Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean

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.

Physiological Influence of Fe and Cu Availability on Nitrogen Isotope Fractionation during Ammonia Oxidation

Microbially mediated cycling processes play central roles in regulating the speciation and availability of nitrogen, a vital nutrient with wide implications for agriculture, water quality, wastewater treatment, ecosystem health, and climate change. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by bacteria (AOB) and archaea (AOA) that require the trace metal micronutrients copper (Cu) and iron (Fe) for growth and metabolic catalysis. While stable isotope analyses for constraining nitrogen cycling are commonly used, it is unclear whether metal availability may modulate expression of stable isotope fractionation during ammonia oxidation, by varying growth or through regulation of metabolic metalloenzymes. We present the first study examining the influence of Fe and Cu availability on the kinetic nitrogen isotope effect in ammonia oxidation (15εAO). We report a general independence of 15εAO from the growth rate in AOB, except at a low temperature (10 °C). With AOA Nitrosopumilus maritimus SCM1, however, 15εAO decreases nonlinearly at lower oxidation rates. We examine assumptions involved in the interpretation of 15εAO values and suggest these dynamics may arise from physiological constraints that push the system toward isotopic equilibrium. These results suggest important links between isotope fractionation and environmental constraints on physiology in these key N cycling microorganisms.

Particle-associated denitrification is the primary source of N2O in oxic coastal waters

The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.

The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean

To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.

Biogeochemical and physical controls on ammonium accumulation on the Chukchi shelf, western Arctic Ocean

Spatial variability of ammonium concentrations along repeat transects were examined on the Chukchi shelf during 2012-2018. Two distinct near-bottom high ammonium pools (>1 μmol/kg) near 67.5°N and 72.5°N of the transects were identified in all years. The accumulation of ammonium in the regions is driven primarily by a combination of biogeochemical processes (e.g., dynamic bacterial remineralization of organic matter) and physical controls (e.g., strong density-contrast barrier limits upward mixing of ammonium). The ammonium pool on the shelf may became larger in the expectation of the stronger bacterial remineralization following elevate primary production, and may have potential impact on the structure and productivity of ecosystem on the Chukchi shelf.

Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre

Nitrite, an intermediate product of the oxidation of ammonia to nitrate (nitrification), accumulates in upper oceans, forming the primary nitrite maximum (PNM). Nitrite concentrations in the PNM are relatively low in the western North Pacific subtropical gyre (wNPSG), where eddies are frequent and intense. To explain these low nitrite concentrations, we investigated nitrification in cyclonic eddies in the wNPSG. We detected relatively low half-saturation constants (i.e., high substrate affinities) for ammonia and nitrite oxidation at 150 to 200 meter water depth. Eddy-induced displacement of high-affinity nitrifiers and increased substrate supply enhanced ammonia and nitrite oxidation, depleting ambient substrate concentrations in the euphotic zone. Nitrite oxidation is more strongly enhanced by the cyclonic eddies than ammonia oxidation, reducing concentrations and accelerating the turnover of nitrite in the PNM. These findings demonstrate a spatial decoupling of the two steps of nitrification in response to mesoscale processes and provide insights into physical-ecological controls on the PNM.

A high-efficiency mixotrophic photoelectroactive biofilm reactor (MPBR) for enhanced simultaneous removal of nutrients and antibiotics by integrating light intensity regulation and microbial extracellular electron extraction

