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The role of sediment oxygen demand (SOD) in causing dissolved oxygen (DO) depletion is widely acknowledged, with previous studies mainly focusing on chemical and biological SOD separately. However, the relationship between the putative functions of sediment microbes and SOD, and their impact on DO depletion in overlying water, remains unclear. In this study, DO depletion was observed in the downstream of the Gan River during the summer. Sediments were sampled from three downstream sites (YZ, Down1, and Down2) and one upstream site (CK) as a control. Aquatic physicochemical parameters and SOD levels were measured, and microbial functions were inferred from taxonomic genes through analyses of the 16S rRNA gene. The results showed that DO depletion sites exhibited a higher SOD rate compared to CK. The microbial community structure was influenced by the spatial variation of Proteobacteria, Chloroflexi, and Bacteroidota, with total organic carbon (TOC) content acting as a significant environmental driver. A negative correlation was observed between microbial diversity and DO concentration (p < 0.05). Aerobic microbes were more abundant in DO depletion sites, particularly Proteobacteria. Microbes involved in various biogeochemical cycles, such as carbon (methane oxidation, methanotrophs, and methylotrophs), nitrogen (nitrification and denitrification), sulfur (sulfide and sulfur compound oxidation), and manganese cycles (manganese oxidation), exhibited higher abundance in DO depletion sites, except for the iron cycle (iron oxidation). These processes were negatively correlated with DO concentration and positively with SOD (p < 0.05). Overall, the results highlight that aerobic bacteria's metabolic processes consume oxygen, increasing the SOD rate and contributing to DO depletion in the overlying water. Additionally, the study underscores the importance of targeting the removal of in situ microbial molecular mechanisms associated with toxic H2S and CH4 to support reoxygenation efforts in rehabilitating DO depletion sites in the Gan River, aiding in identifying factors controlling DO consumption and offering practical value for the river's restoration and management. [ABSTRACT FROM AUTHOR]

Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms – circadian clocks – that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria. [ABSTRACT FROM AUTHOR]

Methane capture via oxidation is considered one of the 'Holy Grails' of catalysis (Tucci and Rosenzweig, 2024). Methane is also a primary greenhouse gas that has to be reduced by 1.2 billion metric tonnes in 10 years to decrease global warming by only 0.23°C (He and Lidstrom, 2024); hence, new technologies are needed to reduce atmospheric methane levels. In Nature, methane is captured aerobically by methanotrophs and anaerobically by anaerobic methanotrophic archaea; however, the anaerobic process dominates. Here, we describe the history and potential of using the two remarkable enzymes that have been cloned with activity for capturing methane: aerobic capture via soluble methane monooxygenase and anaerobic capture via methyl‐coenzyme M reductase. We suggest these two enzymes may play a prominent, sustainable role in addressing our current global warming crisis. [ABSTRACT FROM AUTHOR]

Methane (CH4) is one of the potent greenhouse gases emitted from municipal wastewater treatment plants. The characteristics of methane emission from municipal wastewater treatment plants (WWTPs) have attracted lots of concern from related researchers. The present work investigated the source of methanogens and methane emission properties from two WWTPs in Xi'an, and one is employed in an Orbal oxidation ditch, and the other is anaerobic/anoxic/oxic (A/A/O). The measurement of specific methanogenic activity (SMA) and coenzyme F420 concentration, together with Fluorescence in situ hybridization (FISH), was used to determine the amount and activity of methanogens in two WWTPs. Additionally, a combined activated sludge model was built and predicted the growth of methanogens and other key microorganisms in the sludge. The results showed that the average CH4 emission flux from the Orbal oxidation ditch (22.74 g CH4 /(m2·d)) was much higher than that from A/A/O (9.57 g CH4/(m2·d)). The methane emission factors in the Orbal oxidation ditch and A/A/O processes were 1.18 and 0.21 g CH4 /(m3 INF), respectively. These distinct methane emission characteristics between two WWTPs are mainly attributed to the higher activity and content of methanogens, as well as the discontinuous aeration in the Orbal oxidation ditch. Additionally, dissolved oxygen concentration, water temperature, and the presence of nitrate/nitrite were also important factors that influenced methane emission. The FISH analysis showed that Methanococcus was the dominant methanogen in both WWTPs. In addition, the combined model successfully simulated the growth of methanogens in WWTPs. Methanogens in WWTPs were mainly derived from the sewer system, and the cumulative effect led to an increase in the abundance of methanogens in activated sludge. The outcomes of this study provide new insights in the prediction and management of GHG emission from WWTPs. [ABSTRACT FROM AUTHOR]

