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

Wildfire-Driven Changes in Terrestrial Subsidies Shift Freshwater Microbial and Zooplankton Communities to New Compositional States

Wildfire frequency and intensity are increasing globally, impacting terrestrial and aquatic ecosystems. Deposition of burned materials into aquatic environments can affect biotic communities and nutrient cycling. We investigated how post-fire terrestrial deposition shapes microbial and zooplankton community composition and function across time by manipulating plant material amount (loading; 0-400 g) and chemical composition (burned vs. unburned) in 400 L experimental mesocosms over four months. Burning treatment had minimal effects (1.4%), while loading (6.6%) and time (19.2%) contributed significantly to free-living microbial community variation. Dramatic changes in environmental conditions and microbiome composition occurred at a 50-100 g loading threshold within 30 days. High-loading mesocosms showed hypoxia, increased dissolved organic carbon and aromaticity, elevated bacterial density, and shifts in bacterial community function relating to enhanced carbon degradation, suggesting efficient microbial use of carbon resources despite low oxygen and increased water colour. Zooplankton communities were primarily influenced by time (24.9%), with loading (10.3%) and burning (2.3%) having weaker effects. Zooplankton community composition shifted at a 100 g-150 g threshold that persisted over time, with crustaceans declining and mosquito larvae dominating at higher loading levels. Zooplankton- and plant detritus-associated microbiomes were distinct but showed minimal treatment effects after four months, indicating greater environmental filtering for these microhabitats relative to horizontal transmission from treatment-altered water microbiomes. In contrast, free-living microbiomes maintained loading-driven compositional differences, while predicted genome traits and functions converged across treatments. These results suggest that post-wildfire deposition drives zooplankton and microbial communities into distinct compositional states punctuated by abrupt transitions, but microbiomes may recover community-level functionality over time.

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.

Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins

Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.

IMPORTANCE

Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Short-term negative effects of seawater acidification on the rhodolith holobionts metatranscriptome

Rhodolith holobionts are formed by calcareous coralline algae (e.g., Corallinales) and associated microbiomes. The largest rhodolith bank in the South Atlantic is located in the Abrolhos Bank, in southwestern Brazil, covering an area of 22,000 km2. Rhodoliths serve as nurseries for marine life. However, ocean acidification threatens them with extinction. The acute effects of high pCO₂ levels on rhodolith metatranscriptomes remain unknown. This study investigates the transcriptomic profiles of rhodoliths exposed to short-term (96-h) high pCO₂ levels (up to 1638 ppm). Metatranscriptomes were generated for both dead and alive rhodoliths (15.48 million Illumina reads in total). Alive rhodoliths showed an enrichment of gene transcripts related to environmental stress responses and photosynthesis (Cyanobacteria). In contrast, the metatranscriptomes of dead rhodoliths were dominated by heterotrophic (Proteobacteria and Bacteroidetes) metabolism and virulence factors. The rhodolith holobiont metatranscriptomes respond rapidly to short-term acidification (within 1 h), suggesting that these holobionts may have some capacity to cope with acute acidification effects. However, the negative impacts of prolonged ocean acidification on rhodolith health cannot be overlooked. Rhodoliths exposed to low pH (7.5) for 96 h exhibited a completely altered transcriptomic profile compared to controls. This study highlights the plasticity of rhodolith transcriptomes in the face of ocean acidification and climate change.

