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1. Microbial and Metazoan Activity in Monterey Bay, CA Recorded in Nitrogen Isotope Ratios of Sinking and Suspended Particles

   https://doi.org/10.1029/2025JC022372  

   Doherty, S C; Choy, C A; Paul, N L; Close, H G (October 2025, Journal of Geophysical Research: Oceans)

   Abstract Particulate organic matter supports pelagic food webs, and the activity of these food webs attenuates the flux of carbon into the ocean interior. Understanding the extent to which microbial and metazoan heterotrophs influence particle dynamics is essential to describing the biological carbon pump and nutrient delivery to deep ecosystems. We present results of bulk and compound‐specific nitrogen stable isotope analyses and a Bayesian mixing model of zooplankton fecal pellets (FP), phytoplankton, and microbial detritus end‐members on size‐fractionated particulate organic matter from 10 depths in the upper 500 m of Monterey Bay, CA. Our results suggest three distinct zones of plankton‐particle interactions in Monterey Bay: primary production and grazing from 0 to 60 m, intense microbial reworking from 60 to 200 m, and inclusion into metazoan food webs below 200 m. Zooplankton FP signatures were found in a <20 μm particle size fraction, both at the approximate depth to which zooplankton migrate at night (∼25–60 m) and in the mesopelagic at the approximate depth to which zooplankton migrate during the day (∼200 m). This finding indicates that fecal pellets were rapidly disaggregated at the depth at which they were produced, which has implications for estimates of zooplankton FP contribution to carbon export and modeling efforts. In some water columns, much of zooplankton FP production may be disaggregated and entrained in the epipelagic zone, above the export depth. 

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2. Amino acid carbon isotope fingerprints are unique among eukaryotic microalgal taxonomic groups

   https://doi.org/10.1002/lno.12350  

   Stahl, Angela R.; Rynearson, Tatiana A.; McMahon, Kelton W. (April 2023, Limnology and Oceanography)

   Eukaryotic microalgae play critical roles in the structure and function of marine food webs. The contribution of microalgae to food webs can be tracked using compound-specific isotope analysis of amino acids (CSIA-AA). Previous CSIA-AA studies have defined eukaryotic microalgae as a single functional group in food web mixing models, despite their vast taxonomic and ecological diversity. Using controlled cultures, this work characterizes the amino acid δ13C (δ13CAA) fingerprints—a multivariate metric of amino acid carbon isotope values—of four major groups of eukaryotic microalgae: diatoms, dinoflagellates, raphidophytes, and prasinophytes. We found excellent separation of essential amino acid δ13C (δ13CEAA) fingerprints among four microalgal groups (mean posterior probability reclassification of 99.2 ± 2.9%). We also quantified temperature effects, a primary driver of microalgal bulk carbon isotope variability, on the fidelity of δ13CAA fingerprints. A 10°C range in temperature conditions did not have significant impacts on variance in δ13CAA values or the diagnostic microalgal δ13CEAA fingerprints. These δ13CEAA fingerprints were used to identify primary producers at the base of food webs supporting consumers in two contrasting systems: (1) penguins feeding in a diatom-based food web and (2) mixotrophic corals receiving amino acids directly from autotrophic endosymbiotic dinoflagellates and indirectly from water column diatoms, prasinophytes, and cyanobacteria, likely via heterotrophic feeding on zooplankton. The increased taxonomic specificity of CSIA-AA fingerprints developed here will greatly improve future efforts to reconstruct the contribution of diverse eukaryotic microalgae to the sources and cycling of organic matter in food web dynamics and biogeochemical cycling studies. 

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3. Seasonal dynamics of midwater zooplankton and relation to particle cycling in the North Pacific Subtropical Gyre

   https://doi.org/https://doi.org/10.1016/j.pocean.2020.102266  

   Hannides, CCS; Popp, BN.; Close, HG; Benitez-Nelson, CR; Ka’apu-Lyons, CA; Gloeckler, K; Wallsgrove, N; Uhau, B; Palmer, E; Drazen, JC (January 2020, Progress in oceanography)

   Midwater zooplankton are major agents of biogeochemical transformation in the open ocean; however their characteristics and activity remain poorly known. Here we evaluate midwater zooplankton biomass, amino acid (AA)-specific stable isotope composition (δ15N values) using compound-specific isotope analysis of amino acids (CSIA-AA), trophic position, and elemental composition in the North Pacific Subtropical Gyre (NPSG). We focus on zooplankton collected in the winter, spring, and summer to evaluate midwater trophic dynamics over a seasonal cycle. For the first time we find that midwater zooplankton respond strongly to seasonal changes in production and export in the NPSG. In summer, when export from the euphotic zone is elevated and this ‘summer pulse’ material is transported rapidly to depth, CSIA-AA indicates that large particles (> 53 μm) dominate the food web base for zooplankton throughout the midwaters, and to a large extent even into the upper bathypelagic zone. In winter, when export is low, zooplankton in the mid-mesopelagic zone continue to rely on large particle basal resources, but resident zooplankton in the lower mesopelagic and upper bathypelagic zones switch to include smaller particles (0.7–53 μm) in their food web base, or even a subset of the small particle pool. Midwater zooplankton migration patterns also vary with season, with migrants distributed more evenly at night through the euphotic zone in summer as compared to being more compressed in the upper mixed layer in winter. Deeper zooplankton migration within the mesopelagic zone is also reduced in late summer, likely due to the increased magnitude of large particle material available at depth during this season. Our observed seasonal change in activity and trophic dynamics drives modestly greater biomass in summer than winter through the mesopelagic zone. In contrast midwater zooplankton carbon (C), nitrogen (N), and phosphorus (P) composition does not change with season. Instead we find increasing C:N, C:P, and N:P ratios with greater depths, likely due to decreases in proteinaceous structures and organic P compounds and increases in storage lipids with depth. Our study highlights the importance and diversity of feeding strategies for small zooplankton in NPSG midwaters. Many small zooplankton, such as oncaeid and oithonid copepods, are able to access small particle resources at depth and may be an important trophic link between the microbial loop and deep dwelling micronekton species that also rely on small particle-based food webs. Our observed midwater zooplankton trophic response to export-driven variation in the particle field at depth has important implications for midwater metabolism and the export of C to the deep sea. 