Methane, a potent greenhouse gas, represents both a challenge and an opportunity in the quest for sustainable energy. This work investigates the biotechnology for converting methane into clean, renewable hydrogen. The co-culture of Chlorella sacchrarophila FACHB 4 and Methylomonas sp. HYX-M1 was demonstrated to completely convert 1 mmol of methane to biomass within 96 h. After acid digestion of such biomass, up to 45.05 μmol of glucose, 4.07 μmol of xylose, and 26.5 μmol of lactic acid were obtained. Both Clostridium pasteurianum DSM525 and Clostridium sp. BZ-1 can utilize those sugars to produce hydrogen without any additional organic carbon sources. The higher light intensity in methane oxidation co-culture systems resulted in higher hydrogen production, with the BZ-1 strain producing up to 14.00 μmol of hydrogen, 8.19 μmol of lactate, and 6.09 μmol of butyrate from the co-culture biomass obtained at 12,000 lux. The results demonstrate that the co-culture biomass of microalgae and methanotroph has the potential to serve as a feedstock for dark fermentative hydrogen production. Our study highlights the complexities inherent in achieving efficient and complete methane-to-hydrogen conversion, positioning this biological approach as a pivotal yet demanding area of research for combating climate change and propelling the global energy transition. [ABSTRACT FROM AUTHOR]

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal. [ABSTRACT FROM AUTHOR]

Elimination of plastic waste deposition in landfills is essential to avoid secondary pollution such as microplastics. Under appropriate environments, methanotrophs which proceed through methane oxidation reaction are capable of degrading plastics via their co-metabolisms. Nevertheless, nutrient conditions in landfills to promote methane oxidation and plastic degradation are still unclear. Therefore, the biodegradation of plastic wastes under semi-aerobic conditions with methane oxidation activities and nutrient additions was examined in this study. Various types of plastics (HDPE, LDPE, oxo-degradable plastics) were exposed to methane and air under semi-aerobic conditions in lysimeters where methanotrophic activities were promoted. Nitrate and phosphate and their combination were introduced into waste mixtures to determine their effect on plastic biodegradation. Changes in gas compositions, plastic weight losses, by-products, and microbial consortium were studied. Phosphate supplement resulted in higher methanotrophic population, particularly that of type I (Methylococcus sp., Methylocaldum sp., Methylovorus sp., Methylomonas sp., and Methylobacter sp.) and yielded highest biodegradation for oxo-degradable (15-20%) followed by HDPE (15-19%), and LDPE (4–7%). The plastic degradation was found well correlated to methane oxidation rate. Oppositely, nitrate supplements reduced MOR due to their competition with oxygen for microbial reactions. Semi-aerobic condition with a phosphate supplement is found effective in promoting plastic degradation in landfills.

ABSTRACT Microbial activities in sub-alpine forest soil influence global cycling of the potent greenhouse gas methane. Understanding the dynamics of methane-oxidizing bacterial communities, particularly the roles of potentially active versus total microbial populations, is necessary for reducing uncertainty in global methane budget estimates. However, our understanding of the factors influencing methane cycling in forest soils is limited by our lack of knowledge about the biology of the microbes involved and how these communities are shaped by their environment. Here, we compared the composition and potential activity of microbial communities using 16S rRNA gene amplicon sequencing of total genomic DNA (gDNA) and potentially active complementary DNA (cDNA) from shallow soil in Red Butte Canyon (Salt Lake City, Utah, USA). We compared riparian and upland soils at two time points in the growing season and found distinct differences in both the community composition of the gDNA and cDNA libraries and the potential drivers of these community structures. Aerobic methane-oxidizing bacteria (methanotrophs) were detected in all samples, with cDNA libraries containing a higher average relative abundance and diversity of methanotrophs compared to gDNA libraries. Methane flux at the sample sites did not significantly correlate to the relative abundance (gDNA) or potential activity (cDNA) of methanotrophs. In the cDNA libraries, there were significant positive correlations between the abundance of Methylococcaceae family methanotrophs and several non-methanotrophic methylotrophs previously found to be associated with methane-oxidizing bacterial communities. These findings suggest a complex relationship between methane-cycling bacterial communities and methane flux and highlight the need for further in situ studies to understand the environmental and ecological influences of these microbial consortia.IMPORTANCEMethane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.

IntroductionOrganic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.MethodsCow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.ResultsThe bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.DiscussionIt was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.

The seepage of gaseous compounds from underground reservoirs towards the surface causes abnormalities in the population of microbial communities that consume light hydrocarbons on the surface of the reservoir. This microbial population can serve as indicators for determining the location of gas reservoirs prior to drilling operations. In this study, the simulation of methane gas leakage in the sediments of the Persian Gulf was conducted using a laboratory model. The objective of this simulation was to identify the microbial population consuming methane within the sediments of the Persian Gulf, aiding in the exploration of gas reserves. Continuous injection of methane gas into the system was performed for a period of 3 months to enrich the microbial consortia consuming methane. Subsequently, the microbial population was identified using next-generation sequencing (NGS) analysis. The results indicated that, based on the 16S rRNA sequencing dataset, aerobic methanotrophs, including genera Methylobacter, Methylomarinum, Methylomicrobium, Methylomonas, and Methylophage, were the dominant microbial group on the surface of the sediments. Additionally, anaerobic methane oxidation archaea in sediments were performed by ANME-2 and ANME-3 clades. The findings demonstrate that these microbial communities are capable of coexistence and thrive in long-term exposure to methane in the sediments of the Persian Gulf. Identifying this microbial pattern, alongside other geophysical and geological data, can increase the success rate of gas reservoir exploration.

