The marine nitrogen cycle: new developments and global change

Membraneless channels sieve cations in ammonia-oxidizing marine archaea

Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.

Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past

The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.

Kelps may compensate for low nitrate availability by using regenerated forms of nitrogen, including urea and ammonium

Nitrate, the form of nitrogen often associated with kelp growth, is typically low in summer during periods of high macroalgal growth. More ephemeral, regenerated forms of nitrogen, such as ammonium and urea, are much less studied as sources of nitrogen for kelps, despite the relatively high concentrations of regenerated nitrogen found in the Southern California Bight, where kelps are common. To assess how nitrogen uptake by kelps varies by species and nitrogen form in southern California, USA, we measured uptake rates of nitrate, ammonium, and urea by Macrocystis pyrifera and Eisenia arborea individuals from four regions characterized by differences in nitrogen availability-Orange County, San Pedro, eastern Santa Catalina Island, and western Santa Catalina Island-during the summers of 2021 and 2022. Seawater samples collected at each location showed that overall nitrogen availability was low, but ammonium and urea were often more abundant than nitrate. We also quantified the internal %nitrogen of each kelp blade collected, which was positively associated with ambient environmental nitrogen concentrations at the time of collection. We observed that both kelp species readily took up nitrate, ammonium, and urea, with M. pyrifera taking up nitrate and ammonium more efficiently than E. arborea. Urea uptake efficiency for both species increased as internal percent nitrogen decreased. Our results indicate that lesser-studied, more ephemeral forms of nitrogen can readily be taken up by these kelps, with possible upregulation of urea uptake as nitrogen availability declines.

Inhibitory effect of marine Bacillus sp. and its biomineralization on the corrosion of X65 steel in offshore oilfield produced water

The issue of material failure attributed to microbiologically influenced corrosion (MIC) is escalating in seriousness. Microorganisms not only facilitate corrosion but certain beneficial microorganisms also impede its occurrence. This study explored the impact of marine B. velezensis on the corrosion behavior of X65 steel in simulated offshore oilfield produced water. B. velezensis exhibited rapid growth in the initial stages, and the organic acid metabolites were found to promote corrosion. Subsequently, there was an increase in cross-linked "networked" biofilms products, a significant rise in the prismatic shape of corrosion products, and a tendency for continuous development in the middle and late stages. The organic/inorganic mineralized film layer formed on the surface remained consistently complete. Metabolic products of amino acid corrosion inhibitors were also observed to be adsorbed into the film. B. velezensis altered the kinetics of the X65 steel cathodic reaction, resulting in a deceleration of the electrochemical reaction rate. The mineralization induced by B. velezensis effectively slowed down the corrosion rate of X65 steel.

Unsolved mysteries in marine nitrogen fixation

Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.

Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy

Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.

Understanding the impacts of coastal deoxygenation in nitrogen dynamics: an observational analysis

Biological production and outgassing of greenhouse gasses (GHG) in Eastern Boundary Upwelling Systems (EBUS) are vital for fishing productivity and climate regulation. This study examines temporal variability of biogeochemical and oceanographic variables, focusing on dissolved oxygen (DO), nitrate, nitrogen deficit (N deficit), nitrous oxide (N2O) and air-sea N2O flux. This analysis is based on monthly observations from 2000 to 2023 in a region of intense seasonal coastal upwelling off central Chile (36°S). Strong correlations are estimated among N2O concentrations and N deficit in the 30-80 m layer, and N2O air-sea fluxes with the proportion of hypoxic water (4 < DO < 89 µmol L-1) in the water column, suggesting that N2O accumulation and its exchange are mainly associated with partial denitrification. Furthermore, we observe interannual variability in concentrations and inventories in the water column of DO, nitrate, N deficit, as well as air-sea N2O fluxes in both downwelling and upwelling seasons. These variabilities are not associated with El Niño-Southern Oscillation (ENSO) indices but are related to interannual differences in upwelling intensity. The time series reveals significant nitrate removal and N2O accumulation in both mid and bottom layers, occurring at rates of 1.5 µmol L-1 and 2.9 nmol L-1 per decade, respectively. Particularly significant is the increase over the past two decades of air-sea N2O fluxes at a rate of 2.9 µmol m-2 d-1 per decade. These observations suggest that changes in the EBUS, such as intensification of upwelling and the prevalence of hypoxic waters may have implications for N2O emissions and fixed nitrogen loss, potentially influencing coastal productivity and climate.

