Methylphosphonate metabolism by Pseudomonas sp. populations contributes to the methane oversaturation paradox in an oxic freshwater lake

Reduction of methane and nitrous oxide emissions from stormwater bioretention cells through microbial electrolytic cells

This study investigated the reduction of methane (CH4) and nitrous oxide (N2O) emissions from stormwater bioretention cells through microbial electrolytic cell (MEC), showing the largest reduction of 32.21 % (CH4) at 9.2 μA/m2 of current density and 56.16 % (N2O) at 3.5 μA/m2 of current density, compared with the corresponding in the control (0 μA/m2 of current density). Kinetic of CH4 and N2O emissions could be well fitted by Logistic model with high correlation coefficient (R2 > 0.9500) and model efficiency (ME > 0.95) but low relative root mean square error (RRMSE < 7.88). The increase of pmoA and polysaccharide (PS) were responsible for CH4 reduction, while N2O reduction was attributed to the decrease of nirS and the increase for nosZ and protein (PN), which could explain the lowest GWPd (10.67 mgCO2-eq/m2/h) at 3.5 μA/m2 of current density, suggesting that MEC could be promising for the reduction of CH4 and N2O emissions from bioretention cells.

Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments

Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.

Effects of 17β-Estradiol Pollution on Microbial Communities and Methane Emissions in Aerobic Water Bodies

17β-Estradiol (E2) is a widely present trace pollutant in aquatic environments. However, its impact on microbial communities in aerobic lake waters, which are crucial for methane (CH4) production, remains unclear. This study conducted an E2 contamination experiment by constructing laboratory-simulated aerobic microecosystems. Using 16S rRNA high-throughput sequencing, the effects of E2 on bacterial and archaeal communities were systematically examined. Combined with gas chromatography, the patterns and mechanisms of E2's impact on CH4 emissions in aerobic aquatic systems were uncovered for the first time. Generally, E2 contamination increased the randomness of bacterial and archaeal community assemblies and weakened microbial interactions. Furthermore, changes occurred in the composition and ecological functions of bacterial and archaeal communities under E2 pollution. Specifically, two days after exposure to E2, the relative abundance of Proteobacteria in the low-concentration (L) and high-concentration (H) groups decreased by 6.99% and 4.01%, respectively, compared to the control group (C). Conversely, the relative abundance of Planctomycetota was 1.81% and 1.60% higher in the L and H groups, respectively. E2 contamination led to an increase in the relative abundance of the methanogenesis functional group and a decrease in that of the methanotrophy functional group. These changes led to an increase in CH4 emissions. This study comprehensively investigated the ecotoxicological effects of E2 pollution on microbial communities in aerobic water bodies and filled the knowledge gap regarding aerobic methane production under E2 contamination.

The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities

Methanogenesis is a critical process in the carbon cycle that is applied industrially in anaerobic digestion and biogas production. While naturally occurring in diverse environments, methanogenesis requires anaerobic and reduced conditions, although varying degrees of oxygen tolerance have been described. Microaeration is suggested as the next step to increase methane production and improve hydrolysis in digestion processes; therefore, a deeper understanding of the methanogenic response to oxygen stress is needed. To explore the drivers of oxygen tolerance in methanogenesis, two parallel enrichments were performed under the addition of H2/CO2 in an environment without reducing agents and in a redox-buffered environment by adding redox mediator 9,10-anthraquinone-2,7-disulfonate disodium. The cellular response to oxidative conditions is mapped using proteomic analysis. The resulting community showed remarkable tolerance to high-redox environments and was unperturbed in its methane production. Next to the expression of pathways to mitigate reactive oxygen species, the higher redox potential environment showed an increased presence of selenocysteine and selenium-associated pathways. By including sulfur-to-selenium mass shifts in a proteomic database search, we provide the first evidence of the dynamic and large-scale incorporation of selenocysteine as a response to oxidative stress in hydrogenotrophic methanogenesis and the presence of a dynamic selenoproteome.

