Consolidated bioprocessing of lignocellulosic biomass to lactic acid by a synthetic fungal-bacterial consortium

Advances and prospects for lactic acid production from lignocellulose

Lactic acid is a versatile building block that can be produced via microbial fermentation. Owing to the high optical purity, approximately 90 % of lactic acid is produced by microbes. Recently, the biosynthesis of lactic acid from lignocellulose has concerned much attentions. However, the cost-effective process faces several obstacles because of the complex structure of lignocellulose. This review will comprehensively summarize the state-of-the-art lactic acid production from lignocellulose, including the commonly used lactate-producing microorganisms, the co-utilization of glucose and xylose for the lactic acid production, as well as the lactic acid production from lignocellulose hydrolysate. Furthermore, the strategies regarding the lignocellulosic lactic acid production via consolidated bioprocessing will be also discussed, which can greatly reduce the complexity of the fermentation process.

Bioleaching of rare earth elements from ores and waste materials: Current status, economic viability and future prospects

Rare earth elements (REEs) are critical components of numerous products widely used in many areas, and the demand for REEs is increasing dramatically in recent years. Physical-chemical leaching is commonly adopted for the recovery of REEs from ores and solid wastes, but concerns over the generation of hazards, operation safety, and environmental pollution have urged the transition to greener and more sustainable leaching methods. Bioleaching is considered an excellent alternative for the recovery of REEs. This review provided an overview on the REEs recovery from primary and secondary resources via different bioleaching strategies. The techno-economics of bioleaching for REEs recovery were highlighted, and key factors affecting the economic viability of bioleaching were identified. Finally, strategies including the utilization of low-cost substrates as feedstocks, non-sterile bioleaching, recycling and reutilization of biolixiviants, and development of robust bioleaching strains were proposed to improve the economic competitiveness of bioleaching. It is expected that this review could serve as a useful guideline on the design of more economically competitive bioleaching processes for the recovery REEs from different resources.

Value-added biotransformation of agricultural byproducts by cellulolytic fungi: a review

Agricultural byproducts generally contain abundant bioactive compounds (e.g., cellulose/hemicellulose, phenolic compounds (PCs), and dietary fibers (DFs)), but most of them are neglected and underutilized. Owing to the complicated and rigid structures of agricultural byproducts, a considerable amount of bioactive compounds are entrapped in the polymer matrix, impeding their further development and utilization. In recent years, the prominent performance of cellulolytic fungi to grow and degrade agricultural byproducts has been applied to achieve efficient biotransformation of byproducts to high-value compounds, which is a green and sustainable strategy for the reutilization of agricultural byproducts. This review comprehensively summarizes recent progress in the value-added biotransformation of agricultural byproducts by cellulolytic fungi, including (1) direct utilization of agricultural byproducts for biochemicals and bioethanol production via a consolidated bioprocessing, (2) recovery and biotransformation of bounded PCs from agricultural byproducts for higher bioactive properties, as well as (3) modification and conversion of insoluble DF from agricultural byproducts to produce functional soluble DF. The functional enzymes, potential mechanisms, and metabolic pathways involved are emphasized. Moreover, promising advantages and current bottlenecks using cellulolytic fungi have also been elucidated, shedding further perspectives for sustainable and efficient reutilization of agricultural byproducts by cellulolytic fungi.

Exploring industrial lignocellulosic waste: Sources, types, and potential as high-value molecules

Lignocellulosic biomass has a promising role in a circular bioeconomy and may be used to produce valuable molecules for green chemistry. Lignocellulosic biomass, such as food waste, agricultural waste, wood, paper or cardboard, corresponded to 15.7% of all waste produced in Europe in 2020, and has a high potential as a secondary raw material for industrial processes. This review first presents industrial lignocellulosic waste sources, in terms of their composition, quantities and types of lignocellulosic residues. Secondly, the possible high added-value chemicals obtained from transformation of lignocellulosic waste are detailed, as well as their potential for applications in the food industry, biomedical, energy or chemistry sectors, including as sources of polyphenols, enzymes, bioplastic precursors or biofuels. In a third part, various available transformation treatments, such as physical treatments with ultrasound or heat, chemical treatments with acids or bases, and biological treatments with enzymes or microorganisms, are presented. The last part discusses the perspectives of the use of lignocellulosic waste and the fact that decreasing the cost of transformation is one of the major issues for improving the use of lignocellulosic biomass in a circular economy and green chemistry approach, since it is currently often more expensive than petroleum-based counterparts.

