Stable carbon isotope fractionation as tracer of carbon cycling in anoxic soil ecosystems

Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ13C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42- and NO3- as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.

Carbon-Atom Exchange between [MC2]+ (M = Os and Ir) and Methane: on the Thermodynamic and Dynamic Aspects

Gas-phase reactions of [OsC2]+ and [IrC2]+ with methane at ambient temperature have been studied using quadrupole-ion trap mass spectrometry combined with quantum chemical calculations. Both [OsC2]+ and [IrC2]+ undergo carbon-atom exchange reactions with methane. The associated mechanisms for the two systems are found to be similar. The differences in the rates of carbon isotope exchange reactions of methane with [MC2]+ (M = Os and Ir) are explained by several factors like the energy barrier for the initial H3C-H bond breaking processes, the molecular dynamics, orbital interactions, and the H-binding energies of the pivotal steps. Besides, the number of participating valence orbitals might be one of the keys to regulate the rate in the key step. The present findings may provide useful ideas and inspiration for designing similar processes.

Pig slurry organic matter transformation and methanogenesis at ambient storage temperatures

Manure management is a significant source of global methane emissions, and there is an increased interest in understanding and predicting emissions. The hydrolysis rate of manure organic matter is critical for understanding and predicting methane emissions. We estimated hydrolysis rate constants of crude protein, fibers, and lipids and used the Arrhenius equation to describe its dependency on temperature. Simultaneously, measurements of methane emission, 13/12 C isotope ratios, and methanogen community were conducted. This was achieved by incubating fresh pig manure without inoculum at 10°C, 15°C, 20°C, and 25°C for 85 days in a lab-scale setup. Hydrolysis of hemicellulose and cellulose increased more with temperature than crude protein, but still, hydrolysis rate of crude protein was highest at all temperatures. Results suggested that crude protein consisted of multiple substrate groups displaying large differences in degradability. Lipids and lignin were not hydrolyzed during incubations. Cumulative methane emissions were 7.13 ± 2.69, 24.6 ± 8.00, 66.7 ± 4.8, and 105.7 ± 7.14 gCH4 kgVS -1 at 10°C, 15°C, 20°C, and 25°C, respectively, and methanogenic community shifted from Methanosphaera toward Methanocorpusculum over time and more quickly at higher temperatures. This study provides important parameter estimates and dependencies on temperature, which is important in mechanistic methane emission models. Further work should focus on characterizing quickly degradable substrate pools in the manure organic matter as they might be the main carbon source of methane emission from manure management.

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

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

Stable carbon and nitrogen isotopes identify nuanced dietary changes from the Bronze and Iron Ages on the Great Hungarian Plain

The Great Hungarian Plain (GHP) served as a geographic funnel for population mobility throughout prehistory. Genomic and isotopic research demonstrates non-linear genetic turnover and technological shifts between the Copper and Iron Ages of the GHP, which influenced the dietary strategies of numerous cultures that intermixed and overlapped through time. Given the complexities of these prehistoric cultural and demographic processes, this study aims to identify and elucidate diachronic and culture-specific dietary signatures. We report on stable carbon and nitrogen isotope ratios from 74 individuals from nineteen sites in the GHP dating to a ~ 3000-year time span between the Early Bronze and Early Iron Ages. The samples broadly indicate a terrestrial C₃ diet with nuanced differences amongst populations and through time, suggesting exogenous influences that manifested in subsistence strategies. Slightly elevated δ¹⁵N values for Bronze Age samples imply higher reliance on protein than in the Iron Age. Interestingly, the Füzesabony have carbon values typical of C₄ vegetation indicating millet consumption, or that of a grain with comparable δ¹³C ratios, which corroborates evidence from outside the GHP for its early cultivation during the Middle Bronze Age. Finally, our results also suggest locally diverse subsistence economies for GHP Scythians.

The application and potential non-conservatism of stable isotopes in organic matter source tracing

Organic matter (OM) tracing is critical for understanding the processes of soil redistribution and global carbon cycling. It effectively supports ecological management and global climate change prediction. Stable isotopes are generally more source-specific compared with other tracers and identify OM sources with a higher level of accuracy. Nevertheless, stable isotopes may be enriched or depleted by physical and biochemical processes such as selective migration of particles and OM mineralization in transport and sedimentary environments, making it difficult to establish links between the source and sink regions. Literature on OM source identification tends to assume a direct link between stable isotope sources and sinks, ignoring the non-conservatism of stable isotopes. There is further literature on understanding and modeling the processes that link the sources to sinks in terms of the non-conservatism of stable isotopes. The disagreement in response to the non-conservatism lies in the lack of comprehensive understanding of stable isotope fingerprinting systems and non-conservatism. The development of stable isotope fingerprinting technology is full of challenges. This review outlines the applicability of stable isotope tracers, identification mechanisms, and associated quantitative models, intending to improve the stable isotope fingerprinting system. We highlight the non-conservatism of stable isotopes in space and time caused by physical and biochemical processes. Additionally, a decision tree is established to determine the quantitative tools, evaluation indicators, and procedures related to non-conservatism. This decision tree clarifies the process from non-conservatism detection to threshold determination of statistical quantification, which can guide the end-users to better apply stable isotope to trace OM sources.

