Growth condition optimization for docosahexaenoic acid (DHA) production by Moritella marina MP-1

Strategic nutrient sourcing for biomanufacturing intensification

The successful design of economically viable bioprocesses can help to abate global dependence on petroleum, increase supply chain resilience, and add value to agriculture. Specifically, bioprocessing provides the opportunity to replace petrochemical production methods with biological methods and to develop novel bioproducts. Even though a vast range of chemicals can be biomanufactured, the constraints on economic viability, especially while competing with petrochemicals, are severe. There have been extensive gains in our ability to engineer microbes for improved production metrics and utilization of target carbon sources. The impact of growth medium composition on process cost and organism performance receives less attention in the literature than organism engineering efforts, with media optimization often being performed in proprietary settings. The widespread use of corn steep liquor as a nutrient source demonstrates the viability and importance of "waste" streams in biomanufacturing. There are other promising waste streams that can be used to increase the sustainability of biomanufacturing, such as the use of urea instead of fossil fuel-intensive ammonia and the use of struvite instead of contributing to the depletion of phosphate reserves. In this review, we discuss several process-specific optimizations of micronutrients that increased product titers by twofold or more. This practice of deliberate and thoughtful sourcing and adjustment of nutrients can substantially impact process metrics. Yet the mechanisms are rarely explored, making it difficult to generalize the results to other processes. In this review, we will discuss examples of nutrient sourcing and adjustment as a means of process improvement.

ONE-SENTENCE SUMMARY

The potential impact of nutrient adjustments on bioprocess performance, economics, and waste valorization is undervalued and largely undercharacterized.

Key media microsupplements for boosting de novo lipogenesis in an oleaginic yeast isolate

Present work reports a simple approach of microsupplementing nitrogen starved production media with potential activators of lipogenic enzymes for boosting de novo lipogenesis and demonstrated a 70-117 % rise in lipid content (LC) of yeast isolate Geotrichum candidum NBT-1. A hypothesis was proposed to increase the LC in the isolate at fixed minimum C/N ratio and small molecular activators for 3 key enzymes of lipogenic pathways. ATP citrate lyase, malic enzyme and acetyl CoA-carboxylase were screened in silico. Screened molecules were microsupplemented in nitrogen-starved media for examining the actual influence of their individual and synergistic combination on boosting LC of the isolate, which revealed sodium acetate as a major effector. Acetate in 4 mM concentration, independently and in combination with citric acid and sucrose resulted in a 2-2.2-fold increase in G. candidum LC from 24.8% in control to 49.27% and 53.96%, respectively. A volumetric lipid productivity of 0.0288 g/L/h with appreciable lipid coefficient of 9.77 was achieved in acetate supplemented media. Extracted lipids were 70-90% concentrated in a medium chain fatty acid (MCFA)-caprylic acid (C8:0), which has upsurging nutritional and nutraceutical importance.

Optimizing Eicosapentaenoic Acid Production by Grafting a Heterologous Polyketide Synthase Pathway in the Thraustochytrid Aurantiochytrium

Eicosapentaenoic acid (EPA) is an essential nutritional supplement for human health. The most prominent dietary source of EPA is fish oil, which is unsustainable because of the decline in fishery resources and serious environmental pollution. Alternatively, a heterologous polyketide synthase pathway for EPA biosynthesis was assembled in Thraustochytrid Aurantiochytrium. A 2A peptide-based facile assembly platform that can achieve multigene expression as a polycistron was first established. The platform was then applied to express the EPA biosynthetic gene cluster from Shewanella japonica in Aurantiochytrium. In the shake flask fermentation, the lipid and PUFA yields of the mutant were increased by 26.9 and 36.0%, respectively, and led to about 5-fold increase of the EPA yield. The final EPA titer reached 2.7 g/L in fed-batch fermentation. This study provides a novel metabolic engineering strategy to regulate the EPA ratio in microalgal oil for human nutritional supplementation.