Can three-dimensional nitrate structure be reconstructed from surface information with artificial intelligence? - A proof-of-concept study

Nitrate is one of the essential variables in the ocean that is a primary control of the upper ocean pelagic ecosystem. Its three-dimensional (3D) structure is vital for understanding the dynamic and ecosystem. Although several gridded nitrate products exist, the possibility of reconstructing the 3D structure of nitrate from surface data has never been exploited. In this study, we employed two advanced artificial intelligence (AI) networks, U-net and Earthformer, to reconstruct nitrate concentration in the Indian Ocean from surface data. Simulation from an ecosystem model was utilized as the labeling data to train and test the AI networks, with wind vectors, wind stress, sea surface temperature, sea surface chlorophyll-a, solar radiation, and precipitation as the input. We compared the performance of two networks and different pre-processing methods. With the input features decomposed into climatology and anomaly components, the Earthformer achieved optimal reconstruction results with a lower normalized mean square error (NRMSE = 0.1591), spatially and temporally, outperforming U-net (NRMSE = 0.2007) and the climatology prediction (NRMSE = 0.2089). Furthermore, Earthformer was more capable of identifying interannual nitrate anomalies. With a network interpretation technique, we quantified the spatio-temporal importance of every input feature in the best case (Earthformer with decomposed inputs). The influence of different input features on nitrate concentration in the adjacent Java Sea exhibited seasonal variation, stronger than the interannual one. The feature importance highlighted the role of dynamic factors, particularly the wind, matching our understanding of the dynamic controls of the ecosystem. Our reconstruction and network interpretation technique can be extended to other ecosystem variables, providing new possibilities in studies of marine environment and ecology from an AI perspective.

Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities

o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.

Nitrogen loss in coastal sediments driven by anaerobic ammonium oxidation coupled to microbial reduction of Mn(IV)-oxide

Coastal sediments play a central role in regulating the amount of land-derived reactive nitrogen (Nr) entering the ocean, and their importance becomes crucial in vulnerable ecosystems threatened by anthropogenic activities. Sedimentary denitrification has been identified as the main sink of Nr in marine environments, while anaerobic ammonium oxidation with nitrite (anammox) has also been pointed out as a key player in controlling the nitrogen pool in these locations. Collected evidence in the present work indicates that the microbial biota in coastal sediments from Baja California (northwestern Mexico) has the potential to drive anaerobic ammonium oxidation linked to Mn(IV) reduction (manganammox). Unamended sediment showed ammonification, but addition of vernadite (δMnO2 with nano-crystal size ∼15 Å) as terminal electron acceptor fueled simultaneous ammonium oxidation (up to ∼400 μM of ammonium removed) and production of Mn(II) with a ratio ∆[Mn(II)]/∆[NH4+] of 1.8, which is very close to the stoichiometric value of manganammox (1.5). Additional incubations spiked with external ammonium also showed concomitant ammonium oxidation and Mn(II) production, accounting for ∼30 % of the oxidized ammonium. Tracer analysis revealed that the nitrogen loss associated with manganammox was 4.2 ± 0.4 μg 30N2/g-day, which is 17-fold higher than that related to the feammox process (anaerobic ammonium oxidation linked to Fe(III) reduction, 0.24 ± 0.02 μg 30N2/g-day). Taxonomic characterization based on 16S rRNA gene sequencing revealed the existence of several clades belonging to Desulfobacterota as potential microorganisms catalyzing the manganammox process. These findings suggest that manganammox has the potential to be an additional Nr sink in coastal environments, whose contribution to total Nr losses remains to be evaluated.

Selective Electrocatalytic Conversion of Nitric Oxide to High Value-Added Chemicals

The artificial disturbance in the nitrogen cycle has necessitated an urgent need for nitric oxide (NO) removal. Electrochemical technologies for NO conversion have gained increasing attention in recent years. This comprehensive review presents the recent advancements in selective electrocatalytic conversion of NO to high value-added chemicals, with specific emphasis on catalyst design, electrolyte composition, mass diffusion, and adsorption energies of key intermediate species. Furthermore, the review explores the synergistic electrochemical co-electrolysis of NO with specific carbon source molecules, enabling the synthesis of a range of valuable chemicals with C─N bonds. It also provides in-depth insights into the intricate reaction pathways and underlying mechanisms, offering valuable perspectives on the challenges and prospects of selective NO electrolysis. By advancing comprehension and fostering awareness of nitrogen cycle balance, this review contributes to the development of efficient and sustainable electrocatalytic systems for the selective synthesis of valuable chemicals from NO.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Accelerated nitrogen cycling on Mediterranean seagrass leaves at volcanic CO2 vents

Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO2 vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N2 fixation contributes to 35% of the plant's N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N2 production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.

A genomic view of environmental and life history controls on microbial nitrogen acquisition strategies

Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. In this study, we examine the distribution of 10 major N acquisition strategies in taxonomically and metabolically diverse microbial genomes, including those from the Genomic Catalogue of Earth's Microbiomes dataset. We utilize a marker gene-based approach to assess relationships between N acquisition strategy prevalence and microbial life history strategies. Our results underscore energetic costs of assimilation as a broad control on strategy distribution. The most prevalent strategies are the uptake of ammonium and simple amino acids, which have relatively low energetic costs, while energy-intensive biological nitrogen fixation is the least common. Deviations from the energy-based framework include the higher-than-expected prevalence of the assimilatory pathway for chitin, a large organic polymer. Energy availability is also important, with aerobic chemoorganotrophs  and oxygenic phototrophs notably possessing ~2-fold higher numbers of total strategies compared to anaerobic microbes. Environmental controls are evidenced by the enrichment of inorganic N assimilation strategies among free-living taxa compared to host-associated taxa. Physiological constraints such as pathway incompatibility add complexity to N acquisition strategy distributions. Finally, we discuss the necessity for microbially-relevant spatiotemporal environmental metadata for improving mechanistic and prediction-oriented analyses of genomic data.

