The problem the researchers tackled is fundamentally physical. Eddy-covariance instruments measure the covariance between vertical wind speed and gas concentration at high frequency, typically 10 to 20 hertz, to capture the turbulent eddies that carry gases between the surface and the atmosphere. Yet no instrument is perfect. Limited sampling time, line averaging, the physical separation between the sonic anemometer and the gas analyser’s inlet, and the passage of air through tubes and filters all act like a low-pass filter, smoothing out the fastest fluctuations. Because small eddies contribute disproportionately to the total flux, this smoothing causes a systematic underestimation that can range from a few percent to tens of percent depending on the setup, the site and the weather. Correcting for it is one of the most stubborn technical challenges in micrometeorology.

Two experimental strategies dominate the field. The spectral approach computes the ratio of the attenuated gas concentration power spectrum to the unattenuated sonic temperature spectrum, deriving an empirical transfer function from which a correction factor follows. The co-spectral approach instead uses the co-spectrum of the gas flux itself relative to the sensible heat flux, folding every attenuation source, including sensor separation, into a single empirical characterisation. Each camp has its defenders: spectral methods, championed by widely used software such as EddyPro and embedded in the official ICOS processing pipeline, avoid the complications of time-lag and phase-shift estimation, while co-spectral methods are immune to high-frequency noise and need no separate sensor-separation term. Until now, no systematic, network-wide comparison of the two had ever been attempted.

Ariane Faurès of the University of Liege and her colleagues filled that gap using a full year of carbon dioxide and water vapour flux data from 38 ICOS Class 1 and 2 ecosystem stations, all equipped with an identical enclosed-path LI-7200 gas analyser and a Gill sonic anemometer. This standardisation was a scientific gift: because every site shares the same hardware, the same heated 0.73-metre sampling line, the same rain cap and inlet filter, and flow rates fixed between 10 and 16 litres per minute, differences between sites could be attributed to atmospheric conditions and ecosystem type rather than instrument quirks. The team classified stations into high-measurement-height sites, essentially forests, and low-measurement-height sites such as croplands, grasslands and non-forested peatlands, then computed cut-off frequencies and correction factors for both methods under carefully controlled wind speed, stability and humidity classes.

The first headline finding is reassuring: the standardised ICOS setup performs remarkably well. Cut-off frequencies for carbon dioxide generally exceeded 1 hertz and were strikingly consistent across the continent, with a mean of 2.1 hertz and a tight spread at a wind speed of 3 metres per second. Correction factors for carbon dioxide typically stayed below 1.2, meaning the fluxes needed boosting by less than 20 percent, and often by less than 10. For water vapour the picture was harsher: attenuation was stronger, with correction factors occasionally approaching 2 under humid, windy conditions, reflecting the well-known tendency of water molecules to adsorb onto and desorb from the surfaces of the sampling tube and filter in a manner that varies with relative humidity.

When the two correction methods were compared directly, the differences for carbon dioxide proved small. After the standard turbulence filtering that removes weakly turbulent periods, cumulative annual flux differences between the methods typically stayed below 2 percent, and at high forest towers they were often negligible. The dominant source of carbon dioxide attenuation turned out to be sensor separation, the spatial offset between the anemometer and the analyser inlet, which the spectral approach must add back through a theoretical formulation from Horst and Lenschow. Water vapour told a different story. Here the two methods diverged substantially, with cumulative flux discrepancies frequently reaching 5 to 10 percent, and the largest gaps occurring under stable atmospheric stratification, at low measurement heights, and under strong attenuation.

The reasons for this divergence are methodological as much as physical. Both approaches rest on the assumption of spectral similarity, the idea that gas and temperature fluctuations share the same spectral shape at low frequencies. The study found that this assumption holds well for carbon dioxide but breaks down for water vapour, particularly in humid air, where the gas spectra departed from the ideal reference far more strongly than the co-spectra did. On top of that, the spectral approach was repeatedly plagued by high-frequency noise, requiring a dedicated denoising procedure at 58 percent of sites for carbon dioxide and 84 percent for water vapour, while the theoretical sensor-separation term it depends on produced unrealistically large corrections under stable conditions. The co-spectral approach, by contrast, delivered stable, physically consistent results across all sites and conditions, leading the authors to recommend it for this specific experimental configuration.

