Engineering consortia by polymeric microbial swarmbots

Integrating ecological and evolutionary frameworks for SynCom success

Use of synthetic microbial communities (SynComs) is a promising approach that harnesses nature-based solutions to support soil fertility and food security, mitigate climate change impacts, and restore terrestrial ecosystems. Several microbial products are in the market, and many others are at different stages of development and commercialization. Yet, we are still far from being able to fully harness the potential and successful applications of such biotechnological tools. The limited field efficiency and efficacy of SynComs have significantly constrained commercial opportunities, resulting in market growth falling below expectations. To overcome these challenges and manage expectations, it is critical to address current limitations, failures, and potential environmental consequences of SynComs. In this Viewpoint, we explore how using multiple eco-evolutionary theories can inform SynCom design and success. We further discuss the current status of SynComs and identify the next steps needed to develop and deploy the next generation of tools to boost their ability to support multiple ecosystem services, including food security and environmental sustainability.

In situ intein-mediated multiprotein assembly via engineered cross-species consortia

Inteins can connect flanking external proteins into a new protein fragment and excise themselves. Here, we report the in situ splicing of proteins by engineered microbial consortia. This study pioneers a programmable microbial consortia platform enabling in situ protein splicing through split intein-mediated assembly. Engineered Escherichia coli with the ePop autolysis system release intein-fused protein fragments via synchronized lysis, while Pichia pastoris secretes complementary domains, enabling extracellular reconstitution directly in culture. With the application of integrating quorum-sensing controls and eukaryotic secretion pathways, this approach bypasses in vitro purification, supporting scalable one-pot synthesis of multiple functional proteins. The platform's versatility in logic computation and antibiotic resistance engineering highlights its potential for adaptive biomanufacturing and context-aware biomaterial design.

Roles of the soil microbiome in sustaining grassland ecosystem health on the Qinghai-Tibet Plateau

Soil microbes, as intermediaries in plant-soil interactions, are closely linked to plant health in grassland ecosystems. In recent years, varying degrees of degradation have been observed in the alpine grasslands of the Qinghai-Tibet Plateau (QTP). Addressing grassland degradation, particularly under the influence of climate change, poses a global challenge. Understanding the factors driving grassland degradation on the QTP and developing appropriate mitigation measures is essential for the future sustainability of this fragile ecosystem. In this review, we discuss the environmental and anthropogenic factors affecting grassland degradation and the corresponding impacts on soil microbe community structure. We summarize the current research on the microbiome of the QTP, in particular the effect of vegetation, climate change, grazing, and land use, respectively on the alpine grassland microbiome. The results of these studies indicate that microbially mediated soil bioprocesses are important drivers of grassland ecosystem functional recovery. Therefore, a thorough understanding of the spatial distribution characteristics of the soil microbiome in alpine grasslands is required, and this necessitates an integrated approach in which the interactions among climatic factors, vegetation characteristics, and human activities are evaluated. Additionally, we assess and summarise current technological developments and prospects for applying soil microbiome technologies in sustainable agriculture, including: (i) single-strain inoculation, and (ii) inoculation of synthetic microbial communities, (iii) microbial community transplantation. Grassland restoration projects should be carried out with the understanding that each restoration measure has a unique effect on the soil microbial activity. We propose that the sustainable development of alpine grassland ecosystems can be achieved by adopting advanced microbiome technologies and integrating microbe-based sustainable agricultural practices to maximise grassland biomass, increase soil carbon, and optimise soil nutrient cycling.

Harnessing microbial co-culture to increase the production of known secondary metabolites

Covering: 2019 to 2024Secondary metabolites (SMs) are naturally occurring defense or signaling molecules that are also utilized as human and animal drugs, crop protection agents, and fine chemicals. Currently, SMs are primarily produced in monoculture settings, devoid of the intricate microbial interactions found in natural environments. Monoculture may lead to the silencing of gene clusters, requiring various genetic or bioprocess strategies to activate the biosynthesis of the corresponding metabolites. Less considered is the effect of monoculture on the efficiency of the production of important, known SMs during microbial fermentations. Co-culturing aims to mimic the complexity of natural microbial habitats, thus may increase the titer, the rate and/or the yield of fermentations. This review summarizes the progress in utilizing co-culture to promote the synthesis of known SMs by describing the types of various microbial co-cultures, listing the mechanisms for enhancing the biosynthesis of SMs, and navigating the challenges and strategies for applying such an approach in the biotechnology industries.

