Combined Effects of Carbon and Nitrogen Source to Optimize Growth of Proteobacterial Methanotrophs

Quantitative assessment of methane bioconversion based on kinetics and bioenergetics

The biological conversion of methane under ambient conditions can be performed by methanotrophs that utilize methane as both a sole source of energy and a carbon source. However, compared to the established microbial chassis used for general fermentation with sugar as a feedstock, the productivity of methanotrophs is low. The fundamental knowledge of their metabolic or cellular bottlenecks is limited. In this review, the industrial-scale potential of methane bioconversion was evaluated. In particular, the enzyme kinetics associated with the oxidation and assimilation of methane were investigated to evaluate the potential of methane fermentation. The kinetics of enzymes involved in methane metabolism were compared with those used in the metabolic processes of traditional fermentation (glycolysis). Through this analysis, the current limitations of methane metabolism were identified. Methods for increasing the efficiency of methane bioconversion and directions for the industrial application of methane-based fermentation were discussed.

Different Combinations of Nitrogen and Carbon Sources Influence the Growth and Postbiotic Metabolite Characteristics of Lactiplantibacillus plantarum Strains Isolated from Malaysian Foods

Postbiotic metabolites produced by Lactiplantibacillus plantarum strains isolated from Malaysian food have been extensively reported for their positive effects on health. Understanding the effects of different combinations of carbon and nitrogen sources on the growth and corresponding characteristics of postbiotic metabolites produced by different strains of L. plantarum is important for various applications. Hence, the effects of different combinations of carbon (glucose, lactose, sucrose and dextrose) and nitrogen (X-SEED Kat, X-SEED Peptone, X-SEED Nucleo Advanced, Nucel875 MG, FM888 and FM902) sources on the growth of six strains of L. plantarum (RG11, RG14, RI11, RS5, TL1 and UL4) and the functional characteristics (bacteriocin inhibitory activity, antioxidant activity and lactic acid concentration) of their respective postbiotic metabolites were investigated in this study. UL4 produced the highest viable cell population with sucrose and Nucel875 nitrogen source. The UL4 strain also produced the strongest bacteriocin inhibitory activity with dextrose and FM888 nitrogen source. In comparison, the RI11 strain produced the highest lactic acid concentration with dextrose and Nucel875 nitrogen source and the highest reducing power of RS5 and TL1 postbiotic metabolites was achieved with MRS medium. In the combination of sucrose and X-Seed KAT nitrogen source, RG14 produce the highest hydroxyl radical scavenging activity. The effects of different combinations of carbon and nitrogen sources on the viable cell population of L. plantarum strains and the respective functional characteristics of postbiotic metabolites were strain dependent. The current study also revealed that fermentation media were an important factor that greatly impacted the functionalities of postbiotic metabolites due to the presence of various bioactive compounds that contributed to high antioxidant and antimicrobial properties. The results of this study will facilitate the subsequent medium design and optimisation for the development and production of specific postbiotic metabolites produced by the respective L. plantarum strain for their applications in various industries.

The importance of acetate, pyruvate, and citrate feeding times in improving xanthan production by Xanthomonas citri

Xanthan gum is a microbial polysaccharide produced by Xanthomonas and widely used in various industries. To produce xanthan gum, the native Xanthomonas citri-386 was used in a cheese-whey-based culture medium. The culture conditions were investigated in batch experiments based on the response surface methodology to increase xanthan production and viscosity. Three independent variables in this study included feeding times of acetate, pyruvate, and citrate. The maximum xanthan gum production and viscosity within 120 h by X. citri-386 using Box-Behnken design were 25.7 g/l and 65 500 cP, respectively, with a 151% and 394% increase as compared to the control sample. Overall, the findings of this study recommend the use of X. citri-386 in the cheese-whey-based medium as an economical medium with optimal amounts of acetate, pyruvate, and citrate for commercial production of xanthan gum on an industrial scale. The adjustment of the pyruvate and acetate concentrations optimized xanthan gum production in the environment.