The performance of a mixotrophic photoelectroactive biofilm reactor (MPBR) was improved in order to achieve enhanced simultaneous removal of multiple aqueous pollutants and the production of valuable biomass. The MPBR was optimized by integrating the regulation of light intensity (3000, 8000 and 23000 lux) and microbial extracellular electron extraction (using an electrode at -0.3, 0 and 0.3 V). Results showed that the MPBR operated at a high light intensity (23000 lux) with a potential of -0.3 V (Coulomb efficiency (CE) of 9.65%) achieved maximum pollutant removal efficiencies, effectively removing 65% NH₄⁺-N, 95% PO₄^3--P and 52% sulfadiazine (SDZ) within 72 h, exhibiting an increase by 30%, 56% and 26% compared to an MPBR operated at the same light intensity but without an externally applied potential. The use of an electrode with an applied potential of -0.3V was most suitable for the extraction of photosynthetic electrons from the photoelectroactive biofilm, in which Rhodocyclaceae was highly enriched, effectively alleviating photoinhibition and thereby enhancing N, P assimilation and SDZ degradation under high light conditions. A maximum lipid content of 409.28 mg/g was obtained under low light intensity (3000 lux) conditions with an applied potential of 0.3 V (CE 9.08%), while a maximum protein content of 362.29 mg/g was obtained at a low light intensity (3000 lux) and 0 V (CE 10.71%). The selective enrichment of Chlorobium and the subsequent enhanced conversion of excess available carbon under low light and positive potential stimulation conditions, were responsible for the enhanced accumulation of proteins and lipids in biomass.

Bottom-associated phytoplankton bloom and its expansion in the Arctic Ocean

Phytoplankton production in the Arctic Ocean is increasing due to global warming-induced sea ice loss, which is generally assessed through satellite observations of surface chlorophyll. Here we show that a diatom bloom can occur near the seafloor rather than at the surface in the open Arctic Ocean. Light can reach the seafloor underlying nutrient-rich bottom water after the spring bloom because the surface water becomes oligotrophic and increases transparency in the region of shallow Arctic shelf. Our microcosm experiment demonstrated that diatoms formed a bloom when sediments on the shelf region, which contained abundant viable diatom cells, were exposed to even weak light reaching the seafloor (~1% of the surface irradiance). Repeated shipboard observations in the shelf region suggested that such bottom-associated blooms occurred occasionally and the primary production was significantly underestimated by satellite observations. The average bottom irradiance (2003-2017) in the Arctic Ocean is particularly promoted in summer in the eastern East Siberian Sea and the Foxe Basin, which were ice-covered throughout the year until the 1990s. Our results imply that hidden bottom-associated blooms are now widespread across the shallow Arctic shelf region.

Effects of wastewater effluent-borne nutrients on phytoplankton off the coast of Jeju Island

The spatiotemporal distributions of nutrients in coastal waters surrounding eight wastewater treatment plants (WWTPs) in four seasons were investigated to determine the effects of WWTP effluents on seawater off Jeju Island, Korea. The highest concentrations of nutrients were observed in the outlets of WWTPs with relatively high ammonium concentrations among dissolved inorganic nitrogen (DIN). The reduced DIN (NO₂^- and NH₄⁺)/total DIN ratios are used as a potential short-term index for marine environmental conditions. In seawater surrounding the WWTPs, relatively low nutrient concentrations were observed in spring and fall, due to enhanced biological production, which is closely linked to decreased N/P ratios. Because the highest WWTP effluent fluxes of ammonium in this study were similar to the fluxes of nutrients from submarine groundwater discharge, diffusion from bottom sediments, and discharge from land-based fish farm wastewater, WWTP effluent-derived nutrients are potentially important in oligotrophic environments and can be readily utilized by phytoplankton.

Arbuscular Mycorrhiza and Nitrification: Disentangling Processes and Players by Using Synthetic Nitrification Inhibitors

