Molecular ecology techniques for the study of aerobic methanotrophs

Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake

Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.

Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere

Methanol, the second most abundant volatile organic compound, primarily released from plants, is a major culprit disturbing atmospheric chemistry. Interestingly, ubiquitously found methanol-utilizing bacteria, play a vital role in mitigating atmospheric methanol effects. Despite being extensively characterized, the effect of nitrogen sources on the richness of methanol-utilizers in the bulk soil and rhizosphere is largely unknown. Therefore, the current study was planned to isolate, characterize and explore the richness of cultivable methylotrophs from the bulk soil and rhizosphere of a paddy field using media with varying nitrogen sources. Our data revealed that more genera of methylotrophs, including Methylobacterium, Ancylobacter, Achromobacter, Xanthobacter, Moraxella, and Klebsiella were enriched with the nitrate-based medium compared to only two genera, Hyphomicrobium and Methylobacterium, enriched with the ammonium-based medium. The richness of methylotrophic bacteria also differed substantially in the bulk soil as compared to the rhizosphere. Growth characterization revealed that majority of the newly isolated methanol-utilizing strains in this study exhibited better growth at 37 °C instead of 30 or 45 °C. Moreover, Hyphomicrobium sp. FSA2 was the only strain capable of utilizing methanol even at elevated temperature 45 °C, showing its adaptability to a wide range of temperatures. Differential carbon substrate utilization profiling revealed the facultative nature of all isolated methanol-utilizer strains with Xanthobacter sp. TS3, being an important methanol-utilizer capable of degrading toxic compounds such as acetone and ethylene glycol. Overall, our study suggests the role of nutrients and plant-microbial interaction in shaping the composition of methanol-utilizers in terrestrial environment.

Targeting methanotrophs and isolation of a novel psychrophilic Methylobacter species from a terrestrial Arctic alkaline methane seep in Lagoon Pingo, Central Spitsbergen (78° N)

The microbial diversity associated with terrestrial groundwater seepage through permafrost soils is tightly coupled to the geochemistry of these fluids. Terrestrial alkaline methane seeps from Lagoon Pingo, Central Spitsbergen (78°N) in Norway, with methane-saturated and oxygen-limited groundwater discharge providing a potential habitat for methanotrophy. Here, we report on the microbial community's comparative analyses and distribution patterns at two sites close to Lagoon Pingo's methane emission source. To target methane-oxidizing bacteria from this system, we analysed the microbial community pattern of replicate samples from two sections near the main methane seepage source. DNA extraction, metabarcoding and subsequent sequencing of 16S rRNA genes revealed microbial communities where the major prokaryotic phyla were Pseudomonadota (42-47%), Gemmatimonadota (4-14%) and Actinobacteriota (7-11%). Among the Pseudomonadota, members of the genus Methylobacter were present at relative abundances between 1.6 and 4.7%. Enrichment targeting the methane oxidising bacteria was set up using methane seep sediments as inoculum and methane as the sole carbon and energy source, and this resulted in the isolation of a novel psychrophilic methane oxidizer, LS7-T4AT. The optimum growth temperature for the isolate was 13 °C and the pH optimum was 8.0. The morphology of cells was short rods, and TEM analysis revealed intracytoplasmic membranes arranged in stacks, a distinctive feature for Type I methanotrophs in the family Methylomonadaceae of the class Gammaproteobacteria. The strain belongs to the genus Methylobacter based on high 16S rRNA gene similarity to the psychrophilic species of Methylobacter psychrophilus Z-0021T (98.95%), the psychrophilic strain Methylobacter sp. strain S3L5C (99.00%), and the Arctic mesophilic species of Methylobacter tundripaludum SV96T (99.06%). The genome size of LS7-T4AT was 4,338,157 bp with a G + C content of 47.93%. The average nucleotide identities (ANIb) of strain LS7-T4AT to 10 isolated strains of genus Methylobacter were between 75.54 and 85.51%, lower than the species threshold of 95%. The strain LS7-T4AT represents a novel Arctic species, distinct from other members of the genus Methylobacter, for which the name Methylobacter svalbardensis sp. nov. is proposed. The type of strain is LS7-T4AT (DSMZ:114308, JCM:39463).

