Search Results (75)

Paddy fields are the main agricultural source of greenhouse gas methane (CH₄) emissions. To enhance rice yield, various fertilization practices have been employed in rice paddies. However, the key microbial and abiotic factors driving CH₄ emissions under different fertilization practices in paddy fields remain largely uncharted. This study conducted field experiments in a traditional double-cropping rice area in South China, utilizing five different fertilization practices to investigate the key factors influencing CH₄ emissions. High-throughput sequencing and PICRUSt2 functional prediction were employed to investigate the contributions of soil physicochemical properties, CH₄-metabolizing microorganisms (methanogens and methanotrophs), and key genes (mcrA and pmoA) on CH₄ emissions. The results showed that CH₄ emission fluxes exhibited seasonal variations, with consistent patterns of change observed across all treatments for both early- and late-season rice. Compared to the no-fertilization (NF) treatment, cumulative CH₄ emissions were lower in early-season rice with green manure (GM) and straw returning (SR) treatments, as well as in late-season rice with GM treatment, while rice yields were maintained at higher levels. High-throughput sequencing analysis revealed that potential methanogens were primarily distributed among four orders: Methanobacteriales, Methanocellales, Methanomicrobiales, and Methanosarcinales. Furthermore, there was a significant positive correlation between the relative abundance of the CH₄-related key gene mcrA and these microorganisms. Functional analysis indicated that these potential methanogens primarily produce methane through the acetoclastic and hydrogenotrophic pathways. Aerobic CH₄-oxidizing bacteria, predominantly from the genus Methylocystis, were detected in all the treatments, while the CH₄ anaerobic-oxidizing archaea ANME-1b was only detected in chemical fertilization (CF) and cow manure (CM) treatments. Our random forest analysis revealed that the relative abundance of two methanogens (Methanocellales and Methanosarcinales) and two environmental factors (pH and DOC) had significant impacts on the cumulative CH₄ emissions. The variance decomposition analysis highlighted the CH₄-metabolizing microorganisms explained 50% of the variance in the cumulative CH₄ emissions, suggesting that they are the key microbial factors driving CH₄ emissions. These findings provide guidance for the development of rational measures to reduce CH₄ emissions in paddy fields. Full article

Polyhydroxyalkanoates (PHAs) are polyesters synthesized as a carbon and energy reserve material by a wide number of bacteria. These polymers are characterized by their thermoplastic properties similar to those of plastics derived from the petrochemical industry, such as polyethylene and polypropylene. PHAs are widely used in the medical field and have the potential to be used in other applications due to their biocompatibility and biodegradability. Among PHAs, P(3HB-co-3HV) copolymers are thermo-elastomeric polyesters that are typically soft and flexible with low to no crystallinity, which can expand the range of applications of these bioplastics. Several bacterial species, such as Cupriavidus necator, Azotobacter vinelandii, Halomonas sp. and Bacillus megaterium, have been successfully used for P(3HB-co-3HV) production, both in batch and fed-batch cultures using different low-cost substrates, such as vegetable and fruit waste. Nevertheless, in recent years, several fermentation strategies using other microbial models, such as methanotrophic bacterial strains as well as halophilic bacteria, have been developed in order to improve PHA production in cultivation conditions that are easily implemented on a large scale. This review aims to summarize the recent trends in the production and recovery of PHA copolymers by fermentation, including different cultivation modalities, low-cost raw materials, as well as downstream strategies that have recently been developed with the purpose of producing copolymers, such as P(3HB-co-3HV), with suitable mechanical properties for applications in the biomedical field. Full article

Methanotrophs are bacteria that consume methane (CH₄) as their sole carbon and energy source. These microorganisms play a crucial role in the carbon cycle by metabolizing CH₄ (the greenhouse gas), into cellular biomass and carbon dioxide (CO₂). Polyhydroxyalkanoates (PHAs) are biopolymers produced by various microorganisms, including methanotrophs. PHA production using methanotrophs is a promising strategy to address growing concerns regarding plastic pollution and the need for sustainable, biodegradable materials. Various factors, including nutrient availability, environmental conditions, and metabolic engineering strategies, influence methanotrophic production. Nutrient limitations, particularly those of nitrogen or phosphorus, enhance PHA production by methanotrophs. Metabolic engineering approaches, such as the overexpression of key enzymes involved in PHA biosynthesis or the disruption of competing pathways, can also enhance PHA yields by methanotrophs. Overall, PHA production by methanotrophs represents a sustainable and versatile approach for developing biomedical materials with numerous potential applications. Additionally, alternative feedstocks, such as industrial waste streams or byproducts can be explored to improve the economic feasibility of PHA production. This review briefly describes the potential of methanotrophs to produce PHAs, with recent updates and perspectives. Full article