Adsorption, natural attenuation, and microbial community response of ofloxacin and oxolinic acid in marine sediments

The pollution of quinolone antibiotics in the marine environment has attracted widespread attention, especially for ofloxacin (OFL) and oxolinic acid (OXO) due to their frequent detection. However, few studies have been conducted to assess the behaviors and microbial community response to these antibiotics in marine sediments, particularly for potential antibiotic-resistant bacteria. In this work, the adsorption characteristics, natural attenuation characteristics, and variation of microbial communities of OFL and OXO in marine sediments were investigated. The adsorption process of antibiotics in sediments occurred on the surface and internal pores of organic matter, where OFL was more likely to be transferred from seawater to sediment compared with OXO. Besides, the adsorption of two antibiotics on sediment surfaces was attributed to physisorption (pore filling, electrostatic interaction) and chemisorption (hydrogen bonding). The natural attenuation of OFL and OXO in marine sediment followed second-order reaction kinetics with half-lives of 6.02 and 26.71 days, respectively, wherein biodegradation contributed the most to attenuation, followed by photolysis. Microbial community structure in marine sediments exposure to antibiotics varied by reducing abundance and diversity of microbial communities, as a whole displaying as an increase in the relative abundance of Firmicutes whereas a decrease of Proteobacteria. In detail, Escherichia-Shigella sp., Blautia sp., Bifidobacterium sp., and Bacillus sp. were those antibiotic-resistant bacteria with potential ability to degrade OFL, while Bacillus sp. may be resistant to OXO. Furthermore, functional predictions indicated that the microbial communities in sediment may resist the stress caused by OFL and OXO through cyano-amino acid metabolism, and ascorbate and aldarate metabolism, respectively. The research is key to understanding fate and bacterial resistance of antibiotics in marine sediments.

Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget

Biological methane, a major source of global methane budget, is traditionally thought to be produced in anaerobic environments. However, the recent reports about methane supersaturation occurring in oxygenated water layer, termed as "methane paradox", have challenged this prevailing paradigm. Significantly, growing evidence has indicated that phytoplankton including prokaryotic cyanobacteria and eukaryotic algae are capable of generating methane under aerobic conditions. In this regard, a systematic review of aerobic methane production by phytoplankton is expected to arouse the public attention, contributing to the understanding of methane paradox. Here, we comprehensively summarize the widespread phenomena of methane supersaturation in oxic layers. The remarkable correlation relationships between methane concentration and several key indicators (depth, chlorophyll a level and organic sulfide concentration) indicate the significance of phytoplankton in in-situ methane accumulation. Subsequently, four mechanisms of aerobic methane production by phytoplankton are illustrated in detail, including photosynthesis-driven metabolism, reactive oxygen species (ROS)-driven demethylation of methyl donors, methanogenesis catalyzed by nitrogenase and demethylation of phosphonates catalyzed by CP lyase. The first two pathways occur in various phytoplankton, while the latter two have been specially discovered in cyanobacteria. Additionally, the effects of four crucial factors on aerobic methane production by phytoplankton are also discussed, including phytoplankton species, light, temperature and crucial nutrients. Finally, the measures to control global methane emissions from phytoplankton, the precise intracellular mechanisms of methane production and a more complete global methane budget model are definitely required in the future research on methane production by phytoplankton. This review would provide guidance for future studies of aerobic methane production by phytoplankton and emphasize the potential contribution of aquatic ecosystems to global methane budget.

High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation

The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.

Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply

IMPORTANCE

Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.

Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes

Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, eutrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in 13C-CH4 and 2H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with 13C- and 2H-labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emission to the atmosphere.

Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis

Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na+, and SO42- concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2--N concentration and NO2-/NO3- ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.

The Microbial Degradation of Natural and Anthropogenic Phosphonates

Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.

