Methane to bioproducts: the future of the bioeconomy?

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

High production of ectoine from methane in genetically engineered Methylomicrobium alcaliphilum 20Z by preventing ectoine degradation

BACKGROUND

Methane is a greenhouse gas with a significant potential to contribute to global warming. The biological conversion of methane to ectoine using methanotrophs represents an environmentally and economically beneficial technology, combining the reduction of methane that would otherwise be combusted and released into the atmosphere with the production of value-added products.

RESULTS

In this study, high ectoine production was achieved using genetically engineered Methylomicrobium alcaliphilum 20Z, a methanotrophic ectoine-producing bacterium, by knocking out doeA, which encodes a putative ectoine hydrolase, resulting in complete inhibition of ectoine degradation. Ectoine was confirmed to be degraded by doeA to N-α-acetyl-L-2,4-diaminobutyrate under nitrogen depletion conditions. Optimal copper and nitrogen concentrations enhanced biomass and ectoine production, respectively. Under optimal fed-batch fermentation conditions, ectoine production proportionate with biomass production was achieved, resulting in 1.0 g/L of ectoine with 16 g/L of biomass. Upon applying a hyperosmotic shock after high-cell-density culture, 1.5 g/L of ectoine was obtained without further cell growth from methane.

CONCLUSIONS

This study suggests the optimization of a method for the high production of ectoine from methane by preventing ectoine degradation. To our knowledge, the final titer of ectoine obtained by M. alcaliphilum 20ZDP3 was the highest in the ectoine production from methane to date. This is the first study to propose ectoine production from methane applying high cell density culture by preventing ectoine degradation.

A comprehensive review on methane's dual role: effects in climate change and potential as a carbon-neutral energy source

The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH4) emissions at an alarming rate. Methane is 25 times more potent trapping heat when compared to carbon dioxide (CO2) in the atmosphere. A rise in atmospheric methane, on a 20-year time scale, has an impact of 80 times greater than that of CO2. With increased population growth, waste generation is rising and is predicted to reach 6 Mt by 2025. CH4 emitted from landfills is a significant source that accounts for 40% of overall global methane emissions. Various mitigation and emissions reduction strategies could significantly reduce the global CH4 burden at a cost comparable to the parallel and necessary CO2 reduction measures, reversing the CH4 burden to pathways that achieve the goals of the Paris Agreement. CH4 mitigation directly benefits climate change, has collateral impacts on the economy, human health, and agriculture, and considerably supports CO2 mitigation. Utilizing the CO2 from the environment, methanogens produce methane and lower their carbon footprint. NGOs and the general public should act on time to overcome atmospheric methane emissions by utilizing the raw source for producing carbon-neutral fuel. However, more research potential is required for green energy production and to consider investigating the untapped potential of methanogens for dependable energy generation.

An efficient and eco-friendly approach for the sustainable recovery and properties characterization of polyhydroxyalkanoates produced by methanotrophs

Synthetic biodegradable and bio-based polymers have emerged as sustainable alternatives to nonrenewable petroleum-derived polymers which cause serious environmental issues. In particular, polyhydroxyalkanoates (PHA) are promising biopolymers owing to their outstanding biodegradability and biocompatibility. The production of the homopolymer poly(3-hydroxybutyrate) (PHB) and copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from type II methanotrophs via microbial fermentation was presented. For the efficient extraction and recovery of intracellular PHA from methanotrophs, different extraction approaches were investigated including solvent extraction using 1,3-dioxolane as a green solvent, integrated cell lysis and solvent extraction, and cell digestion without the use of organic solvents. Among various extraction approaches, the integrated method exhibited the highest extraction performance, with PHA recovery and purity exceeding 91 % and 93 %, respectively, even when the PHA content of the cells was low. Furthermore, the molecular weight, thermal stability, and mechanical properties of the recovered PHA were comprehensively analyzed to suggest its suitable practical applications. The obtained properties were comparable to that of the commercial PHA products and PHA produced from other microbial species, indicating an efficient recovery of high-quality PHA produced from methanotrophs.

Continuous polyhydroxybutyrate production from biogas in an innovative two-stage bioreactor configuration

Biogas biorefineries have opened up new horizons beyond heat and electricity production in the anaerobic digestion sector. Added-value products such as polyhydroxyalkanoates (PHAs), which are environmentally benign and potential candidates to replace conventional plastics, can be generated from biogas. This work investigated the potential of an innovative two-stage growth-accumulation system for the continuous production of biogas-based polyhydroxybutyrate (PHB) using Methylocystis hirsuta CSC1 as cell factory. The system comprised two turbulent bioreactors in series to enhance methane and oxygen mass transfer: a continuous stirred tank reactor (CSTR) and a bubble column bioreactor (BCB) with internal gas recirculation. The CSTR was devoted to methanotrophic growth under nitrogen balanced growth conditions and the BCB targeted PHB production under nitrogen limiting conditions. Two different operational approaches under different nitrogen loading rates and dilution rates were investigated. A balanced nitrogen loading rate along with a dilution rate (D) of 0.3 day-1 resulted in the most stable operating conditions and a PHB productivity of ~53 g PHB m-3 day-1 . However, higher PHB productivities (~127 g PHB m-3 day-1 ) were achieved using nitrogen excess at a D = 0.2 day-1 . Overall, the high PHB contents (up to 48% w/w) obtained in the CSTR under theoretically nutrient balanced conditions and the poor process stability challenged the hypothetical advantages conferred by multistage vs single-stage process configurations for long-term PHB production.

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands

Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 +) and low resource (0.2% CH4 and 0.1 mM NH4 +) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

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.