Anaerobic digestion (AD) produces useful biogas and waste streams with high levels of dissolved methane (CH₄) and ammonium (NH₄⁺), among other nutrients. Membrane biofilm reactors (MBfRs), which support dissolved methane oxidation in the same reactor as simultaneous nitrification and denitrification (ME-SND), are a potential bubble-less treatment method. Here, we demonstrate ME-SND taking place in single-stage, AD digestate liquid-fed MBfRs, where oxygen (O₂) and supplemental CH₄ were delivered via pressurized membranes. The effects of two O₂ pressures, leading to different O₂ fluxes, on CH₄ and N removal were examined. MBfRs achieved up to 98% and 67% CH₄ and N removal efficiencies, respectively. The maximum N removal rates ranged from 57 to 94 mg N L⁻¹ d⁻¹, with higher overall rates observed in reactors with lower O₂ pressures. The higher-O₂-flux condition showed NO₂⁻ as a partial nitrification endpoint, with a lower total N removal rate due to low N₂ gas production compared to lower-O₂-pressure reactors, which favored complete nitrification and denitrification. Membrane biofilm 16S rRNA amplicon sequencing showed an abundance of aerobic methanotrophs (especially Methylobacter, Methylomonas, and Methylotenera) and enrichment of nitrifiers (especially Nitrosomonas and Nitrospira) and anammox bacteria (especially Ca. Annamoxoglobus and Ca. Brocadia) in high-O₂ and low-O₂ reactors, respectively. Supplementation of the influent with nitrite supported evidence that anammox bacteria in the low-O₂ condition were nitrite-limited. This work highlights coupling of aerobic methanotrophy and nitrogen removal in AD digestate-fed reactors, demonstrating the potential application of ME-SND in MBfRs for the treatment of AD’s residual liquids and wastewater. Sensor-based tuning of membrane O₂ pressure holds promise for the optimization of bubble-less treatment of excess CH₄ and NH₄⁺ in wastewater. Full article

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH₄ cm⁻³ day⁻¹ in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65–99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO₂ fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes. Full article

The biotechnology of converting methane to single-cell protein (SCP) implies using fast-growing thermotolerant aerobic methanotrophic bacteria. Among the latter, members of the genus Methylococcus received significant research attention and are used in operating commercial plants. Methylococcus capsulatus MIR is a recently discovered member of this genus with the potential to be used for the purpose of SCP production. Like other Methylococcus species, this bacterium stores carbon and energy in the form of glycogen, particularly when grown under nitrogen-limiting conditions. The genome of strain MIR encodes two glycogen synthases, GlgA1 and GlgA2, which are only moderately related to each other. To obtain glycogen-free cell biomass of this methanotroph, glycogen synthase mutants, ΔglgA1, ΔglgA2, and ΔglgA1ΔglgA2, were constructed. The mutant lacking both glycogen synthases exhibited a glycogen-deficient phenotype, whereas the intracellular glycogen content was not reduced in strains defective in either GlgA1 or GlgA2, thus suggesting functional redundancy of these enzymes. Inactivation of the glk gene encoding glucokinase also resulted in a sharp decrease in glycogen content and accumulation of free glucose in cells. Wild-type strain MIR and the mutant strain ΔglgA1ΔglgA2 were also grown in a bioreactor operated in batch and continuous modes. Cell biomass of ΔglgA1ΔglgA2 mutant obtained during batch cultivation displayed high protein content (71% of dry cell weight (DCW) compared to 54% DCW in wild-type strain) as well as a strong reduction in glycogen content (10.8 mg/g DCW compared to 187.5 mg/g DCW in wild-type strain). The difference in protein and glycogen contents in biomass of these strains produced during continuous cultivation was less pronounced, yet biomass characteristics relevant to SCP production were slightly better for ΔglgA1ΔglgA2 mutant. Genome analysis revealed the presence of glgA1-like genes in all methanotrophs of the Gammaproteobacteria and Verrucomicrobia, while only a very few methanotrophic representatives of the Alphaproteobacteria possessed these determinants of glycogen biosynthesis. The glgA2-like genes were present only in genomes of gammaproteobacterial methanotrophs with predominantly halo- and thermotolerant phenotypes. The role of glycogen in terms of energy reserve is discussed. Full article