Facilitated Channeling of Fixed Carbon and Energy into Chemicals in Artificial Phototrophic Communities

Light-driven CO2 biovalorization offers a promising route for coupling carbon mitigation with petrochemical replacement. Synthetic phototrophic communities that mimic lichens can reduce the metabolic burden with improved CO2 utilization. However, inefficient channeling of carbon and energy between species seriously hinders the collaborative CO2-to-molecule route. Herein, we report a universal carbon sequestration (UCS) module based on photosynthetic microbes that provides a high-speed tunnel for channeling carbon and energy to heterotrophs. Compared to that of the traditional CO2-to-sucrose module, the UCS module sequestered 30% more carbon into glycerol, a generally available carbon source with high energy density. We demonstrated that the UCS module can be highly compatible with various industrial chassis and genetically recalcitrant microbes, enabling the rapid development of synthetic phototrophic communities without additional genetic manipulation. Notably, the accelerated electron transport and nutrient recycling systems may facilitate carbon and energy communications between cooperative partners. These UCS module-based communities efficiently channeled CO2 into a wide range of chemicals, with a negative carbon footprint of -25.04 to -440.74 kgCO2e/kg of products. This strategy widens the boundaries of artificial photosynthetic communities and may boost carbon-negative biomanufacturing.

Engineering a Photoautotrophic Microbial Coculture toward Enhanced Biohydrogen Production

The application of synthetic phototrophic microbial consortia holds promise for sustainable bioenergy production. Nevertheless, strategies for the efficient construction and regulation of such consortia remain challenging. Applying tools of genetic engineering, this study successfully constructed a synthetic community of phototrophs using Rhodopseudomonas palustris (R. palustris) and an engineered strain of Synechocystis sp PCC6803 for acetate production (Synechocystis_acs), enabling the production of biohydrogen and fatty acids during nitrogen and carbon dioxide fixation. Elemental balance confirmed carbon capture and nitrogen fixation into the consortium. The strategy of circadian illumination effectively limited oxygen levels in the system, ensuring the activity of the nitrogenase in R. palustris, despite oxygenic photosynthesis happening in Synechocystis. When infrared light was introduced into the circadian illumination, the production of H2 (9.70 μmol mg-1) and fatty acids (especially C16 and C18) was significantly enhanced. Proteomic analysis indicated acetate exchange and light-dependent regulation of metabolic activities. Infrared illumination significantly stimulated the expression of proteins coding for nitrogen fixation, carbohydrate metabolism, and transporters in R. palustris, while constant white light led to the most upregulation of photosynthesis-related proteins in Synechocystis_acs. This study demonstrated the successful construction and light regulation of a phototrophic community, enabling H2 and fatty acid production through carbon and nitrogen fixation.

Whole-genome sequencing and secondary metabolite exploration of the novel Bacillus velezensis BN with broad-spectrum antagonistic activity against fungal plant pathogens

The utilization of chemical pesticides recovers 30%-40% of food losses. However, their application has also triggered a series of problems, including food safety, environmental pollution, pesticide resistance, and incidents of poisoning. Consequently, green pesticides are increasingly seen as viable alternatives to their chemical counterparts. Among these, Plant Growth-Promoting Rhizobacteria (PGPR), which are found within plant rhizosphere, stand out for their capacity to stimulate plant growth. Recently, we isolated a strain, BN, with broad-spectrum antimicrobial activity from the rhizosphere of Lilium brownii. Identification revealed that this strain belongs to the species Bacillus velezensis and exhibits significant inhibitory effects against various fungal plant pathogens. The complete genome sequence of B. velezensis BN consists of a circular chromosome with a length of 3,929,791 bp, includes 3,747 protein-coding genes, 81 small RNAs, 27 rRNAs, and 86 tRNAs. Genomic analysis revealed that 29% of the genes are directly involved in plant growth, while 70% of the genes are indirectly involved. In addition, 12 putative biosynthetic gene clusters were identified, responsible for the synthesis of secondary metabolites, such as non-ribosomal peptides, lanthipeptides, polyketides, siderophores, and terpenes. These findings provide a scientific basis for the development of efficient antimicrobial agents and the construction of biopesticide production platforms in chassis cells.

