In vitro incubations using natural marine communities can provide insight into community structure and function in ways that are challenging through field observations alone. We have designed a minimal metal incubation system for controlled and repeatable experimentation of microbial communities. The systems, dubbed Pelagic Ecosystem Research Incubators (PERIcosms), are 115 L, conical tanks designed to sample suspended, settled, and wall associated material for month long periods. PERIcosms combine some of the ecological advantages of large volume mesocosm incubations with the experimental ease and replication of bottle incubations, and their design is accessible for use by researchers without specialized training or travel to a designated incubation facility. Here, we provide a detailed description for the construction and implementation of PERIcosms and demonstrate their potential to promote replicable, diverse communities for several weeks under clean conditions using time‐series results from two field experiments. One field experiment utilized coastal waters collected from Santa Catalina Island, CA and the other oligotrophic waters collected offshore of Honolulu, HI. Biomass metrics (chlorophyll a and particulate carbon) along with 16S/18S DNA based community composition assessments were conducted to show that communities contained within PERIcosms remained alive and diverse for several weeks using a semi‐continuous culturing approach. We detail trace metal clean techniques that can be used to minimize external contamination, particularly for low dissolved iron environments. PERIcosms have the potential to facilitate natural community incubations which are needed to continue advancing our understanding of microbial ecology and geochemistry.
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Free, publicly-accessible full text available July 1, 2025
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In many oceanic regions, anthropogenic warming will coincide with iron (Fe) limitation. Interactive effects between warming and Fe limitation on phytoplankton physiology and biochemical function are likely, as temperature and Fe availability affect many of the same essential cellular pathways. However, we lack a clear understanding of how globally significant phytoplankton such as the picocyanobacteria
Synechococcus will respond to these co-occurring stressors, and what underlying molecular mechanisms will drive this response. Moreover, ecotype-specific adaptations can lead to nuanced differences in responses between strains. In this study,Synechococcus isolates YX04-1 (oceanic) and XM-24 (coastal) from the South China Sea were acclimated to Fe limitation at two temperatures, and their physiological and proteomic responses were compared. Both strains exhibited reduced growth due to warming and Fe limitation. However, coastal XM-24 maintained relatively higher growth rates in response to warming under replete Fe, while its growth was notably more compromised under Fe limitation at both temperatures compared with YX04-1. In response to concurrent heat and Fe stress, oceanic YX04-1 was better able to adjust its photosynthetic proteins and minimize the generation of reactive oxygen species while reducing proteome Fe demand. Its intricate proteomic response likely enabled oceanic YX04-1 to mitigate some of the negative impact of warming on its growth during Fe limitation. Our study highlights how ecologically-shaped adaptations inSynechococcus strains even from proximate oceanic regions can lead to differing physiological and proteomic responses to these climate stressors.Free, publicly-accessible full text available February 20, 2025 -
Abstract The chemistry of copper (Cu) in seawater is well known to be dominated by complexation with organic ligands. The prevailing paradigm is that Cu forms strong but labile complexes. Recently, a novel procedure revealed that only a small fraction of dissolved Cu exists as labile complexes. The majority is present as a fraction that is relatively inert on timescales of weeks or more and probably does not participate in coordination exchange reactions, including biologically mediated processes. Samples collected from the 2018 GEOTRACES GP15 cruise show that throughout the interior of the Pacific Ocean, this inert fraction comprises about 90% of the dissolved Cu. Labile Cu accumulates in surface waters, probably arising from photochemical decomposition of the inert fraction. There is also a modest accumulation of labile Cu near deep sea sediments and along the Alaskan shelf and slope. The results have important implications for Cu transport and biological availability. Inert Cu may influence Cu transport throughout the water column and contribute to the linear increase in Cu with depth, a distribution which is hard to explain for a biologically active trace metal. The origins of inert Cu are unknown. It may be produced slowly within the water column on the timescale of meridional overturning circulation. In the Columbia River, between 92% and 98% of the dissolved Cu is in the inert fraction, suggesting a possible terrestrial source of inert Cu to the ocean.
