Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy

Rewiring the methanol assimilation pathway in the methylotrophic yeast Pichia pastoris for high-level production of erythritol

Methanol, which is non-food competing, abundant, inexpensive, and potentially renewable, serves as an ideal alternative feedstock for biomanufacturing. Although engineered methylotrophic yeasts have successfully achieved gram-scale production of C2 (acetyl-CoA), C3 (pyruvate), and C6 (fructose-6-phosphate) building blocks from methanol, the production of C4-based (i.e. erythrose-4-phosphate) chemicals remains unexplored. This study demonstrates high-level methanol-to-erythritol production by rewiring the methanol assimilation pathway of Pichia pastoris, achieved through trimming and strengthening the carbon rearrangement network (CRN). Notably, we introduced a bacterial ribulose monophosphate (RuMP) pathway in addition to the native xylulose monophosphate (XuMP) pathway of P. pastoris, creating a hybrid network that significantly improved erythritol production and reduced pentitol byproduct formation. Combining these strategies generated a high-producing recombinant strain, achieving titers up to 31.5 g/L in fermentor culture. This study validates the feasibility of engineering P. pastoris for the efficient conversion of methanol to valuable erythrose-4-phosphate (E4P)-based chemicals. The CRN rewiring strategies employed here offer a valuable reference for engineering methylotrophic cell factories for the production of a wide range of chemicals from methanol.

Bioproducts from renewable methanol: The paraformaldehyde approach

Green methanol as feedstock in biotech operations at large scales is receiving in-depth attention for the production of Single Cell Protein (SCP) and circular chemicals. Several decades ago, cheap fossil-derived methanol was seen as an attractive feedstock. Now, renewable rather than fossil-derived methanol is in focus since its utilization does not depend on fossil resources and importantly it does not compete with food sources. Despite decade-long efforts, the biotech approaches have not been successful in generating economically viable large-scale production based on methanol. This impressive negative track record is to be attributed to the relatively reduced chemical nature of methanol, which implies excessive oxygen demands during fermentations. Hence, for large-scale methanol fermentations, it is essential to minimize oxygen budgets to arrive at economically-viable production processes. In this short communication, a new approach is described in reducing the oxygen footprint by employing the less-reduced compound paraformaldehyde which, via standard procedures, can be obtained chemically from methanol. It is a water-insoluble polymer, which slowly releases formaldehyde at ambient temperatures depending on either pH or temperature. Three methylotrophic microbes were demonstrated to metabolize formaldehyde as chemically released from the non-toxic paraformaldehyde. Methylophilus methylotrophus kept the monomeric formaldehyde below the detection limit in a stirred-tank bioreactor during a 20-hour run on paraformaldehyde. Based on the current work, it is concluded that paraformaldehyde is a highly-suitable feedstock for producing either SCP or numerous circular chemicals as derived from renewable methanol.

Natural coagulants from chestnut shells: A sustainable approach for textile wastewater treatment

The textile industry contributes to 2-10% of global greenhouse gas emissions, water extraction, and biodiversity loss, consuming 93 billion cubic meters of water annually with low reuse rates. Coagulation/flocculation is commonly used for industrial wastewater treatment, typically using conventional coagulants. Recently, interest in natural alternatives, particularly tannin-based coagulants, has grown. Given Portugal's role as a major chestnut producer and textile exporter, this study developed chestnut shell-based coagulants for textile wastewater treatment. Ethanolamine (ETA) and diethanolamine (DEA) were tested in the Mannich reaction, but only ETA produced a coagulant with a positive zeta potential and higher charge density. Five coagulants (CE_1-CE_5) were synthesized using different ETA/tannin and formaldehyde (FA)/tannin ratios. Lower ETA concentrations (7.5 mol L-1) produced the coagulant with the highest charge density and zeta potential. Further testing of FA/tannin ratios (3.5, 6, and 7.5) showed that lower FA levels reduced color removal efficiency and increased toxicity. Comparing synthetic and real textile effluent performance, natural coagulants showed superior color removal, while FeCl3 was more effective for organic matter and nitrogen removal. All coagulants removed phosphorus, with CE_2 achieving nearly 70% removal. Toxicity tests revealed that only CE_5 inhibited V. fischeri bacteria by over 70%. Formaldehyde leaching into treated water was minimal (0.17-0.3 mg L-1), below WHO limits (2.6 mg L-1), but concentrations in sludge were higher, especially in CE_3 and Tanfloc. These findings highlight chestnut shells as a promising source for producing natural, effective coagulants.