Co-Processing Agricultural Residues and Wet Organic Waste Can Produce Lower-Cost Carbon-Negative Fuels and Bioplastics

Scalable, low-cost biofuel and biochemical production can accelerate progress on the path to a more circular carbon economy and reduced dependence on crude oil. Rather than producing a single fuel product, lignocellulosic biorefineries have the potential to serve as hubs for the production of fuels, production of petrochemical replacements, and treatment of high-moisture organic waste. A detailed techno-economic analysis and life-cycle greenhouse gas assessment are developed to explore the cost and emission impacts of integrated corn stover-to-ethanol biorefineries that incorporate both codigestion of organic wastes and different strategies for utilizing biogas, including onsite energy generation, upgrading to bio-compressed natural gas (bioCNG), conversion to poly(3-hydroxybutyrate) (PHB) bioplastic, and conversion to single-cell protein (SCP). We find that codigesting manure or a combination of manure and food waste alongside process wastewater can reduce the biorefinery's total costs per metric ton of CO₂ equivalent mitigated by half or more. Upgrading biogas to bioCNG is the most cost-effective climate mitigation strategy, while upgrading biogas to PHB or SCP is competitive with combusting biogas onsite.

A novel inverse membrane bioreactor for efficient bioconversion from methane gas to liquid methanol using a microbial gas-phase reaction

BACKGROUND

Methane (CH₄), as one of the major energy sources, easily escapes from the supply chain into the atmosphere, because it exists in a gaseous state under ambient conditions. Compared to carbon dioxide (CO₂), CH₄ is 25 times more potent at trapping radiation; thus, the emission of CH₄ to the atmosphere causes severe global warming and climate change. To mitigate CH₄ emissions and utilize them effectively, the direct biological conversion of CH₄ into liquid fuels, such as methanol (CH₃OH), using methanotrophs is a promising strategy. However, supplying biocatalysts in an aqueous medium with CH₄ involves high energy consumption due to vigorous agitation and/or bubbling, which is a serious concern in methanotrophic processes, because the aqueous phase causes a very large barrier to the delivery of slightly soluble gases.

RESULTS

An inverse membrane bioreactor (IMBR), which combines the advantages of gas-phase bioreactors and membrane bioreactors, was designed and constructed for the bioconversion of CH₄ into CH₃OH in this study. In contrast to the conventional membrane bioreactor with bacterial cells that are immersed in an aqueous phase, the filtered cells were placed to face a gas phase in the IMBR to supply CH₄ directly from the gas phase to bacterial cells. Methylococcus capsulatus (Bath), a representative methanotroph, was used to demonstrate the bioconversion of CH₄ to CH₃OH in the IMBR. Cyclopropanol was supplied from the aqueous phase as a selective inhibitor of methanol dehydrogenase, preventing further CH₃OH oxidation. Sodium formate was added as an electron donor to generate NADH, which is necessary for CH₃OH production. After optimizing the inlet concentration of CH₄, the mass of cells, the cyclopropanol concentration, and the gas flow rate, continuous CH₃OH production can be achieved over 72 h with productivity at 0.88 mmol L^-1 h^-1 in the IMBR, achieving a longer operation period and higher productivity than those using other types of membrane bioreactors reported in the literature.

CONCLUSIONS

The IMBR can facilitate the development of gas-to-liquid (GTL) technologies via microbial processes, allowing highly efficient mass transfer of substrates from the gas phase to microbial cells in the gas phase and having the supplement of soluble chemicals convenient.

Recent trends of biotechnological production of polyhydroxyalkanoates from C1 carbon sources

Growing concerns over the use of limited fossil fuels and their negative impacts on the ecological niches have facilitated the exploration of alternative routes. The use of conventional plastic material also negatively impacts the environment. One such green alternative is polyhydroxyalkanoates, which are biodegradable, biocompatible, and environmentally friendly. Recently, researchers have focused on the utilization of waste gases particularly those belonging to C1 sources derived directly from industries and anthropogenic activities, such as carbon dioxide, methane, and methanol as the substrate for polyhydroxyalkanoates production. Consequently, several microorganisms have been exploited to utilize waste gases for their growth and biopolymer accumulation. Methylotrophs such as Methylobacterium organophilum produced highest amount of PHA up to 88% using CH₄ as the sole carbon source and 52-56% with CH₃OH. On the other hand Cupriavidus necator, produced 71-81% of PHA by utilizing CO and CO₂ as a substrate. The present review shows the potential of waste gas valorization as a promising solution for the sustainable production of polyhydroxyalkanoates. Key bottlenecks towards the usage of gaseous substrates obstructing their realization on a large scale and the possible technological solutions were also highlighted. Several strategies for PHA production using C1 gases through fermentation and metabolic engineering approaches are discussed. Microbes such as autotrophs, acetogens, and methanotrophs can produce PHA from CO₂, CO, and CH₄. Therefore, this article presents a vision of C1 gas into bioplastics are prospective strategies with promising potential application, and aspects related to the sustainability of the system.

Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems

Lakes and ponds are considered as a major natural source of CH4 emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane-oxidizing bacteria (MOB), which utilize CH4 using oxygen as an electron acceptor, are one of the dominant microorganisms in the CH4-rich water columns. Metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions. However, experimental proof of these functions, i.e., organic acid production via fermentation, by lake MOB is lacking. In addition, psychrophilic (i.e., cold-loving) MOB and their CH4-oxidizing process have rarely been investigated. In this study, we isolated, provided a taxonomic description, and analyzed the genome of Methylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs, Methylobacter sp. S3L5C represented a ubiquitous cluster of Methylobacter spp. in boreal aquatic ecosystems. At optimal temperatures (3-12 °C) and pH (6.8-8.3), the specific growth rates (µ) and CH4 utilization rate were in the range of 0.018-0.022 h-1 and 0.66-1.52 mmol l-1 d-1, respectively. In batch cultivation, the isolate could produce organic acids, and the concentrations were elevated after replenishing CH4 and air into the headspace. Up to 4.1 mM acetate, 0.02 mM malate, and 0.07 mM propionate were observed at the end of the test under optimal operational conditions. The results herein highlight the key role of Methylobacter spp. in regulating CH4 emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.

