Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness

A megatransposon drives the adaptation of Thermoanaerobacter kivui to carbon monoxide

Acetogens are promising industrial biocatalysts for upgrading syngas, a gas mixture containing CO, H2 and CO2 into fuels and chemicals. However, CO severely inhibits growth of many acetogens, often requiring extensive adaptation to enable efficient CO conversion (carboxydotrophy). Here, we adapt the thermophilic acetogen Thermoanaerobacter kivui to use CO as sole carbon and energy source. Isolate CO-1 exhibits rapid growth on CO and syngas (co-utilizing CO, H2 and CO2) in batch and continuous cultures (µmax ~ 0.25 h-1). The carboxydotrophic phenotype is attributed to the mobilization of a CO-dependent megatransposon originating from the locus responsible for autotrophy in T. kivui. Transcriptomics reveal the crucial role the redox balance plays during carboxydotrophic growth. These insights are exploited to rationally engineer T. kivui to grow on CO. Collectively, our work elucidates a primary mechanism responsible for the acquisition of carboxydotrophy in acetogens and showcases how transposons can orchestrate evolution.

Deep-Sea Cold Seep Campylobacterota: Diversity, Growth, Metabolic Characteristics, and Nutrient Production

Deep-sea chemosynthetic ecosystems, including cold seeps and hydrothermal vents, are widely spread in global oceans. Campylobacterota are important primary producers in deep-sea hydrothermal vents and serve as a vital food source for local invertebrates. However, the nutrients that these bacteria can provide to their hosts are unclear. To date, research on Campylobacterota in cold seeps is very limited. Consequently, little is known about the biological features and ecological potential of Campylobacterota in cold seeps. In the present work, we examined the diversity, growth, metabolic characteristics, and nutrient production of Campylobacterota in a deep-sea cold seep. Over 1000 Campylobacterota ASVs, especially autotrophic Sulfurovum and Sulfurimonas, were identified. By optimizing the culture medium, 9 Sulfurovum and Sulfurimonas strains were isolated, including three potentially novel species. Two novel species were characterized and found to exhibit unique morphological features. These two novel strains possessed complete reverse tricarboxylic acid pathways. One novel strain, FCS5, was a psychrotolerant autotroph with denitrification and phosphorus-removing capacity. FCS5 could grow in the absence of vitamins. Consistently, metabolomics and transcriptome analyses indicated that FCS5 produced multiple vitamins, which regulated the expressions of a large number of genes associated with carbon fixation and multiple-nutrient synthesis. Besides vitamins, autotrophic Campylobacterota also produced abundant free amino acids, fatty acids (short-chain, medium, and long-chain), and proteins. This study indicates that the cold seep abounds with Campylobacterota, which are capable of providing various nutrients for the chemosynthetic ecosystem. In addition, these bacteria may have wide applications, such as in wastewater treatment and carbon emission reduction.

Adaptive laboratory evolution for improving acetogen gas fermentation

Gas fermentation using acetogens can help humankind transition from petroleum-based industries to more sustainable alternatives. Acetogens are a unique set of organisms that efficiently convert carbon oxide waste gases into chemicals, such as ethanol and acetate. While acetogens are already used in commercially operated bioprocess facilities, the field is still affected by challenging genetic manipulation workflows and a developing knowledge of acetogen metabolism. Adaptive laboratory evolution (ALE) can uniquely contribute here, through evolution of organisms guided by synthetically created niches, which delivers strains with industrially relevant phenotypes and helps to resolve genotype-phenotype relationships. Here, we review the expanding use of ALE for acetogens, showcasing results regarding fundamental understanding of acetogens and improvement of phenotypes - faster growth/substrate utilisation, elimination of media components, improving stress tolerance, and improving growth and robustness in bioreactor cultures. These works provide the field with opportunities to further engineer and manipulate acetogen traits for industrial bioprocesses and improve the understanding of genotype-phenotype relationships.