Aerobic methane synthesis and dynamics in a river water environment

Reports of aerobic biogenic methane (CH 4 ) have generated new views about CH 4 sources in nature. We examine this phenomenon in the free-flowing Yellowstone river wherein CH 4 concentrations were tracked as a function of environmental conditions, phototrophic microorganisms (using chlorophyll a , Chl a , as proxy), as well as targeted methylated amines known to be associated with this process. CH 4 was positively correlated with temperature and Chl a , although diurnal measurements showed CH 4 concentrations were greatest during the night and lowest during maximal solar irradiation. CH 4 efflux from the river surface was greater in quiescent edge waters (71-94 μmol m-2 d) than from open flowing current (~ 57 μmol m-2 d). Attempts to increase flux by disturbing the benthic environment in the quiescent water directly below (~ 1.0 m deep) or at varying distances (0-5 m) upstream of the flux chamber failed to increase surface flux. Glycine betaine (GB), dimethylamine and methylamine (MMA) were observed throughout the summer-long study, increasing during a period coinciding with a marked decline in Chl a , suggesting a lytic event led to their release; however, this did not correspond to increased CH 4 concentrations. Spiking river water with GB or MMA yielded significantly greater CH 4 than nonspiked controls, illustrating the metabolic potential of the river microbiome. In summary, this study provides evidence that: (1) phototrophic microorganisms are involved in CH 4 synthesis in a river environment; (2) the river microbiome possesses the metabolic potential to convert methylated amines to CH 4 ; and (3) river CH 4 concentrations are dynamic diurnally as well as during the summer active months.

Evaluation of the methane paradox in four adjacent pre-alpine lakes across a trophic gradient

Contrasting the paradigm that methane is only produced in anoxic conditions, recent discoveries show that oxic methane production (OMP, aka the methane paradox) occurs in oxygenated surface waters worldwide. OMP drivers and their contribution to global methane emissions, however, are not well constrained. In four adjacent pre-alpine lakes, we determine the net methane production rates in oxic surface waters using two mass balance approaches, accounting for methane sources and sinks. We find that OMP occurs in three out of four studied lakes, often as the dominant source of diffusive methane emissions. Correlations of net methane production versus chlorophyll-a, Secchi and surface mixed layer depths suggest a link with photosynthesis and provides an empirical upscaling approach. As OMP is a methane source in direct contact with the atmosphere, a better understanding of its extent and drivers is necessary to constrain the atmospheric methane contribution by inland waters.

Effects of tidal cycle on greenhouse gases emissions from a tropical estuary

The potential effects of tidal and diel cycles on fluxes and concentrations of carbon dioxide (pCO₂), methane (CH₄), and nitrous oxide (N₂O) along with associated biogeochemical processes remain poorly understood in tropical estuaries. The present study, based on six-hourly sampling for nine consecutive days at three locations along the salinity gradient in the Mahanadi estuary of India, revealed that the tidal forcing affected pCO₂ and CH₄ in the mixing zone with elevated concentrations during low tide with maximum concentrations up to 21,606 μatm and 285 μM, respectively. pCO₂ increased with decrease in tidal height within low and high tide duration as well, possibly due to higher relative contribution of freshwater with high CO₂. N₂O, on the other hand, showed no significant variability with tidal cycle or water level fluctuation during high and low tide. Barring the offshore region, the study area was source of greenhouse gases to the atmosphere.

Transformation mechanism of methylphosphonate to methane by Burkholderia sp: Insight from multi-labeled water isotope probing and transcriptomic