Evolution of dissolved organic nitrogen chemistry during transportation to the marginal sea: Insights from nitrogen isotope and molecular composition analyses

Estuaries are hotspots where terrestrially originated dissolved organic matter (DOM) is modified in molecular composition before entering marine environments. However, very few research has considered nitrogen (N) modifications of DOM molecules in estuaries, limiting our understanding of dissolved organic nitrogen (DON) cycling and the associated carbon cycling in estuaries. This study integrated optical, stable isotopes (δ15N and δ13C) and molecular composition (FT-ICR MS) to characterize the transformation of DOM in the Yangtze River Estuary. Both concentration of dissolved organic carbon (DOC) and DON decreased with increasing salinity, while their δ13C and δ15N increased with the increasing salinity. A significant positive correlation was found between δ15N and δ13C during the transportation of DOM to marginal seas, indicating that the behavior of both DOC and DON are primarily controlled by the mixing of freshwater and the seawater in the YRE. During the mixing process, the DON addition was observed using the conservative mixing curves. In the view of molecular composition, DOM molecules became more aromatic as the number of N atoms increased. Spearman correlations reveal that DOM molecules with fewer N atoms exhibited a higher enrichment in protein-like components, while those with more N atoms were more enriched in humic-like components. In addition, the δ15N and δ13C tended to increase as the N content of DOM decreased. Therefore, DON molecules with fewer N atoms were likely to be transformed into those with more N atoms based on the isotopic fractionation theory. This study establishes a linkage between the molecular composition and the δ15N of DOM, and discovers the N transformation pattern within DOM molecules during the transportation to marginal seas.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Microbial regulation of feedbacks to ecosystem change

Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.

Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland

Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.

Phosphorus-driven regime shift from heterotrophic to autotrophic diazotrophs in a deep alpine lake

Biological nitrogen fixation plays a critical role in maintaining primary production, particularly in systematic nitrogen deficiency. However, little is known about the dynamics within diazotrophic community facing ongoing nutrient enrichment in freshwater lakes. Here, a consecutive five-year investigation on diazotrophic community was conducted in Lake Fuxian, an oligotrophic deep alpine lake on the trajectory to eutrophic state. Results showed a regime shift from heterotrophic to autotrophic diazotrophs induced by total phosphorus (TP) enrichment. Specifically, heterotrophic diazotrophs dominated the diazotrophic community when TP was lower than 21.8 μg/L, whereas heterotrophic diazotrophs or diazotrophic Cyanobacteria randomly dominated when TP ranged between 21.8 μg/L and 28.8 μg/L. When TP was higher than 28.8 μg/L, diazotrophic Cyanobacteria accounted for 60.4%-97.7% of the total N2-fixers, indicating diazotrophic biodiversity significantly declined under TP enrichment scenario. Moreover, the dominance of diazotrophic Cyanobacteria further facilitated phytoplankton growth, which strengthened positive feedback between phytoplankton and phosphorus under nitrogen deficiency conditions. This is the first report on the threshold-like state responses of freshwater diazotrophs to environmental drivers. Our study expands the knowledge of the diazotrophic dynamics in freshwater ecosystems and contributes quantitative evidence of ecological thresholds for future environmental policymaking.

Effect of ocean outfall discharge volume and dissolved inorganic nitrogen load on urban eutrophication outcomes in the Southern California Bight

Climate change is increasing drought severity worldwide. Ocean discharges of municipal wastewater are a target for potable water recycling. Potable water recycling would reduce wastewater volume; however, the effect on mass nitrogen loading is dependent on treatment. In cases where nitrogen mass loading is not altered or altered minimally, this practice has the potential to influence spatial patterns in coastal eutrophication. We apply a physical-biogeochemical numerical ocean model to understand the influence of nitrogen management and potable wastewater recycling on net primary productivity (NPP), pH, and oxygen. We model several theoretical management scenarios by combining dissolved inorganic nitrogen (DIN) reductions from 50 to 85% and recycling from 0 to 90%, applied to 19 generalized wastewater outfalls in the Southern California Bight. Under no recycling, NPP, acidification, and oxygen loss decline with DIN reductions, which simulated habitat volume expansion for pelagic calcifiers and aerobic taxa. Recycling scenarios under intermediate DIN reduction show patchier areas of pH and oxygen loss with steeper vertical declines relative to a "no recycling" scenario. These patches are diminished under 85% DIN reduction across all recycling levels, suggesting nitrogen management lowers eutrophication risk even with concentrated discharges. These findings represent a novel application of ocean numerical models to investigate the regional effects of idealized outfall management on eutrophication. Additional work is needed to investigate more realistic outfall-specific water recycling and nutrient management scenarios and to contextualize the benefit of these management actions, given accelerating acidification and hypoxia from climate change.

