nifH sequences and nitrogen fixation in type I and type II methanotrophs

Quantitative assessment of methane bioconversion based on kinetics and bioenergetics

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

Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria

PREMISE

Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity.

METHODS

We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata.

RESULTS

Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19 cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank.

CONCLUSIONS

Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.

Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.

Methylomonas rivi sp. nov., Methylomonas rosea sp. nov., Methylomonas aurea sp. nov. and Methylomonas subterranea sp. nov., type I methane-oxidizing bacteria isolated from a freshwater creek and the deep terrestrial subsurface

Four methane-oxidizing bacteria, designated as strains WSC-6T, WSC-7T, SURF-1T, and SURF-2T, were isolated from Saddle Mountain Creek in southwestern Oklahoma, USA, and the Sanford Underground Research Facility (SURF) in Lead, South Dakota, USA. The strains were Gram-negative, motile, short rods that possessed intracytoplasmic membranes characteristic of type I methanotrophs. All four strains were oxidase-negative and weakly catalase-positive. Colonies ranged from pale pink to orange in colour. Methane and methanol were the only compounds that could serve as carbon and energy sources for growth. Strains WSC-6T and WSC-7T grew optimally at lower temperatures (25 and 20 °C, respectively) compared to strains SURF-1T and SURF-2T (40 °C). Strains WSC-6T and SURF-2T were neutrophilic (optimal pH of 7.5 and 7.3, respectively), while strains WSC-7T and SURF-1T were slightly alkaliphilic, with an optimal pH of 8.8. The strains grew best in media amended with ≤0.5% NaCl. The major cellular fatty acids were C14 : 0, C16 : 1  ω8c, C16 : 1  ω7c, and C16 : 1  ω5c. The DNA G+C content ranged from 51.5 to 56.0 mol%. Phylogenetic analyses indicated that the strains belonged to the genus Methylomonas, with each exhibiting 98.6-99.6% 16S rRNA gene sequence similarity to closely related strains. Genome-wide estimates of relatedness (84.5-88.4% average nucleotide identity, 85.8-92.4% average amino acid identity and 27.4-35.0% digital DNA-DNA hybridization) fell below established thresholds for species delineation. Based on these combined results, we propose to classify these strains as representing novel species of the genus Methylomonas, for which the names Methylomonas rivi (type strain WSC-6T=ATCC TSD-251T=DSM 112293T), Methylomonas rosea (type strain WSC-7T=ATCC TSD-252T=DSM 112281T), Methylomonas aurea (type strain SURF-1T=ATCC TSD-253T=DSM 112282T), and Methylomonas subterranea (type strain SURF-2T=ATCC TSD-254T=DSM 112283T) are proposed.

From genome to evolution: investigating type II methylotrophs using a pangenomic analysis

A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications.

IMPORTANCE

Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Ridge with no-tillage facilitates microbial N2 fixation associated with methane oxidation in rice soil

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.

Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia

Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 μmol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.

Application of nitrogen-rich sunflower husks biochar promotes methane oxidation and increases abundance of Methylobacter in nitrogen-poor soil

