Oxic water column methanogenesis as a major component of aquatic CH4 fluxes

Cold-Temperate Mountainous Freshwater Produces Methane by Algal Metabolism

We reported important environmental drivers of dissolved CH4 concentrations (d-CH4) in nutrient-limited mountainous freshwater in a cold-temperate region and explored the potential for multiple known oxic CH4 production pathways. Field investigation revealed consistent supersaturated d-CH4 in surface water (relative to the theoretical value of d-CH4 at atmospheric equilibrium), with significant seasonal variations. Statistical analysis highlighted the direct impact of algal dynamics and the indirect effect of temperature and nutrients on d-CH4. Further lab-scale incubation demonstrated that CH4 production decreased by 55.25 to 93.65% with algae removal, while it increased 4 to 10 times with methylphosphonate (MPn) amendment. These findings argued that CH4 produced from algal metabolism related to MPn had a high potential for supersaturated d-CH4. It also verified the pivotal role of cyanobacteria in this mechanism, with temperature and light acting as regulatory factors. Through highlighting the role of algae for CH4 characteristics in cold-temperate mountainous freshwater and proposing the potential of oxic CH4 production through MPn metabolism in nutrient-limited lakes, this study enriches comprehension of aquatic CH4 cycle and warns about the importance of preserving environmental balance in freshwater with minimal human disturbance.

Dissolved inorganic carbon input significantly lowers carbon dioxide flux but not methane flux in shallow macrophyte-dominated systems with positive effects on carbon stocks

BACKGROUND

With the increase in the inorganic carbon input from watersheds, elevated dissolved inorganic carbon (DIC) concentrations will significantly impact the carbon cycle in freshwater ecosystems. Moreover, the limited diffusion rate of CO2 in water, coupled with the lack of functional stomata, greatly restricts the ability of submerged macrophytes to absorb CO2 from their aquatic environment. The importance of bicarbonate (HCO3-) for submerged macrophytes becomes more pronounced. Current research focuses on the effects of DIC (notably HCO3-) on the phenotypic plasticity of submerged macrophytes, while its impact on their carbon stock capabilities has rarely been reported.

RESULTS

In this study, Myriophyllum spicatum served as the model macrophyte within a mesocosm experimental system to assess the impact of HCO3- enrichment (0.5 to 2.5 mmol L-1) on carbon stocks and emissions across a one-year period. Our findings indicated that the addition of HCO3- had a non-significant inhibitory effect on the diffusive fluxes of methane (CH4) emissions. Concurrently, it significantly reduced CO2 fluxes within the systems. The annual average CO2 fluxes across the four HCO3- addition levels were -3.48 ± 7.60, -6.78 ± 5.87, -7.15 ± 8.68, and -14.04 ± 14.39 mol m-2 yr-1, respectively, showing significant differences between low /medium- and high- HCO3- addition levels.

CONCLUSION

The addition of HCO3- enhanced carbon stocks in water, macrophytes and the entire system, with minimal effects on carbon sedimentation stocks. Our study provides valuable insights into understanding the carbon sink capacity of aquatic ecosystems and elucidates the underlying mechanisms driving these processes on a system scale.

Terrestrial Organic Matter Inputs Modulate Methane Emissions from a Mega-Reservoir

Reservoirs are hotspots for methane (CH4) emissions. However, to date, the effects of terrestrial organic matter (OM) input and degradation on CH4 emissions from large reservoirs remain largely unknown. From May 2020 to April 2021, we conducted monthly sampling campaigns at 100 sites in Lake Qiandao (580 km2), a mega-reservoir in China, and made monthly vertical profile observations from March to September 2023. We estimated an annual mean FCH4 flux of 0.26 g C m-2 yr-1 (1.51 × 108 g C yr-1). Elevated FCH4 and enriched δ13C-CH4 coincided with low dissolved oxygen (DO) concentrations, high levels of organic suspended solids, terrestrial organic matter, nutrients, depleted δ18O-H2O, and low carbon isotope fractionation (αC) in the inflowing lake regions. Dissolved CH4 (cCH4) correlated positively to the relative abundance of aliphatic compounds. Anoxic bioincubation experiments revealed rapid degradation of riverine organic matter, accompanied by a 56-fold increase in cCH4, δ13C-CH4 enrichment (to -32.25‰), and a significant decrease in αC to 1.02. These findings indicate that acetoclastic CH4 production makes a substantial contribution to cCH4 and thus FCH4. Based on multiple lines of evidence, we conclude that input of terrestrial organic matter and its subsequent degradation lead to DO depletion, and their OM degradation byproducts serve as carbon substrates that promote CH4 emissions.