Nutrient changes in the Bohai Sea over the past two decades

With the growing problem of eutrophication in the Bohai Sea, actions have been taken to reduce nutrient inputs, but it remains to be seen whether nutrient levels and structure have been ameliorated. In this study, the nutrient trends in the Bohai Sea are re-examined based on observations from 2000 to 2019. The results suggest that dissolved inorganic nitrogen (DIN) concentrations and DIN/DIP (dissolved inorganic phosphate) ratios gradually increased from 2000 to 2013 but dramatically decreased from 2013 to 2019. The increase and decrease rates of DIN concentrations decreased with increasing water depth, indicating that DIN concentrations in nearshore waters responded more rapidly to changes in human activities. However, DIP concentrations responded weakly to nutrient inputs, with their trends uncoupled. The DIN/DIP ratios have declined close to and in some seasons even below the canonical Redfield ratio in areas with water depths >20 m recently, implying that relative nutrient limitation in these areas may be shifting from relative phosphorus (P) limitation to absence of relative nutrient limitation or relative nitrogen (N) limitation. Atmospheric deposition, wastewater discharge, and riverine input were responsible for 66 %, 21 %, and 13 % of the variance in the decline of DIN concentration, respectively. Several environmental indicators responded positively to the decrease in DIN concentrations and DIN/DIP ratios, with varying degrees of recovery recently. Our study proves the phased success of various nutrient reduction measures taken by the Chinese government to improve the environment of the Bohai Sea over the past decade.

Natural ocean iron fertilization and climate variability over geological periods

Marine primary producers are largely dependent on and shape the Earth's climate, although their relationship with climate varies over space and time. The growth of phytoplankton and associated marine primary productivity in most of the modern global ocean is limited by the supply of nutrients, including the micronutrient iron. The addition of iron via episodic and frequent events drives the biological carbon pump and promotes the sequestration of atmospheric carbon dioxide (CO2 ) into the ocean. However, the dependence between iron and marine primary producers adaptively changes over different geological periods due to the variation in global climate and environment. In this review, we examined the role and importance of iron in modulating marine primary production during some specific geological periods, that is, the Great Oxidation Event (GOE) during the Huronian glaciation, the Snowball Earth Event during the Cryogenian, the glacial-interglacial cycles during the Pleistocene, and the period from the last glacial maximum to the late Holocene. Only the change trend of iron bioavailability and climate in the glacial-interglacial cycles is consistent with the Iron Hypothesis. During the GOE and the Snowball Earth periods, although the bioavailability of iron in the ocean and the climate changed dramatically, the changing trend of many factors contradicted the Iron Hypothesis. By detangling the relationship among marine primary productivity, iron availability and oceanic environments in different geological periods, this review can offer some new insights for evaluating the impact of ocean iron fertilization on removing CO2 from the atmosphere and regulating the climate.

Dissecting the contributions of organic nitrogen aerosols to global atmospheric nitrogen deposition and implications for ecosystems

Atmospheric deposition of particulate organic nitrogen (ONp) is a significant process in the global nitrogen cycle and may be pivotally important for N-limited ecosystems. However, past models largely overlooked the spatial and chemical inhomogeneity of atmospheric ONp and were thus deficient in assessing global ONp impacts. We constructed a comprehensive global model of atmospheric gaseous and particulate organic nitrogen (ON), including the latest knowledge on emissions and secondary formations. Using this model, we simulated global atmospheric ONp abundances consistent with observations. Our estimated global atmospheric ON deposition was 26 Tg N yr-1, predominantly in the form of ONp (23 Tg N yr-1) and mostly from wildfires (37%), oceans (22%) and aqueous productions (17%). Globally, ONp contributed as much as 40% to 80% of the total N deposition downwind of biomass-burning regions. Atmospheric ONp deposition thus constituted the dominant external N supply to the N-limited boreal forests, tundras and the Arctic Ocean, and its importance may be amplified in a future warming climate.

Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacterium Synechococcus

The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures.

Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.

Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland

Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.

Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs

Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.

Efficient nitrogen removal pathways and corresponding microbial evidence in tidal flow constructed wetlands for saline water treatment

The artificial tidal wetlands ecosystem was believed to be a useful device in treating saline water, and it played a significant part in global nitrogen cycles. However, limited information is available on nitrogen-cycling pathways and related contributions to nitrogen loss in tidal flow constructed wetlands (TF-CWs) for saline water treatment. This study operated seven experimental tidal flow constructed wetlands to remove nitrogen from saline water at salinities of 0-30‰. Stable and high NH4+-N removal efficiency (∼90.3%) was achieved, compared to 4.8-93.4% and 23.5-88.4% for nitrate and total nitrogen (TN), respectively. Microbial analyses revealed the simultaneous occurrence of anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), nitrification and denitrification, contributing to nitrogen (N) loss from the mesocosms. The absolute abundances were 5.54 × 103-8.35 × 107 (nitrogen functional genes) and 5.21 × 107-7.99 × 109 copies/g (16S rRNA), while the related genera abundances ranged from 1.81% to 10.47% (nitrate reduction) and from 0.29% to 0.97% (nitrification), respectively. Quantitative response relationships showed ammonium transformation were controlled by nxrA, hzsB and amoA, and nitrate removal by nxrA, nosZ and narG. Collectively, TN transformation were determined by narG, nosZ, qnorB, nirS and hzsB through denitrification and anammox pathways. The proportion of nitrogen assimilation by plants was 6.9-23.4%. In summary, these findings would advance our understanding of quantitative molecular mechanisms in TF-CW mesocosms for treating nitrogen pollution that caused algal blooms in estuarine/coastal ecosystems worldwide.