The area of sunflower crops is steadily increasing. A beneficial way of managing sunflower waste biomass could be its use as a feedstock for biochar production. Biochar is currently being considered as an additive for improving soil parameters, including the ability to oxidise methane (CH4) - one of the key greenhouse gases (GHG). Despite the high production of sunflower husk, there is still insufficient information on the impact of sunflower husk biochar on the soil environment, especially on the methanotrophy process. To fill this knowledge gap, an experiment was designed to evaluate the effects of addition of sunflower husk biochar (produced at 450-550 °C) at a wide range of doses (1-100 Mg ha-1) to Haplic Luvisol. In the presented study, the CH4 oxidation potential of soil with and without sunflower husk biochar was investigated at 60 and 100% water holding capacity (WHC), and with the addition of 1% CH4 (v/v). The comprehensive study included GHG exchange (CH4 and CO2), physicochemical properties of soil (pH, soil organic carbon (SOC), dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), WHC), and the structure of soil microbial communities. That study showed that even low biochar doses (5 and 10 Mg ha-1) were sufficient to enhance pH, SOC, DOC and NO3--N content. Importantly, sunflower husk biochar was significant source of NO3--N, which soil concentration increased from 9.40 ± 0.09 mg NO3--N kg-1 for the control to even 19.40 ± 0.26 mg NO3--N kg-1 (for 100 Mg ha-1). Significant improvement of WHC (by 11.0-12.4%) was observed after biochar addition at doses of 60 Mg ha-1 and higher. At 60% WHC, application of biochar at a dose of 40 Mg ha-1 brought significant improvements in CH4 oxidation rate, which was 4.89 ± 0.37 mg CH4-C kg-1 d-1. Higher biochar doses were correlated with further improvement of CH4 oxidation rates, which at 100 Mg ha-1 was seventeen-fold higher (8.36 ± 0.84 mg CH4-C kg-1 d-1) than in the biochar-free control (0.48 ± 0.28 mg CH4-C kg-1 d-1). CO2 emissions were not proportional to biochar doses and only grew circa (ca.) twofold from 3.16 to 6.90 mg CO2-C kg-1 d-1 at 100 Mg ha-1. Above 60 Mg ha-1, the diversity of methanotrophic communities increased, with Methylobacter becoming the most abundant genus, which was as high as 7.45%. This is the first, such advanced and multifaceted study of the wide range of sunflower husk biochar doses on Haplic Luvisol. The positive correlation between soil conditions, methanotroph abundance and CH4 oxidation confirmed the multifaceted, positive effect of sunflower husk biochar on Haplic Luvisol. Sunflower husk biochar can be successfully used for Haplic Luvisol supplementation. This additive facilitates soil protection against degradation and has the potential to mitigate GHG emissions.

Microbial gas fermentation technology for sustainable food protein production

The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.

Direct biological fixation provides a freshwater sink for N2O

Nitrous oxide (N2O) is a potent climate gas, with its strong warming potential and ozone-depleting properties both focusing research on N2O sources. Although a sink for N2O through biological fixation has been observed in the Pacific, the regulation of N2O-fixation compared to canonical N2-fixation is unknown. Here we show that both N2O and N2 can be fixed by freshwater communities but with distinct seasonalities and temperature dependencies. N2O fixation appears less sensitive to temperature than N2 fixation, driving a strong sink for N2O in colder months. Moreover, by quantifying both N2O and N2 fixation we show that, rather than N2O being first reduced to N2 through denitrification, N2O fixation is direct and could explain the widely reported N2O sinks in natural waters. Analysis of the nitrogenase (nifH) community suggests that while only a subset is potentially capable of fixing N2O they maintain a strong, freshwater sink for N2O that could be eroded by warming.

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

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

From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering

Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils

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

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Mitigation of greenhouse gas emission by nitrogen-fixing bacteria

Chemical nitrogen fixation by the Haber-Bosch method permitted industrial-scale fertilizer production that supported global population growth, but simultaneously released reactive nitrogen into the environment. This minireview highlights the potential for bacterial nitrogen fixation and mitigation of greenhouse gas (GHG) emissions from soybean and rice fields. Nitrous oxide (N2O), a GHG, is mainly emitted from agricultural use of nitrogen fertilizer and symbiotic nitrogen fixation. Some rhizobia have a denitrifying enzyme system that includes an N2O reductase and are able to mitigate N2O emission from the rhizosphere of leguminous plants. Type II methane (CH4)-oxidizing bacteria (methanotrophs) are endophytes in paddy rice roots and fix N2 using CH4 (a GHG) as an energy source, mitigating the emission of CH4 and reducing nitrogen fertilizer usage. Thus, symbiotic nitrogen fixation shows potential for GHG mitigation in soybean and rice fields while simultaneously supporting sustainable agriculture.

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

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

In Vivo Evidence of Single 13C and 15N Isotope-Labeled Methanotrophic Nitrogen-Fixing Bacterial Cells in Rice Roots

