Search

Coastal upwelling supplies nutrients supporting primary production while also adding the toxic trace metal mercury (Hg) to the mixed layer of the ocean. This could be a concern for human and environmental health if it results in the enhanced bioaccumulation of monomethylmercury (MMHg). Here, we explore how upwelling influences Hg cycling in the California Current System (CCS) biome through particle scavenging and sea-air exchange. We collected suspended and sinking particle samples from a coastal upwelled water parcel and an offshore non-upwelled water parcel and observed higher total particulate Hg and sinking flux in the upwelling region compared to open ocean. To further investigate the full dynamics of Hg cycling, we modeled Hg inventories and fluxes in the upper ocean under upwelling and non-upwelling scenarios. The model simulations confirmed and quantified that upwelling enhances sinking fluxes of Hg by 41% through elevated primary production. Such an enhanced sinking flux of Hg is biogeochemically important to understand in upwelling regions, as it increases the delivery of Hg to the deep ocean where net conversion to MMHg may take place.

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought-providing a time series of short-term transcriptional response during rewetting.

Methane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4 emissions, but with considerable variation, including instances where salinization increased CH4 flux. We measured microbial community composition, biogeochemistry, and CH4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4 emissions are influenced by salinization. CH4 flux was generally, but not always, positively correlated with CO2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4 depending on site. There was mixed support for negative relationships between CH4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site-specific microbes that may respond differently to low-level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.

Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.

Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.

Wetland methane (CH4) emissions over the Boreal-Arctic region are vulnerable to climate change and linked to climate feedbacks, yet understanding of their long-term dynamics remains uncertain. Here, we upscaled and analysed two decades (2002-2021) of Boreal-Arctic wetland CH4 emissions, representing an unprecedented compilation of eddy covariance and chamber observations. We found a robust increasing trend of CH4 emissions (+8.9%) with strong inter-annual variability. The majority of emission increases occurred in early summer (June and July) and were mainly driven by warming (52.3%) and ecosystem productivity (40.7%). Moreover, a 2 °C temperature anomaly in 2016 led to the highest recorded annual CH4 emissions (22.3 Tg CH4 yr-1) over this region, driven primarily by high emissions over Western Siberian lowlands. However, current-generation models from the Global Carbon Project failed to capture the emission magnitude and trend, and may bias the estimates in future wetland CH4 emission driven by amplified Boreal-Arctic warming and greening.

We present a representation of nitrogen and phosphorus cycling in the Functionally Assembled Terrestrial Ecosystem Simulator, a demographic vegetation model within the Energy Exascale Earth System land model. This representation is modular, and designed to allow testing of multiple hypothetical approaches for carbon-nutrient coupling in plants. Novel model hypotheses introduced in this work include, (a) the controls on plant acquisition of aqueous mineralized nutrients in the soil and (b) fairly straight forward methods of allocating nutrients to specific plant organs and their losses through live plant turnover as well as litter fluxes generated through plant mortality. This combines the new with pre-existing hypotheses (such as nitrogen fixation and soil decomposition) into a system that can accommodate plant-soil dynamics for a large number of size- and functional-type-resolved plant cohorts within a time-since-disturbance-resolved ecosystem. Root uptake of nutrients is governed by fine root biomass, and plants vary in their fine root biomass allocation in order to balance carbon and nutrient limitations to growth. We test the sensitivity of the model to a wide range of parameter variations and structural representations, and in the context of observations at Barro Colorado Island, Panama. A key model prediction is that plants in the high-light-availability canopy positions allocate more carbon to fine roots than plants in low-light understory environments, given the widely different carbon versus nutrient constraints of these two niches within a given ecosystem. This model provides a basis for exploring carbon-nutrient coupling with vegetation demography within Earth system models.

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

Wildfire activity in Arctic and boreal regions is rapidly increasing, with severe consequences for climate and human health. Regional long-term variations in fire frequency and intensity characterize fire regimes. The spatial variability in Arctic-boreal fire regimes and their environmental and anthropogenic drivers, however, remain poorly understood. Here we present a fire tracking system to map the sub-daily evolution of all circumpolar Arctic-boreal fires between 2012 and 2023 using 375 m Visible Infrared Imaging Radiometer Suite active fire detections and the resulting dataset of the ignition time, location, size, duration, spread and intensity of individual fires. We use this dataset to classify the Arctic-boreal biomes into seven distinct pyroregions with unique climatic and geographic environments. We find that these pyroregions exhibit varying responses to environmental drivers, with boreal North America, eastern Siberia and northern tundra regions showing the highest sensitivity to climate and lightning density. In addition, anthropogenic factors play an important role in influencing fire number and size, interacting with other factors. Understanding the spatial variability of fire regimes and its interconnected drivers in the Arctic-boreal domain is important for improving future predictions of fire activity and identifying areas at risk for extreme events.

Changes in substrate quality driven by climate, land use, or other forms of global change may represent a strong selective force on microbial communities. Invasion of new taxa into a community through dispersal, evolution, or recolonization could impact the outcome of this environmental selection. Here, we simulated substrate change with a trait-based model of microbial litter decomposition (DEMENTpy) to assess the legacy effects of past substrate quality and the impact of selection by a new substrate on community decomposition activity. Simulations were run with different levels of invasion, including invasion from communities long-adapted to the new substrate. Legacy effects were evident with substrate change for native communities differing in composition. Protein was the only substrate that exerted a strong enough selective force to affect community composition. Legacy effects disappeared when invaders came from substrates similar to the new substrate. Together, our simulations demonstrate that substrate quality changes associated with global change can lead to legacy effects on substrate degradation. In decomposing plant litter, such legacy effects can occur if substrate inputs shift to higher protein content and if invasion is low.

Riverine export of carbon (C) is an important part of the global C cycle; however, most riverine C budgets focus on individual forms of C and fail to comprehensively measure both organic and inorganic C species in concert. To address this knowledge gap, we conducted high frequency sampling of multiple C forms, including dissolved organic C (DOC), inorganic carbon (as alkalinity), particulate organic C (POC), coarse particulate organic C (CPOC), and invertebrate biomass C across the main run-off season in a predominantly rain-fed watershed in Southeast Alaska. Streamwater concentrations were used to model daily watershed C export from May through October. Concentration and modeled yield data indicated that DOC was the primary form of riverine C export (8708 kg C/km2), except during low flow periods when alkalinity (3125 kg C/km2) was the dominant form of C export. Relative to DOC and alkalinity, export of particulate organic C (POC: 992 kg C/km2; CPOC: 313 kg C/km2) and invertebrates (40 kg C/km2) was small, but these forms of organic matter could disproportionately impact downstream food webs because of their higher quality, assessed via C to nitrogen ratios. These seasonal and flow driven changes to C form and export likely provide subsidies to downstream and nearshore ecosystems such that predicted shifts in regional hydroclimate could substantially impact C transfer and incorporation into aquatic food webs. [ABSTRACT FROM AUTHOR]

Hadal trenches represent the deepest oceanic realm and were once considered to be deprived of life. However, trenches act as important depocenters for organic matter with highly elevated microbial activity. In this forum, we discuss the biogeochemistry of the hadal realm and its microbial communities thriving at extreme hydrostatic pressure. [ABSTRACT FROM AUTHOR]