Perhaps the most provocative result emerged when the team compared their independently computed corrections with the official fluxes produced by the ICOS Ecosystem Thematic Centre. Since the network pipeline also uses a spectral method, one might expect close agreement, but the opposite was true: differences between the study’s spectral corrections and the official products were often larger than the differences between the spectral and co-spectral approaches themselves. For water vapour, cumulative flux differences against the ICOS pipeline averaged 10.7 percent at low-measurement-height sites, with some stations showing gaps exceeding 20 percent, and even carbon dioxide showed average differences of 1.6 percent and station-level extremes above 10 percent. The causes are a cascade of small choices: different low-pass and anemometer correction equations, a different sensor-separation formulation, different filtering thresholds and fitting ranges, and a contested use of the transfer function when computing correction factors, a choice that earlier work suggests can bias fluxes by up to 10 percent.

These numbers matter far beyond the technical community. Eddy-covariance fluxes feed the global carbon budgets that inform climate policy, underpin assessments of whether forests and peatlands are net sinks or sources of greenhouse gases, and enter the long-running debate over the surface energy balance closure problem. A systematic 10 percent uncertainty in water vapour fluxes propagates directly into estimates of evapotranspiration and ecosystem water use, while even a few percent in carbon dioxide can shift the calculated carbon balance of a young forest or a drained peatland. The study also carries a practical design lesson: because attenuation grows as the measurement height approaches the canopy, mounting sensors as high as feasible, within footprint constraints, dramatically reduces the correction burden, and at many forest towers the carbon dioxide correction is now so small it could arguably be skipped altogether.

The authors have released their analysis as an open-source Python tool, FreqCor, designed to be configurable across setups and trace gases, and they argue that the high-frequency correction step deserves a broader reassessment within the ICOS processing pipeline. They are candid that a fully automated, network-scale procedure remains elusive: thresholds, fitting ranges and denoising decisions still involve user judgement, and future work should replace uniform flux thresholds with signal-to-noise criteria and validate denoising across many sites. The study’s scope is limited to enclosed-path analysers, and the authors note that closed-path systems with long tubes, common for methane and nitrous oxide measurements, could show even larger method differences and merit a similar network-wide test. For now, one thing is clear: the quiet correction applied inside every flux tower’s software is not a formality, and choosing the right way to do it can change what Europe’s ecosystems appear to breathe.

Subject of Research: Comparison of spectral and co-spectral high-frequency attenuation corrections for eddy-covariance flux measurements across the ICOS ecosystem network

Article Title: Spectral versus co-spectral correction of eddy-covariance fluxes: a multi-site assessment across the ICOS network

Article References: Faurès, A., Fratini, G., Nicolini, G., Papale, D., Sabbatini, S., & Heinesch, B. (2026). Spectral versus co-spectral correction of eddy-covariance fluxes: a multi-site assessment across the ICOS network. Atmospheric Measurement Techniques, 19(18), 6037-6074. https://doi.org/10.5194/amt-19-6037-2026

Image Credits: AI Generated

DOI: 10.5194/amt-19-6037-2026

Keywords: eddy covariance, ICOS, spectral correction, co-spectral correction, high-frequency attenuation, carbon dioxide flux, water vapour flux, gas analyser, sensor separation, micrometeorology, ecosystem monitoring, Atmospheric Measurement Techniques

The Beinan River drains a catchment of roughly 1,600 square kilometers composed primarily of schist and slate, rocks that are being uplifted at rates of up to several centimeters per year. This rapid uplift, combined with torrential monsoon rains and frequent typhoons, generates extraordinary sediment loads that rank among the highest in the world. Rivers like the Beinan carry pulverized rock fragments downstream, keeping the water chronically turbid and physically unstable. For decades, scientists assumed that such conditions would suppress planktonic life, because suspended sediment blocks sunlight and because thin soils provide few organic substrates for microbial respiration. The new research demonstrates that this assumption is only partially correct, and that the reality is far more nuanced and biologically interesting than previously imagined.

