the world with its waste. The approach of waste to wealth in the recent era has made many Eco-economical suggestions for the industries. The valuable products in biorefinery aspects of the eco-economical suggestions include; energy products, high-value drugs and novel materials. Bio-lipids are found to be the major influencing eco-economical products in the process. Production of bio-lipid from microbial sources has paved the way for future research on lipid-bioproducts. The yeast cell is a unique organism with a large unicellular structure capable of accumulating a high amount of lipids. It constitutes 90% of neutral lipids. Various strategies enhance the lipid profile of yeast cells: usage of oleaginous yeast, usage of low cost (or) alternative substrates, developing stress conditions in the growth medium, using genetically modified yeast, altering metabolic pathways of yeast and by using the symbiotic cultures of yeast with other microbes. The metabolic alterations of lipid pathways such as lipid biosynthesis, lipid elongation, lipid accumulation and lipid degradation have been a striking feature of research in lipid-based microbial work. The lipid-bioproducts have also made a strong footprint in the history of alternative energy products. It includes partial acyl glycerol, oleochemicals, phospholipids and biofuels. This report comprises the recent approaches carried out in the yeast cell for enhancing its lipid content. The limitations, challenges and future scope of individual strategies were also highlighted in this article.

Tracking gene expression, metabolic profiles, and biochemical analysis in the halotolerant basidiomycetous yeast Rhodotorula mucilaginosa EXF-1630 during benzo[a]pyrene and phenanthrene biodegradation under hypersaline conditions

Polyaromatic phenanthrene (Phe) and benzo[a]pyrene (BaP) are highly toxic, mutagenic, and carcinogenic contaminants widely dispersed in nature, including saline environments. Polyextremotolerant Rhodotorula mucilaginosa EXF-1630, isolated from Arctic sea ice, was grown on a huge concentration range -10 to 500 ppm- of Phe and BaP as sole carbon sources at hypersaline conditions (1 M NaCl). Selected polycyclic aromatic hydrocarbons (PAHs) supported growth as well as glucose, even at high PAH concentrations. Initially, up to 40% of Phe and BaP were adsorbed, followed by biodegradation, resulting in 80% removal in 10 days. While extracellular laccase, peroxidase, and un-specific peroxygenase activities were not detected, NADPH-cytochrome c reductase activity peaked at 4 days. The successful removal of PAHs and the absence of toxic metabolites were confirmed by toxicological tests on moss Physcomitrium patens, bacterium Aliivibrio fischeri, human erythrocytes, and pulmonary epithelial cells (A549). Metabolic profiles were determined at the midpoint of the biodegradation exponential phase, with added Phe and BaP (100 ppm) and 1 M NaCl. Different hydroxylated products were found in the culture medium, while the conjugative metabolite 1-phenanthryl-β-D-glucopyranose was detected in the medium and in the cells. Transcriptome analysis resulted in 870 upregulated and 2,288 downregulated transcripts on PAHs, in comparison to glucose. Genomic mining of 61 available yeast genomes showed a widespread distribution of 31 xenobiotic degradation pathways in different yeast lineages. Two distributions with similar metabolic capacities included black yeasts and mainly members of the Sporidiobolaceae family (including EXF-1630), respectively. This is the first work describing a metabolic profile and transcriptomic analysis of PAH degradation by yeast.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

Harnessing pongamia shell hydrolysate for triacylglycerol agglomeration by novel oleaginous yeast Rhodotorula pacifica INDKK

BACKGROUND

To meet the present transportation demands and solve food versus fuel issue, microbial lipid-derived biofuels are gaining attention worldwide. This study is focussed on high-throughput screening of oleaginous yeast by microwave-aided Nile red spectrofluorimetry and exploring pongamia shell hydrolysate (PSH) as a feedstock for lipid production using novel oleaginous yeast Rhodotorula pacifica INDKK.