Methylococcus capsulatus MIR is a strain of methanotrophic bacteria that is potentially suitable for production of feed protein and other value-added compounds from methane. Genomic analysis did not reveal in Mc. capsulatus MIR any known pathways of C3-carboxylation necessary for the replenishment of the tricarboxylic acid cycle intermediates and the full-scale metabolic functioning. The pepc gene encoding PEP carboxylase in Methylomonas rapida 12 was introduced into Mc. capsulatus MIR cells on a plasmid under the control of a medium-strength promoter. Expression of heterologous PEP carboxylase led to an increase in the content of glutamate, glycine, and lysine in the cells of the recombinant strain, but did not increase the growth rate of the culture. Consequently, the introduction of heterologous PEP carboxylase, which carries out the C3-carboxylation reaction, helps to increase the nutritional value of the methanotroph biomass. [ABSTRACT FROM AUTHOR]

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Waste glycerol is produced in excess by several industries, such as during biodiesel production. In this work, the metabolic versatility of anaerobic sludge was explored towards waste glycerol valorization. By applying different environmental (methanogenic and sulfate-reducing) conditions, three distinct microbial cultures were obtained from the same inoculum (anaerobic granular sludge), with high microbial specialization, within three different phyla (Thermodesulfobacteriota, Euryarchaeota and Pseudomonadota). The cultures are capable of glycerol conversion through different pathways: (i) glycerol conversion to methane by a bacterium closely related to Solidesulfovibrio alcoholivorans (99.8% 16S rRNA gene identity), in syntrophic relationship with Methanofollis liminatans (98.8% identity), (ii) fermentation to propionate by Propionivibrio pelophilus strain asp66 (98.6% identity), with a propionate yield of 0.88 mmol mmol−1 (0.71 mg mg−1) and a propionate purity of 80–97% and (iii) acetate production coupled to sulfate reduction by Desulfolutivibrio sulfoxidireducens (98.3% identity). In conclusion, starting from the same inoculum, we could drive the metabolic and functional potential of the microbiota towards the formation of several valuable products that can be used in industrial applications or as energy carriers. Key points: Versatility of anaerobic cultures was explored for waste glycerol valorization Different environmental conditions lead to metabolic specialization Biocommodities such as propionate, acetate and methane were produced [ABSTRACT FROM AUTHOR]

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria. [ABSTRACT FROM AUTHOR]

Small intestinal bacterial overgrowth (SIBO) is characterized by an increase in the bacterial population of the small intestine due to an imbalance between the amount of bacteria and the intestinal barrier. Pediatric SIBO presents with a wide spectrum of symptoms, ranging from mild gastrointestinal complaints to malabsorption or malnutrition. Breath tests are commonly used as noninvasive diagnostic tools for SIBO, but a standardized methodology is currently unavailable. Intestinal flora produces methane which slows intestinal transit and increases the contractile activity of small intestine. Emerging literature suggests a correlation between overgrowth of methanogenic bacteria in the intestines and constipation. Treatment of SIBO involves administration of antibacterial therapy in addition to management of underlying conditions and optimal dietary adjustments. However, research on antibiotic treatment for pediatric patients with constipation and SIBO is limited and has yielded conflicting results. In the current review, we summarize the state-of-the-art of the field and discuss previous treatment attempts and currently used regimens for SIBO patients with constipation, with a focus on pediatric populations. [ABSTRACT FROM AUTHOR]

Background: Microbial methane oxidation, methanotrophy, plays a crucial role in mitigating the release of the potent greenhouse gas methane from aquatic systems. While aerobic methanotrophy is a well-established process in oxygen-rich environments, emerging evidence suggests their activity in hypoxic conditions. However, the adaptability of these methanotrophs to such environments has remained poorly understood. Here, we explored the genetic adaptability of aerobic methanotrophs to hypoxia in the methanogenic sediments of Lake Kinneret (LK). These LK methanogenic sediments, situated below the oxidic and sulfidic zones, were previously characterized by methane oxidation coupled with iron reduction via the involvement of aerobic methanotrophs. Results: In order to explore the adaptation of the methanotrophs to hypoxia, we conducted two experiments using LK sediments as inoculum: (i) an aerobic "classical" methanotrophic enrichment with ambient air employing DNA stable isotope probing (DNA-SIP) and (ii) hypoxic methanotrophic enrichment with repeated spiking of 1% oxygen. Analysis of 16S rRNA gene amplicons revealed the enrichment of Methylococcales methanotrophs, being up to a third of the enriched community. Methylobacter, Methylogaea, and Methylomonas were prominent in the aerobic experiment, while hypoxic conditions enriched primarily Methylomonas. Using metagenomics sequencing of DNA extracted from these experiments, we curated five Methylococcales metagenome-assembled genomes (MAGs) and evaluated the genetic basis for their survival in hypoxic environments. A comparative analysis with an additional 62 Methylococcales genomes from various environments highlighted several core genetic adaptations to hypoxia found in most examined Methylococcales genomes, including high-affinity cytochrome oxidases, oxygen-binding proteins, fermentation-based methane oxidation, motility, and glycogen use. We also found that some Methylococcales, including LK Methylococcales, may denitrify, while metals and humic substances may also serve as electron acceptors alternative to oxygen. Outer membrane multi-heme cytochromes and riboflavin were identified as potential mediators for the utilization of metals and humic material. These diverse mechanisms suggest the ability of methanotrophs to thrive in ecological niches previously thought inhospitable for their growth. Conclusions: Our study sheds light on the ability of enriched Methylococcales methanotrophs from methanogenic LK sediments to survive under hypoxia. Genomic analysis revealed a spectrum of genetic capabilities, potentially enabling these methanotrophs to function. The identified mechanisms, such as those enabling the use of alternative electron acceptors, expand our understanding of methanotroph resilience in diverse ecological settings. These findings contribute to the broader knowledge of microbial methane oxidation and have implications for understanding and potential contribution methanotrophs may have in mitigating methane emissions in various environmental conditions. [ABSTRACT FROM AUTHOR]