Microbial biofilms as a platform for diverse biocatalytic applications

Microbial biofilms have gained significant traction in commercial wastewater treatment due to their inherent resilience, well-organized structure, and potential for collaborative metabolic processes. As our understanding of their physiology deepens, these living catalysts are finding exciting applications beyond wastewater treatment, including the production of bulk and fine chemicals, bioelectricity generation, and enzyme immobilization. While the biological applications of biofilms in different biocatalytic systems have been extensively summarized, the applications of artificially engineered biofilms were rarely discussed. This review aims to bridge this gap by highlighting the untapped potential of engineered microbial biofilms in diverse biocatalytic applications, with a focus on strategies for biofilms engineering. Strategies for engineering biofilm-based systems will be explored, including genetic modification, synthetic biology approaches, and targeted manipulation of biofilm formation processes. Finally, the review will address key challenges and future directions in developing robust biofilm-based biocatalytic platforms for large-scale production of chemicals, pharmaceuticals, and biofuels.

CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Replacing petrochemicals with compounds from bio-based manufacturing processes remains an important part of the global effort to move towards a sustainable future. However, achieving economic viability requires both optimized cell factories and innovative processes. Here, we address this challenge by developing a fermentation platform, which enables two concurrent fermentations in one bioreactor. We first construct a xylitol producing Escherichia coli strain in which CRISPRi-mediated gene silencing is used to switch the metabolism from aerobic to anaerobic, even when the bacteria are under oxic conditions. The switch also decouples growth from production, which further increases the yield. The strain produces acetate as a byproduct, which is subsequently metabolized under oxic conditions by a secondary E. coli strain. Through constraint-based metabolic modelling this strain is designed to co-valorize glucose and the excreted acetate to a secondary product. This unique syntrophic consortium concept facilitates the implementation of "two fermentations in one go", where the concurrent fermentation displays similar titers and productivities as compared to two separate single strain fermentations.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

Strategies to enhance production of metabolites in microbial co-culture systems

Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.

Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia

Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.

Research advances on the consolidated bioprocessing of lignocellulosic biomass

Lignocellulosic biomass is an abundant and renewable bioresource for the production of biofuels and biochemical products. The classical biorefinery process for lignocellulosic degradation and conversion comprises three stages, i.e., pretreatment, enzymatic saccharification, and fermentation. However, the complicated pretreatment process, high cost of cellulase production, and insufficient production performance of fermentation strains have restricted the industrialization of biorefinery. Consolidated bioprocessing (CBP) technology combines the process of enzyme production, enzymatic saccharification, and fermentation in a single bioreactor using a specific microorganism or a consortium of microbes and represents another approach worth exploring for the production of chemicals from lignocellulosic biomass. The present review summarizes the progress made in research of CBP technology for lignocellulosic biomass conversion. In this review, different CBP strategies in lignocellulose biorefinery are reviewed, including CBP with natural lignocellulose-degrading microorganisms as the chassis, CBP with biosynthetic microorganisms as the chassis, and CBP with microbial co-culturing systems. This review provides new perspectives and insights on the utilization of low-cost feedstock lignocellulosic biomass for production of biochemicals.

Enhanced production of lactic acid from pretreated rice straw using co-cultivation of Bacillus licheniformis and Bacillus sonorenesis

Lactic acid (LA) production from sugar mixture derived from lignocellulosic rice straw employing co- culture system of thermotolerant and inhibitor tolerant Bacillus licheniformis DGB and Bacillus sonorenesis DGS15 was carried out. In minimal media, both the strains of Bacillus DGB and DGS15 worked together by efficiently utilising glucose and xylose respectively. Response Surface Methodology (RSM) was used for optimisation of pretreatment of rice straw to achieve maximum yield of 50.852 g/L total reducing sugar (TRS) from 100 gm of rice straw biomass. Pretreatment of rice straw resulted in its delignification, as confirmed by FTIR spectroscopy, since the peak at 1668 cm-1 disappeared due to removal of lignin and scanning electron microscopy (SEM) revealed disruption in structural and morphological features. Crystallinity index (CrI) of treated rice straw increased by 15.54% in comparison to native biomass. DGB and DGS15 individually yielded 0.64 g/g and 0.82 g/g lactic acid respectively, where as their co-cultivation led to effective utilisation of both glucose and xylose within 15 h (70%) and complete utilisation in 48 h, producing 49.75 g/L LA with a yield of 0.98 g/g and productivity of 1.036 g/L/h, and resulting in reduction in fermentation time. Separate hydrolysis of rice straw and co-fermentation (SHCF) of hydrolysates by Bacillus spp. enhanced the production of lactic acid, can circumvent challenges in biorefining of lignocellulosic biomass.

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Aim: Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Methods: Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. Results: SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. Conclusion: A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

Evaluation of ruminal methane and ammonia formation and microbiota composition as affected by supplements based on mixtures of tannins and essential oils using Rusitec

BACKGROUND

Dietary supplements based on tannin extracts or essential oil compounds (EOC) have been repeatedly reported as a promising feeding strategy to reduce the environmental impact of ruminant husbandry. A previous batch culture screening of various supplements identified selected mixtures with an enhanced potential to mitigate ruminal methane and ammonia formation. Among these, Q-2 (named after quebracho extract and EOC blend 2, composed of carvacrol, thymol, and eugenol) and C-10 (chestnut extract and EOC blend 10, consisting of oregano and thyme essential oils and limonene) have been investigated in detail in the present study with the semi-continuous rumen simulation technique (Rusitec) in three independent runs. For this purpose, Q-2 and C-10, dosed according to the previous study, were compared with a non-supplemented diet (negative control, NC) and with one supplemented with the commercial EOC-based Agolin® Ruminant (positive control, PC).

RESULTS

From d 5 to 10 of fermentation incubation liquid was collected and analysed for pH, ammonia, protozoa count, and gas composition. Feed residues were collected for the determination of ruminal degradability. On d 10, samples of incubation liquid were also characterised for bacterial, archaeal and fungal communities by high-throughput sequencing of 16S rRNA and 26S ribosomal large subunit gene amplicons. Regardless of the duration of the fermentation period, Q-2 and C-10 were similarly efficient as PC in mitigating either ammonia (-37% by Q-2, -34% by PC) or methane formation (-12% by C-10, -12% by PC). The PC was also responsible for lower feed degradability and bacterial and fungal richness, whereas Q-2 and C-10 effects, particularly on microbiome diversities, were limited compared to NC.

CONCLUSIONS

All additives showed the potential to mitigate methane or ammonia formation, or both, in vitro over a period of 10 d. However, several differences occurred between PC and Q-2/C-10, indicating different mechanisms of action. The pronounced defaunation caused by PC and its suggested consequences apparently determined at least part of the mitigant effects. Although the depressive effect on NDF degradability caused by Q-2 and C-10 might partially explain their mitigation properties, their mechanisms of action remain mostly to be elucidated.

Sustainable management and valorization of biomass wastes using synthetic microbial consortia

In response to the persistent expansion of global resource demands, considerable attention has been directed toward the synthetic microbial consortia (SMC) within the domain of microbial engineering, aiming to address the sustainable management and valorization of biomass wastes. This comprehensive review systematically encapsulates the most recent advancements in research and technological applications concerning the utilization of SMC for biomass waste treatment. The construction strategies of SMC are briefly outlined, and the diverse applications of SMC in biomass wastes treatment are explored, with particular emphasis on its potential advantages in waste degradation, hazardous substances control, and high value-added products conversion. Finally, recommendations for the future development of SMC technology are proposed, and prospects for its sustainable application are discussed.