Use of biochar derived from Spartina alterniflora to reduce sediment methane (CH4) production potential during non-farming period in earthen aquaculture ponds

Biochar has been proposed as an effective material for mitigating greenhouse gas emissions from farmlands, but comparable information for earthen aquaculture ponds is limited. A field study was conducted to investigate the effects of adding biochar (200-1600 kg ha-1) derived from the invasive plant Spartina alterniflora on sediment physico-chemical properties, CH4 production potential (PCH4), and the relevant functional gene abundances in earthen aquaculture ponds during the non-farming period. The results indicated that biochar treatments increased sediment porosity and salinity, while decreasing dissolved organic carbon and microbial biomass carbon. Biochar-treated sediments also exhibited a significantly lower abundance of mcrA gene especially in the early drainage stage, and a higher abundance of pmoA gene especially in the intermediate and final drainage stages. Consequently, the mean PCH4 in biochar-treated sediments (1.28-21.12 ng g-1 d-1) was 57-73% lower than in the control group (5.41-39.45 ng g-1 d-1). The reduction in PCH4 did not differ between biochar produced at 300 °C vs. 500 °C and was not dependent on the amount of biochar added. The findings suggest that using biochar derived from S. alterniflora can be a cost-effective method to control the spread of this invasive plant and reduce CH4 production in aquaculture pond sediment during the non-farming period.

Dark carbon fixation is a common process in the water column of stratified boreal lakes

CO2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water.

Strong Subseasonal Variability of Oxic Methane Production Challenges Methane Budgeting in Freshwater Lakes

Methane (CH4) accumulation in the well-oxygenated lake epilimnion enhances the diffusive atmospheric CH4 emission. Both lateral transport and in situ oxic methane production (OMP) have been suggested as potential sources. While the latter has been recently supported by increasing evidence, quantifying the exact contribution of OMP to atmospheric emissions remains challenging. Based on a large high-resolution field data set collected during 2019-2020 in the deep stratified Lake Stechlin and on three-dimensional hydrodynamic modeling, we improved existing CH4 budgets by resolving each component of the mass balance model at a seasonal scale and therefore better constrained the residual OMP. All terms in our model showed a large temporal variability at scales from intraday to seasonal, and the modeled OMP was most sensitive to the surface CH4 flux estimates. Future efforts are needed to reduce the uncertainties in estimating OMP rates using the mass balance approach by increasing the frequency of atmospheric CH4 flux measurements.

Epilimnetic oligotrophication increases contribution of oxic methane production to atmospheric methane flux from stratified lakes

Although considerable attention has been paid to the effects of eutrophication on aquatic methane (CH4) emissions to the atmosphere, the ecosystem-level effects of oligotrophication/re-oligotrophication on aquatic CH4 production and subsequent ecological responses remain to be elucidated. It has been hypothesized that dissolved inorganic phosphorus (DIP)-deficient conditions drive the ecosystem to utilize poorly bioavailable organic phosphorus for biomass formation, thereby generating CH4 as a by-product. To test this hypothesis, a mass balance approach was used to estimate in situ oxic methane production (OMP) in an oligotrophic, deep Lake Fuxian. The isotopic signature of dissolved 13C-CH4, the potential substrates for OMP, and the phnJ/phnD genes associated with microbial demethylation of organic phosphorus compounds were analyzed. Our results indicate that CH4 accumulation was maximal in the surface mixed layer (SML, i.e., Epilimnion) during lake stratification, and ∼ 86 % of the total CH4 flux to the atmosphere was due to OMP. Decomposition of methylphosphonate (MPn) by Alphaproteobacteria (genera Sphingomonas and Mesorhizobium) contributed significantly to OMP. Furthermore, water temperature (Temp), chlorophyll a (Chla), and DIP were the most critical predictors of water OMP potential. Meta-analysis of currently available global data showed that OMP had a negative exponential distribution with DIP (OMP = 2.0 e-0.71DIP, R2 = 0.57, p < 0.05). DIP concentrations below a threshold of 3.40 ∼ 9.35 μg P L-1 triggered OMP processes and increased the atmospheric CH4 emissions. Under future warming scenarios, stratification and catchment management induced oligotrophication or re-oligotrophication may systematically affect the biogeochemical cycling of phosphorus and the OMP contribution to CH4 emission in stratified lakes.

S-containing molecular markers of dissolved organic carbon attributing to riverine dissolved methane production across different land uses

The emission of methane (CH4) from streams and rivers contributes significantly to its global inventory. The production of CH4 is traditionally considered as a strictly anaerobic process. Recent investigations observed a "CH4 paradox" in oxic waters, suggesting the occurrence of oxic methane production (OMP). Human activities promoted dissolved organic carbon (DOC) in streams and rivers, providing significant substrates for CH4 production. However, the underlying DOC molecular markers of CH4 production in river systems are not well known. The identification of these markers will help to reveal the mechanism of methanogenesis. Here, Fourier transform ion cyclotron mass spectrometry and other high-quality DOC characterization, ecosystem metabolism, and in-situ net CH4 production rate were employed to investigate molecular markers attributing to riverine dissolved CH4 production across different land uses. We show that endogenous CH4 production supports CH4 oversaturation and positively correlates with DOC concentrations and gross primary production. Furthermore, sulfur (S)-containing molecules, particularly S-aliphatics and S-peptides, and fatty acid-like compounds (e.g., acetate homologs) are characterized as markers of water-column aerobic and anaerobic CH4 production. Watershed characterization, including riverine discharge, allochthonous DOC input, turnover, as well as autochthonous DOC, affects the CH4 production. Our study helps to understand riverine aerobic or anaerobic CH4 production relating to DOC molecular characteristics across different land uses.

