Engineering biological systems toward a sustainable bioeconomy

Ammonia Production Using Bacteria and Yeast toward a Sustainable Society

Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.

The Emergence of Genome Editing—Innovation Network Dynamics of Academic Publications, Patents, and Business Activities

Transformative societal change can both be triggered and influenced by both macro-level political means and the emergence of technologies. Key enabling technologies and therein biotechnology hold the power to drive those changes forward, evolving from breakthrough academic discoveries into business activities. Due to its increasing empirical relevance, we picked genome editing as an example for an emerging technology and extracted publication, patent, and company data from the years 2000 to 2020. By drawing upon social network analysis, we identify major networks and clusters that are dominating the respective time and layer. Based on these networks, we draw vertical connections between scientific knowledge, patented technologies, and business activities to visualize the interlevel relationships between actors through technological development. Thereby, we identify network dynamics of the emergence of genome editing, the most important actors and clusters evolving, and its spread into different areas.

Sustainable Biological Ammonia Production towards a Carbon-Free Society

A sustainable society was proposed more than 50 years ago. However, it is yet to be realised. For example, the production of ammonia, an important chemical widely used in the agriculture, steel, chemical, textile, and pharmaceutical industries, still depends on fossil fuels. Recently, biological approaches to achieve sustainable ammonia production have been gaining attention. Moreover, unlike chemical methods, biological approaches have a lesser environmental impact because ammonia can be produced under mild conditions of normal temperature and pressure. Therefore, in previous studies, nitrogen fixation by nitrogenase, including enzymatic ammonia production using food waste, has been attempted. Additionally, the production of crops using nitrogen-fixing bacteria has been implemented in the industry as one of the most promising approaches to achieving a sustainable ammonia economy. Thus, in this review, we described previous studies on biological ammonia production and showed the prospects for realising a sustainable society.

Reuniting the Biogeochemistry of Algae for a Low-Carbon Circular Bioeconomy

Given their advantages of high photosynthetic efficiency and non-competition with land-based crops, algae, that are carbon-hungry and sunlight-driven microbial factories, are a promising solution to resolve energy crisis, food security, and pollution problems. The ability to recycle nutrient and CO₂ fixation from waste sources makes algae a valuable feedstock for biofuels, food and feeds, biochemicals, and biomaterials. Innovative technologies such as the bicarbonate-based integrated carbon capture and algae production system (BICCAPS), integrated algal bioenergy carbon capture and storage (BECCS), as well as ocean macroalgal afforestation (OMA), can be used to realize a low-carbon algal bioeconomy. We review how algae can be applied in the framework of integrated low-carbon circular bioeconomy models, focusing on sustainable biofuels, low-carbon feedstocks, carbon capture, and advances in algal biotechnology.

Improved ammonia production from soybean residues by cell surface-displayed l-amino acid oxidase on yeast

Ammonia is critical for agricultural and chemical industries. The extracellular production of ammonia by yeast (Saccharomyces cerevisiae) using cell surface engineering can be efficient approach because yeast can avoid growth deficiencies caused by knockout of genes for ammonia assimilation. In this study, we produced ammonia outside the yeast cells by displaying an l-amino acid oxidase with a wide substrate specificity derived from Hebeloma cylindrosporum (HcLAAO) on yeast cell surfaces. The HcLAAO-displaying yeast successfully produced 12.6 m m ammonia from a mixture of 20 proteinogenic amino acids (the theoretical conversion efficiency was 63%). We also succeeded in producing ammonia from a food processing waste, soybean residues (okara) derived from tofu production. The conversion efficiency was 88.1%, a higher yield than reported in previous studies. Our study demonstrates that ammonia production outside of yeast cells is a promising strategy to utilize food processing wastes.

Renewable Biomass Utilization: A Way Forward to Establish Sustainable Chemical and Processing Industries

Lignocellulosic biomass feedstocks are promising alternatives to fossil fuels for meeting raw material needs of processing industries and helping transit from a linear to a circular economy and thereby meet the global sustainability criteria. The sugar platform route in the biochemical conversion process is one of the promising and extensively studied methods, which consists of four major conversion steps: pretreatment, hydrolysis, fermentation, and product purification. Each of these conversion steps has multiple challenges. Among them, the challenges associated with the pretreatment are the most significant for the overall process because this is the most expensive step in the sugar platform route and it significantly affects the efficiency of all subsequent steps on the sustainable valorization of each biomass component. However, the development of a universal pretreatment method to cater to all types of feedstock is nearly impossible due to the substantial variations in compositions and structures of biopolymers among these feedstocks. In this review, we have discussed some promising pretreatment methods, their processing and chemicals requirements, and the effect of biomass composition on deconstruction efficiencies. In addition, the global biomass resources availability and process intensification ideas for the lignocellulosic-based chemical industry have been discussed from a circularity and sustainability standpoint.