Extreme drought alters methane uptake but not methane sink in semi-arid steppes of Inner Mongolia

Global climate change, particularly drought, is expected to alter grassland methane (CH4) oxidation, a key natural process against atmospheric greenhouse gas accumulation, yet the extent of this effect and its interaction with future atmospheric CH4 concentrations increases remains uncertain. To address this research gap, we measured CH4 flux during an imposed three-month rain-free period corresponding to a 100-year recurrence drought in soil mesocosms collected from 16 different Eurasian steppe sites. We also investigated the abundance and composition of methanotrophs. Additionally, we conducted a laboratory experiment to explore the impact of elevated CH4 concentration on the CH4 uptake capacity of grassland soil under drought conditions. We found that regardless of the type of grassland, CH4 flux was still being absorbed at its peak, meaning that all grasslands functioned as persistent CH4 sinks even when the soil water content (SWC) was <5 %. A bell-shaped relationship between SWC and CH4 uptake was observed in the soils. The average maximum CH4 oxidation rate in the meadow steppe was higher than that in the typical and desert steppe soils during extreme drought. The experimental elevation of atmospheric CH4 concentration counteracted the anticipated reduction in CH4 uptake related to physiological water stress on methanotrophic soil microbes under the drought stress. On the contrary, we found that across the regional scale, nitrogen, phosphorous, and total soil organic content played a crucial role in moderating the duration and magnitude of CH4 uptake with respect to SWC. USC-γ (Upland Soil Cluster γ) and JR-3 (Jasper Ridge Cluster) were the dominant group of soil methanotrophic bacteria in three types of grassland. However, the methanotrophic abundance, rather than the methanotrophic community composition, was the dominant microbiological factor governing CH4 uptake during the drought.

Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions

In this study, the biodegradability of trifluoroacetate (TFA), perfluorooctanoic acid (PFOA), and perfluoro-2-methyl-3-oxahexanoic acid (HFPO-DA) by a native microbial community was evaluated over a 10-month incubation period. The observed microbial defluorination ratios and removal efficiency were 3.46 ( ± 2.73) % and 8.03 ( ± 3.03) %, 8.44 ( ± 1.88) % and 13.52 ( ± 4.96) %, 3.02 ( ± 0.62) % and 5.45 ( ± 2.99) % for TFA, PFOA and HFPO-DA, respectively. The biodegradation intermediate products, TFA and pentafluoropropionic acid (PFA), of PFOA and HFPO-DA were detected in their biodegradation treatment groups. Furthermore, the concentrations of the PFOA metabolites, perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), in the aqueous solutions after incubation were quantified to be 0.21 and 4.14 µg/L. TFA, PFOA and HFPO-DA significantly reduced the microbial diversity and changed the structure of the community. The co-occurrence network analysis showed that low abundance species, such as Flexilinea flocculi, Bacteriovorax stolpii, and g_Sphingomonas, are positively correlated with the generation of fluoride ion, implying their potential collaborative functions contributing to the observed biodefluorination. The findings in this study can provide insights for the biodegradation of perfluoroalkyl carboxylic acids and their emerging alternatives by indigenous microorganisms in the environment.

Floating plants reduced methane fluxes from wetlands by creating a habitat conducive to methane oxidation

Wetlands are one of the important natural sources of atmospheric methane (CH4), as an important part of wetlands, floating plants can be expected to affect methane release. However, the effects of floating plants on methane release are limited. In this study, methane fluxes, physiochemical properties of the overlying water, methane oxidation potential and rhizospheric bacterial community were investigated in simulated wetlands with floating plants Eichhornia crassipes, Hydrocharis dubia, and Trapa natans. We found that E. crassipes, H. dubia, and T. natans plants could inhibit 84.31% - 97.31%, 4.98% - 88.91% and 43.62% - 92.51% of methane fluxes at interface of water-atmosphere compared to Control, respectively. Methane fluxes were negatively related to nutrients concentration in water column but positively related to the aerenchyma proportions of roots, stems, and leaves. At the same biomass, root of E. crassipes (36.44%) had the highest methane oxidation potential, followed by H. dubia (12.99%) and T. natans (11.23%). Forty-five bacterial phyla in total were identified on roots of three plants and 7 bacterial genera (2.10% - 3.33%) were known methanotrophs. Type I methanotrophs accounted for 95.07% of total methanotrophs. The pmoA gene abundances ranged from 1.90 × 1016 to 2.30 × 1018 copies/g fresh weight of root biofilms. Abundances of pmoA gene was significantly positively correlated with environmental parameters. Methylotrophy (5.40%) and methanotrophy (3.75%) function were closely related to methane oxidation. This study highlights that floating plant restoration can purify water and promote carbon neutrality partially by reducing methane fluxes through methane oxidation in wetlands.