Methane-oxidizing bacteria (methanotrophs) play an ecological role in methane and nitrogen fluxes because they are capable of nitrogen fixation and methane oxidation, as indicated by genomic and cultivation-dependent studies. However, the chemical relationships between methanotrophy and diazotrophy and aerobic and anaerobic reactions, respectively, in methanotrophs remain unclear. No study has demonstrated the cooccurrence of both bioactivities in a single methanotroph bacterium in its natural environment. Here, we demonstrate that both bioactivities in type II methanotrophs occur at the single-cell level in the root tissues of paddy rice (Oryza sativa L. cv. Nipponbare). We first verified that difluoromethane, an inhibitor of methane monooxygenase, affected methane oxidation in rice roots. The results indicated that methane assimilation in the roots mostly occurred due to oxygen-dependent processes. Moreover, the results indicated that methane oxidation-dependent and methane oxidation-independent nitrogen fixation concurrently occurred in bulk root tissues. Subsequently, we performed fluorescence in situ hybridization and NanoSIMS analyses, which revealed that single cells of type II methanotrophs (involving six amplicon sequence variants) in paddy rice roots simultaneously and logarithmically fixed stable isotope gases ¹⁵N₂ and ¹³CH₄ during incubation periods of 0, 23, and 42 h, providing in vivo functional evidence of nitrogen fixation in methanotrophic cells. Furthermore, ¹⁵N enrichment in type II methanotrophs at 42 h varied among cells with an increase in ¹³C accumulation, suggesting that either the release of fixed nitrogen into root systems or methanotroph metabolic specialization is dependent on different microenvironmental niches in the root.

Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N₂ fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N₂ fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. ¹⁵N₂-stable isotope probing showed that N₂-fixing activity was stimulated 160-fold by CH₄ oxidation from 0.27 to 43.3 μmol N g^–1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of ¹⁵N-NH₄⁺ through microbial mineralization. Nitrate amendment almost completely abolished N₂ fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N₂ fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N₂ fixation in CH₄-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N₂ fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.

Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h-1 g-1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h-1 g-1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h-1 g-1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h-1 g-1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.

Transcriptomic profiling of nitrogen fixation and the role of NifA in Methylomicrobium buryatense 5GB1

Methanotrophs capable of converting C1-based substrates play an important role in the global carbon cycle. As one of the essential macronutrient components in the medium, the uptake of nitrogen sources severely regulates the cell's metabolism. Although the feasibility of utilizing nitrogen gas (N₂) by methanotrophs has been predicted, the mechanism remains unclear. Herein, the regulation of nitrogen fixation by an essential nitrogen-fixing regulator (NifA) was explored based on transcriptomic analyses of Methylomicrobium buryatense 5GB1. A deletion mutant of the nitrogen global regulator NifA was constructed, and the growth of M. buryatense 5GB1ΔnifA exhibited significant growth inhibition compared with wild-type strain after the depletion of nitrate source in the medium. Our transcriptome analyses elucidated that 22.0% of the genome was affected in expression by NifA in M. buryatense 5GB1. Besides genes associated with nitrogen assimilation such as nitrogenase structural genes, genes related to cofactor biosynthesis, electron transport, and post-transcriptional modification were significantly upregulated in the presence of NifA to enhance N₂ fixation; other genes related to carbon metabolism, energy metabolism, membrane transport, and cell motility were strongly modulated by NifA to facilitate cell metabolisms. This study not only lays a comprehensive understanding of the physiological characteristics and nitrogen metabolism of methanotrophs, but also provides a potentially efficient strategy to achieve carbon and nitrogen co-utilization.Key points• N₂ fixation ability of M. buryatense 5GB1 was demonstrated for the first time in experiments by regulating the supply of N₂.• NifA positively regulates nif-related genes to facilitate the uptake of N₂ in M. buryatense 5GB1.• NifA regulates a broad range of cellular functions beyond nif genes in M. buryatense 5GB1.

Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction

Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO₂ fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.

Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates

Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.

Elevated Atmospheric CO2 and Nitrogen Fertilization Affect the Abundance and Community Structure of Rice Root-Associated Nitrogen-Fixing Bacteria

Elevated atmospheric CO2 (eCO2) results in plant growth and N limitation, yet how root-associated nitrogen-fixing bacterial communities respond to increasing atmospheric CO2 and nitrogen fertilization (eN) during the growth stages of rice is unclear. Using the nifH gene as a molecular marker, we studied the combined effect of eCO2 and eN on the diazotrophic community and abundance at two growth stages in rice (tillering, TI and heading, HI). Quantitative polymerase chain reaction (qPCR) showed that eN had no obvious effect on nifH abundance in rice roots under either ambient CO2 (aCO2) or eCO2 treatment at the TI stage; in contrast, at the HI, nifH copy numbers were increased under eCO2 and decreased under aCO2. For rhizosphere soils, eN significantly reduced the abundance of nifH under both aCO2 and eCO2 treatment at the HI stage. Elevated CO2 significantly increased the nifH abundance in rice roots and rhizosphere soils with nitrogen fertilization, but had no obvious effect without N addition at the HI stage. There was a significant interaction [CO2 × N fertilization] effect on nifH abundance in root zone at the HI stage. In addition, the nifH copy numbers in rice roots were significantly higher at the HI stage than at the TI stage. Sequencing analysis indicated that the root-associated diazotrophic community structure tended to cluster according to the nitrogen fertilization treatment and that Rhizobiales were the dominant diazotrophs in all root samples at the HI stage. Additionally, nitrogen fertilization significantly increased the relative abundance of Methylosinus (Methylocystaceae) under eCO2 treatment, but significantly decreased the relative abundance of Rhizobium (Rhizobiaceae) under aCO2 treatment. Overall, the combined effect of eN and eCO2 stimulates root-associated diazotrophic methane-oxidizing bacteria while inhibits heterotrophic diazotrophs.

