Carbon Cycle Research Articles

Metal-Organic Frameworks for Electrocatalytic CO2 Reduction: From Catalytic Site Design to Microenvironment Modulation.

The electrochemical reduction of CO2 to high-value carbon-based chemicals provides a sustainable approach to achieving an artificial carbon cycle. In the decade, metal-organic frameworks (MOFs), a kind of porous crystalline porous materials featuring well-defined structures, large surface area, high porosity, diverse components, easy tailorability, and controllable morphology, have attracted considerable research attention, serving as electrocatalysts to drive CO2 reduction. In this review, the reaction mechanisms of electrochemical CO2 reduction and the structure/component advantages of MOFs meeting the requirements of electrocatalysts for CO2 reduction are analyzed. After that, the representative progress for the precise fabrication of MOF-based electrocatalysts for CO2 reduction, focusing on catalytic site design and microenvironment modulation, are systemically summarized. Furthermore, the emerging applications and promising research for more practical scenarios related to electrochemical CO2 conversion are specifically proposed. Finally, the remaining challenges and future outlook of MOFs for electrochemical CO2 reduction are further discussed.

Organic carbon oxidation and the associated pyrite formation in deep sediments at the Nankai subduction zone

The preservation of organic carbon (OC) in marine sediments is crucial for Earth's climate by sequestering CO2. While OC is mostly remineralized before it reaches the seafloor, a notable fraction is buried in deep-sea sediments, particularly at subduction zones known for their enhanced sedimentation rates that promote OC burial. The mechanisms behind OC recycling and decomposition within subduction zone sediments are governed by biologically mediated redox reactions involving a range of electron acceptors, which facilitate the sequential oxidation of OC. However, direct evidence regarding such effects on OC in deep sediments remains limited. In this study, we examine the contents of pyrite and trace metals of molybdenum (Mo), vanadium (V), and cesium (Cs) in organic-rich deep sediments from the Nankai subduction zone. We find that the pyrite, sulfate, diagenetic illite, and OC contents covary in Unit V, highlighting the important role of organoclastic sulfate reduction and biotic smectite-to-illite reaction at 60–70 °C in OC oxidation and pyrite formation. The profiles of Mo, V, and Cs also align with these processes in the same interval. Our findings contribute to an in-depth understanding of OC dynamics in subduction zones, emphasizing the complex interactions within deep sediments that may influence the global carbon cycle.

Divergent metabolism estimates from dissolved oxygen and inorganic carbon: Implications for river carbon cycling

Divergent metabolism estimates from dissolved oxygen and inorganic carbon: Implications for river carbon cycling

Impact of Plant Community Diversity on Greenhouse Gas Emissions in Riparian Zones.

Plant community succession can impact greenhouse gas (GHG) emissions from the soil by altering the soil carbon and nitrogen cycles. However, the effects of community landscape diversity on soil GHG emissions have rarely been fully understood. Therefore, this study investigated how plant landscape diversity, structure type, and species composition, affect soil GHG emissions in a riparian zone. Soil GHG emissions were assessed by measuring the air samples collected from four study sites, which have different plant community structure types and species compositions (natural sites with complex plants, landscaped sites with fruit trees and grasses, untended sites with ruderals, and farmland sites), using the static chamber method. Significant differences were observed in soil carbon dioxide (CO2; p < 0.001), nitrous oxide (N2O; p < 0.001), and methane (CH4; p = 0.005) emissions. The untended site with ruderals exhibited the highest CO2 emissions, while N2O emissions increased as plant community diversity decreased. All sites acted as sinks for CH4 emissions, with decreased CH4 uptake efficiency in more diverse plant communities. The Mantel test and variance partitioning analysis revealed soil microbial biomass as an indirect influencer of GHG emissions. This study could help predict soil GHG emissions and their global warming potential under future changes in the island riparian zones.

Uncovering the roles of the scaffolding protein CsoS2 in mediating the assembly and shape of the α-carboxysome shell.