Sustainable value chain management based on dynamic capabilities in small and medium-sized enterprises (SMEs)

Purpose

The aim of this research is to analyze sustainable value chain management based on dynamic capabilities in small and medium-sized enterprises (SMEs).

Design/methodology/approach

A qualitative methodology is used, through a multiple case study with three SMEs, to identify the conceptual relationship between the sustainable value chain and dynamic capabilities. Interviews are conducted with managers, and the data are analyzed through content analysis.

Findings

It is observed that breaking down barriers in processes is important for establishing the sustainable value chain, generating dynamic capabilities with the readaptation of activities.

Research limitations/implications

It is recommended that studies be conducted in other sectors and in large companies, to identify new perspectives.

Practical implications

The findings of this study demonstrate the constant processes of SMEs in response to legal, bureaucratic and logistical changes, in the generation of dynamic capabilities and sustainable value chain management, to achieve their customers' goals.

Social implications

The research contributes to the literature on the management of dynamic capabilities in the value chain in Brazilian companies and to the supply chain field, particularly in relation to SMEs.

Originality/value

This research analyzes sustainable value chain management based on dynamic capabilities in Brazilian SMEs, gathering the managers' perceptions regarding changes in the external environment that influence adaptations and alignments, impacting on their businesses.

The transition of Rhodobacter sphaeroides into a microbial cell factory

Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.

CRISPR with a Happy Ending: Non-Templated DNA Repair for Prokaryotic Genome Engineering

The exploration of microbial metabolism is expected to support the development of a sustainable economy and tackle several problems related to the burdens of human consumption. Microorganisms have the potential to catalyze processes that are currently unavailable, unsustainable and/or inefficient. Their metabolism can be optimized and further expanded using tools like the clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) systems. These tools have revolutionized the field of biotechnology, as they greatly streamline the genetic engineering of organisms from all domains of life. CRISPR-Cas and other nucleases mediate double-strand DNA breaks, which must be repaired to prevent cell death. In prokaryotes, these breaks can be repaired through either homologous recombination, when a DNA repair template is available, or through template-independent end joining, of which two major pathways are known. These end joining pathways depend on different sets of proteins and mediate DNA repair with different outcomes. Understanding these DNA repair pathways can be advantageous to steer the results of genome engineering experiments. In this review, we discuss different strategies for the genetic engineering of prokaryotes through either non-homologous end joining (NHEJ) or alternative end joining (AEJ), both of which are independent of exogenous DNA repair templates.

Construction of engineered yeast producing ammonia from glutamine and soybean residues (okara)

Ammonia is an essential substance for agriculture and the chemical industry. The intracellular production of ammonia in yeast (Saccharomyces cerevisiae) by metabolic engineering is difficult because yeast strongly assimilates ammonia, and the knockout of genes enabling this assimilation is lethal. Therefore, we attempted to produce ammonia outside the yeast cells by displaying a glutaminase (YbaS) from Escherichia coli on the yeast cell surface. YbaS-displaying yeast successfully produced 3.34 g/L ammonia from 32.6 g/L glutamine (83.2% conversion rate), providing it at a higher yield than in previous studies. Next, using YbaS-displaying yeast, we also succeeded in producing ammonia from glutamine in soybean residues (okara) produced as food waste from tofu production. Therefore, ammonia production outside cells by displaying ammonia-lyase on the cell surface is a promising strategy for producing ammonia from food waste as a novel energy resource, thereby preventing food loss.

Anticipating governance challenges in synthetic biology: Insights from biosynthetic menthol

This paper advances an anticipatory governance framework to investigate and prepare for the potential implications of an emerging technology. Within the growing domain of synthetic biology, we draw on an end-to-end assessment of biosynthetic menthol that incorporates consideration of multiple dimensions of production and use. Based on documentary analysis, available data, and interviews, our approach unfolds in three steps. First, we map the sociotechnical transition in menthol production, comparing existing agricultural and chemical production methods with new biosynthetic processes - or what we call the biological (bio) turn. Second, we explore the rationales, promises and expectations of menthol's bio-turn and explore the drivers of transition so as to clarify which goals and values innovation is addressing. Third, we reflect on the opportunities and challenges of such a transition to put forward an agenda for responsible innovation and anticipatory governance. The bio-turn in menthol is analysed through five responsible innovation dimensions: the potential distribution of benefits and burdens; social resilience; environmental sustainability; infrastructure and business models; and public perception and public interest. We consider the implications of our analysis both for the responsible development and application of synthetic biology for menthol and for the broader assessment and sociotechnical construction of emerging technologies.