Energy and nutrient recovery from municipal and industrial waste and wastewater-a perspective

This publication highlights the latest advancements in the field of energy and nutrient recovery from organics rich municipal and industrial waste and wastewater. Energy and carbon rich waste streams are multifaceted, including municipal solid waste, industrial waste, agricultural by-products and residues, beached or residual seaweed biomass from post-harvest processing, and food waste, and are valuable resources to overcome current limitations with sustainable feedstock supply chains for biorefining approaches. The emphasis will be on the most recent scientific progress in the area, including the development of new and innovative technologies, such as microbial processes and the role of biofilms for the degradation of organic pollutants in wastewater, as well as the production of biofuels and value-added products from organic waste and wastewater streams. The carboxylate platform, which employs microbiomes to produce mixed carboxylic acids through methane-arrested anaerobic digestion, is the focus as a new conversion technology. Nutrient recycling from conventional waste streams such as wastewater and digestate, and the energetic valorization of such streams will also be discussed. The selected technologies significantly contribute to advanced waste and wastewater treatment and support the recovery and utilization of carboxylic acids as the basis to produce many useful and valuable products, including food and feed preservatives, human and animal health supplements, solvents, plasticizers, lubricants, and even biofuels such as sustainable aviation fuel.

ONE-SENTENCE SUMMARY

Multifaceted waste streams as the basis for resource recovery are essential to achieve environmental sustainability in a circular economy, and require the development of next-generation waste treatment technologies leveraging a highly adaptive mixed microbial community approach to produce new biochemicals, biomaterials, and biofuels from carbon-rich organic waste streams.

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted.

ONE-SENTENCE SUMMARY

This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

Engineered co-culture for consolidated production of phenylpropanoids directly from aromatic-rich biomass

Consolidated bioprocesses for the in situ hydrolysis and conversion of biomass feedstocks into value-added products offers great potential for both process and cost reduction. However, to date few consolidated bioprocesses have been developed that target aromatic rich feedstock fractions. Reported here is the development of synthetic co-cultivation for the consolidated hydrolysis and valorisation of corncob hydroxycinnamic acids. Biomass hydrolysis was achieved via a secretion module developed in B. subtilis using a genetically encoded biosensor-actuator to secrete hydrolytic enzymes. Conversion was achieved via a biotransformation module developed in E. coli using a suite of plug-and-play encoded enzymes to convert the released hydroxycinnamic acids into high-value phenylpropanoid target compounds. Finally, employing cellulolytic pre-treatment, extractive fermentation and in situ product recovery multiple aromatic products, coniferol and chavicol, were isolated from the same process in high purity.

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.

Construction of stable microbial consortia for effective biochemical synthesis

Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.

Microbial co-cultures for biochemicals production from lignocellulosic biomass: A review

Global reliance on fossil oil should shift to cleaner alternatives to get a decarbonized society. One option to achieve this ambitious goal is the use of biochemicals produced from lignocellulosic biomass (LCB). The inherent low biodegradability of LCB and the inhibitory compounds that might be released during pretreatment are two main challenges for LCB valorization. At microbiological level, constraints are mostly linked to the need for axenic cultures and the preference for certain carbon sources (i.e., glucose). To cope with these issues, this review focuses on efficient LCB conversion via the sugar platform as well as an innovative carboxylate platform taking advantage of the co-cultivation of microorganisms. This review discusses novel trends in the use of microbial communities and co-cultures aiming at different bioproducts co-generation in single reactors as well as in sequential bioprocess combination. The outlook and further perspectives of these alternatives have been outlined for future successful development.

Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors

Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.

Microbial tolerance engineering for boosting lactic acid production from lignocellulose

Lignocellulosic biomass is an attractive non-food feedstock for lactic acid production via microbial conversion due to its abundance and low-price, which can alleviate the conflict with food supplies. However, a variety of inhibitors derived from the biomass pretreatment processes repress microbial growth, decrease feedstock conversion efficiency and increase lactic acid production costs. Microbial tolerance engineering strategies accelerate the conversion of carbohydrates by improving microbial tolerance to toxic inhibitors using pretreated lignocellulose hydrolysate as a feedstock. This review presents the recent significant progress in microbial tolerance engineering to develop robust microbial cell factories with inhibitor tolerance and their application for cellulosic lactic acid production. Moreover, microbial tolerance engineering crosslinking other efficient breeding tools and novel approaches are also deeply discussed, aiming to providing a practical guide for economically viable production of cellulosic lactic acid.