Carboxysomes are a paradigm of organelle-like structures in cyanobacteria and many proteobacteria. These nanoscale compartments enclose Rubisco and carbonic anhydrase within an icosahedral virus-like shell to improve CO2 fixation, playing a vital role in the global carbon cycle. Understanding how the carboxysomes are formed is not only important for basic research studies but also holds promise for repurposing carboxysomes in bioengineering applications. In this study, we focuses on a specific scaffolding protein called CsoS2, which is involved in facilitating the assembly of α-type carboxysomes. By deciphering the functions of different parts of CsoS2, especially its middle region, we provide new insights into how CsoS2 drives the stepwise assembly of the carboxysome at the molecular level. This knowledge will guide the rational design and reprogramming of carboxysome nanostructures for many biotechnological applications.

Eocene maar sediments record warming of up to 3.5 °C during a hyperthermal event 47.2 million years ago

Eocene hyperthermal events reflect profound perturbations of the global carbon cycle. Most of our knowledge about their onset, timing, and rates originates from marine records. Hence, the pacing and magnitude of hyperthermal continental warming remains largely unaccounted for due to a lack of high-resolution climate records. Here we use terrestrial biomarkers and carbon isotopes retrieved from varved lake deposits of the UNESCO World Heritage site ‘Messel Fossil Pit’ (Germany) to quantify sub-millennial to millennial-scale temperature and carbon isotope changes across hyperthermal event C21n-H1 (47.2 million years ago). Our results show maximum warming of ca. 3.5 °C during C21n-H1. We propose that two components are responsible for the warming pattern across the hyperthermal: (1) the massive release of greenhouse gases into the atmosphere-ocean system and (2) half-precession orbital forcing indicated by ~12.000-year temperature cycles. The carbon isotope record of bulk organic matter indicates a sharp, 7‰ decrease at the peak of the hyperthermal, corresponding to increased organic carbon content and a shift in the lake algal community. Collectively, our proxy data reveal the structure of continental temperature response during the hyperthermal event that is characterized by overall warming with a superimposed pattern of sub-orbital scale temperature fluctuations.

Microbial Metabolism and Environmental Controls of Acetate Cycling in the Northwest Pacific Ocean

AbstractMicrobial acetate metabolism is an important part of marine carbon cycling. We present a comprehensive study to constrain microbial acetate metabolism and its regulation in surface seawater of the northwest Pacific Ocean. We found that acetate oxidation (rate constant k: 0.016–0.506 day−1) accounted for 77.6%–99.4% of the total microbial acetate uptake, suggesting that acetate was predominantly used as a microbial energy source. Acetate also served as a significant biomass carbon source, as reflected by the elevated contribution of acetate assimilation to bacterial carbon production. Acetate turnover was largely influenced by water mass mixing and nutrient conditions. Atmospheric deposition was a source of acetate in surface water and this process can also impact the microbial acetate uptake. Microbial utilization of acetate could account for up to 25.9% of the bacterial carbon demand, suggesting the significant role of acetate metabolism in microbial carbon cycling in the open ocean.

Synthesis of In Situ Marine Calcium Carbonate Dissolution Kinetic Measurements in the Water Column

AbstractCalcium carbonate (CaCO3) dissolution is an integral part of the ocean's carbon cycle. However, laboratory measurements and ocean alkalinity budgets disagree on the rate and loci of dissolution. In situ dissolution studies can help to bridge this gap, but so far published studies have not been utilized as a whole because they have not previously been compiled into one data set and lack carbonate system data to compare between studies. Here, we compile all published measurements of CaCO3 dissolution rates in the water column (11 studies, 752 data points). Combining World Ocean Atlas data (temperature, salinity) with the neural network CANYON‐B (carbonate system variables), we estimate seawater saturation state (Ω) for each rate measurement. We find that dissolution rates at the same Ω vary by 2 orders of magnitude. Using a machine learning approach, we show that while Ω is the main driver of dissolution rate, most variability can be attributed to differences in experimental design, above all bias due to (diffusive) transport and the synthetic or biogenic nature of CaCO3. The compiled data set supports previous findings of a change in the mechanism driving dissolution at Ωcrit = 0.8 that separates two distinct dissolution regimes: rslow = 0.29 · (1 − Ω)0.68(±0.16) mass% day−1 and rfast = 2.95 · (1 − Ω)2.2(±0.2) mass% day−1. Above the saturation horizon, one study shows significant dissolution that cannot solely be explained by established theories such as zooplankton grazing and organic matter degradation. This suggests that other, non‐biological factors may play a role in shallow dissolution.