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.

Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill

Microbial communities mediate the transformation of organic matter within landfills into methane (CH₄). Yet their ecological role in CH₄ production is rarely evaluated. To characterize the microbiome associated with this biotransformation, the overall community and methanogenic Archaea were surveyed in an arid landfill using leachate collected from distinctly aged landfill cells (i.e., younger, intermediate, and older). We hypothesized that distinct methanogenic niches exist within an arid landfill, driven by geochemical gradients that developed under extended and age-dependent waste biodegradation stages. Using 16S rRNA and mcrA gene amplicon sequencing, we identified putative methanogenic niches as follows. The order Methanomicrobiales was the most abundant order in leachate from younger cells, where leachate temperature and propionate concentrations were measured at 41.8°C ± 1.7°C and 57.1 ± 10.7 mg L⁻¹. In intermediate-aged cells, the family Methanocellaceae was identified as a putative specialist family under intermediate-temperature and -total dissolved solid (TDS) conditions, wherein samples had a higher alpha diversity index and near CH₄ concentrations. In older-aged cells, accumulating metals and TDS supported Methanocorpusculaceae, “Candidatus Bathyarchaeota,” and “Candidatus Verstraetearchaeota” operational taxonomic units (OTUs). Consistent with the mcrA data, we assayed methanogenic activity across the age gradient through stable isotopic measurements of δ¹³C of CH₄ and δ¹³C of CO₂. The majority (80%) of the samples’ carbon fractionation was consistent with hydrogenotrophic methanogenesis. Together, we report age-dependent geochemical gradients detected through leachate in an arid landfill seemingly influencing CH₄ production, niche partitioning, and methanogenic activity.

IMPORTANCE Microbiome analysis is becoming common in select municipal and service ecosystems, including wastewater treatment and anaerobic digestion, but its potential as a microbial-status-informative tool to promote or mitigate CH₄ production has not yet been evaluated in landfills. Methanogenesis mediated by Archaea is highly active in solid-waste microbiomes but is commonly neglected in studies employing next-generation sequencing techniques. Identifying methanogenic niches within a landfill offers detail into operations that positively or negatively impact the commercial production of methane known as biomethanation. We provide evidence that the geochemistry of leachate and its microbiome can be a variable accounting for ecosystem-level (coarse) variation of CH₄ production, where we demonstrate through independent assessments of leachate and gas collection that the functional variability of an arid landfill is linked to the composition of methanogenic Archaea.

Novel Insights into Dissolved Organic Matter Processing Pathways in a Coastal Confined Aquifer System with the Highest Known Concentration of Geogenic Ammonium

High levels of geogenic ammonium in groundwater is a highly neglected nitrogen pool in coastal aquatic systems. Although organic matter (OM) mineralization is known to significantly influence geogenic ammonium enrichment, the detailed mechanism underlying ammonium enrichment based on dissolved organic matter (DOM) characterization in coastal aquifer systems remains unclear. In this study, we characterized the optical and molecular signatures of DOM coupled with hydrogeochemistry and multiple isotopes (H/O/C/N) to elucidate in detail the mechanisms underlying the anomalously high ammonium in the coastal confined aquifer system of the Pearl River Delta, which exhibits the highest reported geogenic ammonium concentration in groundwater on the Earth. We identified three DOM fluorescent components, a marine humic-like component (C1) and two other humic-like components (C2 and C3). The autochthonous OM was first processed to the C1 component, which was further transformed to C2 and C3 components. In terms of molecular classes, the processing pathway from bacterial- or algal-derived OM to aliphatic compounds and highly unsaturated-low O compounds was identified, and highly unsaturated-low O compounds were accumulated as the main products. Compounds containing two or three N atoms were processed, and compounds with one N atom gradually accumulated, which was further degraded into CHO compounds. The ammonium (up to 179 mg/L as N) was gradually enriched due to the decomposition of CHO+3N to CHO+2N, CHO+1N, and CHO compounds. Owing to the longer residence time and less frequent fresh water flushing, the produced ammonium was retained in the aquifer as a "long-term result". The contrasting DOM characteristics, together with the differing depositional and hydrogeological conditions, give rise to the higher levels of geogenic ammonium in coastal confined aquifer systems compared with inland alluvial-lacustrine confined aquifer systems. To our knowledge, this is the first study to characterize DOM and its relationship with geogenic ammonium in coastal aquifer systems.