Greenhouse Gas Emissions and Lateral Carbon Dynamics at an Eroding Yedoma Permafrost Site in Siberia (Duvanny Yar)

Rapid Arctic warming is accelerating permafrost thaw and mobilizing previously frozen organic carbon (OC) into waterways. Upon thaw, permafrost-derived OC can become susceptible to microbial degradation that may lead to greenhouse gas emissions (GHG), thus accelerating climate change. Abrupt permafrost thaw (e.g., riverbank erosion, retrogressive thaw slumps) occurs in areas rich in OC. Given the high OC content and the increase in frequency of abrupt thaw events, these environments may increasingly contribute to permafrost GHG emissions in the future. To better assess these emissions from abrupt permafrost thaw, we incubated thaw stream waters from an abrupt permafrost thaw site (Duvanny Yar, Siberia) and additionally, waters from their outflow to the Kolyma River. Our results show that CO2 release by volume from thaw streams was substantially higher than CO2 emissions from the river outflow waters, while the opposite was true for CO2 release normalized to the suspended sediment weight (gram dry weight). The CH4 emissions from both thaw streams and outflow waters were at a similar range, but an order of magnitude lower than those of CO2. Additionally, we show that nearshore riverbank waters differ in their biogeochemistry from thaw streams and Kolyma River mainstem: particles resemble thaw streams while dissolved fraction is more alike to the Kolyma River thalweg. In these waters dissolved OC losses are faster than in the river thalweg. Our incubations offer a first insight into the GHG release from permafrost thaw streams that connect exposed and degrading permafrost outcrops to larger river systems.

Controls on spatial variation in porewater methane concentrations across United States tidal wetlands

Tidal wetlands can be a substantial sink of greenhouse gases, which can be offset by variable methane (CH4) emissions under certain environmental conditions and anthropogenic interventions. Land managers and policymakers need maps of tidal wetland CH4 properties to make restoration decisions and inventory greenhouse gases. However, there is a mismatch in spatial scale between point-based sampling of porewater CH4 concentration and its predictors, and the coarser resolution mapping products used to upscale these data. We sampled porewater CH4 concentrations, salinity, sulfate (SO42-), ammonium (NH4+), and total Fe using a spatially stratified sampling at 27 tidal wetlands in the United States. We measured porewater CH4 concentrations across four orders of magnitude (0.05 to 852.9 μM). The relative contribution of spatial scale to variance in CH4 was highest between- and within-sites. Porewater CH4 concentration was best explained by SO42- concentration with segmented linear regression (p < 0.01, R2 = 0.54) indicating lesser sensitivity of CH4 to SO42- below 0.62 mM SO42-. Salinity was a significant proxy for CH4 concentration, because it was highly correlated with SO42- (p < 0.01, R2 = 0.909). However, salinity was less predictive of CH4 with segmented linear regression (p < 0.01, R2 = 0.319) relative to SO42-. Neither NH4+, total Fe, nor relative tidal elevation correlated significantly with porewater CH4; however, NH4+ was positively and significantly correlated with SO42- after detrending CH4 for its relationship with SO42- (p < 0.01, R2 = 0.194). Future sampling should focus on within- and between-site environmental gradients to accurately map CH4 variation. Mapping salinity at sub-watershed scales has some potential for mapping SO42-, and by proxy, constraining spatial variation in porewater CH4 concentrations. Additional work is needed to explain site-level deviations from the salinity-sulfate relationship and elucidate other predictors of methanogenesis. This work demonstrates a unique approach to remote team science and the potential to strengthen collaborative research networks.

Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China

Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g-1 d-1, which was higher than that in reservoirs sediment (1.92 to 11.56 μg g-1 d-1). Similarly, the average AeOM in the water column of lake (104.7 μg L-1 d-1) was much higher than that of reservoirs (46 μg L-1 d-1). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.

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.

Light-driven differences in bacterial networks and organic matter decomposition: Insights from an analysis of the harmful cyanobacterium Microcystis aeruginosa PCC 7806