Dissolved inorganic carbon (DIC) and its stable carbon isotope (δ13C‐DIC) are valuable parameters for studying the aquatic carbon cycle and quantifying ocean anthropogenic carbon accumulation rates. However, the potential of this coupled pair is underexploited as only 15% or less of cruise samples have been analyzed for δ13C‐DIC because the traditional isotope analysis is labor‐intensive and restricted to onshore laboratories. Here, we improved the analytical precision and reported the protocol of an automated, efficient, and high‐precision method for ship‐based DIC and δ13C‐DIC analysis based on cavity ring‐down spectroscopy (CRDS). We also introduced a set of stable in‐house standards to ensure accurate and consistent DIC and δ13C‐DIC measurements, especially on prolonged cruises. With this method, we analyzed over 1600 discrete seawater samples over a 40‐d cruise along the North American eastern ocean margin in summer 2022, representing the first effort to collect a large dataset of δ13C‐DIC onboard of any oceanographic expedition. We evaluated the method's uncertainty, which was 1.2 μmol kg−1 for the DIC concentration and 0.03‰ for the δ13C‐DIC value (1σ). An interlaboratory comparison of onboard DIC concentration analysis revealed an average offset of 2.0 ± 3.8 μmol kg−1 between CRDS and the coulometry‐based results. The cross‐validation of δ13C‐DIC in the deep‐ocean data exhibited a mean difference of only −0.03‰ ± 0.07‰, emphasizing the consistency with historical data. Potential applications in aquatic biogeochemistry are discussed. [ABSTRACT FROM AUTHOR]

Denitrification, anaerobic ammonium oxidation (Anammox), and ferric iron reduction coupled with anaerobic ammonium oxidation (Feammox) are the nitrogen removal pathways in natural ecosystems. In this study, the differences between these three nitrogen removal pathways in a Phragmites australis covered site (LW), artificial grassland covered site (CD), poplar covered site (YD), and topsoil tillage after harvesting reed site (GD) in the Yinchuan Yellow River wetland were investigated using isotope tracing, metagenome, and quantitative polymerase chain reaction (Q-PCR) techniques. No 30N2 accumulation was detected in 15NH4 + addition incubations, indicating that Feammox was weak in all sites, which is consistent with a low abundance of the Feammox functional bacteria Acidimiprobiaceae sp. A6. The denitrification rates were 0.36 (LW), 0.5 (CD), 0.76 (YD) and 0.12 (GD) mg N/kg/day. The Anammox rates were 0.18 (LW) and 0.26 (GD) mg N/kg/day; other sites did not detect Anammox rate. Denitrification was the dominant pathway except for the CD site. The YD site had the highest abundance of denitrification genes, which was consistent with the denitrification rate. [ABSTRACT FROM AUTHOR]

This study aims to characterize how eddies shape the biogeochemistry of the Mozambique Channel using a physical-biogeochemical model that realistically simulates its interannual dynamics. The 20-year-long numerical simulation provides a comprehensive dataset for robust statistical analysis of thousands of mesoscale features using an eddy detection method. We show that all eddy types significantly shape the biogeochemical landscape over the Mozambique Channel, with varying effects across different areas: (1) Sofala Bank and Delagoa Bay: Cyclonic eddies enhance diatom production. (2) Comoros Basin: Cyclonic eddies favor diatom growth via nutrient-rich waters from the NEMC. (3) Central Mozambique Channel: Anticyclonic eddies and rings promote nanophytoplankton through eddy-topography interactions. (4) Southern Mozambique Channel: A mix of eddies from the MC and South Madagascar influences diverse responses due to coastal upwelling. This diversity of processes results in distinct biological signatures of eddy types, leading to diverse ecosystem assemblages with a clear oligotrophic signature. [ABSTRACT FROM AUTHOR]

We introduce an novel approach to compare Earth System Model output using a causality-based approach. The method is based on the PCMCI+ algorithm, which identifies causal relationships between multiple variables. We aim to investigate the causal relationships between atmospheric (North Atlantic Oscillation – NAO), oceanic (gyre strength, stratification, circulation), and biogeochemical variables (nitrate, iron, silicate, net primary production) in the North Atlantic subpolar gyre, a critical region for the global climate system with a well characterised multi-year variability in physical and biogeochemical properties in response to the North Atlantic Oscillation. We test a specific multivariate conceptual scheme, involving causal links between these variables. Applying the PCMCI+ method allows us to differentiate between the influence of vertical mixing and horizontal advection on nutrient concentrations, spring bloom intensity, as well as to highlight model-specific dynamics. The analysis of the causal links suggests a dominant contribution of vertical mixing to peak spring bloom intensity compared to transport. The strength of the links is variable among models. Stratification is identified as an important factor controlling spring bloom NPP in some, but not all, models. Horizontal transport also significantly influences biogeochemistry. However, horizontal transport generally exhibits lower contributions than vertical mixing. Most of the links found are model-specific, hence likely contributing to inter-model spread. The limitations of the method are discussed and directions for future research are suggested. [ABSTRACT FROM AUTHOR]

Copper, a malleable and ductile transition metal, possesses two stable isotopes. These copper isotopic composition data have recently found diverse applications in various fields and disciplines. In geology, copper isotopes serve as tracers that aid in investigating ore formation processes and the mechanisms of copper deposits Likewise, it has emerged as a valuable tracer in polluted environments. In plant biology, copper acts as an essential micronutrient crucial for photosynthesis, respiration, and growth. Copper isotopes contribute to understanding how plants uptake and dispense copper from the soil within their tissues. Similarly, in animals, copper serves as an essential trace element, playing a vital role in growth, white blood cell function, and enzyme activity. In humans, copper acts as an antioxidant, neutralising harmful free radicals within the body. It also helps in maintaining the nervous and immune system. Furthermore, copper isotopes find medical applications, particularly in cancer diagnostics, neurodegenerative diseases, and targeted radiotherapy. However, excessive copper can have detrimental effects in humans such as it can cause liver damage, nausea, and abdominal pain, whilst in plants it can affect the growth of plants, photosynthesis, and membrane permeability. This review emphasises the significance of copper and its isotopes in geology, the environment, and human health. [ABSTRACT FROM AUTHOR]

The parameterization of fluxes associated with representing unresolved dynamics in turbulent flows, especially in the atmosphere and ocean (which have a vast range of scales), remains a challenging task. This is especially true for Earth system models including complex biogeochemistry and requiring very long simulations. The problem of representing the dependence of the mean flux of a passive tracer in terms of the mean has a very long history; in this study, we take a somewhat different approach. We use a formalism showing that the mean flux will be a functional of the mean gradients, a formalism that can be used to calculate the structure of the functional which is non-local in both space and time. Two-dimensional turbulent simulations are used to explore the weight of nearby (in space or time) gradients. We also use stochastic velocities and iterated maps to show that the results are similar. The functional formalism provides an understanding of when non-locality needs to be considered and when a local eddy diffusivity can be a reasonably good approximation. Furthermore, the formalism provides guidance for the development of data-driven parameterizations. [ABSTRACT FROM AUTHOR]

Rapidly changing permafrost landscapes are a potential key terrestrial source of greenhouse gases (GHGs) at a global scale, yet, remain poorly characterized regarding GHG origins and environmental controls on emissions. Subsurface ice wedges, commonly found across many permafrost landscapes, harbor GHG‐rich gas bubbles. Analyzing these bubbles aids comprehension of subzero temperature GHG formation in permafrost. The Batagay megaslump, Earth's largest known thaw slump in northern Yakutia, provides an opportunity to study mixing ratios and isotopic compositions of both GHGs and non‐GHG in ice wedge samples from two stratigraphic units: the Upper Ice Complex (UIC) and the Lower Ice Complex (LIC). The Ar/N2/O2 compositions and bubble shapes indicated that the studied ice wedges were likely formed through dry snow and/or hoarfrost compaction, and microbial activity remained active after ice wedge formation. The high CO2 and CH4 mixing ratios and carbon stable isotope values suggested that CO2 and CH4 primarily originated from microbial sources. N2O showed an "exclusive relation" with CH4—meaning that high N2O is observed only when CH4 is low, and vice versa—and N2O mixing ratios vary at different depths. These findings suggest that GHG formation in ice wedges is not solely controlled by physiochemical conditions, but involves a complex interplay between microbial activity and environmental conditions. Our study contributes to a better understanding of the dynamics involved in GHG formation within degrading permafrost landscapes. [ABSTRACT FROM AUTHOR]