Microbial upcycling of methane to phytoene using metabolically engineered Methylocystis sp. MJC1 strain

Methane, a potent greenhouse gas, requires sustainable mitigation strategies. Here, the microbial upcycling of methane to phytoene, a valuable colorless carotenoid with applications in the cosmeceutical industry was demonstrated. To achieve this goal, a stepwise metabolic engineering approach was employed in Methylocystis sp. MJC1, a methane-oxidizing bacterium. The incorporation of crtE and crtB genes from Deinococcus radiodurans R1 established the phytoene biosynthetic pathway. This pathway was fine-tuned through promoter optimization, resulting in a phytoene production of 450 μg/L from 37 mmol/L methane. Disrupting the ackA gene reduced a by-product, acetate, by 50 % and increased phytoene production by 56 %. Furthermore, overexpressing the dxs gene boosted phytoene titer 3-fold. The optimized strain produced 15 mg/L phytoene from 2 mol/L methane in fed-batch fermentation, a 4-fold increase in phytoene titer and 4-fold in yield. This demonstrates Methylocystis sp. MJC1's potential for efficient phytoene production and presents a novel approach for greenhouse gas reduction.

Enrichment of mixed methanotrophic cultures producing polyhydroxyalkanoates (PHAs) from various environmental sources

Methanotrophic bacteria can use atmospheric methane (CH4) as a sole carbon source for the growth and production of polyhydroxyalkanoates (PHA). The development of CH4 bioconversion processes relies heavily on the selection of an efficient methanotrophic culture. This research assessed the effect of selected growth conditions, such as nitrogen sources on the enrichment of methanotrophic cultures from various environments for PHA accumulation. Nitrate-based medium favoured the culture growth and selection for PHA-producing methanotrophic cultures with Methylocystis sp. as a major genus and accumulation of up to 27 % polyhydroxybutyrate (PHB) in the biomass. Three PHB-producing cultures: enriched from waste activated sludge (AS), peat bog soil (PB) and landfill biocover soil (LB) were then tested for their ability to produce PHA copolymer at different CH4:O2 ratios. All enriched cultures were able to utilise valeric acid as a cosubstrate for the accumulation of PHA with a 3-hydroxyvaleric (3HV) fraction of 21-41 mol% depending on the inoculum source and CH4 concentration. The process performance of selected cultures was evaluated and compared to the culture of reference strain Methylocystis hirsuta DSM 18500. All mixed cultures irrespective of their inoculum source had similar levels of 3HV fraction in the PHA (38 ± 2 mol%). The highest poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production was observed for AS culture at 10 % CH4 with an accumulation of 27 ± 3 % of dry cell weight (DCW), 3HV fraction of 39 ± 2 mol% and yield of 0.42 ± 0.02 g-PHA/g-substrate.

Imbalanced metabolism induced NH4+ accumulation and its effect on the central metabolism of Methylomonas sp. ZR1

Nitrogen and carbon are the two most essential nutrient elements, and their metabolism is tightly coupled in single carbon metabolic microorganisms. However, the nitrogen metabolism and the nitrogen/carbon (N/C) metabolic balance in single-carbon metabolism is poorly studied. In this study, the nitrogen metabolism pattern of the fast growing methanotrophs Methylomonas sp. ZR1 grown in methane and methanol was studied. Effect study of different nitrogen sources on the cell growth of ZR1 indicates that nitrate salts are the best nitrogen source supporting the growth of ZR1 using methane and methanol as carbon source. However, its metabolic intermediate ammonium was found to accumulate with high N/C ratio in the medium and consequently inhibit the growth of ZR1. Studies of carbon and nitrogen metabolic kinetic under different N/C ratio conditions indicate that the accumulation of NH4+ is caused by the imbalanced nitrogen and carbon metabolism in ZR1. Feeding carbon skeleton α-ketoglutaric acid could effectively relieve the inhibition effect of NH4+ on the growth of ZR1, which further confirms this assumption. qPCR analysis of the expression level of the central metabolic key enzyme gene indicates that the nitrogen metabolic intermediate ammonium has strong regulation effect on the central nitrogen and carbon metabolism in ZR1. qPCR-combined genomic analysis confirms that a third ammonium assimilation pathway glycine synthesis system is operated in ZR1 to balance the nitrogen and carbon metabolism. Based on the qPCR result, it was also found that ZR1 employs two strategies to relieve ammonium stress in the presence of ammonium: assimilating excess ammonium or cutting off the nitrogen reduction reactions according to the available C1 substrate. Validating the connections between single-carbon and nitrogen metabolism and studying the accumulation and assimilation mechanism of ammonium will contribute to understand how nitrogen regulates cellular growth in single-carbon metabolic microorganisms.

