Cyanobacterial photo-driven mixotrophic metabolism and its advantages for biosynthesis

Interplay between photosynthetic electron flux and organic carbon sinks in sucrose-excreting Synechocystis sp. PCC 6803 revealed by omics approaches

BACKGROUND

Advancing the engineering of photosynthesis-based prokaryotic cell factories is important for sustainable chemical production and requires a deep understanding of the interplay between bioenergetic and metabolic pathways. Rearrangements in photosynthetic electron flow to increase the efficient use of the light energy for carbon fixation must be balanced with a strong carbon sink to avoid photoinhibition. In the cyanobacterium Synechocystis sp. PCC 6803, the flavodiiron protein Flv3 functions as an alternative electron acceptor of photosystem I and represents an interesting engineering target for reorganizing electron flow in attempts to enhance photosynthetic CO2 fixation and increase production yield.

RESULTS

We have shown that inactivation of Flv3 in engineered sucrose-excreting Synechocystis (S02:Δflv3) induces a transition from photoautotrophic sucrose production to mixotrophic growth sustained by sucrose re-uptake and the formation of intracellular carbon sinks such as glycogen and polyhydroxybutyrate. The growth of S02:Δflv3 exceeds that of the sucrose-producing strain (S02) and demonstrates unforeseen proteomic and metabolomic changes over the course of the nine-day cultivation. In the absence of Flv3, a down-regulation of proteins related to photosynthetic light reactions and CO2 assimilation occurred concomitantly with up-regulation of those related to glycolytic pathways, before any differences in sucrose production between S02 and S02:Δflv3 strains were observed. Over time, increased sucrose degradation in S02:Δflv3 led to the upregulation of respiratory pathway components, such as the plastoquinone reductase complexes NDH-11 and NDH-2 and the terminal respiratory oxidases Cyd and Cox, which transfer electrons to O2. While glycolytic metabolism is significantly up-regulated in S02:Δflv3 to provide energy for the cell, the accumulation of intracellular storage compounds and the increase in respiration serve as indirect sinks for photosynthetic electrons.

CONCLUSIONS

Our results show that the presence of strong carbon sink in the engineered sucrose-producing Synechocystis S02 strain, operating under high light, high CO2 and salt stress, cannot compensate for the lack of Flv3 by directly balancing the light transducing source and carbon fixing sink reactions. Instead, the cells immediately sense the imbalance, leading to extensive reprogramming of cellular bioenergetic, metabolic and ion transport pathways that favor mixotrophic growth rather than enhancing photoautotrophic sucrose production.

Glycogen synthesis prevents metabolic imbalance and disruption of photosynthetic electron transport from photosystem II during transition to photomixotrophy in Synechocystis sp. PCC 6803

Some cyanobacteria can grow photoautotrophically or photomixotrophically by using simultaneously CO2 and glucose. The switch between these trophic modes and the role of glycogen, their main carbon storage macromolecule, was investigated. We analysed the effect of glucose addition on the physiology, metabolic and photosynthetic state of Synechocystis sp. PCC 6803 and mutants lacking phosphoglucomutase and ADP-glucose pyrophosphorylase, with limitations in glycogen synthesis. Glycogen acted as a metabolic buffer: glucose addition increased growth and glycogen reserves in the wild-type (WT), but arrested growth in the glycogen synthesis mutants. Already 30 min after glucose addition, metabolites from the Calvin-Benson-Bassham cycle and the oxidative pentose phosphate shunt increased threefold more in the glycogen synthesis mutants than the WT. These alterations substantially affected the photosynthetic performance of the glycogen synthesis mutants, as O2 evolution and CO2 uptake were both impaired. We conclude that glycogen synthesis is essential during transitions to photomixotrophy to avoid metabolic imbalance that induces inhibition of electron transfer from PSII and subsequently accumulation of reactive oxygen species, loss of PSII core proteins, and cell death. Our study lays foundations for optimising photomixotrophy-based biotechnologies through understanding the coordination of the crosstalk between photosynthetic electron transport and metabolism.

