Remineralization Of Organic Matter Research Articles

A missing link in the carbon cycle: phytoplankton light absorption under RCP emission scenarios

Abstract. Marine biota and biogeophysical mechanisms, such as phytoplankton light absorption, have attracted increasing attention in recent climate studies. Under global warming, the influence of phytoplankton on the climate system is expected to change. Previous studies analyzed the impact of phytoplankton light absorption under prescribed future atmospheric CO2 concentrations. However, the role of this biogeophysical mechanism under freely evolving atmospheric CO2 concentration and future CO2 emissions remains unknown. To shed light on this research gap, we perform simulations with the EcoGEnIE Earth system model (ESM) and prescribe CO2 emissions out to the year 2500 following the four Extended Concentration Pathway (ECP) scenarios, which for practical purposes we call Representative Concentration Pathway (RCP) scenarios. Under all RCP scenarios, our results indicate that phytoplankton light absorption leads to a shallower remineralization of organic matter and a reduced export efficiency, weakening the biological carbon pump. In contrast, this biogeophysical mechanism increases the surface chlorophyll by ∼ 2 %, the sea surface temperature (SST) by 0.2 to 0.6 °C, the atmospheric CO2 concentrations by 8 %–20 % and the atmospheric temperature by 0.3 to 0.9 °C. Under the RCP2.6, RCP4.5 and RCP6.0 scenarios, the magnitude of changes due to phytoplankton light absorption is similar. However, under the RCP8.5 scenario, the changes in the climate system are less pronounced due to decreasing ecosystem productivity as temperature increases, highlighting a reduced effect of phytoplankton light absorption under strong warming. Additionally, this work highlights the major role of phytoplankton light absorption on the climate system, suggesting highly uncertain feedbacks on the carbon cycle with uncertainties that may be in the range of those known from the land biota.

First lacustrine application of the diatom‐bound nitrogen isotope paleo‐proxy reveals coupling of denitrification and N2 fixation in a hyper‐eutrophic lake

AbstractPast changes in the input/output, and internal cycling, of bioavailable nitrogen (N) in marine and lacustrine environments can be reconstructed by analyzing the N isotopic composition (δ15N) of organic matter in the sedimentary record. To verify, and eliminate, potential biases of bulk sedimentary δ15N (δ15Nbulk) signatures by diagenetic alteration and external N inputs, we applied, for the first time, the diatom‐bound N isotope (δ15Ndb) paleo‐proxy to lake sediments. By comparing δ15Nbulk and δ15Ndb in a sedimentary record from eutrophic Lake Lugano (Switzerland), we demonstrate that changing redox conditions influence the degree of N‐isotopic alteration of the bulk sediment, emphasizing the need for caution when interpreting δ15Nbulk in paleolimnological studies. Furthermore, in combining δ15Ndb measurements with X‐ray fluorescence scanning and state‐of‐the‐art molecular biomarker analyses, we reconstruct nutrient cycling and paleoenvironmental conditions in the lake over the past ~ 125 yr. Coeval with the period of severe eutrophication in Lake Lugano in the 1960s, our proxy data indicate that export production, δ15Ndb, and the concentration of heterocyst glycolipids (a biomarker for N2‐fixing cyanobacteria) increased simultaneously. Together, these data suggest that the rise in δ15Ndb is likely the result of enhanced water‐column denitrification in response to increased phytoplankton productivity. We hypothesize that greater export production during eutrophication led to anoxic conditions in the hypolimnion as a result of enhanced organic matter remineralization, raising water‐column denitrification. Enhanced N loss and remobilization of phosphorous (P) from the sediments under anoxic conditions lowered the N : P ratio in the lake, fostering cyanobacterial N2 fixation in surface waters.

Primary to post-depositional microbial controls on the stable and clumped isotope record of shoreline sediments at Fayetteville Green Lake.

Lacustrine carbonates are a powerful archive of paleoenvironmental information but are susceptible to post-depositional alteration. Microbial metabolisms can drive such alteration by changing carbonate saturation insitu, thereby driving dissolution or precipitation. The net impact these microbial processes have on the primary δ18O, δ13C, and Δ47 values of lacustrine carbonate is not fully known. We studied the evolution of microbial community structure and the porewater and sediment geochemistry in the upper ~30 cm of sediment from two shoreline sites at Green Lake, Fayetteville, NY over 2 years of seasonal sampling. We linked seasonal and depth-based changes of porewater carbonate chemistry to microbial community composition, insitu carbon cycling (using δ13C values of carbonate, dissolved inorganic carbon (DIC), and organic matter), and dominant allochems and facies. We interpret that microbial processes are a dominant control on carbon cycling within the sediment, affecting porewater DIC, aqueous carbon chemistry, and carbonate carbon and clumped isotope geochemistry. Across all seasons and sites, microbial organic matter remineralization lowers the δ13C of the porewater DIC. Elevated carbonate saturation states in the sediment porewaters (Ω > 3) were attributed to microbes from groups capable of sulfate reduction, which were abundant in the sediment below 5 cm depth. The nearshore carbonate sediments at Green Lake are mainly composed of microbialite intraclasts/oncoids, charophytes, larger calcite crystals, and authigenic micrite-each with a different origin. Authigenic micrite is interpreted to have precipitated insitu from the supersaturated porewaters from microbial metabolism. The stable carbon isotope values (δ13Ccarb) and clumped isotope values (Δ47) of bulk carbonate sediments from the same depth horizons and site varied depending on both the sampling season and the specific location within a site, indicating localized (μm to mm) controls on carbon and clumped isotope values. Our results suggest that biological processes are a dominant control on carbon chemistry within the sedimentary subsurface of the shorelines of Green Lake, from actively forming microbialites to pore space organic matter remineralization and micrite authigenesis. A combination of biological activity, hydrologic balance, and allochem composition of the sediments set the stable carbon, oxygen, and clumped isotope signals preserved by the Green Lake carbonate sediments.

Picocyanobacterial-bacterial interactions sustain cyanobacterial blooms in nutrient-limited aquatic environments

Cyanobacterial blooms (CBs) and concomitant water quality issues in oligotrophic/mesotrophic waters have been recently reported, challenging the conventional understanding that CBs are primarily caused by eutrophication. To elucidate the underlying mechanism of CBs in nutrition-deficient waters, the changes in Chlorophyll a (Chl-a), cyanobacterial-bacterial community composition, and certain microbial function in Qingcaosha Reservoir, the global largest tidal estuary storage reservoir, were analyzed systematically and comprehensively after its pilot run (2011–2019) in this study. Although the water quality was improved and stabilized, more frequent occurrences of bloom level of Chl-a (>20 μg L−1) in warm seasons were observed during recent years. The meteorological changes (CO2, sunshine duration, radiation, precipitation, evaporation, and relative humidity), water quality variations (pH, total organic carbon content, dissolved oxygen, and turbidity), accumulated sediments as an endogenous source, as well as unique estuarine conditions collectively facilitated picocyanobacterial-bacterial coexistence and community functional changes in this reservoir. A stable and tight co-occurrence pattern was established between dominant cyanobacteria (Synechococcus, Cyanobium, Planktothrix, Chroococcidiopsis, and Prochlorothrix) and certain heterotrophic bacteria (Proteobacteria, Actinobacteria, and Bacteroidetes), which contributed to the remineralization of organic matter for cyanobacteria utilization. The relative abundance of chemoorganoheterotrophs and bacteria related to nitrogen transformation (Paracoccus, Rhodoplanes, Nitrosomonas, and Zoogloea) increased, promoting the emergence of CBs in nutrient-limited conditions through enhanced nutrient recycling. In environments with limited nutrients, the interaction between photosynthetic autotrophic microorganisms and heterotrophic bacteria appears to be non-competitive. Instead, they adopt complementary roles within their ecological niche over long-term succession, mutually benefiting from this association. This long-term study confirmed that enhanced nutrient cycling, facilitated by cyanobacterial-bacterial symbiosis following long-term succession, could promote CBs in oligotrophic aquatic environments devoid of external nutrient inputs. This study advances understanding of the mechanisms that trigger and sustain CBs under nutritional constraints, contributing to developing more effective mitigation strategies, ensuring water safety, and maintaining ecological balance.

Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion.

The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves 13C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of 12C into organic carbon and CH4. Extreme and variable 13C enrichments in carbonates were caused by 13C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly 13C enriched. Thus, the loss of extreme 13C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.

Model exploration of microplastic effects on zooplankton grazing reveal potential impacts on the global carbon cycle

Amongst the increasing number of anthropogenic stress factors threatening ocean equilibrium, microplastics (MP; < 5 mm) have emerged as particularly worrisome. In situ observations have shown that MP accumulate in large areas at the surface ocean where it may threaten the functioning marine species. In particular, experimental evidence has shown that the grazing rates of several zooplankton species may be significantly altered by MP. These direct impacts on zooplankton may alter nutrient and carbon cycling. However, how these laboratory results may translate into impacts on the global ocean is yet unknown. Here, we use a global coupled physical-biogeochemical model including MP (NEMO/PISCES-PLASTIC) to investigate the impacts of MP exposure on zooplankton grazing rates. Drawing from experimental results, we use varying water contamination impact thresholds to explore the biogeochemical consequences of MP impacts on short (10 years) and long timescales (100 years). Our simulations show that the geographical extent of MP impacts on zooplankton remains restricted to about 10% of the global ocean surface, even after 100 years of constant MP contamination. However, in the most contaminated regions (e.g. the sub-tropical gyres), [MP] has surged from a few mg m−3 to > 50 mg m−3. Despite their oligotrophic nature and limited contribution to the overall ocean carbon cycle, MP impacts on zooplankton grazing could disrupt carbon cycling in these highly contaminated regions (up to 50% reduction in yearly primary production, carbon export fluxes and organic matter remineralisation after 100 years). Our research suggests that persistent MP pollution in the ocean could diminish primary production by 4%. In spite of the large sensitivity of our results to the water contamination impact threshold, we suggest MP impacts on zooplankton grazing may cause an annual loss of 1 Gt yr−1 of exported carbon after 100 years, if MP inputs remain constant globally.

Multiple Ba Phases in Marine Sediments elucidate environmental processes and conditions for the Holocene Mediterranean

Mediterranean sediments are known for their major shifts in sedimentary composition associated with dramatic changes in environmental and climate conditions. A typical expression for this in Holocene sediments is the occurrence of a distinctly organic-rich unit, sapropel S1, thought to be related with humid climate conditions. The S1 is accompanied by major changes in Ba content and in other elemental composition, respectively related to biological upper water column productivity and shifts in detrital sediment provenance. Here, we focus on changes in Ba and in its various phases to unravel shifts in environmental conditions around S1.Using selective extractions for sediments in cores MP37PC, MP39PC and MP50PC, respectively at 1908, 1359 and 775m water depth, we distinguish different Ba-phases: detrital Ba (Ba-det), barite Ba (Ba-bar), Mn-oxide-related Ba (Ba-ox), carbonate- and pyrite-associated Ba (Ba-carb and Ba-pyr). The predominant Ba-phase during S1 is Ba-bar (∼70%), whereas before and after S1 it is Ba-det (>90%). All other phases are mostly relatively small but have diagnostic value for environmental conditions and processes.The detrital (Ba/Al) is distinctly lower during S1 than before and after. The (Ba/Al). det variability, and enhanced values for Ba-carb and Ba-ox may have substantial influence on the traditional way to derive barite-Ba or excess-Ba content.The steep gradients in Ba-bar at onset and ending of S1and its high level during S1, clearly identify this period. In addition, and due to the exclusive nature of extraction results, we unequivocally demonstrate for the first time that there is a small gradual ‘early onset’ Ba-bar preceding the major increase in sapropel S1 formation sensu stricto.The ending of S1 formation is relatively abrupt with a well-defined reventilation event (’6 ka reventilation event’). This reventilation is associated with a rapid change in environmental conditions such as oxygenation and related remineralization of organic matter and recrystallization of carbonate. This rapid change and associated diagenetic processes are authentically recorded in Ba-carb and Ba-ox. For the period during sapropel S1 formation, the Ba-carb and Ba-ox results point to different levels of ventilation in the Eastern Mediterranean, i.e. a relatively mixed water mass down to ∼800m, a moderately mixed water mass from ∼800-to ∼1500 m, and a more stagnant water mass below 1500 m.

Emission of CO2 and its related carbonate system dynamics in a hotspot area during winter and summer: The Changjiang River estuary

The carbonate chemistry in river-dominated marginal seas is highly heterogeneous, and there is ongoing debate regarding the definition of atmospheric CO2 source or sink. On this basis, we investigated the carbonate chemistry and air-sea CO2 fluxes in a hotspot estuarine area: the Changjiang Estuary during winter and summer. The spatial characteristics of the carbonate system were influenced by water mixing of three end-members in winter, including the Changjiang freshwater with low total alkalinity (TA) concentration, the less saline Yellow Sea Surface Water with high TA, and the saline East China Sea (ECS) offshore water with moderate TA. While in summer with increased river discharge, the carbonate system was regulated by simplified two end-member mixing between the Changjiang freshwater and the ECS offshore water. By performing the end-member mixing model on DIC variations in the river plume region, significant biological addition of DIC was found in winter with an estimation of −120 ± 113 μmol kg−1 caused by wintertime organic matter remineralization from terrestrial source. While this biological addition of DIC shifted to DIC removal due to biological production in summer supported by the increased nutrient loading from Changjiang River. The pCO2 dynamics in the river plume and the ECS offshore were both subjected to physical mixing of freshwater and seawater, whether in winter and summer. In the inner estuary without horizontal mixing, the pCO2 dynamics were mainly influenced by biological uptake in winter and temperature in summer. The inner estuary, the river plume, and the ECS offshore were sources of atmospheric CO2, with their contributions varying seasonally. The Changjiang runoff enhanced the inner estuary's role as a CO2 source in summer, while intensive biological uptake reduced the river plume's contribution.

Loss of nitrogen via anaerobic ammonium oxidation (anammox) in the California Current system during the late Quaternary

Abstract. The California Current system (CCS) hosts one of the largest oxygen minimum zones (OMZs) in the world: the eastern North Pacific (ENP) OMZ, which is dissociated into subtropical and tropical regions (i.e. the ESTNP and ETNP). In the modern ENP OMZ, bioavailable nitrogen (N) is lost via denitrification and anaerobic ammonium oxidation (anammox). Even so, paleo-reconstructions of N loss have focused solely on denitrification. Fluctuations in bulk sedimentary δ15N over glacial–interglacial cycles have been interpreted to reflect variations in denitrification rates in response to ETNP OMZ intensity changes. This δ15N signal is thought to be transported northwards to the ESTNP OMZ. Here, we present the first CCS sedimentary record of ladderane lipids, biomarkers for anammox, located within the ESTNP OMZ (32° N, 118° W). Over the last two glacial terminations (∼ 160 kyr cal BP), ladderane concentrations were analysed in combination with the index of ladderanes with five cyclobutane moieties (NL5), short-chain (SC) ladderane degradation products, and productivity proxies. This shows that (1) ladderanes were derived from anammox bacteria living within the ESTNP OMZ water column; (2) ladderanes were continuously present, with relatively high concentrations during both glacial and interglacial periods, showcasing that the ESTNP OMZ must have retained an anoxic core in which N loss occurred; and (3) anammox abundance appears to have been driven by both organic matter (OM) remineralization and advection changes, which regulated nutrient and oxygen levels. Our study shows that anammox was an important feature in the CCS, and it provides a more holistic picture of N-loss dynamics and the development of the ESTNP OMZ over glacial–interglacial cycles. Lastly, ladderanes and their SC products were also detected in 160–500 kyr cal BP sediments (15.7–37.5 m b.s.f., metres below sea floor; analysed at a low temporal resolution), highlighting their potential as anammox biomarkers in relatively deeper buried sediments for future studies.

Planktonic Marine Fungi: A Review

AbstractFungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of marine fungi has evolved over the past century. Currently, “marine fungi” are defined as any fungi recovered repeatedly from marine habitats that are able to grow and/or sporulate in marine environments, form symbiotic relationships with other marine organisms, adapt and evolve at the genetic level, or are active metabolically in marine environments. While there are a number of recent reviews synthesizing our knowledge derived from over a century of research on marine fungi, this review article focuses on the state of knowledge on planktonic marine fungi from the coastal and open ocean, defined as fungi that are in suspension or attached to particles, substrates or in association with hosts in the pelagic zone of the ocean, and their roles in remineralization of organic matter and major biogeochemical cycles. This review differs from previous ones by focusing on biogeochemical impacts of planktonic marine fungi and methodological considerations for investigating their diversity and ecological functions. Importantly, we point out gaps in our knowledge and the potential methodological biases that might have contributed to these gaps. Finally, we highlight recommendations that will facilitate future studies of marine fungi. This article first provides a brief overview of the diversity of planktonic marine fungi, followed by a discussion of the biogeochemical impacts of planktonic marine fungi, and a wide range of methods that can be used to study marine fungi.

Molybdenum Isotope Fingerprinting of Microbial Sulfate Reduction in Seep Carbonate Rocks

AbstractUnderstanding the interaction between molybdenum (Mo) and organic matter during microbial sulfate reduction is critical for the use of Mo to reconstruct marine redox conditions throughout Earth's history. However, little is known about Mo isotope fractionation and how it relates to organic matter remineralization during microbial sulfate reduction. Here, we report Mo abundances and isotopic (δ98Mo) compositions for bulk‐rock, non‐lithogenic and sequentially extracted fractions, including carbonate (carb), pyrite, and organic matter (OM), of seep carbonate rocks. Our data indicate that the difference between δ98Mocarb and δ98MoOM (Δ98Mocarb‐OM) displays significant variability in the studied samples, ranging between 0.72 and 1.01‰. Remarkably, the obtained Δ98Mocarb‐OM values indicate correlative trends with stable carbon isotope ratios and bulk abundances of (a) total organic carbon, (b) Mo, and (c) pyrite in seep carbonates, which we interpret as reflecting sustained adsorption of isotopically light Mo onto organic matter during enhanced sulfate reduction. On this basis, we put forward the concept that Δ98Mocarb‐OM of authigenic carbonate rocks can be used as a measure of the intensity of sulfate reduction and for reconstructing past interactions between Mo and organic matter in marine sediments.

Physical and Biogeochemical Properties of California Current Upwelled Source Waters

AbstractCoastal upwelling variability in the California Current region, one of the four main eastern boundary current upwelling systems, is controlled by processes acting over a wide range of spatial and temporal scales. While the ensuing ecosystem response depends strongly on upwelled water properties, determining their exact physical and biogeochemical characteristics is notoriously difficult as it requires tracking water masses backward in space and time from the moment they upwell near the coast to their subsurface origin. Adjoint model simulations have been used successfully to track water masses in coastal upwelling systems and the work presented here extends these applications to determining the co‐variability of physical and biogeochemical properties of source waters at spatial scales that resolve the known alongshore variability of coastal upwelling in the region. Notably, the results identify that the modulation of coastal upwelling efficiency by onshore/offshore geostrophic meanders is the dominant mechanism explaining alongshore variability in source depth and properties of upwelled waters. The simulations also reveal that source water properties vary seasonally in response to different balances between coastal upwelling intensity and biogeochemical processes. During spring, interannual variability of physical and biogeochemical properties is directly tied to the intensity of upwelling‐favorable alongshore winds, whereas, during summer, biogeochemical properties respond more strongly to biological activity and subsequent organic matter remineralization at depth. Overall, the present work provides important insight into the mechanisms responsible for the alongshore mosaic and seasonal variation of upwelled source water properties in the central California Current region.