Toward optimal use of biomass as carbon source for chemical bioproduction

Biomass is widely identified as a promising, renewable replacement for fossil feedstocks in the production of energy, fuels, and chemicals. However, the sustainable supply of biomass is limited. Economic and ecological criteria support prioritization of biomass as a carbon source for organic chemicals; however, utilization for energy currently dominates. Therefore, to optimize the use of available biomass feedstock, biorefining development must focus on high carbon efficiencies and enabling the conversion of all biomass fractions, including lignin and fermentation-derived CO₂. Additionally, novel technological platforms should allow the incorporation of nontraditional, currently underutilized carbon feedstocks (e.g. manure) into biorefining processes. To this end, funneling of waste feedstocks to a single product (e.g. methane) and subsequent conversion to chemicals is a promising approach.

Fungal–Lactobacteria Consortia and Enzymatic Catalysis for Polylactic Acid Production

Polylactic acid (PLA) is the main biobased plastic manufactured on an industrial scale. This polymer is synthetized by chemical methods, and there is a strong demand for the implementation of clean technologies. This work focuses on the microbial fermentation of agro-industrial waste rich in starch for the production of lactic acid (LA) in a consolidated bioprocess, followed by the enzymatic synthesis of PLA. Lactic acid bacteria (LAB) and the fungus Rhizopus oryzae were evaluated as natural LA producers in pure cultures or in fungal–lactobacteria co-cultures formed by an LAB and a fungus selected for its metabolic capacity to degrade starch and to form consortia with LAB. Microbial interaction was analyzed by scanning electron microscopy and biofilm production was quantified. The results show that the fungus Talaromyces amestolkiae and Lactiplantibacillus plantarum M9MG6-B2 establish a cooperative relationship to exploit the sugars from polysaccharides provided as carbon sources. Addition of the quorum sensing molecule dodecanol induced LA metabolism of the consortium and resulted in improved cooperation, producing 99% of the maximum theoretical yield of LA production from glucose and 65% from starch. Finally, l-PLA oligomers (up to 19-LA units) and polymers (greater than 5 kDa) were synthetized by LA polycondensation and enzymatic ring-opening polymerization catalyzed by the non-commercial lipase OPEr, naturally produced by the fungus Ophiostoma piceae.

Enhancement of Biomass Conservation and Bioethanol Production of Sweet Sorghum Silage by Constructing Synergistic Microbial Consortia

The efficient storage of materials before bioethanol production could be key to improving pretreatment protocol and facilitating biodegradation, in turn improving the cost-effectiveness of biomass utilization. Biological inoculants were investigated for their effects on ensiling performance, biodegradability of silage materials, and final bioethanol yield from sweet sorghum. Two cellulolytic microbial consortia (CF and PY) were used to inoculate silages of sweet sorghum, with and without combined lactic acid bacteria (Xa), for up to 60 days of ensiling. We found that the consortia notably decreased pH and ammonia nitrogen content while increasing lactic acid/acetic acid ratios. The microbes also functioned in synergy with Xa, significantly reducing lignocellulose content and improving biomass preservation. First-order exponential decay models captured the kinetics of nonstructural carbohydrates and suggested high water-soluble carbohydrate (grams per kilogram dry matter [DM]) preservation potential in PY-Xa (33.48), followed by CF-Xa (30.51). Combined addition efficiently improved enzymatic hydrolysis and enhanced bioethanol yield, and sweet sorghum treated with PY-Xa had the highest ethanol yield (28.42 g L-1). Thus, combined bioaugmentation of synergistic microbes provides an effective method of improving biomass preservation and bioethanol production from sweet sorghum silages. IMPORTANCE Ensiling is an effective storage approach to ensure stable year-round supply for downstream biofuel production; it offers combined facilities of storage and pretreatment. There are challenges in ensiling sweet sorghum due to its coarse structure and high fiber content. This study provides a meaningful evaluation of the effects of adding microbial consortia, with and without lactic acid bacteria, on changes in key properties of sweet sorghum. This study highlighted the bioaugmented ensiling using cellulolytic synergistic microbes to outline a cost-effective strategy to store and pretreat sweet sorghum for bioethanol production.