Both plants and their associated arbuscular mycorrhizal (AM) fungi require nitrogen (N) for their metabolism and growth. This can result in both positive and negative effects of AM symbiosis on plant N nutrition. Either way, the demand for and efficiency of uptake of mineral N from the soil by mycorrhizal plants are often higher than those of nonmycorrhizal plants. In consequence, the symbiosis of plants with AM fungi exerts important feedbacks on soil processes in general and N cycling in particular. Here, we investigated the role of the AM symbiosis in N uptake by Andropogon gerardii from an organic source (¹⁵N-labeled plant litter) that was provided beyond the direct reach of roots. In addition, we tested if pathways of ¹⁵N uptake from litter by mycorrhizal hyphae were affected by amendment with different synthetic nitrification inhibitors (dicyandiamide [DCD], nitrapyrin, or 3,4-dimethylpyrazole phosphate [DMPP]). We observed efficient acquisition of ¹⁵N by mycorrhizal plants through the mycorrhizal pathway, independent of nitrification inhibitors. These results were in stark contrast to ¹⁵N uptake by nonmycorrhizal plants, which generally took up much less ¹⁵N, and the uptake was further suppressed by nitrapyrin or DMPP amendments. Quantitative real-time PCR analyses showed that bacteria involved in the rate-limiting step of nitrification, ammonia oxidation, were suppressed similarly by the presence of AM fungi and by nitrapyrin or DMPP (but not DCD) amendments. On the other hand, abundances of ammonia-oxidizing archaea were not strongly affected by either the AM fungi or the nitrification inhibitors. IMPORTANCE Nitrogen is one of the most important elements for all life on Earth. In soil, N is present in various chemical forms and is fiercely competed for by various microorganisms as well as plants. Here, we address competition for reduced N (ammonia) between ammonia-oxidizing prokaryotes and arbuscular mycorrhizal fungi. These two functionally important groups of soil microorganisms, participating in nitrification and plant mineral nutrient acquisition, respectively, have often been studied in separation in the past. Here, we showed, using various biochemical and molecular approaches, that the fungi systematically suppress ammonia-oxidizing bacteria to an extent similar to that of some widely used synthetic nitrification inhibitors, whereas they have only a limited impact on abundance of ammonia-oxidizing archaea. Competition for free ammonium is a plausible explanation here, but it is also possible that the fungi produce some compounds acting as so-called biological nitrification inhibitors.

Plankton food webs in the oligotrophic Gulf of Mexico spawning grounds of Atlantic bluefin tuna

We used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic bluefin tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show extensive nutrient regeneration fueling primary productivity (mostly by cyanobacteria and other picophytoplankton) in the upper euphotic zone. The food web is dominated by the microbial loop (>70% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). By contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <10% of the net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on podonid cladocerans and other suspension-feeding zooplankton, which in turn derive much of their nutrition from nano- and micro-phytoplankton (mixotrophic flagellates, and to a lesser extent, diatoms). This allows ABT larvae to maintain a comparatively low trophic level (~4.2 for preflexion and postflexion larvae), which increases trophic transfer from phytoplankton to larval fish.

Spatio-Temporal Variations in the Abundance and Community Structure of Nitrospira in a Tropical Bay

Nitrospira is the most diverse genus of nitrite-oxidizing bacteria, and its members are widely spread in various natural and engineered ecosystems. In this study, the phylogenetic diversity of Nitrospira and monthly changes of its abundance from Zhanjiang Bay were investigated. Phylogenetic analysis showed that among 58 OTUs with high abundance, 74% were not affiliated with any previously described Nitrospira species, revealing a previously unrecognized diversity of coastal Nitrospira. The abundances of both Nitrospira and Nitrospina exhibited a significantly monthly change. During most of the months, abundance of Nitrospina was greater than that of Nitrospira. In particle-attached communities, either abundance of Nitrospina or Nitrospira was highly correlated with that of ammonia-oxidizing archaea (AOA), whereas abundance of ammonia-oxidizing bacteria was only highly correlated with that of Nitrospina. In free-living communities, either abundance of Nitrospina or Nitrospira was correlated only with that of AOA. These results suggest that both Nitrospira and Nitrospina can be involved in nitrite oxidation by coupling with AOA, but Nitrospina may play a greater role than Nitrospira in this tropical bay.