Impact of Intercropping on the Diazotrophic Community in the Soils of Continuous Cucumber Cropping Systems

Diazotrophs are important soil components that help replenish biologically available nitrogen (N) in the soil and contribute to minimizing the use of inorganic N fertilizers in agricultural ecosystems. However, there is little understanding of how diazotrophs respond to intercropping and soil physicochemical properties in cucumber continuous cropping systems. In this study, using the nifH gene as a marker, we have examined the impacts of seven intercropping plants on diazotrophic community diversity and composition compared to a cucumber continuous cropping system during two cropping seasons. The results showed that intercropping increased the abundance of the nifH gene, which was negatively correlated with available phosphorous in the fall. Diazotrophic diversity and richness were higher in the rape-cucumber system than in the monoculture. Multivariate regression tree analysis revealed that the diversity of the diazotrophic communties was shaped mainly by soil moisture and available phosphorous. Skermanella were the dominant genera in all of the samples, which increased significantly in the mustard-cucumber system in the fall. There was no effect of intercropping on the structure of the diazotrophic community in this case. Non-metric multidimensional scaling analysis showed that cropping season had a greater effect than intercropping on the community structure of the diazotrophs. Overall, our results suggest that intercropping altered the abundance and diversity rather than the structure of the diazotrophic community, which may potentially affect the N fixation ability of continuous cropping systems.

Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining

Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using ¹³C-CH₄ to a co-occurrence network analysis derived from the ¹³C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.

Type II methanotrophs: A promising microbial cell-factory platform for bioconversion of methane to chemicals

Methane, the predominant element in natural gas and biogas, represents a promising alternative to carbon feedstocks in the biotechnological industry due to its low cost and high abundance. The bioconversion of methane to value-added products can enhance the value of gas and mitigate greenhouse gas emissions. Methanotrophs, methane-utilizing bacteria, can make a significant contribution to the production of various valuable biofuels and chemicals from methane. Type II methanotrophs in comparison with Type I methanotrophs have distinct advantages, including high acetyl-CoA flux and the co-incorporation of two important greenhouse gases (methane and CO₂), making it a potential microbial cell-factory platform for methane-derived biomanufacturing. Herein, we review the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. Representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.

Do methanotrophs drive phosphorus mineralization in soil ecosystem?

Experiments were carried out to elucidate linkage between methane consumption and mineralization of phosphorous (P) from different P sources. The treatments were (i) no CH₄ + no P amendment (absolute control), (ii) with CH₄ + no P amendment (control), (iii) with CH₄ + inorganic P as Ca₃(PO₄)₂, and (iv) with CH₄ + organic P as sodium phytate. P sources were added at 25 µg P·(g soil)^-1. Soils were incubated to undergo three repeated CH₄ feeding cycles, referred to as feeding cycle I, feeding cycle II, and feeding cycle III. CH₄ consumption rate k (µg CH₄ consumed·(g soil)^-1·day^-1) was 0.297 ± 0.028 in no P amendment control, 0.457 ± 0.016 in Ca₃(PO₄)₂, and 0.627 ± 0.013 in sodium phytate. Rate k was stimulated by 2 to 6 times over CH₄ feeding cycles and followed the trend of sodium phytate > Ca₃(PO₄)₂ > no P amendment control. CH₄ consumption stimulated P solubilization from Ca₃(PO₄)₂ by a factor of 2.86. Acid phosphatase (µg paranitrophenol released·(g soil)^-1·h^-1) was higher in sodium phytate than the no P amendment control. Abundance of 16S rRNA and pmoA genes increased with CH₄ consumption rates. The results of the study suggested that CH₄ consumption drives mineralization of unavailable inorganic and organic P sources in the soil ecosystem.