Mediterranean Sea bacteria as a potential source of long-chain polyunsaturated fatty acids

Long-chain polyunsaturated fatty acids (LC-PUFAs), including EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) are important nutritional ingredients in fish feed. So far, fish oil has been used as a main source of LC-PUFAs; however, the limited global supply of fish oil is not able to meet the demand of the growing aquaculture sector. Hence, sustainability of aquaculture industry could be supported by searching alternative sources of these compounds. Marine microorganisms represent a sustainable and stable supply source of LC-PUFAs. A collection of 209 bacterial isolates obtained from sediment samples recovered in the Mediterranean Sea was screened in order to select new LC-PUFAs producers. Among 95 putative producers selected based on colourimetric screening, 31 quickly growing were selected for further studies. The detection of LC-PUFAs was confirmed from 15 isolates belonging to the genera Marinobacter, Halomonas and Thalassospira by GC-FID analysis. Among them, the isolate Marinobacter sp. G16.20 was found to be a potentially high LC-PUFA producer exhibiting relatively high levels of DHA in particular (maximum productivity of 1.85 ± 0.371 mg/g, representing 45.89% of the total fatty acids detected and identified). Microorganisms belonging to the genera reported in this study showed biotechnological traits interesting for their potential future application in aquaculture.

Nitrogen Feeding Strategies and Metabolomic Analysis To Alleviate High-Nitrogen Inhibition on Docosahexaenoic Acid Production in Crypthecodinium cohnii

It is well-known that high-nitrogen content inhibits cell growth and docosahexaenoic acid (DHA) biosynthesis in heterotrophic microalgae Crypthecodinium cohnii. In this study, two nitrogen feeding strategies, pulse-feeding and continuous-feeding, were evaluated to alleviate high-nitrogen inhibition effects on C. cohnii. The results showed that continuous-feeding with a medium solution containing 50% ( w/v) yeast extract at 2.1 mL/h during 12-96 h was the optimal nitrogen feeding strategy for the fermentation process, when glucose concentration was maintained at 15-27 g/L during the same period. With the optimized strategy, 71.2 g/L of dry cell weight and DHA productivity of 57.1 mg/L/h were achieved. In addition, metabolomic analysis was applied to determine the metabolic changes during different nitrogen feeding conditions, and the changes in amino acids, polysaccharides, purines, and pentose phosphate pathway were observed, providing valuable metabolite-level information for exploring the mechanism of the high-nitrogen inhibition effect and further improving DHA productivity in C. cohnii.

Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production

Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.

Improving Escherichia coli membrane integrity and fatty acid production by expression tuning of FadL and OmpF

Background

Construction of microbial biocatalysts for the production of biorenewables at economically viable yields and titers is frequently hampered by product toxicity. Membrane damage is often deemed as the principal mechanism of this toxicity, particularly in regards to decreased membrane integrity. Previous studies have attempted to engineer the membrane with the goal of increasing membrane integrity. However, most of these works focused on engineering of phospholipids and efforts to identify membrane proteins that can be targeted to improve fatty acid production have been unsuccessful.

Results

Here we show that deletion of outer membrane protein ompF significantly increased membrane integrity, fatty acid tolerance and fatty acid production, possibly due to prevention of re-entry of short chain fatty acids. In contrast, deletion of fadL resulted in significantly decreased membrane integrity and fatty acid production. Consistently, increased expression of fadL remarkably increased membrane integrity and fatty acid tolerance while also increasing the final fatty acid titer. This 34% increase in the final fatty acid titer was possibly due to increased membrane lipid biosynthesis. Tuning of fadL expression showed that there is a positive relationship between fadL abundance and fatty acid production. Combinatorial deletion of ompF and increased expression of fadL were found to have an additive role in increasing membrane integrity, and was associated with a 53% increase the fatty acid titer, to 2.3 g/L.

Conclusions

These results emphasize the importance of membrane proteins for maintaining membrane integrity and production of biorenewables, such as fatty acids, which expands the targets for membrane engineering.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0650-8) contains supplementary material, which is available to authorized users.

Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia

The current study describes the taxonomic and functional composition of metagenomic sequences obtained from a filamentous microbial mat isolated from the Comau fjord, located in the northernmost part of the Chilean Patagonia. The taxonomic composition of the microbial community showed a high proportion of members of the Gammaproteobacteria, including a high number of sequences that were recruited to the genomes of Moritella marina MP-1 and Colwelliapsycherythraea 34H, suggesting the presence of populations related to these two psychrophilic bacterial species. Functional analysis of the community indicated a high proportion of genes coding for the transport and metabolism of amino acids, as well as in energy production. Among the energy production functions, we found protein-coding genes for sulfate and nitrate reduction, both processes associated with Gammaproteobacteria-related sequences. This report provides the first examination of the taxonomic composition and genetic diversity associated with these conspicuous microbial mat communities and provides a framework for future microbial studies in the Comau fjord.