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.

Construction of microbial consortia for microbial degradation of complex compounds

Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use

Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.

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.

Opportunities in the microbial valorization of sugar industrial organic waste to biodegradable smart food packaging materials

Many petroleum-derived plastics, including food packaging materials are non-biodegradable and designed for single-use applications. Annually, around 175 Mt. of plastic enters the land and ocean ecosystems due to mismanagement and lack of techno economically feasible plastic waste recycling technologies. Renewable sourced, biodegradable polymer-based food packaging materials can reduce this environmental pollution. Sugar production from sugarcane or sugar beet generates organic waste streams that contain fermentable substrates, including sugars, acids, and aromatics. Microbial metabolism can be leveraged to funnel those molecules to platform chemicals or biopolymers to generate biodegradable food packaging materials that have active or sensing molecules embedded in biopolymer matrices. The smart package can real-time monitor food quality, assure health safety, and provide economic and environmental benefits. Active packaging materials display functional properties such as antimicrobial, antioxidant, and light or gas barrier. This article provides an overview of potential biodegradable smart/active polymer packages for food applications by valorizing sugar industry-generated organic waste. We highlight the potential microbial pathways and metabolic engineering strategies to biofunnel the waste carbon efficiently into the targeted platform chemicals such as lactic, succinate, muconate, and biopolymers, including polyhydroxyalkanoates, and bacterial cellulose. The obtained platform chemicals can be used to produce biodegradable polymers such as poly (butylene adipate-co-terephthalate) (PBAT) that could replace incumbent polyethylene and polypropylene food packaging materials. When nanomaterials are added, these polymers can be active/smart. The process can remarkably lower the greenhouse gas emission and energy used to produce food-packaging material via sugar industrial waste carbon relative to the petroleum-based production. The proposed green routes enable the valorization of sugar processing organic waste into biodegradable materials and enable the circular economy.

Consolidated bioprocessing of lignocellulosic biomass: Technological advances and challenges

Consolidated bioprocessing (CBP) is characterized by a single-step production of value-added compounds directly from biomass in a single vessel. This strategy has the capacity to revolutionize the whole biorefinery concept as it can significantly reduce the infrastructure input and use of chemicals for various processing steps which can make it economically and environmentally benign. Although the proof of concept has been firmly established in the past, commercialization has been limited due to the low conversion efficiency of the technology. Either a native single microbe, genetically modified microbe or a consortium can be employed. The major challenge in developing a cost-effective and feasible CBP process is the recognition of bifunctional catalysts combining the capability to use the substrates and transform them into value-added products with high efficiency. This article presents an in-depth analysis of the current developments in CBP around the globe and the possibilities of advancements in the future.

Direct conversion of cellulose to L-lactic acid by a novel thermophilic Caldicellulosiruptor strain

Background

Consolidated bioprocessing (CBP) of lignocellulosic biomass to l-lactic acid using thermophilic cellulolytic/hemicellulolytic bacteria provides a promising solution for efficient lignocellulose conversion without the need for additional cellulolytic/hemicellulolytic enzymes. Most studies on the mesophilic and thermophilic CBP of lignocellulose to lactic acid concentrate on cultivation of non-cellulolytic mesophilic and thermophilic bacteria at temperatures of 30–55 °C with external addition of cellulases/hemicellulases for saccharification of substrates.

Results

l-Lactic acid was generated by fermenting microcrystalline cellulose or lignocellulosic substrates with a novel thermophilic anaerobic bacterium Caldicellulosiruptor sp. DIB 104C without adding externally produced cellulolytic/hemicellulolytic enzymes. Selection of this novel bacterium strain for lactic acid production is described as well as the adaptive evolution towards increasing the l-lactic acid concentration from 6 to 70 g/l on microcrystalline cellulose. The evolved strains grown on microcrystalline cellulose show a maximum lactic acid production rate of 1.0 g/l*h and a lactic acid ratio in the total organic fermentation products of 96 wt%. The enantiomeric purity of the l-lactic acid generated is 99.4%. In addition, the lactic acid production by these strains on several other types of cellulose and lignocellulosic feedstocks is also reported.