Influence of operational conditions on the performance of biogas bioconversion into ectoines in pilot bubble column bioreactors

The application of biogas as a low-priced substrate for the production of ectoines constitutes an opportunity to decrease their production costs and to enhance the viability of anaerobic digestion. The influence of operational conditions on CH₄-biogas biodegradation and on ectoines production yields was assessed in continuous pilot bubble column bioreactors. The rise in biomass concentration from 1 to 3 g L^-1 resulted in a decrease in the specific ectoine content from 42 ± 8 to 30 ± 4 mg_ectoine g_VSS^-1. The concentration of Cu²⁺ and Mg²⁺ did not impact process performance, while the use of ammonium as N source resulted in low CH₄ biodegradation and ectoine yields (13 ± 7 mg_ectoine g_VSS^-1). The increase in CH₄ content from 4.5 to 9 %v·v^-1 enhanced CH₄ removal efficiency. Process operation at NaCl concentrations of 3 %w·w^-1 instead of 6 %w·w^-1 decreased the ectoine yield to 17 mg_ectoine g_VSS^-1. Finally, Methylomicrobiumburyatense was identified as the dominant species.

RNA Biomarker Trends across Type I and Type II Aerobic Methanotrophs in Response to Methane Oxidation Rates and Transcriptome Response to Short-Term Methane and Oxygen Limitation in Methylomicrobium album BG8

Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker pmoA were found to vary quantitatively with respect to methane oxidation rates in the model aerobic methanotroph Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures grown in membrane bioreactors, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per-cell pmoA mRNA transcript levels strongly correlated with per-cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). The inclusion of both type I and type II aerobic methanotrophs suggests a universal trend between in situ activity level and pmoA RNA biomarker levels which can aid in improving estimates of both subsurface and atmospheric methane. Additionally, genome-wide expression data (obtained by transcriptome sequencing [RNA-seq]) were used to explore transcriptomic responses of steady-state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response. IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane, having an impact on global net methane emissions. Additionally, they have also gained interest for their biotechnological applications in single-cell protein production, biofuels, and bioplastics. Having better ways of measuring methanotroph activity and understanding how methanotrophs respond to changing conditions is imperative for both optimization in controlled-growth applications and understanding in situ methane oxidation rates. In this study, we explored the applicability of methane oxidation biomarkers as a universal indicator of methanotrophic activity and explored methanotroph transcriptomic response to short-term changes in substrate availability. Our results contribute to better understanding the activity of aerobic methanotrophs, their core metabolic pathways, and their stress responses.

Recycling carbon for sustainable protein production using gas fermentation

Current food production practices contribute significantly to climate change. To transition into a sustainable future, a combination of new food habits and a radical food production innovation must occur. Single-cell protein from microbial fermentation can profoundly impact sustainability. This review paper explores opportunities offered by gas fermentation to completely replace our reliance on fossil fuels for the production of food. Together with synthetic biology, designed microbial proteins from gas fermentation have the potential to reduce our dependence on fossil fuels and make food production more sustainable.

Crucial role of the chaperonin GroES/EL for heterologous production of the soluble methane monooxygenase from Methylomonas methanica MC09

Methane is a widespread energy source and can serve as an attractive C1 building block for a future bioeconomy. The soluble methane monooxygenase (sMMO) is able to break the strong C−H bond of methane and convert it to methanol. The high structural complexity, multiplex cofactors, and unfamiliar folding or maturation procedures of sMMO have hampered the heterologous production and thus biotechnological applications. Here, we demonstrate the heterologous production of active sMMO from the marine Methylomonas methanica MC09 in Escherichia coli by co‐synthesizing the GroES/EL chaperonin. Iron determination, electron paramagnetic resonance spectroscopy, and native gel immunoblots revealed the incorporation of the non‐heme diiron centre and homodimer formation of active sMMO. The production of recombinant sMMO will enable the expansion of the possibilities of detailed studies, allowing for a variety of novel biotechnological applications.

Adapting isotopic tracer and metabolic flux analysis approaches to study C1 metabolism

Single-carbon (C1, or one-carbon) substrates are promising feedstocks for sustainable biofuel and biochemical production. Crucial to the goal of engineering C1-utilizing strains for improved production is a quantitative understanding of the organization, regulation and rates of the reactions that underpin C1 metabolism. ¹³C Metabolic flux analysis (MFA) is a well-established platform for interrogating these questions with multi-carbon substrates, and uses the differential labeling of metabolites that results from feeding a substrate with position-specific incorporation of ¹³C in order to infer quantitative fluxes and pathway topology. Adapting isotopic tracer approaches to C1 metabolism, where position-specific substrate labeling is impossible, requires additional experimental considerations. Here we review recent studies that have developed isotopic tracer approaches to overcome the challenge of uniform metabolite labeling and provide quantitative insight into C1 metabolism.

Ectoine Production from Biogas in Waste Treatment Facilities: A Techno-Economic and Sensitivity Analysis

The capacity of haloalkaliphilic methanotrophic bacteria to synthesize ectoine from CH₄-biogas represents an opportunity for waste treatment plants to improve their economic revenues and align their processes to the incoming circular economy directives. A techno-economic and sensitivity analysis for the bioconversion of biogas into 10 t ectoine·y^-1 was conducted in two stages: (I) bioconversion of CH₄ into ectoine in a bubble column bioreactor and (II) ectoine purification via ion exchange chromatography. The techno-economic analysis showed high investment (4.2 M€) and operational costs (1.4 M€·y^-1). However, the high margin between the ectoine market value (600-1000 €·kg^-1) and the estimated ectoine production costs (214 €·kg^-1) resulted in a high profitability for the process, with a net present value evaluated at 20 years (NPV₂₀) of 33.6 M€. The cost sensitivity analysis conducted revealed a great influence of equipment and consumable costs on the ectoine production costs. In contrast to alternative biogas valorization into heat and electricity or into low added-value bioproducts, biogas bioconversion into ectoine exhibited high robustness toward changes in energy, water, transportation, and labor costs. The worst- and best-case scenarios evaluated showed ectoine break-even prices ranging from 158 to 275 €·kg^-1, ∼3-6 times lower than the current industrial ectoine market value.