Awakening of the RuMP cycle for partial methylotrophy in the thermophile Parageobacillus thermoglucosidasius

Given sustainability and scalability concerns of using sugar feedstocks for microbial bioproduction of bulk chemicals, widening the feedstock range for microbial cell factories is of high interest. Methanol is a one-carbon alcohol that stands out as an alternative feedstock for the bioproduction of chemicals, as it is electron-rich, water-miscible and can be produced from several renewable resources. Bioconversion of methanol into products under thermophilic conditions (>50 °C) could be highly advantageous for industrial biotechnology. Although progress is being made with natural, thermophilic methylotrophic microorganisms, they are not yet optimal for bioproduction and establishing alternative thermophilic methylotrophic bioproduction platforms can widen possibilities. Hence, we set out to implement methanol assimilation in the emerging thermophilic model organism Parageobacillus thermoglucosidasius. We engineered P. thermoglucosidasius to be strictly dependent for its growth on methanol assimilation via the core of the highly efficient ribulose monophosphate (RuMP) cycle, while co-assimilating ribose. Surprisingly, this did not require heterologous expression of RuMP enzymes. Instead, by laboratory evolution we awakened latent, native enzyme activities to form the core of the RuMP cycle. We obtained fast methylotrophic growth in which ∼17 % of biomass was strictly obtained from methanol. This work lays the foundation for developing a versatile thermophilic bioproduction platform based on renewable methanol.

Recent advances in enzymes active on lignin-derived aromatic compounds

Lignin is an attractive alternative to fossil fuels as a feedstock for the sustainable manufacture of chemicals. Emergent strategies for lignin valorization include tandem processes whereby thermochemical fractionation of the biomass yields a mixture of lignin-derived aromatic compounds (LDACs), which are then transformed into target compounds by a microbial cell factory. Identifying LDAC-degrading pathways is critical to optimize carbon yield from diverse depolymerization mixtures. Characterizing enzymes - especially those that catalyze the rate-limiting steps of O-demethylation, hydroxylation, and decarboxylation - informs and enables biocatalyst design. Rational, structure-based engineering of key enzymes, as well as untargeted, evolution-based approaches, further optimize biocatalysis. In this review we outline recent advances in these fields which are critical in developing biocatalysts to efficiently synthesize lignin-based bioproducts.

Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms

A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m2/d during the summer. The δ13C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.

Bringing carbon to life via one-carbon metabolism

One-carbon (C1) compounds found in greenhouse gases and industrial waste streams are underutilized carbon and energy sources. While various biological and chemical means exist for converting C1 substrates into multicarbon products, major challenges of C1 conversion lie in creating net value. Here, we review metabolic strategies to utilize carbon across oxidation states. Complications arise in biochemical C1-utilization approaches because of the need for cellular energy currency ATP. ATP supports cell maintenance and proliferation and drives thermodynamically challenging reactions by coupling them with ATP hydrolysis. Powering metabolism through substrate cofeeding and energy transduction from light and electricity improves ATP availability, relieves metabolic bottlenecks, and upcycles carbon. We present a bioenergetic, engineering, and technoeconomic outlook for bringing elements to life.