Carbon dioxide and methane as carbon source for the production of polyhydroxyalkanoates and concomitant carbon fixation

The currently used plastics are non-biodegradable, and cause greenhouse gases (GHGs) emission as they are petroleum-based. Polyhydroxyalkanoates (PHAs) are biopolymers with excellent biodegradability and biocompatibility, which can be used to replace petroleum-based plastics. A variety of microorganisms have been found to synthesize PHAs by using typical GHGs: carbon dioxide and methane as carbon sources. Converting carbon dioxide (CO2) and methane (CH4) to PHAs is an attractive option for carbon capture and biodegradable plastic production. In this review, the microorganisms capable of using CO2 and CH4 to produce PHAs were summarized. The metabolic mechanism, PHAs production process, and the factors influencing the production process are illustrated. The currently used optimization techniques to improve the yield of PHAs are discussed. The challenges and future prospects for developing economically viable PHAs production using GHGs as carbon source are identified. This work provides an insight for achieving carbon sequestration and bioplastics based circular economy.

Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Methanol bioconversion in Methylotuvimicrobium buryatense 5GB1C through self-cycling fermentation

Methanol is an abundant and low-cost next-generation carbon source. While many species of methanotrophic bacteria can convert methanol into valuable bioproducts in bioreactors, Methylotuvimicrobium buryatense 5GB1C stands out as one of the most promising strains for industrialization. It has a short doubling time compared to most methanotrophs, remarkable resilience against contamination, and a suite of tools enabling genetic engineering. When approaching industrial applications, growing M. buryatense 5GB1C on methanol using common batch reactor operation has important limitations; for example methanol toxicity leads to mediocre biomass productivity. Advanced bioreactor operation strategies, such as fed-batch and self-cycling fermentation, have the potential to greatly improve the industrial prospects of methanotrophs growing on methanol. Herein, implementation of fed-batch operation led to a 26-fold increase in biomass density, while two different self-cycling fermentation (SCF) strategies led to 3-fold and 10-fold increases in volumetric biomass productivity. Interestingly, while synchronization is a typical trait of microbial populations undergoing SCF, M. buryatense 5GB1C cultures growing under this mode of operation led to stable, reproducible cycles but no significant synchronization.

Biotransformation of gluten-free composite flour mediated by probiotics via solid-state fermentation process conducted under different moisture contents

Staple foods produced from composite flour are considered feasible to alleviate protein-energy malnutrition (PEM). However, one of the major limitations of composite flour is poor protein digestibility. The biotransformation process mediated by probiotics via solid-state fermentation (SSF) holds a promising potential to address the poor protein digestibility in composite flour. Yet, there is no report established in this regard to the best of our knowledge. Therefore, 4 strains of Lactiplantibacillus plantarum and Pediococcus pentosaceus UP2 isolated from Malaysian foods that were previously reported to produce versatile extracellular hydrolytic enzymes were employed to biotransform gluten-free composite flour derived from rice, sorghum, and soybean. The SSF process was performed under 30-60% (v/w) moisture content for 7 days, where samples were withdrawn at 24 h intervals for various analyses such as pH, total titratable acidity (TTA), extracellular protease activity, soluble protein concentration, crude protein content, and in vitro protein digestibility. The pH of the biotransformed composite flour showed a significant reduction from the initial range of pH 5.98-6.67 to the final pH of 4.36-3.65, corresponding to the increase in the percentage of TTA in the range of 0.28-0.47% to 1.07-1.65% from days 0 to 4 and remained stable till day 7 of the SSF process. The probiotics strains exhibited high extracellular proteolytic activity (0.63-1.35 U/mg to 4.21-5.13 U/mg) from days 0 to 7. In addition, the treated composite flour soluble protein increased significantly (p ≤ 0.05) (0.58-0.60 mg/mL to 0.72-0.79 mg/mL) from days 0 to 7, crude protein content (12.00-12.18% to 13.04-14.39%) and protein digestibility (70.05-70.72% to 78.46-79.95%) from days 0 to 4 of SSF. The results of biotransformation of 50% (v/w) moisture content were mostly comparable to 60% (v/w) moisture content, implying 50% (v/w) moisture content was the most suitable moisture content for the effective biotransformation of gluten-free composite flour mediated by probiotics via SSF since flour quality is better at lower moisture content. As for the overall performance, L. plantarum RS5 was ranked the best strain, attributed to the general improvement in the physicochemical properties of composite flour.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils

CH₄ emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH₄ oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH₄ produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH₄ oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH₄ oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH₄ emissions via the reduction of CH₄ oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO₃^- is responsible for the decrease in CH₄ oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH₄ oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH₄ emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH₄ dynamics in Arctic regions.