Freshwater systems are critical yet often underestimated components of global carbon cycling, functioning both as carbon sinks and sources. Cyanobacteria play a key role in this cycle by capturing atmospheric carbon dioxide through photosynthesis. The captured carbon is either released back into the atmosphere or sequestered in sediments following organismal decay. This study examines the pivotal role of cyanobacteria, specifically Microcystis aeruginosa PCC 7806, in the biogeochemical cycling of carbon in freshwater ecosystems, with a focus on how light influences the degradation of cyanobacteria-derived organic matter. Using a combination of 16S rDNA sequencing and excitation-emission matrix coupled with parallel factor (EEM-PARAFAC) analysis, we conducted a 50-day experiment to investigate the dynamics of dissolved organic matter (DOM) and lysate organic matter (LOM) derived from M. aeruginosa PCC 7806 under light and dark conditions. Our results demonstrate that light significantly impacts bacterial community composition, gene functionality, and the decomposition of organic matter. The findings emphasize the crucial role of light in facilitating microbial adaptation, stabilizing microbial networks and driving organic substrate transformation. These insights underscore the influence of light on microbial community dynamics and organic matter degradation, revealing shifts in microbial populations under varying light conditions. This suggests a strong link between photochemical processes and microbial activity, with significant ecological implications.

Cyanobacteria decay alters CH4 and CO2 produced hotspots along vertical sediment profiles in eutrophic lakes

Cyanobacteria-derived organic carbon has been reported to intensify greenhouse gas emissions from lacustrine sediments. However, the specific processes of CH4 and CO2 production and release from sediments into the atmosphere remain unclear, especially in eutrophic lakes. To investigate the influence of severe cyanobacteria accumulation on the production and migration of sedimentary CH4 and CO2, this study examined the different trophic level lakes along the middle and lower reaches of the Yangtze River. The results demonstrated that eutrophication amplified CH4 and CO2 emissions, notably in Lake Taihu, where fluxes peaked at 929.9 and 7222.5 μmol/m2·h, mirroring dissolved gas levels in overlying waters. Increased sedimentary organic carbon raised dissolved CH4 and CO2 concentrations in pore-water, with isotopic tracking showing cyanobacteria-derived carbon specifically elevated CH4 and CO2 in surface sediment pore-water more than in deeper layers. Cyanobacteria-derived carbon deposition on surface sediment boosted organic carbon and moisture levels, fostering an anaerobic microenvironment conducive to enhanced biogenic CH4 and CO2 production in surface sediments. In the microcosm systems with the most severe cyanobacteria accumulation, average CH4 and CO2 concentrations in surface sediments reached 6.9 and 2.3 mol/L, respectively, surpassing the 4.7 and 1.4 mol/L observed in bottom sediments, indicating upward migration of CH4 and CO2 hotspots from deeper to surface layers. These findings enhance our understanding of the mechanisms underlying lake sediment carbon emissions induced by eutrophication and provide a more accurate assessment of lake carbon emissions.

Ebullition dominates methane emissions in stratified coastal waters

Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δ13C-CH4 across the sediment and water column, it became apparent that the surface water δ13C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.

Rethinking microbially driven methane formation in mangrove wetlands

Mangrove wetlands contribute to climate change mitigation through efficient carbon burial, yet microbial methanogenesis offsets these climate benefits. We review the diversity of methanogenic microorganisms in mangrove sediments, present the unrecognized role of bacteria on methanogenesis, and highlight the significance of distinguishing various methanogenic pathways to assess mangrove climate benefits.

Distribution and sea-to-air fluxes of nitrous oxide and methane from a seasonally hypoxic coastal zone in the southeastern Arabian Sea