Effect of variation in temperature on malodor generation from different units of a wastewater treatment plant

This study investigates the effect of temperature variation on malodor generation across different units of a wastewater treatment plant (WWTP). The results demonstrate that higher temperatures exacerbated odor emission due to increased microbial activity with all the different units showing maximum odorous gas production at the highest temperatures used (35 °C and 45 °C) in this study. The maximum total odor activity value (OAV) of 353106 was obtained for anoxic and anaerobic unit at 45 °C. The variation in composition of odor-causing gases was also dependent on wastewater characteristics than temperature alone. Volatile reduced sulfur compounds, including hydrogen sulfide and methyl mercaptan, were dominant in most wastewater samples, while units with higher dissolved oxygen (DO) content, such as aeration and sedimentation units, exhibited elevated levels of phenol and dimethyl disulfide and reduced H2S concentration. Analysis of the liquid composition following incubations revealed presence of mainly aldehydes (> 75%) which are produced due to incomplete organic matter degradation, particularly at lower temperatures. Statistical analysis showed positive correlation between temperature and odor generation. DO had negative correlation with H2S (r =  - 0.78, - 0.93) along with total gas concentration and total OAV, but positively correlated with other gases, namely methyl mercaptan (r = 0.22, 0.97), dimethyl disulfide (r = 0.93, 0.98), phenol (r = 0.99, 0.97), and ammonia (r = 0.99, 0.98). Solids concentration and volatile solids to total solids (VS/TS) ratio had positive correlation with H2S, total gas concentration, and total OAV (r = 0.68, 0.54, and 0.90). These findings highlight the need for tailored odor management strategies based on temperature fluctuations and unit-specific conditions to optimize WWTP operations and reduce odor emissions effectively.

Converting Bacillus subtilis 168 to a Synthetic Methylotroph by Combinatorial Metabolic Regulation Strategies

Methanol, which can come from methane or carbon dioxide, is a valuable renewable one-carbon (C1) feedstock for the production of biofuels and food chemicals. A new method was developed to create a multienzyme complex by combining methanol dehydrogenase (Mdh), 3-hexulose-6-phosphate synthase (Hps), and 6-phospho-3-hexuloseisomerase (Phi) in equal parts using SpyTag/Catcher and DogTag/Catcher systems. This self-assembly of multiple enzymes improves the conversion of methanol to fructose-6-phosphate (F6P) and was used to engineer a synthetic methylotroph from B. subtilis 168 that could efficiently utilize methanol. Various metabolic regulations related to key carbon pathways were tested and integrated to boost methanol consumption in this engineered strain. The final strain, B. subtilis SM6, could consume 3.87 g/L of methanol, marking the highest level of coutilization with xylose to date. The strategies employed in this research optimized the distribution of metabolic flow for formaldehyde and xylose, offering valuable insights for future studies on synthetic methylotrophs.

A Patent Landscape on Methane Oxidizing Bacteria (MOB) or Methanotrophs

Methane-oxidizing bacteria (MOB) or methanotrophs are a category of bacteria that rely on methane as their primary carbon and energy source. Methane is the second most abundant greenhouse gas after carbon dioxide and is comparatively far more potent in trapping heat in the atmosphere. MOBs are important microorganisms in the global carbon cycle where they play a crucial role in the oxidation of methane. The present review provides a comprehensive patent landscape on technology development using MOB. The first patent in this technology domain was recorded in 1971, with a notable surge in activity observed in 2020. A detailed patent analysis revealed that the early inventions were mainly focused on the production of various metabolites and bioremediation using MOB. In the later years, patents were filed in the area of identification of various species of MOB and their large-scale production. From 2010 onwards, consistent patent filing was observed in the genetic engineering of MOB to enhance their methane oxidizing capacity. The United States and China have emerged as the global leaders in terms of patent filing in this technology space. Precigen Inc. and Exxon Research Engineering Co., US were the top patent assignees followed by the University of Tsinghua and Calysta Inc. The Highest number of patent applications have claimed metabolite production by using MOB followed by their use in bioremediation. Methylosinus has emerged as the predominant microorganism of choice for methane oxidation applications.