Effects of dissolved organic matter from sediment and soil samples on the growth and physiology of four bloom-forming algal species

Algal blooms negatively impact the water quality of reservoirs; however, the role of dissolved organic matter (DOM) in bloom formation in reservoirs has not been investigated. Therefore, we assessed the compositions of sediment- and soil-derived DOM and their effects on the growth, physiology, and photosynthetic activity of Microcystis aeruginosa, Anabaena sp., Chlamydomonas sp., and Peridiniopsis sp. (bloom-forming species). Sediment DOM promoted the growth of all algal species, whereas soil DOM significantly promoted the growth of Chlamydomonas sp. and Peridiniopsis sp.; this effect was due to enhanced stress tolerance and photosynthetic efficiency exhibited by these algae under DOM treatment. However, soil DOM slightly inhibited the growth of Anabaena sp. by increasing reactive oxygen species levels and inactivating some photosystem II reaction centers. The tyrosine-like substance, humic acid-like substances, and unsaturated aliphatic compounds were the main DOM components that affected algal growth. The findings of this study will provide a theoretical foundation for the development of bloom-prevention strategies for river-type reservoirs.

Effects of dissolved organic matter derived from two herbs on the growth, physiology, and physico-chemical characteristics of four bloom-forming algae species

While algal blooms occur frequently in lakes and reservoirs worldwide, the effects of dissolved organic matter (DOM) from lakeside and riparian zones on bloom formation are not well understood. In this study, we characterized the molecular composition of DOM from Cynodon dactylon (L.) Pers. (CD-DOM) and Xanthium sibiricum Patrin ex Widder (XS-DOM) and assessed their effects on the growth, physiology, volatile organic compounds (VOCs), and stable carbon isotope in four bloom-forming algae species (Microcystis aeruginosa, Anabaena sp., Chlamydomonas sp., and Peridiniopsis sp.). Stable carbon isotope analysis showed that the four species were affected by DOM. Both DOM types increased the cell biomass, polysaccharide and protein contents, chlorophyll fluorescence parameter values, and VOCs release of Anabaena sp., Chlamydomonas sp. and Microcystis aeruginosa, suggesting that DOM stimulated algal growth by increasing nutrient sources, photosynthetic efficiency, and stress tolerance. And in general, these three strains exhibited better growth at higher DOM concentrations. However, DOM treatment inhibited the growth of Peridiniopsis sp., as indicated by the increases in reactive oxygen species, damage in photosystem II reaction centers, and blockage in electron transport. Fluorescence analysis showed that tryptophan-like compounds were the main DOM components that affected algal growth. Molecular-level analysis suggested that unsaturated aliphatic compounds may be the most important DOM components. The findings indicate that CD-DOM and XS-DOM promote the blue-green algal blooms formation and thus should be considered in the management of natural water quality.

Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.

Metabolic transformation of cyanobacteria for biofuel production

World-wide, an emerging demand is moving towards the biofuels to replace the fossil fuels. In alternative biofuel production strategies, cyanobacteria have unique characteristic of accumulating glycogen, lipid, and fuel molecules through natural mechanisms. Moreover, the cyanobacteria can be easily engineered to synthesis a plenty of fuel molecules from CO₂. To obtain the fuel molecule from cyanobacteria, various techniques were invented in which the metabolic engineering is found to be a prerequisite to develop an economically feasible process. The expression of indigenous or heterologous pathways plays an important role in developing successful production process. In addition, the engineering of photosynthetic apparatus, destruction of competitive pathways and improvement of tolerance were also proven to improve the product specific synthesis. Although various metabolic engineering approaches have been developed, there are certain obstacles when it comes to implementation for the production. In this review, the important biosynthetic pathways for biofuels, alteration of other genes to improve the actual pathway and possibilities of developing cyanobacterial fuel production have been elaborated.