Conclusions

The evolved strains originating from Caldicellulosiruptor sp. DIB 104C were capable of producing unexpectedly large amounts of l-lactic acid from microcrystalline cellulose in fermenters. These strains produce l-lactic acid also from lignocellulosic feedstocks and thus represent an ideal starting point for development of a highly integrated commercial l-lactic acid production process from such feedstocks.

Fermentative Lactic Acid Production From Lignocellulosic Feedstocks: From Source to Purified Product

The second (lignocellulosic biomass and industrial wastes) and third (algal biomass) generation feedstocks gained substantial interest as a source of various value-added chemicals, produced by fermentation. Lactic acid is a valuable platform chemical with both traditional and newer applications in many industries. The successful fractionation, separation, and hydrolysis of lignocellulosic biomass result in sugars' rich raw material for lactic acid fermentation. This review paper aims to summarize the investigations and progress in the last 5 years in lactic acid production from inexpensive and renewable resources. Different aspects are discussed-the type of raw materials, pretreatment and detoxification methods, lactic acid-producers (bacteria, fungi, and yeasts), use of genetically manipulated microorganisms, separation techniques, different approaches of process organization, as well as main challenges, and possible solutions for process optimization.

Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles

In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.

Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion

Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.

Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere

Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1–T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4–5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions

Anaerobic digestion is a promising method for energy recovery through conversion of organic waste to biogas and other industrial valuables. However, to tap the full potential of anaerobic digestion, deciphering the microbial metabolic pathway activities and their underlying bioenergetics is required. In addition, the behavior of organisms in consortia along with the analytical abilities to kinetically measure their metabolic interactions will allow rational optimization of the process. This review aims to explore the metabolic bottlenecks of the microbial communities adopting latest advances of profiling and ¹³C tracer-based analysis using state of the art analytical platforms (GC, GC-MS, LC-MS, NMR). The review summarizes the phases of anaerobic digestion, the role of microbial communities, key process parameters of significance, syntrophic microbial interactions and the bottlenecks that are critical for optimal bioenergetics and enhanced production of valuables. Considerations into the designing of efficient synthetic microbial communities as well as the latest advances in capturing their metabolic cross talk will be highlighted. The review further explores how the presence of additives and inhibiting factors affect the metabolic pathways. The critical insight into the reaction mechanism covered in this review may be helpful to optimize and upgrade the anaerobic digestion system.

Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans

BACKGROUND

Lignocellulosic biomass is an attractive and sustainable alternative to petroleum-based feedstock for the production of a range of biochemicals, and pretreatment is generally regarded as indispensable for its biorefinery. However, various inhibitors that severely hinder the growth and fermentation of microorganisms are inevitably produced during the pretreatment of lignocellulose. Presently, there are few reports on a single microorganism that can detoxify or tolerate toxic mixtures of pretreated lignocellulose hydrolysate while effectively transforming sugar components into valuable compounds. Alternatively, microbial coculture provides a simpler and more efficacious way to realize this goal by distributing metabolic functions among different specialized strains.

RESULTS

In this study, a novel synthetic microbial consortium, which is composed of a responsible for detoxification bacterium engineered Pseudomonas putida KT2440 and a lactic acid production specialist Bacillus coagulans NL01, was developed to directly produce lactic acid from highly toxic lignocellulosic hydrolysate. The engineered P. putida with deletion of the sugar metabolism pathway was unable to consume the major fermentable sugars of lignocellulosic hydrolysate but exhibited great tolerance to 10 g/L sodium acetate, 5 g/L levulinic acid, 10 mM furfural and HMF as well as 2 g/L monophenol compound. In addition, the engineered strain rapidly removed diverse inhibitors of real hydrolysate. The degradation rate of organic acids (acetate, levulinic acid) and the conversion rate of furan aldehyde were both 100%, and the removal rate of most monoaromatic compounds remained at approximately 90%. With detoxification using engineered P. putida for 24 h, the 30% (v/v) hydrolysate was fermented to 35.8 g/L lactic acid by B. coagulans with a lactic acid yield of 0.8 g/g total sugars. Compared with that of the single culture of B. coagulans without lactic acid production, the fermentation performance of microbial coculture was significantly improved.