Active Methanotrophs in Suboxic Alpine Swamp Soils of the Qinghai-Tibetan Plateau

Methanotrophs are the only biofilters for reducing the flux of global methane (CH4) emissions in water-logged wetlands. However, adaptation of aerobic methanotrophs to low concentrations of oxygen and nitrogen in typical swamps, such as that of the Qinghai-Tibetan Plateau, is poorly understood. In this study, we show that Methylobacter-like methanotrophs dominate methane oxidation and nitrogen fixation under suboxic conditions in alpine swamp soils. Following incubation with 13C-CH4 and 15N-N2 for 90 days under suboxic conditions with repeated flushing using an inert gas (i.e., argon), microbial carbon and nitrogen turnover was measured in swamp soils at different depths: 0-20 cm (top), 40-60 cm (intermediate), and 60-80 cm (deep). Results show detectable methane oxidation and nitrogen fixation in all three soil depths. In particular, labeled carbon was found in CO2 enrichment (13C-CO2), and soil organic carbon (13C-SOC), whereas labeled nitrogen (15N) was detected in soil organic nitrogen (SON). The highest values of labeled isotopes were found at intermediate soil depths. High-throughput amplicon sequencing and Sanger sequencing indicated the dominance of Methylobacter-like methanotrophs in swamp soils, which comprised 21.3-24.0% of the total bacterial sequences, as measured by 13C-DNA at day 90. These results demonstrate that aerobic methanotroph Methylobacter is the key player in suboxic methane oxidation and likely catalyzes nitrogen fixation in swamp wetland soils in the Qinghai-Tibetan Plateau.

Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

Changes in Methane Emission and Community Composition of Methane-Cycling Microorganisms Along an Elevation Gradient in the Dongting Lake Floodplain, China

Methane (CH4) emission and environmental controls of CH4-cycling microorganisms are unclear in inland floodplains. Here, we examined soil CH4 emissions and the community composition of CH4-cycling microorganisms under three vegetation types—mudflat (MF, no vegetation cover), Carex meadow (CM, mainly Carex brevicuspis), and reed land (RL, mainly Miscanthus sacchariflorus)—from water-adjacent areas to higher-elevation land in the Dongting Lake floodplain, China. The results showed that CH4 emission is the highest in CM, while significant absorption was observed in the RL site. The abundance ratio of methanogen/methanotroph was the highest in CM, intermediate in MF, and lowest in RL. The Methanosarcinaceae family represented the dominant methanogens in the three sampling sites (41.32–75.25%). The genus Methylocystis (60.85%, type II methanotrophs) was dominant in CM, while Methylobacter and Methylosarcina (type I methanotrophs) were the dominant genera in MF (51.00%) and RL (50.24%), respectively. Structural equation model analysis showed that methanogen and methanotroph abundance were affected by water table depth, soil water content, and pH indirectly through soil organic content, total nitrogen, microbial biomass carbon, and microbial biomass nitrogen. These results indicated that the Dongting Lake floodplain may change from a CH4 source to a CH4 sink with vegetation succession with an increase in elevation, and the methanogen/methanotroph ratio can be used as a proxy for CH4 emission in wetland soils. The continuous increase in reed area combined with the decrease in Carex meadow may mitigate CH4 emission and enhance the CH4 sink function during the non-flood season in the Dongting Lake floodplain.

Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics

High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.

Molecular Mechanism Associated With the Impact of Methane/Oxygen Gas Supply Ratios on Cell Growth of Methylomicrobium buryatense 5GB1 Through RNA-Seq