Production and fluxes of inorganic carbon and alkalinity in a subarctic subterranean estuary

In this study, we focus on the biogeochemical processes that produce both dissolved inorganic carbon (DIC) and total alkalinity (TA) along a subarctic subterranean estuary (STE) located in the Gulf of St. Lawrence (Magdalen Island, Qc, Canada) in order to evaluate the DIC and TA fluxes as well as the buffering capacity of the exported groundwater to coastal waters. DIC and TA do not behave conservatively during mixing along the groundwater flow path and this implies the occurrence of internal redox reactions that control both their production and consumption. In addition, we show that the origin and composition of the organic carbon within the system alter the carbonate parameters by generating low pH conditions (5.9 - 7.2) and contributing to non-carbonate alkalinity (NCA) that accounts for more than 30% of TA. Whereas iron cycling plays a key role in the production of DIC in the fresh and low-salinity groundwaters, the precipitation of sulfide minerals neutralize the acidity produced by the metabolically produced CO2, in the saline groundwater where sulfate is available. The STE pCO2, computed from the DIC-pHNBS pair ranged from a few ppm to 16000 ppm that results in a CO2 evasion rate of up to 310 mol m−2d−1 to the atmosphere. Based on Darcy flow and the mean concentrations of DIC and carbonate alkalinity (Ac = TA - NCA) in the discharge zone, fluxes derived from submarine groundwater discharge were estimated at 1.43 and 0.70 mol m−2d−1 for DIC and Ac, respectively. Despite a major part of the metabolic CO2 being lost along the groundwater flow path, the SGD-derived DIC flux was still greater than the Ac flux, implying that groundwater discharge reduces the buffering capacity of the receiving coastal waters. This site-specific scale study demonstrates the importance of diagenetic reactions and organic matter remineralization processes on carbonate system parameters in STE. Our results highlight that subarctic STEs could be hot spots of CO2 evasion and a source of acidification to coastal waters that should be considered in carbon budgets.

Labyrinthulomycetes thrives in organic matter-rich waters with ecological partitioning in the Pearl River Estuary.

Labyrinthulomycetes play an important role in marine biogeochemical cycles, but their diversity, distribution patterns, and key regulatory factors remain unclear. This study measured the abundance and diversity of Labyrinthulomycetes in the Pearl River Estuary (PRE) to understand its distribution pattern and relationship with environmental and biological factors. The abundance of Labyrinthulomycetes ranged from 24 to 500 cells·mL-1, with an average of 144.37 ± 94.65 cells·mL-1, and its community composition showed obvious ecological partitioning in the PRE. The results of statistical analysis indicated that CDOM, salinity, and chlorophyll a contributed significantly (P < 0.01) to the community composition, explaining 46.59%, 11.34%, and 4.38% of the variance, respectively. The Labyrinthulomycetes distribution pattern combined with the niches of dominant species was revealed; low-salinity species mainly use terrigenous organic matter occupied dominant positions in the upper estuary and showed the highest abundance; moderate-salinity species that can use phytoplankton-derived resources thrived in the middle estuary; and seawater species dominated the lower estuary with the highest diversity but the lowest abundance. In addition, the results of phylogenetic tree analysis indicated that the existence of a novel lineage, and further study on the diversity and ecological functions of Labyrinthulomycetes is needed.IMPORTANCELabyrinthulomycetes play important roles in organic matter remineralization, carbon sinks, and food webs. However, the true diversity of Labyrinthulomycetes is still unclear due to limitations in isolation and culture methods. In addition, previous studies on their relationship with environmental factors are inconsistent and even contradictory, and it is speculated that their community composition may have spatial heterogeneity along the environmental gradient. In this study, the distribution pattern and key regulators of Labyrinthulomycetes in the PRE were revealed. Combining the niche of dominant species, it is suggested that salinity determines the spatial differences in Labyrinthulomycetes diversity, and the resources of substrate (terrestrial input or phytoplankton-derived) determine the dominant species, and its abundance is mainly determined by organic matter concentrations. Our study provided new information on the Labyrinthulomycetes diversity and verified the spatial heterogeneity of Labyrinthulomycetes community composition, providing reliable explanations for the inconsistencies in previous studies.