Photo-methanification of aquatic dissolved organic matters with different origins under aerobic conditions: Non-negligible role of hydroxyl radicals

Lingering inconsistencies in the global methane (CH4) budget and ambiguity in CH4 sources and sinks triggered efforts to identify new CH4 formation pathways in natural ecosystems. Herein, we reported a novel mechanism of light-induced generation of hydroxyl radicals (•OH) that drove the production of CH4 from aquatic dissolved organic matters (DOMs) under ambient conditions. A total of five DOM samples with different origins were applied to examine their potential in photo-methanification production under aerobic conditions, presenting a wide range of CH4 production rates from 3.57 × 10-3 to 5.90 × 10-2 nmol CH4 mg-C-1 h-1. Experiments of •OH generator and scavenger indicated that the contribution of •OH to photo-methanificaiton among different DOM samples reached about 4∼42 %. In addition, Fourier transform infrared spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry showed that the carbohydrate- and lipid-like substances containing nitrogen-bonded methyl groups, methyl ester, acetyl groups, and ketones, were the potential precursors for light-induced CH4 production. Based on the experimental results and simulated calculations, the contribution of photo-methanification of aquatic DOMs to the diffusive CH4 flux across the water-air interface in a typical eutrophic shallow lake (e.g., Lake Chaohu) ranged from 0.1 % to 18.3 %. This study provides a new perspective on the pathways of CH4 formation in aquatic ecosystems and a deeper understanding on the sources and sinks of global CH4.

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.

Experimental Ecosystem Eutrophication Causes Offsetting Effects on Emissions of CO2, CH4, and N2O from Agricultural Reservoirs

Despite decades of research and management efforts, eutrophication remains a persistent threat to inland waters. As nutrient pollution intensifies in the coming decades, the implications for aquatic greenhouse gas (GHG) emissions are poorly defined, particularly the responses of individual GHGs: carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). The biogeochemical controls of each gas can differ, making it difficult to predict the overall effect of nutrient pollution on the net radiative forcing of aquatic ecosystems. Here, we induced eutrophication of small nitrogen (N)-limited agricultural reservoirs and measured changes in diffusive GHG emissions within a before-after-control-impact (BACI) study design during June to September 2021. Each gas exhibited a unique response to 300% increases in primary production, with a shift from an overall CO2 source to a sink, a modest increase in N2O flux, and, unexpectedly, no significant change in CH4 emissions. The lack of net directional change in CO2-equivalent GHG emissions in fertilized reservoirs during the summer contrasts findings from empirical studies of eutrophic lakes. Our findings illustrate the difficulty in extrapolating among different sized ecosystems and suggest that forecast 2-fold increases in agricultural N fertilization by 2050 may not result in consistently elevated GHG emissions during summer, at least from small reservoirs in continental grassland regions.

Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake

Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.

All tidal wetlands are blue carbon ecosystems

Managing coastal wetlands is one of the most promising activities to reduce atmospheric greenhouse gases, and it also contributes to meeting the United Nations Sustainable Development Goals. One of the options is through blue carbon projects, in which mangroves, saltmarshes, and seagrass are managed to increase carbon sequestration and reduce greenhouse gas emissions. However, other tidal wetlands align with the characteristics of blue carbon. These wetlands are called tidal freshwater wetlands in the United States, supratidal wetlands in Australia, transitional forests in Southeast Asia, and estuarine forests in South Africa. They have similar or larger potential for atmospheric carbon sequestration and emission reductions than the currently considered blue carbon ecosystems and have been highly exploited. In the present article, we suggest that all wetlands directly or indirectly influenced by tides should be considered blue carbon. Their protection and restoration through carbon offsets could reduce emissions while providing multiple cobenefits, including biodiversity.

CO2 and CH4 dynamics in a eutrophic tropical Andean reservoir

We studied the dynamics of methane (CH4) and carbon dioxide (CO2) in a eutrophic tropical reservoir located in the Colombian Andes. Temporal and spatial dynamics were addressed through sampling during six field campaigns conducted throughout a two-year period. We monitored fluxes at the air-water interface, dissolved gas concentrations, physical and chemical properties of the water column, microstructure profiles of turbulence, and meteorological conditions. Throughout the study period, the reservoir was a persistent source of CH4 to the atmosphere with higher emissions occurring in the near inflow region. During periods of low water levels, both the emissions and surface concentrations of CH4 were higher and more spatially heterogeneous. The measured CO2 fluxes at the air-water interface changed direction depending on the time and location, showing alternating uptake and emissions by the water surface. Mass balances of dissolved CH4 in the surface mixed layer revealed that biochemical reactions and gas evasion were the most significant processes influencing the dynamics of dissolved CH4, and provided new evidence of possible oxic methane production. Our results also suggest that surface CH4 concentrations are higher under more eutrophic conditions, which varied both spatially and temporally.

Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir

Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103-1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.

Is ebullition or diffusion more important as methane emission pathway in a shallow subsaline lake?

Methane (CH4) emissions via ebullition contribute significantly to greenhouse gas emissions from freshwater bodies. According to the literature, the ebullition pathway may even be the most important pathway in some cases, particularly in shallow lakes. Ebullition rates are not often estimated because of the high uncertainty associated with episodic releases, leading to difficulties in their determination. This study provides an estimate of such emissions in a large, shallow, subsaline lake in eastern Austria, Lake Neusiedl, and compares them to the diffusion pathway. Ebullition gas sampling was conducted every 5-10 days over a period of 107 days from late March to mid-July 2021, using ebullition traps placed in three distinct locations: Reed belt, Channel and Open water/Lake. The aim was to study the temporal and spatial heterogeneity of ebullition and its contribution to total emissions. At the same time, several water quality and other environmental parameters were measured and then tested against the CH4 ebullition rates to explore them as potential drivers for this pathway. The carbon isotope fractionation factor (αC) of the measured CH4 ebullition gas, ranging from 1.03 to 1.06, indicates a dominance of the acetoclastic methanogenesis in the sediments of Lake Neusiedl, regardless of the location. The Reed belt location showed the highest mean CH4 ebullition rate (17 ± 28 mg CH4 m-2 d-1), which is >340-fold higher than the mean of the other two locations, and demonstrated also a strong temperature dependency. In all locations at Lake Neusiedl, the median CH4 fluxes via diffusion are significantly higher than via ebullition. Our analyses do not confirm the dominance of the ebullition pathway in any of the studied locations. Whereas at the Reed belt, ebullition accounts for 48 % of the CH4 emissions, in the other two locations, is responsible only for about 1 %.

Significant inter-annual fluctuation in CO2 and CH4 diffusive fluxes from subtropical aquaculture ponds: Implications for climate change and carbon emission evaluations

Aquaculture ponds are potential hotspots for carbon cycling and emission of greenhouse gases (GHGs) like CO2 and CH4, but they are often poorly assessed in the global GHG budget. This study determined the temporal variations of CO2 and CH4 concentrations and diffusive fluxes and their environmental drivers in coastal aquaculture ponds in southeastern China over a five-year period (2017-2021). The findings indicated that CH4 flux from aquaculture ponds fluctuated markedly year-to-year, and CO2 flux varied between positive and negative between years. The coefficient of inter-annual variation of CO2 and CH4 diffusive fluxes was 168% and 127%, respectively, highlighting the importance of long-term observations to improve GHG assessment from aquaculture ponds. In addition to chlorophyll-a and dissolved oxygen as the common environmental drivers, CO2 was further regulated by total dissolved phosphorus and CH4 by dissolved organic carbon. Feed conversion ratio correlated positively with both CO2 and CH4 concentrations and fluxes, showing that unconsumed feeds fueled microbial GHG production. A linear regression based on binned (averaged) monthly CO2 diffusive flux data, calculated from CO2 concentrations, can be used to estimate CH4 diffusive flux with a fair degree of confidence (r2 = 0.66; p < 0.001). This algorithm provides a simple and practical way to assess the total carbon diffusive flux from aquaculture ponds. Overall, this study provides new insights into mitigating the carbon footprint of aquaculture production and assessing the impact of aquaculture ponds on the regional and global scales.

Archaeal blooms and busts in an estuarine time series

Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.

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.

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.

Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau

Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.

Fluxes in CO2 and CH4 and influencing factors at the sediment-water interface in a eutrophic saline lake

Although saline aquatic ecosystems are significant emitters of greenhouse gases (GHGs), dynamic changes in GHGs at the sediment-water interface remain unclear. The present investigation carried out a total of four sampling campaigns in Daihai Lake, which is a eutrophic saline lake situated in a semi-arid area of northern China. The aim of this study was to investigate the spatio-temporal dynamics of carbon dioxide (CO2) and methane (CH4) fluxes at the sediment-water interface and the influencing factors. The mean concentrations of porewater CO2 and CH4 were 44.98 ± 117.99 μmol L-1 and 124.36 ± 97.00 μmol L-1, far exceeding those in water column of 11.14 ± 2.16 μmol L-1 and 0.33 ± 0.23 μmol L-1, respectively. The CO2 and CH4 fluxes at the sediment-water interface (FS-WCO2 and FS-WCH4) exhibited significant spatial and temporal variations, with mean values of 9.24 ± 13.84 μmol m-2 d-1 and 3.53 ± 4.36 μmol m-2 d-1, respectively, indicating that sediment is the source of CO2 and CH4 in the water column. However, CO2 and CH4 fluxes were much lower than those measured at the water-air interface in a companion study (17.54 ± 14.54 mmol m-2d-1 and 0.50 ± 0.50 mmol m-2d-1, respectively), indicating that the diffusive flux of gases at the sediment-water interface was not the primary source of CO2 and CH4 emissions to the atmosphere. Regression and correlation analyses revealed that salinity (Sal) and nutrients were the most influential factors on porewater gas concentrations, and that gas fluxes increased with increasing gas concentrations and porosity. The microbial activity of sediment is greatly affected by nutrients and Sal. Additionally, Sal has the ability to regulate biogeochemical processes, thereby regulating GHG emissions. The present investigation addresses the research gap concerning GHG emissions from sediments of eutrophic saline lakes. The study suggests that controlling the eutrophication and salinization of lakes could be a viable strategy for reducing carbon emissions from lakes. However, further investigations are required to establish more conclusive results.