Strategies and tools to construct stable and efficient artificial coculture systems as biosynthetic platforms for biomass conversion

Inspired by the natural symbiotic relationships between diverse microbial members, researchers recently focused on modifying microbial chassis to create artificial coculture systems using synthetic biology tools. An increasing number of scientists are now exploring these systems as innovative biosynthetic platforms for biomass conversion. While significant advancements have been achieved, challenges remain in maintaining the stability and productivity of these systems. Sustaining an optimal population ratio over a long time period and balancing anabolism and catabolism during cultivation have proven difficult. Key issues, such as competitive or antagonistic relationships between microbial members, as well as metabolic imbalances and maladaptation, are critical factors affecting the stability and productivity of artificial coculture systems. In this article, we critically review current strategies and methods for improving the stability and productivity of these systems, with a focus on recent progress in biomass conversion. We also provide insights into future research directions, laying the groundwork for further development of artificial coculture biosynthetic platforms.

Assembly strategies for microbe-material hybrid systems in solar energy conversion

Microbe-material hybrid systems which facilitate the solar-driven synthesis of high-value chemicals, harness the unique capabilities of microbes, maintaining the high-selectivity catalytic abilities, while concurrently incorporating exogenous materials to confer novel functionalities. The effective assembly of both components is essential for the overall functionality of microbe-material hybrid systems. Herein, we conducted a critical review of microbe-material hybrid systems for solar energy conversion focusing on the perspective of interface assembly strategies between microbes and materials, which are categorized into five types: cell uptake, intracellular synthesis, extracellular mineralization, electrostatic adsorption, and cell encapsulation. Moreover, this review elucidates the mechanisms by which microbe-material hybrid systems convert elementary substrates, such as carbon dioxide, nitrogen, and water, into high-value chemicals or materials for energy generation.

Regulating Bacterial Culture through Tailored Silk Inverse Opal Scaffolds

Controlling the growth of microbial consortia is of great significance in the biomedical field. Selective bacterial growth is achieved by fabricating silk inverse opal (SIO) scaffolds with varying pore sizes ranging from 0.3 to 4.5 µm. Pore size significantly influences the growth dynamics of bacteria in both single and mixed-strain cultures. Specially, the SIO-4.5 µm scaffold is observed to be more favorable for cultivating S. aureus, whereas the SIO-0.3 µm scaffold is more suitable for cultivating E. coli and P. aeruginosa. By adjusting the secondary conformation of silk fibroin, the stiffness of the SIO substrate will be altered, which results in the increase of bacteria on the SIO by 16 times compared with that on the silk fibroin film. Manipulating the pore size allows for the adjustment of the S. aureus to P. aeruginosa ratio from 0.8 to 9.3, highlighting the potential of this approach in regulating bacterial culture.

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.

Ultrasound-visible engineered bacteria for tumor chemo-immunotherapy

Our previous work developed acoustic response bacteria, which enable the precise tuning of transgene expression through ultrasound. However, it is still difficult to visualize these bacteria in order to guide the sound wave to precisely irradiate them. Here, we develop ultrasound-visible engineered bacteria and chemically modify them with doxorubicin (DOX) on their surfaces. These engineered bacteria (Ec@DIG-GVs) can produce gas vesicles (GVs), providing a real-time imaging guide for remote hyperthermia high-intensity focused ultrasound (hHIFU) to induce the expression of the interferon (IFN)-γ gene. The production of IFN-γ can kill tumor cells, induce macrophage polarization from the M2 to the M1 phenotype, and promote the maturation of dendritic cells. DOX can be released in the acidic tumor microenvironment, resulting in immunogenic cell death of tumor cells. The concurrent effects of IFN-γ and DOX activate a tumor-specific T cell response, producing the synergistic anti-tumor efficacy. Our study provides a promising strategy for bacteria-mediated tumor chemo-immunotherapy.