To probe the metabolic activity of river microorganisms directly, the research team led by Jhen-Nien Chen and Pei-Ling Wang of National Taiwan University employed a technique that goes beyond the traditional reliance on dissolved oxygen sensors. They collected river water from five sites spanning the catchment, from forested headwater tributaries down to the river mouth near the estuary, and incubated it with carbon-13 labeled compounds. By adding isotopically labeled dissolved inorganic carbon, they could track how much carbon dioxide microorganisms fixed into biomass through photosynthesis and chemosynthesis. By adding carbon-13 labeled amino acids, specifically glycine and leucine, they could measure how rapidly heterotrophic microbes consumed organic molecules and respired them back into carbon dioxide. This dual approach allowed the team to separate the contributions of autotrophy, the process by which organisms build their own biomass from inorganic carbon, and heterotrophy, the process by which organisms consume organic matter and release carbon dioxide as a waste product.

The results revealed a striking seasonal pattern. Metabolic rates were consistently higher during the wet season, which runs from June through November, than during the dry season. Water temperatures were roughly six degrees Celsius warmer in the wet season, suspended sediment concentrations increased by an average factor of eleven, and ammonium concentrations rose significantly. All of these factors appeared to stimulate microbial activity. More remarkably, the team found that heterotrophic catabolic rates, meaning the speed at which microbes respired organic carbon into carbon dioxide, exceeded autotrophic carbon fixation rates by one to two orders of magnitude. This imbalance indicates that the planktonic community of the Beinan River is strongly net heterotrophic, functioning as a net producer of carbon dioxide rather than a net consumer.

When the researchers scaled their measured rates up to the entire catchment, they calculated that planktonic microbial metabolism produces approximately 7.89 times ten to the seventh moles of carbon dioxide per year. This figure represents about 3.8 percent of the total carbon dioxide flux generated by the catchment, which includes contributions from pyrite-induced carbonate weathering, the oxidation of ancient petrogenic carbon buried in the bedrock, and the physical exchange of carbon dioxide between the river surface and the atmosphere. While 3.8 percent may seem modest, the researchers emphasize that this is a substantial and previously unquantified component of the carbon budget in a system where geological processes overwhelmingly dominate. The total river-atmosphere carbon dioxide evasion for the catchment was estimated at roughly 2.08 times ten to the ninth moles per year, a figure consistent with the extraordinarily high weathering rates documented for active mountain belts worldwide.

One of the most intriguing discoveries concerns the identity of the microorganisms responsible for carbon fixation in the absence of light. At sites where suspended sediment concentrations were highest, dark incubations revealed significant uptake of labeled dissolved inorganic carbon even when photosynthesis was impossible. Genetic sequencing of the microbial communities showed that taxa capable of oxidizing sulfur compounds and ammonia were abundant during the wet season, particularly members of the genera Thiobacillus and Sulfuricurvum. These lithoautotrophic bacteria derive their energy not from sunlight but from chemical reactions involving reduced inorganic compounds, such as the sulfide and ferrous iron supplied by eroding pyrite-bearing rocks and by groundwater discharge. The team proposes that the constant pulverization and abrasion of slate and schist in the river channel exposes fresh mineral surfaces that fuel these chemoautotrophic communities, effectively linking geological erosion directly to biological carbon fixation in the water column.

The microbial community composition shifted dramatically between seasons and along the river’s length. In the dry season, when waters ran clearer and suspended sediment loads were lower, phototrophic organisms such as cyanobacteria dominated at upstream sites, taking advantage of the improved light penetration. In the wet season, these photosynthetic populations were displaced by sulfur-oxidizing and nitrogen-oxidizing lithoautotrophs that thrived on the chemical substrates released by sediment mobilization. At the most downstream site near the river mouth, heterotrophic bacteria capable of degrading complex dissolved organic matter predominated year-round, reflecting the accumulation of organic compounds transported from the entire upstream catchment. This longitudinal transition from rock-driven to organic-matter-driven metabolism echoes classical ecological frameworks such as the River Continuum Concept, but with a geological twist unique to tectonically active settings.

The study also revealed fascinating details about how these microbes process organic substrates. Glycine was consistently preferred over leucine as an energy source, a selectivity the authors attribute to the metabolic efficiency of glycine-centered biochemical pathways. The reductive glycine pathway and the glycine cleavage system require less energy to operate than the multi-step enzymatic breakdown required for leucine catabolism. In the dry season, when nutrient supplies were scarce, microbial communities diverted nearly all available amino acids toward respiration for basic cellular maintenance rather than biomass production. In the wet season, with abundant particulate organic matter available, a larger fraction of consumed substrates was channeled into growth and biosynthesis. These physiological shifts underscore how tightly microbial carbon processing is coupled to the hydrological and geological rhythms of the catchment.