Soil is an important source and sink of greenhouse gas carbon dioxide (CO2) and methane (CH4). During CH4 consumption CO2 is produced as an end product. It is generally assumed that CO2 would inhibit CH4 consumption due to feedback inhibition. To test the effect of CO2 on methanotrophy, experiments were conducted in microcosms with different initial concentration of CO2 and CH4. Changes in CH4 consumption potential and abundance of pmoA gene copies in relation to CO2 concentration were estimated. In general, CH4 consumption ceased in the absence of CO2. In presence of CO2, rate of CH4 consumption (ng CH4 consumed g−1 soil d−1) varied from 0.283 to 0.481 at 1000 ppm of CH4 and 2.958 to 4.994 at 10,000 ppm of CH4. Abundance of methanotrophs (pmoA gene copies g−1 soil) ranged from 4.5 × 105 to 107 × 105 g−1 soil. A follow up experiment was carried out to evaluate CH4 consumption in the presence or absence of CO2, which proved that CO2 is essential for CH4 consumption. Study concludes that CO2 is a precursor molecule for CH4 consumption in soil ecosystem and methanotrophs are capable of mitigating both the greenhouse gases, CH4 and CO2. [ABSTRACT FROM AUTHOR]

As the main contributor to greenhouse gas (GHG) in paddy soil, information on methane (CH4) emission characteristics under different tillage and cultivation practices are limited. A five-year field trial was conducted from 2019 in a single-cropping rice system in Taihu Lake region, east of China. The experiment had a completely randomized block design, and the treatments included rotary tillage plus rice dry direct seeding (RD), rotary tillage plus rice mechanical transplanting (RT), and plowing tillage plus rice mechanical transplanting (PT). We determined the rice yield, GHG emission, soil traits, and methanogens and methanotrophs in 2022 and 2023. The results revealed that PT and RT significantly increased rice yield compared to RD, whereas PT simultaneously increased CH4 emissions. The year-averaged cumulative CH4 emissions in PT were increased by 38.5% and 61.4% higher than RT and RD, respectively. Meanwhile, yield-scaled global warming potentials (GWPs) in RT and RD were lower than those in PT. Tillage and cultivation practices shifted mcrA and pmoA abundances, and PT significantly decreased pmoA abundance. The community structure and diversity of the methanogens and methanotrophs were not significantly affected. Structural equation model analyses illustrated that CH4 emissions were regulated by mcrA and pmoA directly, which in turn, regulated by soil carbon and nitrogen. Overall, rotary tillage plus mechanism transplanting was a feasible agronomic technology in a single-cropping rice system in Taihu Lake region, exhibiting higher and more stable rice productivity, accompanied with lower CH4 emissions and yield-scaled GWP. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Understanding methane flux dynamics in Arctic cold seep systems and the influence of oceanic currents on microbial methane-oxidizing bacteria (MOB) is crucial for assessing their impact on Arctic methane emissions. Here, we investigate methane dynamics and associated microbial communities at two cold seep areas, Norskebanken and Hinlopen Trough, North of Svalbard. Methane concentrations and methane oxidation rates (MOx) were measured in bottom and surface waters, with higher values observed in bottom waters, particularly at Hinlopen Trough. Dominant water column MOB clusters were Milano-WF1B-03 and Methyloprofundus. Methane availability drove MOx activity, as indicated by higher concentrations in bottom waters and sediments where MOx was elevated, too. Sediment MOB communities varied among locations, with Hinlopen featuring higher diversity and abundance. Similarities between sediments and water column MOBs suggest potential recruitment from sediments, possibly via a bubble shuttle mechanism. In addition, bottom water MOB community composition also showed similarities between the Norskebanken and Hinlopen seeps, implying an exchange of water column microbes between the two seep areas, which may likely be driven by the regional current regime. Together, our results show that bubble-mediated transport and translocation via currents are important processes shaping the community structure and efficiency of the microbial methane filter in the water column. [ABSTRACT FROM AUTHOR]

