Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre

Unveiling the contribution of particle-associated non-cyanobacterial diazotrophs to N2 fixation in the upper mesopelagic North Pacific Gyre

Dinitrogen (N2) fixation supports marine life through the supply of reactive nitrogen. Recent studies suggest that particle-associated non-cyanobacterial diazotrophs (NCDs) could contribute significantly to N2 fixation contrary to the paradigm of diazotrophy as primarily driven by cyanobacterial genera. We examine the community composition of NCDs associated with suspended, slow, and fast-sinking particles in the North Pacific Subtropical Gyre. Suspended and slow-sinking particles showed a higher abundance of cyanobacterial diazotrophs than fast-sinking particles, while fast-sinking particles showed a higher diversity of NCDs including Marinobacter, Oceanobacter and Pseudomonas. Using single-cell mass spectrometry we find that Gammaproteobacteria N2 fixation rates were higher on suspended and slow-sinking particles (up to 67 ± 48.54 fmol N cell⁻¹ d⁻¹), while putative NCDs' rates were highest on fast-sinking particles (121 ± 22.02 fmol N cell⁻¹ d⁻¹). These rates are comparable to previous diazotrophic cyanobacteria observations, suggesting that particle-associated NCDs may be important contributors to pelagic N2 fixation.

Particle-associated N2 fixation by heterotrophic bacteria in the global ocean

N2-fixing microorganisms (diazotrophs) sustain life on our planet by providing biologically available nitrogen to plants. In the oceans, cyanobacterial diazotrophs, mostly prevalent in warm tropical and subtropical waters, were traditionally considered the sole contributors to marine N2 fixation. Recently, an almost ubiquitous distribution of N2-fixing heterotrophic bacteria has been discovered in the pelagic ocean. However, the mechanisms enabling heterotrophic diazotrophs to thrive in cold high-latitude waters and their contribution to the global nitrogen budget are unknown. Using a data-driven cell-based metabolic model, we show that heterotrophic bacteria inside sinking particles can fix N2 over a wide range of temperatures, explaining their ubiquitous presence in the oceans. We estimate that heterotrophic diazotrophs account for about 10% of global marine N2 fixation, with the highest contribution in oxygen minimum zones. These findings call for a reassessment of the N2 fixation patterns and the biogeochemical cycling of nitrogen in the global ocean.

Single-cell imaging reveals efficient nutrient uptake and growth of microalgae darkening the Greenland Ice Sheet

Blooms of dark pigmented microalgae accelerate glacier and ice sheet melting by reducing the surface albedo. However, the role of nutrient availability in regulating algal growth on the ice remains poorly understood. Here, we investigate glacier ice algae on the Greenland Ice Sheet, providing single-cell measurements of carbon:nitrogen:phosphorus (C:N:P) ratios and assimilation rates of dissolved inorganic carbon (DIC), ammonium and nitrate following nutrient amendments. The single-cell analyses reveal high C:N and C:P atomic ratios in algal biomass as well as intracellular P storage. DIC assimilation rates are not enhanced by ammonium, nitrate, or phosphate addition. Our combined results demonstrate that glacier ice algae can optimise nutrient uptake, facilitating the potential colonization of newly exposed bare ice surfaces without the need for additional nutrient inputs. This adaptive strategy is particularly important given accelerated climate warming and the expansion of melt areas on the Greenland Ice Sheet.

Coupling effect of cyanobacterial blooms with migration and transformation of typical pollutants in lake or reservoir: Enhanced or decreased?

Eutrophication of lake and reservoir caused by cyanobacterial harmful algal blooms (cyanoHABs) become a global ecological problem because of massive destruction of ecosystems, which have attracted attentions widely. In addition to the production of cyanotoxins by certain bloom-forming species, there may also be direct or indirect interactions between cyanobacteria blooms and various pollutants in lakes or reservoirs. Based on bibliometrics, 19110 papers in Web of Science (WOS) and 2998 papers in the China National Knowledge Infrastructure (CNKI) on eutrophication and cyanobacterial blooms in lakes and reservoirs were analyzed, which showed that research on this topic has been ongoing for nearly 80 years with a gradual increase in its popularity. The research on the coupling process of cyanobacterial blooms with five typical pollutants, including microcystins (MCs), heavy metals, viruses, antibiotics and antibiotic resistance genes (ARGs), indicate that the coupling process between cyanobacteria blooms and certain pollutants is indeed generated through direct or indirect interactions by adsorption, changing the physical and chemical conditions of water environment, and changing the structure of microbial community. For instance, the production, toxicity would be likely enhanced by cyanobacteria blooms directly. And the microorganisms may play a significant role in the interaction between cyanobacteria blooms and ARGs. Generally, the risk of some typical pollutants would be likely enhanced or decreased directly or indirectly by these processes. It is recommended that further attention be paid to the interrelationships between the process of cyanobacterial bloom and typical pollutants' migration and transformation, to provide the scientific basis for the risk assessment and thus multi-objective synergistic control and management of nutrients and typical pollutants in eutrophic lakes or reservoirs.

Puzzling out the ecological niche construction for nitrogen fixers in a coastal upwelling system

Diazotrophs are a diverse group of microorganisms that can fertilize the ocean through biological nitrogen fixation (BNF). Due to the high energetic cost of this process, diazotrophy in nitrogen-replete regions remains enigmatic. We use multidisciplinary observations to propose a novel framework for the ecological niche construction of nitrogen fixers in the upwelling region off NW Iberia-one of the most productive coastal regions in Europe-characterized by weak and intermittent wind-driven upwelling and the presence of bays. The main diazotroph detected (UCYN-A2) was more abundant and active during summer and early autumn, coinciding with relatively high temperatures (>16°C), low nitrogen:phosphorus ratios (N:P < 7.2), and a large contribution of ammonium (>75%) to the total dissolved inorganic nitrogen available. Furthermore, nutrient amendment experiments showed that BNF is detectable when phytoplankton biomass and productivity are nitrogen limited. Seasonally recurrent biogeochemical processes driven by hydrography create an ecological niche for nitrogen fixers in this system. During the spring-summer upwelling, nondiazotroph autotrophs consume nitrate and produce organic matter inside the bays. Thereafter, the combined effect of intense remineralization on the shelf and sustained positive circulation within the bays in late summer-early autumn, conveys enhanced ammonium content and excess phosphate into the warm surface layer. The low N:P ratio confers a competitive advantage to diazotrophs since they are not restricted by nitrogen supply. The new nitrogen supply mediated by BNF could extend the productivity period, and may be a key reason why upwelling bays are more productive than upwelled offshore waters.

Distribution of protoporphyrin IX during Prorocentrum donghaiense blooms and its relationship with particle-attached and free-living bacterial communities

Particle-attached (PA) and free-living (FL) bacterial communities are essential for nutrient cycles and metabolite production and serve as a food source in aquatic systems. However, our understanding of how biotic factors influence community interactions, co-occurrence patterns, and niche occupancy remains limited. This study investigated the influence of protoporphyrin IX (PPIX) on bacteria with different lifestyles during Prorocentrum donghaiense bloom. The findings revealed that PPIX distribution responded variably to changes in physicochemical parameters induced by red tide bloom. Large-sized or particle-attached (PA) phytoplankton (cell size >3 μm) were identified as the primary contributors to environmental PPIX, while small-sized plankton or free-living (FL) microorganisms (<3 μm) contributed less. In red tide-affected areas, PPIX and its derivatives were significantly more abundant than in non-red tide areas, indicating an increased demand for porphyrins by plankton during red tides. Additionally, the red tide also significantly influenced the preference of bacterial lineages for PA or FL lifestyles, highlighting a close interaction between bacteria with different lifestyles and PPIX levels. This study quantitatively analyzed the distribution of PPIX across different cell sizes in red tide and non-red tide marine environments, providing insights into microbial interactions and dynamics in changing ecosystems and offering a reference for using PPIX to predict red tide ecological disasters.

The NanoSIMS-HR: The Next Generation of High Spatial Resolution Dynamic SIMS

The high lateral resolution and sensitivity of the NanoSIMS 50 and 50L series of dynamic SIMS instruments have enabled numerous scientific advances over the past 25 years. Here, we report on the NanoSIMS-HR, the first major upgrade to the series, and analytical tests in a suite of sample types, including an aluminum sample containing silicon crystals, microalgae, and plant roots colonized with a symbiotic fungus. Significant improvements have been made in the Cs+ ion source, high voltage (HV) control, stage reproducibility, and other aspects of the instrument that affect performance. The modified design of the NanoSIMS-HR thermal-ionization Cs+ source enables a 5 pA primary ion beam to be focused into a 100 nm spot, a ∼2.5-fold increase compared to Cs+ sources on previous instruments (∼2 pA at 100 nm). The brightness of the new Cs+ source enables an ultimate lateral resolution as high as 30 nm and improved detection limits for a given analysis area. Sample stage movement accuracy is higher than 500 nm, enabling many-fold higher throughput automated analyses. With the new HV control, the primary ion beam impact energy can be reduced from 16 to 2 keV, which enables higher depth resolution during depth profiling (a 2-fold improvement), albeit with a 5-fold decrease in lateral resolution. In the NanoSIMS-HR, the secondary ion column and detection system are identical to those used in the previous series, and the isotopic analysis performance is as precise as in previous NanoSIMS instruments.

Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed

Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.

Fronts divide diazotroph communities in the Southern Indian Ocean

Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well-explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here, we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multifrontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving high N2 fixation rates (up to 13.96 nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.

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.

Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium

IMPORTANCE

The contribution of non-cyanobacterial diazotrophs (NCDs) to total N2 fixation in the marine water column is unknown, but their importance is likely constrained by the limited availability of dissolved organic matter and low O2 conditions. Light could support N2 fixation and growth by NCDs, yet no examples from bacterioplankton exist. In this study, we show that the phototrophic NCD, Rhodopseudomonas sp. BAL398, which is a member of the diazotrophic community in the surface waters of the Baltic Sea, can utilize light. Our study highlights the significance of biofilm formation for utilizing light and fixing N2 under oxic conditions and the role of cell plasticity in regulating these processes. Our findings have implications for the general understanding of the ecology and importance of NCDs in marine waters.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard)

Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.

Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

Dinitrogen (N₂) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N₂ fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N₂ fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.