Methylphosphonate (MPn), has been identified as a likely source of methane in aerobic ocean and may be responsible for the "ocean methane paradox", that is oversaturation of dissolved methane in oxic sea waters. However, the mechanism underlying the cleavage of C-P bonds during microbial degradation is not well understood. Using multi-labeled water isotope probing (MLWIP) and transcriptome analysis, we investigated the phosphate oxygen isotope systematics and mechanisms of microbial-mediated degradation of MPn in this study. In the aerobic culture containing MPn as the only phosphorus source, there was a significant release of inorganic phosphate (149.4 μmol/L) and free methane (268.3 mg/L). The oxygen isotopic composition of inorganic phosphorus (δ¹⁸O_P) of accumulated released phosphate was 4.50‰, 23.96‰, and 40.88‰, respectively, in the corresponding ¹⁸O-labeled waters of -10.3‰, 9.9‰, and 30.6‰, and the slope obtained in plots of δ¹⁸O_P versus the oxygen isotopic composition of water (δ¹⁸O_W) was 0.89. Consequently, 89% of the oxygen atoms (Os) in phosphate (PO₄) were exchanged with ¹⁸O-labeled waters in the medium, while the rest were exchanged with intracellular metabolic water. It has been confirmed that the C-P bond cleavage of MPn occurs in the cell with both ambient and metabolic water participation. Moreover, phn gene clusters play significant roles to cleave the C-P bond of MPn for Burkholderia sp. HQL1813, in which phnJ, phnM and phnI genes are significantly up-regulated during MPn decomposition to methane. In conclusion, the aerobic biotransformation of MPn to free methane by Burkholderia sp. HQL1813 has been elucidated, providing new insights into the mechanism that bio-cleaves C-P bonds to produce methane aerobically in aqueous environments for representative phosphonates.

Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis

Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the 'methane paradox'), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.

Magnitude and Drivers of Oxic Methane Production in Small Temperate Lakes

Methanogenesis is traditionally considered as a strictly anaerobic process. Recent evidence suggests instead that the ubiquitous methane (CH₄) oversaturation found in freshwater lakes is sustained, at least partially, by methanogenesis in oxic conditions. Although this paradigm shift is rapidly gaining acceptance, the magnitude and regulation of oxic CH₄ production (OMP) have remained ambiguous. Based on the summer CH₄ mass balance in the surface mixed layer (SML) of five small temperate lakes (surface area, SA, of 0.008-0.44 km²), we show that OMP (range of 0.01 ± 0.01 to 0.52 ± 0.04 μmol L^-1 day^-1) is linked to the concentrations of chlorophyll-a, total phosphorus, and dissolved organic carbon. The stable carbon isotopic mass balance of CH₄ (δ¹³C-CH₄) indicates direct photoautotrophic release as the most likely source of oxic CH₄. Furthermore, we show that the oxic CH₄ contribution to the SML CH₄ saturation and emission is an inverse function of the ratio of the sediment area to the SML volume in lakes as small as 0.06 km². Given that global lake CH₄ emissions are dominated by small lakes (SA of <1 km²), the large contribution of oxic CH₄ production (up to 76%) observed in this study suggests that OMP can contribute significantly to global CH₄ emissions.

Sustained stoichiometric imbalance and its ecological consequences in a large oligotrophic lake

Considerable attention is given to absolute nutrient levels in lakes, rivers, and oceans, but less is paid to their relative concentrations, their nitrogen:phosphorus (N:P) stoichiometry, and the consequences of imbalanced stoichiometry. Here, we report 38 y of nutrient dynamics in Flathead Lake, a large oligotrophic lake in Montana, and its inflows. While nutrient levels were low, the lake had sustained high total N: total P ratios (TN:TP: 60 to 90:1 molar) throughout the observation period. N and P loading to the lake as well as loading N:P ratios varied considerably among years but showed no systematic long-term trend. Surprisingly, TN:TP ratios in river inflows were consistently lower than in the lake, suggesting that forms of P in riverine loading are removed preferentially to N. In-lake processes, such as differential sedimentation of P relative to N or accumulation of fixed N in excess of denitrification, likely also operate to maintain the lake's high TN:TP ratios. Regardless of causes, the lake's stoichiometric imbalance is manifested in P limitation of phytoplankton growth during early and midsummer, resulting in high C:P and N:P ratios in suspended particulate matter that propagate P limitation to zooplankton. Finally, the lake's imbalanced N:P stoichiometry appears to raise the potential for aerobic methane production via metabolism of phosphonate compounds by P-limited microbes. These data highlight the importance of not only absolute N and P levels in aquatic ecosystems, but also their stoichiometric balance, and they call attention to potential management implications of high N:P ratios.