The methane (CH₄)/oxygen (O₂) gas supply ratios significantly affect the cell growth and metabolic pathways of aerobic obligate methanotrophs. However, few studies have explored the CH₄/O₂ ratios of the inlet gas, especially for the CH₄ concentrations within the explosion range (5∼15% of CH₄ in air). This study thoroughly investigated the molecular mechanisms associated with the impact of different CH₄/O₂ ratios on cell growth of a model type I methanotroph Methylomicrobium buryatense 5GB1 cultured at five different CH₄/O₂ supply molar ratios from 0.28 to 5.24, corresponding to CH₄ content in gas mixture from 5% to 50%, using RNA-Seq transcriptomics approach. In the batch cultivation, the highest growth rate of 0.287 h^-1 was achieved when the CH₄/O₂ supply molar ratio was 0.93 (15% CH₄ in air), and it is crucial to keep the availability of carbon and oxygen levels balanced for optimal growth. At this ratio, genes related to methane metabolism, phosphate uptake system, and nitrogen fixation were significantly upregulated. The results indicated that the optimal CH₄/O₂ ratio prompted cell growth by increasing genes involved in metabolic pathways of carbon, nitrogen and phosphate utilization in M. buryatense 5GB1. Our findings provided an effective gas supply strategy for methanotrophs, which could enhance the production of key intermediates and enzymes to improve the performance of bioconversion processes using CH₄ as the only carbon and energy source. This research also helps identify genes associated with the optimal CH₄/O₂ ratio for balancing energy metabolism and carbon flux, which could be candidate targets for future metabolic engineering practice.

Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants

Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N₂) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N₂ fixation in non-leguminous plants. Identification of the involved N₂-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N₂ fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N₂. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N₂ by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.

Large-scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters

Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial-aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation.

Biofiltration of methane

The on-going annual increase in global methane (CH₄) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH₄ emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH₄ concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH₄ biofiltration studies that have been performed in the last decades.

Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives

The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.

Biofiltration of methane using hybrid mixtures of biochar, lava rock and compost

Using hybrid packing materials in biofiltration systems takes advantage of both the inorganic and organic properties offered by the medium including structural stability and a source of available nutrients, respectively. In this study, hybrid mixtures of compost with either lava rock or biochar in four different mixture ratios were compared against 100% compost in a methane biofilter with active aeration at two ports along the height of the biofilter. Biochar outperformed lava rock as a packing material by providing the added benefit of participating in sorption reactions with CH₄. This study provides evidence that a 7:1 volumetric mixture of biochar and compost can successfully remove up to 877 g CH₄/m³·d with empty-bed residence times of 82.8 min. Low-affinity methanotrophs were responsible for the CH₄ removal in these systems (K_M(app) ranging from 5.7 to 42.7 µM CH₄). Sequencing of 16S rRNA gene amplicons indicated that Gammaproteobacteria methanotrophs, especially members of the genus Methylobacter, were responsible for most of the CH₄ removal. However, as the compost medium was replaced with more inert medium, there was a decline in CH₄ removal efficiency coinciding with an increased dominance of Alphaproteobacteria methanotrophs like Methylocystis and Methylocella. As a biologically-active material, compost served as the sole source of nutrients and inoculum for the biofilters which greatly simplified the operation of the system. Higher elimination capacities may be possible with higher compost content such as a 1:1 ratio of either biochar or lava rock, while maintaining the empty-bed residence time at 82.8 min.

Paenibacillus maysiensis sp. nov., a Nitrogen-Fixing Species Isolated from the Rhizosphere Soil of Maize

A novel bacterium SX-49^T with nitrogen-fixing capability was isolated from the rhizosphere soil of maize. Phylogenetic analysis of nifH gene fragment and 16S rRNA gene sequence revealed that the strain SX-49^T is a member of the genus Paenibacillus. Values of 16S rRNA gene sequence similarity were highest between SX-49^T and P. jamilae DSM 13815^T (97.0%), P. brasiliensis DSM 14914^T (97.8%), P. polymyxa DSM 36^T (97.5%), and P. terrae DSM 15891^T (98.8%). The similarity between SX-49^T and other Paenibacillus species was < 97.0%. DNA-DNA hybridization values between strain SX-49^T and the four type strains were P. jamilae DSM 13815^T: 40.6%, P. brasiliensis DSM 14914^T: 27.9%, P. polymyxa DSM 36^T: 29.2%, and P. terrae DSM 15891^T: 66.4%. The DNA G+C content of SX-49^T was 46.4 mol%. The predominant fatty acids were anteiso-C_15:0, C_16:0 and iso-C_16:0. The predominant isoprenoid quinone was MK-7. The genome contains 5628 putative protein-coding sequences (CDS), 6 rRNAs and 56 tRNAs. The phenotypic and genotypic characteristics, DNA-DNA relatedness, and genome features suggest that SX-49^T represents a novel species of the genus Paenibacillus, and the name Paenibacillus maysiensis sp. nov. is proposed.