Engineering functional materials through bacteria-assisted living grafting

Functionalizing materials with biomacromolecules such as enzymes has broad applications in biotechnology and biomedicine. Here, we introduce a grafting method mediated by living cells to functionalize materials. We use polymeric scaffolds to trap engineered bacteria and micron-sized particles with chemical groups serving as active sites for grafting. The bacteria synthesize the desired protein for grafting and autonomously lyse to release it. The released functional moieties are locally grafted onto the active sites, generating the materials engineered by living grafting (MELGs). MELGs are resilient to perturbations because of both the bonding and the regeneration of functional domains synthesized by living cells. The programmability of the bacteria enables us to fabricate MELGs that can respond to external input, decompose a pollutant, reconstitute synthetic pathways for natural product synthesis, and purify mismatched DNA. Our work establishes a bacteria-assisted grafting strategy to functionalize materials with a broad range of biological activities in an integrated, flexible, and modular manner. A record of this paper's transparent peer review process is included in the supplemental information.

Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes

The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.

Deciphering the potential role of quorum quenching in efficient aerobic denitrification driven by a synthetic microbial community

Low efficiency is one of the main challenges for the application of aerobic denitrification technology in wastewater treatment. To improve denitrification efficiency, a synthetic microbial community (SMC) composed of denitrifiers Acinetobacter baumannii N1 (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas hydrophila (AH) were constructed. The nitrate (NO3--N) reduction efficiency of the SMC reached 97 % with little nitrite (NO2--N) accumulation, compared to the single-culture systems and co-culture systems. In the SMC, AH proved to mainly contribute to NO3--N reduction with the assistance of AC, while PA exerted NO2--N reduction. AC and AH secreted N-hexanoyl-DL-homoserine lactone (C6-HSL) to promote the electron transfer from the quinone pool to nitrate reductase. The declined N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL), resulting from quorum quenching (QQ) by AH, stimulated the excretion of pyocyanin, which could improve the electron transfer from complex III to downstream denitrifying enzymes for NO2--N reduction. In addition, C6-HSL mainly secreted by PA led to the up-regulation of TCA cycle-related genes and provided sufficient energy (such as NADH and ATP) for aerobic denitrification. In conclusion, members of the SMC achieved efficient denitrification through the interactions between QQ, electron transfer, and energy metabolism induced by N-acyl-homoserine lactones (AHLs). This study provided a theoretical basis for the engineering application of synthetic microbiome to remove nitrate wastewater.

Self-lysis microbial consortia for predictable multi-proteins assembly

The scope of bioengineering is expanding from the design of single strain to the microbial communities, allowing for the division-of-labor in synthesizing the multi-protein systems. Predicting the composition of the final product during the biomanufacturing process, however, can be difficult. Consortia-based manufacturing has the potential to boost production efficiency, but this benefit primarily holds in the upstream. The current format of downstream process heavily relies on the centralized facility, and is not economical and flexible to address the demands in small-scale. Here, we present a concise and manageable platform to enable the multi-protein system assembly. We engineer a self-lysis microbial consortium, where each strain lyses autonomously at high densities and produces a single protein component. The product fraction can be precisely tuned by varying the inoculation ratio. Utilizing this platform, we assemble a classical 34-component PURE (protein synthesis using recombinant elements) system. We have further optimized the downstream process of the biomanufacturing by incorporating the porous structure of polymeric materials. The encapsulated autolysis consortium can produce and release the proteins while maintaining the cell factories enclosed in the materials by exporting the multi-protein system for collection. Our research provides a novel approach to the flexible and controllable production of multi-protein systems, opening up new possibilities for pathway assembly and portable biomanufacturing.

Microbiome-functionality in anaerobic digesters: A critical review

Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.

Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature

Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.