A shortcut to carbon-neutral bioplastic production: Recent advances in microbial production of polyhydroxyalkanoates from C1 resources

Since the 20th century, plastics that are widely being used in general life and industries are causing enormous plastic waste problems since improperly discarded plastics barely degrade and decompose. Thus, the demand for polyhydroxyalkanoates (PHAs), biodegradable polymers with material properties similar to conventional petroleum-based plastics, has been increased so far. The microbial production of PHAs is an environment-friendly solution for the current plastic crisis, however, the carbon sources for the microbial PHA production is a crucial factor to be considered in terms of carbon-neutrality. One‑carbon (C1) resources, such as methane, carbon monoxide, and carbon dioxide, are greenhouse gases and are abundantly found in nature and industry. C1 resources as the carbon sources for PHA production have a completely closed carbon loop with much advances; i) fast carbon circulation with direct bioconversion process and ii) simple fermentation procedure without sterilization as non-preferable nutrients. This review discusses the biosynthesis of PHAs based on C1 resource utilization by wild-type and metabolically engineered microbial host strains via biorefinery processes.

Recent trends in methane to bioproduct conversion by methanotrophs

Methane is an abundant and low-cost gas with high global warming potential and its use as a feedstock can help mitigate climate change. Variety of valuable products can be produced from methane by methanotrophs in gas fermentation processes. By using methane as a sole carbon source, methanotrophic bacteria can produce bioplastics, biofuels, feed additives, ectoine and variety of other high-value chemical compounds. A lot of studies have been conducted through the years for natural methanotrophs and engineered strains as well as methanotrophic consortia. These have focused on increasing yields of native products as well as proof of concept for the synthesis of new range of chemicals by metabolic engineering. This review shows trends in the research on key methanotrophic bioproducts since 2015. Despite certain limitations of the known production strategies that makes commercialization of methane-based products challenging, there is currently much attention placed on the promising further development.

Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions

Methane-oxidizing bacteria (methanotrophs) often coexist with methylotrophs that utilize methanol excreted by methanotrophs. Recently, we found that a facultative methylotroph, Methyloceanibacter caenitepidi Gela4T, possibly utilizes acetate rather than methanol in the coculture with a methanotroph, Methylocaldum marinum S8. Here, we examined the effects of oxygen concentrations on growth of and acetate excretion by M. marinum S8 in pure culture and the coculture with M. caenitepidi Gela4T. M. marinum S8 excreted acetate during the exponential growth phase not only under microaerobic (O2 concentrations of 3.5%-6%) but also under aerobic (O2 concentrations of 20%-31%) conditions. RNA-Seq analyses of M. marinum S8 cells grown under aerobic conditions suggested that phosphoketolase and acetate kinase were candidate genes involved in acetate production. Nonmethylotrophic bacteria, Cupriavidus necator NBRC 102504, could grow when cocultured with M. marinum S8, also supporting the existence of methanol-independent cross-feeding from M. marinum S8 under aerobic conditions.

Abiotic-biotic hybrid for CO2 biomethanation: From electrochemical to photochemical process

Converting CO₂ into sustainable fuels (e.g., CH₄) has great significance to solve carbon emission and energy crisis. Generally, CO₂ methanation needs abundant of energy input to overcome the eight-electron-transfer barrier. Abiotic-biotic hybrid system represents one of the cutting-edge technologies that use renewable electric/solar energy to realize eight-electron-transfer CO₂ biomethanation. However, the incompatible abiotic-biotic hybrid can result in low efficiency of electron transfer and CO₂ biomethanation. Herein, we present the comprehensive review to highlight how to design abiotic-biotic hybrid for electric/solar-driven CO₂ biomethanation. We primarily introduce the CO₂ biomethanation mechanism, and further summarize state-of-the-art electrochemical and photochemical CO₂ biomethanation in hybrid systems. We also propose excellent synthetic biology strategies, which are useful to design tunable methanogenic microorganisms or enzymes when cooperating with electrode/semiconductor in hybrid systems. This review provides theoretical guidance of abiotic-biotic hybrid and also shows the bright future of sustainable fuel production in the form of CO₂ biomethanation.

Bioproduction of l- and d-lactic acids: advances and trends in microbial strain application and engineering

Lactic acid is an important platform chemical used in the food, agriculture, cosmetic, pharmaceutical, and chemical industries. It serves as a building block for the production of polylactic acid (PLA), a biodegradable polymer, which can replace traditional petroleum-based plastics and help to reduce environmental pollution. Cost-effective production of optically pure l- and d-lactic acids is necessary to achieve a quality and thermostable PLA product. This paper evaluates research advances in the bioproduction of l- and d-lactic acids using microbial fermentation. Special emphasis is given to the development of metabolically engineered microbial strains and processes tailored to alternative and flexible feedstock concepts such as: lignocellulose, glycerol, C1-gases, and agricultural-food industry byproducts. Alternative fermentation concepts that can improve lactic acid production are discussed. The potential use of inducible gene expression systems for the development of biosensors to facilitate the screening and engineering of lactic acid-producing microorganisms is discussed.