Engineering a Xylose-Utilizing Synechococcus elongatus UTEX 2973 Chassis for 3-Hydroxypropionic Acid Biosynthesis under Photomixotrophic Conditions

Photomixotrophic cultivation of cyanobacteria is considered a promising strategy to achieve both high cell density and product accumulation, since cyanobacteria can obtain carbon and energy sources from organic matter in addition to those obtained from CO₂ and sunlight. Acetyl coenzyme A (acetyl-CoA) is a key precursor used for the biosynthesis of a wide variety of important value-added chemicals. However, the acetyl-CoA content in cyanobacteria is typically low under photomixotrophic conditions, which limits the productivity of the derived chemicals. In this study, a xylose utilization pathway from Escherichia coli was first engineered into fast-growing Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973), enabling the xylose based photomixotrophy. Metabolomics analysis of the engineered strain showed that the utilization of xylose enhanced the carbon flow to the oxidative pentose phosphate (OPP) pathway, along with an increase in the intracellular abundance of metabolites such as fructose-6-phosphate (F6P), fructose-1,6-bisphosphate (FBP), ribose-5-phosphate (R5P), erythrose-4-phosphate (E4P), and glyceraldehyde-3-phosphate (G3P). Then, the native glycolytic pathway was rewired via heterologous phosphoketolase (Pkt) gene expression, combined with phosphofructokinase (Pfk) gene knockout and fructose-1,6-bisphosphatase (Fbp) gene overexpression, to drive more carbon flux from xylose to acetyl-CoA. Finally, a heterologous 3-hydroxypropionic acid (3-HP) biosynthetic pathway was introduced. The results showed that 3-HP biosynthesis was improved by up to approximately 4.1-fold (from 22.5 mg/L to 91.3 mg/L) compared with the engineered strain without a rewired metabolism under photomixotrophic conditions and up to approximately 14-fold compared with the strain under photoautotrophic conditions. Using 3-HP as a "proof-of-molecule", our results demonstrated that this strategy could be applied to improve the intracellular pool of acetyl-CoA for the photomixotrophic production of value-added chemicals that require acetyl-CoA as a precursor in a cyanobacterial chassis.

A review on cyanobacteria cultivation for carbohydrate-based biofuels: Cultivation aspects, polysaccharides accumulation strategies, and biofuels production scenarios

Cyanobacterial biomass has constituted a crucial third and fourth-generation biofuel material, with great potential to synthesize a wide range of metabolites, mainly carbohydrates. Lately, carbohydrate-based biofuels from cyanobacteria, such as bioethanol, biohydrogen, and biobutanol, have attracted attention as a sustainable alternative to petroleum-based products. Cyanobacteria can perform a simple process of saccharification, and extracted carbohydrates can be converted into biofuels with two alternatives; the first one consists of a fermentative process based on bacteria or yeasts, while the second alternative consists of an internal metabolic process of their own in intracellular carbohydrate content, either by the natural or genetic engineered process. This study reviewed carbohydrate-enriched cyanobacterial biomass as feedstock for biofuels. Detailed insights on technical strategies and limitations of cultivation, polysaccharide accumulation strategies for further fermentation process were provided. Advances and challenges in bioethanol, biohydrogen, and biobutanol production by cyanobacteria synthesis and an independent fermentative process are presented. Critical outlook on life-cycle assessment and techno-economical aspects for large-scale application of these technologies were discussed.

Engineering microbial metabolic energy homeostasis for improved bioproduction

Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.

Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces

Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

Engineering a Central Carbon Metabolism Pathway to Increase the Intracellular Acetyl-CoA Pool in Synechocystis sp. PCC 6803 Grown under Photomixotrophic Conditions

In cyanobacteria, photomixotrophic growth is considered as a promising strategy to achieve both high cell density and product accumulation. However, the conversion of glucose to acetyl coenzyme A (acetyl-CoA) in the native glycolytic pathway is insufficient, which decreases the carbon utilization and productivity of engineered cyanobacteria under photomixotrophic conditions. To increase the carbon flux from glucose to key intracellular precursor acetyl-CoA in Synechocystis sp. PCC 6803 (hereafter, Synechocystis 6803) under photomixotrophic conditions, a synthetic nonoxidative cyclic glycolysis (NOG) pathway was introduced into the wild type strain, which successfully increased the intracellular pool of acetyl-CoA by approximately 1-fold. To minimize the competition for glucose, the native Embden-Meyerhof-Parnas (EMP) and Entner-Doudoroff (ED) pathways were knocked out, respectively. Notably, eliminating the native ED pathway in the engineered strain carrying the NOG pathway further increased the intracellular pool of acetyl-CoA up to 2.8-fold. Another carbon consuming pathway in Synechocystis 6803, the glycogen biosynthesis pathway, was additionally knocked out in the above-mentioned engineered strain, which enabled an increase of the intracellular acetyl-CoA pool by up to 3.5-fold when compared with the wild type strain. Finally, the content of intracellular lipids was analyzed as an index of the productive capacity of the engineered Synechocystis 6803 cell factory under photomixotrophic conditions. The results showed the total lipids yield increased about 26% compared to the wild type (from 15.71% to 34.12%, g/g glucose), demonstrating that this integrated approach could represent a general strategy not only for the improvement of the intracellular concentration of acetyl-CoA, but also for the production of value-added chemicals that require acetyl-CoA as a key precursor in cyanobacteria.