Excessive intake of iodine will do harm to human health. In recent years, high iodine groundwater has become a global concern after high arsenic and high fluorine groundwater. A deep understanding of the environmental factors affecting iodine accumulation in groundwater and the mechanism of migration and transformation is the scientific prerequisite for effective prevention and control of iodine pollution in groundwater. The paper comprehensively investigated the relevant literature on iodine pollution of groundwater and summarized the present spatial distribution and hydrochemical characteristics of iodine-enriched groundwater. Environmental factors and hydrogeological conditions affecting iodine enrichment in aquifers are systematically summarized. An in-depth analysis of the hydrologic geochemistry, physical chemistry, biogeochemistry and human impacts of iodine transport and transformation in the surface environment was conducted, the results and conclusions in the field of high iodine groundwater research are summarized comprehensively and systematically. Stable isotope can be used as a powerful tool to track the sources of hydrochemical components, biogeochemistry processes, recharge sources and flow paths of groundwater in hydrogeological systems, to provide effective research methods and means for the study of high iodine groundwater system, and deepen the understanding of the formation mechanism of high iodine groundwater, the application of isotopic technique in high iodine groundwater is also systematically summarized, which enriches the method and theory of high iodine groundwater research. This paper provides more scientific basis for the prevention and control of groundwater iodine pollution and the management of groundwater resources in water-scarce areas. [ABSTRACT FROM AUTHOR]

Background subsurface vertical mixing rates in the Southern Ocean (SO) are known to vary by an order of magnitude temporally and spatially, due to variability in their generating mechanisms, which include winds and shear instabilities at the surface, and the interaction of tides and lee waves with rough bottom topography. There is great uncertainty in the parameterization of this mixing in coarse resolution Earth System Models (ESM), and in the impact that this has on SO biological productivity on sub decadal timescales. Using a data assimilating biogeochemical ocean model we show that SO phytoplankton productivity is highly sensitive to differences in background diapycnal mixing over short timescales. Changes in the background vertical mixing rates alter key biogeochemical and physical conditions. The greatest changes to the distribution of physical and biogeochemical tracers occur in regions with very strong tracer vertical gradients. A combination of reduced nutrient limitation and reduced light limitation causes a strong increase in SO phytoplankton productivity with higher background mixing. This leads to increased summer carbon export but reduced wintertime export over the mixed layer depth, which could alter the strength of the SO biological carbon pump and atmospheric CO2 ${\text{CO}}_{2}$ concentrations on centennial to millennial timescales. This study demonstrates the importance of accurately representing diapycnal mixing in ESM to predict SO biogeochemical dynamics and their broader climatic implications. Plain Language Summary: The vertical mixing of water beneath the surface of the Southern Ocean varies significantly over time and space due to factors such as winds, tides, and the interaction of waves with the ocean floor's topography. This is hard to represent in ocean climate models, which are essential for understanding the ocean's role in global climate systems. In this work, we investigate how this mixing affects the productivity of phytoplankton, tiny plants crucial to the ocean's ecosystem. We demonstrate that even small changes in background mixing rates can profoundly impact phytoplankton productivity in the Southern Ocean over short time periods. Alterations in mixing rates influence key environmental conditions, particularly nutrient and light availability, which are vital for phytoplankton growth. This heightened productivity enhances the ocean's ability to absorb carbon dioxide from the atmosphere, potentially affecting long‐term atmospheric CO2 ${\text{CO}}_{2}$ levels. Key Points: The rate of background vertical mixing is a key control of Southern Ocean phytoplankton productivity over annual timescalesIncreased mixing enhances the vertical flux of nutrients to the surface, increasing productivity and altering phytoplankton assemblagesMixing rates alter the physical and biogeochemical environment, reducing the carbon exported to below the winter mixed layer depth [ABSTRACT FROM AUTHOR]

Superoxide is a reactive oxygen species that is influential in the redox chemistry of a wide range of biological processes and environmental cycles. Using a novel in situ sensor we report the first water column profiles of superoxide in the Baltic Sea, at concentrations higher than previously observed in other oceans. Our data revealed consistent peaks of superoxide (2.0–15.1 nM) in dark waters just below the mixed layer. The oxic waters, low metal concentrations, and lack of sunlight imply that the peak is likely of biological origin. Several profiles displayed a concomitant dip in dissolved oxygen mirroring this superoxide peak, strongly suggesting a link between the two features. The magnitude and distribution of superoxide observed warrants re‐evaluation of the most relevant sources and controls of superoxide in seawater. Locally, these high concentrations of superoxide may create environments conducive to reactions with trace metals and organic matter and present an overlooked sink of oxygen in the Baltic Sea. Plain Language Summary: The combination of unusual inflow activity and topographic conditions with strong anthropogenic influence in the Baltic Sea, offer a unique environment to study redox chemistry. To gain further insight into the biogeochemical cycles in this area we made the first measurements of superoxide, a reactive oxygen species that plays significant roles in organismal health, as well as the chemistry of metals and carbon in seawater. We made direct measurements of superoxide in seawater, leading to continuous profiles between 2 and 80 m at 7 different locations in the Baltic Sea. Our results revealed the presence of widespread superoxide maxima that consistently appeared in dark waters at depths between 23 and 35 m. In some instances, the superoxide peaks are mirrored by dips in oxygen concentrations. This work demonstrates that light‐independent processes were the dominant source of superoxide in the Baltic Sea in September, and point to an association between heterotrophic activity, oxygen loss, and superoxide production. The high levels of superoxide observed in this study suggest that a reevaluation of the abundances of this compound in seawater is necessary, and underline the advantages of in situ techniques for capturing total superoxide concentrations. Key Points: Superoxide maxima consistently appear in dark waters below the mixed layerCorresponding dips in oxygen at depths of superoxide maxima suggest link between heterotrophic respiration and superoxide production [ABSTRACT FROM AUTHOR]