Interactions of functional microorganisms and their contributions to methane bioconversion to short-chain fatty acids

Methane bioconversion to value-added liquid chemicals has been proposed as a promising solution to augment the petroleum-dominated chemical market. Recent investigations have reported that various electron acceptors (e.g., nitrite and nitrate) are available to drive methane bioconversion to short-chain fatty acids (SCFAs). However, little is known about effects of the rate electron acceptor supplied on liquid chemical production from methane. Herein, three independent membrane biofilm reactors (MBfRs) feeding with respective nitrate, nitrite, combined nitrate and nitrite were operated under high and low rate condition in succession, to study whether feeding rate of electron acceptors could impact the methane bioconversion to SCFAs and the associated microbiological features. Long-term operation showed that all tested electron acceptors with a high supply rate were favorable for methane bioconversion to SCFAs (990.9 mg L^-1d^-1, 1695.7 mg L^-1d^-1, and 2425.7 mg L^-1d^-1), while under a low electron acceptor feeding rate, the SCFA production rate decreased to 8.9 mg L^-1d^-1, 16.8 mg L^-1d^-1, and 260.1 mg L^-1d^-1, respectively. Microbial community characterization showed that the biofilm was predominated by Methanosarcina, Methanobacterium, Propionispora and Clostridium. On the basis of the known metabolism characteristics of these microorganisms, it was assumed that these methanogens and fermenters contributed jointly to methane bioconversion to SCFAs. The findings could be helpful to understand the role of electron acceptor rate in methane bioconversion to liquid chemicals.

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production

Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.

An Aldolase-Based New Pathway for Bioconversion of Formaldehyde and Ethanol into 1,3-Propanediol in Escherichia coli

Formaldehyde (HCHO) is a reactive one-carbon compound that is interesting for biosynthesis. The assimilation of HCHO depends on the catalysis of aldolase. Here, we present a novel synthetic pathway in E. coli to convert HCHO and ethanol into 1,3-propanediol (PDO) using a deoxyribose-5-phosphate aldolase (DERA). DERA condenses HCHO and acetaldehyde to form 3-hydroxypropionaldehyde, the direct precursor of PDO formation. This new pathway opens up the possibility to synthesize an appealing C3 compound from a C1 compound and a C2 compound without carbon loss in contrast to all the other known PDO synthetic pathways where typically 30-50% of the carbons are lost as CO₂ and other byproducts. The pathway is successfully demonstrated by elaborating three metabolic modules. First, DERA from Thermotoga maritima was found to be efficient for the aldol condensation and PDO production module. For the module of acetaldehyde supply from ethanol, an alcohol dehydrogenase from Hansenula polymorpha was selected. For the HCHO supply module, the control of HCHO concentration and its utilization were shown to be important for achieving the assimilation of HCHO in recombinant E. coli cells. By deleting the gene frmA for endogenous conversion of HCHO to formate and controlling HCHO at a level of about 0.6 mM, the concentration and yield of PDO were increased from initially 5.67 mM (0.43 g/L) and 0.057 mol/mol to 17.35 mM (1.32 g/L) and 0.096 mol/mol in bioconversion of ethanol and HCHO with resting E. coli cells. Further engineering of DERA and the HCHO supply module is necessary to realize the potential of this promising metabolic pathway.

Cellulose nanocrystals coated with a tannic acid-Fe3+ complex as a significant medium for efficient CH4 microbial biotransformation

Microbial biotransformation of CH₄ gas has been attractive for the production of energy and high-value chemicals. However, insufficient supply of CH₄ in a culture medium needs to be overcome for the efficient utilization of CH₄. Here, we utilized cellulose nanocrystals coated with a tannic acid-Fe³⁺ complex (TA-Fe³⁺CNCs) as a medium component to enhance the gas-liquid mass-transfer performance. TA-Fe³⁺CNCs were well suspended in water without agglomeration, stabilized gas bubbles without coalescence, and increased the gas solubility by 20 % and the k_La value at a rapid inlet gas flow rate. Remarkably, the cell growth rate of Methylomonas sp. DH-1 as model CH₄-utilizing bacteria improved with TA-Fe³⁺CNC concentration without any cytotoxic or antibacterial properties, resulting in higher metabolite production ability such as methanol, pyruvate, formate, and succinate. These results showed that TA-Fe³⁺CNCs could be utilized as a significant component in the culture medium applicable as a promising nanofluid for efficient CH₄ microbial biotransformation.

Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications

Worldwide, the use of methane is limited to generating power, electricity, heating, and for production of chemicals. We believe this valuable gas can be employed more widely. Here we review the possibility of using methane as a feedstock for biotechnological processes based on the application of synthetic methanotrophs. Methane monooxygenase (MMO) enables aerobic methanotrophs to utilize methane as a sole carbon and energy source, in contrast to industrial microorganisms that grow on carbon sources, such as sugar cane, which directly compete with the food market. However, naturally occurring methanotrophs have proven to be difficult to manipulate genetically and their current industrial use is limited to generating animal feed biomass. Shifting the focus from genetic engineering of methanotrophs, towards introducing metabolic pathways for methane utilization in familiar industrial microorganisms, may lead to construction of efficient and economically feasible microbial cell factories. The applications of a technology for MMO production are not limited to methane-based industrial synthesis of fuels and value-added products, but are also of interest in bioremediation where mitigating anthropogenic pollution is an increasingly relevant issue. Published research on successful functional expression of MMO does not exist, but several attempts provide promising future perspectives and a few recent patents indicate that there is an ongoing research in this field. Combining the knowledge on genetics and metabolism of methanotrophy with tools for functional heterologous expression of MMO-encoding genes in non-methanotrophic bacterial species, is a key step for construction of synthetic methanotrophs that holds a great biotechnological potential.

