Light-driven synthetic microbial consortia:playing with an oxygen dilemma

Background:Light-driven synthetic microbial consortia are composed of photoautotrophs and heterotrophs.They exhibited better performance in stability,robustness and capacity for handling complex tasks when comparing with axenic cultures.Different from general microbial consortia,the intrinsic property of photosynthetic oxygen evolution in light-driven synthetic microbial consortia is an important factor affecting the functions of the consortia.Results:In light-driven microbial consortia,the oxygen liberated by photoautotrophs will result in an aerobic environment,which exerts dual effects on different species and processes.On one hand,oxygen is favorable to the synthetic microbial consortia when they are used for wastewater treatment and aerobic chemical production,in which biomass accumulation and oxidized product formation will benefit from the high energy yield of aerobic respiration.On the other hand,the oxygen is harmful to the synthetic microbial consortia when they were used for anaerobic processes including biohydrogen production and bioelectricity generation,in which the presence of oxygen will deactivate some biological components and compete for electrons.Conclusions:Developing anaerobic processes in using light-driven synthetic microbial consortia represents a costeffective alternative for production of chemicals from carbon dioxide and light.Thus,exploring a versatile approach addressing the oxygen dilemma is essential to enable light-driven synthetic microbial consortia to get closer to practical applications.

Design and construction of synthetic microbial consortia in China

The rapid development of synthetic biology enables the design,construction and optimization of synthetic microbial consortia to achieve specific functions.In China,the“973”project-“Design and Construction of Microbial Consortia”was funded by the National Basic Research Program of China in January 2014.It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands.In this review,we will introduce this“973”project,including the significance of microbial consortia,the fundamental scientific issues,the recent research progresses,and some case studies about synthetic microbial consortia in the past two and a half years.

Construction of synthetic microbial consortia for 2-keto-L-gulonic acid biosynthesis

Currently,the establishment of synthetic microbial consortia with rational strategies has gained extensive attention,becoming one of the important frontiers of synthetic biology.Systems biology can offer insights into the design and construction of synthetic microbial consortia.Taking the high-efficiency production of 2-keto-L-gulonic acid(2-KLG)as an example,we constructed a synthetic microbial consortium“Saccharomyces cerevisiae-Ketogulonigenium vulgare”based on systems biology analysis.In the consortium,K.vulgare was the 2-KLG pro-ducing strain,and S.cerevisiae acted as the helper strain.Comparative transcriptomic analysis was performed on an engineered S.cerevisiae(VTC2)and a wild-type S.cerevisiae BY4741.The results showed that the up-regulated genes in VTC2,compared with BY4741,were mainly involved in glycolysis,TCA cycle,purine metabolism,and biosynthesis of amino acids,B vitamins,and antioxidant proteases,all of which play important roles in pro-moting the growth of K.vulgare.Furthermore,Vitamin C produced by VTC2 could further relieve the oxidative stress in the environment to increase the production of 2-KLG.Therefore,VTC2 would be of great advantage in working with K.vulgare.Thus,the synthetic microbial consortium"VTC2-K.vulgare"was constructed based on transcriptomics analyses,and the accumulation of 2-KLG was increased by 1.49-fold compared with that of mono-cultured K.vulgare,reaching 13.2±0.52 g/L.In addition,the increased production of 2-KLG was accompanied by the up-regulated activities of superoxide dismutase and catalase in the medium and the up-regulated oxidative stress-related genes(sod,cat and gpd)in K.vulgare.The results indicated that the oxida-tive stress in the synthetic microbial consortium was efficiently reduced.Thus,systems analysis confirmed a favorable symbiotic relationship between microorganisms,providing guidance for further engineering synthetic consortia.

Bistability and oscillations in co-repressive synthetic microbial consortia

Background： Synthetic microbial consortia are conglomerations of genetically engineered microbes programmed to cooperatively bring about population-level phenotypes. By coordinating their activity, the constituent strains can display emergent behaviors that are difficult to engineer into isogenic populations. To do so, strains are engineered to communicate with one another through intercellular signaling pathways that depend on cell density. Methods： Here, we used computational modeling to examine how the behavior of synthetic microbial consortia results from the interplay between population dynamics governed by cell growth and internal transcriptional dynamics governed by cell-ceil signaling. Specifically, we examined a synthetic microbial consortium in which two strains each produce signals that down-regulate transcription in the other. Within a single strain this regulatory topology is called a ＂co-repressive toggle switch＂ and can lead to bistability. Results： We found that in co-repressive synthetic microbial consortia the existence and stability of different states depend on population-level dynamics. As the two strains passively compete for space within the colony, their relative fractions fluctuate and thus alter the strengths of intercellular signals. These fluctuations drive the consortium to alternative equilibria. Additionally, if the growth rates of the strains depend on their transcriptional states, an additional feedback loop is created that can generate oscillations. Conclusions： Our findings demonstrate that the dynamics of microbial consortia cannot be predicted from their regulatory topologies alone, but are also determined by interactions between the strains. Therefore, when designing synthetic microbial consortia that use intercellular signaling, one must account for growth variations caused by the production of protein.