The broader implications of this work extend well beyond Taiwan. Mountainous catchments cover 27 percent of Earth’s land surface and drain more than 30 percent of global runoff, yet they remain severely underrepresented in global carbon models. Inland waters collectively release between 0.65 and 2.1 petagrams of carbon per year as carbon dioxide, a flux comparable in magnitude to the ocean’s annual carbon dioxide uptake. If planktonic metabolism contributes a measurable fraction of this flux even in the most physically hostile river environments, then current global estimates that neglect or underestimate microbial contributions from mountain rivers may require revision. The researchers note that their planktonic measurements exclude the benthic and hyporheic compartments, the riverbed and subsurface zones where additional microbial processing almost certainly occurs, particularly during the dry season when clear water allows light to reach coarse streambed sediments.

Looking forward, the team advocates for high-frequency monitoring during storm events, kinetic experiments that measure substrate uptake at environmentally realistic concentrations, and RNA-based molecular approaches that can distinguish actively metabolizing microorganisms from merely abundant ones. They also emphasize the need for parallel measurements of benthic and hyporheic metabolism to construct a complete picture of river carbon cycling in these dynamic systems. What is already clear, however, is that even in oligotrophic, sediment-choked, tectonically restless rivers, planktonic microorganisms constitute a vital and quantifiable link in the chain that connects mountain erosion to atmospheric carbon dioxide. As climate change intensifies both monsoon precipitation and the frequency of extreme hydrological events in mountainous regions worldwide, understanding how these microbial communities respond to disturbance will become increasingly important for predicting future carbon fluxes and refining the global carbon inventory.

Subject of Research: Planktonic microbial metabolism and carbon dioxide fluxes in a tectonically active mountainous river catchment in Taiwan

Article Title: Roles of planktonic metabolism in CO2 fluxes along the river-estuary continuum in a rapidly uplifting catchment of eastern Taiwan

Article References: Chen, J.-N., Chen, P.-E., Yen, Y.-S., Tu, T.-H., Wang, L.-Y., Lien, W.-Y., Lin, Y.-T., & Wang, P.-L. (2026). Roles of planktonic metabolism in CO 2 fluxes along the river-estuary continuum in a rapidly uplifting catchment of eastern Taiwan. Biogeosciences, 23(19), 6781-6802. https://doi.org/10.5194/bg-23-6781-2026

Image Credits: AI Generated

DOI: 10.5194/bg-23-6781-2026

Keywords: river metabolism, carbon dioxide flux, planktonic microbes, mountain rivers, Taiwan, Biogeosciences, heterotrophy, autotrophy, carbon-13 labeling, microbial communities, chemical weathering, tectonic uplift

The stakes behind this engineering effort are considerable. As countries and companies scramble to verify carbon sinks in forests, farmland, and wetlands, the demand for trustworthy, affordable flux measurements has exploded. Carbon markets, carbon farming schemes, and land-use regulations such as the European Union’s LULUCF framework all depend on knowing precisely how much carbon dioxide an ecosystem absorbs or releases. Yet the standard tool for this job, the eddy covariance technique, relies on instruments that can cost tens of thousands of euros, limiting how widely the method can be deployed.

Eddy covariance works by measuring the vertical wind speed and the gas concentration fluctuations at high frequency, typically ten times per second, allowing researchers to calculate the net exchange of carbon dioxide or water vapour between the surface and the atmosphere over half-hour intervals. The technique is the backbone of global flux networks, but its expense has kept it largely confined to academic observatories. Inventory-based alternatives, such as repeated soil carbon sampling, take five to ten years to yield results, far too slow for markets that need timely verification.