The seasonal variability, pathways, and sea-to-air fluxes of nitrous oxide (N2O) and methane (CH4) in the coastal environment, where coastal upwelling and mudbanks co-exist are presented based on the monthly time-series measurements from November 2021 to December 2022. Upwelling-driven hypoxic water's shoreward propagation and persistence were the major factors controlling the N2O concentrations, while the freshwater influx and sedimentary fluxes modulate CH4 concentrations. The N2O concentrations were high during the southwest monsoon (up to 35 nM; 19 ± 8 nM)), followed by spring inter-monsoon (up to 19 nM; 10 ± 5 nM), and lowest during the northeast monsoon (up to 13 nM; 8 ± 2 nM), whereas the CH4 levels were high during the spring inter-monsoon (8.4 to 65 nM), followed by southwest monsoon (6.8 to 53.1 nM) and relatively lower concentrations during the northeast monsoon (3.3 to 32.6 nM). The positive correlations of excess N2O with Apparent Oxygen Utilisation (AOU) and the sum of nitrate and nitrite (NOx) indicate that nitrification is the primary source of N2O in the mudbank regime. The negative correlation of CH4 concentrations with salinity indicates considerable input of CH4 through freshwater influx. CH4 exhibited a highly significant positive correlation with Chlorophyll-a throughout the study period. Furthermore, it displayed a statistically significant positive correlation with phosphate (PO43-) during the northeast monsoon while a strong negative correlation with PO43- during the spring inter-monsoon, pointing towards the role of aerobic CH4 production pathways in the mudbank regime. N2O and CH4 exhibited a contrasting seasonal pattern of sea-to-air fluxes, characterised by the highest N2O fluxes during the southwest monsoon (hypoxia) (13 ± 10 μM m-2 d-1), followed by spring inter-monsoon (12 ± 16 μM m-2 d-1), and the lowest during the northeast monsoon (0.6 ± 3 μM m-2 d-1). Conversely, the highest sea-to-air fluxes of CH4 were noticed during the spring inter-monsoon (74 ± 56 μM m-2 d-1), followed by the southwest monsoon (45 ± 35 μM m-2 d-1), and the lowest values during the northeast monsoon (19 ± 16 μM m-2d-1). Long-term time-series measurements will be invaluable in understanding the longer-term impacts of climate-driven variability on marine biogeochemical cycles in dynamic nearshore systems.

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.

Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle

Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.

Nitrous oxide and methane production and consumption at five full-size denitrifying bioreactors treating subsurface drainage water

Nitrate (NO3-) removal in denitrifying bioreactors is influenced by flow, water chemistry, and design, but it is not known how these widely varying factors impact the production of nitrous oxide (N2O) or methane (CH4) across sites. Woodchip bioreactors link the hydrosphere and atmosphere in this respect, so five full-size bioreactors in Illinois, USA, were monitored for NO3-, N2O, and CH4 to better document where this water treatment technology resides along the pollution swapping to climate smart spectrum. Both surface fluxes and dissolved forms of N2O and CH4 were measured (n = 7-11 sampling campaigns per site) at bioreactors ranging from <1 to nearly 5 years old and treating subsurface drainage areas from between 6.9 and 29 ha. Across all sites, N2O surface and dissolved volumetric production rates averaged 1.0 ± 1.6 mg N2O-N/m3-d and 24 ± 62 mg dN2O-N/m3-d, respectively, and CH4 production rates averaged 6.0 ± 26 mg CH4-C/m3-d and 310 ± 520 mg dCH4-C/m3-d for surface and dissolved, respectively. However, N2O was consistently consumed at one bioreactor, and only three of the five sites produced notable CH4. Surface fluxes of CH4 were significantly reduced by the presence of a soil cover. Bioreactor denitrification was relatively efficient, with only 0.51 ± 3.5 % of removed nitrate emitted as N2O (n = 48). Modeled indirect N2O emissions factors were significantly lower when a bioreactor was present versus absent (EF5: 0.0055 versus 0.0062 kg N2O-N/kg NO3-N; p = 0.0011). While further greenhouse gas research on bioreactors is recommended, this should not be used as an excuse to slow adoption efforts. Bioreactors provide a practical option for voluntary water quality improvement in the heavily tile-drained US Midwest and elsewhere.

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.