Microbial methane emissions from the non-methanogenesis processes: A critical review

Methane, a potent greenhouse gas of global importance, has traditionally been considered as an end product of microbial methanogenesis of organic matter. Paradoxically, growing evidence has shown that some microbes, such as cyanobacteria, algae, fungi, purple non-sulfur bacteria, and cryptogamic covers, produce methane in oxygen-saturated aquatic and terrestrial ecosystems. The non-methanogenesis process could be an important potential contributor to methane emissions. This systematic review summarizes the knowledge of microorganisms involved in the non-methanogenesis process and the possible mechanisms of methane formation. Cyanobacteria-derived methane production may be attributed to either demethylation of methyl phosphonates or linked to light-driven primary productivity, while algae produce methane by utilizing methylated sulfur compounds as possible carbon precursors. In addition, fungi produce methane by utilizing methionine as a possible carbon precursor, and purple non-sulfur bacteria reduce carbon dioxide to methane by nitrogenase. The microbial methane distribution from the non-methanogenesis processes in aquatic and terrestrial environments and its environmental significance to global methane emissions, possible mechanisms of methane production in each open water, water-to-air methane fluxes, and the impact of climate change on microorganisms are also discussed. Finally, future perspectives are highlighted, such as establishing more in-situ experiments, quantifying methane flux through optimizing empirical models, distinguishing individual methane sources, and investigating nitrogenase-like enzyme systems to improve our understanding of microbial methane emission from the non-methanogenesis process.

Aerobic bacterial methane synthesis

Reports of biogenic methane (CH₄) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy and in most cases the process is poorly understood at the gene and enzyme levels. In marine and freshwater environments, CH₄ supersaturation of oxic surface waters has been termed the "methane paradox" because biological CH₄ synthesis is viewed to be a strictly anaerobic process carried out by O₂-sensitive methanogens. Interest in this phenomenon has surged within the past decade because of the importance of understanding sources and sinks of this potent greenhouse gas. In our work on Yellowstone Lake in Yellowstone National Park, we demonstrate microbiological conversion of methylamine to CH₄ and isolate and characterize an Acidovorax sp. capable of this activity. Furthermore, we identify and clone a gene critical to this process (encodes pyridoxylamine phosphate-dependent aspartate aminotransferase) and demonstrate that this property can be transferred to Escherichia coli with this gene and will occur as a purified enzyme. This previously unrecognized process sheds light on environmental cycling of CH₄, suggesting that O₂-insensitive, ecologically relevant aerobic CH₄ synthesis is likely of widespread distribution in the environment and should be considered in CH₄ modeling efforts.

Spatial methane pattern in a deep freshwater lake: Relation to water depth and topography

Freshwater lakes are regarded as important methane (CH₄) sources, accounting for ~20% of natural emission. To improve the assessment of the global greenhouse effect, it is necessary to consider spatial variability within lakes. Here, CH₄ concentrations in the water column and sediment layers, as well as the sediment CH₄ production potentials and diffusive fluxes, were studied in the littoral, intermediate, and profundal zones of the medium-sized (425 ha), deep (maximum depth 69.5 m) Lake Stechlin (Germany). Sediment CH₄ concentrations, production potentials and sediment-water interface diffusive fluxes showed significant spatial heterogeneity and were highest in the profundal zone. CH₄ concentrations in the surface water did not differ among the studied locations, indicating a decoupling from the production sites in the sediment. The high amount of CH₄ in profundal sediments that might potentially be released to the atmosphere is either trapped or oxidized within the water column, while the surface water dissolved CH₄ is more related to the dynamics in the epilimnion. The divergence in sediment physical (water content, grain size) and chemical (organic matter quantity or quality, sulfate) properties across the lake leads to variations in CH₄ dynamics which are restricted to deeper habitats in this type of lake.