CONCLUSIONS

The microbial coculture system constructed in this study demonstrated the strong potential of the process for the biosynthesis of valuable products from lignocellulosic hydrolysates containing high concentrations of complex inhibitors by specifically recruiting consortia of robust microorganisms with desirable characteristics and also provided a feasible and attractive method for the bioconversion of lignocellulosic biomass to other value-added biochemicals.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Challenges and Future Perspectives of Promising Biotechnologies for Lignocellulosic Biorefinery

Lignocellulose is a kind of renewable bioresource containing abundant polysaccharides, which can be used for biochemicals and biofuels production. However, the complex structure hinders the final efficiency of lignocellulosic biorefinery. This review comprehensively summarizes the hydrolases and typical microorganisms for lignocellulosic degradation. Moreover, the commonly used bioprocesses for lignocellulosic biorefinery are also discussed, including separated hydrolysis and fermentation, simultaneous saccharification and fermentation and consolidated bioprocessing. Among these methods, construction of microbial co-culturing systems via consolidated bioprocessing is regarded as a potential strategy to efficiently produce biochemicals and biofuels, providing theoretical direction for constructing efficient and stable biorefinery process system in the future.

Techno-economic assessment of bioethanol production from lignocellulose by consortium-based consolidated bioprocessing at industrial scale

Lignocellulose-based biofuels are of major importance to mitigate the impact of international traffic and transport on climate change while sustaining agricultural land for food supply. Highly integrated systems like consolidated bioprocessing (CBP), where enzyme production, enzymatic hydrolysis and fermentation of the released sugars are carried out in one reactor, offer the highest potential to save costs and to make lignocellulose-based biofuels economically competitive. The work described here showed that CBP based on a microbial consortium operated at full-scale (2,000 t/d) saves up to 27.5% of the total ethanol production costs compared to conventional ethanol production from lignocellulose in individual process steps. The cost savings are mainly achieved through lower CAPEX due to less apparatus requirements because of the integrated process, as well as through lower OPEX since no glucose is needed for enzyme production. A comparison with literature estimations of cost savings of CBP based on genetically modified microorganisms results in approximately the same range. As a result of a detailed sensitivity analysis, scale and yield were identified as the main cost-pushers from a process point of view, whereas the price level of the plant location has the highest impact on the investment conditions. In the EU, CBP yields enough margin for profitable production and the possibility to decentralize biomass valorization, whereas in the world's largest ethanol market, the U.S, profitable production of lignocellulosic ethanol can only be achieved by CBP combined with other cost saving techniques, such as utilization of cost-free waste feedstocks, since ethanol has undergone a considerable price slump.

Modelling microbial communities: Harnessing consortia for biotechnological applications

Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.

Life cycle and economic assessment of sugarcane bagasse valorization to lactic acid

In this work, detailed life cycle assessment (LCA) and techno-economic analysis (TEA) of a novel lactic acid (LA) production process from sugarcane bagasse is performed, with the objective of identifying process improvement opportunities. Moreover, this is first such study in the Indian context. Experimental data generated at the Vasantdada Sugar Institute (VSI) for upstream processes is combined with ASPEN Plus simulation of the downstream steps for a commercial plant producing 104 tonnes per day of LA. Equipment sizing is performed and costing is done using standard approaches. OpenLCA is used to develop the LCA model and Ecoinvent database is used to quantify life cycle impacts for 1 kg of LA. Different scenarios for the LA plant are studied. Results showed that the pretreatment stage was crucial from both economic and environmental perspectives. The total life cycle climate change impact for production of 1 kg of lactic acid was 4.62 kg CO₂ eq. The product cost of LA was USD 2.9/kg, and a payback time of 6 years was achieved at a selling price of USD 3.21/kg. Scenario analysis has revealed that lactic acid plant annexed to a sugar mill led to significant environmental and economic benefits. Sensitivity analysis has identified opportunities to reduce the life cycle climate change impact to 2.29 kg CO₂ eq. and product cost to USD 1.42/kg through reduced alkali consumption, higher solid loading, and reduced enzyme loading.

Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.