Changes in the Red Sea overturning circulation during Marine Isotope Stage 3

Abstract. The oceanography of the Red Sea is controlled by the restricted exchange of water masses with the Indian Ocean and by high evaporation rates due to the arid climate of the surrounding land areas. In the northern Red Sea, the formation of oxygen-rich subsurface water ventilates the deeper parts of the basin, but little is known about the variability in this process in the past. The stable oxygen and carbon isotope records of epibenthic foraminifera from a sediment core of the central Red Sea and comparison with existing isotope records allow for the reconstruction of changes in the Red Sea overturning circulation (ROC) during Marine Isotope Stage 3. The isotope records imply millennial-scale variations in the ROC, in phase with the climate variability in the high northern latitudes. This suggests an immediate response of dense-water formation to the regional climate and hydrology of the northern Red Sea. Deep-water formation was intensified under the influence of cold and hyper-arid conditions during Heinrich stadials and was diminished during Dansgaard–Oeschger interstadials. While these changes are reflected in both stable oxygen and carbon isotope records, the latter data also exhibit changes in phase with the African–Indian monsoon system. The decoupling of the stable carbon and oxygen isotope records at the summer monsoon maximum centered around 55–60 ka may be associated with an increased inflow of nutrient-rich intermediate waters from the Arabian Sea to the central Red Sea. This process fueled local surface water productivity, resulting in enhanced remineralization of sinking organic matter and release of 12C at intermediate water depths.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The sensitivity of the equatorial pacific ODZ to particulate organic matter remineralization in a climate model under pre-industrial conditions

Marine oxygen plays a fundamental role in regulating the transfer of organic carbon and nutrients to their dissolved inorganic forms, serving as the terminal electron acceptor for heterotrophic respiration. Oxygen can become limiting to these processes in coastal and open-ocean oxygen deficient zones (ODZs). The maintenance of ODZs depends on the balance between physical processes such as ventilation and biogeochemical processes such as remineralization. These two processes act in opposing directions on ODZs, with ventilation responsible for transporting oxygen from the surface, where it is near saturation with the partial pressure of O2 in the atmosphere, to deeper oxygen-depleted layers, and remineralization acting to consume oxygen through biogeochemical processes such as microbial degradation throughout the water column. Remineralization is represented in all CMIP6 models, but the actual parameterizations, as well as their magnitude, are widely varying.In this study, we examine the sensitivity to remineralization of the equatorial Pacific ODZ (O2<60μmol/kg) in a model; the NASA GISS Ocean Biogeochemical Model (NOBM-G) embedded in the NASA-GISS coupled atmosphere-ocean model. We find that increasing the remineralization rate shoals the ODZ onset depth (i.e. the regionally averaged upper bound of the ODZ), and decreases ODZ volume and regional-averaged thickness. Changes in biological consumption and vertical convergence of oxygen are identified as the primary contributors to changes in ODZ onset depth. ODZ thickness is mainly influenced by the shoaling of the bottom boundary of the ODZ, which decreases with maximum remineralization rate due to decreasing oxygen consumption and increasing horizontal oxygen convergence in deep waters. On the other hand, vertically-averaged ODZ area has a more complex, non-monotonic relationship with maximum remineralization rate. While these findings suggest an important role for remineralization in determining the shape of the ODZ in our model, the relative importance of remineralization vs. other physical parameterizations remains to be established. While our results reflect the structure of our ocean biogeochemical model, the relationship of remineralization to ODZ characteristics in other models should be examined to better inform model inter-comparisons.

Iron, Nickel, Copper, Zinc, and their stable isotopes along a salinity gradient in the Pearl River Estuary, southeastern China

