Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes

Autofluorescence for the Visualization of Microorganisms in Biodeteriorated Materials in the Context of Cultural Heritage

Microorganisms, including fungi, bacteria, cyanobacteria, and algae, frequently colonize the surfaces of cultural heritage materials. These biological agents can cause biodeterioration through various mechanisms, resulting in aesthetic alteration, physical disruption, or compromise of mechanical integrity. To assess the presence and diversity of microorganisms, a combination of microscopy techniques is commonly used in conjunction with results from both culture-dependent and culture-independent methods. However, microbial populations are often underestimated. To address this issue, microorganisms can be detected by their intrinsic fluorescence, which can be observed via fluorescence microscopy. This approach facilitates the mapping of the spatial arrangement of microorganisms and the understanding of colonization patterns, thereby complementing established imaging techniques and providing insight into the interactions of microbial communities with the substrate. Given the limited research in this area, we examine the potential of microorganism autofluorescence as a molecular tool for investigating biodeterioration in artistic and architectural heritage, with a particular focus on paper and stone materials. Identifying and understanding the diverse microbiota that may be present is crucial for developing tailored and effective preventive measures and conservation treatments, as some of the species discovered may pose significant risks to both artifacts and human health.

Microbial electrosynthesis: opportunities for microbial pure cultures

Microbial electrosynthesis (MES) is an emerging technology that couples renewable electricity to microbial production processes. Although advances in MES performance have been driven largely by microbial mixed cultures, we see a great limitation in the diversity, and hence value, of products that can be achieved in undefined mixed cultures. By contrast, metabolic control of pure cultures and genetic engineering could greatly expand the scope of MES, and even of broader electrobiotechnology, to include targeted high-value products. To leverage this potential, we advocate for more efforts and activities to develop engineered electroactive microbes for synthesis, and we highlight the need for a standardized electrobioreactor infrastructure that allows the establishment and engineering of electrobioprocesses with these novel biocatalysts.

The repertoire and levels of secondary metabolites in microbial cocultures depend on the inoculation ratio: a case study involving Aspergillus terreus and Streptomyces rimosus

OBJECTIVE

The aim of this study was to determine the influence of the inoculation volume ratio on the production of secondary metabolites in submerged cocultures of Aspergillus terreus and Streptomyces rimosus.

RESULTS

The shake flask cocultures were initiated by using 23 inoculum variants that included different volumes of A. terreus and S. rimosus precultures. In addition, the axenic controls were propagated in parallel with the cocultures. UPLC‒MS analysis revealed the presence of 15 secondary metabolites, 12 of which were found both in the "A. terreus vs. S. rimosus" cocultures and axenic cultures of either A. terreus or S. rimosus. The production of the remaining 3 molecules was recorded solely in the cocultures. The repertoire and quantity of secondary metabolites were evidently dependent on the inoculation ratio. It was also noted that detecting filamentous structures resembling typical morphological forms of a given species was insufficient to predict the presence of a given metabolite.

CONCLUSIONS

The modification of the inoculation ratio is an effective strategy for awakening and enhancing the production of secondary metabolites that are not biosynthesized under axenic conditions.

Synthetic microbial ecology: engineering habitats for modular consortia

Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems

The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.

Mixed culture biotechnology and its versatility in dark fermentative hydrogen production

Over the years, extensive research has gone into fermentative hydrogen production using pure and mixed cultures from waste biomass with promising results. However, for up-scaling of hydrogen production mixed cultures are more appropriate to overcome the operational difficulties such as a metabolic shift in response to environmental stress, and the need for a sterile environment. Mixed culture biotechnology (MCB) is a robust and stable alternative with efficient waste and wastewater treatment capacity along with co-generation of biohydrogen and platform chemicals. Mixed culture being a diverse group of bacteria with complex metabolic functions would offer a better response to the environmental variations encountered during biohydrogen production. The development of defined mixed cultures with desired functions would help to understand the microbial community dynamics and the keystone species for improved hydrogen production. This review aims to offer an overview of the application of MCB for biohydrogen production.

Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans

Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.

Synthetic biology tools for environmental protection

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.

Effects of the Coculture Initiation Method on the Production of Secondary Metabolites in Bioreactor Cocultures of Penicillium rubens and Streptomyces rimosus

Bioreactor cocultures involving Penicillium rubens and Streptomyces rimosus were investigated with regard to secondary metabolite production, morphological development, dissolved oxygen levels, and carbon substrate utilization. The production profiles of 22 secondary metabolites were analyzed, including penicillin G and oxytetracycline. Three inoculation approaches were tested, i.e., the simultaneous inoculation of P. rubens with S. rimosus and the inoculation of S. rimosus delayed by 24 or 48 h relative to P. rubens. The delayed inoculation of S. rimosus into the P. rubens culture did not prevent the actinomycete from proliferating and displaying its biosynthetic repertoire. Although a period of prolonged adaptation was needed, S. rimosus exhibited growth and the production of secondary metabolites regardless of the chosen delay period (24 or 48 h). This promising method of coculture initiation resulted in increased levels of metabolites tentatively identified as rimocidin B, 2-methylthio-cis-zeatin, chrysogine, benzylpenicilloic acid, and preaustinoid D relative to the values recorded for the monocultures. This study demonstrates the usefulness of the delayed inoculation approach in uncovering the metabolic landscape of filamentous microorganisms and altering the levels of secondary metabolites.

Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea

Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.

Biomaterial approaches for engineering and analyzing structure and metabolic states of microbial consortia within biofilms

Microbial consortia within biofilms are frequently found in structured organization in nature and are thought to bear great potential for productive biotechnological applications, such as the degradation of complex substrates, biosensing, or the production of chemical compounds. However, in-depth understanding of their organizational principles, as well as comprehensive design criteria of structured microbial consortia for industrial applications are still limited. It is hypothesized that biomaterial engineering of such consortia within scaffolds can advance the field by providing defined in vitro mimics of naturally occurring and industrially applicable biofilms. Such systems will allow for adjustment of important microenvironmental parameters and in-depth analysis with high temporal and spatial resolution. In this review, we provide the background of biomaterial engineering of structured biofilm consortia, show approaches for their design, and demonstrate tools to analyze their metabolic state.

Fermentation performance of oleaginous yeasts on Eucommia ulmoides Oliver hydrolysate: Impacts of the mixed strains fermentation

This present study mainly focused on the investigation and optimization of the fermentation performance of oleaginous yeasts on Eucommia ulmoides Oliver hydrolysate (EUOH), which contains abundant and diverse sugars. More importantly, the impacts of the mixed strains fermentation compared with the single strain fermentation were analyzed and evaluated, through systematic investigations of substrate metabolism, cell growth, polysaccharide and lipid production, COD and ammonia-nitrogen removals. It was found that the mixed strains fermentation could effectively promote a more comprehensive and thorough utilization of the various sugars in EUOH, greatly improve COD removal effect, biomass and yeast polysaccharide production, but could not significantly improve the overall lipid content and ammonia nitrogen removal effect. In this study, when the two strains with the highest lipid content (i.e. L. starkeyi and R. toruloides) were mixed-cultured, the maximum lipid yield of 3.82 g/L was achieved, and the yeast polysaccharide yield, COD and ammonia-nitrogen removal rates of the fermentation (LS+RT) were 1.64 g/L, 67.4% and 74.9% respectively. When the strain with the highest polysaccharide content (i.e. R. toruloides) was mixed-cultured with the strains with strong growth activity (i.e. T. cutaneum and T. dermatis), a large amount of yeast polysaccharides could be obtained, which were 2.33 g/L (RT+TC) and 2.38 g/L (RT+TD) respectively. And the lipid yield, COD and ammonia-nitrogen removal rates of the fermentation (RT+TC), (RT+TD) were 3.09 g/L, 77.7%, 81.4% and 2.54 g/L, 74.9%, 80.4%, respectively.

Artificial microbial consortia for bioproduction processes

The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO2 through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.

Reliable online measurement of population dynamics for filamentous co-cultures

Understanding population dynamics is a key factor for optimizing co-culture processes to produce valuable compounds. However, the measurement of independent population dynamics is difficult, especially for filamentous organisms and in presence of insoluble substrates like cellulose. We propose a workflow for fluorescence-based online monitoring of individual population dynamics of two filamentous microorganisms. The fluorescent tagged target co-culture is composed of the cellulolytic fungus Trichoderma reesei RUT-C30-mCherry and the pigment-producing bacterium Streptomyces coelicolor A3(2)-mNeonGreen (mNG) growing on insoluble cellulose as a substrate. To validate the system, the fluorescence-to-biomass and fluorescence-to-scattered-light correlation of the two strains was characterized in depth under various conditions. Thereby, especially for complex filamentous microorganisms, microbial morphologies have to be considered. Another bias can arise from autofluorescence or pigments that can spectrally interfere with the fluorescence measurement. Green autofluorescence of both strains was uncoupled from different green fluorescent protein signals through a spectral unmixing approach, resulting in a specific signal only linked to the abundance of S. coelicolor A3(2)-mNG. As proof of principle, the population dynamics of the target co-culture were measured at varying inoculation ratios in presence of insoluble cellulose particles. Thereby, the respective fluorescence signals reliably described the abundance of each partner, according to the variations in the inocula. With this method, conditions can be fine-tuned for optimal growth of both partners along with natural product formation by the bacterium.