Dissolved organic nitrogen cycling revealed at the molecular level in the Bohai and Yellow Sea

Marginal seas play a crucial role in the cycling of dissolved organic nitrogen (DON) between the terrestrial and marine environments. However, very few studies have considered the molecular transformation of DON in marginal seas, leaving the DON molecular modifications in its cycling largely unknown. Therefore, this study examined DON cycling in the Bohai Sea and Yellow Sea, two semi-closed marginal seas in northern China, using stable isotopes (δ15N and δ13C), optical characteristics, and molecular compositions. Compared to the Yellow Sea, the Bohai Sea had a weaker exchange with the open ocean, resulting in higher concentrations, lower δ15N, and more recalcitrant properties in DON. The DON cycling showed significant differences inside and outside the Yellow Sea Cold Water (YSCW). Degradation was the major sink of DON in the YSCW, during which more highly unsaturated compounds and carboxyl-rich alicyclic molecules were produced. Nitrogen atoms were found to be removed from the molecules with more N atoms to those with fewer ones during the DON degradation. This study discovered the molecular modifications in DON cycling and highlighted the intrinsic mechanisms in the cycling of DON in marginal seas.

Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series

UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A's rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A's microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.

Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast

The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.

Inter-seasonal variation in nitrogen uptake rates of the eutrophic Cochin estuary and adjacent coastal Arabian Sea

The study assessed the Cochin estuary and adjacent coastal Arabian Sea for their seasonal variation in nitrate (NO3-) and ammonium (NH4+) uptake rates by total and nano + picoplankton using the 15N tracer technique. The results suggested that the NO3- and NH4+ uptake rates in the Cochin estuary are higher than those in the adjacent coastal Arabian Sea. NO3- and NH4+ uptake rates in the nearshore stations in the off Cochin station were high, indicating the influence of the eutrophic estuary. NO3- and NH4+ uptake rates conducted in off Mangalore transect were significantly lower than those of the off Cochin as it does not have an exchange with eutrophic systems. The nano + picoplankton's contribution to the total DIN uptake rates in the Cochin estuary was 77-98 %, indicating the relevance of nano + pico phytoplankton in the N cycling of the region.

Diversity of the protease-producing bacteria and their extracellular protease in the coastal mudflat of Jiaozhou Bay, China: in response to clam naturally growing and aquaculture

The booming mudflat aquaculture poses an accumulation of organic matter and a certain environmental threat. Protease-producing bacteria are key players in regulating the nitrogen content in ecosystems. However, knowledge of the diversity of protease-producing bacteria in coastal mudflats is limited. This study investigated the bacterial diversity in the coastal mudflat, especially protease-producing bacteria and their extracellular proteases, by using culture-independent methods and culture-dependent methods. The clam aquaculture area exhibited a higher concentration of carbon, nitrogen, and phosphorus when compared with the non-clam area, and a lower richness and diversity of bacterial community when compared with the clam naturally growing area. The major classes in the coastal mud samples were Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria. The Bacillus-like bacterial community was the dominant cultivated protease-producing group, accounting for 52.94% in the non-clam area, 30.77% in the clam naturally growing area, and 50% in the clam aquaculture area, respectively. Additionally, serine protease and metalloprotease were the principal extracellular protease of the isolated coastal bacteria. These findings shed light on the understanding of the microbes involved in organic nitrogen degradation in coastal mudflats and lays a foundation for the development of novel protease-producing bacterial agents for coastal mudflat purification.

Microplastics trigger the Matthew effect on nitrogen assimilation in marine diatoms at an environmentally relevant concentration

Microplastics (MPs, diameter <5 mm) are widely distributed on Earth, especially in the oceans. Diatoms account for ∼40% of marine primary productivity and affect the global biogeochemical cycles of macroelements. However, the effects of MPs on marine nitrogen cycling remain poorly understood, particularly comparisons between nitrogen-replete and nitrogen-limited conditions. We found that MPs trigger the Matthew effect on nitrogen assimilation in diatoms, where MPs inhibited nitrogen assimilation under nitrogen-limited conditions while enhancing nitrogen metabolism under nitrogen-replete conditions in Phaeodactylum tricornutum. Nitrate reductase (NR) and nitrite reductase (NIR) are upregulated, but nitrate transporter (NRT) and glutamine synthetase (GS) are downregulated by MPs under nitrogen-limited conditions. In contrast, NR, NIR, and GS are all upregulated by MPs under nitrogen-replete conditions. MPs accelerate nitrogen anabolic processes with an increase in the accumulation of carbohydrates by 80.7 ± 7.9% and enhance the activities of key nitrogen-metabolizing enzymes (8.20-44.90%) under nitrogen-replete conditions. In contrast, the abundance of carbohydrates decreases by 22.0-34.4%, and NRT activity is inhibited by 79.0-86.5% in nitrogen-limited algae exposed to MPs. Metabolomic and transcriptomic analyses were performed to further explore the molecular mechanisms of reprogrammed nitrogen assimilation, including carbon metabolism, nitrogen transport and ammonia assimilation. The aforementioned spatial redistribution (e.g., the Matthew effect between nitrogen-replete and -limited conditions) of nitrogen assimilation highlights the potential risks of MP contamination in the ocean.