Methane Oxidation Coupled to Selenate Reduction in a Membrane Bioreactor under Oxygen-Limiting Conditions

Microbial methane oxidation coupled to a selenate reduction process has been proposed as a promising solution to treat contaminated water, yet the underlying microbial mechanisms are still unclear. In this study, a novel methane-based membrane bioreactor system integrating hollow fiber membranes for efficient gas delivery and ultrafiltration membranes for biomass retention was established to successfully enrich abundant suspended cultures able to perform methane-dependent selenate reduction under oxygen-limiting conditions. The microbial metabolic mechanisms were then systematically investigated through a combination of short-term batch tests, DNA-based stable isotope probing (SIP) microcosm incubation, and high-throughput sequencing analyses of 16S rRNA gene and functional genes (pmoA and narG). We confirmed that the methane-supported selenate reduction process was accomplished by a microbial consortia consisting of type-II aerobic methanotrophs and several heterotrophic selenate reducers. The mass balance and validation tests on possible intermediates suggested that methane was partially oxidized into acetate under oxygen-limiting conditions, which was consumed as a carbon source for selenate-reducing bacteria. High-throughput 16S rRNA gene sequencing, DNA-SIP incubation with 13CH4, and subsequent functional gene (pmoA and narG) sequencing results collectively proved that Methylocystis actively executed partial methane oxidation and Acidovorax and Denitratisoma were dominant selenate-reducing bacteria, thus forming a syntrophic partnership to drive selenate reduction. The findings not only advance our understanding of methane oxidation coupled to selenate reduction under oxygen-limiting conditions but also offer useful information on developing methane-based biotechnology for bioremediation of selenate-contaminated water.

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.

Experimental erosion of microbial diversity decreases soil CH4 consumption rates

Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.

Effects of microplastics on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications

Microplastics (MPs), as a new type of pollutant, widely exist in livestock and poultry breeding and agricultural soils. However, research on MPs pollution on greenhouse gas emissions in combined planting and breeding systems is lacking, especially from the perspective of phage horizontal gene transfer. Therefore, this paper explores the effects of MPs on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications. The results of the study indicated that the addition of MPs had an impact on both the physicochemical properties and microbial community structure of manure during the composting process and on the compost-applied rhizosphere soil of lactuca (Lactuca sativa). Specifically, on day 7 of composting, mcrA/pmoA and (nirS+nirK) levels in bacteria in the MP group significantly increased. Additionally, it was observed that the MP group had higher average temperatures during the high-temperature period of composting, which led to a rapid reduction in phages. However, the phage levels quickly recovered during the cooling period. Furthermore, the addition of MPs to the rhizosphere soil resulted in higher levels of nirK. These changes may affect greenhouse gas emissions.

Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.

Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.

Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments

In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.

Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm

In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

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.

Reduced methane emissions in former permafrost soils driven by vegetation and microbial changes following drainage

In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon-rich wetlands, although 71% of this carbon pool is stored in faster-thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short-term thawing experiments, investigations of the long-term changes following final thaw and co-occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25 years of natural drainage, that resulted in a 10-fold decrease in CH₄ emissions (3.2 ± 2.2 vs. 0.3 ± 0.4 mg C-CH₄  m^-2  day^-1 ), while CO₂ emissions were comparable. These data extend the time perspective from earlier studies based on short-term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH₄ oxidation due to the longer residence time of CH₄ in the oxidation zone, while the observed loss of aerenchyma plants reduced CH₄ diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long-term effects of climate change on CH₄ emissions and underscores the need for data from different soil types and thaw histories.

Unexpected Parabolic Temperature Dependency of CH4 Emissions from Rice Paddies

Global warming is expected to affect methane (CH₄) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH₄ emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH₄ emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH₄ emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH₄ emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH₄ emissions need to consider both plant and microbial responses to warming.

Environmental Factors Affecting the Community of Methane-oxidizing Bacteria

Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000‍ ‍mg N L^–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH₄⁺ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.

Spatiotemporal dynamics in microbial communities mediating biogeochemical cycling of nutrients across the Xiaowan Reservoir in Lancang River