The new prototype was designed to be 50 to 60 percent cheaper than commercially available fast-response analysers without significant compromises in performance. It is an enclosed-path instrument based on Vaisala’s CARBOCAP technology, which uses a single-beam, dual-wavelength non-dispersive infrared method. Instead of fixed emission lines, the sensor employs an electrically tunable Fabry–Pérot interferometer filter that alternates between an absorption wavelength near 4.3 micrometres for carbon dioxide and a nearby reference wavelength with no absorption, with a second band near 2.6 micrometres serving water vapour measurements. A thermopile detector, a small 30.3 cubic centimetre gas cell, and a proprietary micro-hotplate infrared light source complete the optical package.

Two design choices stand out. First, the instrument contains internal temperature and pressure sensors that compensate for temperature, pressure, and water vapour dilution effects in real time. Second, and arguably most important, it features a built-in autocalibration routine that periodically checks the signal against an internal reference. This feature proved to be the crux of the entire project. Early in the field campaign, the autocalibration, which ran roughly every thirty minutes, produced visible jumps in the carbon dioxide signal because the underlying drift, primarily driven by temperature, could not be described by a simple functional relationship.

A major software update on 21 July 2022 changed everything. The firmware was rewritten to apply step-wise corrections for the drift between calibrations using internal signals from the instrument’s components, so that corrections became continuous and the discontinuities after each autocalibration virtually disappeared. Further updates followed in late August, after a maintenance visit in September, and in late October. By the end of the roughly six-month campaign, laboratory testing showed no significant calibration drift at all, a striking result for a low-cost sensor operating outdoors through a Finnish summer and autumn.

The field test took place at the Haltiala cropland in Vantaa, southern Finland, from late June to mid-November 2022, with the site planted in oats. The prototype system and a reference setup built around a Li-Cor LI-7200RS analyser were mounted at the same 2.9 metre measurement height, each paired with a Metek uSonic-3 Scientific sonic anemometer. The prototype sampled at 5 hertz rather than the standard 10 hertz, a deliberate cost-saving choice. The researchers showed that this halving of the sampling rate has essentially no impact on calculated fluxes, since disjunct sampling introduces no systematic bias as long as the sampling interval remains shorter than the integral time scale of the turbulent signal; only the random uncertainty grows slightly.

The performance numbers are impressive for the price class. The prototype achieved a first-order response time of 0.17 to 0.18 seconds for carbon dioxide, close to its laboratory value of 0.2 seconds and only modestly slower than the reference analyser’s 0.08 seconds. This fast response matters because turbulent fluctuations near the surface shift toward higher frequencies under stable stratification, and a sluggish sensor misses them, biasing fluxes low. The prototype’s noise level, initially 2 to 2.5 parts per million, rose temporarily to about 3 ppm when the stability-focused software update traded some noise for signal continuity, then dropped to roughly 1 ppm after the September improvements. That noise corresponds to a flux random uncertainty of about 0.2 to 0.24 micromoles per square metre per second, well below the 10 to 20 percent random uncertainty that the stochastic nature of turbulence itself imposes on any eddy covariance measurement.

The flux comparison told a consistent story. Half-hourly carbon dioxide fluxes from the two systems were highly correlated, with coefficients of determination between 0.85 and 0.96 for carbon dioxide and around 0.90 for water vapour, and the slight underestimation by the prototype diminished after the July software update. In July, the oat field absorbed up to about 30 micromoles of carbon dioxide per square metre per second during the day and released roughly 10 at night, with both systems tracking the strong diurnal cycle and its decline as the crop senesced. Cumulative carbon dioxide fluxes diverged by 13 percent before the software update but by only 18 percent of a much smaller cumulative total afterwards, a difference the authors consider small given the near-zero exchange conditions of late summer. Water vapour fluxes agreed well early on, though cumulative differences grew later in the season, likely reflecting the difficulty of correcting high-frequency losses when water is absorbed and desorbed in the sampling line at high humidity.

There is a bittersweet coda. The researchers conclude that the prototype came close to being a production-ready analyser that could balance a substantially lower price against scientific-grade accuracy, potentially enabling dense networks of flux towers across heterogeneous landscapes or redundant installations at single sites to sharpen annual carbon budgets. Yet a market analysis by Vaisala concluded that in 2022 the market was not large enough to justify the investment, and further development was frozen. The study stands as a proof of concept: the engineering barriers to cheap, reliable ecosystem carbon monitoring have largely fallen, and what remains is the economic and institutional will to deploy such tools at scale as carbon accounting becomes a fixture of the global economy.