Setting the stage for plant–soil feedback: Mycorrhizal influences over conspecific recruitment, plant and fungal communities, and coevolution

Abstract Plant–soil feedback (PSF) plays a central role in determining plant community dynamics, yet our understanding of how different combinations of plants and microbes influence PSF remains limited. Plants of different mycorrhizal types often exhibit contrasting PSF outcomes, influencing plant recruitment and spatial structure. Generalizing across plant species based on mycorrhizal type creates the potential to examine broader effects on ecological communities. We review mechanisms contributing to different PSF outcomes between arbuscular mycorrhizal and ectomycorrhizal trees. We focus on how plant and fungal traits that differ between mycorrhizal types interact with pathogenic and saprotrophic microorganisms and nutrient and carbon cycling. Synthesis. Building on this framework, we propose several new research directions. First, mycorrhizal‐induced changes in soils can operate beyond the conspecific level, spilling over from abundant plant species onto less abundant ones. This community‐level ‘mycorrhizal spillover’ is hypothesized to affect PSF in ways that are additive and interactive with conspecific density dependence. Second, we describe how mycorrhizal effects on PSF could structure the way plant communities respond to global change. Third, we discuss how they may influence plant evolution by altering the balance of selection pressures on traits and genes related to pathogen defence and mutualism formation.

Long-term Autotrophic Growth and Solar-to-chemical Conversion in Shewanella Oneidensis MR-1 through Light-driven Electron Transfer.

Members of the genus Shewanella are known for their versatile electron accepting routes, which allow them to couple decomposition of organic matter to reduction of various terminal electron acceptors for heterotrophic growth in diverse environments. Here, we report autotrophic growth of Shewanella oneidensis MR-1 with photoelectrons provided by illuminated biogenic CdS nanoparticles. This hybrid system enables photosynthetic oscillatory acetate production from CO2 for over five months, far exceeding other inorganic-biological hybrid system that can only sustain for hours or days. Biochemical, electrochemical and transcriptomic analyses reveal that the efficient electron uptake of S. oneidensis MR-1 from illuminated CdS nanoparticles supplies sufficient energy to stimulate the previously overlooked reductive glycine pathway for CO2 fixation. The continuous solar-to-chemical conversion is achieved by photon induced electric recycling in sulfur species. Overall, our findings demonstrate that this mineral-assisted photosynthesis, as a widely existing and unique model of light energy conversion, could support the sustained photoautotrophic growth of non-photosynthetic microorganisms in nutrient-lean environments and mediate the reversal of coupled carbon and sulfur cycling, consequently resulting in previously unknown environmental effects. In addition, the hybrid system provides a sustainable and flexible platform to develop a variety of solar products for carbon neutrality.

The Validity of Optical Properties as Tracers of Terrigenous Dissolved Organic Carbon During Extensive Remineralization in Coastal Waters