Transcriptome analysis and reverse engineering verification of SNZ3Val125Ile and Pho3Asn134Asp revealed the mechanism of adaptive laboratory evolution to increase the yield of tyrosol in Saccharomyces cerevisiae strain S26-AE2

BACKGROUND

Tyrosol is an important drug precursor, and Saccharomyces cerevisiae is one of the main microorganisms that produces tyrosol. Although excessive metabolic modification increases the production of tyrosol, it also causes a decrease in the growth rate of yeast. Therefore, this study attempted to restore the growth of S. cerevisiae through adaptive evolution and further improve tyrosol production.

RESULTS

After the adaptive laboratory evolution of S. cerevisiae S26, three evolutionary strains were obtained. The biomass of strain S26-AE2 reached 17.82 g DCW/L in the presence of 100 g/L glucose, which was 15.33% higher than that of S26, and its tyrosol production reached 817.83 mg/L. The transcriptome analysis revealed that, upon exposure to 100 g/L glucose, the S26-AE2 strain may reduce the transcriptional regulation of glucose repression through decreased HXK2 expression. The expression of genes related to pyruvate synthesis was increased in strain S26-AE2. Meanwhile, the expression levels of most tricarboxylic acid cycle-related genes in S26-AE2 were increased when cultured with 20 g/L glucose. Furthermore, the amount of tyrosol produced by strain S26 with the SNZ3Val125Ile mutation increased by 17.01% compared with that of the control strain S26 following exposure to 100 g/L glucose.

CONCLUSIONS

In this study, a strain, S26-AE2, with good growth and tyrosol production performance was obtained by adaptive evolution. The transcriptome analysis revealed that the differences in the expression of genes involved in metabolic pathways in adaptive evolutionary strains may be related to yeast growth and tyrosol production. Further reverse engineering verified that the mutation of SNZ3 promoted tyrosol synthesis in S. cerevisiae in glucose-rich medium. This study provides a theoretical basis for the metabolic engineering of S. cerevisiae to synthesise tyrosol and its derivatives.

Metabolic Versatility of acetogens in syngas Fermentation: Responding to varying CO availability

Syngas fermentation using acetogenic bacteria offers a promising route for sustainable chemical production. However, gas-liquid mass transfer limitations and efficient co-utilization of CO and H2 pose significant challenges. This study investigated the kinetics of syngas conversion to acetate by Acetobacterium wieringae and Clostridium species in batch conditions under varying initial CO partial pressures (19 - 110 kPa). A. wieringae strains, exhibited superior growth in all gas compositions, with a maximum growth rate of 0.104 h-1. The distinct CO, H2, and CO2 consumption patterns revealed metabolic flexibility and adaptation to varying syngas compositions. Notably, A. wieringae strains and C. autoethanogenum achieved complete CO and H2 conversion, with C. autoethanogenum also exhibiting net CO2 uptake. These findings provide valuable insights into the distinct metabolic capabilities of these acetogens and contribute to the development of efficient and sustainable syngas fermentation processes.

Directed Evolution of Microbial Communities in Fermented Foods: Strategies, Mechanisms, and Challenges

Directed Evolution of Microbial Communities (DEMC) offers a promising approach to enhance the functional attributes of microbial consortia in fermented foods by mimicking natural selection processes. This review details the application of DEMC in fermented foods, focusing on optimizing community traits to improve both fermentation efficiency and the sensory quality of the final products. We outline the core techniques used in DEMC, including the strategic construction of initial microbial communities, the systematic introduction of stress factors to induce desirable traits, and the use of artificial selection to cultivate superior communities. Additionally, we explore the integration of genomic tools and dynamic community analysis to understand and guide the evolutionary trajectories of these communities. While DEMC shows substantial potential for refining fermented food products, it faces challenges such as maintaining genetic diversity and functional stability of the communities. Looking ahead, the integration of advanced omics technologies and computational modeling is anticipated to significantly enhance the predictability and control of microbial community evolution in food fermentation processes. By systematically improving the selection and management of microbial traits, DEMC serves as a crucial tool for enhancing the quality and consistency of fermented foods, directly contributing to more robust and efficient food production systems.