From the perspective of a circular economy, the bioconversion of methane into valuable protein and carbohydrates can provide alternative food resources, while reducing greenhouse gas emissions. In this study, a nutritional induction strategy for artificial biomanufacturing by an industrial-promising methanotrophic bacterium was proposed for the first time. Three different scenarios of methanotrophic cultivations were carried out by manipulating the availability of oxygen and nitrogen during fermentation to investigate the flexible and efficient biosynthesis of cell proteins, glycogen, and extracellular polysaccharides (EPS). The highest titer of glycogen (5.21 g L−1) and EPS (15.81 g L−1) was observed in scenario I and scenario II, respectively. However, the maximum cell protein productivity (640.05 mg L−1 h−1) was achieved in scenario III with nutrimental balance, resulting in a 2.1-fold enhancement compared to scenario I under nutrient depletion. Further transcriptomic analysis revealed the nutritional induction mechanism, with central carbon and nitrogen metabolisms being boosted with sufficient key nutrients in scenario III, leading to the significant up-regulation of related genes towards protein synthesis. Additionally, a preliminary economic and environmental assessment highlighted the potential benefits of methane-based biomanufacturing in reducing production expenses and greenhouse gas emissions, which may help drive innovation and the development of sustainable and environmentally friendly products. [ABSTRACT FROM AUTHOR]

Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d−1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity. The occurrence of aerobic methane-oxidizing bacteria in anoxic environments is puzzling, as oxygen is thought to be required for methane oxidation. Here, Schorn et al. show that the methane assimilation activity of these bacteria is similar under hypoxic and anoxic conditions in a stratified lake, and the bacteria use fermentation-based methanotrophy as well as denitrification under anoxic conditions. [ABSTRACT FROM AUTHOR]

The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2‐producing intra‐aerobic methanotrophic pathway. Although numerous amplicon‐based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep‐sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep‐sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome‐assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite‐dependent anaerobic methane oxidation (n‐DAMO) occurs within deep‐sea sediments. In addition, the identification of the Wood–Ljungdahl (WL) and 3‐hydroxypropionate/4‐hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep‐sea environments. Indeed, we found that for their survival in the oligotrophic deep‐sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl‐CoA from the carbonyl branch for citric acid cycle‐based energy production and methane from the methyl branch for n‐DAMO. The observed low ratios of non‐synonymous substitutions to synonymous substitutions (pN/pS) in n‐DAMO‐related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep‐sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep‐sea ecosystems, driven by this bacterial phylum. [ABSTRACT FROM AUTHOR]

A study of the distribution of methane cycle microbial communities in the upper layers of bottom sediments above large hydrocarbon reservoirs in the South Kara petroleum region of the West Siberian Province revealed the presence in these layers of both aerobic methanotrophic bacteria and anaerobic methanogenic archaea, as well as numerous heterotrophic microorganisms of various phylogenetic groups. Research was carried out in the Baydaratskaya Bay and in the east of the Pukhuchan Depression (southern part of the Kara Sea). Aerobic methanotrophic bacteria belonged to the families Methyloligellaceae, Methylophagaceae and Methylomonaceae were detected in the surface oxidized layers (0–2 cm, Eh from 60 to 175 mV) of bottom sediments. Moreover, representatives of Methyloligellaceae were found in quite significant amount (1.52–2.61% of all 16S rRNA gene sequence reads) at all studied stations of the Kara Sea. In the subsurface reduced layers (18–20 cm, Eh from –63 to –246 mV), methanogenic archaea were dominated by representatives of the order Methanomassiliicoccales (up to 3.3% of all 16S rRNA gene sequence reads). Methanogenic archaea of the orders Methanofastidiosales, Methanobacteriales and Methanomicrobiales were also discovered. In addition, aerobic/facultative anaerobic methanotrophic bacteria of the families Methylococcaceae and Methylomonadaceae were found on these reduced layers of the bottom sediments, but the relative abundance (in percentage of sequence reads of their total number) of anaerobic methanotrophic archaea was extremely low there. Apparently, the oxidation of methane in bottom sediments of the Kara Sea, where its concentration at most of the studied stations dramatically increased with sediment depth, occurs predominantly under aerobic conditions in the surface layers, where the relative abundance and phylogenetic diversity of methanotrophs are higher. [ABSTRACT FROM AUTHOR]

Biogas digestive effluent (BDE) is a nutrient-enriched source that can be utilized as an organic fertilizer for rice cultivation without synthetic fertilizer (SF) application. However, a primary concern is the stimulation of methane (CH4) emissions due to the enrichment of the labile organic carbon, a favorite substrate of methanogenic archaea. Methanotrophs potentially reduce greenhouse gas (GHG) emissions from rice fields owing to metabolizing CH4 as a carbon source and energy. We therefore examined the effect of the application of methanotroph-inoculated BDE to the rice cultivated paddy soil on GHG emissions and rice productivity under a pot experiment. Methanotrophs (Methylosinus sp. and Methylocystis sp.), isolated from the Vietnamese Mekong Delta's rice fields, were separately inoculated to the heated BDE, followed by a 5-day preincubation. Methanotroph-inoculated BDE was supplied to rice cultivation to substitute SF at 50% or 100% in terms of nitrogen amount. The results showed that the total CH4 emissions increased ~34% with the application of BDE. CH4 emissions were significantly reduced by ~17–21% and ~28–44% under the application of methanotroph-inoculated BDE at 100% and 50%, respectively. The reduction in CH4 was commensurate with the augmentation of pmoA transcript copy number under methanotroph-inoculated BDE. In addition, methanotroph-inoculated BDE application did not increase nitrous oxide (N2O) emissions and adversely affect rice growth and grain productivity. This study highlighted the BDE-recirculated feasibility for a lower CH4 emission rice production based on methanotrophs where high CH4-emitting fields were confirmed. [ABSTRACT FROM AUTHOR]

Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner–Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes. [ABSTRACT FROM AUTHOR]

Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable products. These bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse gases. Several genetic tools have previously been developed for genetic and metabolic engineering of methanotrophs. However, the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria, which hinders genetic and metabolic engineering of these biocatalysts. As such, expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable products. Here, we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b, representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs, respectively. Further, we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in M. capsulatus and M. trichosporium OB3b, but the synthetic series had limited range. Thus, we mutagenized the native M. capsulatus particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic, constitutive promoters functional not only in M. capsulatus, but also in Escherichia coli. Collectively, the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria. [ABSTRACT FROM AUTHOR]

Simple Summary: Humanity faced the hottest year in observational history in 2023. If the trend of rising temperatures on Earth continues, irreversible changes in the environment will occur with negative consequences for the lives of us all. In order to limit the further increase in temperatures on Earth, it is necessary to reduce the emissions of greenhouse gases (GHGs) in various sectors. Since ruminant farming is a significant contributor to anthropogenic GHG emissions due to methane emissions, we attempted to reduce methane emissions in dairy cows by using brown seaweed (Ascophyllum nodosum) in cow rations. Indeed, we achieved a reduction in methane emissions, without disturbing the productivity of cows. We also found a more favorable metabolic status and milk composition in supplemented cows. Additional studies are needed to define precisely how brown seaweeds can be included into strategies to reduce methane emissions from the dairy industry. The dairy industry contributes significantly to anthropogenic methane emissions, which have an impact on global warming. This study aimed to investigate the effects of a dietary inclusion of brown seaweed Ascophyllum nodosum on enteric methane emissions (EMEs), hematological and blood biochemical profiles, and milk composition in dairy cows. Eighteen Holstein cows were divided into three groups: CON (non-supplemented cows), BS50 (50 mL of 10% A. nodosum), and BS100 (100 mL of 10% A. nodosum). In each cow, measurements of EME, dry matter intake (DMI), and milk yield (MY), as well as blood and milk sampling with respective analyzes, were performed before supplementation (P1), after 15 (P2) days, and after 30 (P3) days of supplementation. A. nodosum reduced (p < 0.05) methane production, methane yield, and methane intensity in both BS50 and BS100, and raised DMI (p < 0.05) only in BS50. Total bilirubin (p < 0.05) was higher in BS50 compared to CON cows in P2, and triacylglycerols were lower (p < 0.05) in BS50 than in CON cows in P3. Higher milk fat content was found in BS50 than in CON cows in P3. C16:0 proportions were higher (p < 0.05) in BS50 and BS100 than in CON cows, while C18:3n-3 was higher (p < 0.05) in BS100 than in BS50 and CON cows in P3. Dietary treatment with A. nodosum reduced EMEs and showed the potential to increase DMI and to improve energy status as well as milk composition in peak-lactating dairy cows. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The escalating global demand for protein and the imperative to meet sustainable development goals have driven the emergence of biotransformation platforms, with methanotrophs showing significant potential in this field. In this paper, the metabolism, nutritional requirements, cultivation strategies, and bioreactors of methanotrophs are reviewed. Integrating upstream and downstream technologies is also advocated to advance the development of methanotroph biotransformation platforms toward a circular economy model. The advancements in utilizing biogas as a viable carbon source and wastewater as a nitrogen source are discussed, emphasizing the need for detailed quality control and safety assessments to ensure the suitability of single-cell protein as animal feed. In general, by integrating advanced nutrient recovery technologies to define new process routes, methanotroph biotransformation platforms can bring better environmental benefits by reducing carbon emissions and saving resources. Shifting to renewable energy is crucial for achieving environmental sustainability. By using renewable energy to power microbial fermentation, biomass dehydration, and waste recycling, the platform can offset high energy consumption and attain significant market competitiveness with traditional protein sources. [ABSTRACT FROM AUTHOR]