Customized spatial niches for synthetic microbial consortia

The construction of synthetic microbial consortia has been considered a new frontier. However, maintaining artificial microbial communities remains challenging because the dominant strain eventually outcompetes the others. Inspired by natural ecosystems, one promising approach to assemble stable consortia is to construct spatial niches partitioning subpopulations and overlapping abiotic requirements.

Synthetic phylogenetically diverse communities promote denitrification and stability

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.

A Synthetic Signaling Network Imitating the Action of Immune Cells in Response to Bacterial Metabolism

State-of-the-art bottom-up synthetic biology allows to replicate many basic biological functions in artificial-cell-like devices. To mimic more complex behaviors, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here, a sophisticated biological response is considered, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. A consortium consisting of two synthetic agents is designed-responsive DNA-based particles and antibiotic-loaded lipid vesicles-whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilization and exposure to antibiotics. The results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.

Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal

The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.

A Microbial Community Cultured in Gradient Hydrogel for Investigating Gut Microbiome-Drug Interaction and Guiding Therapeutic Decisions

Despite the recognition that the gut microbiota acts a clinically significant role in cancer chemotherapy, both mechanistic understanding and translational research are still limited. Maximizing drug efficacy requires an in-depth understanding of how the microbiota contributes to therapeutic responses, while microbiota modulation is hindered by the complexity of the human body. To address this issue, a 3D experimental model named engineered microbiota (EM) is reported for bridging microbiota-drug interaction research and therapeutic decision-making. EM can be manipulated in vitro and faithfully recapitulate the human gut microbiota at the genus/species level while allowing co-culture with cells, organoids, and isolated tissues for testing drug responses. Examination of various clinical and experimental drugs by EM reveales that the gut microbiota affects drug efficacy through three pathways: immunological effects, bioaccumulation, and drug metabolism. Guided by discovered mechanisms, custom-tailored strategies are adopted to maximize the therapeutic efficacy of drugs on orthotopic tumor models with patient-derived gut microbiota. These strategies include immune synergy, nanoparticle encapsulation, and host-guest complex formation, respectively. Given the important role of the gut microbiota in influencing drug efficacy, EM will likely become an indispensable tool to guide drug translation and clinical decision-making.

Spontaneously established syntrophic yeast communities improve bioproduction

Nutritional codependence (syntrophy) has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not result in cooperative growth. Here we employ high-throughput phenotypic screening to systematically test pairwise combinations of auxotrophic Saccharomyces cerevisiae deletion mutants. Although most coculture pairs do not enter syntrophic growth, we identify 49 pairs that spontaneously form syntrophic, synergistic communities. We characterized the stability and growth dynamics of nine cocultures and demonstrated that a pair of tryptophan auxotrophs grow by exchanging a pathway intermediate rather than end products. We then introduced a malonic semialdehyde biosynthesis pathway split between different pairs of auxotrophs, which resulted in increased production. Our results report the spontaneous formation of stable syntrophy in S. cerevisiae auxotrophs and illustrate the biotechnological potential of dividing labor in a cooperating intraspecies community.

A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast

Secondary natural products (NPs) are a rich source for drug discovery. However, the low abundance of NPs makes their extraction from nature inefficient, while chemical synthesis is challenging and unsustainable. Saccharomyces cerevisiae and Pichia pastoris are excellent manufacturing systems for the production of NPs. This Perspective discusses a comprehensive platform for sustainable production of NPs in the two yeasts through system-associated optimization at four levels: genetics, temporal controllers, productivity screening, and scalability. Additionally, it is pointed out critical metabolic building blocks in NP bioengineering can be identified through connecting multilevel data of the optimized system using deep learning.