Subject of Research: Field intercomparison of a low-cost fast-response carbon dioxide sensor with a standard eddy covariance system

Article Title: Good performance of low-cost fast-response carbon dioxide sensor based on intercomparison with the standard eddy-covariance system

Article References: Rannik, Ü., Mammarella, I., Vesala, T., Väkimies, P., Heiskari-Tuohiniemi, H., & Korkiakoski, M. (2026). Good performance of low-cost fast-response carbon dioxide sensor based on intercomparison with the standard eddy-covariance system. Atmospheric Measurement Techniques, 19(18), 6159-6169. https://doi.org/10.5194/amt-19-6159-2026

Image Credits: AI Generated

DOI: 10.5194/amt-19-6159-2026

Keywords: eddy covariance, carbon dioxide flux, low-cost sensors, NDIR spectroscopy, autocalibration, ecosystem carbon monitoring, water vapour flux, carbon markets, atmospheric measurement, Vaisala, University of Helsinki, cropland

The choice of study site was deliberate. Volcanic lakes are usually treated as special cases in greenhouse gas budgets because they can receive magmatic and hydrothermal carbon from below, potentially inflating their emissions far above those of ordinary lakes. The Azores, with active volcanism and widespread hydrothermal manifestations, is an ideal place to test how much of a lake’s carbon output is geological and how much is biological. Previous work across the archipelago estimated that 45 Azorean lakes together emit roughly 171,000 tonnes of carbon dioxide per year, of which about 42 percent was attributed to volcanic origin. But the Flores lakes had only been measured once before, leaving large uncertainties, and their methane emissions had never been quantified at all.

The three lakes differ dramatically despite sitting within a few kilometers of each other inside the Seven Lakes Caldera. Comprida is the smallest and shallowest, just 14.3 meters deep with a surface area of 0.06 square kilometers, occupying an elongated maar formed by a row of at least five craters during a single eruption dated to 3,180 calibrated years before present. Negra, formed in the same eruption, is the deepest lake in the entire Azores at 119 meters, with water that can linger for 17 years before being flushed out. Funda, the largest at 0.38 square kilometers, lies in a steep-walled maar created by a phreatomagmatic eruption around 3,250 years ago and drains a watershed more than eight times its own surface area. These differences in depth, volume and residence time turned out to matter enormously for how the lakes behave chemically and biologically.

The team conducted four field surveys between May 2023 and February 2024, capturing the full seasonal cycle of these monomictic lakes, which stratify thermally in summer and mix completely in winter. They measured diffuse carbon dioxide flux using a static floating chamber equipped with an infrared detector, mapping the lake surfaces point by point, and applied both the Graphical Statistical Approach and sequential Gaussian simulation to convert those measurements into total lake-wide emission estimates. For methane, they deployed floating chambers along transects during the November and February surveys and also calculated theoretical fluxes from dissolved gas concentrations using a thin boundary layer model, finding the two methods agreed closely. Water chemistry was profiled at depth intervals in every lake, and sediment cores were collected for microbial analysis using full-length 16S rRNA gene sequencing on a PacBio platform.

The headline numbers show that carbon dioxide dominates these systems by two to three orders of magnitude over methane. Funda Lake emerged as the strongest emitter, releasing about 1.06 tonnes of carbon dioxide per day during the first survey and 1.02 tonnes during the second, while Comprida and Negra released at most around 0.39 and 0.22 tonnes per day respectively. Yet crucially, none of the measured fluxes came close to the threshold of 35 grams per square meter per day above which a magmatic contribution cannot be excluded. Carbon isotope data reinforced this conclusion: the delta-13C values of dissolved inorganic carbon in all three lakes were more negative than both the atmospheric and mantle signatures, pointing to a biogenic origin for the escaping carbon dioxide rather than a deep volcanic source.

Seasonality left a clear fingerprint on the emissions. Carbon dioxide fluxes were consistently lower during the August survey than in May, a counterintuitive result the researchers attribute to warmer surface waters boosting photosynthetic activity, which strips dissolved carbon dioxide from the water before it can escape. In eutrophic lakes this effect can be strong enough to push surface waters below atmospheric equilibrium, turning them into temporary carbon dioxide sinks. Methane behaved differently: fluxes were two to three times higher during the November survey, when Negra and Funda were still stratified and bottom waters were warm, than in February after full mixing. Warmer sediments favor methane-producing archaea, so the stratified autumn conditions gave methanogenesis a head start that winter mixing then erased.