RESULTS

A new oleaginous yeast R. pacifica INDKK was identified and selected for microbial lipid production. R. pacifica INDKK produced maximum 12.8 ± 0.66 g/L of dry cell weight and 6.78 ± 0.4 g/L of lipid titre after 120 h of growth, showed high tolerance to pre-treatment-derived inhibitors such as 5-hydroxymethyl furfural (5-HMF), (2 g/L), furfural (0.5 g/L) and acetic acid (0.5 g/L), and ability to assimilate C3, C5 and C6 sugars. Interestingly, R. pacifica INDKK showed higher lipid accumulation when grown in alkali-treated saccharified PSH (AS-PSH) (0.058 ± 0.006 g/L/h) as compared to acid-treated detoxified PSH (AD-PSH) (0.037 ± 0.006 g/L/h) and YNB medium (0.055 ± 0.003 g/L/h). The major fatty acid constituents are oleic, palmitic, linoleic and linolenic acids with an estimated cetane number (CN) of about 56.7, indicating the good quality of fuel.

CONCLUSION

These results suggested that PSH and R. pacifica INDKK could be considered as potential feedstock for sustainable biodiesel production.

Mechanistic investigations in ultrasound-assisted biodegradation of phenanthrene

This study has addressed the biodegradation of polycyclic aromatic hydrocarbon, phenanthrene using Candida tropicalis. Optimization using central composite statistical design yielded optimum experimental parameters as: pH = 6.2, temperature = 33.4 °C, mechanical shaking = 190 rpm and % inoculum = 9.26% v/v. Sonication of biodegradation mixture at 33 kHz and 10% duty cycle in log phase (12 h per day for 4 days) resulted in a 25% enhancement in phenanthrene removal. Profiles of specific growth rate (µ) and specific degradation rate (q) versus initial substrate concentration were fitted to Haldane substrate inhibition model. Both µ and q showed maxima for initial concentration of 100 mg L^-1. Kinetic analysis of degradation profiles showed higher biomass yield coefficient and smaller decay coefficient in presence of sonication. Expression of total intracellular proteins in control and test experiments were analyzed using SDS-PAGE. This analysis revealed overexpression of enzyme catechol 2,3-dioxygenase (in meta route metabolism) during sonication which is involved in ring cleavage of phenanthrene. Evaluation of cell viability after sonication by flow cytometry analysis revealed > 80% live cells. These effects are attributed to enhanced cellular transport induced by intense microturbulence generated by sonication.

Identification of oleaginous yeasts that metabolize aromatic compounds

The valorization of lignin is critical for the economic viability of the bioeconomy. Microbial metabolism is advantageous for handling the myriad of aromatic compounds resulting from lignin chemical or enzymatic depolymerization. Coupling aromatic metabolism to fatty acid biosynthesis makes possible the production of biofuels, oleochemicals, and other fine/bulk chemicals derived from lignin. Our previous work identified Cutaneotrichosporon oleaginosus as a yeast that could accumulate nearly 70% of its dry cell weight as lipids using aromatics as a sole carbon source. Expanding on this, other oleaginous yeast species were investigated for the metabolism of lignin-relevant monoaromatics. Thirty-six oleaginous yeast species from the Phaff yeast collection were screened for growth on several aromatic compounds representing S-, G-, and H- type lignin. The analysis reported in this study suggests that aromatic metabolism is largely segregated to the Cutaenotrichosporon, Trichosporon, and Rhodotorula clades. Each species tested within each clade has different properties with respect to the aromatics metabolized and the concentrations of aromatics tolerated. The combined analysis suggests that Cutaneotrichosporon yeast are the best suited to broad spectrum aromatic metabolism and support its development as a model system for aromatic metabolism in yeast.

Economical lipid production from Trichosporon oleaginosus via dissolved oxygen adjustment and crude glycerol addition

The effect of dissolved oxygen concentration on lipid accumulation in Trichosporon oleaginosus has been investigated. The experiment was performed in 15 L fermenters. The dissolved oxygen concentration varied by adjusting the agitation and aeration. High dissolved oxygen level at 50%-60% enhanced cell growth. Maintaining low dissolved oxygen concentration at 20%-30% during lipogenesis phase led to high final lipid content (51%) in Trichosporon oleaginosus. The consumptions of energy and cost of the process were evaluated. The energy consumption in the dissolved oxygen level optimized process was 41% less than that with dissolved oxygen level at 50%-60%. In addition, the cost was also reduced around one time in the dissolved oxygen level optimized process compared to the one with dissolved oxygen level at 50%-60%. The study provided a feasible way of enhancing lipid accumulation in Trichosporon oleaginosus and reducing the consumption of energy and cost of lipid production from Trichosporon oleaginosus.