Changes in the abundance and diversity of bacterial and archaeal communities at different depths in a eutrophic freshwater lake in southwestern Mexico

Bacteria and archaea play a fundamental role in the biogeochemical cycles of organic matter, pollutants, and nutrients to maintain the trophic state of aquatic ecosystems. However, very little is known about the composition patterns of microbial communities in vertical distribution (water column) in freshwater lakes and their relationship with the physicochemical properties of water. "La Encantada" lake in the Lagunas de Montebello National Park (LMNP) is a site of interest due to the anthropogenic impact received and the little information about it. In this study, 3 sites were evaluated; samples were collected using 0-15 m deep water columns and analyzed using Illumina MiSeq sequencing technology based on the 16S rRNA gene. The physical parameters of pH, temperature, dissolved oxygen, electrolytic conductivity, and PO-4 were determined. The results revealed clear differences in the microbial composition of the water throughout the column; the most abundant phyla in bacterial communities were Proteobacteria (23.2%), Cyanobacteria (17.3%), and Bacteroidetes (17.2%), and for archaea were Crenarchaeota (35.9%) and Euryarchaeota (33.2%). PICRUSt metabolic inference analysis revealed that the main functional genes were related to cellular processes and biodegradation of xenobiotics, indicating an increasing trend of contaminants and residual discharges that may act as a precursor to alter microbial communities and stability of the lakes. At depths of 10 and 15 m, the microbial diversity was greater; likewise, the correlation between the physicochemical parameters and the microbial communities at the genus level showed that Chlorobaculum, Desulfomonile, and Candidatus Xiphinematobacter were favored by an increase in dissolved phosphates and by the decrease in pH and temperature. These results highlight that the microbial communities exhibit variation in their composition due to the effect of depth and physicochemical parameters, which could play a role as biological factors in the trophic states of a lake.

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.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

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.

Widespread natural methane and oil leakage from sub-marine Arctic reservoirs

Parceling the anthropogenic and natural (geological) sources of fossil methane in the atmosphere remains problematic due to a lack of distinctive chemical markers for their discrimination. In this light, understanding the distribution and contribution of potential geological methane sources is important. Here we present empirical observations of hitherto undocumented, widespread and extensive methane and oil release from geological reservoirs to the Arctic Ocean. Methane fluxes from >7000 seeps significantly deplete in seawater, but nevertheless reach the sea surface and may transfer to the air. Oil slick emission spots and gas ebullition are persistent across multi-year observations and correlate to formerly glaciated geological structures, which have experienced km-scale glacial erosion that has left hydrocarbon reservoirs partially uncapped since the last deglaciation ~15,000 years ago. Such persistent, geologically controlled, natural hydrocarbon release may be characteristic of formerly glaciated hydrocarbon-bearing basins which are common across polar continental shelves, and could represent an underestimated source of natural fossil methane within the global carbon cycle.

Greenhouse gases emissions and dissolved carbon export affected by submarine groundwater discharge in a maricultural bay, Hainan Island, China

Greenhouse gases (GHG) emissions in coastal areas are influenced by both mariculture and submarine groundwater discharge (SGD). In this study, we first conducted a comprehensive investigation on carbon dioxide (CO₂) and methane (CH₄) emissions affected by SGD in a typical maricultural bay in north-eastern Hainan Island, China. A radon (²²²Rn) mass balance model revealed considerable high SGD rates (179 ± 92 cm d^-1) in the bay, and the fluxes of SGD-derived dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) were 150.36 and 3.65 g C m^-2 d^-1, respectively. Time-series measurement results, including those for ²²²Rn, CH₄, CO₂, and physicochemical parameters, indicated that GHG dynamics in the maricultural bay mainly varied with tidal fluctuations, and isotopic evidence further revealed that acetate fermentation was the main mechanism of methanogenesis in the maricultural waters. The water-air fluxes in the maricultural area were 1.05 ± 0.32 and 9.49 ± 3.96 mmol m^-2 day^-1 for CH₄ and CO₂, respectively, implying that Qinglan Bay was a potential source of GHG released into the atmosphere. At the bay-scale, the CO₂ emissions followed a spatial pattern, and the CH₄ emissions were mainly affected by mariculture. The high CH₄ emissions in the maricultural waters caused by maricultural activities, SGD, high temperature, and special hydrology resulted in the formation of the CH₄-dominated total CO₂-equivalent emissions model. Our study highlights the importance of considering the link between SGD and GHG emissions in maricultural bays when constraining global GHG fluxes.