Microbes drive biogeochemical cycles of nutrients controlling water quality in freshwater ecosystems, yet little is known regarding how spatiotemporal variation in the microbial community affects this ecosystem-level functional processes to resist perturbations. Here we examined spatiotemporal dynamics of microbial communities in paired stratified water columns and sediments collected from the Xiaowan Reservoir of Lancang-Mekong River over a year long period. Results highlighted distinctive spatiotemporal patterns of microbial communities in water columns mainly driven by sulfate, dissolved oxygen, nitrate and temperature, whilst sediment communities only showed a seasonal variation pattern governed by pH, reduced inorganic sulfur, sulfate, organic matter and total nitrogen. Microbial co-occurrence networks revealed the succession of keystone taxa in both water columns and sediments, reflecting core ecological functions in response to altered environmental conditions. Specifically, in shallow water, keystone nitrogen fixers and denitrifiers were responsible for providing nitrogen nutrients in summer, while recalcitrant substance degraders likely supplied microbially available organic matters to maintain ecosystem stability in winter. But in deep water, methane oxidation was the critical process linked to microbial-mediated cycle of carbon, nitrogen and sulfur. In addition, carbon metabolism and mercury methylation mediated by sulfate reducers, denitrifiers and nitrogen fixers were core functioning features of sediments in summer and winter, respectively. This work expands our knowledge of the importance of keystone taxa in maintaining stability of reservoir ecosystems under changing environments, providing new perspectives for water resource conservation and management.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH₄) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH₄ oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH₄ gdw^–1 day^–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH₄ oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH₄ emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH₄ oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

Sediment Disturbance Negatively Impacts Methanogen Abundance but Has Variable Effects on Total Methane Emissions

Methane emissions from aquatic ecosystems are increasingly recognized as substantial, yet variable, contributions to global greenhouse gas emissions. This is in part due to the challenge of modeling biologic parameters that affect methane emissions from a wide range of sediments. For example, the impacts of fish bioturbation on methane emissions in the literature have been shown to result in a gradient of reduced to enhanced emissions from sediments. However, it is likely that variation in experimental fish density, and consequently the frequency of bioturbation by fish, impacts this outcome. To explore how the frequency of disturbance impacts the levels of methane emissions in our previous work we quantified greenhouse gas emissions in sediment microcosms treated with various frequencies of mechanical disturbance, analogous to different levels of activity in benthic feeding fish. Greenhouse gas emissions were largely driven by methane ebullition and were highest for the intermediate disturbance frequency (disturbance every 7 days). The lowest emissions were for the highest frequency treatment (3 days). This work investigated the corresponding impacts of disturbance treatments on the microbial communities associated with producing methane. In terms of total microbial community structure, no statistical difference was observed in the total community structure of any disturbance treatment (0, 3, 7, and 14 days) or sediment depth (1 and 3 cm) measured. Looking specifically at methanogenic Archaea however, a shift toward greater relative abundance of a putatively oxygen-tolerant methanogenic phylotype (ca. Methanothrix paradoxum) was observed for the highest frequency treatments and at depths impacted by disturbance (1 cm). Notably, quantitative analysis of ca. Methanothrix paradoxum demonstrated no change in abundance, suggesting disturbance negatively and preferentially impacted other methanogen populations, likely through oxygen exposure. This was further supported by a linear decrease in quantitative abundance of methanogens (assessed by qPCR of the mcrA gene), with increased disturbance frequency in bioturbated sediments (1 cm) as opposed to those below the zone of bioturbation (3 cm). However, total methane emissions were not simply a function of methanogen populations and were likely impacted by the residence time of methane in the lower frequency disturbance treatments. Low frequency mechanical disruption results in lower methane ebullition compared to higher frequency treatments, which in turn resulted in reduced overall methane release, likely through enhanced methanotrophic activities, though this could not be identified in this work. Overall, this work contributes to understanding how animal behavior may impact variation in greenhouse gas emissions and provides insight into how frequency of disturbance may impact emissions.

Distinct Co-occurrence Relationships and Assembly Processes of Active Methane-Oxidizing Bacterial Communities Between Paddy and Natural Wetlands of Northeast China

Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a ¹³C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.

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

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

Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes

Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways; the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modeling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modeling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modeling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, providing a predictive framework for assessing gene absences for these functions. We present this adaptation of macroecology’s occupancy modeling to metagenomics as a tool to quantify the uncertainty in predictions of the presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future.

IMPORTANCE Metagenomics is maturing rapidly as a field but is hampered by a lack of available statistical tools. A primary area of uncertainty is around missing genes or functions from a metagenomic data set. Here, we borrow an established modeling approach from macroecology and adapt it to metagenomic data sets. Rather than multiple sampling trips to a specific area to detect a species of interest (e.g., identifying a cardinal in a forest), we leverage the enormous amount of information within a metagenome and use multiple gene markers for a function of interest (e.g., subunits of an enzyme complex). We applied our adapted occupancy modeling to a case study examining methane cycling capacity. Our models show methanogens and methanotrophs are both more likely to cooccur than be present in the absence of the other guild. The lack of consistent and complete metadata is a significant hurdle for increasing the statistical rigor of metagenomic analyses.

Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps

Methane availability in freshwaters is usually associated with spatial-temporal variation in methanogenesis. Unusually, however, natural gas macro-seeps occur along the Condamine River in eastern Australia which elevate ambient water-column methane concentrations more than 3,000 times. We quantified the spatial-temporal variation in methane oxidation rates and the total microbial and methanotroph community composition (through the amplification and sequencing of 16S rRNA and particulate methane monooxygenase (pmoA) genes), and the factors mediating this variation, in reaches with and without macro-seeps. Sediment methane oxidation rates were, on average, 29 times greater, and the abundance of methanotrophs significantly higher, in the vicinity of methane macro-seeps compared to non-seep sites. Methylocystis was the most abundant methanotroph group at all sites, but type Ib methanotrophs showed the steepest increase in abundance at seep sites. pmoA gene analysis identified these as clade 501, while 16S rRNA gene analysis identified these as the closely related genus Methylocaldum. Sediment methane oxidation rates and the relative abundance and composition of benthic microbial communities were primarily influenced by methane availability which was in turn related to variation in river discharge. Methane-derived carbon may be an important energy source for the aquatic food webs in reaches affected by natural gas macro-seeps.

Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay

Seabed hydrocarbon seeps present natural laboratories for investigating responses of marine ecosystems to petroleum input. A hydrocarbon seep near Scott Inlet, Baffin Bay, was visited for in situ observations and sampling in the summer of 2018. Video evidence of an active hydrocarbon seep was confirmed by methane and hydrocarbon analysis of the overlying water column, which is 260 m at this site. Elevated methane concentrations in bottom water above and down current from the seep decreased to background seawater levels in the mid-water column >150 m above the seafloor. Seafloor microbial mats morphologically resembling sulfide-oxidizing bacteria surrounded areas of bubble ebullition. Calcareous tube worms, brittle stars, shrimp, sponges, sea stars, sea anemones, sea urchins, small fish and soft corals were observed near the seep, with soft corals showing evidence for hydrocarbon incorporation. Sediment microbial communities included putative methane-oxidizing Methyloprofundus, sulfate-reducing Desulfobulbaceae and sulfide-oxidizing Sulfurovum. A metabolic gene diagnostic for aerobic methanotrophs (pmoA) was detected in the sediment and bottom water above the seep epicentre and up to 5 km away. Both 16S rRNA gene and pmoA amplicon sequencing revealed that pelagic microbial communities oriented along the geologic basement rise associated with methane seepage (running SW to NE) differed from communities in off-axis water up to 5 km away. Relative abundances of aerobic methanotrophs and putative hydrocarbon-degrading bacteria were elevated in the bottom water down current from the seep. Detection of bacterial clades typically associated with hydrocarbon and methane oxidation highlights the importance of Arctic marine microbial communities in mitigating hydrocarbon emissions from natural geologic sources.

Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change

Methane oxidizing bacteria (methanotrophs) within the genus Methylobacter constitute the biological filter for methane (CH₄) in many Arctic soils. Multiple Methylobacter strains have been identified in these environments but we seldom know the ecological significance of the different strains. High-Arctic peatlands in Svalbard are heavily influenced by herbivory, leading to reduced vascular plant and root biomass. Here, we have measured potential CH₄ oxidation rates and identified the active methantrophs in grazed peat and peat protected from grazing by fencing (exclosures) for 18 years. Grazed peat sustained a higher water table, higher CH₄ concentrations and lower oxygen (O₂) concentrations than exclosed peat. Correspondingly, the highest CH₄ oxidation potentials were closer to the O₂ rich surface in the grazed than in the protected peat. A comparison of 16S rRNA genes showed that the majority of methanotrophs in both sites belong to the genus Methylobacter. Further analyses of pmoA transcripts revealed that several Methylobacter OTUs were active in the peat but that different OTUs dominated the grazed peat than the exclosed peat. We conclude that grazing influences soil conditions, the active CH₄ filter and that different Methylobacter populations are responsible for CH₄ oxidation depending on the environmental conditions.

Spatiotemporal patterns and drivers of methane uptake across a climate transect in Inner Mongolia Steppe

Steppe soils are important biological sinks for atmospheric methane (CH₄), but the strength of CH₄ uptake remains uncertain due to large spatiotemporal variation and the lack of in situ measurements at regional scale. Here, we report the seasonal and spatial patterns of CH₄ uptake across a 1200 km transect in arid and semi-arid steppe ecosystems in Inner Mongolia, ranging from meadow steppe in the east plain to typical and desert steppes on the west plateau. In general, seasonal patterns of CH₄ uptake were site specific, with unimodal seasonal curves in meadow and typical steppes and a decreasing seasonal trend in desert steppe. Soil moisture was the dominant factor explaining the seasonal patterns of CH₄ uptake, and CH₄ uptake rate decreased with an increase in soil moisture. Across the transect, CH₄ uptake showed a skewed unimodal spatial pattern, with the peak rate observed in the typical steppe sites and with generally higher uptake rates in the west plateau than in the east plain. Soil moisture, together with soil temperature, soil total carbon, and aboveground plant biomass, were the main drivers of the regional patterns of CH₄ uptake rate. These findings are important for model development to more precisely estimate the soil CH₄ sink capacity in arid and semi-arid regions.