A Eukaryote-Featured Membrane Phospholipid Enhances Bacterial Formaldehyde Tolerance and Assimilation of One-Carbon Feedstocks

Efficient bioassimilation of one-carbon (C1) feedstocks is often hindered by the toxicity of C1 substrates and/or intermediates. We compared the toxicity of several common C1 substrates/intermediates and found that formaldehyde imposes the highest toxicity on the representative bacterium Escherichia coli. Besides causing chromosomal DNA and protein damage effects, here, we revealed that formaldehyde greatly impairs cell membranes. To this end, here, we sought to remodel the cell membrane of E. coli by introducing a non-native, eukaryote-featured membrane phospholipid composition, phosphatidylcholine (PC). This engineered E. coli strain exhibited significantly increased membrane integrity, resulting in enhanced formaldehyde tolerance. When applied to C1 assimilation, the PC-harboring E. coli consumed up to 4.7 g/L methanol, which is 23-fold higher than that of the control strain (0.2 g/L). In summary, the present study highlights the detrimental impact of formaldehyde-induced membrane damage and thus underscores the significance of membrane remodeling in enhancing formaldehyde tolerance and facilitating the assimilation of C1 substrates.

Identification and characterization of a novel formaldehyde dehydrogenase in Bacillus subtilis

Formaldehyde is a known toxic compound, and functional formaldehyde detoxification is crucial for the survival of all living cells. Such detoxification systems are of particular importance for methylotrophic microorganisms that rely on formaldehyde as a central metabolite in their one-carbon metabolism. Understanding formaldehyde dissimilation pathways in non-methylotrophic industrial microorganisms is necessary for ongoing research aiming at engineering methylotrophy into their metabolism (synthetic methylotrophy). There is a variety of formaldehyde dissimilation pathways across microorganisms, often based on the activity of formaldehyde dehydrogenases. In this study, we investigated the role of the yycR gene of Bacillus subtilis putatively encoding a novel, uncharacterized zinc-type alcohol dehydrogenase-like protein. We showed that the B. subtilis ΔyycR mutant displayed a reduced formaldehyde tolerance level and confirmed the enzymatic activity of recombinantly produced and purified YycR as formaldehyde dehydrogenase in vitro. Biochemical analyses demonstrated that YycR activity is optimal at 40°C, with the highest measured activity at pH 9.5, formaldehyde is the preferred substrate, and the kinetic constants are Km of 0.19 ± 0.05 mM and Vmax of 2.24 ± 0.05 nmol min-1. Altogether, we showed that YycR is a novel formaldehyde dehydrogenase with a role in formaldehyde detoxification in B. subtilis, providing valuable insights for future research on synthetic methylotrophy in this organism.

IMPORTANCE

Formaldehyde is a key metabolite in methanol assimilation for many methylotrophic microorganisms, and at the same time, it is toxic to all living cells, which means its intracellular concentrations must be tightly controlled. An in-depth understanding of methanol detoxification systems in industrially relevant microorganisms is a prerequisite for the introduction of methanol utilization pathways into their metabolism (synthetic methylotrophy). Bacillus subtilis, an industrial workhorse conventionally used for the production of enzymes, is known to possess two formaldehyde detoxification pathways. Here, we identify a novel formaldehyde dehydrogenase in this bacterium as a path towards creating innovative prospect strategies for strain engineering towards synthetic methylotrophy.

Fabrication and characterization of antibacterial nanofiber membranes modified with chitosan and imidazolidinyl urea for potential use in biological waste treatments

An ion exchange nanofiber membrane (AEA-COOH) was developed from polyacrylonitrile (PAN) nanofibers through chemical hydrolysis. It was further modified by grafting chitosan (CS) onto its surface, creating the AEA-COOH-CS membrane. Then, both membranes were covalently immobilized with imidazolidinyl urea (IU), resulting in AEA-COOH-IU and AEA-COOH-CS-IU membranes. This study analyzed their physical properties, antibacterial efficacy (AE), and reusability. Optimal conditions were identified: 50 kDa molecular weight of chitosan, pH 8 for IU modification, and 0.05 % IU concentration. The AEA-COOH-IU membrane achieved 96.15 % AE against Escherichia coli at an initial concentration of 2.0 × 107 CFU/mL, while the AEA-COOH-CS-IU membrane achieved 100 % AE. The AEA-COOH-CS-IU membrane maintained 95.04 % efficacy over 5 cycles, demonstrating superior durability. As a result, the AEA-COOH-CS-IU membrane has high potential for environmental applications such as water purification and wastewater treatment. Its robust antibacterial properties and reusability suggest a significant impact on ensuring cleaner water resources and prospective uses in the biomedical field, including medical device coatings and healthcare applications.

Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol

As methanol can be derived from either CO2 or methane, methanol economy can play an important role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain with a doubling time of 3.5 hours under optimal conditions, comparable or faster than native model methylotrophs Methylorubrum extorquens AM1 (Td~4hr) and Bacillus methanolicus at 37°C (Td~5hr). To accomplish this, we develop a bacterial artificial chromosome (BAC) with dynamic copy number variation (CNV) to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. We track the genome variations of 75 cultures along the evolution process by next-generation sequencing, and identified the features of the fast-growing strain. After stabilization, the final strain (SM8) grows to 20 g/L of cell mass within 77 hrs in a bioreactor. This study illustrates the potential of dynamic CNV as an evolution tool and synthetic methylotrophs as a platform for sustainable biotechnological applications.

The influence of urban environmental effects on the orchard soil microbial community structure and function: a case study in Zhejiang, China

The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture.

Exploring NAD+ metabolism and NNAT: Insights from structure, function, and computational modeling

Nicotinamide Adenine Dinucleotide (NAD+), a coenzyme, is ubiquitously distributed and serves crucial functions in diverse biological processes, encompassing redox reactions, energy metabolism, and cellular signalling. This review article explores the intricate realm of NAD + metabolism, with a particular emphasis on the complex relationship between its structure, function, and the pivotal enzyme, Nicotinate Nucleotide Adenylyltransferase (NNAT), also known as nicotinate mononucleotide adenylyltransferase (NaMNAT), in the process of its biosynthesis. Our findings indicate that NAD + biosynthesis in humans and bacteria occurs via the same de novo synthesis route and the pyridine ring salvage pathway. Maintaining NAD homeostasis in bacteria is imperative, as most bacterial species cannot get NAD+ from their surroundings. However, due to lower sequence identity and structurally distant relationship of bacteria, including E. faecium and K. pneumonia, to its human counterpart, inhibiting NNAT, an indispensable enzyme implicated in NAD + biosynthesis, is a viable alternative in curtailing infections orchestrated by E. faecium and K. pneumonia. By merging empirical and computational discoveries and connecting the intricate NAD + metabolism network with NNAT's crucial role, it becomes clear that the synergistic effect of these insights may lead to a more profound understanding of the coenzyme's function and its potential applications in the fields of therapeutics and biotechnology.

The Moraxella catarrhalis AdhC-FghA system is important for formaldehyde detoxification and protection against pulmonary clearance

Multidrug-resistant clinical isolates of Moraxella catarrhalis have emerged, increasing the demand for the identification of new treatment and prevention strategies. A thorough understanding of how M. catarrhalis can establish an infection and respond to different stressors encountered in the host is crucial for new drug-target identification. Formaldehyde is a highly cytotoxic compound that can be produced endogenously as a by-product of metabolism and exogenously from environmental sources. Pathways responsible for formaldehyde detoxification are thus essential and are found in all domains of life. The current work investigated the role of the system consisting of the S-hydroxymethyl alcohol dehydrogenase (AdhC), a Zn-dependent class III alcohol dehydrogenase, and the S-formyl glutathione hydrolase (FghA) in the formaldehyde detoxification process in M. catarrhalis. Bioinformatics showed that the components of the system are conserved across the species and are highly similar to those of Streptococcus pneumoniae, which share the same biological niche. Isogenic mutants were constructed to study the function of the system in M. catarrhalis. A single fghA knockout mutant did not confer sensitivity to formaldehyde, while the adhC-fghA double mutant is formaldehyde-sensitive. In addition, both mutants were significantly cleared in a murine pulmonary model of infection as compared to the wild type, demonstrating the system's importance for this pathogen's virulence. The respective phenotypes were reversed upon the genetic complementation of the mutants. To date, this is the first study investigating the role of the AdhC-FghA system in formaldehyde detoxification and pathogenesis of M. catarrhalis.

Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.

Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics

As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.

Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology

Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.