Hydrocarbon transformation pathways and soil organic carbon stability in the biostimulation of oil-contaminated soil: Implications of 13C natural abundance

Mineralization, assimilation, and humification are key processes to detoxify oil-contaminated soil by biostimulation remediation strategies, and these processes are affected by stimulants. In this study, we investigated the effects of either inorganic salts or organic stimulants (organic compost and sawdust) on hydrocarbon transformation. Total petroleum hydrocarbons (TPH) and hydrocarbon components were determined by gravimetry and gas chromatography, and the ¹³C of CO₂, microbial biomass carbon (MBC), and humus were measured by stable isotope mass spectrometry. The results showed that organic compost was the most beneficial for the dissipation of hydrocarbons. After 60 days of remediation, the removal rates of TPH, saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were 35.7%, 39.6%, 15.9%, 80.5%, and 8.8%, respectively. A total of 84.7%-88.5% of the removed hydrocarbons were mineralized in all the treatments. The hydrocarbon degradation pathway in the control soil (without stimulant addition) was "assimilation → humification → mineralization". The hydrocarbon transformation pathways in the biostimulation treatments were "assimilation → mineralization → humification". The soil organic carbon (SOC) stability decreased during remediation, which was attributed to the enhanced microbial activity and the removal of recalcitrant hydrocarbons.

A multiple isotope (H, O, N, C and S) approach to elucidate the hydrochemical evolution of shallow groundwater in a rapidly urbanized area of the Pearl River Delta, China

A comprehensive understanding of the impacts of natural and human activities on groundwater evolution is critical for sustainable groundwater resource management, as groundwater quality degradation from urbanization has raised widespread concerns. However, conclusions based only on basic hydrochemical data would be fragmentary because complex processes occur with high concentrations of pollutants in rapidly urbanized areas. Thus, the hydrogeochemical and multi-isotope approaches were combined to elucidate the groundwater hydrogeochemical evolution in such an area. The results demonstrated that the major hydrochemical types of groundwater were ClNa and HCO₃-Ca in 2018 and that the hydrochemical patterns had changed since 1980. The predominant controlling factors for groundwater hydrochemistry were rock weathering due to carbonic, sulfuric and nitric acids, while the cation exchange and evaporation processes acted as natural factors; redox reactions, including denitrification, sulfate reduction, and methanogenesis, also affected groundwater hydrochemistry. The impacts of anthropogenic activities on groundwater hydrochemistry consisted of direct impacts that referred to the infiltration of manure and septic waste responsible for the occurrence of high NO₃^- content and part of the SO₄^2- content in groundwater and indirect impacts that included the following issues: (1) acid rain accelerated water-rock interactions and resulted in the accumulation of SO₄^2-; (2) sulfate reduction and methanogenesis increased the HCO₃^- content and expanded the distribution of HCO₃-type water; (3) organic matter associated with manure and septic waste accelerated the development of a reducing environment in groundwater; and (4) the occurrence of a strong reducing environment promoted the release of Mn, aggravated heavy metal pollution and imposed adverse effects on the ecological system.

Enrichment of Geogenic Ammonium in Quaternary Alluvial-Lacustrine Aquifer Systems: Evidence from Carbon Isotopes and DOM Characteristics

Geogenic ammonium in groundwater owing to mineralization of natural organic matter (NOM) has been reported in different geologic settings, but detailed mechanisms responsible for high ammonium concentration levels are poorly understood. To this end, we chose Quaternary high ammonium aquifer systems in central Yangtze River basins and used carbon isotopes in both dissolved organic carbon and inorganic carbon together with characterization of dissolved organic matter (DOM) and groundwater chemistry to reveal mechanisms related to the genesis of ammonium. The results indicate that high levels of geogenic ammonium (up to 33.50 mg/L as N) occur due to long-term water-rock interactions in a relatively sluggish hydrogeological environment with abundant organic matter that is rich in both C and N. The stable carbon isotope data suggest that ammonium in the groundwater is released from intensive degradation of organic matter with higher contents of ammonium associated with methanogenesis. The optical signatures of DOM indicate ammonium in the groundwater is mostly associated with terrestrial humic-like components rather than protein-like components. Molecular characterization of DOM by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) shows that, compared to low ammonium groundwater, high ammonium groundwater has larger mass weights, greater abundance of CHO+N compounds, higher percentages of lignin- and condensed-hydrocarbon-like components, lower H/C ratios, higher nominal oxidation state of carbon (NOSC) values and more double bonds, rings, and aromatic structures. Strong degradation of NOM and preferential utilization of energetically more favorable, terrestrial humic-like components (lignin-like as the main class) with high NOSC values facilitates the formation of high ammonium groundwater. To the best of our knowledge, this is the first effort to use carbon isotopes and DOM characteristics to identify enrichment mechanisms for geogenic ammonium in alluvial-lacustrine aquifer systems.