Laboratory scale bioreactor designs in the processes of methane bioconversion: Mini-review

Global methane emissions have been steadily increasing over the past few decades, exerting a negative effect on the environment. Biogas from landfills and sewage treatment plants is the main anthropogenic source of methane. This makes methane bioconversion one of the priority areas of biotechnology. This process involves the production of biochemical compounds from non-food sources through microbiological synthesis. Methanotrophic bacteria are a promising tool for methane bioconversion due to their ability to use this greenhouse gas and to produce protein-rich biomass, as well as a broad range of useful organic compounds. Currently, methane is used not only to produce biomass and chemical compounds, but also to increase the efficiency of water and solid waste treatment. However, the use of gaseous substrates in biotechnological processes is associated with some difficulties. The low solubility of methane in water is one of the major problems. Different approaches have been involved to encounter these challenges, including different bioreactor and gas distribution designs, solid carriers and bulk sorbents, as well as varying air/oxygen supply, the ratio of volumetric flow rate of gas mixture to its consumption rate, etc. The aim of this review was to summarize the current data on different bioreactor designs and the aspects of their applications for methane bioconversion and wastewater treatment. The bioreactors used in these processes must meet a number of requirements such as low methane emission, improved gas exchange surface, and controlled substrate supply to the reaction zone.

From Acetate to Bio-Based Products: Underexploited Potential for Industrial Biotechnology

Currently, most biotechnological products are based on microbial conversion of carbohydrate substrates that are predominantly generated from sugar- or starch-containing plants. However, direct competitive uses of these feedstocks in the food and feed industry represent a dilemma, so using alternative carbon sources has become increasingly important in industrial biotechnology. A promising alternative carbon source that may be generated in substantial amounts from lignocellulosic biomass and C1 gases is acetate. This review discusses the underexploited potential of acetate to become a next-generation platform substrate in future industrial biotechnology and summarizes alternative sources and routes for acetate production. Furthermore, biotechnological aspects of microbial acetate utilization and the state of the art of biotechnological acetate conversion into value-added bioproducts are highlighted.

Polyhydroxyalkanoates (PHA) production from biogas in waste treatment facilities: Assessing the potential impacts on economy, environment and society

Using the biogas generated from organic waste anaerobic treatment to produce polyhydroxyalkanoates (PHAs) has emerged as an attractive alternative to heat and power generation (CHP) in waste treatment plants. The sustainability of biogas combustion for CHP, biogas bioconversion into PHA and a combination of both scenarios was compared in terms of environmental impact, process economics and social responsibility according to the IChemE Sustainability Metrics. Although PHA production presented higher investment and operational costs, a comparable economic performance was observed in all biogas valorization scenarios regarding net present value (0.77 M€) and internal rate of return (6.4 ± 0.2%) due to the higher market value of biopolymers. The PHA production entailed a significant reduction of atmospheric acidification and odor emissions compared to CHP despite showing higher land, water, chemicals and energy requirements. Job creation associated to biopolymer industry and the increasing public demand for bioproducts were identified as fundamental aspects for enhancing social and local acceptance of waste processing facilities. This study demonstrated that PHA production from biogas constitutes nowadays a realistic alternative to CHP in waste treatment plants and that PHA can be produced at a competitive market price when biogas is used for internal energy provision (4.2 €·kg^-1 PHA).

Methanol Production by "Methylacidiphilum fumariolicum" SolV under Different Growth Conditions

The production of methanol, an important chemical, is completely dependent on natural gas. The current multistep chemical process uses high temperature and pressure to convert methane in natural gas to methanol. In this study, we used the methanotroph “Methylacidiphilum fumariolicum” SolV to achieve continuous methanol production from methane as the substrate. The production rate was highly dependent on the growth rate of this microorganism, and high conversion efficiencies were obtained. Using microorganisms for the production of methanol might enable the use of more sustainable sources of methane, such as biogas, rather than natural gas.

Industrial methanol production converts methane from natural gas into methanol through a multistep chemical process. Biological methane-to-methanol conversion under moderate conditions and using biogas would be more environmentally friendly. Methanotrophs, bacteria that use methane as an energy source, convert methane into methanol in a single step catalyzed by the enzyme methane monooxygenase, but inhibition of methanol dehydrogenase, which catalyzes the subsequent conversion of methanol into formaldehyde, is a major challenge. In this study, we used the thermoacidophilic methanotroph “Methylacidiphilum fumariolicum” SolV for biological methanol production. This bacterium possesses a XoxF-type methanol dehydrogenase that is dependent on rare earth elements for activity. By using a cultivation medium nearly devoid of lanthanides, we reduced methanol dehydrogenase activity and obtained a continuous methanol-producing microbial culture. The methanol production rate and conversion efficiency were growth-rate dependent. A maximal conversion efficiency of 63% mol methanol produced per mol methane consumed was obtained at a relatively high growth rate, with a methanol production rate of 0.88 mmol/g (dry weight)/h. This study demonstrates that methanotrophs can be used for continuous methanol production. Full-scale application will require additional increases in the titer, production rate, and efficiency, which can be achieved by further decreasing the lanthanide concentration through the use of increased biomass concentrations and novel reactor designs to supply sufficient gases, including methane, oxygen, and hydrogen.

IMPORTANCE The production of methanol, an important chemical, is completely dependent on natural gas. The current multistep chemical process uses high temperature and pressure to convert methane in natural gas to methanol. In this study, we used the methanotroph “Methylacidiphilum fumariolicum” SolV to achieve continuous methanol production from methane as the substrate. The production rate was highly dependent on the growth rate of this microorganism, and high conversion efficiencies were obtained. Using microorganisms for the production of methanol might enable the use of more sustainable sources of methane, such as biogas, rather than natural gas.

Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs

Methane, a non-expensive natural substrate, is used by Methylocystis spp. as a sole source of carbon and energy. Here, we assessed whether Methylocystis sp. strain SC2 is able to also utilize hydrogen as an energy source. The addition of 2% H₂ to the culture headspace had the most significant positive effect on the growth yield under CH₄ (6%) and O₂ (3%) limited conditions. The SC2 biomass yield doubled from 6.41 (±0.52) to 13.82 (±0.69) mg cell dry weight per mmol CH₄, while CH₄ consumption was significantly reduced. Regardless of H₂ addition, CH₄ utilization was increasingly redirected from respiration to fermentation-based pathways with decreasing O₂/CH₄ mixing ratios. Theoretical thermodynamic calculations confirmed that hydrogen utilization under oxygen-limited conditions doubles the maximum biomass yield compared to fully aerobic conditions without H₂ addition. Hydrogen utilization was linked to significant changes in the SC2 proteome. In addition to hydrogenase accessory proteins, the production of Group 1d and Group 2b hydrogenases was significantly increased in both short- and long-term incubations. Both long-term incubation with H₂ (37 d) and treatments with chemical inhibitors revealed that SC2 growth under hydrogen-utilizing conditions does not require the activity of complex I. Apparently, strain SC2 has the metabolic capacity to channel hydrogen-derived electrons into the quinone pool, which provides a link between hydrogen oxidation and energy production. In summary, H₂ may be a promising alternative energy source in biotechnologically oriented methanotroph projects that aim to maximize biomass yield from CH_4, such as the production of high-quality feed protein.

Biomethanol Production from Methane by Immobilized Co-cultures of Methanotrophs

Methanol production by co-culture of methanotrophs Methylocystis bryophila and Methyloferula stellata was examined from methane, a greenhouse gas. Co-culture exhibited higher methanol yield of 4.72 mM at optimum ratio of M. bryophila and M. stellata (3:2) compared to individual cultures. The immobilized co-culture within polyvinyl alcohol (PVA) showed relative efficiency of 90.1% for methanol production at polymer concentration of 10% (v/v). The immobilized co-culture cells within PVA resulted in higher bioprocess stability over free cells at different pH, and temperatures. Free and encapsulated co-cultures showed maximum methanol production of 4.81 and 5.37 mM under optimum conditions, respectively. After five cycles of reusage under batch conditions, free and encapsulated co-cultures retained methanol production efficiency of 23.8 and 61.9%, respectively. The present investigation successfully revealed the useful influence of co-culture on the methanol production over pure culture. Further, encapsulation within the polymeric matrix proved to be a better approach for the enhanced stability of the bioprocess.

Methanol production by polymer-encapsulated methanotrophs from simulated biogas in the presence of methane vector

Type I (Methylomicrobium album) and II (Methyloferula stellata) methanotrophs were encapsulated by alginate and polyvinyl alcohol (PVA) to improve methanol production from simulated biogas [methane (CH₄) and carbon dioxide (CO₂)] in the presence of CH₄ vector. Polymeric matrix alginate (2%) and PVA (10%) were found to be optimum for the immobilization of both the methanotrophs, with a relative efficiency of methanol production up to 80.6 and 88.7%, respectively. The stability of methanol production by immobilized cells was improved up to 13.2-fold under repeated batch-culture over free cells. The addition of CH₄ vectors showed 1.7-fold higher methanol production on using simulated biogas than in the control. The maximum methanol production of 7.46 and 7.14 mmol/L was noted for PVA-encapsulated M. album and M. stellata, respectively. This study successfully established the beneficial effects of CH₄ vectors on methanol production by methanotrophs from greenhouse gases that can be applied for real biogas feedstock.

Elucidating the influence of environmental factors on biogas-based polyhydroxybutyrate production by Methylocystis hirsuta CSC1

The valorization of biogas as a feedstock for the generation of added-value bioproducts will play a key role on the sustainability of anaerobic digestion. The present work assessed the influence of key environmental parameters (O₂:CH₄ ratio, temperature and nitrogen source) on the growth and polyhydroxybutyrate (PHB) synthesis under nitrogen limiting conditions of the type II methanotroph Methylocystis hirsuta CSC1 using biogas as a feedstock. The O₂:CH₄ ratios tested (1:1, 1.5:1 and 2:1) did not affect significantly M. hirsuta CSC1 growth yields (~5 g TSS mol^-1 CH₄), although lower CH₄ removal rates were reached under O₂-limiting conditions (ratio 1:1). The highest PHB content (45 wt%) was achieved at a ratio 2:1 and was threefold higher than those obtained at lower ratios (~15 wt%). The increase in temperature from 15 to 25 °C resulted in increases in the growth yield (from 5 to 6 g TSS mol^-1 CH₄) and PHB content (from 32 to 40 wt%). Conversely, the lowest PHB content (30 wt%) was reached at 37 °C, together with a negligible growth under nutrient sufficient conditions. The nitrogen source also played a key role on both M. hirsuta CSC1 growth and PHB synthesis. Thus, ammonium resulted in the highest growth yield (7 g TSS mol^-1 CH₄), although the maximum PHB content was achieved when biomass was previously grown in nitrate as the nitrogen source (41 wt%). Nitrite exerted an inhibitory effect on M. hirsuta CSC1 growth.