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4. Vertical trophic structure and niche partitioning of gelatinous predators in a pelagic food web: Insights from stable isotopes of siphonophores

   https://doi.org/10.1002/lno.12536  

   Hetherington, Elizabeth D; Close, Hilary G; Haddock, Steven_H D; Damian‐Serrano, Alejandro; Dunn, Casey W; Wallsgrove, Natalie J; Doherty, Shannon C; Choy, C Anela (April 2024, Limnology and Oceanography)

   Abstract Gelatinous zooplankton are increasingly recognized as key components of pelagic ecosystems, and there have been many recent insights into their ecology and roles in food webs. To examine the trophic ecology of siphonophores (Cnidaria, Hydrozoa), we used bulk (carbon and nitrogen) and compound‐specific (nitrogen) isotope analysis of individual amino acids (CSIA‐AA). We collected samples of 15 siphonophore genera using blue‐water diving, midwater trawls, and remotely operated vehicles in the California Current Ecosystem, from 0 to 3000 m. We examined the basal resources supporting siphonophore nutrition by comparing their isotope values to those of contemporaneously collected sinking and suspended particles (0–500 m). Stable isotope values provided novel insights into siphonophore trophic ecology, indicating considerable niche overlap between calycophoran and physonect siphonophores. However, there were clear relationships between siphonophore trophic positions and phylogeny, and the highest siphonophore trophic positions were restricted to physonects. Bulk and source amino acid nitrogen isotope (δ¹⁵N) values of siphonophores and suspended particles all increased significantly with increasing collection depth. In contrast, siphonophore trophic positions did not increase with increasing collection depth. This suggests that microbially reworked, deep, suspended particles with higher δ¹⁵N values than surface particles, likely indirectly support deep‐pelagic siphonophores. Siphonophores feed upon a range of prey, from small crustaceans to fishes, and we show that their measured trophic positions reflect this trophic diversity, spanning 1.5 trophic levels (range 2.4–4.0). Further, we demonstrate that CSIA‐AA can elucidate the feeding ecology of gelatinous zooplankton and distinguish between nutritional resources across vertical habitats. These findings improve our understanding of the functional roles of gelatinous zooplankton and energy flow through pelagic food webs. 

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5. Quantifying the  d15N trophic offset in a cold-water scleractinian coral (CWC): implications for the CWC diet and coral  15N as a marine N cycle proxy

   Mottram, J; Gothmann, A; Prokopenko, M; Cordova, A; Rollinson, V; Dobkowski, K; Granger, J (March 2024, Biogeosciences)

   The nitrogen (N) isotope composition (δ15N) of cold-water corals is a promising proxy for reconstructing past ocean N cycling, as a strong correlation was found between the δ15N of the organic nitrogen preserved in coral skeletons and the δ15N of particulate organic matter exported from the surface ocean. However, a large offset of 8 ‰–9 ‰ between the δ15N recorded by the coral and that of exported particulate organic matter remains unexplained. The 8 ‰–9 ‰ offset may signal a higher trophic level of coral dietary sources, an unusually large trophic isotope effect or a biosynthetic δ15N offset between the coral's soft tissue and skeletal organic matter, or some combinations of these factors. To understand the origin of the offset and further validate the proxy, we investigated the trophic ecology of the asymbiotic scleractinian cold-water coral Balanophyllia elegans, both in a laboratory setting and in its natural habitat. A long-term incubation experiment of B. elegans fed on an isotopically controlled diet yielded a canonical trophic isotope effect of 3.0 ± 0.1 ‰ between coral soft tissue and the Artemia prey. The trophic isotope effect was not detectably influenced by sustained food limitation. A long N turnover of coral soft tissue, expressed as an e-folding time, of 291 ± 15 d in the well-fed incubations indicates that coral skeleton δ15N is not likely to track subannual (e.g., seasonal) variability in diet δ15N. Specimens of B. elegans from the subtidal zone near San Juan Channel (WA, USA) revealed a modest difference of 1.2 ± 0.6 ‰ between soft tissue and skeletal δ15N. The δ15N of the coral soft tissue was 12.0 ± 0.6 ‰, which was ∼6 ‰ higher than that of suspended organic material that was comprised dominantly of phytoplankton – suggesting that phytoplankton is not the primary component of B. elegans' diet. An analysis of size-fractionated net tow material suggests that B. elegans fed predominantly on a size class of zooplankton ≥500 µm, implicating a two-level trophic transfer between phytoplankton material and coral tissue. These results point to a feeding strategy that may result in an influence of the regional food web structure on the cold-water coral δ15N. This factor should be taken into consideration when applying the proxy to paleo-oceanographic studies of ocean N cycling. 

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