Ecosystem maturity modulates greenhouse gases fluxes from artificial lakes

Lentic ecosystems play a major role in the global carbon cycling but the understanding of the environmental determinants of lake metabolism is still limited, notably in small artificial lakes. Here the effects of environmental conditions on lake metabolism and CO₂ and CH₄ emissions were quantified in 11 small artificial gravel pit lakes covering a gradient of ecosystem maturity, ranging from young oligotrophic to older, hypereutrophic lakes. The diffusive fluxes of CO₂ and CH₄ ranged from -30.10 to 37.78 mmol m^-2 d^-1 and from 3.05 to 25.45 mmol m^-2 d^-1 across gravel pit lakes, respectively. Nutrients and chlorophyll a concentrations were negatively correlated with CO₂ concentrations and emissions but positively correlated with CH₄ concentrations and emissions from lakes. These findings indicate that, as they mature, gravel pit lakes switch from heterotrophic to autotrophic-based metabolism and hence turn into CO₂-sinks. In contrast, the emission of CH₄ increased along the maturity gradient. As a result, eutrophication occurring during ecosystem maturity increased net emissions in terms of climate impact (CO_{2 equivalent}) due to the higher contribution of CH₄ emissions. Overall, mean CO_2equivalent emission was 7.9 g m^-2 d^-1, a value 3.7 and 4.7 times higher than values previously reported in temperate lakes and reservoirs, respectively. While previous studies reported that lakes represent emitters of C to the atmosphere, this study highlights that eutrophication may reverse lake contribution to global C budgets. However, this finding is to be balanced with the fact that eutrophication also increased CH₄ emissions and hence, enhanced the potential impact of these ecosystems on climate. Implementing mitigation strategies for maintaining intermediate levels of maturity is therefore needed to limit the impacts of small artificial waterbodies on climate. This could be facilitated by their small size and should be planned at the earliest stages of artificial lake construction.

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.

High Spatiotemporal Dynamics of Methane Production and Emission in Oxic Surface Water

The discovery of methane (CH₄) accumulation in oxic marine and limnic waters has redefined the role of aquatic environments in the regional CH₄ cycle. Although CH₄ accumulation in oxic surface waters became apparent in recent years, the sources are still subject to controversial discussions. We present high-resolution in situ measurements of CH₄ concentration and its stable isotope composition in a stratified mesotrophic lake. We show that CH₄ accumulation in surface waters originates from a highly dynamic interplay between (oxic) CH₄ production and emission to the atmosphere. Laboratory incubations of different phytoplankton types and application of stable isotope techniques provide a first unambiguous evidence that major phytoplankton classes in Lake Stechlin per se produce CH₄ under oxic conditions. Combined field and lab results show that the photoautotroph community is an important driver for CH₄ production and its highly dynamic accumulation in oxic surface waters.

Linking Stoichiometric Organic Carbon–Nitrogen Relationships to planktonic Cyanobacteria and Subsurface Methane Maximum in Deep Freshwater Lakes

Our understanding of the source of methane (CH4) in freshwater ecosystems is being revised because CH4 production in oxic water columns, a hitherto inconceivable process of methanogenesis, has been discovered for lake ecosystems. The present study surveyed nine Japanese deep freshwater lakes to show the pattern and mechanisms of such aerobic CH4 production and subsurface methane maximum (SMM) formation. The field survey observed the development of SMM around the metalimnion in all the study lakes. Generalized linear model (GLM) analyses showed a strong negative nonlinear relationship between dissolved organic carbon (DOC) and dissolved inorganic nitrogen (DIN), as well as a similar curvilinear relationship between DIN and dissolved CH4, suggesting that the availability of organic carbon controls N accumulation in lake waters thereby influences the CH4 production process. The microbial community analyses revealed that the distribution of picocyanobacteria (i.e., Synechococcus), which produce CH4 in oxic conditions, was closely related to the vertical distribution of dissolved CH4 and SMM formation. Moreover, a cross-lake comparison showed that lakes with a more abundant Synechococcus population exhibited a greater development of the SMM, suggesting that these microorganisms are the most likely cause of methane production. Thus, we conclude that the stoichiometric balance between DOC and DIN might cause the cascading responses of biogeochemical processes, from N depletion to picocyanobacterial domination, and subsequently influence SMM formation in lake ecosystems.

