Cell mass energetic yields of fed-batch culture by Lipomyces starkeyi

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.

A metabolic model of Lipomyces starkeyi for predicting lipogenesis potential from diverse low-cost substrates

BACKGROUND

Lipomyces starkeyi has been widely regarded as a promising oleaginous yeast with broad industrial application prospects because of its wide substrate spectrum, good adaption to fermentation inhibitors, excellent fatty acid composition for high-quality biodiesel, and negligible lipid remobilization. However, the currently low experimental lipid yield of L. starkeyi prohibits its commercial success. Metabolic model is extremely valuable to comprehend the complex biochemical processes and provide great guidance for strain modification to facilitate the lipid biosynthesis.

RESULTS

A small-scale metabolic model of L. starkeyi NRRL Y-11557 was constructed based on the genome annotation information. The theoretical lipid yields of glucose, cellobiose, xylose, glycerol, and acetic acid were calculated according to the flux balance analysis (FBA). The optimal flux distribution of the lipid synthesis showed that pentose phosphate pathway (PPP) independently met the necessity of NADPH for lipid synthesis, resulting in the relatively low lipid yields. Several targets (NADP-dependent oxidoreductases) beneficial for oleaginicity of L. starkeyi with significantly higher theoretical lipid yields were compared and elucidated. The combined utilization of acetic acid and other carbon sources and a hypothetical reverse β-oxidation (RBO) pathway showed outstanding potential for improving the theoretical lipid yield.

CONCLUSIONS

The lipid biosynthesis potential of L. starkeyi can be significantly improved through appropriate modification of metabolic network, as well as combined utilization of carbon sources according to the metabolic model. The prediction and analysis provide valuable guidance to improve lipid production from various low-cost substrates.

Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils

Application of biochar (BC) derived from rice straw has generated increasing interest in long-term storage of soil organic carbon (SOC), however its carbon (C) sequestration potential vary widely among agricultural soils despite the same BC dose used. These discrepancies in the ability of soils to sequester C after BC application are poorly understood. Metabolic quotient (qCO₂) is a reflection of "microbial efficiency" and linked to SOC turnover across ecosystems. Therefore, we investigated the SOC sequestration and qCO₂ in a Yellow River alluvium paddy soil (YP) and a quaternary red clay paddy soil (QP) under rice-wheat annual rotation following 4-year of BC application rate of 11.3 Mg ha^-1 per cropping season. BC application consistently brought 65.3 Mg C ha^-1 into the soils over 4-year experimental period but increased SOC by 57.6 Mg C ha^-1 in YP and 64.5 Mg C ha^-1 in QP. Calculating SOC mass balance showed 11.7% of BC-C losses from YP and only 1.16% from QP. BC application stimulated the G⁺ bacterial, fungi, and actinomycetes by increasing O-alkyl C content in YP, while decreased the same microorganisms by decreasing anomeric C-H content in QP. Importantly, higher clay and amorphous Fe (Fe_o) contents in QP after BC application protected SOC from further decomposition, which in turn decreased microorganisms and resulted in higher SOC sequestration than YP. Our results indicated that soil properties controlled the extent of SOC sequestration after BC application and site-specific soil properties must be carefully considered to maximize long-term SOC sequestration after BC application.

Evaluation of Yarrowia lipolytica Oil for Biodiesel Production: Land Use Oil Yield, Carbon, and Energy Balance

Oils from yeasts have emerged as a suitable alternative raw material to produce biodiesel, due to their similar composition to common raw materials such as vegetable oils. Additionally, they have the advantage of not competing with human or animal feed, and, furthermore, they do not compete for arable land. In this work, a carbon and energy balance was evaluated for Yarrowia lipolytica as a model yeast, using crude glycerol from biodiesel as the only carbon source, which improves biodiesel overall yield by 6%. The process presented a positive energy balance. Feasibility of yeast oil as biodiesel substrate was also evaluated by determination of the lipid fatty acid profile and cetane number. Moreover, a comparison of oil yields, in terms of land use, between vegetable, microalgae, and yeast oils is also presented. The results showed that Y. lipolytica oil yield is considerably higher than vegetable oils (767 times) and microalgae (36 times).

Porous cellulose as promoter of oil production by the oleaginous yeast Lipomyces starkeyi using mixed agroindustrial wastes

Enhanced single cell oil (SCO) production by the oleaginous yeast Lipomyces starkeyi DSM 70296, immobilised on delignified porous cellulose, is reported. Pure glucose media were initially used. The effects of substrate pH and treatment temperature were evaluated, showing that 30°C and pH 5.0 were the optimum conditions for SCO production by the immobilised yeast. The immobilisation technique led to increased lipid accumulation and cell growth by 44% and 8%, respectively, in the glucose media, compared to free cells in suspension. This positive effect was also shown when low concentration mixed agro-industrial waste suspensions were used as substrates, leading to 85% enhanced SCO production in comparison with free cells. Higher fatty acid (HFA) analysis showed that yeast immobilisation led to increased formation of unsaturated HFAs (6%) and reduced saturated HFAs (5%) compared to free cells.