Katherine A. Barbeau

This study quantifies the fecal pellet production and pellet sinking rates of the pyrosome Pyrosoma atlanticum in the Southern California Current across a range of conditions, from the productive nearshore to the oligotrophic offshore. Fecal pellet production rates averaged 1310 ± 76 pellets h ⁻¹ , resulting in the production of up to 390,380 pellets h ⁻¹ m ⁻² in locations with high densities of 298 ind. m ⁻² . Fecal pellet mean size was 354 ± 111 μ m, and sinking rates of fresh pellets averaged 47 ± 38 m d ⁻¹ , while aged pellets had lower rates averaging 31 ± 28 m d ⁻¹ . We estimate ingestion rates of 55.5 ± 9.5 mg C m ⁻² d ⁻¹ in the offshore and 41.1 ± 8.28 mg C m ⁻² d ⁻¹ in nearshore coastal waters. Based on pellet production rates, colony abundance, carbon content per pellet, and literature values of assimilation efficiencies, we estimate that pyrosomes consume the carbon equivalent of ~ 30% of net primary production in offshore waters and 1–26% in coastal waters. We present novel measurements of biogenic silica in pyrosome fecal pellets, indicating that pyrosomes can directly remove 0.5–4% of the euphotic zone‐integrated diatom standing stock, with higher rates in nearshore environments. Direct observation of fecal pellets showed unassimilated diatom chains, confirming direct consumption. Our results suggest that pyrosomes contribute to both carbon and silica export, important processes to constrain for understanding biogeochemistry in the region.

In the ocean, dissolved organic phosphorus (DOP) supports the health and productivity of marine phytoplankton, a phenomenon most often investigated under inorganic phosphate (Pi) scarcity. However, microbial DOP acquisition occurring in Pi replete ocean environments remains poorly understood. Here, we conducted a combination of nutrient addition experiments, alkaline phosphatase (AP) rate measurements, and metatranscriptomics analyses along an onshore-to-offshore gradient in the California Current Ecosystem (CCE), a relatively Pi-rich upwelling region. We found that AP activity (APA) and eukaryotic transcripts for DOP utilization were present throughout the CCE. In bottle incubations, APA was upregulated in response to iron (Fe) and nitrogen (N) additions. Major contributors to these trends included atypical alkaline phosphatases (AP _aty ) of diatoms in the coastal upwelling area, and unclassified non-cytoplasmic P-diesterases (PDE _nc ) of multiple eukaryotic taxa in the offshore regime. APA and gene expression dynamics were not coupled to phytoplankton growth, suggesting that these organisms experience underlying P stress, a state of cellular metabolism caused by Pi scarcity, even in regions primarily growth-limited by other elements. While AP _aty and PDE _nc were highly abundant among the microbial community phosphatase pool, these genes were missing from a widely used annotation database, highlighting the importance of manual curation for the detection of these atypical and unclassified proteins. Altogether, these results emphasize the functional diversity of phosphatases sustaining microbial community health in diverse and productive marine habitats.

Bacteria compete for iron by producing small-molecule chelators known as siderophores. The triscatechol siderophores trivanchrobactin and ruckerbactin, produced by Vibrio campbellii DS40M4 and Yersinia ruckeri YRB, respectively, are naturally occurring diastereomers that form chiral ferric complexes in opposing enantiomeric configurations. Chiral recognition is a hallmark of specificity in biological systems, yet the biological consequences of chiral coordination compounds are relatively unexplored. We demonstrate stereoselective discrimination of microbial growth and iron uptake by chiral Fe(III)–siderophores. The siderophore utilization pathway in V. campbellii DS40M4 is stereoselective for Λ-Fe(III)–trivanchrobactin, but not the mismatched Δ-Fe(III)–ruckerbactin diastereomer. Chiral recognition is likely conferred by the stereospecificity of both the outer membrane receptor (OMR) protein FvtA and the periplasmic binding protein (PBP) FvtB, both of which must interact preferentially with the Λ-configured Fe(III)-coordination complexes.

Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO₂for up to four days_.Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.

In the spring and summer, high rates of primary production occur in the California Current Ecosystem (CCE) when nutrients are supplied to the euphotic zone. During periods of intense coastal upwelling, a flux of the micronutrient iron comes from nearshore sedimentary sources. In this upwelling region, mesoscale filament features distribute iron laterally, leading to distinct iron‐influenced ecological zones. This study is the first to focus on the biogeochemical links between iron, the macronutrients, and particulates in coastal upwelling filaments. Broad spatial patterns of iron and biogenic silica concentrations, and proxies of iron‐stress of diatoms, support results from microcosm amendment studies conducted during CCE Long Term Ecological Research process cruises in the summers of 2017 and 2019. We found that the benthic boundary layer and shoreward filament endmember supply dissolved and total dissolvable iron to this feature, but rapid assimilation and sinking by biogenic particles (e.g., diatoms) depletes the surface concentrations. Subsequently, diatom blooms which form in recently upwelled water masses become iron limited over time, thereby affecting the ratios of surface macronutrient reservoirs and biogeochemical advective fluxes. The development of Fe‐limitation during lateral advection may lead to efficient carbon export downstream and offshore of the region with the highest phytoplankton growth rates and productivity.

It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::km^r, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.

We investigated nutrient patterns and their relationship to vertical carbon export using results from 38 Lagrangian experiments in the California Current Ecosystem. The dominant mode of variability reflected onshore‐offshore nutrient gradients. A secondary mode of variability was correlated with silica excess and dissolved iron and likely reflects regional patterns of iron limitation. The biological carbon pump was enhanced in high‐nutrient and Fe‐stressed regions. Patterns in the nutrient landscape proved to be better predictors of the vertical flux of sinking particles than contemporaneous measurements of net primary production. Our results suggest an important role for Fe‐stressed diatoms in vertical carbon flux. They also suggest that either preferential recycling of N or non‐Redfieldian nutrient uptake by diatoms may lead to high PO₄³⁻:NO₃⁻ and Si(OH)₄:NO₃⁻ ratios, following export of P‐ and Si‐enriched organic matter. Increased export following Fe stress may partially explain inverse relationships between net primary productivity and export efficiency.

Iron uptake by diatoms is a biochemical process with global biogeochemical implications. In large regions of the surface ocean diatoms are both responsible for the majority of primary production and frequently experiencing iron limitation of growth. The strategies used by these phytoplankton to extract iron from seawater constrain carbon flux into higher trophic levels and sequestration into sediments. In this study we use reverse genetic techniques to target putative iron-acquisition genes in the model pennate diatom Phaeodactylum tricornutum. We describe components of a reduction-dependent siderophore acquisition pathway that relies on a bacterial-derived receptor protein and provides a viable alternative to inorganic iron uptake under certain conditions. This form of iron uptake entails a close association between diatoms and siderophore-producing organisms during low-iron conditions. Homologs of these proteins are found distributed across diatom lineages, suggesting the significance of siderophore utilization by diatoms in the marine environment. Evaluation of specific proteins enables us to confirm independent iron-acquisition pathways in diatoms and characterize their preferred substrates. These findings refine our mechanistic understanding of the multiple iron-uptake systems used by diatoms and help us better predict the influence of iron speciation on taxa-specific iron bioavailability. Significance Diatoms can access inorganic iron with remarkable efficiency, but this process is contingent on carbonate ion concentration. As ocean acidification reduces carbonate concentration, inorganic iron uptake may be discouraged in favor of carbonate-independent uptake. We report details of an iron assimilation process that needs no carbonate but requires exogenous compounds produced by cooccurring organisms. We show this process to be critical for diatom growth at high siderophore concentrations, but ineffective at acquiring iron from low-affinity organic chelators or lithogenic particulates. Understanding the caveats associated with iron source preference in diatoms will help predict the impacts of climate change on microbial community structure in high-nitrate low-chlorophyll ecosystems.