Much of the Antarctic coast is covered by seasonal landfast sea ice (fast ice), which serves as an important habitat for ice algae. Fast‐ice algae provide a key early season food source for pelagic and benthic food webs, and contribute to biogeochemical cycling in Antarctic coastal ecosystems. Summertime fast ice is undergoing a decline, leading to more seasonal fast ice with unknown impacts on interconnected Earth system processes. Our understanding of the spatiotemporal variability of Antarctic fast ice, and its impact on polar ecosystems is currently limited. Evaluating the overall productivity of fast‐ice algae has historically been hampered by limitations in observations and models. By linking new fast‐ice extent maps with a one‐dimensional sea‐ice biogeochemical model, we provide the first estimate of the spatio‐seasonal variability of Antarctic fast‐ice algal gross primary production (GPP) and its annual primary production on a circum‐Antarctic scale. Experiments conducted for the 2005–2006 season provide a mean fast ice‐algal production estimate of 2.8 Tg C/y. This estimate represents about 12% of overall Southern Ocean sea‐ice algae production (estimated in a previous study), with the mean fast‐ice algal production per area being 3.3 times higher than that of pack ice. Our Antarctic fast‐ice GPP estimates are probably underestimated in the Ross Sea and Weddell Sea sectors because the sub‐ice platelet layer habitats and their high biomass are not considered. Plain Language Summary: Antarctic landfast sea ice (fast ice) is sea ice fastened to the coastline of Antarctica and provides a prolific habitat for microalgae. These ice algae are ecologically important because their production takes place early in the season when water column primary production is low. By combining a new satellite data set and a biogeochemical sea‐ice algal growth model, this study provides the first estimate of circum‐Antarctic fast‐ice algal production: 2.8 million tonnes of carbon per year, which is about 12% of the total Antarctic sea‐ice algal production. The mean algal primary production per area in fast ice is 3.3 times higher than that of pack ice. Key Points: First estimate of circum‐Antarctic landfast sea‐ice annual gross primary production, with a focus on the 2005–2006 seasonMean landfast sea‐ice algal primary production is 2.8 TgC/y, representing 12% (range 5%–19%) of total Southern Ocean ice algal productivityMean modeled landfast sea‐ice algal production per area is 3.3 times higher than that of pack ice [ABSTRACT FROM AUTHOR]

Riverine nutrient export is an important process in marine coastal biogeochemistry and also impacts global marine biology. The nitrogen cycle is a key player here. Internal feedbacks are shown to regulate not only nitrogen distribution, but also primary production and thereby oxygen concentrations. Phosphorus is another essential nutrient and interacts with the nitrogen cycle via different feedback mechanisms. After a previous study of the marine nitrogen cycle response to riverine nitrogen supply, here we include phosphorus from river export with different phosphorus burial scenarios and study the impact of phosphorus alone and in combination with nitrogen in a global 3D ocean biogeochemistry model. Again, we analyse the effects on near-coastal and open-ocean biogeochemistry. We find that riverine export of bioavailable phosphorus alone or in conjunction with nitrogen affects marine biology on millennial timescales more than riverine nitrogen alone. Biogeochemical feedbacks in the marine nitrogen cycle are strongly influenced by additional phosphorus. Where bioavailable phosphorus increases with river input, nitrogen concentration increases as well, except for in regions with diminishing oxygen concentrations. High phosphorus burial rates decrease biological production significantly. Globally, the addition of riverine phosphorus in the modelled ocean leads to elevated primary production rates in the coastal and open oceans. [ABSTRACT FROM AUTHOR]

Marginal seas are usually fulfilled with strongly varying mesoscale eddies (MEs), which evolutions plays vital roles in regulating global oceanic energy equilibrium, triggering subemesoscale processes with strong vertical velocity, and inducing high biogeochemistry transport. But the temporal evolutions of MEs and submesoscale processes with several kilometers' resolutions are difficult to be measured by traditional observations with passive working mode. The automatic underwater gliders (AUGs) and vehicles (AUVs) positively observe oceanic motion, and could provide us spatiotemporal synchronization information for strongly varying MEs. Here, we present a 9-year high dense dataset of AUVs/AUGs observations in 2014–2022 in the South China Sea (SCS) can be downloaded from https://doi.org/10.57760/sciencedb.11996 (Qiu et al., 2024b). Totally, 9 AUG and 2 AUV cruise experiments were conducted, and 83 AUGs (2 AUVs) equipment were deployed with zonal and temporal resolutions of < 7 km and <6 hour. It covers the area of eddy's birth, propagation, and dissipation, presenting us the most complete data to investigate the evolution of MEs at different life stages. 40 % of them reach resolutions < 1 km and < 1 hour, which provides us the dynamic characteristics of submesoscale instabilities across and along front at the eddy edge. This dataset has potential in improving the forecast accuracy in physical and biogeochemistry numerical model. Much more aggressive field investigation programs will be promoted by the NSFC in future. [ABSTRACT FROM AUTHOR]

Global declines in animal populations suggest global causes. Herbivores are uniquely vulnerable to declines in the nutrient density of the plants they consume. CO 2 pollution is a global agent of nutrient dilution: the impoverishment of plant tissue, bite for bite, of the elements essential for herbivore survival. As plants assimilate higher levels of CO 2 , nutrient dilution can create flammable 'green deserts' of low-quality food for herbivores already limited by elements from nitrogen to sodium to zinc. We posit that nutrient dilution is a key driver – rich in testable predictions – of global declines in herbivore abundance. Its impact should be highest in productive and/or nutrient-poor ecosystems like tropical forests and the open oceans. It is reversed by fertilization. It acts regardless of habitat size or pesticide use. It thus complements these and other agents of herbivore decline. Nutrient dilution (ND) – the decrease in the concentration of nutritional elements in plant tissue – arises from an increase in the mass of carbohydrates and/or a decrease in the 20+ essential elements. Increasing CO 2 levels and its promotion of biomass are linked to nutrient dilution. We build a case for nutrient dilution as a key driver in global declines in herbivore abundance. Herbivores must build element-rich animal tissue from nutrient-poor plant tissue, and their abundance commonly increases with fertilization of both macro- and micronutrients. We predict the global impacts of nutrient dilution will be magnified in some of Earth's most biodiverse, highly productive, and/or nutrient-poor ecosystems and should favor specific traits of herbivores, including sap-feeding and ruminant microbiomes. [ABSTRACT FROM AUTHOR]

Humans have profoundly altered phosphorus (P) cycling across scales. Agriculturally driven changes (e.g., excessive P‐fertilization and manure addition), in particular, have resulted in pronounced P accumulations in soils, often known as "soil legacy P." These legacy P reserves serve as persistent and long‐term nonpoint sources, inducing downstream eutrophication and ecosystem services degradation. While there is considerable scientific and policy interest in legacy P, its fine‐scale spatial heterogeneity, underlying drivers, and scales of variance remain unclear. Here we present an extensive field sampling (150‐m interval grid) and analysis of 1438 surface soils (0–15 cm) in 2020 for two typical subtropical grassland types managed for livestock production: Intensively managed (IM) and Semi‐natural (SN) pastures. We ask the following questions: (1) What is the spatial variability, and are there hotspots of soil legacy P? (2) Does soil legacy P vary primarily within pastures, among pastures, or between pasture types? (3) How does soil legacy P relate to pasture management intensity, soil and geographic characteristics? and (4) What is the relationship between soil legacy P and aboveground plant tissue P concentration? Our results showed that three measurements of soil legacy P (total P, Mehlich‐1, and Mehlich‐3 extractable P representing labile P pools) varied substantially across the landscape. Spatial autoregressive models revealed that soil organic matter, pH, available Fe and Al, elevation, and pasture management intensity were crucial predictors for spatial patterns of soil P, although models were more reliable for predicting total P (68.9%) than labile P. Our analysis further demonstrated that total variance in soil legacy P was greater in IM than SN pastures, and intensified pasture management rescaled spatial patterns of soil legacy P. In particular, after controlling for sample size, soil P was extremely variable at small scales, with variance diminished as spatial scale increased. Our results suggest that broad pasture‐ or farm‐level best management practices may be limited and less efficient, especially for more IM pastures. Rather, management to curtail soil legacy P and mitigate P loading and losses should be implemented at fine scales designed to target spatially distinct P hotspots across the landscape. [ABSTRACT FROM AUTHOR]