Predicting Personalized Diets Based on Microbial Characteristics between Patients with Superficial Gastritis and Atrophic Gastritis

BACKGROUND

gastritis is a common stomach disease with a high global incidence and can potentially develop into gastric cancer. The treatment of gastritis focuses on medication or diets based on national guidelines. However, the specific diet that can alleviate gastritis remains largely unknown.

METHODS

we propose a microbiota-directed dietary strategy that investigates potential food factors using microbial exogenous metabolites. Given the current lack of understanding of the repeatable characteristics of gastric microbiota, we conducted a meta-analysis to identify the features of gastric bacteria. Local samples were collected as validation cohorts. Furthermore, RevEcoR was employed to identify bacteria's exogenous metabolites, and FooDB was used to retrieve foods that can target specific bacteria.

RESULTS

Bacteroides, Weissella, Actinomyces, Atopobium, Oribacterium, Peptostreptococcus, and Rothia were biomarkers between superficial gastritis (SG) and atrophic gastritis (AG) (AG_N) without H. pylori infection, whereas Bacillus, Actinomyces, Cutibacterium, Helicobacter, Novosphingobium, Pseudomonas, and Streptococcus were signatures between SG and AG (AG_P) with H. pylori infection. According to the exogenous metabolites, adenosyloobalamin, soybean, common wheat, dates, and barley were regarded as potential candidates for AG_N treatment, while gallate was regarded as a candidate for AG_P treatment.

CONCLUSIONS

this study firstly profiled the gastric microbiota of AG and SG with or without H. pylori and provided a recommended diet for global AG according to exogenous metabolites.

The potential of CO2-based production cycles in biotechnology to fight the climate crisis

Rising CO2 emissions have pushed scientists to develop new technologies for a more sustainable bio-based economy. Microbial conversion of CO2 and CO2-derived carbon substrates into valuable compounds can contribute to carbon neutrality and sustainability. Here, we discuss the potential of C1 carbon sources as raw materials to produce energy, materials, and food and feed using microbial cell factories. We provide an overview of potential microbes, natural and synthetic C1 utilization pathways, and compare their metabolic driving forces. Finally, we sketch a future in which C1 substrates replace traditional feedstocks and we evaluate the costs associated with such an endeavor.

Achieving net zero CO2 emission in the biobased production of reduced platform chemicals using defined co-feeding of methanol

Next-generation bioprocesses of a future bio-based economy will rely on a flexible mix of readily available feedstocks. Renewable energy can be used to generate sustainable CO₂-derived substrates. Metabolic engineering already enables the functional implementation of different pathways for the assimilation of C1 substrates in various microorganisms. In addition to feedstocks, the benchmark for all future bioprocesses will be sustainability, including the avoidance of CO₂ emissions. Here we review recent advances in the utilization of C1-compounds from different perspectives, considering both strain and bioprocess engineering technologies. In particular, we evaluate methanol as a co-feed for enabling the CO₂ emission-free production of acetyl-CoA-derived compounds. The possible metabolic strategies are analyzed using stoichiometric modeling combined with thermodynamic analysis and prospects for industrial-scale implementation are discussed.

Unique alcohol dehydrogenases involved in algal sugar utilization by marine bacteria

Marine algae produce complex polysaccharides, which can be degraded by marine heterotrophic bacteria utilizing carbohydrate-active enzymes. The red algal polysaccharide porphyran contains the methoxy sugar 6-O-methyl-D-galactose (G6Me). In the degradation of porphyran, oxidative demethylation of this monosaccharide towards D-galactose and formaldehyde occurs, which is catalyzed by a cytochrome P450 monooxygenase and its redox partners. In direct proximity to the genes encoding for the key enzymes of this oxidative demethylation, genes encoding for zinc-dependent alcohol dehydrogenases (ADHs) were identified, which seem to be conserved in porphyran utilizing marine Flavobacteriia. Considering the fact that dehydrogenases could play an auxiliary role in carbohydrate degradation, we aimed to elucidate the physiological role of these marine ADHs. Although our results reveal that the ADHs are not involved in formaldehyde detoxification, a knockout of the ADH gene causes a dramatic growth defect of Zobellia galactanivorans with G6Me as a substrate. This indicates that the ADH is required for G6Me utilization. Complete biochemical characterizations of the ADHs from Formosa agariphila KMM 3901T (FoADH) and Z. galactanivorans DsijT (ZoADH) were performed, and the substrate screening revealed that these enzymes preferentially convert aromatic aldehydes. Additionally, we elucidated the crystal structures of FoADH and ZoADH in complex with NAD+ and showed that the strict substrate specificity of these new auxiliary enzymes is based on a narrow active site. KEY POINTS: • Knockout of the ADH-encoding gene revealed its role in 6-O-methyl-D-galactose utilization, suggesting a new auxiliary activity in marine carbohydrate degradation. • Complete enzyme characterization indicated no function in a subsequent reaction of the oxidative demethylation, such as formaldehyde detoxification. • These marine ADHs preferentially convert aromatic compounds, and their strict substrate specificity is based on a narrow active site.