Increasing lysine level improved methanol assimilation toward butyric acid production in Butyribacterium methylotrophicum

BACKGROUND

Methanol, a promising non-food fermentation substrate, has gained increasing interest as an alternative feedstock to sugars for the bio-based production of value-added chemicals. Butyribacterium methylotrophicum, one of methylotrophic-acetogenic bacterium, is a promising host to assimilate methanol coupled with CO₂ fixation for the production of organic acids, such as butyric acid. Although the methanol utilization pathway has been identified in B. methylotrophicum, little knowledge was currently known about its regulatory targets, limiting the rational engineering to improve methanol utilization.

RESULTS

In this study, we found that methanol assimilation of B. methylotrophicum could be significantly improved when using corn steep liquor (CSL) as the co-substrate. The further investigation revealed that high level of lysine was responsible for enhanced methanol utilization. Through the transcriptome analysis, we proposed a potential mechanism by which lysine confers improved methylotrophy via modulating NikABCDE and FhuBCD transporters, both of which are involved in the uptake of cofactors essential for enzymes of methanol assimilation. The improved methylotrophy was also confirmed by overexpressing NikABCDE or FhuBCD operon. Finally, the de novo synthetic pathway of lysine was further engineered and the methanol utilization and butyric acid production of B. methylotrophicum were improved by 63.2% and 79.7%, respectively. After an optimization of cultivation medium, 3.69 g/L of butyric acid was finally achieved from methanol with a yield of 76.3%, the highest level reported to date.

CONCLUSION

This study revealed a novel mechanism to regulate methanol assimilation by lysine in B. methylotrophicum and engineered it to improve methanol bioconversion to butyric acid, culminating in the synthesis of the highest butyric acid titer reported so far in B. methylotrophicum. What's more, our work represents a further advancement in the engineering of methylotrophic-acetogenic bacterium to improve C1-compound utilization.

Screening, and Optimization of Fermentation Medium to Produce Secondary Metabolites from Bacillus amyloliquefaciens, for the Biocontrol of Early Leaf Spot Disease, and Growth Promoting Effects on Peanut (Arachis hypogaea L.)

A novel Bacillus amyloliquefaciens BAM strain, with novel fermentation nutrient mediums and compositions, could produce potent antifungal secondary metabolites, as the existing strains face resistance from fungus pathogens. In the current study, we introduced two novel nutrient mediums for the fermentation process, semolina and peanut root extract, as carbon and nitrogen sources in order to maximize the antifungal effects of B. amyloliquefaciens against Cercaspora arachidichola to control early leaf spot disease in peanuts. Based on a single-factor test and the central composite design of response surface methodology, the optimum fermentation medium for Bacillus amyloliquefaciens antagonistic substance was determined, containing 15 gm/L of semolina flour, 12.5 gm/L of beef extract, and 0.5 gm/L of magnesium sulfate, which inhibited the fungal growth by 91%. In vitro, antagonistic activity showed that the fermentation broth of B. amyloliquefaciens BAM with the optimized medium formulation had an inhibition rate of (92.62 ± 2.07)% on the growth of C. arachidichola. Disease control effects in pot experiments show that the pre-infection spray of B. amyloliquefaciens BAM broth had significant efficiency of (92.00 ± 3.79)% in comparison to post-infection spray. B. amyloliquefaciens BAM broth significantly promoted peanut plant growth and physiological parameters and reduced the biotic stress of C. archidechola. Studies revealed that B. amyloliquefaciens BAM with a novel fermentation formulation could be an ideal biocontrol and biofertilizer agent and help in early disease management of early leaf spots in peanuts.

The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis

Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH₄) and nitrous oxide (N₂O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH₄ at the global scale. We also address the effects of N enrichment on N₂O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH₄ oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH₄⁺ enrichment, inhibits CH₄ oxidation, resulting in higher CH₄ emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N₂O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.