Plastic responses lead to increased neurotoxin production in the diatom Pseudo-nitzschia under ocean warming and acidification

Ocean warming (OW) and acidification (OA) are recognized as two major climatic conditions influencing phytoplankton growth and nutritional or toxin content. However, there is limited knowledge on the responses of harmful algal bloom species that produce toxins. Here, the study provides quantitative and mechanistic understanding of the acclimation and adaptation responses of the domoic acid (DA) producing diatom Pseudo-nitzschia multiseries to rising temperature and pCO2 using both a one-year in situ bulk culture experiment, and an 800-day laboratory acclimation experiment. Ocean warming showed larger selective effects on growth and DA metabolism than ocean acidification. In a bulk culture experiment, increasing temperature +4 °C above ambient seawater temperature significantly increased DA concentration by up to 11-fold. In laboratory when the long-term warming acclimated samples were assayed under low temperatures, changes in growth rates and DA concentrations indicated that P. multiseries did not adapt to elevated temperature, but could instead rapidly and reversibly acclimate to temperature shifts. However, the warming-acclimated lines showed evidence of adaptation to elevated temperatures in the transcriptome data. Here the core gene expression was not reversed when warming-acclimated lines were moved back to the low temperature environment, which suggested that P. multiseries cells might adapt to rising temperature over longer timescales. The distinct strategies of phenotypic plasticity to rising temperature and pCO2 demonstrate a strong acclimation capacity for this bloom-forming toxic diatom in the future ocean.

Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters

In the context of an increasing atmospheric carbon dioxide (CO₂) level, acidification of estuarine and coastal waters is greatly exacerbated by land-derived nutrient inputs, coastal upwelling, and complex biogeochemical processes. A deeper understanding of how nitrifiers respond to intensifying acidification is thus crucial to predict the response of estuarine and coastal ecosystems and their contribution to global climate change. Here, we show that acidification can significantly decrease nitrification rate but stimulate generation of byproduct nitrous oxide (N₂O) in estuarine and coastal waters. By varying CO₂ concentration and pH independently, an expected beneficial effect of elevated CO₂ on activity of nitrifiers ("CO₂-fertilization" effect) is excluded under acidification. Metatranscriptome data further demonstrate that nitrifiers could significantly up-regulate gene expressions associated with intracellular pH homeostasis to cope with acidification stress. This study highlights the molecular underpinnings of acidification effects on nitrification and associated greenhouse gas N₂O emission, and helps predict the response and evolution of estuarine and coastal ecosystems under climate change and human activities.

Ammonia Production Using Bacteria and Yeast toward a Sustainable Society

Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.

The Co-Evolution Aspects of the Biogeochemical Role of Phytoplankton in Aquatic Ecosystems: A Review

In freshwater and marine ecosystems, the phytoplankton community is based on microalgae and cyanobacteria, which include phylogenetically very diverse groups of oxygenic photoautotrophs. In the process of evolution, they developed a wide range of bio(geo)chemical adaptations that allow them to effectively use solar radiation, CO₂, and nutrients, as well as major and trace elements, to form O₂ and organic compounds with a high chemical bond energy. The inclusion of chemical elements in the key processes of energy and plastic metabolism in the cell is determined by redox conditions and the abundance and metabolic availability of elements in the paleoenvironment. Geochemical evolution, which proceeded simultaneously with the evolution of biosystems, contributed to an increase in the number of metals and trace elements acting as cofactors of enzymes involved in metabolism and maintaining homeostasis in the first photoautotrophs. The diversity of metal-containing enzymes and the adaptive ability to replace one element with another without losing the functional properties of enzymes ensured the high ecological plasticity of species and allowed microalgae and cyanobacteria to successfully colonize a wide variety of habitats. In this review, we consider the main aspects of the modern concepts of the biogeochemical evolution of aquatic ecosystems and the role of some metals in the main bioenergetic processes in photosynthetic prokaryotes and eukaryotes. We present generalized data on the efficiency of the assimilation of key nutrients by phytoplankton and their importance in the cycle of carbon, silicon, nitrogen, phosphorus, sulfur, and iron. This article presents modern views on the evolutionary prerequisites for the formation of elemental signatures in different systematic groups of microalgae, as well as the possibility of using the stoichiometric ratio in the study of biological and geochemical processes in aquatic ecosystems.

How elevated nitrogen load affects bacterial community structure and nitrogen cycling services in coastal water

Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively correlated with elevated dissimilatory nitrate reduction and denitrification pathway abundances. Fallowed fish farms were characterized by a predicted high abundance of nirA and narB genes contributing to assimilatory nitrate reduction pathway due to the prevalence of Cyanobacteria. Overall, these results suggested active operation and short hiatus in coastal aquaculture practices could rapidly impact planktonic bacterial communities and further influence nitrogen cycling and associated processes. These findings will improve the understanding of the responses and interactions between microbiome and aquaculture activities. In a world of increasing aquaculture demands, this work has important implications for sustainable water resource management and development.