Background: Wastewater treatment plants contribute approximately 6% of anthropogenic methane emissions. Methanotrophs, capable of converting methane into polyhydroxybutyrate (PHB), offer a promising solution for utilizing methane as a carbon source, using activated sludge as a seed culture for PHB production. However, maintaining and enriching PHB-accumulating methanotrophic communities poses challenges. Results: This study investigated the potential of Methylosinus trichosporium OB3b to bioaugment PHB-accumulating methanotrophic consortium within activated sludge to enhance PHB production. Waste-activated sludges with varying ratios of M. trichosporium OB3b (1:0, 1:1, 1:4, and 0:1) were cultivated. The results revealed substantial growth and methane consumption in waste-activated sludge with M. trichosporium OB3b-amended cultures, particularly in a 1:1 ratio. Enhanced PHB accumulation, reaching 37.1% in the same ratio culture, indicates the dominance of Type II methanotrophs. Quantification of methanotrophs by digital polymerase chain reaction showed gradual increases in Type II methanotrophs, correlating with increased PHB production. However, while initial bioaugmentation of M. trichosporium OB3b was observed, its presence decreased in subsequent cycles, indicating the dominance of other Type II methanotrophs. Microbial community analysis highlighted the successful enrichment of Type II methanotrophs-dominated cultures due to the addition of M. trichosporium OB3b, outcompeting Type I methanotrophs. Methylocystis and Methylophilus spp. were the most abundant in M. trichosporium OB3b-amended cultures. Conclusions: Bioaugmentation strategies, leveraging M. trichosporium OB3b could significantly enhance PHB production and foster the enrichment of PHB-accumulating methanotrophs in activated sludge. These findings contribute to integrating PHB production in wastewater treatment plants, providing a sustainable solution for resource recovery. [ABSTRACT FROM AUTHOR]

In a semi-closed visualization pipeline, this experiment studied the inhibitory effect of ultra-fine pure water mist, ultra-fine water mist containing inorganic salt and ultra-fine water mist containing bacteria-inorganic salt on 9.8% methane explosion under five different quality of spray volume. Combined with the methane explosion suppression experiment, the ability of methane-oxidizing bacteria to degrade 9.8% of methane was studied in a simulated pipeline. Experiments showed that the addition of inorganic salt and the degradation of methane-oxidizing bacteria could improve the suppression explosion effect of ultra-fine water mist, and the suppression explosion effect was related to the volume of water mist. Under the same ultra-fine water mist condition, with the increase of the volume of water mist, the explosion suppression effect was improved. Compared with pure methane, pure water ultra-fine water mist, and inorganic salt ultra-fine water mist, the maximum explosion overpressure and flame propagation speed under the condition of bacteria-inorganic salt ultra-fine water mist were significantly reduced. Compared with the explosion of pure methane, due to the degradation of methane by methane-oxidizing bacteria, when the degradation time was 10 h, and the volume of ultra-fine water mist containing bacteria-inorganic salt was 12.5 mL, the maximum explosion overpressure dropped significantly from 0.663 to 0.343 MPa, a decrease of 48.27%. The appearance time of the maximum explosion overpressure was delayed from 208.8 to 222.6 ms. The peak flame velocity was 4 m s−1, which was 83.3% lower than that of 9.8% pure methane explosion. This study will contribute to the development of efficient ultrafine water mist synergistic inhibitors for the prevention of methane explosion disasters. [ABSTRACT FROM AUTHOR]

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O. Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic or anoxic environments. Here, the authors show that acidophilic methanotrophs can respire nitrous oxide and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species‐rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial‐mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen‐fixing and methane‐oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes. [ABSTRACT FROM AUTHOR]

Nutrient subsidy of methane‐oxidising bacteria (MOB), an alternative basal resource, to plankton communities through pelagic‐benthic coupling is expected to alter carbon‐to‐nitrogen (C/N) ratios and biomass of zooplankton, and affect biological processes in aquatic food webs. Previous studies indicate that most MOB nutrient subsidies to zooplankton are focused largely on C subsidies; nevertheless, considering that N is important to zooplankton and phytoplankton growth, a better understanding of MOB N subsidies to plankton communities is needed.We examined changes in nutrients, phytoplankton mass‐specific productivity, MOB reliance, C/N ratios and biomass of zooplankton between summer stratification and winter mixing periods based on in situ investigation in a subtropical deep oligotrophic freshwater ecosystem during 2010–2014.The results revealed that with increasing reliance on MOB during the winter mixing period, zooplankton C/N ratios decreased and had a significantly nonlinearly inverse relationship with zooplankton biomass. The negative relationship between zooplankton biomass and phytoplankton mass‐specific productivity was further observed in synchronous time.The profundal MOB enhanced pelagic‐profundal coupling and served as an alternative N support for pelagic plankton food webs during the winter and/or less productive seasons, adding to greater understanding of the role of methanotrophs in aquatic food webs. [ABSTRACT FROM AUTHOR]