Sustainable Process for the Production of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from Renewable Resources: A Simulation Study

Bacterially produced polyhydroxyalkanoates are valuable substitutes for petrochemical plastics, but their current production capacities are very scarce. Producing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-co-HV) from methane and odd-chain carbon fatty acids could make the production of this biodegradable polymer cost-effective. This study analyzes the main factors affecting methanotrophic growth and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) accumulation, simulating a pilot-scale process based on a double-stage approach. The effects of the nitrogen source and the oxygen partial pressure during a 20 day growth phase were studied; the cosubstrate concentration, the culture selected, and the methane partial pressure were investigated during the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production stage performed within 15 days under nutrient starvation. Methylocystis parvus OBBP and Methylosinus thricosporum OB3b reached the maximum growth productivities with ammonium as the nitrogen source and oxygen at high partial pressure. The simulation of the PHB-co-HV accumulation revealed that methanotrophs could better accumulate the polymer with low valeric acid concentrations. A methane-abundant gas stream (0.5 atm of methane) could increase process yields up to 0.32 kg m^-3 d^-1.

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.

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.

Spatial and seasonal dynamics of the methane cycle in a tropical coastal lagoon and its tributary river

Coastal aquatic ecosystems such as estuaries and coastal lagoons are important atmospheric methane sources that must be better constrained. This work presents a detailed characterization of the methane cycle in a tropical coastal lagoon (La Mancha, Veracruz, Mexico) and its tributary river over three distinct seasons, along a transect from the river to the sea connection. In addition to several physicochemical parameters, the dissolved methane, carbon dioxide, and oxygen concentrations were measured with high resolution in the sediments and the water column, combined with production/uptake rates. Methane and carbon dioxide cycles were further constrained by determining atmospheric flux over the entire river and lagoon sections. The results indicate that La Mancha is a highly contrasted ecosystem. The river section is characterized by a strong pycnocline, relatively high methane concentration, and active methanogenesis and methanotrophy, discharging into a relatively homogeneous lagoon section where the methane and carbon cycles are less active. Overall, both the river and the lagoon were a net source of methane and carbon dioxide, with an annual emission of 2.9 metric tons of methane and 2757 metric tons of carbon dioxide. The spatial structure of the main components of the methane, carbon dioxide, and oxygen cycles was established, and it was observed that depthwise heterogeneities predominated in the river section. In contrast, lengthwise heterogeneities dominated in the lagoon section.

Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8

Methylomicrobium album BG8 is an aerobic methanotrophic bacterium with promising features as a microbial cell factory for the conversion of methane to value-added chemicals. However, the lack of a genome-scale metabolic model (GEM) of M. album BG8 has hindered the development of systems biology and metabolic engineering of this methanotroph. To fill this gap, a high-quality GEM was constructed to facilitate a system-level understanding of the biochemistry of M. album BG8. Flux balance analysis, constrained with time-series data derived from experiments with various levels of methane, oxygen, and biomass, was used to investigate the metabolic states that promote the production of biomass and the excretion of carbon dioxide, formate, and acetate. The experimental and modeling results indicated that M. album BG8 requires a ratio of ∼1.5:1 between the oxygen- and methane-specific uptake rates for optimal growth. Integrative modeling revealed that at ratios of  >2:1 oxygen-to-methane uptake flux, carbon dioxide and formate were the preferred excreted compounds, while at ratios of <1.5:1 acetate accounted for a larger fraction of the total excreted flux. Our results showed a coupling between biomass production and the excretion of carbon dioxide that was linked to the ratio between the oxygen- and methane-specific uptake rates. In contrast, acetate excretion was experimentally detected during exponential growth only when the initial biomass concentration was increased. A relatively lower growth rate was also observed when acetate was produced in the exponential phase, suggesting a trade-off between biomass and acetate production.

IMPORTANCE A genome-scale metabolic model (GEM) is an integrative platform that enables the incorporation of a wide range of experimental data. It is used to reveal system-level metabolism and, thus, clarify the link between the genotype and phenotype. The lack of a GEM for Methylomicrobium album BG8, an aerobic methane-oxidizing bacterium, has hindered its use in environmental and industrial biotechnology applications. The diverse metabolic states indicated by the GEM developed in this study demonstrate the versatility in the methane metabolic processes used by this strain. The integrative GEM presented here will aid the implementation of the design-build-test-learn paradigm in the metabolic engineering of M. album BG8. This advance will facilitate the development of a robust methane bioconversion platform and help to mitigate methane emissions from environmental systems.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

In vivo quantification of polyhydroxybutyrate (PHB) in the alphaproteobacterial methanotroph, Methylocystis sp. Rockwell