Although the crucial role that dissolved trace metals (dTMs) play in both carbon cycling and climate have been revealed over the past three decades, much about the oceanic budgets of dTMs remains unknown. Rivers are one of the most important dTM sources to the ocean, and estuaries are a key interface between land and ocean. However, our understanding of how dTMs behave as they pass through the estuarine transition is limited, leading to uncertainties in estimating fluvial metal fluxes to the ocean and balancing oceanic dTM budgets. Alongside concentrations, metal stable isotopes offer an additional dimension to constrain estuarine processes, but data on metal isotopes in estuaries are scarce. Here we present dTM concentrations and their stable isotope ratios along a full salinity gradient in the Pearl River Estuary (PRE), southeastern China. Concentration data show a large apparent loss of dFe (86%) during estuarine mixing, moderate losses of dNi (13%) and dZn (36%), and nearly conservative behavior for dCu. However, examination of metal isotope data (δ56Fe, δ60Ni, δ65Cu, and δ66Zn) reveals more complex biogeochemistry, requiring either a two-stage scenario or a three-endmember mixing process. The two-stage process involves fractionation of dTM isotopes at low salinities, likely driven by particle adsorption and colloidal flocculation, followed by conservative mixing between intermediate-salinity estuarine waters and South China Sea waters. Alternatively, the three-endmember mixing process includes influences from riverine, oceanic endmembers, and external sources such as benthic flux and industrial activities, shaping dTM isotope distributions. Specifically, capturing δ56Fe fully proves challenging, yet it appears strongly influenced by inputs of benthic Fe within the PRE, characterized by dFe > 13 nmol kg−1 and δ56Fe < −0.80‰. δ60Ni and δ66Zn can be described by either two-stage or there-endmember mixing processes. In the former, the Rayleigh fractionation with αd-p of 1.00004 for δ60Ni and 1.0001 for δ66Zn, or the steady state fractionation with αd-p of 1.00005 for δ60Ni and 1.0002 for δ66Zn, could be derived to explain their patterns at low salinity, likely driven by colloidal flocculation. Additionally, a third source with dNi > 33 nmol kg−1 and δ60Ni > +1.26‰ and a third source with dZn > 13 nmol kg−1 and δ66Zn > +0.96‰, both influenced by human activities, could also shape the δ60Ni and δ66Zn patterns in the PRE, respectively. The description of δ65Cu is best achieved by a three-endmember mixing process, with the external source having dCu > 20 nmol kg−1 andδ65Cu < +1.3‰, indicative of processes like organic matter remineralization or discharge from wastewater treatment plant. Our study highlights the need for more extensive and detailed studies on estuarine settings to elucidate their potentially crucial role in global dTMs budgets.

Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis

Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2 as an electron donor to reduce CO2 to CH4, but in the absence of H2 many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for reduction of coenzyme F420 or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is unknown. Using Methanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420 at similar rates. F420 reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1 mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth, and metal content of the proteins suggested that isoforms are dependent on either molybdenum or tungsten for activity. These data suggest that both isoforms of Fdh are functionally redundant, but their activities in vivo may be limited by gene regulation or metal availability under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.

Biological carbon pump estimate based on multidecadal hydrographic data

The transfer of photosynthetically produced organic carbon from surface to mesopelagic waters draws carbon dioxide from the atmosphere1. However, current observation-based estimates disagree on the strength of this biological carbon pump (BCP)2. Earth system models (ESMs) also exhibit a large spread of BCP estimates, indicating limited representations of the known carbon export pathways3. Here we use several decades of hydrographic observations to produce a top-down estimate of the strength of the BCP with an inverse biogeochemical model that implicitly accounts for all known export pathways. Our estimate of total organic carbon (TOC) export at 73.4 m (model euphotic zone depth) is 15.00 ± 1.12 Pg C year−1, with only two-thirds reaching 100 m depth owing to rapid remineralization of organic matter in the upper water column. Partitioned by sequestration time below the euphotic zone, τ, the globally integrated organic carbon production rate with τ > 3 months is 11.09 ± 1.02 Pg C year−1, dropping to 8.25 ± 0.30 Pg C year−1 for τ > 1 year, with 81% contributed by the non-advective-diffusive vertical flux owing to sinking particles and vertically migrating zooplankton. Nevertheless, export of organic carbon by mixing and other fluid transport of dissolved matter and suspended particles remains regionally important for meeting the respiratory carbon demand. Furthermore, the temperature dependence of the sequestration efficiency inferred from our inversion suggests that future global warming may intensify the recycling of organic matter in the upper ocean, potentially weakening the BCP.