Enrichments of methanotrophic-heterotrophic cultures with high poly-β-hydroxybutyrate (PHB) accumulation capacities

Methanotrophic-heterotrophic communities were selectively enriched from sewage sludge to obtain a mixed culture with high levels of poly-β-hydroxybutyrate (PHB) accumulation capacity from methane. Methane was used as the carbon source, N₂ as sole nitrogen source, and oxygen and Cu content were varied. Copper proved essential for PHB synthesis. All cultures enriched with Cu could accumulate high content of PHB (43.2%-45.9%), while only small amounts of PHB were accumulated by cultures enriched without Cu (11.9%-17.5%). Batch assays revealed that communities grown with Cu and a higher O₂ content synthesized more PHB, which had a wider optimal CH₄:O₂ range and produced a high PHB content (48.7%) even though in the presence of N₂. In all methanotrophic-heterotrophic communities, both methanotrophic and heterotrophic populations showed the ability to accumulate PHB. Although methane was added as the sole carbon source, heterotrophs dominated with abundances between 77.2% and 85.6%. All methanotrophs detected belonged to type II genera, which formed stable communities with heterotrophs of different PHB production capacities.

Effect of biomass concentration on methane oxidation activity using mature compost and graphite granules as substrata

Reported methane oxidation activity (MOA) varies widely for common landfill cover materials. Variation is expected due to differences in surface area, the composition of the substratum and culturing conditions. MOA per methanotrophic cell has been calculated in the study of natural systems such as lake sediments to examine the inherent conditions for methanotrophic activity. In this study, biomass normalised MOA (i.e., MOA per methanotophic cell) was measured on stabilised compost, a commonly used cover in landfills, and on graphite granules, an inert substratum widely used in microbial electrosynthesis studies. After initially enriching methanotrophs on both substrata, biomass normalised MOA was quantified under excess oxygen and limiting methane conditions in 160ml serum vials on both substrata and blends of the substrata. Biomass concentration was measured using the bicinchoninic acid assay for microbial protein. The biomass normalised MOA was consistent across all compost-to-graphite granules blends, but varied with time, reflecting the growth phase of the microorganisms. The biomass normalised MOA ranged from 0.069±0.006μmol CH4/mg dry biomass/h during active growth, to 0.024±0.001μmol CH4/mg dry biomass/h for established biofilms regardless of the substrata employed, indicating the substrata were equally effective in terms of inherent composition. The correlation of MOA with biomass is consistent with studies on methanotrophic activity in natural systems, but biomass normalised MOA varies by over 5 orders of magnitude between studies. This is partially due to different methods being used to quantify biomass, such as pmoA gene quantification and the culture dependent Most Probable Number method, but also indicates that long term exposure of materials to a supply of methane in an aerobic environment, as can occur in natural systems, leads to the enrichment and adaptation of types suitable for those conditions.

Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase

Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.

Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field

N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input.

Draft Genome Sequences of Eight Obligate Methane Oxidizers Occupying Distinct Niches Based on Their Nitrogen Metabolism

The genome sequences of Methylomonas methanica (NCIMB 11130^T, R-45363, and R-45371), Methylomonas koyamae (R-45378, R-45383, and R-49807), Methylomonas lenta (R-45370), and Methylosinus sp. (R-45379) were obtained. These aerobic methanotrophs were isolated from terrestrial ecosystems, and their distinct phenotypes related to nitrogen assimilation and dissimilation were previously reported.

Biologically derived fertilizer: A multifaceted bio-tool in methane mitigation

Methane emissions are affected by agricultural practices. Agriculture has increased in scale and intensity because of greater food, feed and energy demands. The application of chemical fertilizers in agriculture, particularly in paddy fields, has contributed to increased atmospheric methane emissions. Using organic fertilizers may improve crop yields and the methane sink potential within agricultural systems, which may be further improved when combined with beneficial microbes (i.e. biofertilizers) that improve the activity of methane oxidizing bacteria such as methanotrophs. Biofertilizers may be an effective tool for agriculture that is environmentally beneficial compared to conventional inorganic fertilizers. This review highlights and discusses the interplay between ammonia and methane oxidizing bacteria, the potential interactions of microbial communities with microbially-enriched organic amendments and the possible role of these biofertilizers in augmenting the methane sink potential of soils. It is suggested that biofertilizer applications should not only be investigated in terms of sustainable agriculture productivity and environmental management, but also in terms of their effects on methanogen and methanotroph populations.