Methane is a common industrial by-product that can be used as feedstock for production of the biopolymer polyhydroxybutyrate (PHB) by alphaproteobacterial methanotrophs. In vivo assessment of PHB production would shed light on the biosynthesis process and guide design of improved production strategies, but it is currently difficult to perform efficiently. In this study, the alphaproteobacterial methanotroph Methylocystis sp. Rockwell was grown on methane with three different nitrogen sources (ammonium, nitrate, and atmospheric nitrogen), and biomass samples were harvested at defined time points during lag, exponential, and stationary growth phases. PHB cell content was analyzed at these sampling points via a standard gas chromatography-flame ionization detector method, which requires hydrolysis of PHB and esterification of the resulting monomer under acidic conditions, and a novel, rapid, cost-effective approach based on fixation and staining of bacterial cells via Nile Blue A fluorescent dye enabling differential staining of cell membranes and intracellular PHB granules for single-cell analysis through fluorescence microscopy. Overall, the two PHB quantification approaches were in agreement at all stages of growth and in all three growing conditions tested. The PHB cell content was greatest with atmospheric nitrogen as a nitrogen source, followed by ammonium and nitrate. Under atmospheric nitrogen and ammonium conditions, PHB cell content decreased with growth progression, while under nitrate conditions PHB cell content remained unchanged in all growth phases. In addition to presenting a rapid, efficient method enabling in vivo quantification of PHB production, the present study highlights the impact of nitrogen source on PHB production by Methylocystis sp. Rockwell. KEY POINTS: • A novel fluorescence microscopy method to quantify PHB in single cells was developed • The microscopy method was validated by the derivation/gas chromatography method • Methylocystis sp. Rockwell synthesizes PHB granules without nutrient stress.

The Influence of Above-Ground Herbivory on the Response of Arctic Soil Methanotrophs to Increasing CH4 Concentrations and Temperatures

Rising temperatures in the Arctic affect soil microorganisms, herbivores, and peatland vegetation, thus directly and indirectly influencing microbial CH₄ production. It is not currently known how methanotrophs in Arctic peat respond to combined changes in temperature, CH₄ concentration, and vegetation. We studied methanotroph responses to temperature and CH₄ concentration in peat exposed to herbivory and protected by exclosures. The methanotroph activity was assessed by CH₄ oxidation rate measurements using peat soil microcosms and a pure culture of Methylobacter tundripaludum SV96, qPCR, and sequencing of pmoA transcripts. Elevated CH₄ concentrations led to higher CH₄ oxidation rates both in grazed and exclosed peat soils, but the strongest response was observed in grazed peat soils. Furthermore, the relative transcriptional activities of different methanotroph community members were affected by the CH₄ concentrations. While transcriptional responses to low CH₄ concentrations were more prevalent in grazed peat soils, responses to high CH₄ concentrations were more prevalent in exclosed peat soils. We observed no significant methanotroph responses to increasing temperatures. We conclude that methanotroph communities in these peat soils respond to changes in the CH₄ concentration depending on their previous exposure to grazing. This “conditioning” influences which strains will thrive and, therefore, determines the function of the methanotroph community.

Cultivation of Important Methanotrophs From Indian Rice Fields

Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10^–6–10^–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.

Metabolome profiles of the alphaproteobacterial methanotroph Methylocystis sp. Rockwell in response to carbon and nitrogen source

Methanotrophs use methane as a sole carbon source and thus play a critical role in its global consumption. Intensified interest in methanotrophs for their low-cost production of value-added products and large-scale industrialization has led to investigations of strain-to-strain variation in parameters for growth optimization and metabolic regulation. In this study, Methylocystis sp. Rockwell was grown with methane or methanol as a carbon source and ammonium or nitrate as a nitrogen source. The intracellular metabolomes and production of polyhydroxybutyrate, a bioplastic precursor, were compared among treatments to determine how the different combinations of carbon and nitrogen sources affected metabolite production. The methane-ammonium condition resulted in the highest growth, followed by the methane-nitrate, methanol-nitrate and methanol-ammonium conditions. Overall, the methane-ammonium and methane-nitrate conditions directed metabolism toward energy-conserving pathways, while methanol-ammonium and methanol-nitrate directed the metabolic response toward starvation pathways. Polyhydroxybutyrate was produced at greater abundances in methanol-grown cells, independent of the nitrogen source. Together, the results revealed how Methylocystis sp. Rockwell altered its metabolism with different combinations of carbon and nitrogen source, with implications for production of industrially relevant metabolites.