A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria

Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally at 55 °C (with a growth range spanning 30 to 60 °C). The pure isolate was recovered from a methane-utilizing mixed culture enrichment from an alkaline thermal spring in the Ethiopia Rift Valley, and utilized methanol, methylamine, glucose and a variety of multi-carbon compounds. Phylogenetic analysis of the 16S rRNA gene sequences demonstrated that strain LS7-MT represented a new facultatively methylotrophic bacterium within the order Hyphomicrobiales of the class Alphaproteobacteria. This new strain showed 94 to 96% 16S rRNA gene identity to the two methylotroph genera, Methyloceanibacter and Methyloligella. Analysis of the draft genome of strain LS7-MT revealed genes for methanol dehydrogenase, essential for methanol oxidation. Functional and comparative genomics of this new isolate revealed genomic and physiological divergence from extant methylotrophs. Strain LS7-MT contained a complete mxaF gene cluster and xoxF1 encoding the lanthanide-dependent methanol dehydrogenase (XoxF). This is the first report of methanol oxidation at 55 °C by a moderately thermophilic bacterium within the class Alphaproteobacteria. These findings expand our knowledge of methylotrophy by the phylum Proteobacteria in thermal ecosystems and their contribution to global carbon and nitrogen cycles.

Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

Enhancement of nitrite reduction and enrichment of Methylomonas via conductive materials in a nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane-oxidizing (n-damo) process has a promising prospect in anaerobic wastewater treatment, utilizing methane as the sole electron source to remove nitrite. However, the metabolic activity of n-damo bacteria is too low for practical application. This study aimed to stimulate n-damo process by introducing conductive nano-magnetite and/or electron shuttle anthraquinone-2,6-disulfonate (AQDS), and also set a comparative treatment of adding insulated ferrihydrite. The results showed that the nitrite reduction rate was enhanced the most significantly in treatment with nano-magnetite, approximately 1.6 times higher than that of the control without any supplement. While ferrihydrite application showed an adverse effect on n-damo process. The well-known aerobic methane oxidizer Methylomonas spp. was found to be enriched under n-damo condition with the supplementation of nano-magnetite and/or AQDS, but abundance of n-damo bacteria did not exhibit significant increase. It was hypothesized that Methylomonas spp. could be survived under anaerobic n-damo condition using oxygen produced by n-damo bacteria for the self-growth, and the nitrite reduction could be promoted through the enhancement of microbial interspecies electron transfer triggered by the introduction of conductive materials. It opens a new direction for the stimulation of n-damo activity, which needs more evidences to verify the hypothetic mechanism.

Filamentous green algae Spirogyra regulates methane emissions from eutrophic rivers

Excessive growth of filamentous green algae in rivers has attracted much attention due to their functional importance to primary production and carbon cycling. However, comprehensive knowledge of how filamentous green algae affect carbon cycling, especially the CH₄ emissions from river ecosystems, remains limited. In this study, incubation experiments were conducted to examine the factors regulating CH₄ emissions from a eutrophic river with dense growth of filamentous green algae Spirogyra through combinations of biogeochemical, molecular biological, and stable carbon isotope analyses. Results showed that although water dissolved oxygen (DO) in the algae+sediment (A+S) incubation groups increased up to 19 mg L^-1, average CH₄ flux of the groups was 13.09 μmol m^-2 day^-1, nearly up to two times higher than that from sediments without algae (S groups). The significant increase of sediment CH₄ oxidation potential and methanotroph abundances identified the enhancing sediment CH₄ oxidation during Spirogyra bloom. However, the increased water CH₄ concentration was consistent with depleted water [Formula: see text] and decreased apparent fractionation factor (α_app), suggesting the important contribution of Spirogyra to the oxic water CH₄ production. It can thus be concluded that high DO concentration during the algal bloom promoted the CH₄ consumption by enhancing sediment CH₄ oxidation, while algal-linked oxic water CH₄ production as a major component of water CH₄ promoted the CH₄ emissions from the river. Our study highlights the regulation of Spirogyra in aquatic CH₄ fluxes and will help to estimate accurately CH₄ emissions from eutrophic rivers with dense blooms of filamentous green algae. Graphical abstract.