Land use drivers of riverine methane dynamics in a tropical river basin, India

Rivers are globally significant natural sources of atmospheric methane (CH₄). However, the effect of land use changes on riverine CH₄ dynamics, particularly in tropical zones, remain ambiguous, yet important to predict and anticipate the present and future contribution of rivers to the global CH₄ budget. The present study examines the magnitude and drivers of riverine CH₄ concentration and emission in the tropical Krishna River (KR) basin, India. The large spatial variability of CH₄ concentration (0.03 to 185.34 μmol L ^-1) and emissions (0.04 mmol m^-2 d^-1 to 1666.24 mmol m^-2 d^-1) in the KR basin was linked to the site-specific features of the catchments through which rivers are draining. Several fold higher CH₄ concentration and emission was observed for the urban river sites (64.63 ± 53.17 µmol L^-1 and 294.15 ± 371.52 mmol m² d^-1, respectively) than the agricultural (1.05 ± 2.22 µmol L^-1 and 3.45 ± 9.72 mmol m² d^-1, respectively) and forested (0.49 ± 0.23 µmol L^-1 and 1.26 ± 0.73 mmol m² d^-1, respectively) sites. The concentrations of dissolved oxygen, total phosphorus, and Chlorophyll-a were significant hydrochemical variables strongly coupled with the dissolved CH₄ concentrations. On the other hand, percentage of built-up area emerged as the most important landscape-level driver indicating that urbanization has an overriding effect on riverine CH₄ concentration in the agriculture dominated KR basin. Our study supports the growing notion that tropical urban rivers are hotspot of CH₄ emission. Furthermore, we show that the pattern of increasing in riverine CH₄ concentration with built-up area (%) is a general feature of Asian river basins. As the urban land cover and population following an exponential increase, Asian rivers might contribute substantially to the regional and global CH₄ budget.

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.

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.

Summer greenhouse gas fluxes in different types of hemiboreal lakes

Lakes are considered important regulators of atmospheric greenhouse gases (GHG). We estimated late summer open water GHG fluxes in nine hemiboreal lakes in Estonia classified under different lake types according to the European Water Framework Directive (WFD). We also used the WFD typology to provide an improved estimate of the total GHG emission from all Estonian lakes with a gross surface area of 2204 km² representing 45,227 km² of hemiboreal landscapes (the territory of Estonia). The results demonstrate largely variable CO₂ fluxes among the lake types with most active emissions from Alkalitrophic (Alk), Stratified Alkalitrophic (StratAlk), Dark Soft and with predominant binding in Coastal, Very Large, and Light Soft lakes. The CO₂ fluxes correlated strongly with dissolved CO₂ saturation (DCO₂) values at the surface. Highest CH₄ emissions were measured from the Coastal lake type, followed by Light Soft, StratAlk, and Alk types; Coastal, Light Soft, and StratAlk were emitting CH₄ partly as bubbles. The only emitter of N₂O was the Alk type. We measured weak binding of N₂O in Dark Soft and Coastal lakes, while in all other studied lake types, the N₂O fluxes were too small to be quantified. Diversely from the common viewpoint of lakes as net sources of both CO₂ and CH₄, it turns out from our results that at least in late summer, Estonian lakes are net sinks of both CO₂ alone and the sum of CO₂ and CH₄. This is mainly caused by the predominant CO₂ sink function of Lake Peipsi forming ¾ of the total lake area and showing negative net emissions even after considering the Global Warming Potential (GWP) of other GHGs. Still, by converting CH₄ data into CO₂ equivalents, the combined emission of all Estonian lakes (8 T C day^-1) is turned strongly positive: 2720 T CO₂ equivalents per day.

Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland

Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.

Large alpine deep lake as a source of greenhouse gases: A case study on Lake Fuxian in Southwestern China

Freshwater lakes are recognized as potential sources of greenhouse gases (GHGs) that contribute to global warming. However, the spatiotemporal patterns of GHG emissions have not been adequately quantified in large deep lakes, resulting in substantial uncertainties in the estimated GHG budgets in global lakes. In this study, the spatial and seasonal variability of diffusive GHG (CO₂, CH₄, and N₂O) emissions from Lake Fuxian located on a plateau in Southwestern China were quantified. The results showed that the surface lake water was oversaturated with dissolved GHG concentrations, and the average concentrations were 24.25 μM CO₂, 0.044 μM CH₄, and 14.28 nM N₂O, with diffusive emission rates of 8.82 mmol CO₂ m^-2 d^-1, 31.94 μmol CH₄ m^-2 d^-1, and 4.94 μmol N₂O m^-2 d^-1, respectively. Diffusive CH₄ flux exhibited high temporal and spatial variability similar to that in most lakes. In contrast, diffusive CO₂ and N₂O flux showed distinct seasonal variability and similar spatial patterns, emphasizing the necessity for increasing the temporal resolution in GHG flux measurements for integrated assessments. Water temperature and/or oxygen concentrations were crucial in regulating seasonal variability in GHG emissions. However, no limnological parameter was found to govern the spatial GHG patterns. The frequent advection mixing caused by wind-driven currents might be the reason for the low spatial heterogeneity in GHGs, in which the inconspicuous mechanism requires further research. It was recommended that at least 11 locations were needed for representative whole lake flux estimates at each sampling campaign. In addition, the maximum peak of CH₄ in the oxycline from Lake Fuxian indicated that low CH₄ oxidation occurred in oxic waters. Overall, this study suggests that, compared to other tropical and temperate lakes, this alpine deep lake is a minor CO₂ and CH₄ source, but a moderate N₂O source, which are horizontally uniform.