Long-term metal remediation in wetland treatment systems (WTSs) involves facilitating dissimilatory sulfate reduction to produce sulfide and mineralize metals in deep sediments. We evaluated seasonal sulfur cycling in two constructed wetlands (Maintained WTS constructed in 2007, and the Unmaintained WTS constructed in 2000) on the Savannah River Site in Aiken, South Carolina, USA. Significant interactions in sulfide concentration were observed between sediment depth, season, and wetland (F = 4.64, df = 11, P = 3.28 × 10 − 5). In the Maintained WTS, dissimilatory sulfate reduction dominated the surface sediments during the warm season (0–2 cm depth, t=-2.66, P = 9.70 × 10 − 3), unlike the Unmaintained system. Sulfate concentrations in pore waters increased in the warm season (F = 7.84, df = 1, P = 6.50 × 10 − 3), contrary to expectations. Sulfur limitation in the Unmaintained WTS during the warm season correlated with increased sulfur assimilation in giant bulrush. Lower sulfide concentrations in surface sediments of the Unmaintained WTS illustrated aging effects. The Maintained WTS shows potential for managing erosion, pH reduction, and sulfur limitation observed in the older Unmaintained WTS. [ABSTRACT FROM AUTHOR]

Climate change and anthropogenic impacts drastically affect the biogeochemical regime of the Black Sea, which contains the largest volume of sulphidic water in the world. The Sea's oxygen inventory depends on vertical mixing that transports dissolved oxygen (DO) from the upper euphotic layer to deeper layers and on dissolved oxygen consumption for the oxidation of organic matter (OM) and reduced species of S, Fe, and Mn. Here we use a vertical one-dimensional transport model, 2DBP, forced by Copernicus data, that was coupled with the FABM-family N-P-Si-C-O-S-Mn-Fe Bottom RedOx Model BROM. The research objective of this study was to analyze the oxygen budget in the upper 350 m of the Sea and demonstrate the role of the parameterization of the acceleration of the sinking of particles covered by precipitated Mn(IV). The analysis of the oxygen budget revealed distinct patterns in oxygen consumption within different depths. In the oxic zone, the primary sink for DO is the mineralization of organic matter, whereas in the suboxic zone, dissolved Mn(II) oxidation becomes the predominant sink. The produced Mn(IV) sinks down and reacts with hydrogen sulphide several meters below, making possible the existence of the suboxic layer without detectable concentrations of DO and H2S. [ABSTRACT FROM AUTHOR]

This study evaluates the ability of Earth System Models (ESMs) from the Coupled Model Intercomparison Project Phase 6 (CMIP6) to simulate biogeochemical variables in the southern South China Sea (SCS). The analysis focuses on key biogeochemical variables: chlorophyll, phytoplankton, nitrate, and oxygen based on their availability in the selected models at annual and seasonal scales. The models' performance is assessed against Copernicus Marine Environment Monitoring Service (CMEMS) data using statistical metrics such as the Taylor diagram and Taylor skill score. The results show that the models generally capture the observed spatial patterns of surface biogeochemical variables. However, they exhibit varying degrees of overestimation or underestimation in their quantitative measures. Specifically, their mean bias error ranges from -0.02 to +2.5 mg m -3 for chlorophyll, -0.5 to +1 mmol m -3 for phytoplankton, -0.1 to +1.3 mmol m -3 for nitrate, and -2 to +2.5 mmol m -3 for oxygen. The performance of the models is also influenced by the season, with some models showing better performance during June, July, and August than December, January, and February. Overall, the top five best-performing models for biogeochemical variables are MIROC-ES2H, GFDL-ESM4, CanESM5-CanOE, MPI-ESM1-2-LR, and NorESM2-LM. The findings of this study have implications for researchers and end users of the datasets, providing guidance for model improvement and understanding the impacts of climate change on the southern SCS ecosystem. [ABSTRACT FROM AUTHOR]

Abstract Climate change is causing widespread impacts on seawater pH through ocean acidification (OA). Kelp forests, in some locations can buffer the effects of OA through photosynthesis. However, the factors influencing this variation remain poorly understood. To address this gap, we conducted a literature review and field deployments of pH and dissolved oxygen (DO) loggers within four habitats: intact kelp forest, moderate kelp cover, sparse kelp cover and barrens at one site in Port Phillip Bay, a wind-wave dominated coastal embayment in Victoria, Australia. Additionally, a wave logger was placed directly in front of the intact kelp forest and barrens habitats. Most studies reported that kelp increased seawater pH and DO during the day, compared to controls without kelp. This effect was more pronounced in densely populated forests, particularly in shallow, sheltered conditions. Our field study was broadly consistent with these observations, with intact kelp habitat having higher seawater pH than habitats with less kelp or barrens and higher seawater DO compared to barrens, particularly in the afternoon and during calmer wave conditions. Although kelp forests can provide local refuges to biota from OA, the benefits are variable through time and may be reduced by declines in kelp density and increased wave exposure.

Abstract Nutrient limitations play a key regulatory role in plant growth, thereby affecting ecosystem productivity and carbon uptake. Experimental observations identifying the most limiting nutrients are lacking, particularly in Afrotropical forests. We conducted an ecosystem-scale, full factorial nitrogen (N)-phosphorus (P)-potassium (K) addition experiment consisting 32 40 × 40 m plots (eight treatments × four replicates) in Uganda to investigate which (if any) nutrient limits fine root growth. After two years of observations, added N rapidly decreased fine root biomass by up to 36% in the first and second years of the experiment. Added K decreased fine root biomass by 27% and fine root production by 30% in the second year. These rapid reductions in fine root growth highlight a scaled-back carbon investment in the costly maintenance of large fine root network as N and K limitations become alleviated. No fine root growth response to P addition was observed. Fine root turnover rate was not significantly affected by nutrient additions but tended to be higher in N added than non-N added treatments. These results suggest that N and K availability may restrict the ecosystem’s capacity for CO2 assimilation, with implications for ecosystem productivity and resilience to climate change.

Deception Island (DI) is an active volcanic caldera in the South Shetland Islands, Antarctica, with an inner bay, Port Foster, formed by an ancient eruption. The bay's seafloor hydrofracture system contains hydrothermal seeps and submarine vents, which are a source of trace metals (TMs) like Fe, Ni, Co, V, and greenhouse gases (GHGs) such as CO2 and CH4. This study presents measurements of TMs and GHGs in Port Foster's surface waters during January-February 2021 to characterize their spatial distribution. TMs concentrations in the northeastern region of the bay, particularly V (74 nM), Fe (361 nM), Co (3.9 nM) and Ni (17.2 nM), were generally higher than in the Southern Ocean, likely due to hydrothermal activity. As some TMs such as Fe are scarce in the SO and limit primary productivity, inputs of these nutrients from DI into surrounding waters may also regionally promote increased primary productivity. Higher surface temperature (ST), elevated partial pressure of CO2 (pCO2), and lower salinity were found near submarine fumaroles, with ST positively correlated with pCO2 and negatively with salinity. Although hydrothermal sites showed localized CO2 outgassing, the bay overall acted as a CO2 sink, with a median flux of -2.78 mol m-2 yr-1 with an interquartile range (IQR) of 3.84 mol m-2 yr-1. CH4 highest concentration levels were found in the southeastern sector. The median concentration was 8.9 nM with an IQR of 1.9 nM, making Port Foster a regional net CH4 source with a median flux of 9.7 μmol m-2 d-1 and an IQR of 3.4 μmol m-2 d-1. Ultimately, the analysis of spatial patterns of the measured variables suggested that fumaroles of DI may be playing a significant role in the alteration of regional seawater biogeochemistry. [ABSTRACT FROM AUTHOR]