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming

In the context of continuously increasing anthropogenic nitrogen inputs, knowledge of how ammonia oxidation (AO) in the ocean responds to warming is crucial to predicting future changes in marine nitrogen biogeochemistry. Here, we show divergent thermal response patterns for marine AO across a wide onshore/offshore trophic gradient. We find ammonia oxidizer community and ambient substrate co-regulate optimum temperatures (T_opt), generating distinct thermal response patterns with T_opt varying from ≤14 °C to ≥34 °C. Substrate addition elevates T_opt when ambient substrate is unsaturated. The thermal sensitivity of kinetic parameters allows us to predict responses of both AO rate and T_opt at varying substrate and temperature below the critical temperature. A warming ocean promotes nearshore AO, while suppressing offshore AO. Our findings reconcile field inconsistencies of temperature effects on AO, suggesting that predictive biogeochemical models need to include such differential warming mechanisms on this key nitrogen cycle process.

Microbial ammonia oxidation is important in marine nutrient cycling and greenhouse gas dynamics, but the responses to ocean warming are unclear. Here coast to open ocean incubations show that projected year 2100 temperatures might be too hot for these microbes in oligotrophic regions to handle, but may facilitate oxidation rates in coastal waters.

Effects of different light conditions on ammonium removal in a consortium of microalgae and partial nitrifying granules

Ammonium removal by a coupling process of microalgae (Chlorella sorokiniana) with partial nitrifying granules was evaluated in batch reactors illuminated in a wide range of light intensities (0, 100, 450, and 1600 μmol photons m^-2 s^-1). Ammonium oxidation performance for different light exposure time showed that the granules had a light stress tolerance at 1600 μmol photons m^-2 s^-1 for up to 12 h, but continuous illumination induced severe inhibition on nitrifying bacteria thereafter. Ammonium removal efficiencies at the end of tests were 66%, 62%, 5%, and -10% (due to ammonification) for 0, 100, 450, and 1600 μmol photons m^-2 s^-1, respectively. The nitrogen mass balance shows co-occurrence of microalgal growth taking up 24% of fed ammonium and nitrifying bacteria oxidizing 38% of fed ammonium at 100 μmol photons m^-2 s^-1, while both nitrification and microalgal growth are inhibited at light intensity above 450 μmol photons m^-2 s^-1. In comparing results from this study with previous results, it was found that the ammonium removal pathway, i.e., nitrification or microalgal uptake, is regulated more strongly by daily average light intensity than by instantaneous light intensity. Empirical model equations to estimate the oxygen balance in consortium reactors categorized the effect of daily average light intensities on process performance as follows: (i) below 27 μmol photons m^-2 s^-1: insufficient oxygen for nitrification; (ii) 27 to 35: sufficient oxygen for nitrification via nitrite; (iii) 35 to 180: sufficient oxygen for nitrification via nitrate; (iv) above approximately 200-300: oversaturated dissolved oxygen, excess free ammonia and/or intensive light inhibitions.

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.

Dominance of nitrous oxide production by nitrification and denitrification in the shallow Chaohu Lake, Eastern China: Insight from isotopic characteristics of dissolved nitrous oxide

In recent decades, most lakes in Eastern China have suffered unprecedented nitrogen pollution, making them potential "hotspots" for N₂O production and emission. Understanding the mechanisms of N₂O production and quantifying emissions in these lakes is essential for assessing regional and global N₂O budgets and for mitigating N₂O emissions. Here, we measure isotopic compositions (δ¹⁵N-N₂O and δ¹⁸O-N₂O) and site preference (SP) of dissolved N₂O in an attempt to differentiate the relative contribution of N₂O production processes in the shallow, eutrophic Chaohu Lake, Eastern China. Our results show that the bulk isotope ratios for δ¹⁵N-N₂O, δ¹⁸O-N₂O, and SP were 5.8 ± 3.9‰, 29.3 ± 13.4‰, and 18.6 ± 3.2‰, respectively. More than 76.8% of the dissolved N₂O was produced via microbial processes. Findings suggest that dissolved N₂O is primarily produced via nitrification (between 27.3% and 48.0%) and denitrification (between 31.9% and 49.5%). In addition, isotopic data exhibit significant N₂O consumption during denitrification. We estimate the average N₂O emission rate (27.5 ± 26.0 μg N m^-2 h^-1), which is higher than that from rivers in the Changjiang River network (CRN). We scaled-up the regional N₂O emission (from 1.98 Gg N yr^-1 to 4.58 Gg N yr^-1) using a N₂O emission factor (0.51 ± 0.63%) for shallow lakes in the middle and lower region of the CRN. We suggest that beneficial circumstances for promoting complete denitrification may be helpful for reducing N₂O production and emissions in fresh surface waters.

Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies

Trichodesmium is an important dinitrogen (N₂)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N₂ fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N₂ fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.

Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes

Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.

Variations in the phytoplankton community due to dust additions in eutrophication, LNLC and HNLC oceanic zones

Dust deposition can bring nutrients and trace elements to the upper ocean and affect phytoplankton growth and community structure. We conducted a comparative study using on-board microcosm experiments amended with varying amounts of dust (0.2, 1, and 2 mg L^-1) in the East China Sea (eutrophic zone), the subtropical gyre (low-nutrient and low-chlorophyll zone, LNLC), and the Kuroshio-Oyashio transition region (high-nutrient and low-chlorophyll zone, HNLC) of the Northwest Pacific Ocean. The additions of dust supplied a considerable amount of nitrogen (N) and negligible phosphorus (P) relative to the seawater collected for incubation experiments (baseline), contributing to increases in Chlorophyll a with increasing dust additions. Significant linear correlations were observed between the net growth rates of larger cells (i.e., micro-size: >20 μm and nano-size: 2-20 μm) and available N (sum of baseline and added N) at each zone, demonstrating that phytoplankton size structure shifts towards larger cells with the increasing dust additions. In the experiments conducted in LNLC and HNLC zones, micro-sized phytoplankton (primarily consisting of diatoms) benefited most from dust additions. In the experiments conducted in eutrophic zone, however, the primary beneficiary was the nano-sized phytoplankton (primarily consisting of dinoflagellates). When a time lag of one day in relative abundance of diatoms (RAD, the abundance of diatoms divided by the sum of diatoms and dinoflagellates) relative to the N:P ratio was considered, we found the RAD increased substantially with increases in the N:P ratio until the ratio approached the Redfield ratio (N:P = 16:1), and then the RAD decreased gradually as the N:P ratio increased. This was ascribed to the lower sensitivity of dinoflagellates to nutrient shortage, relative to diatoms. Overall, our results suggested that the overwhelming input of N relative to P by dust deposition might cause significant ecological impacts by altering the N:P ratio of varying trophic seawaters.

Untangling hidden nutrient dynamics: rapid ammonium cycling and single-cell ammonium assimilation in marine plankton communities

Ammonium is a central nutrient in aquatic systems. Yet, cell-specific ammonium assimilation among diverse functional plankton is poorly documented in field communities. Combining stable-isotope incubations (¹⁵N-ammonium, ¹⁵N₂ and ¹³C-bicarbonate) with secondary-ion mass spectrometry, we quantified bulk ammonium dynamics, N₂-fixation and carbon (C) fixation, as well as single-cell ammonium assimilation and C-fixation within plankton communities in nitrogen (N)-depleted surface waters during summer in the Baltic Sea. Ammonium production resulted from regenerated (≥91%) and new production (N₂-fixation, ≤9%), supporting primary production by 78–97 and 2–16%, respectively. Ammonium was produced and consumed at balanced rates, and rapidly recycled within 1 h, as shown previously, facilitating an efficient ammonium transfer within plankton communities. N₂-fixing cyanobacteria poorly assimilated ammonium, whereas heterotrophic bacteria and picocyanobacteria accounted for its highest consumption (~20 and ~20–40%, respectively). Surprisingly, ammonium assimilation and C-fixation were similarly fast for picocyanobacteria (non-N₂-fixing Synechococcus) and large diatoms (Chaetoceros). Yet, the population biomass was high for Synechococcus but low for Chaetoceros. Hence, autotrophic picocyanobacteria and heterotrophic bacteria, with their high single-cell assimilation rates and dominating population biomass, competed for the same nutrient source and drove rapid ammonium dynamics in N-depleted marine waters.

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.