New insights into mechanisms of sunlight- and dark-mediated high-temperature accelerated diurnal production-degradation of fluorescent DOM in lake waters

The production of fluorescent dissolved organic matter (FDOM) by phytoplankton and its subsequent degradation, both of which occur constantly under diurnal-day time sunlight and by night time dark-microbial respiration processes in the upper layer of surface waters, influence markedly several biogeochemical processes and functions in aquatic environments and can be feasibly related to global warming (GW). In this work sunlight-mediated high-temperature was shown to accelerate the production of FDOM, but also its complete disappearance over a 24-h diurnal period in July at the highest air and water temperatures (respectively, 41.1 and 33.5 °C), differently from lower temperature months. Extracellular polymeric substances (EPS), an early-state DOM, were produced by phytoplankton in July in the early morning (6:00-9:00), then they were degraded into four FDOM components over midday (10:00-15:00), which was followed by simultaneous production and almost complete degradation of FDOM with reformation of EPS during the night (2:00-6:00). Such transformations occurred simultaneously with the fluctuating production of nutrients, dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and the two isotopes (δ¹⁵N and δ¹⁸O) of NO₃^-. It was estimated that complete degradation of FDOM in July was associated with mineralization of approximately 15% of the initial DOC, which showed a nighttime minimum (00:00) in comparison to a maximum at 13:00. FDOM identified by excitation-emission matrix spectroscopy combined with parallel factor analysis consisted of EPS, autochthonous humic-like substances (AHLS) of C- and M-types, a combined form of C- and M-types of AHLS, protein-like substances (PLS), newly-released PLS, tryptophan-like substances, tyrosine-like substances (TYLS), a combined form of TYLS and phenylalanine-like substances (PALS), and their degradation products. Finally, stepwise degradation and production processes are synthesized in a pathway for FDOM components production and their subsequent transformation under different diurnal temperature conditions, which provided a broader paradigm for future impacts on GW-mediated DOM dynamics in lake water.

Enhanced Production of Photosynthetic Pigments and Various Metabolites and Lipids in the Cyanobacteria Synechocystis sp. PCC 7338 Culture in the Presence of Exogenous Glucose

Synechocystis strains are cyanobacteria that can produce useful biomaterials for biofuel and pharmaceutical resources. In this study, the effects of exogenous glucose (5-mM) on cell growth, photosynthetic pigments, metabolites, and lipids in Synechocystis sp. PCC 7338 (referred to as Synechocystis 7338) were investigated. Exogenous glucose increased cell growth on days 9 and 18. The highest production (mg/L) of chlorophyll a (34.66), phycocyanin (84.94), allophycocyanin (34.28), and phycoerythrin (6.90) was observed on day 18 in Synechocystis 7338 culture under 5-mM glucose. Alterations in metabolic and lipidomic profiles under 5-mM glucose were investigated using gas chromatography-mass spectrometry (MS) and nanoelectrospray ionization-MS. The highest production (relative intensity/L) of aspartic acid, glutamic acid, glycerol-3-phosphate, linolenic acid, monogalactosyldiacylglycerol (MGDG) 16:0/18:1, MGDG 16:0/20:2, MGDG 18:1/18:2, neophytadiene, oleic acid, phosphatidylglycerol (PG) 16:0/16:0, and PG 16:0/17:2 was achieved on day 9. The highest production of pyroglutamic acid and sucrose was observed on day 18. We suggest that the addition of exogenous glucose to Synechocystis 7338 culture could be an efficient strategy for improving growth of cells and production of photosynthetic pigments, metabolites, and intact lipid species for industrial applications.