Introduction: Cold-water coral reefs form complex benthic habitats, supporting thousands of species. The broadscale environmental tolerances of reef-forming species such as Lophelia pertusa are well studied, but small-scale differences between different reef settings have received little attention so far. The controlling factors of thriving cold-water coral reefs and how these habitats differ in terms of framework extent, coral colony morphology, and associated fauna could reveal how these benthic ecosystems formand expand. Information on the natural range of environmental fluctuations could provide a better understanding of the resilience of such ecosystems towards environmental changes. Our study aimed to elaborate small-scale forces on local hydrodynamics and oceanographic parameters at two geographically close but contrasting reef sites in mid-Norway. Methods: We investigated natural fluctuations and the seasonal variability of environmental conditions of an inshore and an offshore Lophelia-dominated reef over an annual cycle by time series monitoring of physical properties by benthic landers and water sampling for biogeochemical variables using CTD casts. Results and discussion: The flow fields at the extensive reef on the offshore Sula Ridge and a bank reef at Nord-Leksa in a fjord-system differed regarding both short-term and seasonal levels. The inshore flow field was strong and tidally driven, whereas the offshore flow field was slower with large seasonal variability. The local flow regimes and the seasonal atmospheric forcing could explain the observed seasonality of the hydrographic variables and the observed inter-annual variability in biogeochemical variables. Comparison with a flow model showed that the natural short-term and seasonal variability are driven by small-scale forcing that is not represented in model analyses. These results suggest that local hydrodynamics together with sea-floor topography control the reef extent and the morphology of cold-water coral colonies. [ABSTRACT FROM AUTHOR]

This paper is an attempt to generalize the nitrogen isotope information of the molecules that make up the cell from our point of view. Nitrogen in the cell exists as 20 proteinaceous amino acids, nucleobases, hemes, chlorophylls, and others, and their composition is similar among organisms. Based on a physiologically simple autonomous system that maintains a balance between inputs and outputs, it is theoretically predicted that 15N is distributed to each cellular compound with a certain regularity, and thus a specific relationship in nitrogen isotopic ratios among compounds. Previous studies essentially confirm this. The nitrogen isotopic ratio of compound i constituting the cell can be generalized as δ15Ni = δ15Nplant + Δi (TP − 1) + γi, where TP represents the trophic position, and Δi and γi are the trophic discrimination factor and the intracellular 15N distribution of compound i, respectively. Knowing reliable values of Δi and γi will help us to better understand nitrogen dynamics in the biosphere and advance our understanding of the picture of the Earth's environment through biogeochemistry. [ABSTRACT FROM AUTHOR]

The paper reports the detailed studies of drilling cores from peat deposits of the Vydrino bog with a thickness of 4.4 m and an age of 13 100 cal. years. The peat is composed of fen, transitional, and raised types. The early-diagenetic transformations of peat sediments are considered, and the distribution of elements, the formation of authigenic minerals, and the chemical composition of bog waters are studied. The destruction of organic matter begins from the upper intervals of peat at the early diagenetics stage. Pyrograms do not have clearly defined high-temperature peaks, "rudiments" of the macromolecular structure of kerogen, which indicates a low degree of transformation of peat organic matter. The high abundance of organotrophic, ammonifying, nitrifying, and phosphate-mobilizing microorganisms, and the low abundance of Fe- and Mn-oxidizing microorganisms, and sulfate-reducing bacteria are revealed. The presence of organotrophic microorganisms throughout the section indicates that the biogeochemical processes of the carbon cycle span the entire peat sequence. The low S(II) content indicates the low intensity of sulfate reduction. The fen peat is characterized by the high contents of Si, Al, Fe, Ca, Sr, Ba, Zr, La and anomalous contents of Cu, Zn, which is caused by the peatland formation under conditions of rich mineral nutrition. The ash part of the transitional peat demonstrates a decrease in the contents of Si, Fe, Sr, Br, K Si, Ca, Ba, Cu, Zn and La, which reflects the gradual weakening of the connection of the peat deposit with the underlying rocks. The near-surface horizon of raised peat is characterized by an increase in the contents of K, Mn, Zn, Hg, Pb and As, which is accompanied by an increase in atmospheric dust and anthropogenic impact on the bog ecosystem in the 20th and 21st centuries. The bog waters of the fen peat are characterized by the high contents of the main ions, Al, Fe, Mn, Sr, while the transitional peat shows a decrease in DOC, , , Al, Fe, Ni, Ca, Mg. The oligotrophic stage peat deposit layer is characterized by the development of Fe oxides and hydroxides, the presence of vivianite is noted for transitional peats, and the eutrophic stage layer includes rhodochrosite and sulfides of Fe, Cu, and Zn. [ABSTRACT FROM AUTHOR]

Animals interact with nutrient cycles by consuming and depositing nutrients, interactions studied separately in nutritional ecology and zoogeochemistry. Recent theoretical work bridges these disciplines, highlighting that animal‐driven nutrient recycling could be crucial in helping animals meet their nutritional needs. When animals exhibit site fidelity, they consistently deposit nutrients, potentially improving vegetation quality. We investigated this potential feedback by analysing changes in forage nitrogen stocks following simulated caribou calving. We found that forage nitrogen stocks increased after 2 weeks and remained elevated after 1 year, a change due to increased forage quality, not quantity. We also developed a nutrient budget within calving grounds, demonstrating that natal fluid and calf carcasses contribute substantial nitrogen subsidies. We, thus, highlight a positive zoogeochemical feedback whereby nutrients deposited during calving become bioavailable during lactation and provide evidence that site fidelity creates a biogeochemical boomerang in which animals deposit nutrients that can be reused later. [ABSTRACT FROM AUTHOR]

Mapping spatial variation in stable isotope values (isoscapes) of primary producers and consumers can provide insight into regional patterns of biogeochemistry and be used to trace the movements of mobile animals. Here we present carbon (δ13C) and nitrogen (δ15N) isoscapes for an expansive region of the continental United States (Mid Atlantic Bight to the NW Gulf of Mexico) derived from inshore lizardfish (Synodus foetens) and explore temporal stability and environmental drivers of observed isotopic variation. We observed significant spatial variation in lizardfish δ13C and δ15N values throughout much of the Atlantic and Gulf coasts, reflecting local biogeochemistry regimes. Extensive sampling throughout the northern Gulf of Mexico (NGOM) revealed positive relationships between lizardfish δ13C values and bottom temperature, likely reflecting lower carbon isotope discrimination between CO2 and phytoplankton in highly productive, warm, inshore environments. Conversely, δ15N values were not well explained by environmental parameters, but appeared higher in nearshore environments of the NGOM, which are heavily influenced by nitrogenous run-off from land. An isotopically unique region of high δ13C values and low δ15N values were observed for lizardfish sampled in the Eastern NGOM off the southwest coast of Florida, reflecting a potential influence of seagrass and/or macroalgal productivity supporting the base of the food web. Overall, these findings underscore the utility of benthic lizardfish stable isotopes for inferring local patterns of ocean biogeochemistry throughout expansive ocean environments. In application, these data can be used to define migratory histories of mobile taxa and support contemporary critical habitat assessments. [ABSTRACT FROM AUTHOR]