Combined application of biochar with urease and nitrification inhibitors have synergistic effects on mitigating CH4 emissions in rice field: A three-year study

Biochar and inhibitors applications have been proposed for mitigating soil greenhouse gas emissions. However, how biochar, inhibitors and the combination of biochar and inhibitors affect CH₄ emissions remains unclear in paddy soils. The objective of this study was to explore the effects of biochar application alone, and in combination with urease (hydroquinone) and nitrification inhibitors (dicyandiamide) on CH₄ emissions and yield-scaled CH₄ emissions during three rice growing seasons in the Taihu Lake region (Suzhou and Jurong), China. In Suzhou, N fertilization rates of 120-280 kg N ha^-1 increased CH₄ emissions compared to no N fertilization (Control) (P < 0.05), and the highest emission was observed at 240 kg N ha^-1, possibly due to the increase in rice-derived organic carbon (C) substrates for methanogens. Biochar amendment combined with N fertilization reduced CH₄ emissions by 13.2-27.1% compared with optimal N (ON, Suzhou) and conventional N application (CN-J, Jurong) (P < 0.05). This was related to the reduction in soil dissolved organic C and the increase in soil redox potential. Addition of urease and nitrification inhibitor (ONI) decreased CH₄ emissions by 15.7% compared with ON treatment. Combined application of biochar plus urease, nitrification and double inhibitors further decreased CH₄ emissions by 22.2-51.0% compared with ON and CN-J treatment. ON resulted in the highest yield-scaled CH₄ emissions, while combined application of biochar alone and in combination with the inhibitors decreased yield-scaled CH₄ emissions by 12.7-54.9% compared with ON and CN-J treatment (P < 0.05). The lowest yield-scaled CH₄ emissions were observed under combined application of 7.5 t ha^-1 biochar with both urease and nitrification inhibitors. These findings suggest that combined application of biochar and inhibitors could mitigate total CH₄ and yield-scaled CH₄ emissions in paddy fields in this region.

Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China

Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH₄⁺-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.

The Impact of Methane on Microbial Communities at Marine Arctic Gas Hydrate Bearing Sediment

Cold seeps are characterized by high biomass, which is supported by the microbial oxidation of the available methane by capable microorganisms. The carbon is subsequently transferred to higher trophic levels. South of Svalbard, five geological mounds shaped by the formation of methane gas hydrates, have been recently located. Methane gas seeping activity has been observed on four of them, and flares were primarily concentrated at their summits. At three of these mounds, and along a distance gradient from their summit to their outskirt, we investigated the eukaryotic and prokaryotic biodiversity linked to 16S and 18S rDNA. Here we show that local methane seepage and other environmental conditions did affect the microbial community structure and composition. We could not demonstrate a community gradient from the summit to the edge of the mounds. Instead, a similar community structure in any methane-rich sediments could be retrieved at any location on these mounds. The oxidation of methane was largely driven by anaerobic methanotrophic Archaea-1 (ANME-1) and the communities also hosted high relative abundances of sulfate reducing bacterial groups although none demonstrated a clear co-occurrence with the predominance of ANME-1. Additional common taxa were observed and their abundances were likely benefiting from the end products of methane oxidation. Among these were sulfide-oxidizing Campilobacterota, organic matter degraders, such as Bathyarchaeota, Woesearchaeota, or thermoplasmatales marine benthic group D, and heterotrophic ciliates and Cercozoa.

Methanobactin from methanotrophs: genetics, structure, function and potential applications

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Niche Differentiation of Active Methane-Oxidizing Bacteria in Estuarine Mangrove Forest Soils in Taiwan

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10-15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils.

Molecular Ecology of Isoprene-Degrading Bacteria

Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth's climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle.

Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China

Root-associated aerobic methanotrophs play an important role in regulating methane emissions from the wetlands. However, the influences of the plant genotype on root-associated methanotrophic structures, especially on active flora, remain poorly understood. Transcription of the pmoA gene, encoding particulate methane monooxygenase in methanotrophs, was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland. High-throughput sequencing of pmoA based on DNA and cDNA was used to analyze the methanotrophic community. Sequencing of cDNA pmoA amplicons confirmed that the structure of active methanotrophic was not always consistent with DNA. A type I methanotroph, Methylomonas, was the most active group in P. australis, whereas Methylocystis, a type II methanotroph, was the dominant group in S. triqueter. In T. angustifolia, these two types of methanotroph existed in similar proportions. However, at the DNA level, Methylomonas was predominant in the roots of all three plants. In addition, vegetation type could have a profound impact on root-associated methanotrophic community at both DNA and cDNA levels. These results indicate that members of the genera Methylomonas (type I) and Methylocystis (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland.