Methanotrophy is a biological process that effectively reduces global methane emissions by utilizing microorganisms that can utilize methane as a source of energy under both oxic and anoxic conditions, using a variety of different electron acceptors. Methanotrophic microbes, which utilize methane as their primary source of carbon and energy, are microorganisms found in various environments, such as soil, sediments, freshwater, and marine ecosystems. These microbes play a significant role in the global carbon cycle by consuming methane, a potent greenhouse gas, and converting it into carbon dioxide, which is less harmful. However, methane is known to be the primary contributor to ozone formation and is considered a major greenhouse gas. Methane alone contributes to 30% of global warming; its emissions increased by over 32% over the last three decades and thus affect humans, animals, and vegetation adversely. There are different sources of methane emissions, like agricultural activities, wastewater management, landfills, coal mining, wetlands, and certain industrial processes. In view of the adverse effects of methane, urgent measures are required to reduce emissions. Methanotrophs have attracted attention as multifunctional bacteria with potential applications in biological methane mitigation and environmental bioremediation. Methanotrophs utilize methane as a carbon and energy source and play significant roles in biogeochemical cycles by oxidizing methane, which is coupled to the reduction of various electron acceptors. Methanotrophy, a natural process that converts methane into carbon dioxide, presents a promising solution to mitigate global methane emissions and reduce their impact on climate change. Nonetheless, additional research is necessary to enhance and expand these approaches for extensive use. In this review, we summarize the key sources of methane, mitigation strategies, microbial aspects, and the application of methanotrophs in global methane sinks with increasing anthropogenic methane emissions. Full article

An ever-increasing amount of research is being performed on the stability and recovery of soil methane-oxidizing bacteria since this is one of the fundamental processes controlling the amount of methane in the atmosphere. Mineral fertilizers may alter the methane oxidation processes in agricultural soils when they are introduced. Although ammonium (NH₄⁺) is believed to have a significant impact on aerobic methane oxidation activity in soils, there is still little data on how it reacts with lanthanum (La). The recent identification of a novel class of lanthanum-containing enzymes in methanotrophic bacteria may be the foundation for controlling the function of the soil “methane filter” and related microbiota. In the current study, microcosms with agricultural sod-podzolic soils were created and incubated in air or 20% CH₄ in the gas phase with the addition of NH₄⁺ (100 µg/g) and La (5 µg/g) to the soil. Using GC analysis and high-performance 16S rRNA sequencing, the methane oxidation potential and composition of soil bacterial communities were studied over the month of incubation. A negative impact of NH₄⁺ on the oxidation of methane was observed, whereas La had a somewhat beneficial effect. Ammonium had an impact on the composition of methanotrophs, and a significant shift was observed upon La addition. Proteobacteria made up a larger share of the soil microbial community, and Gammaproteobacteria dominated the methanotrophic populations. Methylobacter, a methanotroph, and Methylotenera, an obligatory methylotroph, were the two absolute dominants in the La-amended variants. These findings could help evaluate how lanthanum regulates methanotrophic communities in agricultural soils and lead to the creation of new strategies for controlling the “methane filter” in soil. Full article