High abundances of gelatinous zooplankton (GZ) can significantly impact marine ecosystem by acting as both sink and source of organic matter (OM) and nutrients. The decay of GZ bloom can introduce significant amount of OM to the ocean interior, with its variability influenced by GZ life traits and environmental factors, impacting microbial communities vital to marine biogeochemical cycles. The invasive ctenophores Mnemiopsis leidyi has formed massive blooms in the northern Adriatic Sea since 2016. However, the variability in the chemical composition and egg production of blooming populations, as well as the role of environmental factors in governing this variability, remains largely unknown. Our analysis of biometry, chemical composition, and fecundity of M. leidyi sampled in the Gulf of Trieste in 2021 revealed stable carbon and nitrogen content throughout bloom development, with no significant correlation with seawater temperature, salinity, oxygen, and chlorophyll a concentration. Although the studied population exhibited homogeneity in terms of biometry and chemical composition, the number of produced eggs varied substantially, showing no clear correlation with environmental variables and being somewhat lower than previously reported for the study area and other Mediterranean areas. We observed a positive correlation between the wet weight of individuals and the percentage of hatched eggs, as well as a significant positive correlation between the percentage of hatched eggs and ambient seawater temperature. Additionally, we noted that the speed of hatching decreased with decreasing seawater temperature in autumn, corresponding to the end of M. leidyi bloom. [ABSTRACT FROM AUTHOR]

Human interactions have led to the emergence of a higher complexity of urban metabolic networks; hence, traditional natural- or agriculture-oriented biogeochemical models might not be transferred well to urban environments. Increasingly serious environmental problems require the development of new concepts and models. Here, we propose a basic paradigm for urban–rural complex nitrogen (N) metabolic network reconstruction (NMNR) by introducing new concepts and methodologies from systems biology at the molecular scale, analyzing both local and global structural properties and exploring optimization and regulation methods. Using the Great Hangzhou Areas System (GHA) as a case study, we revealed that pathway fluxes follow a power law distribution, which indicates that human-dominated pathways constitute the principal part of the functions of the whole network. However, only 1.16% of the effective cycling pathways and an average hamming distance of only 5.23 between the main pathways indicate that the network lacks diverse pathways and feedback loops, which could lead to low robustness. Furthermore, more than half of the N fluxes did not pass through core metabolism, causing waste and pollution. We also provided strategies to design network structures and regulate system function: improving robustness and reducing pollution by referring to the characteristics of biochemical metabolic networks (e.g., the bow-tie structure). This method can be used to replace the trial-and-error method in system regulation and design. By decomposing the GHA N metabolic network into 4398 metabolic pathways and the corresponding fluxes with a power law distribution, NMNR helps us quantify the vulnerability in the current urban nitrogen cycle. The basic ideas and methodology in NMNR can be applied to coupled human and natural systems to advance global sustainable development studies, and they can also extend systems biology from the molecule to complex ecosystems and lead to the development of multi-scale unified theory in systems biology. [ABSTRACT FROM AUTHOR]

The main purpose of this study is to set up a biogeochemistry model for the Ria de Aveiro ecosystem and evaluate the relative importance of the main parameters and the processes occurring at the interface between the water column and the upper layer of the bottom sediment. It addresses a gap in modeling the interactions between the biogeochemical status of the water column and the upper sediment layer in the Ria de Aveiro lagoon ecosystem. Traditional modeling studies treated the bottom sediment as a rigid boundary, ignoring significant biogeochemical interactions at the interface between the water column and the upper layer of the bottom sediment. Therefore, the model integrates, besides the main biogeochemical processes within the water column, those occurring at the upper benthic layer, focusing on nitrogen (N) and phosphorus (P) cycles. This approach aims to enhance the accuracy of model predictions and understanding of the Ria de Aveiro lagoon's biogeochemical dynamics. The study will be focused on the following coupled state variables: TN/IN and TP/IP, for total and inorganic nitrogen (N) and total and inorganic phosphorus (P), respectively, where total stands for the sum of organic and inorganic components of those elements. The model was set up and validated for some water quality stations of the Ria de Aveiro. Analysis has identified key parameters influencing TN and TP, such as nitrification, denitrification rates, and oxygen penetration. TN was found sensitive to nitrate and ammonium diffusion coefficients, while TP was influenced by iron–phosphate interactions and phosphorus mineralization. Concerning the model validation, the results demonstrated that the RMSE and MAPE values for the main variables fall within an acceptable range, given the uncertainty related to data. The model was applied to assess the impact of the following physical forcing: river flow, water temperature, and salinity on N and P status of the water column. The results clearly demonstrate that bottom layer and water column interactions play an important role in the N and P status of the water column and contribute to the N and P concentration changes of the water. The influence of river flows alone led to contrasting behaviors among the lagoon stations, with significant increases in TP levels, which may be attributed to sediment release from the sediment layer. Nevertheless, the combination of high river flows and elevated nutrient levels at the river boundaries has led to significantly increased nitrogen (N) and phosphorus (P) levels, underscoring the influence of river flow on the interaction between bottom layer sediment and the water column. High water temperatures typically lead to an increase in total phosphorus (TP) levels, indicating a possible release from the sediment layer. Meanwhile, TN levels remained stable. Salinity changes had a minor impact compared to river flow and temperature. The study emphasizes the importance of understanding interactions between the water column and sediment, particularly in shallow intertidal areas. Overall, the inclusion of biogeochemical interactions between the benthic and pelagic layers represents progress in ecosystem modeling of the Ria de Aveiro. [ABSTRACT FROM AUTHOR]

Data assimilation (DA) in marine and freshwater systems combines numerical models and observations to deliver the best possible characterization of a waterbody's physical and biogeochemical state. DA underpins the widely used 3D ocean state reanalyses and forecasts produced operationally by, e.g., the Copernicus Marine Service. The use of DA in natural waters is an active field of research, but testing new developments in realistic setting can be challenging as operational DA systems are demanding in terms of computational resources and technical skill. There is a need for test beds that are sufficiently realistic but also efficient to run and easy to operate. Here, we present the Ensemble and Assimilation Tool (EAT), a flexible and extensible software package that enables data assimilation of physical and biogeochemical variables in a one-dimensional water column. EAT builds on established open-source components for hydrodynamics (GOTM), biogeochemistry (FABM), and data assimilation (PDAF). It is easy to install and operate and is flexible through support for user-written plugins. EAT is well suited to explore and advance the state of the art in DA in natural waters thanks to its support for (1) strongly and weakly coupled data assimilation, (2) observations describing any prognostic and diagnostic element of the physical–biogeochemical model, and (3) the estimation of biogeochemical parameters. Its range of capabilities is demonstrated with three applications: ensemble-based coupled physical–biogeochemical assimilation, the use of variational methods (3D-Var) to assimilate sea surface chlorophyll, and the estimation of biogeochemical parameters. [ABSTRACT FROM AUTHOR]

The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15N- and 13C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry. The biogeochemical roles of the plastisphere regulating N cycling are elusive. This study reveals the plastisphere as an emerging nitrifying niche, featured by distinct shifts in nitrifiers and potential substrate exchanges compared to seawater. [ABSTRACT FROM AUTHOR]

Chemosynthesis fixes carbon using energy acquired from reduced chemical compounds and is a primordial process that occurs ubiquitously throughout contemporary marine ecosystems. Diverse and abundant marine bacteria and archaea gain energy from inorganic compounds such as ammonia, nitrite, sulfide, hydrogen, carbon monoxide, and iron using specific enzymes. Chemosynthesis is enriched relative to photosynthesis in aphotic waters, including at increased ocean depths, and may show diel, seasonal, and latitudinal variations. Some regions of the ocean are primarily driven by chemosynthesis, ranging from highly productive geologically fuelled hydrothermal vents to oligotrophic below-shelf waters. Dark carbon fixation through chemosynthetic processes may play a quantitatively significant role in oceanic primary production, though carbon budgets remain poorly resolved. Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times. [ABSTRACT FROM AUTHOR]