A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley

Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M.capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy.

Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes

Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.

Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave

Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.

The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review

New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.

Perchlorate bio-reduction in a methane-based membrane biofilm reactor in the presence and absence of oxygen

Perchlorate has been widely detected in various water environments and could cause serious health problems. Methane has been proposed as a promising electron donor to remove perchlorate from contaminated water, yet it is unclear whether and how microbial methane oxidation couples with perchlorate reduction, in particular under anoxic conditions. Here, the feasibility and performance of perchlorate reduction driven by methane in the presence and absence of oxygen were investigated and compared in a lab-scale methane-based membrane biofilm reactor. Long-term operational performance suggested that perchlorate was reduced to chloride, with 4 mg Cl/L/d of perchlorate removal rate under anoxic conditions. Differently, perchlorate removal rate increased to 16 mg Cl/L/d, and volatile fatty acids (VFAs) were produced from methane partial oxidation when a limited oxygen (10 mg/L/d) was externally supplied. Regardless of oxygen conditions, microbial perchlorate reduction driven by methane might be mediated through synergistic interactions by a microbial consortium, but with different key microbial members under both oxygen regimes. Under anoxic conditions, aerobic methanotrophs (likely Methylocystaceae and Methylococcaceae) might micro-aerobically oxidize methane by utilizing internal oxygen from microbial perchlorate reduction, which might be mediated by Rhodocyclaceae. In contrast, under oxygen-limiting conditions, methanogens (e.g., Methanosarcina) and fermenters (e.g., Veillonellaceae) likely jointly converted methane into VFAs, then dissimilatory perchlorate-reducing bacteria (e.g., Rhodocyclaceae) utilized the produced VFAs to reduce perchlorate to chloride. Our findings provide evidence to link methane oxidation with perchlorate reduction under both oxygen regimes, which could be facilitated to design a process to remove perchlorate from groundwater.

ATP- and Polyphosphate-Dependent Glucokinases from Aerobic Methanotrophs

The genes encoding adenosine triphosphate (ATP)- and polyphosphate (polyP)-dependent glucokinases (Glk) were identified in the aerobic obligate methanotroph Methylomonas sp. 12. The recombinant proteins were obtained by the heterologous expression of the glk genes in Esherichia coli. ATP-Glk behaved as a multimeric protein consisting of di-, tri-, tetra-, penta- and hexamers with a subunit molecular mass of 35.5 kDa. ATP-Glk phosphorylated glucose and glucosamine using ATP (100% activity), uridine triphosphate (UTP) (85%) or guanosine triphosphate (GTP) (71%) as a phosphoryl donor and exhibited the highest activity in the presence of 5 mM Mg²⁺ at pH 7.5 and 65 °C but was fully inactivated after a short-term incubation at this temperature. According to a gel filtration in the presence of polyP, the polyP-dependent Glk was a dimeric protein (2 × 28 kDa). PolyP-Glk phosphorylated glucose, mannose, 2-deoxy-D-glucose, glucosamine and N-acetylglucosamine using polyP as the phosphoryl donor but not using nucleoside triphosphates. The K_m values of ATP-Glk for glucose and ATP were about 78 μM, and the K_m values of polyP-Glk for glucose and polyP_(n=45) were 450 and 21 μM, respectively. The genomic analysis of methanotrophs showed that ATP-dependent glucokinase is present in all sequenced methanotrophs, with the exception of the genera Methylosinus and Methylocystis, whereas polyP-Glks were found in all species of the genus Methylomonas and in Methylomarinum vadi only. This work presents the first characterization of polyphosphate specific glucokinase in a methanotrophic bacterium.

Molecular biological tools in concrete biodeterioration - a mini review

Concrete structures develop biofilms when exposed to various environments. At a certain stage, the microbial films destroy the concrete structures leading to significant deterioration. Culture-dependent techniques give an incomplete picture of the microbial communities on the concrete surface. Culture-independent techniques or molecular biological tools pave a new way to analyse microbial communities involved in concrete biodeterioration. This study highlights the need to 'build' a database, for Microbiologically Influenced Concrete Corrosion (MICC) involving microbial groups that are being identified using culture-dependent and independent techniques. The role of molecular tools such as 16S rRNA sequencing, denaturing gradient gel electrophoresis (DGGE), Fluorescent in situ hybridization (FISH), Real-time Polymerase Chain Reaction (RT-PCR), microarray analysis, 2-Dimensional gel electrophoresis (2-DE) in analysing microbial communities on the concrete structures have been reviewed in this paper.