Synthetic methylotrophic yeasts for the sustainable fuel and chemical production

Global energy-related emissions, in particular carbon dioxide, are rapidly increasing. Without immediate and strong reductions across all sectors, limiting global warming to 1.5 °C and thus mitigating climate change is beyond reach. In addition to the expansion of renewable energies and the increase in energy efficiency, the so-called Carbon Capture and Utilization technologies represent an innovative approach for closing the carbon cycle and establishing a circular economy. One option is to combine CO₂ capture with microbial C₁ fermentation. C₁-molecules, such as methanol or formate are considered as attractive alternative feedstock for biotechnological processes due to their sustainable production using only CO₂, water and renewable energy. Native methylotrophic microorganisms can utilize these feedstock for the production of value-added compounds. Currently, constraints exist regarding the understanding of methylotrophic metabolism and the available genetic engineering tools are limited. For this reason, the development of synthetic methylotrophic cell factories based on the integration of natural or artificial methanol assimilation pathways in biotechnologically relevant microorganisms is receiving special attention. Yeasts like Saccharomyces cerevisiae and Yarrowia lipolytica are capable of producing important products from sugar-based feedstock and the switch to produce these in the future from methanol is important in order to realize a CO₂-based economy that is independent from land use. Here, we review historical biotechnological applications, the metabolism and the characteristics of methylotrophic yeasts. Various studies demonstrated the production of a broad set of promising products from fine chemicals to bulk chemicals by applying methylotrophic yeasts. Regarding synthetic methylotrophy, the deep understanding of the methylotrophic metabolism serves as the basis for microbial strain engineering and paves the way towards a CO₂-based circular bioeconomy. We highlight design aspects of synthetic methylotrophy and discuss the resulting chances and challenges using non-conventional yeasts as host organisms. We conclude that the road towards synthetic methylotrophic yeasts can only be achieved through a combination of methods (e.g., metabolic engineering and adaptive laboratory evolution). Furthermore, we presume that the installation of metabolic regeneration cycles such as supporting carbon re-entry towards the pentose phosphate pathway from C₁-metabolism is a pivotal target for synthetic methylotrophy.

Toward Methanol-Based Biomanufacturing: Emerging Strategies for Engineering Synthetic Methylotrophy in Saccharomyces cerevisiae

The global expansion of biomanufacturing is currently limited by the availability of sugar-based microbial feedstocks, which require farmland for cultivation and therefore cannot support large increases in production without impacting the human food supply. One-carbon feedstocks, such as methanol, present an enticing alternative to sugar because they can be produced independently of arable farmland from organic waste, atmospheric carbon dioxide, and hydrocarbons such as biomethane, natural gas, and coal. The development of efficient industrial microorganisms that can convert one-carbon feedstocks into valuable products is an ongoing challenge. This review discusses progress in the field of synthetic methylotrophy with a focus on how it pertains to the important industrial yeast, Saccharomyces cerevisiae. Recent insights generated from engineering synthetic methylotrophic xylulose- and ribulose-monophosphate cycles, reductive glycine pathways, and adaptive laboratory evolution studies are critically assessed to generate novel strategies for the future engineering of methylotrophy in S. cerevisiae.