Methane (CH4) emissions from wetland ecosystems are controlled by redox conditions in the soil, which are currently underrepresented in Earth system models. Plant-mediated radial oxygen loss (ROL) can increase soil O2 availability, affect local redox conditions, and cause heterogeneous distribution of redox-sensitive chemical species at the root scale, which would affect CH4 emissions integrated over larger scales. In this study, we used a subsurface geochemical simulator (PFLOTRAN) to quantify the effects of incorporating either spatially homogeneous ROL or more complex heterogeneous ROL on model predictions of porewater solute concentration depth profiles (dissolved organic carbon, methane, sulfate, sulfide) and column integrated CH4 fluxes for a tidal coastal wetland. From the heterogeneous ROL simulation, we obtained 18% higher column averaged CH4 concentration at the rooting zone but 5% lower total CH4 flux compared to simulations of the homogeneous ROL or without ROL. This difference is because lower CH4 concentrations occurred in the same rhizosphere volume that was directly connected with plant-mediated transport of CH4 from the rooting zone to the atmosphere. Sensitivity analysis indicated that the impacts of heterogeneous ROL on model predictions of porewater oxygen and sulfide concentrations will be more important under conditions of higher ROL fluxes or more heterogeneous root distribution (lower root densities). Despite the small impact on predicted CH4 emissions, the simulated ROL drastically reduced porewater concentrations of sulfide, an effective phytotoxin, indicating that incorporating ROL combined with sulfur cycling into ecosystem models could potentially improve predictions of plant productivity in coastal wetland ecosystems. [ABSTRACT FROM AUTHOR]

Community‐type conversions, such as replacement of perennials by exotic annual grasses in semiarid desert communities, are occurring due to plant invasions that often create positive plant–soil feedbacks, which favor invaders and make restoration of native perennials difficult. Exotic annual grass control measures, such as pre‐emergent herbicides, can also alter soil ecosystems directly or indirectly (i.e. via the plant community), yet there are few studies on the topic in natural, non‐cropped landscapes. We asked how spray treatments applied to soil post‐fire with the intention of inhibiting invasive annual grasses (such as Bromus tectorum L.) and releasing existing native perennial grasses affected soil resources, a microbial process, and invertebrates in three climatically varied sagebrush steppe sites. Spray treatments included chemical herbicides (imazapic and rimsulfuron) that strongly affected plant communities and a bioherbicide (Pseudomonas fluorescens strain D7) that did not. Chemical herbicides increased soil mineral nitrogen in proportion to their negative effects on plant cover for 2 years after treatments in all sites and increased soil water and net N mineralization (measured at one site) but did not affect total carbon, nitrogen, or organic matter. Invertebrate responses to herbicides varied by site, and invertebrates increased with chemical herbicides at the highest, wettest site. We show that herbicide treatments can exacerbate pulses of mineral nutrients, which previous studies have shown can weaken ecosystem resistance to invasion. Thus, restoration strategies that increase the likelihood that desired plants can capture mineralized nutrients after herbicide application will likely be more successful. [ABSTRACT FROM AUTHOR]

Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significant ly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities. [ABSTRACT FROM AUTHOR]

Databases of 3D paleoclimate model simulations are increasingly used within global biogeochemical models for the Phanerozoic Eon. This improves the accuracy of the surface processes within the biogeochemical models, but the approach is limited by the availability of large numbers of paleoclimate simulations at different p CO 2 levels and for different continental configurations. In this paper we apply the Frame Interpolation for Large Motion (FILM) deep learning method to a set of Phanerozoic paleoclimate model simulations to upscale their time resolution from one model run every ∼25 million years to one model run every 1 million years (Myr). Testing the method on a 5 Myr time-resolution set of continental configurations and paleoclimates confirms the accuracy of our approach when reconstructing intermediate frames from configurations separated by up to 40 Myr. We then apply the method to upscale the paleoclimate data structure in the SCION climate-biogeochemical model. The interpolated surface temperature and runoff are reasonable and present a logical progression between the original key frames. When updated to use the high-time-resolution climate data structure, the SCION model predicts climate shifts that were not present in the original model outputs due to its previous use of widely spaced datasets and simple linear interpolation. We conclude that a time resolution of ∼10 Myr in Phanerozoic paleoclimate simulations is likely sufficient for investigating the long-term carbon cycle and that deep learning methods may be critical in attaining this time resolution at reasonable computational expense, as well as for developing new fully continuous methods in which 3D continental processes are able to translate over a moving continental surface in deep time. However, the efficacy of deep learning methods in interpolating runoff data, compared to that of paleogeography and temperature, is diminished by the heterogeneous distribution of runoff. Consequently, interpolated climates must be confirmed by running a paleoclimate model if scientific conclusions are to be based directly on them. [ABSTRACT FROM AUTHOR]

Estimating global river solids, nitrogen (N), and phosphorus (P), in both quantity and composition, is necessary for understanding the development and persistence of many harmful algal blooms, hypoxic events, and other water quality issues in inland and coastal waters. This requires a comprehensive freshwater model that can resolve intertwined algae, solid, and nutrient dynamics, yet previous global watershed models have limited mechanistic resolution of instream biogeochemical processes. Here we develop the global, spatially explicit, and process-based Freshwater Algae, Nutrient, and Solid cycling and Yields (FANSY) model and incorporate it within the Land Model (LM3). The resulting model, LM3-FANSY v1.0, is intended as a baseline for eventual linking of global terrestrial and ocean biogeochemistry in next-generation Earth system models to project global changes that may challenge empirical approaches. LM3-FANSY explicitly resolves interactions between algae, N, P, and solid dynamics in rivers and lakes at 1° spatial and 30 min temporal resolution. Simulated suspended solids (SS), N, and P in multiple forms (particulate or dissolved, organic or inorganic) agree well with measurement-based yield (kg km -2 yr -1), load (kt yr -1), and concentration (mg L -1) estimates across a globally distributed set of large rivers, with an accuracy comparable to other global nutrient and SS models. Furthermore, simulated global river loads of SS, N, and P in different forms to the coastal ocean are consistent with published ranges, though regional biases are apparent. River N loads are estimated to contain approximately equal contributions by dissolved inorganic N (41 %) and dissolved organic N (39 %), with a lesser contribution by particulate organic N (20 %). For river P load estimates, particulate P, which includes both organic and sorbed inorganic forms, is the most abundant form (64 %), followed by dissolved inorganic and organic P (25 % and 11 %). Time series analysis of river solid and nutrient loads in large US rivers for the period ∼ 1963–2000 demonstrates that simulated SS and N loads in different N forms covary with variations of measurement-based loads. LM3-FANSY, however, has less capability to capture interannual variability of P loads, likely due to the lack of terrestrial P dynamics in LM3. Analyses of the model results and sensitivity to components, parameters, and inputs suggest that fluxes from terrestrial litter and soils, wastewater, and weathering are the most critical inputs to the fidelity of simulated river nutrient loads for observation-based estimates. Sensitivity analyses further demonstrate a critical role of algal dynamics in controlling the ratios of inorganic and organic nutrient forms in freshwaters. While the simulations are able to capture significant cross-watershed contrasts at a global scale, disagreement for individual rivers can be substantial. This limitation is shared by other global river models and could be ameliorated through further refinements in nutrient sources, freshwater model dynamics, and observations. Current targets for future LM3-FANSY development include the additions of terrestrial P dynamics, freshwater carbon, alkalinity, enhanced sediment dynamics, and anthropogenic hydraulic controls. [ABSTRACT FROM AUTHOR]