Anthropogenic regulation governs nutrient cycling and biological succession in hydropower reservoirs

Hydropower plays an important role in the supply of renewable energy, but it also exerts a great influence on the river continuum. Understanding nutrient cycling and microbial community succession in hydropower reservoirs is key to weighing hydroelectric pros and cons. However, the underlying control mechanisms are still not well known, especially with respect to the impacts of hydrological conditions. Based on a comprehensive survey of hydropower reservoirs along the Wujiang River in SW China and an integration of published data, we found that reservoir physicochemical and biological stratifications and planktonic microbial community assembly were synergistically evolving, and reservoir hydraulic load (i.e., mean water depth per unit retention time) was a key factor controlling the strength of stratifications, CO₂ and N₂O fluxes, nutrient retention efficiency, and bacterioplankton diversity. Hydraulic loads are artificially designed for hydropower reservoirs, and nutrient cycling and biological succession in reservoirs are thus governed by anthropogenic regulation. This study provides a theoretical basis to mitigate the environmental impacts of hydropower dams by regulating reservoir hydraulic load.

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.

Terrigenous organic carbon drives methane dynamics in cascade reservoirs in the upper Yangtze China

Methane (CH₄) emissions from freshwaters to the atmosphere have a profound impact on global atmospheric greenhouse gas (GHG) concentrations. Anthropogenic footprints such as dam construction and reservoir operation significantly changed the fate and transport of CH₄ in freshwaters. The source of particulate organic carbon (POC) in reservoirs is a critical factor controlling CH₄ production and emissions. However, little is known of how reservoir operation mediates the transport of POC and regulates CH₄ accumulation in cascade hydroelectric reservoirs. Here, spatial and temporal variations in POC and CH₄ were explored in the Xiluodu (XLD) and Xiangjiaba (XJB) reservoirs which are deep valley cascade reservoirs located in the main channel of the upper Yangtze River. Based on the δ¹³C-POC and N/C mole ratio of particulate organic matter, the results of multi-endmember stable isotope mixing models by a Bayesian model showed that terrigenous POC and autochthonous POC accounted for approximately 55% ± 18% and 43% ± 19% (SD, n = 179) of POC, respectively. Together with other hydrological and environmental parameters, we found that the input of terrigenous POC was dominantly influenced by water level variations and flow regulation due to reservoir operation. The cumulative effect of POC caused by cascade dams was not apparent. Terrigenous POC were more likely to drive CH₄ accumulation in our study. Evident low level of CH₄ in both reservoirs were likely affected by low sedimentation of POC and microbial CH₄ oxidation. We hope our study could provide a conceptual framework for further modeling of CH₄ dynamics in cascade reservoirs.

Greenhouse gas emissions from African lakes are no longer a blind spot

Natural lakes are thought to be globally important sources of greenhouse gases (CO2, CH4, and N2O) to the atmosphere although nearly no data have been previously reported from Africa. We collected CO2, CH4, and N2O data in 24 African lakes that accounted for 49% of total lacustrine surface area of the African continent and covered a wide range of morphology and productivity. The surface water concentrations of dissolved CO2 were much lower than values attributed in current literature to tropical lakes and lower than in boreal systems because of a higher productivity. In contrast, surface water-dissolved CH4 concentrations were generally higher than in boreal systems. The lowest CO2 and the highest CH4 concentrations were observed in the more shallow and productive lakes. Emissions of CO2 may likely have been substantially overestimated by a factor between 9 and 18 in African lakes and between 6 and 26 in pan-tropical lakes.

Exploring the microbial mechanism of reducing methanogenesis during dairy manure membrane-covered aerobic composting at industrial scale

In this study, the microbial mechanism of reducing methanogenesis during membrane-covered aerobic composting from solid dairy manure was investigated. An industrial-scale experiment was carried out to compare a static composting group (SC) and a forced aeration composting group (AC) with a semipermeable membrane-covered composting group (MC + AC). The results showed that the semipermeable membrane-covered could improve the oxygen utilization rate and inhibit the anaerobic bacterial genus Hydrogenispora and archaea order Methanobacteriales. During the membrane-covered period, the acetoclastic methanogenesis module in MC + AC, AC and SC decreased by 0.58%, 0.05% and 0.04%, respectively, and the cdhC gene in the acetoclastic pathway was found to be decreased by 65.51% only in MC + AC. Changes in methane metabolism pathways resulted in a 27.48% lower average methane concentration in MC + AC than in SC. Therefore, the semipermeable membrane-covered strategy can effectively reduce methane production during dairy manure aerobic composting by restricting the methanogenesis of the acetoclastic pathway.