The microbial data provide the mechanistic explanation for these patterns. In summer, Negra Lake was dominated by autotrophic Nostocaceae, cyanobacteria that fix carbon dioxide through photosynthesis, consistent with its relatively low surface fluxes. Meanwhile Comprida and Funda harbored abundant fermentative taxa such as Clostridiaceae and Enterobacteriaceae, which break down organic matter anaerobically and release carbon dioxide in deeper sediments. When winter mixing broke down the stratification in Negra and Funda, the microbial balance shifted sharply: fermenters, sulfate-reducing Desulfatiglandaceae and syntrophic Syntrophaceae all surged, indicating intensified anaerobic respiration and a potential pulse of carbon dioxide from sediments that had been accumulating organic matter under oxygen-poor conditions.

Methane cycling followed its own microbial logic. In Funda Lake, syntrophic families that feed methanogens, including Smithellaceae, Syntrophaceae and Syntrophorhabdaceae, were already well established during summer stratification and grew further in winter, but so did Methylomonadaceae, aerobic bacteria that oxidize methane. The researchers suggest that winter mixing oxygenates deeper water, giving methanotrophs the oxygen they need to consume methane before it reaches the surface, which helps explain the lower winter fluxes. Comprida Lake told a different story: syntrophic groups were scarce, but methane-oxidizing Methylococcaceae and Methylomonadaceae exploded in winter, suggesting that in this less productive lake, biological oxidation is the dominant brake on methane escape. In deep Negra Lake, by contrast, methanotrophs declined in winter, possibly because even full mixing could not deliver enough oxygen to the lake’s great depths, allowing methane to accumulate.

Trophic status emerged as a unifying theme. Negra and Funda are classified as being in poor and bad ecological status respectively under the EU Water Framework Directive, with chlorophyll-a values reaching 45 and 86.4 micrograms per liter, while Comprida remains in good status with far lower productivity. The eutrophic lakes support larger microbial communities engaged in anaerobic degradation, which translates into higher greenhouse gas production. The study’s total emission estimates reflect this: when the lakes were stratified, Funda released about 1.23 tonnes of carbon dioxide equivalent per day, compared with 0.33 and 0.23 tonnes for Comprida and Negra. Methane emissions, ranging from 0.64 to 6.28 kilograms per day across the lakes, remained below global averages for lakes of comparable size, but the authors warn that ongoing eutrophication, potentially worsened by climate-driven increases in nutrient runoff, could push these numbers upward.

The broader message is that volcanic setting alone does not make a lake a carbon hotspot. In Flores’s maar lakes, the geology provides the basin, but the biology writes the emissions budget. Microbial communities act as dynamic regulators, mediating the balance between carbon fixation and respiration, between methanogenesis and methane oxidation, and shifting that balance with every seasonal turn of the water column. As climate change alters stratification patterns and nutrient loading in lakes worldwide, the authors argue that integrating microbial functional profiles into biogeochemical assessments will be essential for predicting how these small but numerous ecosystems will feed back on the global carbon cycle.

Subject of Research: Carbon dioxide and methane fluxes and their microbial controls in monomictic volcanic crater lakes on Flores Island, Azores

Article Title: CO2 and CH4 fluxes from monomictic volcanic lakes in a remote oceanic island: Flores island case study (Azores)

Article References: Ferreira, L., Andrade, C., Cruz, J. V., Tassi, F., Pimentel, A., Braga, D., Frias, J., Raposeiro, P., & Toubarro, D. (2026). CO2 and CH4 fluxes from monomictic volcanic lakes in a remote oceanic island: Flores island case study (Azores). Environmental Earth Sciences, 85(16), Article 417. https://doi.org/10.1007/s12665-026-13139-1

Image Credits: AI Generated

DOI: 10.1007/s12665-026-13139-1

Keywords: volcanic lakes, greenhouse gases, carbon dioxide flux, methane emissions, Azores, Flores Island, maar lakes, microbial communities, eutrophication, biogeochemistry, lake stratification, methanotrophs