Considering the increasing interest in understanding the biotic component of methane removal from our atmosphere, it becomes essential to study the physiological characteristics and genomic potential of methanotroph isolates, especially their traits allowing them to adapt to elevated growth temperatures. The genetic signatures of Methylocaldum species have been detected in many terrestrial and aquatic ecosystems. A small set of representatives of this genus has been isolated and maintained in culture. The genus is commonly described as moderately thermophilic, with the growth optimum reaching 50 °C for some strains. Here, we present a comparative analysis of genomes of three Methylocaldum strains—two terrestrial M. szegediense strains (O-12 and Norfolk) and one marine strain, Methylocaldum marinum (S8). The examination of the core genome inventory of this genus uncovers significant redundancy in primary metabolic pathways, including the machinery for methane oxidation (numerous copies of pmo genes) and methanol oxidation (duplications of mxaF, xoxF1-5 genes), three pathways for one-carbon (C1) assimilation, and two methods of carbon storage (glycogen and polyhydroxyalkanoates). We also investigate the genetics of melanin production pathways as a key feature of the genus. Full article

The ongoing yearly rise in worldwide methane (CH₄) emissions is mostly due to human activities. Nevertheless, since over half of these emissions are scattered and have a concentration of less than 3% (v/v), traditional physical–chemical methods are not very effective in reducing them. In this context, biotechnologies like biofiltration using methane-consuming bacteria, also known as methanotrophs, offer a cost-efficient and practical approach to addressing diffuse CH₄ emissions. The present review describes recent findings in biofiltration processes as one of the earliest biotechnologies for treating polluted air. Specifically, impacts of biotic (such as cooperation between methanotrophs and non-methanotrophic bacteria and fungi) and abiotic factors (such as temperature, salinity, and moisture) that influence CH₄ biofiltration were compiled. Understanding the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural practices and industrial procedures that contribute to a more favourable equilibrium of greenhouse gases. The integration of advanced genetic analyses can enable holistic approaches for unravelling the potential of biological systems for methane mitigation. This study pioneers a holistic approach to unravelling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. Full article

Methane-oxidizing bacteria (MOB) have long been recognized as an important bioindicator for oil and gas exploration. However, due to their physiological and ecological diversity, the distribution of MOB in different habitats varies widely, making it challenging to authentically reflect the abundance of active MOB in the soil above oil and gas reservoirs using conventional methods. Here, we selected the Puguang gas field of the Sichuan Basin in Southwest China as a model system to study the ecological characteristics of methanotrophs using culture-independent molecular techniques. Initially, by comparing the abundance of the pmoA genes determined by quantitative PCR (qPCR), no significant difference was found between gas well and non-gas well soils, indicating that the abundance of total MOB may not necessarily reflect the distribution of the underlying gas reservoirs. ¹³C-DNA stable isotope probing (DNA-SIP) in combination with high-throughput sequencing (HTS) furthermore revealed that type II methanotrophic Methylocystis was the absolutely predominant active MOB in the non-gas-field soils, whereas the niche vacated by Methylocystis was gradually filled with type I RPC-2 (rice paddy cluster-2) and Methylosarcina in the surface soils of gas reservoirs after geoscale acclimation to trace- and continuous-methane supply. The sum of the relative abundance of RPC-2 and Methylosarcina was then used as specific biotic index (BI) in the Puguang gas field. A microbial anomaly distribution map based on the BI values showed that the anomalous zones were highly consistent with geological and geophysical data, and known drilling results. Therefore, the active but not total methanotrophs successfully reflected the microseepage intensity of the underlying active hydrocarbon system, and can be used as an essential quantitative index to determine the existence and distribution of reservoirs. Our results suggest that molecular microbial techniques are powerful tools for oil and gas prospecting. Full article

The seasonal feeding patterns of the cold-adapted fish, Coregonus albula, are poorly studied in high-latitude lakes but could provide insight for predicting the effects of global warming. We examined vendace’s diet composition, traced the carbon and nitrogen isotope ratios from producers to consumers in the food web, and estimated vendace’s trophic position in a subarctic lake (the White Sea basin). Results showed the vendace to be a typical euryphagous fish, but clear seasonal differences were found in the relative importance of plankton and benthos in the diet. The vendace consumed primarily benthic amphipods in the summer, planktonic cladocerans in the autumn, and copepods in the winter–spring (under ice); larvae of aquatic insects were the second-most important food items throughout the year. Because of the substantial proportion of fish embryos in its diet, the vendace had a trophic position similar to that of a predatory fish (perch). The Bayesian food source-mixing model revealed that the majority of vendace energy derives from planktonic copepods. The dominant Cyclops had the lowest carbon isotope values, suggesting a carbon-depleted diet typical for methanotrophic bacteria, as its probable food source was in a lake under ice. Understanding the feeding patterns of vendace provides information to better predict the potential biotic effects of environmental change on lake ecosystems. Full article