Research progress of bio-slurry remediation technology for organic contaminated soil

Bio-slurry remediation technology, as a controllable bioremediation method, has the significant advantage of high remediation efficiency and can effectively solve the problems of high energy consumption and secondary pollution of traditional organic pollution site remediation technology. To further promote the application of this technology in the remediation of organically polluted soil, this paper summarizes the importance and advantages of bio-slurry remediation technology compared with traditional soil remediation technologies (physical, chemical, and biological). It introduces the technical infrastructure and its technological processes. Then, various factors that may affect its remediation performance are discussed. By analyzing the applications of this technology to the remediation of typical organic pollutant-(polycyclic aromatic hydrocarbons(PAHs), polychlorinated biphenyls(PCBs), total petroleum hydrocarbons(TPH), and pesticide) contaminated sites, the following key features of this remediation technology are summarised: (1) the technology has a wide range of applications and can be used in a versatile way in the remediation projects of various types of organic-contaminated soil sites such as in clay, sand, and high organic matter content soil; (2) the technology is highly controllable. Adjusting environmental parameters and operational conditions, such as nutrients, organic carbon sources (bio-stimulation), inoculants (bio-augmentation), water-to-soil ratio, etc., can control the remediation process, thus improving the restoration performance. To sum up, this bio-slurry remediation technology is an efficient, controllable and green soil remediation technology that has broad application prospects.

Engineered Living Materials For Sustainability

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

Engineering living materials by synthetic biology

Natural biological materials are programmed by genetic information and able to self-organize, respond to environmental stimulus, and couple with inorganic matter. Inspired by the natural system and to mimic their complex and delicate fabrication process and functions, the field of engineered living materials emerges at the interface of synthetic biology and materials science. Here, we review the recent efforts and discuss the challenges and future opportunities.

Cyanobacteria as cell factories for the photosynthetic production of sucrose

Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.

On-demand biomanufacturing through synthetic biology approach

Biopharmaceuticals including protein therapeutics, engineered protein-based vaccines and monoclonal antibodies, are currently the mainstay products of the biotechnology industry. However, the need for specialized equipment and refrigeration during production and distribution poses challenges for the delivery of these technologies to the field and low-resource area. With the development of synthetic biology, multiple studies rewire the cell-free system or living cells to impact the portable, on-site and on-demand manufacturing of biomolecules. Here, we review these efforts and suggest future directions.

A Highly Compatible Phototrophic Community for Carbon-Negative Biosynthesis

CO₂ sequestration engineering is promising for carbon-negative biosynthesis, and artificial communities can solve more complex problems than monocultures. However, obtaining an ideal photosynthetic community is still a great challenge. Herein, we describe the development of a highly compatible photosynthetic community (HCPC) by integrating a sucrose-producing CO₂ sequestration module and a super-coupled module. The cyanobacteria CO₂ sequestration module was obtained using stepwise metabolic engineering and then coupled with the efficient sucrose utilization module Vibrio natriegens. Integrated omics analysis indicated that enhanced photosynthetic electron transport and extracellular vesicles promote intercellular communication. Additionally, the HCPC was used to channel CO₂ into valuable chemicals, enabling the overall release of -22.27 to -606.59 kgCO₂ e kg^-1 in the end products. This novel light-driven community could facilitate circular economic implementation in the future.

Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors

Genetically engineered (GE) bacteria were utilized for developing functional systems upon confinement within a restricted space. Use of natural soft hydrogel such as alginate, gelatin, and agarose, have been investigated as promising approaches to design functional architectures. Nevertheless, a challenge is to develop functional microenvironments that support biofilm-like confinement in a relevant three-dimensional (3D) format for long-term studies. We demonstrate a natural soft hydrogel bioactuator based on alginate core-shell structures (0.25-2 mm core and 50-300 μm shell thickness) that enables 3D microbial colonization upon confinement with high cell density. Specially, our study evaluates the efficiency of bacteria-functional system by recapitulating various GE bacteria which can produce common reporter proteins, to demonstrate their actuator functions as well as dynamic pair-wise interactions. The structural design of the hydrogel can endure continued growth of various bacteria colonies within the confined space for over 10 days. The total amount of cellular biomass upon hydrogel-shell confinement was increased 5-fold compared to conventional techniques without hydrogel-shell. Furthermore, the enzymatic activity increased 3.8-fold and bioluminescence signal by 8-fold compared to the responses from conventional hydrogel systems. The conceptualized platform and our workflow represent a reliable strategy with core-shell structures to develop artificial hydrogel habitats as bacteria-based functional systems for bioactuation.