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Abstract Copper (Cu) is an important micronutrient for marine organisms, which can also be toxic at elevated concentrations. Here, we present a new model of global ocean Cu biogeochemical cycling, constrained by GEOTRACES observations, with key processes including sources from rivers, dust, and sediments, biological uptake and remineralization of Cu, reversible scavenging of Cu onto sinking particles, conversion of Cu between labile and inert species, and ocean circulation. In order for the model to match observations, in particular the relatively small increase in Cu concentrations along the global “conveyor belt,” we find it is necessary to include significant external sources of Cu with a magnitude of roughly 1.3 Gmol yr−1, having a relatively stronger impact on the Atlantic Ocean, though the relative contributions of river, dust, and sediment sources are poorly constrained. The observed nearly linear increase in Cu concentrations with depth requires a strong benthic source of Cu, which includes the sedimentary release of Cu that was reversibly scavenged from the water column. The processes controlling Cu cycling in the Arctic Ocean appear to be unique, requiring both relatively high Cu concentrations in Arctic rivers and reduced scavenging in the Arctic. Observed partitioning of Cu between labile and inert phases is reproduced in the model by the slow conversion of labile Cu to inert in the whole water column with a half‐life of ∼250 years, and the photodegradation of inert Cu to labile in the surface ocean with a minimum half‐life of ∼2 years at the equator.
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Abstract Siderophores are strong iron‐binding molecules produced and utilized by microbes to acquire the limiting nutrient iron (Fe) from their surroundings. Despite their importance as a component of the iron‐binding ligand pool in seawater, data on the distribution of siderophores and the microbes that use them are limited. Here, we measured the concentrations and types of dissolved siderophores during two cruises in April 2016 and June 2017 that transited from the iron‐replete, low‐macronutrient North Pacific Subtropical Gyre through the North Pacific Transition Zone (NPTZ) to the iron‐deplete, high‐macronutrient North Pacific Subarctic Frontal Zone (SAFZ). Surface siderophore concentrations in 2017 were higher in the NPTZ (4.0–13.9 pM) than the SAFZ (1.2–5.1 pM), which may be partly attributed to stimulated siderophore production by environmental factors such as dust‐derived iron concentrations (up to 0.51 nM). Multiple types of siderophores were identified on both cruises, including ferrioxamines, amphibactins, and iron‐free forms of photoreactive siderophores, which suggest active production and use of diverse siderophores across latitude and depth. Siderophore biosynthesis and uptake genes and transcripts were widespread across latitude, and higher abundances of these genes and transcripts at higher latitudes may reflect active siderophore‐mediated iron uptake by the local bacterial community across the North Pacific. The variability in the taxonomic composition of bacterial communities that transcribe putative ferrioxamine, amphibactin, and salmochelin transporter genes at different latitudes further suggests that the microbial groups involved in active siderophore production and usage change depending on local conditions.
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Abstract. Spatially distant sources of neodymium (Nd) to the ocean that carry different isotopic signatures (εNd) have been shown to trace out major water masses and have thus been extensively used to study large-scale features of the ocean circulation both past and current. While the global marine Nd cycle is qualitatively well understood, a complete quantitative determination of all its components and mechanisms, such as the magnitude of its sources and the paradoxical conservative behavior of εNd, remains elusive. To make sense of the increasing collection of observational Nd and εNd data, in this model description paper we present and describe the Global Neodymium Ocean Model (GNOM) v1.0, the first inverse model of the global marine biogeochemical cycle of Nd. The GNOM is embedded in a data-constrained steady-state circulation that affords spectacular computational efficiency, which we leverage to perform systematic objective optimization, allowing us to make preliminary estimates of biogeochemical parameters. Owing to its matrix representation, the GNOM model is additionally amenable to novel diagnostics that allow us to investigate open questions about the Nd cycle with unprecedented accuracy. This model is open-source and freely accessible, is written in Julia, and its code is easily understandable and modifiable for further community developments, refinements, and experiments.more » « less