Insights into constructing a stable and efficient microbial consortium

Microbial consortia are ubiquitous in nature,in which multiple microbial species cooperate to complete some important tasks such as lignocellulose degradation.Because of the advantages such as reduced metabolic burden and robustness to environment disturbances,developing a microbial consortium is a promising approach for valuable product synthesis,lignocellulose utilization,human health care,bioremediation and sustainable energy,etc.Despite the benefits,however,most artificial microbial consortia confront the problems of instability and low efficiency due to growth competition and metabolite incompatibility.To overcome these challenges,multiple strategies to design efficient synthetic microbial consortia have been reported.In this review,the interactions that determine the stability and performance of microbial consortia were described.Progress of artificial microbial consortia research was summarized,and the key strategies i.e.,spatial or temporal segregation,separated utilization of nutrients,nutrient cross-feeding and division of labor,that will be of great importance for achieving a stable and efficient microbial consortium were highlighted.Two novel advanced tools,signaling molecule systems and computational models,were also introduced and discussed.We believed that combining the universal cell–cell signaling molecule systems with computational models will be promising for synthetic microbial consortia construction in the future.

Design and construction of microbial cell factories based on systems biology

Environmental sustainability is an increasingly important issue in industry.As an environmentally friendly and sustainable way,constructing microbial cell factories to produce all kinds of valuable products has attracted more and more attention.In the process of constructing microbial cell factories,systems biology plays a crucial role.This review summarizes the recent applications of systems biology in the design and construction of microbial cell factories from four perspectives,including functional genes/enzymes discovery,bottleneck pathways identification,strains tolerance improvement and design and construction of synthetic microbial consortia.Systems biology tools can be employed to identify functional genes/enzymes involved in the biosynthetic pathways of products.These discovered genes are introduced into appropriate chassis strains to build engineering microorganisms capable of producing products.Subsequently,systems biology tools are used to identify bottleneck pathways,improve strains tolerance and guide design and construction of synthetic microbial consortia,resulting in increasing the yield of engineered strains and constructing microbial cell factories successfully.

Claroideoglomus etunicatum and Pantoea dispersa significantly enhance growth and nutrition of broom grass

Broom grass(Thysanolaena maxima)is an evergreen non-timber forest produce species.This grass is now domesticated for cultivation by farmers.It is a multi-purpose grass providing mainly inflorescence used as brooms for cleaning every household and also fodder for cattle,fuel wood for cooking and thus enhance farmers income.An earlier pot culture study brought out that Claroideoglomus etunicatum as the best arbuscular mycorrhizal fungus(AMF)and Pantoea dispersa as the best plant growth promoting rhizobacteria(PGPR)for inoculating broom grass.In the present investigation,a pot culture experiment was conducted in glasshouse to study the effect of individual and combined inoculation of C.etunicatum and P.dispersa on the growth of broom grass.The plant height,stem girth,biovolume index,plant dry weight,major and minor nutrient concentrations were significantly higher in plants inoculated with C.etunicatum+P.dispersa compared to inoculation with either of them.It was concluded that dual inoculation with the two selected beneficial microorganisms is best for enhancing the growth and yield of broom grass which in turn will improve the livelihood of the farmers.

Interactions among microorganisms functionally active for electron transfer and pollutant degradation in natural environments

Compared to single microbial strains,complex interactions between microbial consortia composed of various microorganisms have been shown to be effective in expanding ecological functions and accomplishing biological processes.Electroactive microorganisms(EMs)and degradable microorganisms(DMs)play vital roles in bioenergy production and the degradation of organic pollutants hazardous to human health.These microorganisms can strongly interact with other microorganisms and promote metabolic cooperation,thus facilitating electricity production and pollutant degradation.In this review,we describe several specific types of EMs and DMs based on their ability to adapt to different environments,and summarize the mechanism of EMs in extracellular electron transfer.The effects of interactions between EMs and DMs are evaluated in terms of electricity production and degradation efficiency.The principle of the enhancement in microbial consortia is also introduced,such as improved biomass,changed degradation pathways,and biocatalytic potentials,which are directly or indirectly conducive to human health.