Regenerative water purification for space applications: Needs, challenges, and technologies towards 'closing the loop'

Human missions to establish surface habitats on the Moon and Mars are planned in the coming decades. Extraplanetary surface habitat life support systems (LSS) will require new capabilities to withstand anticipated unique, harsh conditions. In order to provide safe, habitable environments for the crew, water purification systems that are robust and reliable must be in place. These water purification systems will be required to treat all sources of water in order to achieve the necessary levels of recovery needed to sustain life over the long-duration missions. Current water recovery and purification systems aboard the International Space Station (ISS) are only partially closed, requiring external inputs and resupply. Furthermore, organic wastes, such as fecal and food wastes, are currently discarded and not recycled. For long-duration missions and habitats, this is not a viable approach. The inability to recycle organic wastes represents a lost opportunity to recover critical elements (e.g., C, H, O, N, P) for subsequent food production, water purification, and atmospheric regeneration. On Earth, a variety of technologies are available to meet terrestrial wastewater treatment needs; however, these systems are rarely completely closed-loop, due to lack of economic drivers, legacy infrastructure, and the (perceived) abundance of resources on Earth. Extraplanetary LSS provides a game-changing opportunity to incentivize the development of completely closed-loop systems. Candidate technologies may be biological, physical, or chemical, with associated advantages and disadvantages. This paper presents a survey of potential technologies, along with their inputs, outputs and requirements, which may be suitable for next-generation regenerative water purification in space. With this information, particular technologies can be down-selected for subsystem integration testing and optimization. In order for future space colonies to have closed-loop systems which minimize consumable inputs and maximize recovery, strategic implementation of a variety of complementary subsystems is needed.

Biotransformation of methane into methanol by methanotrophs immobilized on coconut coir

This study aimed to establish a unique approach for the production of methanol from methane (CH₄) in the presence of paraffin oil mediated by methanotrophs immobilized on coconut coir (CC). Immobilization of different methanotrophs through covalent method increased the immobilization yield and relative efficiency for methanol production to 48.6% and 96.8%, respectively. In the presence of paraffin oil, methanol production was 1.6-fold higher by Methylocystis bryophila than by control. Compared to free cells, whole cells immobilized on CC showed higher stability for methanol production. Under repeated batch conditions, cumulative methanol production by immobilized cells and free cells, after eight cycles of reuse, was 52.9 and 30.9 mmol/L, respectively. This study effectively demonstrated the beneficial influence of lignocellulosic biowaste CC as support for immobilization of methanotrophs and paraffin oil on bioconversion of CH₄ to methanol.

An Aldolase-Catalyzed New Metabolic Pathway for the Assimilation of Formaldehyde and Methanol To Synthesize 2-Keto-4-hydroxybutyrate and 1,3-Propanediol in Escherichia coli

Formaldehyde (HCHO) is an important intermediate in the metabolism of one-carbon (C1) compounds such as methanol, formate, and methane. The ribulose monophosphate (RuMP) pathway is the most-studied HCHO assimilation route and the 3-hexulose-6-phosphate synthase (Hps) plays an important role for HCHO fixation. In this study, we proposed and selected a pyruvate-dependent aldolase to channel HCHO into 2-keto-4-hydroxybutyrate as an important intermediate for biosynthesis. By combining this reaction with three further enzymes we demonstrated a pyruvate-based C1 metabolic pathway for biosynthesis of the appealing compound 1,3-propanediol (1,3-PDO). This novel pathway is first confirmed in vitro using HCHO and pyruvate as substrates. It is then demonstrated in vivo in E. coli for 1,3-PDO production from HCHO and methanol with glucose as a cosubstrate. This de novo pathway has several decisive advantages over the known metabolic pathways for 1,3-PDO: (1) C1 carbon is directly channeled into a precursor of 1,3-PDO; (2) the use of pyruvate as an acceptor of HCHO is glycerol-independent, circumventing thus the need of coenzyme B₁₂ as cofactor for glycerol dehydration; (3) the pathway is much shorter and more simple than the recently proposed l-homoserine-dependent pathway, thus avoiding complicated regulations involving precursors for essential amino acids. In addition to proof-of-concept we further improved the host strain by deleting a gene (frmA) responsible for the conversion of HCHO to formate, thereby increasing the production of 1,3-PDO from 298.3 ± 11.4 mg/L to 508.3 ± 9.1 mg/L and from 3.8 mg/L to 32.7 ± 0.8 mg/L with HCHO and methanol as cosubstrate of glucose fermentation, respectively. This work is the first study demonstrating a genetically engineered E. coli that can directly use HCHO or methanol for the synthesis of 2-keto-4-hydroxybutyrate and its further conversion to 1,3-PDO.

Microbial consortia including methanotrophs: some benefits of living together

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

Polyhydroxyalkanoates production from methane emissions in Sphagnum mosses: Assessing the effect of temperature and phosphorus limitation

The isolation of highly efficient methanotrophic communities is crucial for the optimization of methane bioconversion into products with a high market value such as polyhydroxyalkanoates (PHA). The research here presented aimed at enriching a methanotrophic consortium from two different inocula (Sphagnum peat moss (Sp) and Sphagnum and activated sludge (M)) able to accumulate PHA while efficiently oxidizing CH₄. Moreover, the effect of the temperature and phosphorus limitation on the biodegradation rate of CH₄ and the PHA accumulation potential was investigated. Higher CH₄ degradation rates were obtained under P availability at increasing temperature (25, 30 and 37 °C). The biomass enriched from the mixed inoculum always exhibited a superior biodegradation performance regardless of the temperature (a maximum value of 84.3 ± 8.4 mg CH₄ h^-1 g biomass^-1 was recorded at 37 °C). The results of the PHB production showed that phosphorus limitation is required to promote PHB accumulation, the highest PHB content being observed with the Sphagnum inoculum at 25 °C (13.6 ± 5.6%). The differential specialization of the microbial communities depending on the enrichment temperature supported the key role of this parameter on the results obtained. In all cases after the completion of the enrichment process and of the P limitation tests, Methylocystis, a type II methanotroph known for its ability to accumulate PHA, was the genus that became dominant (reaching percentages from 16 to 46% depending on the enrichment temperature). Thus, the results here obtained demonstrated for the first time the relevance of the temperature used for the enrichment of the methanotrophic bacteria to boost PHA production yields under P limiting condition, highlighting the importance of optimizing culture conditions to improve the cost-efficiency of bioprocesses based on using methane as the primary feedstock for the PHA industrial market.