The external/internal sources and sinks of greenhouse gases (CO2, CH4, N2O) in the Pearl River Estuary and adjacent coastal waters in summer

Estuary acts as a hotspot of greenhouse gases (GHGs, including CO2, CH4 and N2O) to the atmosphere. However, the GHGs budgets, including input/output fluxes through interfaces and biogeochemical source/sink processes in water columns, of the estuarine systems are still not well constrained due to the lacking of comprehensive observational data. Here, we presented the spatial distributions of GHGs of surface/bottom water and sediment porewater along the Pearl River Estuary (PRE) and adjacent region during summertime. The incorporation of the monitoring for the sediment-water interface (SWI) with these of the water-air interface (WAI) allows us to close the budget revealing additional information of internal consumption/production processes of the three GHGs. The oversaturated CO2 (481-7573 μatm), CH4 (289-16,990 %) and N2O (108-649 %) in surface water suggested PRE is a significant GHGs source to the atmosphere, in which CO2 is the major contributor accounting for 90 % of total global warming potential (GWP), leaving 2.8 % from CH4, and 7.2 % from N2O. Addition to the river input, the SWI releases GHGs to the overlying water with fluxes of 3.5 × 107, 10.8 × 104 and 0.7 × 104 mol d-1 for CO2, CH4 and N2O, respectively. Although all three GHGs exhibited emission to the atmosphere, our mass balance calculation showed that 16.9× 107 mol d-1 of CO2 and 1.0 × 104 mol d-1 of N2O were consumed, respectively, inside the estuary water body, while extra-production (13.8 × 104 mol d-1) of CH4 was demanded in the water body to support its output flux. This is the first experiment quantitatively assessing the importance of internal carbon and nitrogen biogeochemical processes in the PRE. Our finding is of guiding significance to constrain the GHGs budget and draw up realistic pathways for modeling works of GHGs prediction.

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.

Greenhouse gas emissions from constructed wetlands: A bibliometric analysis and mini-review

Constructed wetlands (CWs) have been widely applied in wastewater treatment; however, the degradation of organic pollutants within CWs leads to substantial emissions of greenhouse gases (GHGs), such as carbon dioxide, methane and nitrous oxide. Under the low-carbon economy, GHG emissions have emerged as a major concern, and have been intensively studied in the CW field. In this study, we conducted a bibliometric review using CiteSpace and a global-scale analysis of GHG emission levels based on 286 records and proposed potential approaches for the future control of GHG emissions in CWs. We found that the research has generally evolved through three stages over the past 15 years: GHG emission level assessment (2007-2010), mechanisms (2011-2016), and control (2017-2022). The type of CWs is closely related to GHG emissions, with free water surface CWs emitting higher levels of methane and vertical subsurface flow CWs emitting higher levels of carbon dioxide and nitrous oxide. By optimizing CW operation, it is conceivable to synergistically reduce GHG emissions while enhancing pollutant removal.

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.

Untapped talents: insight into the ecological significance of methanotrophs and its prospects

The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.

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.

Stable Isotope Approach to Assess the Production and Consumption of Methylphosphonate and Its Contribution to Oxic Methane Formation in Surface Waters

Recent studies in aquatic environments have indicated that microbial methane production is not limited to strictly anoxic conditions and is widespread in the oxic water column. Based on recent investigations proposing linkage between the microbial turnover of methylphosphonate (MPn) and the widespread methane oversaturation in surface waters, we conducted an MPn/13C-MPn tracer approach that combines liquid chromatography-mass spectrometry and gas chromatography-stable isotope ratio mass spectrometry to assess concentrations of the MPn tracer and its contribution to oxic methane formation. In our study, conducted during summer 2020 in the Baltic Sea, we show that MPn is a potent methanogenic substrate in the surface water. However, we found that MPn was produced within the surface and subthermocline water bodies and that its turnover was not limited to the phosphorus-stressed and cyanobacteria-rich surface water. However, our study revealed that most of the MPn was probably degraded via alternative pathways, not releasing methane. Our assessment indicates that the contribution of the MPn degradation pathway only contributed marginally to oxic methane production at the study site in the Baltic Sea and that a variety of methanogenic pathways are probably responsible for the surface-water methane enrichments.

Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic

Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.

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.