AbstractTerrestrial dissolved organic carbon (tDOC) is significant for coastal carbon cycling, and spectroscopy of chromophoric and fluorescent dissolved organic matter (CDOM, FDOM) is widely used to study tDOC cycling. However, CDOM and FDOM are often amongst the more labile components of tDOC. Because few studies have compared spectroscopy to measurements of both bulk tDOC concentration and tDOC remineralization, it remains unclear how accurately CDOM and FDOM actually trace tDOC in coastal waters when tDOC undergoes extensive remineralization. We collected a 4‐year coastal timeseries in Southeast Asia, where tropical peatlands provide a large tDOC input. A carbon stable isotope mass balance shows that on average 53% of tDOC was remineralized upstream of our site, while 74% of CDOM was bleached. Despite this extensive tDOC remineralization and preferential CDOM loss, optical properties could still reliably quantify tDOC. CDOM spectral slope properties, such as S275–295, are exponentially related to tDOC; these are highly sensitive tDOC tracers at low, but not at high, tDOC concentrations. Other properties are linearly related to tDOC, and both specific ultraviolet absorbance (SUVA254) and DOC‐normalized fluorescence intensity may be suitable to quantify tDOC over a wider range of concentrations. However, the optical properties did not show consistent changes with the extent of tDOC remineralization. Our data support the validity of CDOM and FDOM spectroscopy to trace tDOC across coastal gradients even after the majority of tDOC has been remineralized, but they also show that these measurements may not provide direct information about the degree of natural tDOC processing.

Metagenomic Analysis of Bottom Sediments of the Karst Meromictic Lake Black Kichier Revealed Abundant Unculturable Thermoplasmatota

Investigations into the microbial community of bottom sediments in the karst lake Black Kichier were conducted. These sediments exhibited elevated levels of sulfide, dissolved methane, and organic matter. Direct radiotracer experiments revealed substantial rates of microbial processes involved in the decomposition of organic matter. Uncultivated archaea belonging to the phylum Thermoplasmatota were identified within the microbial community. Metagenomic analysis unveiled representatives from five orders: Methanomassiliicoccales, Thermoprofundales (formerly known as Marine Benthic Group D and DHVEG-1), DTX01, SG8-5, and Candidatus Gimiplasmatales (formerly UBA10834). These archaea were previously believed to occur exclusively in deep marine sediments characterized by extreme organic matter scarcity. This discovery reshapes our understanding of the role played by Thermoplasmatota archaea, spanning five orders, in the degradation segment of the carbon cycle.

Alterations in carbon and nitrogen cycling mediated by soil microbes due to the conversion of karst mountainous forests into urban parks

The conversion of mountainous karst forests into urban parks necessitates a critical analysis of its impact on existing ecosystems, particularly regarding soil microbial diversity and its role in carbon and nitrogen cycling. Our study targeted three established mountain parks in Guiyang, China, to discern the effects of habitat alteration and park age on the soil microbiota’s functional genes. The findings indicated pronounced differences in functional gene profiles between original remnant forests and created greenspaces. The artificial green spaces exhibited a heightened presence of genes related to aerobic methane oxidation, anaerobic carbon fixation, denitrification and nitrification, indicating that artificial green spaces may cultivate soil microbial communities with enhanced metabolic versatility. We revealed a positive correlation between soil nitrogen levels and the abundance of genes involved in various processes of the carbon and nitrogen cycles in these artificial green areas, highlighting the critical role of nitrogen in influencing the structure of microbial communities. Soil chemical properties (namely C, N, P, K content) and habitat type emerged as the most consequential for the gene composition related to the carbon and nitrogen cycles. The co-occurrence networks of functional genes constructed for these cycles suggest a tendency towards synergistic microbial interactions. To safeguard the interplay between human recreation and the conservation of native ecosystems, we recommend the integration of native flora preservation and meticulous soil condition management into the strategies for developing urban mountain parks.

Land use and cover change accelerated China’s land carbon sinks limits soil carbon

Land use and cover change (LUCC) significantly impacts global carbon cycles and land surface properties, accounting for 25% of the historical atmospheric CO2 increase. We explore a previously overlooked role of LUCC in driving the land carbon cycle by using a three-level meta-analysis and Land Use Harmonization data to drive an ecosystem model. Our findings reveal that a loss of 39.2% of soil organic carbon (SOC) change in China due to LUCC, mitigated by afforestation, doubles gross primary productivity at 0.02 Pg C yr−1, countering central China’s urbanization decline. Indirect climate effects, especially soil bulk density, significantly impact SOC compared to direct climate effects. LUCC has significantly increased the Chinese terrestrial carbon sink, with net ecosystem productivity reaching 0.02 ± 0.12 Pg C yr−1. Our study underscores the importance of reforestation and afforestation in addressing climate change and enhancing carbon sinks in future carbon management.

Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant

Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.

Analysis of bacterial community structure, functional variation, and assembly mechanisms in multi-media habitats of lakes during the frozen period

Ice, water, and sediment represent three interconnected habitats in lake ecosystems, and bacteria are crucial for maintaining ecosystem equilibrium and elemental cycling across these habitats. However, the differential characteristics and driving mechanisms of bacterial community structures in the ice, water, and sediments of seasonally frozen lakes remain unclear. In this study, high-throughput sequencing technology was used to analyze and compare the structure, function, network characteristics, and assembly mechanisms of bacterial communities in the ice, water, and sediment of Wuliangsuhai, a typical cold region in Inner Mongolia. The results showed that the bacterial communities in the ice and water phases had similar diversity and composition, with Proteobacteria, Bacteroidota, Actinobacteria, Campilobacterota, and Cyanobacteria as dominant phyla. The bacterial communities in sediments displayed significant differences from ice and water, with Chloroflexi, Proteobacteria, Firmicutes, Desulfobacterota, and Acidobacteriota being the dominant phyla. Notably, the bacterial communities in water exhibited higher spatial variability in their distribution than those in ice and sediment. This study also revealed that during the frozen period, the bacterial community species in the ice, water, and sediment media were dominated by cooperative relationships. Community assembly was primarily influenced by stochastic processes, with dispersal limitation and drift identified as the two most significant factors within this process. However, heterogeneous selection also played a significant role in the community composition. Furthermore, functions related to nitrogen, phosphorus, sulfur, carbon, and hydrogen cycling vary among bacterial communities in ice, water, and sediment. These findings elucidate the intrinsic mechanisms driving variability in bacterial community structure and changes in water quality across different media phases (ice, water, and sediment) in cold-zone lakes during the freezing period, offering new insights for water environmental protection and ecological restoration efforts in such environments.

Tropical peat composition may provide a negative feedback on fire occurrence and severity

Loss of peat through increased burning will have major impacts on the global carbon cycle. In a normal hydrological state, the risk of fire propagation is largely controlled by peat bulk density and moisture content. However, where humans have interfered with the moisture status of peat either via drainage, or indirectly via climate change, we hypothesise that its botanical composition will become important to flammability, such that peats from different latitudes might have different compositionally-driven susceptibility to ignition. We use pyrolysis combustion flow calorimetry to determine the temperature of maximum thermal decomposition (Tmax) of peats from different latitudes, and couple this to a botanical composition analysis. We find that tropical peat has higher Tmax than other regions, likely on account of its higher wood content which appears to convey a greater resistance to ignition. This resistance also increases with depth, which means that loss of surface peat in tropical regions may lead to a reduction in the subsequent ignitability of deeper peat layers as they are exposed, potentially resulting in a negative feedback on increased fire occurrence and severity.

Effects of fire on tree species composition and carbon stocks of a peat swamp forest in Central Kalimantan, Indonesia

ABSTRACT Peat swamp forests are important in the global carbon (C) budget because of the huge amount of C stored in these ecosystems, particularly in below-ground components. Indonesia has some of the greatest extent of peat swamp forests globally, yet many of them are being disturbed by fires that are becoming increasingly frequent. In Kalampangan, Central Kalimantan, the tree species (≥4.8 cm diameter) composition, aboveground biomass (AGB) and litter standing crop of peat swamp forests were sampled, and the overall ecosystem C stock estimated, within two 1-ha sampling plots, one of which was undisturbed (natural) and the other previously burned. The AGB and litter standing crop found in the natural forest totaled 341 and 6.77 Mg ha−1, respectively. The AGB declined more than six-fold to 53.2 Mg ha−1, and the litter standing crop declined by about half to 3.30 Mg ha−1 in the disturbed forest; the total number of tree species declined from 114 to 80 per hectare. The disturbed peat swamp lost just over 200 Mg C ha−1 to the atmosphere due to the combustion of tree biomass and the upper layer of the peat, but C stocks still remained very high overall (c. 1100 Mg ha−1) due to the thick layer of peat (>2 m) making peat swamp forest conservation imperative due to their huge carbon stocks.