Understanding microbial syngas fermentation rates

Syngas fermentation to ethanol has reached industrial production. Further improvement of this process would be aided by quantitative understanding of the influence of imposed reaction conditions on the fermentation performance. That requires a reliable model of the microbial kinetics. Data were collected from 37 steady states in chemostats and from many batch experiments that use Clostridium authoethanogenum. Biomass-specific rates from CO conversion experiments were related to each other according to simple reaction stoichiometries and the Pirt equation, with only the ratio of ethanol to acetate production remaining as degree of freedom. No clear dependency of this ratio on dissolved concentrations, such as CO or acetic acid concentration, was found. This is largely caused by the lack of knowledge about the dependency of the CO uptake rate (and hence all other rates) on the CO concentration. This knowledge gap is caused by a lack of dissolved CO measurements. For dissolved H2, a similar gap applies. Modelling H2 consumption adds more degrees of freedom to the system, so that more structured experiments with H2 is needed. The inhibition of gas consumption by acetate and ethanol is partly known but needs further study. KEY POINTS: • Set of Clostridium autoethanogenum syngas fermentation data from chemostats. • Unstructured kinetic models can relate most biomass-specific rates to dilution rates. • Lack of dissolved gas measurements limits deeper understanding.

Quantitative physiology and biomass composition of Cyberlindnera jadinii in ethanol-grown cultures

BACKGROUND

Elimination of greenhouse gas emissions in industrial biotechnology requires replacement of carbohydrates by alternative carbon substrates, produced from CO2 and waste streams. Ethanol is already industrially produced from agricultural residues and waste gas and is miscible with water, self-sterilizing and energy-dense. The yeast C. jadinii can grow on ethanol and has a history in the production of single-cell protein (SCP) for feed and food applications. To address a knowledge gap in quantitative physiology of C. jadinii during growth on ethanol, this study investigates growth kinetics, growth energetics, nutritional requirements, and biomass composition of C. jadinii strains in batch, chemostat and fed-batch cultures.

RESULTS

In aerobic, ethanol-limited chemostat cultures, C. jadinii CBS 621 exhibited a maximum biomass yield on ethanol ( Y X / S max ) of 0.83 gbiomass (gethanol)-1 and an estimated maintenance requirement for ATP (mATP) of 2.7 mmolATP (gbiomass)-1 h-1. Even at specific growth rates below 0.05 h-1, a stable protein content of approximately 0.54 gprotein (gbiomass)-1 was observed. At low specific growth rates, up to 17% of the proteome consisted of alcohol dehydrogenase proteins, followed by aldehyde dehydrogenases and acetyl-CoA synthetase. Of 13 C. jadinii strains evaluated, 11 displayed fast growth on ethanol (μmax > 0.4 h-1) in mineral medium without vitamins, and CBS 621 was found to be a thiamine auxotroph. The prototrophic strain C. jadinii CBS 5947 was grown on an inorganic salts medium in fed-batch cultures (10-L scale) fed with pure ethanol. Biomass concentrations in these cultures increased up to 100 gbiomass (kgbroth)-1, with a biomass yield of 0.65 gbiomass (gethanol)-1. Model-based simulation, based on quantitative parameters determined in chemostat cultures, adequately predicted biomass production. A different protein content of chemostat- and fed-batch-grown biomass (54 and 42%, respectively) may reflect the more dynamic conditions in fed-batch cultures.

CONCLUSIONS

Analysis of ethanol-grown batch, chemostat and fed-batch cultures provided a quantitative physiology baseline for fundamental and applied research on C. jadinii. Its high maximum growth rate, high energetic efficiency of ethanol dissimilation, simple nutritional requirements and high protein content, make C. jadinii a highly interesting platform for production of SCP and other products from ethanol.