Biogeochemical and physical controls on methane fluxes from two ferruginous meromictic lakes

Meromictic lakes with anoxic bottom waters often have active methane cycles whereby methane is generally produced biogenically under anoxic conditions and oxidized in oxic surface waters prior to reaching the atmosphere. Lakes that contain dissolved ferrous iron in their deep waters (i.e., ferruginous) are rare, but valuable, as geochemical analogues of the conditions that dominated the Earth's oceans during the Precambrian when interactions between the iron and methane cycles could have shaped the greenhouse regulation of the planet's climate. Here, we explored controls on the methane fluxes from Brownie Lake and Canyon Lake, two ferruginous meromictic lakes that contain similar concentrations (max. >1 mM) of dissolved methane in their bottom waters. The order Methanobacteriales was the dominant methanogen detected in both lakes. At Brownie Lake, methanogen abundance, an increase in methane concentration with respect to depths closer to the sediment, and isotopic data suggest methanogenesis is an active process in the anoxic water column. At Canyon Lake, methanogenesis occurred primarily in the sediment. The most abundant aerobic methane-oxidizing bacteria present in both water columns were associated with the Gammaproteobacteria, with little evidence of anaerobic methane oxidizing organisms being present or active. Direct measurements at the surface revealed a methane flux from Brownie Lake that was two orders of magnitude greater than the flux from Canyon Lake. Comparison of measured versus calculated turbulent diffusive fluxes indicates that most of the methane flux at Brownie Lake was non-diffusive. Although the turbulent diffusive methane flux at Canyon Lake was attenuated by methane oxidizing bacteria, dissolved methane was detected in the epilimnion, suggestive of lateral transport of methane from littoral sediments. These results highlight the importance of direct measurements in estimating the total methane flux from water columns, and that non-diffusive transport of methane may be important to consider from other ferruginous systems.

Aquatic and terrestrial cyanobacteria produce methane

Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.

Contribution of oxic methane production to surface methane emission in lakes and its global importance

Recent discovery of oxic methane production in sea and lake waters, as well as wetlands, demands re-thinking of the global methane cycle and re-assessment of the contribution of oxic waters to atmospheric methane emission. Here we analysed system-wide sources and sinks of surface-water methane in a temperate lake. Using a mass balance analysis, we show that internal methane production in well-oxygenated surface water is an important source for surface-water methane during the stratified period. Combining our results and literature reports, oxic methane contribution to emission follows a predictive function of littoral sediment area and surface mixed layer volume. The contribution of oxic methane source(s) is predicted to increase with lake size, accounting for the majority (>50%) of surface methane emission for lakes with surface areas >1 km².

Microcapillary sampling of Baltic Sea copepod gut microbiomes indicates high variability among individuals and the potential for methane production

The paradox of methane oversaturation in oxygenated surface water has been described in many pelagic systems and still raises the question of the source. Temora sp. and Acartia sp. commonly dominate the surface and subsurface waters of the central Baltic Sea. It is hypothesised that their gut microbiome at least partly contributes to the methane anomaly in this ecosystem. However, the potential pathway for this methane production remains unclear. Using a microcapillary technique, we successfully overcame the challenge of sampling the gut microbiome of copepods <1 mm. 16S rRNA gene amplicon sequencing revealed differences among the dominant bacterial communities associated with Temora sp. (Actinobacteria, Betaproteobacteria and Flavobacteriia) and Acartia sp. (Actinobacteria, Alphaproteobacteria and Betaproteobacteria) and the surrounding water (Proteobacteria, Cyanobacteria and Verrucomicrobia), but also intraspecific variability. In both copepods, gut-specific prokaryotic taxa and indicative species for methane production pathways (methanogenesis, dimethylsulfoniopropionate or methylphosphonate) were present. The relative abundance of archaea and methanogens was investigated using droplet digital polymerase chain reaction and showed a high variability among copepod individuals, underlining intra- and interspecific differences in copepod-associated prokaryotic communities. Overall, this work highlights that the guts of Temora sp. and Acartia sp. have the potential for methane production but are probably no hotspot.