A Cyanobacteria-Based Biofilm System for Advanced Brewery Wastewater Treatment

Algal/cyanobacterial biofilm photobioreactors provide an alternative technology to conventional photosynthetic systems for wastewater treatment based on high biomass production and easy biomass harvesting at low cost. This study introduces a novel cyanobacteria-based biofilm photobioreactor and assesses its performance in post-treatment of brewery wastewater and biomass production. Two different supporting materials (glass/polyurethane) were tested to investigate the effect of surface hydrophobicity on biomass attachment and overall reactor performance. The reactor exhibited high removal efficiency (over 65%) of the wastewater’s pollutants (chemical oxygen demand, nitrate, nitrite, ammonium, orthophosphate, and total Kjeldahl nitrogen), while biomass per reactor surface reached 13.1 and 12.8 g·m−2 corresponding to 406 and 392 mg·L−1 for glass and polyurethane, respectively, after 15 days of cultivation. The hydrophilic glass surface favored initial biomass adhesion, although eventually both materials yielded complete biomass attachment, highlighting that cell-to-cell interactions are the dominant adhesion mechanism in mature biofilms. It was also found that the biofilm accumulated up to 61% of its dry weight in carbohydrates at the end of cultivation, thus making the produced biomass a suitable feedstock for bioethanol production.

Crosstalk of two-component signal transduction systems in regulating central carbohydrate and energy metabolism during autotrophic and photomixotrophic growth of Synechocystis sp. PCC 6803

Unicellular model cyanobacterium Synechocystis sp. PCC 6803 has received considerable attention as a sustainable energy resource because of its photosynthetic machinery. However, two-component signal transduction systems (TCSTSs) in regulating central carbohydrate and energy metabolism of cyanobacteria are still poorly understood due to their diversity and functional complication. In this study, by comparing the growth of knockout mutants of 44 response regulators (RRs) of TCSTSs in Synechocystis, several RR mutants demonstrating differential growth patterns were identified under auto- or photomixotrophic conditions. However, in spite of no growth difference observed for the remaining RR mutants, liquid chromatography-mass spectrometry based metabolomic profile analysis showed that a widespread crosstalk of TCSTSs in regulating central carbohydrate and energy metabolism of Synechocystis was identified, while most of them showed diverse patterns during different trophic types or growth stages. Furthermore, an integrative analysis between evolutionary relationships and metabolomic profiles revealed some pairs of paralogous RRs with highly functional convergence, suggesting the possible conserved functions of Synechocystis TCSTSs during evolution. This study laid an important basis for understanding the function of TCSTSs in photosynthetic cyanobacteria.

Synthetic biology for manufacturing chemicals: constraints drive the use of non-conventional microbial platforms

Genetically modified microbes have had much industrial success producing protein-based products (such as antibodies and enzymes). However, engineering microbial workhorses for biomanufacturing of commodity compounds remains challenging. First, microbes cannot afford burdens with both overexpression of multiple enzymes and metabolite drainage for product synthesis. Second, synthetic circuits and introduced heterologous pathways are not yet as "robust and reliable" as native pathways due to hosts' innate regulations, especially under suboptimal fermentation conditions. Third, engineered enzymes may lack channeling capabilities for cascade-like transport of metabolites to overcome diffusion barriers or to avoid intermediate toxicity in the cytoplasmic environment. Fourth, moving engineered hosts from laboratory to industry is unreliable because genetic mutations and non-genetic cell-to-cell variations impair the large-scale fermentation outcomes. Therefore, synthetic biology strains often have unsatisfactory industrial performance (titer/yield/productivity). To overcome these problems, many different species are being explored for their metabolic strengths that can be leveraged to synthesize specific compounds. Here, we provide examples of non-conventional and genetically amenable species for industrial manufacturing, including the following: Corynebacterium glutamicum for its TCA cycle-derived biosynthesis, Yarrowia lipolytica for its biosynthesis of fatty acids and carotenoids, cyanobacteria for photosynthetic production from its sugar phosphate pathways, and Rhodococcus for its ability to biotransform recalcitrant feedstock. Finally, we discuss emerging technologies (e.g., genome-to-phenome mapping, single cell methods, and knowledge engineering) that may facilitate the development of novel cell factories.