Peanut–cotton intercropping to enhance soil ecosystem multifunctionality: Roles of microbial keystone taxa, assembly processes, and C-cycling profiles

Legume-based intercropping, such as the peanut–cotton system, stands out as a promising strategy for enhancing soil ecosystem multifunctionality (EMF); however, the underlying microbial mechanisms driving these enhancements remain inadequately explored. In this study, after implementing peanut–cotton intercropping for six consecutive years, a data set of 13 ecosystem functional indicators including 41 soil variables, was obtained and used to quantify the average EMF index. We investigated changes in microbial keystone taxa in co-occurrence networks, community assembly processes, carbon (C) cycling profiles, and their collective impacts on soil EMF. Soil EMF increased by an average of 140.0 % in the peanut–cotton intercropping system, compared with monoculture systems of both peanut and cotton, driven by significant increases in C-cycling (159.9 %), nutrient provisioning (91.2 %), and microbial growth efficiency functions (53.9 %). The peanut–cotton intercropping system significantly increased the average well-color developments (AWCD), abundance of C-fixation and C-degradation genes, and related pathways, resulting in a highly vigorous microbial C-cycling profile. The microbial community assembly processes shifted from a balance of stochastic and deterministic processes in monocultures to predominantly deterministic processes (> 70 %) in the intercropping system. Additionally, the peanut–cotton intercropping system fostered a more efficient and stable bacterial–fungal cross-kingdom network than the monocultures, characterized by a higher average clustering coefficient, higher robustness, and shorter average path length. This intercropping system also recruited a group of keystone taxa affiliated with Proteobacteria, Actinobacteria, and Ascomycota phyla. The enhancement of EMF in the peanut–cotton intercropping system resulted from the positive impact of key microbial community members and their assembly, C/N ratios, AWCD, and C-fixation and C-degradation genes. Our study provides insights into the complex ecological linkages between microbial communities, C-cycling profiles, and soil ecosystem functions, providing valuable insights into the microbial mechanisms underlying the benefits of intercropping systems.

Disentangling how the opportunistic parasitic fungus Armillaria affects the flammability of coarse deadwood in exotic pine plantations

Parasitic wood fungi are important to forest carbon cycles globally. However, whether or how they affect the flammability of coarse deadwood is poorly understood. Given the predicted climate-driven increase in wildfires and associated carbon emissions into the atmosphere, potentially amplifying climate warming, filling this knowledge gap should have high priority. We thereto investigated coastal plantations of the exotic black pine, Pinus nigra J.F. Arnold, in the Netherlands, which are widely suffering from Armillaria infection. We hypothesized that branches from forest stands with a visible Armillaria infection will burn differently compared with branches from stands without a visible Armillaria infection, due to Armillaria infection having an additional effect on the branch traits. We tested this hypothesis by burning coarse Pinus nigra branches across a range of densities from infected and uninfected forest patches under standardized conditions in a fire lab and by measuring Armillaria biomass (via ddPCR), deadwood traits and key flammability parameters. Armillaria infection did enhance the flammability of Pinus nigra branches (e.g. more ignitable, longer flame duration and higher percentage mass loss). This higher flammability originated from both direct Armillaria influences, e.g. via changing wood structure (before and/or after wood death), and indirect influences, e.g. by facilitating nitrogen fixation in wood, thereby increasing wood decomposability and consequently reducing wood density. Our findings also have important implications for understanding the role of pathogens in fire regimes more broadly.