An Oxidative Pathway for Microbial Utilization of Methylphosphonic Acid as a Phosphate Source

Methylphosphonic acid is synthesized by marine bacteria and is a prominent component of dissolved organic phosphorus. Consequently, methylphosphonic acid also serves as a source of inorganic phosphate (Pi) for marine bacteria that are starved of this nutrient. Conversion of methylphosphonic acid into Pi is currently only known to occur through the carbon-phosphorus lyase pathway, yielding methane as a byproduct. In this work, we describe an oxidative pathway for the catabolism of methylphosphonic acid in Gimesia maris DSM8797. G. maris can use methylphosphonic acid as Pi sources despite lacking a phn operon encoding a carbon-phosphorus lyase pathway. Instead, the genome contains a locus encoding homologues of the non-heme Fe(II) dependent oxygenases HF130PhnY* and HF130PhnZ, which were previously shown to convert 2-aminoethylphosphonic acid into glycine and Pi. GmPhnY* and GmPhnZ1 were produced in E. coli and purified for characterization in vitro. The substrate specificities of the enzymes were evaluated with a panel of synthetic phosphonates. Via ³¹P NMR spectroscopy, it is demonstrated that the GmPhnY* converts methylphosphonic acid to hydroxymethylphosphonic acid, which in turn is oxidized by GmPhnZ1 to produce formic acid and Pi. In contrast, 2-aminoethylphosphonic acid is not a substrate for GmPhnY* and is therefore not a substrate for this pathway. These results thus reveal a new metabolic fate for methylphosphonic acid.

A role for phosphorus redox in emerging and modern biochemistry

Phosphorus is a major biogeochemical element controlling growth in many ecosystems. It has presumably been an important element since the onset of life. In most chemical and biochemical considerations, phosphorus is synonymous with phosphates, a pentavalent oxidation state that includes the phosphate backbone of DNA and RNA, as well as major metabolites such as ATP. However, redox processing of phosphates to phosphites and phosphonates, and to even lower oxidation states provides a work-around to many of the problems of prebiotic chemistry, including phosphorus's low solubility and poor reactivity. In addition, modern phosphorus cycling has increasingly identified reduced P compounds as playing a role, sometimes significant, in biogeochemical processes. This suggests that phosphorus is not redox-insensitive and reduced P compounds should be considered as part of the phosphorus biogeochemical cycle.

Full-scale evaluation of methane production under oxic conditions in a mesotrophic lake

Oxic lake surface waters are frequently oversaturated with methane (CH₄). The contribution to the global CH₄ cycle is significant, thus leading to an increasing number of studies and stimulating debates. Here we show, using a mass balance, on a temperate, mesotrophic lake, that ~90% of CH₄ emissions to the atmosphere is due to CH₄ produced within the oxic surface mixed layer (SML) during the stratified period, while the often observed CH₄ maximum at the thermocline represents only a physically driven accumulation. Negligible surface CH₄ oxidation suggests that the produced 110 ± 60 nmol CH₄ L^-1 d^-1 efficiently escapes to the atmosphere. Stable carbon isotope ratios indicate that CH₄ in the SML is distinct from sedimentary CH₄ production, suggesting alternative pathways and precursors. Our approach reveals CH₄ production in the epilimnion that is currently overlooked, and that research on possible mechanisms behind the methane paradox should additionally focus on the lake surface layer.