Transcriptomic and Metabolomic Responses to Carbon and Nitrogen Sources in Methylomicrobium album BG8

Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled the phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated hydroxylamine dehydrogenase (haoAB) and overall central metabolic activity, whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species. IMPORTANCE Methanotrophs are gaining increasing interest for their biotechnological potential to convert single-carbon compounds into value-added products such as industrial chemicals, fuels, and bioplastics. Optimizing these species for biotechnological applications requires a detailed understanding of how cellular activity and metabolism vary across different growth substrates. Although each of the two most commonly used carbon sources (methane or methanol) and nitrogen sources (ammonium or nitrate) in methanotroph growth media have well-described advantages and disadvantages in an industrial context, their effects on global cellular activity remain poorly characterized. Here, we comprehensively describe the transcriptomic and metabolomic changes that characterize the growth of an industrially promising methanotroph strain on multiple combinations of carbon and nitrogen sources. Our results represent a more holistic evaluation of cellular activity than previous studies of core metabolic pathways and provide a valuable basis for the future biotechnological optimization of these species.

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.

Screening for Methane Utilizing Mixed Communities with High Polyhydroxybutyrate (PHB) Production Capacity Using Different Design Approaches

With the adverse environmental ramifications of the use of petroleum-based plastic outweighing the challenges facing the industrialization of bioplastics, polyhydroxyalkanoate (PHA) biopolymer has gained broad interest in recent years. Thus, an efficient approach for maximizing polyhydroxybutyrate (PHB) polymer production in methanotrophic bacteria has been developed using the methane gas produced in the anaerobic digestion process in wastewater treatment plants (WWTPS) as a carbon substrate and an electron donor. A comparison study was conducted between two experimental setups using two different recycling strategies, namely new and conventional setups. The former setup aims to recycle PHB producers into the system after the PHB accumulation phase, while the latter recycles the biomass back into the system after the exponential phase of growth or the growth phase. The goal of this study was to compare both setups in terms of PHB production and other operational parameters such as growth rate, methane uptake rate, and biomass yield using two different nitrogen sources, namely nitrate and ammonia. The newly proposed setup is aimed at stimulating PHB accumulating type II methanotroph growth whilst enabling other PHB accumulators to grow simultaneously. The success of the proposed method was confirmed as it achieved highest recorded PHB accumulation percentages for a mixed culture community in both ammonia- and nitrate-enriched media of 59.4% and 54.3%, respectively, compared to 37.8% and 9.1% for the conventional setup. Finally, the sequencing of microbial samples showed a significant increase in the abundance of type II methanotrophs along with other PHB producers, confirming the success of the newly proposed technique in screening for PHB producers and achieving higher PHB accumulation.

Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum

The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.

Bioconversion of wastewater to single cell protein by methanotrophic bacteria

Single cell protein (SCP) provides an alternative protein source to partially replace the conventional agricultural resources and support the increased nutritional needs. Inexpensive feeding source is one of the key limiting factors for the expansion of SCP production. The present study examined the valorization of biogas derived from the anaerobic digestion (AD) of sewage sludge and the discarded effluent as nutrients source to produce SCP using methanotrophic bacteria. Results indicated that the mixed methanotrophic culture can grow well on the pasteurized AD supernatant and biogas, succeeding in promising dry weight (DW) yield (0.66 ± 0.01 g-DW/g-CH₄ and 11.54 ± 0.12 g-DW/g-NH₄⁺). Methylomonas (56.26%) and Methylophilus (24.60%) spp. were the two main representatives of the mixed culture. The produced dried biomass had a protein content higher than 41% w/w, including essential amino acids like histidine, valine, phenylalanine, isoleucine, leucine, threonine and lysine. The cultivated SCP shows potential utilization as protein source for animal diets.

Valorization of methane from environmental engineering applications: A critical review

Wastewater and waste management sectors alone account for 18% of the anthropogenic methane (CH₄) emissions. This study presents a critical overview of methanotrophs ("methane oxidizing microorganisms") for valorizing typically discarded CH₄ from environmental engineering applications, focusing on wastewater treatment plants. Methanotrophs can convert CH₄ into valuable bioproducts including chemicals, biodiesel, DC electricity, polymers, and S-layers, all under ambient conditions. As discarded CH₄ and its oxidation products can also be used as a carbon source in nitrification and annamox processes. Here we discuss modes of CH₄ assimilation by methanotrophs in both natural and engineered systems. We also highlight the technical challenges and technological breakthroughs needed to enable targeted CH₄ oxidation in wastewater treatment plants.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.