This study designed surface flow constructed wetlands (SFCWs) with Myriophyllum aquaticum (M. aquaticum) to evaluate how different influent C/N ratios (0:1 (C₀N), 5:1 (C₅N), 10:1 (C₁₀N), and 15:1 (C₁₅N)) affect pollutant removal, greenhouse gas (GHG) emissions, and microbial communities. The results showed that effluent ammonia nitrogen (${\mathrm{N}\mathrm{H}}_4^{+}$-N), nitrate nitrogen (${\mathrm{N}\mathrm{O}}_3^{-}$-N), and total nitrogen (TN) concentrations decreased, but effluent chemical oxygen demand (COD) concentration increased with increasing influent C/N ratios. The highest removal rates of TN (73.17%) and COD (74.56%) were observed with C₅N. Regarding GHG emissions, a few changes in CO₂ fluxes were caused by the influent C/N ratio, whereas CH₄ fluxes obviously increased with the increasing influent C/N ratio. The highest N₂O emission occurred with C₀N (211.03 ± 44.38 mg-N·m⁻²·h⁻¹), decreasing significantly with higher C/N ratios. High-throughput sequencing revealed that different influent C/N ratios directly influenced the microbial distribution and composition related to CH₄ and N₂O metabolism in SFCWs. The highest abundance (46.24%) of denitrifying bacteria (DNB) was observed with C₅N, which helped to achieve efficient nitrogen removal with a simultaneous reduction in N₂O emissions. Methanogen abundance rose with higher C/N ratios, whereas methanotrophs peaked under C₅N and C₁₀N conditions. Additionally, the random forest model identified influent C/N ratio and Rhodopseudomonas as primary factors influencing CH₄ and N₂O emissions, respectively. This highlights the importance of the influent C/N ratio in regulating both pollutant removal and GHG emissions in constructed wetlands. Full article

Methanotrophy is the ability of an organism to capture and utilize the greenhouse gas, methane, as a source of energy-rich carbon. Over the years, significant progress has been made in understanding of mechanisms for methane utilization, mostly in bacterial systems, including the key metabolic pathways, regulation and the impact of various factors (iron, copper, calcium, lanthanum, and tungsten) on cell growth and methane bioconversion. The implementation of -omics approaches provided vast amount of heterogeneous data that require the adaptation or development of computational tools for a system-wide interrogative analysis of methanotrophy. The genome-scale mathematical modeling of its metabolism has been envisioned as one of the most productive strategies for the integration of muti-scale data to better understand methane metabolism and enable its biotechnological implementation. Herein, we provide an overview of various computational strategies implemented for methanotrophic systems. We highlight functional capabilities as well as limitations of the most popular web resources for the reconstruction, modification and optimization of the genome-scale metabolic models for methane-utilizing bacteria. Full article

Bioplastics hold significant promise in replacing conventional plastic materials, linked to various serious issues such as fossil resource consumption, microplastic formation, non-degradability, and limited end-of-life options. Among bioplastics, polyhydroxyalkanoates (PHA) emerge as an intriguing class, with poly(3-hydroxybutyrate) (P3HB) being the most utilized. The extensive application of P3HB encounters a challenge due to its high production costs, prompting the investigation of sustainable alternatives, including the utilization of waste and new production routes involving CO₂ and CH₄. This study provides a valuable comparison of two P3HBs synthesized through distinct routes: one via cyanobacteria (Synechocystis sp. PCC 6714) for photoautotrophic production and the other via methanotrophic bacteria (Methylocystis sp. GB 25) for chemoautotrophic growth. This research evaluates the thermal and mechanical properties, including the aging effect over 21 days, demonstrating that both P3HBs are comparable, exhibiting physical properties similar to standard P3HBs. The results highlight the promising potential of P3HBs obtained through alternative routes as biomaterials, thereby contributing to the transition toward more sustainable alternatives to fossil polymers. Full article