Tunable population dynamics in a synthetic filamentous coculture

Microbial cocultures are used as a tool to stimulate natural product biosynthesis. However, studies often empirically combine different organisms without a deeper understanding of the population dynamics. As filamentous organisms offer a vast metabolic diversity, we developed a model filamentous coculture of the cellulolytic fungus Trichoderma reesei RUT-C30 and the noncellulolytic bacterium Streptomyces coelicolor A3(2). The coculture was set up to use α-cellulose as a carbon source. This established a dependency of S. coelicolor on hydrolysate sugars released by T. reesei cellulases. To provide detailed insight into coculture dynamics, we applied high-throughput online monitoring of the respiration rate and fluorescence of the tagged strains. The respiration rate allowed us to distinguish the conditions of successful cellulase formation. Furthermore, to dissect the individual strain contributions, T. reesei and S. coelicolor were tagged with mCherry and mNeonGreen (mNG) fluorescence proteins, respectively. When evaluating varying inoculation ratios, it was observed that both partners outcompete the other when given a high inoculation advantage. Nonetheless, adequate proportions for simultaneous growth of both partners, cellulase, and pigment production could be determined. Finally, population dynamics were also tuned by modulating abiotic factors. Increased osmolality provided a growth advantage to S. coelicolor. In contrast, an increase in shaking frequency had a negative effect on S. coelicolor biomass formation, promoting T. reesei. This comprehensive analysis fills important knowledge gaps in the control of complex cocultures and accelerates the setup of other tailor-made coculture bioprocesses.

Production of secondary metabolites in stirred tank bioreactor co-cultures of Streptomyces noursei and Aspergillus terreus

The focus of the study was to characterize the bioprocess kinetics and secondary metabolites production in the novel microbial co-cultivation system involving Streptomyces noursei ATCC 11455 (the producer of an antifungal substance known as nystatin) and Aspergillus terreus ATCC 20542 (the source of lovastatin, a cholesterol-lowering drug). The investigated “A. terreus vs. S. noursei” stirred tank bioreactor co-cultures allowed for the concurrent development and observable biosynthetic activity of both species. In total, the production profiles of 50 secondary metabolites were monitored over the course of the study. The co-cultures were found to be effective in terms of enhancing the biosynthesis of several metabolic products, including mevinolinic acid, an acidic form of lovastatin. This work provided a methodological example of assessing the activity of a given strain in the co-culture by using the substrates which can be metabolized exclusively by this strain. Since S. noursei was shown to be incapable of lactose utilization, the observed changes in lactose levels were attributed to A. terreus and thus confirmed its viability. The study was complemented with the comparative microscopic observations of filamentous morphologies exhibited in the co-cultures and corresponding monocultures.

The potential of amoeba-based processes for natural product syntheses

The identification of novel platform organisms for the production and discovery of small molecules is of high interest for the pharmaceutical industry. In particular, the structural complexity of most natural products with therapeutic potential restricts an industrial production since chemical syntheses often require complex multistep routes. The amoeba Dictyostelium discoideum can be easily cultivated in bioreactors due to its planktonic growth behavior and contains numerous polyketide and terpene synthase genes with only a few compounds being already elucidated. Hence, the amoeba both bears a wealth of hidden natural products and allows for the development of new bioprocesses for existing pharmaceuticals. In this mini review, we present D. discoideum as a novel platform for the production of complex secondary metabolites and discuss its suitability for industrial processes. We also provide initial insights into future bioprocesses, both involving bacterial coculture setups and for the production of plant-based pharmaceuticals.

Advances in automated real-time flow cytometry for monitoring of bioreactor processes

Flow cytometry and its technological possibilities have greatly advanced in the past decade as analysis tool for single cell properties and population distributions of different cell types in bioreactors. Along the way, some solutions for automated real-time flow cytometry (ART-FCM) were developed for monitoring of bioreactor processes without operator interference over extended periods with variable sampling frequency. However, there is still great potential for ART-FCM to evolve and possibly become a standard application in bioprocess monitoring and process control. This review first addresses different components of an ART-FCM, including the sampling device, the sample-processing unit, the unit for sample delivery to the flow cytometer and the settings for measurement of pre-processed samples. Also, available algorithms are presented for automated data analysis of multi-parameter fluorescence datasets derived from ART-FCM experiments. Furthermore, challenges are discussed for integration of fluorescence-activated cell sorting into an ART-FCM setup for isolation and separation of interesting subpopulations that can be further characterized by for instance omics-methods. As the application of ART-FCM is especially of interest for bioreactor process monitoring, including investigation of population heterogeneity and automated process control, a summary of already existing setups for these purposes is given. Additionally, the general future potential of ART-FCM is addressed.

Bioprocess Control: Current Progress and Future Perspectives

Typical bioprocess comprises of different unit operations wherein a near optimal environment is required for cells to grow, divide, and synthesize the desired product. However, bioprocess control caters to unique challenges that arise due to non-linearity, variability, and complexity of biotech processes. This article presents a review of modern control strategies employed in bioprocessing. Conventional control strategies (open loop, closed loop) along with modern control schemes such as fuzzy logic, model predictive control, adaptive control and neural network-based control are illustrated, and their effectiveness is highlighted. Furthermore, it is elucidated that bioprocess control is more than just automation, and includes aspects such as system architecture, software applications, hardware, and interfaces, all of which are optimized and compiled as per demand. This needs to be accomplished while keeping process requirement, production cost, market value of product, regulatory constraints, and data acquisition requirements in our purview. This article aims to offer an overview of the current best practices in bioprocess control, monitoring, and automation.