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a biodegradable polymer with excellent thermal and mechanical properties comparable to fossil-based plastics. Scaling up the production of this polymer could provide a viable solution for reducing the use of fossil-based materials. However, its current production capacities are limited, with only a few facilities implementing the process at pilot or semi-industrial scales. The primary challenge lies in the high production costs, with 40% of the expenses attributed to the feedstock used for fermentation. Additionally, the energy required for sterilization in processes using pure methanotrophic cultures further reduces its economic viability. In this study, the economic aspects of the PHBV production process were assessed at an industrial level (100,000 t/y PHBV), using cheap and renewable substrates such as valeric acid and methane. A mixed methanotrophic consortium was used to reduce the need for sterility. The techno-economic analysis was based on estimating both fixed investment and operating costs. Then, a sensitivity analysis was performed to analyse the effect that the polymer content has on the final selling price: the initial biomass concentration was set to 30 g L-1, and the PHBV content was considered to be 20, 30, 40, 50 and 70% wt on a dry weight basis. The results revealed that increasing the polymer content beyond 40% wt led to a more competitive PHBV selling price, thus opening significant market opportunities. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In the present study, soil physico-chemical properties, hexachlorocyclohexane (HCH) isomers, lindane degrading soil methanotrophs and soil microbial biomass-C, N and P were investigated by selecting 6 study sites in Lucknow and Renukoot region of Uttar Pradesh, Northern India. The ANOVA revealed significant variations soil physico-chemical properties (P SBRJS01> SBIJS02> ControlURRH3. A positive linear relationship (R2=0.7951) was noted between lindane degradation and Cl− release during the methanotrophic isolates incubation period. A greater SMB–C, –N and –P values (365.2, 65.5, and 26.8 μg g−1 soil, respectively), having higher HCH residues were, recorded in the soil samples of Renukoot region, compared to the soils of Lucknow region.The negative correlation between SMB–C, –N, and –P values and different soil HCH isomers suggests that higher concentrations of lethal HCH residues persisting in soils negatively impacts the quantity of soil microbial biomass. Therefore, on-site monitoring and methanotrophic mediated bioremediation of HCH soil residues might be a viable and eco-friendly option in removal of this particular persistent soil pesticide from the contaminated area.

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

The effects of the influent nitrate (NO3−-N) concentration on reactor performance and microbial communities of anaerobic methane oxidation coupled to denitrification in a membrane biofilm reactor were emphatically investigated after prolonged storage. The system was run for a period of 185 days including the storage period, reactivating process, and stable operation phase. The influent NO3−-N concentrations varied from 10, 20, and 30 mg/L, and the reactor was continuously operated for 135 days. The denitrification rate in the reactor was activated first and then inhibited, with the average value of NO3−-N consumed of 0.42 mg/L·h−1 at influent NO3−-N of 20 mg/L; there was no obvious nitrite and ammonia–nitrogen accumulation in the whole stage. Illumina MiSeq sequencing results showed that increases in NO3−-N loading could improve the microbial abundance in the system. The highest value for variety and the lowest value for the evenness of the microbial community corresponded to the ideal value of 20 mg/L. It speculated that promoting biofilm bacteria (PBB) became the key functional bacterial group after prolonged storage. Besides, the abundance of methane-oxidizing bacteria was significantly increased in synergy with PBB and denitrifiers to achieve reactivating and stable operation of anaerobic methane oxidation coupled to denitrification. [ABSTRACT FROM AUTHOR]

Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2, CH4, H2S and H2. These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid‐tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF‐ and MxaFI‐type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1. [ABSTRACT FROM AUTHOR]

The paper presents the results of a study of carbonate and sulfate–carbonate–clayey rocks of the Lower Maeotian in the sections of the bays of Cape Kazantip using a complex of analytical methods. It is established that the greatest variation of chemical, bituminological, phase, and carbon-isotope composition is characterized by carbonate–clay and clayey rocks of the section bottom. It is proved that the initial OM was accumulated mainly under reducing conditions, but has some variations in composition; it is characterized by a low degree of its catagenetic transformation, which indicates the preservation of the primary isotopic composition. The diverse phase composition of the clay fraction is revealed: dioctahedral illite, kaolinite, chlorite, glauconite, and weakly ordered mixed-layer formations of illite/smectite type with different ratios of illite and smectite components and varying degrees of ordering. Modeling of their diffraction profiles showed that the illite/smectite structure may indicate significant depths of sediment mobilization by mud volcanoes. The isotopic composition of the 13Сorg ranges widely from –33.72 to –19.27‰ the mode being –22.1...–24.93‰. The isotopic composition of 13Сorg below –25.6‰ may be related to the entry of isotope-light mass of methane-oxidizing bacteria into the OM. It was revealed that variations of isotopic composition curves 13Сcarb and 13Сorg along the section of the studied rocks are rarely characterized by unidirectional (positive or negative) variations and have different trends along the section. Direction of the 13Сcarb isotope composition curve with some variations has a pronounced upward trend toward heavier weighting, whereas the isotopic values of the 13Сorg reveals reverse tendency. The results obtained prove that the revealed variations in the composition of OM and carbon isotope composition in the Lower Maeotian sections of Cape Kazantip reflect variations in the sedimentation conditions of temperature, salinity, freshwater ingression, bioproductivity fluctuations, and the influence of local gas–fluid deposition. It is proposed to use such accessory minerals as zircon, monazite, and ilmenite as an indicator of mud paleovolcanism. [ABSTRACT FROM AUTHOR]

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function. [ABSTRACT FROM AUTHOR]

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water–air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water–air fluxes remained below 0.6 mmol m−2 d−1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water–air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]