Molecular analysis of microbial nitrogen transformation and removal potential in the plant rhizosphere of artificial tidal wetlands across salinity gradients

This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0-30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 10³-9.12 × 10⁸ (nitrogen functional genes) and 1.24 × 10⁸-8.43 × 10⁹ copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23-9.23, 400.03-755.91, 3.12-35.24 and 30.51-300.04 nmolN₂·g^-1·d^-1, respectively. The denitrification process contributed to 73.59-88.65% of NO_x^- reduction, compared to 0.71-13.20% and 8.20-15.42% via DNRA and anammox, as 83.83-90.74% of N₂ production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28-99.23% of NH₄⁺ oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.

MXene-Derived Metal-Organic Framework@MXene Heterostructures toward Electrochemical NO Sensing

The electrochemical sensing of nitric oxide (NO) molecules by metal-organic framework (MOF) catalysts has been impeded, to a large extent, owing to their poor electrical conductivity and weak NO adsorption. In this work, incomplete in situ conversion of V₂ CT_x (T = terminal atoms) MXene to MOF is adopted, forming MOF@MXene heterostructures, which outperform MXene and MOF monocomponents toward electrochemical NO sensing. Density functional theory (DFT) calculation results indicate metal-like electronic characters for the heterostructure benefiting from the dominating contribution of the V 3d orbitals of the metallic MXene. Moreover, plane-averaged charge density difference shows substantial charge redistribution occurs at the heterointerfaces, producing a built-in field, which facilitates charge transfer. Besides, molecular mechanics-based simulated annealing calculation reveals greatly enhanced adsorption energies of NO molecules on the heterointerfaces than that on separate MOFs and MXenes. Hence, the facilitated charge transfer and preferential NO adsorption are responsible for the dramatically promoted performance toward NO sensing. The prudent design of MOF@MXene heterostructure may spur advanced electrocatalysts for electrochemical sensing.

Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera

In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.

Integrating the impact of global change on the niche and physiology of marine nitrogen-fixing cyanobacteria

Marine nitrogen fixation is a major source of new nitrogen to the ocean, which interacts with climate driven changes to physical nutrient supply to regulate the response of ocean primary production in the oligotrophic tropical ocean. Warming and changes in nutrient supply may alter the ecological niche of nitrogen-fixing organisms, or 'diazotrophs', however, impacts of warming on diazotroph physiology may also be important. Lab-based studies reveal that warming increases the nitrogen fixation-specific elemental use efficiency (EUE) of two prevalent marine diazotrophs, Crocosphaera and Trichodesmium, thus reducing their requirements for the limiting nutrients iron and phosphorus. Here, we coupled a new diazotroph model based upon observed diazotroph energetics of growth and resource limitation to a state-of-the-art global model of phytoplankton physiology and ocean biogeochemistry. Our model is able to address the integrated response of nitrogen fixation by Trichodesmium and Crocosphaera to warming under the IPCC high emission RCP8.5 scenario for the first time. Our results project a global decline in nitrogen fixation over the coming century. However, the regional response of nitrogen fixation to climate change is modulated by the diazotroph-specific thermal performance curves and EUE, particularly in the Pacific Ocean, which shapes global trends. Spatially, the response of both diazotrophs is similar with expansion towards higher latitudes and reduced rates of nitrogen fixation in the lower latitudes. Overall, 95%-97% of the nitrogen fixation climate signal can be attributed to the combined effect of temperature on the niche and physiology of marine diazotrophs, with decreases being associated with a reduced niche and increases resulting due to a combination of expanding niche and temperature driven changes to EUE. Climate change impacts on both the niche and physiology of marine diazotrophs interact to shape patterns of marine nitrogen fixation, which will have important implications for ocean productivity in the future.

Microbial diversity and biogeochemical cycling potential in deep-sea sediments associated with seamount, trench, and cold seep ecosystems

Due to their extreme water depths and unique physicochemical conditions, deep-sea ecosystems develop uncommon microbial communities, which play a vital role in biogeochemical cycling. However, the differences in the compositions and functions of the microbial communities among these different geographic structures, such as seamounts (SM), marine trenches (MT), and cold seeps (CS), are still not fully understood. In the present study, sediments were collected from SM, MT, and CS in the Southwest Pacific Ocean, and the compositions and functions of the microbial communities were investigated by using amplicon sequencing combined with in-depth metagenomics. The results revealed that significantly higher richness levels and diversities of the microbial communities were found in SM sediments, followed by CS, and the lowest richness levels and diversities were found in MT sediments. Acinetobacter was dominant in the CS sediments and was replaced by Halomonas and Pseudomonas in the SM and MT sediments. We demonstrated that the microbes in deep-sea sediments were diverse and were functionally different (e.g., carbon, nitrogen, and sulfur cycling) from each other in the seamount, trench, and cold seep ecosystems. These results improved our understanding of the compositions, diversities and functions of microbial communities in the deep-sea environment.