Sources of seasonal wetland methane emissions in permafrost regions of the Qinghai-Tibet Plateau

In this study, systematic soil methane cycle geochemical monitoring was carried out in a typical gas hydrate region in the Qinghai-Tibet Plateau. Soil gas samples were collected for hydrocarbon components and carbon isotope analysis. Meanwhile, soil-methane fluxes from the upper active layer (20-30 cm) were monitored during six months of one year. The results of this research provide evidence of a new source of methane emission from wetland soils in permafrost regions: gas hydrate release. Sites with large methane emissions were found using flux monitoring, the characteristics of thermogenic methane were identified using carbon isotope tracing, and the relationship between emission by soils and effusion from gas hydrates was determined through correlation analyses of soil-adsorbed hydrocarbons. Seasonal variation of methane emissions are also discussed by considering the emission of bacterial methane, thermogenic methane, and the absorption of methane from the soil active layer. These comprehensive findings provide valuable information for carbon cycle research of wetlands in permafrost regions.

Sub-oxycline methane oxidation can fully uptake CH4 produced in sediments: case study of a lake in Siberia

It is commonly assumed that methane (CH₄) released by lakes into the atmosphere is mainly produced in anoxic sediment and transported by diffusion or ebullition through the water column to the surface of the lake. In contrast to that prevailing idea, it has been gradually established that the epilimnetic CH₄ does not originate exclusively from sediments but is also locally produced or laterally transported from the littoral zone. Therefore, CH₄ cycling in the epilimnion and the hypolimnion might not be as closely linked as previously thought. We utilized a high-resolution method used to determine dissolved CH₄ concentration to analyze a Siberian lake in which epilimnetic and hypolimnetic CH₄ cycles were fully segregated by a section of the water column where CH₄ was not detected. This layer, with no detected CH₄, was well below the oxycline and the photic zone and thus assumed to be anaerobic. However, on the basis of a diffusion-reaction model, molecular biology, and stable isotope analyses, we determined that this layer takes up all the CH₄ produced in the sediments and the deepest section of the hypolimnion. We concluded that there was no CH₄ exchange between the hypolimnion (dominated by methanotrophy and methanogenesis) and the epilimnion (dominated by methane lateral transport and/or oxic production), resulting in a vertically segregated lake internal CH₄ cycle.

Evaluating the potential use of a dairy industry residue to induce denitrification in polluted water bodies: A flow-through experiment

Improving the effectiveness and economics of strategies to remediate groundwater nitrate pollution is a matter of concern. In this context, the addition of whey into aquifers could provide a feasible solution to attenuate nitrate contamination by inducing heterotrophic denitrification, while recycling an industry residue. Before its application, the efficacy of the treatment must be studied at laboratory-scale to optimize the application strategy in order to avoid the generation of harmful intermediate compounds. To do this, a flow-through denitrification experiment using whey as organic C source was performed, and different C/N ratios and injection periodicities were tested. The collected samples were analyzed to determine the chemical and isotopic composition of N and C compounds. The results proved that whey could promote denitrification. Nitrate was completely removed when using either a 3.0 or 2.0 C/N ratio. However, daily injection with C/N ratios from 1.25 to 1.5 seemed advantageous, since this strategy decreased nitrate concentration to values below the threshold for water consumption while avoiding nitrite accumulation and whey release with the outflow. The isotopic results confirmed that nitrate attenuation was due to denitrification and that the production of DIC was related to bacterial whey oxidation. Furthermore, the isotopic data suggested that when denitrification was not complete, the outflow could present a mix of denitrified and nondenitrified water. The calculated isotopic fractionation values (ε¹⁵N_NO3/N2 and ε¹⁸O_NO3/N2) might be applied in the future to quantify the efficiency of the bioremediation treatments by whey application at field-scale.

Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures

In many anaerobic environments methane (CH₄) is produced by methanogens, with either H₂/CO₂ or acetate (i.e., the methyl group) as precursors, through what are referred to as hydrogenotrophic and acetoclastic methanogenic pathways respectively. Their relative contribution to total CH₄ production can be quantified by determining the stable carbon isotopic fractionation factors for both pathways as well as the isotopic signatures of CO₂, CH₄, and the methyl group in acetate of the sample. The procedures for measuring carbon isotopic fractionation factors of both methanogenic pathways and isotopic composition of these compounds by isotope ratio mass spectrometry are described in this chapter. The results are very helpful in evaluating the activity of the methanogens involved in each methanogenic pathway as well as those of other biological pathways with different fractionation factors.