Engineered Methanotrophy: A Sustainable Solution for Methane-Based Industrial Biomanufacturing

Methane is a promising feedstock with high abundance and low cost for the sustainable production of biochemicals and biofuels. Methanotrophic bacteria are particularly interesting platforms for methane bioconversion as they can utilize methane as a carbon substrate. Recently, breakthroughs in the understanding of methane metabolism in methanotrophs as well as critical advances in systems metabolic engineering of methanotrophic bacteria have been reported. Here, we discuss the important gaps in the understanding of methanotrophic metabolism that have been uncovered recently and the current trends in systems metabolic engineering in both methanotrophic bacteria and non-native hosts to advance the potential of methane-based biomanufacturing.

Exploration and enrichment of methane-oxidizing bacteria derived from a rice paddy field emitting highly concentrated methane

Methane-oxidizing bacteria (MOB) possess the metabolic potential to assimilate the highly potent greenhouse gas, CH₄, and can also synthesize valuable products. Depending on their distinct and fastidious metabolic pathways, MOB are mainly divided into Type I and Type II; the latter are known as producers of polyhydroxyalkanoate (PHA). Despite the metabolic potential of MOB to synthesize PHA, the ecophysiology of MOB, especially under high CH₄ flux conditions, is yet to be understood. Therefore, in this study, a rice paddy soil receiving a high CH₄ flux from underground was used as an inoculum to enrich MOB using fed-batch operation, then the enriched Type II MOB were characterized. The transitions in the microbial community composition and CH₄ oxidation rates were monitored by 16S rRNA gene amplicon sequencing and degree of CH₄ consumption. With increasing incubation time, the initially dominant Methylomonas sp., affiliated with Type I MOB, was gradually replaced with Methylocystis sp., Type II MOB, resulting in a maximum CH₄ oxidation rate of 1.40 g-CH₄/g-biomass/day. The quantification of functional genes encoding methane monooxygenase, pmoA and PHA synthase, phaC, by quantitative PCR revealed concomitant increases in accordance with the Type II MOB enrichment. These increases in the functional genes underscore the significance of Type II MOB to mitigate greenhouse gas emission and produce PHA.

Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b

Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism.

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.

Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol

Methylotuvimicrobium alcaliphilum 20Z is a promising platform strain for bioconversion of one-carbon (C1) substrates into value-added products. To carry out robust metabolic engineering with methylotrophic bacteria and to implement C1 conversion machinery in non-native hosts, systems-level evaluation and understanding of central C1 metabolism in methanotrophs under various conditions is pivotal but yet elusive. In this study, a genome-scale integrated approach was used to provide in-depth knowledge on the metabolic pathways of M. alcaliphilum 20Z grown on methane and methanol. Systems assessment of core carbon metabolism indicated the methanol assimilation pathway is mostly coupled with the efficient Embden-Meyerhof-Parnas (EMP) pathway along with the serine cycle. In addition, an incomplete TCA cycle operated in M. alcaliphilum 20Z on methanol, which might only supply precursors for de novo synthesis but not reducing powers. Instead, it appears that the direct formaldehyde oxidation pathway supply energy for the whole metabolic system. Additionally, a comparative transcriptomic analysis in multiple gammaproteobacterial methanotrophs also revealed the transcriptional responses of central metabolism on carbon substrate change. These findings provided a systems-level understanding of carbon metabolism and new opportunities for strain design to produce relevant products from different C1-feedstocks.

Biochar can mitigate methane emissions by improving methanotrophs for prolonged period in fertilized paddy soils

Biochar application to fertilized paddy soils has been recommended as an effective countermeasure to mitigate methane (CH₄) emissions, but its mechanism and effective duration has not yet been adequately elucidated. A laboratory incubation experiment was performed to gain insight into the combined effects of fresh and six-year aged biochar on potential methane oxidation (PMO) in paddy soils with ammonium or nitrate-amendment. Results showed that both ammonium and nitrate were essential for CH₄ oxidation though high ammonium (4 mM) inhibited PMO as compared to low ammonium (1 mM and 2 mM), and that nitrate was better in promoting PMO than ammonium. Moreover, ammonium-amendment promoted type I pmoA, and nitrate-amendment enhanced type II pmoA abundance. Both fresh and aged biochar increased PMO as well as nitrification by enhancing the total, type I and type II methanotrophs as compared to the control. Increased soil PMO with mineral N input in both six-year aged biochar and fresh biochar amendment, indicating that biochar mitigated CH₄ by promoting PMO for prolonged period in fertilized paddy soils.