Ambiguous controls on simulated diazotrophs in the world oceans

Nitrogen fixers, or diazotrophs, play a key role in the nitrogen and carbon cycle of the world oceans. Diazotrophs are capable of utilising atmospheric dinitrogen which is a competitive advantage over generally faster growing ordinary phytoplankton in nitrogen-depleted conditions in the sun-lit surface ocean. In this study we argue that additional competitive advantages must be at play in order to explain the dynamics and distribution of diazotrophs in the global oceans. Backed by growing published evidence we test the effects of preferential grazing (where zooplankton partly avoids diazotrophs) and high-affinity diazotrophic phosphorus uptake in an Earth System Model of intermediate complexity. Our results illustrate that these fundamentally different model assumptions result in a very similar match to observation-based estimates of nitrogen fixation while, at the same time, they imply very different trajectories into our warming future. The latter applies to biomass, fixation rates as well as to the ratio of the two. We conclude that a more comprehensive understanding of the competition between ordinary and diazotrophic phytoplankton will reduce uncertainties in model-based projections of the oceanic N cycle.

A case for an active eukaryotic marine biosphere during the Proterozoic era

The microfossil record demonstrates the presence of eukaryotic organisms in the marine ecosystem by about 1,700 million years ago (Ma). Despite this, steranes, a biomarker indicator of eukaryotic organisms, do not appear in the rock record until about 780 Ma in what is known as the "rise of algae." Before this, it is argued that eukaryotes were minor ecosystem members, with prokaryotes dominating both primary production and ecosystem dynamics. In this view, the rise of algae was possibly sparked by increased nutrient availability supplying the higher nutrient requirements of eukaryotic algae. Here, we challenge this view. We use a size-based ecosystem model to show that the size distribution of preserved eukaryotic microfossils from 1,700 Ma and onward required an active eukaryote ecosystem complete with phototrophy, osmotrophy, phagotrophy, and mixotrophy. Model results suggest that eukaryotes accounted for one-half or more of the living biomass, with eukaryotic algae contributing to about one-half of total marine primary production. These ecosystems lived with deep-water phosphate levels of at least 10% of modern levels. The general lack of steranes in the pre-780-Ma rock record could be a result of poor preservation.

Sinking Trichodesmium fixes nitrogen in the dark ocean

The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.

Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.

Real-Time Underway Mapping of Nutrient Concentrations of Surface Seawater Using an Autonomous Flow Analyzer

High-frequency field nutrient analyzers offer a promising technology to solve time-consuming and laborious sampling problems in dynamic and complex river-estuarine-coastal ecosystems. However, few studies on the simultaneous underway analysis of five key nutrients (ammonium, nitrite, nitrate, phosphate, and silicate) in seawaters are available because of the limitations of the technique. In this study, a state-of-the-art autonomous portable analyzer for the shipboard analysis of nutrients in the environment of varied salinities and concentration ranges was reported. The analyzer consisted of compact hardware that was well suited for shipboard deployment with minimal maintenance. Moreover, a novel LabVIEW-based software program was developed, containing additional functions such as automated calibration curve generation, autodilution of high-concentration samples, and a user-friendly interface for multiparameter analysis using a single instrument. After the optimization of chemical reactions and work flow chart, the analyzer exhibited low limits of detection, a large linear range with automated dilution, and relative standard deviations of less than 2% (n = 11). Compared to other flow-based techniques, this analyzer is more portable and consumes less reagent with an autonomous data processing function and applicability within a broad salinity range (0-35). The analyzer was successfully applied for real-time analysis in the Jiulong River Estuary-Xiamen Bay with excellent on-site accuracy and applicability. The relationship between high spatial resolution nutrient concentrations and salinities showed very different patterns in estuarine and coastal areas, indicating the benefit of using an underway automated analyzer for chemical mapping in a dynamic environment.

A Synthesis of Viral Contribution to Marine Nitrogen Cycling

Nitrogen is an essential component of major cellular macromolecules, such as DNA and proteins. Its bioavailability has a fundamental influence on the primary production of both terrestrial and oceanic ecosystems. Diverse marine microbes consume nitrogen, while only a limited taxon could replenish it, leaving nitrogen one of the most deficient nutrients in the ocean. A variety of microbes are involved in complex biogeochemical transformations of nitrogen compounds, and their ecological functions might be regulated by viruses in different manners. First and foremost, viruses drive marine nitrogen flow via host cell lysis, releasing abundant organic nitrogen into the surrounding environment. Secondly, viruses can also participate in the marine nitrogen cycle by expressing auxiliary metabolic genes (AMGs) to modulate host nitrogen metabolic pathways, such as nitrification, denitrification, anammox, and nitrogen transmembrane transport. Additionally, viruses also serve as a considerable reservoir of nitrogen element. The efficient turnover of viruses fundamentally promotes nitrogen flow in the oceans. In this review, we summarize viral contributions in the marine nitrogen cycling in different aspects and discuss challenges and issues based on recent discoveries of novel viruses involved in different processes of nitrogen biotransformation.