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.

Contribution of periphytic biofilm of paddy soils to carbon dioxide fixation and methane emissions

Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane (CH₄) flux. The accurate quantification of CH₄ emissions from rice paddies remains problematic, in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes. Herein, we comprehensively evaluated the contribution of one form of microbial aggregates, periphytic biofilm (PB), to carbon dioxide (CO₂) and CH₄ emissions from paddies distributed across three climatic zones, and quantified the pathways that drive net CH₄ production as well as CO₂ fixation. We found that PB accounted for 7.1%-38.5% of CH₄ emissions and 7.2%-12.7% of CO₂ fixation in the rice paddies. During their growth phase, PB fixed CO₂ and increased the redox potential, which promoted aerobic CH₄ oxidation. During the decay phase, PB degradation reduced redox potential and increased soil organic carbon availability, which promoted methanogenic microbial community growth and metabolism and increased CH₄ emissions. Overall, PB acted as a biotic converter of atmospheric CO₂ to CH₄, and aggravated carbon emissions by up to 2,318 kg CO₂ equiv ha^-1 season^-1. Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates (i.e., PB) from soil microbes, and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH₄ emissions by manipulating PB growth.

Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments

Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.

Diel variation of CH4 emission fluxes in a small artificial lake: Toward more accurate methods of observation

Lakes are significant sources in global methane (CH₄) budgets. However, estimations of the magnitude of global CH₄ emissions from lakes may be highly biased owing to the uncertainties in data originating from observation times, methods, and parameterizations of the gas transfer velocity (k). Here, we conducted continuous 48-hour measurements of CH₄ fluxes using the floating chamber method seasonally at Lake Baihua, a small reservoir in southwestern China, and compared the results with estimates derived from boundary layer models. Results showed that there was a weak dependency of k on wind speed, indicating that wind speed was not the major factor regulating gas exchange in such small lakes. It is thus concluded that the wind speed-dependent boundary layer model method is not suitable for CH₄ flux observations in small and medium-sized lake, and that the floating chamber method is recommended for use instead. The measured CH₄ fluxes displayed remarkably diurnal patterns, therefore the use of single observations to represent daily average values comes with unacceptably large uncertainties. A reasonable alternative is averaging observations made at sunrise and at sunset to represent daily values, which has a much smaller uncertainty (ranging from 0.8% to 13.6%). The coincident peaks of CH₄ and chlorophyll concentrations in the subsurface indicate that CH₄ originated mainly from aerobic methanogenesis. Solar radiation is likely one of the major factors regulating CH₄ production and emissions in the lake through enhancing CH₄ production, inhibiting CH₄ oxidation, and probably changing hydrodynamics conditions. Therefore, irradiation should be taken into consideration as a key factor in observing CH₄ fluxes in lakes. As sampling times are limited, observations during both sunny and cloudy weather should be proportionally included. This is the first time, to the best of our knowledge, that solar radiation has been proposed as a key driver of CH₄ emissions from lakes.

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

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

"Greenhouse gas dynamics in a coastal lagoon during the recovery of the macrophyte meadow (Mar Menor, SE Spain)"

The Mar Menor is a hypersaline coastal lagoon with salinity values ranging from 41.9 to 45.5. The system is subjected to a high anthropic pressure that causes an intense eutrophication process, followed by a recovery of the macrophyte meadows. This study focuses on the distribution of the main greenhouse gases (CO₂, CH₄ and N₂O) and was carried out in the extreme seasonal conditions of winter and summer during the year 2018. Sediment-water-atmosphere exchanges and biochemical processes in the water column appeared to be the main factors to explain the variability of these gases. Dissolved Inorganic Carbon (DIC), CH₄ and N₂O benthic fluxes values obtained in this study, were of 91 ± 29 mmol m^-2 d^-1, 3.9 ± 1.9 μmol m^-2 d^-1 and -0.65 μmol m^-2 d^-1, respectively, along with an important seasonal variation observed, with an increase of DIC and CH₄ benthic fluxes during the summer season. Mean values of partial pressure of CO₂ (pCO₂) in surface water were of 579 μatm in winter and 464 μatm in summer, therefore we can establish that the Mar Menor acts as a source of this gas emitting 3.3 ± 3.0 mmol CO₂ m^-2 d^-1 to the atmosphere. In spite of this, the Mar Menor has a strong autotrophic behaviour partly due to the recovery of the macrophyte meadows, presenting an estimated NEP of 101 mmol m^-2 d^-1. Regarding to CH₄, the mean fluxes to the atmosphere were of 8.0 ± 5.8 μmol m^-2 d^-1 and there was evidence of CH₄ production in the water column that increased in summer. Last of all, in the case of N₂O the system acts as a sink with values of -0.65 ± 0.5 μmol m^-2 d^-1, presenting an intake of N₂O that is usually detected in pristine systems.

High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water

The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH₄ oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L⁻¹). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH₄. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates.

Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.