A review on microbial lipids as a potential biofuel

Energy security, environmental concerns, and unstable oil prices have been the driving trifecta of demand for alternative fuels in the United States. The United States' dependence on energy resources, often from unstable oil-producing countries has created political insecurities and concerns. As we try to gain energy security, unconventional oil becomes more common, flooding the market, and causing the major downshift of the usual unstable oil prices. Meanwhile, consumption of fossil fuels and the consequent CO₂ emissions have driven disruptions in the Earth's atmosphere and are recognized to be responsible for global climate change. While the significance of each of these three factors may fluctuate with global politics or new technologies, transportation energy will remain the prominent focus of multi-disciplined research. Bioenergy future depends on the price of oil. Current energy policy of the United States heavily favors petroleum industry. In this review, the current trend in microbial lipids as a potential biofuel is discussed.

On-Site Production of Cellulolytic Enzymes by the Sequential Cultivation Method

The conversion of renewable lignocellulosic biomass into fuels, chemicals, and high-value materials using the biochemical platform has been considered the most sustainable alternative for the implementation of future biorefineries. However, the high cost of the cellulolytic enzymatic cocktails used in the saccharification step significantly affects the economics of industrial large-scale conversion processes. The on-site production of enzymes, integrated to the biorefinery plant, is being considered as a potential strategy that could be used to reduce costs. In such approach, the microbial production of enzymes can be carried out using the same lignocellulosic biomass as feedstock for fungal development and biofuels production. Most of the microbial cultivation processes for the production of industrial enzymes have been developed using the conventional submerged fermentation. Recently, a sequential solid-state followed by submerged fermentation has been described as a potential alternative cultivation method for cellulolytic enzymes production. This chapter presents the detailed procedure of the sequential cultivation method, which could be employed for the on-site production of the cellulolytic enzymes required to convert lignocellulosic biomass into simple sugars.

Alcohols enhance the rate of acetic acid diffusion in S. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance

Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. n-butanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes.

Corn bran bioprocessing: Development of an integrated process for microbial lipids production

This study investigated the potential of corn bran as a feedstock for microbial lipid production using oleaginous yeast, Trichosporon oleaginosus ATCC20509. Different conditions (solid loading of biomass, acid loading, and pretreatment duration) were applied to optimize pretreatment processes using the Box-Behnken design. The highest sugar yield of 0.53g/g was obtained from corn bran hydrolysates at a pretreatment condition of 5% solid loading and 1% acid loading for 30min. Compared with synthetic media, up to 50% higher lipid accumulations in T. oleaginosus were achieved using corn bran hydrolysates during fermentation. Also, the direct effect of pretreatment condition on the lipid accumulation of T. oleaginosus was investigated using response surface methodology (RSM). Solid loading of biomass during the pretreatment process significantly affected the fermentation process for lipid accumulation of T. oleaginosus. The RSM model can provide useful information to design an integrated bioconversion platform.

Engineering Saccharomyces cerevisiae fatty acid composition for increased tolerance to octanoic acid

Biorenewable chemicals such as short and medium chain fatty acids enable functional or direct substitution of petroleum-derived building blocks, allowing reduction of anthropogenic greenhouse gases while meeting market needs of high-demand products like aliphatic alcohols and alpha olefins. However, producing these fatty acids in microorganisms can be challenging due to toxicity issues. Octanoic acid (C8) can disrupt the integrity of the cell membrane in yeast, and exogenous supplementation of oleic acid has been shown to help alleviate this. We recently engineered the Saccharomyces cerevisiae enzyme acetyl-CoA carboxylase by replacing serine residue 1157 with alanine to prevent deactivation by phosphorylation. Expression of Acc1^S1157A in S. cerevisiae resulted in an increase in total fatty acid production, with the largest increase for oleic acid. In this study, we evaluated the effect of this modified lipid profile on C8 toxicity to the yeast. Expression of Acc1^S1157A in S. cerevisiae BY4741 increased the percentage of oleic acid 3.1- and 1.6-fold in the absence and presence of octanoic acid challenge, respectively. Following exposure to 0.9 mM of C8 for 24 h, the engineered yeast had a 10-fold higher cell density relative to the baseline strain. Moreover, overexpressing Acc1^S1157A allowed survival at C8 concentrations that were lethal for the baseline strain. This marked reduction of toxicity was shown to be due to higher membrane integrity as an 11-fold decrease in leakage of intracellular magnesium was observed. Due to the increase in oleic acid, this approach has the potential to reduce toxicity of other valuable bioproducts such as shorter chain aliphatic acids and alcohols and other membrane stressors. In an initial screen, increased resistance to n-butanol, 2-propanol, and hexanoic acid was demonstrated with cell densities 3.2-, 1.8-, and 29-fold higher than the baseline strain, respectively. Biotechnol. Bioeng. 2017;114: 1531-1538. © 2017 Wiley Periodicals, Inc.

Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803

Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc.