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Nitrification, the microbial conversion of ammonium to nitrite then to nitrate, occurs throughout the oceanic water column, yet the environmental factors influencing the production of nitrate in the euphotic zone (EZ) remain unclear. In this study, the natural abundances of N and O isotopes (δ¹⁵N and δ¹⁸O, respectively) in nitrate were used in an existing model framework to quantify nitrate contributed by EZ nitrification in the California Current Ecosystem (CCE) during two anomalously warm years. Model data estimated that between 6% and 36% of the EZ nitrate reservoirs were derived from the combined steps of nitrification within the EZ. The CCE data set found nitrification contributions to EZ nitrate to be positively correlated with nitrite concentrations () at the depth of the primary nitrite maximum (PNM). Building on this correlation, EZ nitrification in the southern California Current was estimated to contribute on average 20% ± 6% to EZ nitrate as inferred using the PNMof the long‐term California Cooperative Oceanic Fisheries Investigation (CalCOFI) survey record. A multiple linear regression analysis of the CalCOFI PNMtime series identified two conditions that led to positive deviations in. Enhanced PNM, and potentially enhanced EZ nitrification, may be linked to (1) reduced phytoplankton competition for ammonium () andas interpreted from particulate organic carbon:chlorophyll ratios, and/or (2) to increased supply of(and thenoxidation to) from the degradation of organic nitrogen as interpreted from particulate organic nitrogen concentrations.

 

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.

 

Transitions in phytoplankton community composition are typically attributed to ecological succession even in physically dynamic upwelling systems like the California Current Ecosystem (CCE). An expected succession from a high‐chlorophyll (~ 10μg L⁻¹) diatom‐dominated assemblage to a low‐chlorophyll (< 1.0μg L⁻¹) non‐diatom dominated assemblage was observed during a 2013 summer upwelling event in the CCE. Using an interdisciplinary field‐based space‐for‐time approach leveraging both biogeochemical rate measurements and metatranscriptomics, we suggest that this successional pattern was driven primarily by physical processes. An annually recurring mesoscale eddy‐like feature transported significant quantities of high‐phytoplankton‐biomass coastal water offshore. Chlorophyll was diluted during transport, but diatom contributions to phytoplankton biomass and activity (49–62% observed) did not decline to the extent predicted by dilution (18–24% predicted). Under the space‐for‐time assumption, these trends infer diatom biomass and activity and were stimulated during transport. This is hypothesized to result from decreased contact rates with mortality agents (e.g., viruses) and release from nutrient limitation (confirmed by rate data nearshore), as predicted by the Disturbance‐Recovery hypothesis of phytoplankton bloom formation. Thus, the end point taxonomic composition and activity of the phytoplankton assemblage being transported by the eddy‐like feature were driven by physical processes (mixing) affecting physiological (release from nutrient limitation, increased growth) and ecological (reduced mortality) factors that favored the persistence of the nearshore diatoms during transit. The observed connection between high‐diatom‐biomass coastal waters and non‐diatom‐dominated offshore waters supports the proposed mechanisms for this recurring eddy‐like feature moving seed populations of coastal phytoplankton offshore and thereby sustaining their activity.

 

ABSTRACT Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many coastal Vibrio spp. can infect humans, representing a growing threat linked to increasing seawater temperatures. Interactions with eukaryotic organisms may provide attachment substrate and critical nutrients that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp. However, vibrio interactions with planktonic organisms in an environmental context are poorly understood. We quantified the pathogenic Vibrio species V. cholerae , V. parahaemolyticus , and V. vulnificus monthly for 1 year at five sites and observed high abundances, particularly during summer months, with species-specific temperature and salinity distributions. Using metabarcoding, we established a detailed profile of both prokaryotic and eukaryotic coastal microbial communities. We found that pathogenic Vibrio species were frequently associated with distinct eukaryotic amplicon sequence variants (ASVs), including diatoms and copepods. Shared environmental conditions, such as high temperatures and low salinities, were associated with both high concentrations of pathogenic vibrios and potential environmental reservoirs, which may influence vibrio infection risks linked to climate change and should be incorporated into predictive ecological models and experimental laboratory systems. IMPORTANCE Many species of coastal vibrio bacteria can infect humans, representing a growing health threat linked to increasing seawater temperatures. However, their interactions with surrounding microbes in the environment, especially eukaryotic organisms that may provide nutrients and attachment substrate, are poorly understood. We quantified three pathogenic Vibrio species monthly for a duration of 1 year, finding that all three species were abundant and exhibited species-specific temperature and salinity distributions. Using metabarcoding, we investigated associations between these pathogenic species and prokaryotic and eukaryotic microbes, revealing genus and amplicon sequence variant (ASV)-specific relationships with potential functional implications. For example, pathogenic species were frequently associated with chitin-producing eukaryotes, such as diatoms in the genus Thalassiosira and copepods. These associations between high concentrations of pathogenic vibrios and potential environmental reservoirs should be considered when predicting infection risk and developing ecologically relevant model systems. 

Micronutrients control phytoplankton growth in the ocean, influencing carbon export and fisheries. It is currently unclear how micronutrient scarcity affects cellular processes and how interdependence across micronutrients arises. We show that proximate causes of micronutrient growth limitation and interdependence are governed by cumulative cellular costs of acquiring and using micronutrients. Using a mechanistic proteomic allocation model of a polar diatom focused on iron and manganese, we demonstrate how cellular processes fundamentally underpin micronutrient limitation, and how they interact and compensate for each other to shape cellular elemental stoichiometry and resource interdependence. We coupled our model with metaproteomic and environmental data, yielding an approach for estimating biogeochemical metrics, including taxon-specific growth rates. Our results show that cumulative cellular costs govern how environmental conditions modify phytoplankton growth. 

The Southern Ocean (SO) harbors some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how these changes will influence community composition and downstream biogeochemical processes. We performed light-saturated experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea to examine the effects of increased iron availability (+2 nM) and warming (+3 and +6 °C) on nutrient uptake, as well as the growth and transcriptional responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia . We found that community nutrient uptake and primary productivity were elevated under both warming conditions without iron addition (relative to ambient −0.5 °C). This effect was greater than additive under concurrent iron addition and warming. Pseudo-nitzschia became more abundant under warming without added iron (especially at 6 °C), while Fragilariopsis only became more abundant under warming in the iron-added treatments. We attribute the apparent advantage Pseudo-nitzschia shows under warming to up-regulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia ’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters and thereby influence global nutrient distribution and carbon cycling. 

Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum . Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae. 

Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone. 

Vast and diverse microbial communities exist within the ocean. To better understand the global influence of these microorganisms on Earth’s climate, we developed a robot capable of sampling dissolved and particulate seawater biochemistry across ocean basins while still capturing the fine-scale biogeochemical processes therein. Carbon and other nutrients are acquired and released by marine microorganisms as they build and break down organic matter. The scale of the ocean makes these processes globally relevant and, at the same time, challenging to fully characterize. Microbial community composition and ocean biochemistry vary across multiple physical scales up to that of the ocean basins. Other autonomous underwater vehicles are optimized for moving continuously and, primarily, horizontally through the ocean. In contrast,Clio, the robot that we describe, is designed to efficiently and precisely move vertically through the ocean, drift laterally in a Lagrangian manner to better observe water masses, and integrate with research vessel operations to map large horizontal scales to a depth of 6000 meters. We present results that show howClioconducts high-resolution sensor surveys and sample return missions, including a mapping of 1144 kilometers of the Sargasso Sea to a depth of 1000 meters. We further show how the samples obtain filtered biomass from seawater that enable genomic and proteomic measurements not possible through in situ sensing. These results demonstrate a robotic oceanography approach for global-scale surveys of ocean biochemistry.

 

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.