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We combine consistently dated benthic carbon isotopic records distributed over the entire Atlantic Ocean with numerical simulations performed by a glacial configuration of the Norwegian Earth System Model with active ocean biogeochemistry, in order to interpret the observed Cibicides δ13C changes at the stadial-interstadial transition corresponding to the end of Heinrich Stadial 4 (HS4) in terms of ocean circulation and remineralization changes. We show that the marked increase in Cibicides δ13C observed at the end of HS4 between ~2000 and 4200 m in the Atlantic can be explained by changes in nutrient concentrations as simulated by the model in response to the halting of freshwater input in the high latitude glacial North Atlantic. Our model results show that this Cibicides δ13C signal is associated with changes in the ratio of southern-sourced (SSW) versus northern-sourced (NSW) water masses at the core sites, whereby SSW is replaced by NSW as a consequence of the resumption of deep water formation in the northern North Atlantic and Nordic Seas after the freshwater input is halted. Our results further suggest that the contribution of ocean circulation changes to this signal increases from ~40 % at 2000 m to ~80 % at 4000 m. Below ~4200 m, the model shows little ocean circulation change but an increase in remineralization across the transition marking the end of HS4. The simulated lower remineralization during stadials than interstadials is particularly pronounced in deep subantarctic sites, in agreement with the decrease in the export production of carbon to the deep Southern Ocean during stadials found in previous studies.

Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011). Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).

Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from scanning mobility particle sizer ([SMPS], SMPS-C GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) instruments acquiring continuously during the full course of the campaign. Aerosols pumped through one of the ([MAST-PUMP]) inlets were channeled through a conductive tubing of 1.9 cm inner diameter to four parallel 47mm filter holders installed in the rear hold using a vacuum pump (Diaphragm pumpME16 NT, VACUUBRAND BmbH & Co KG, Wertheim, Germany) at a minimum flow rate of 30 lpm (20lpm prior to may 2016). Air was conducted to a scanning mobility particle sizer ([SMPS], SMPS-C GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) measuring particles in the size range 0.025 – 0.70 µm. The SMPS was set to perform a full scan of particle distribution every 5 min. Data from [SMPS] are averaged at the 30 minute scale and provided both at the scale of particle concentration (nb cm-3) together with its normalized size distribution (dN/dlogDp (nb cm-3) i.e., the concentration divided by the log of the width of the bin).

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) instrument acquiring continuously during the full course of the campaign. Aerosols pumped through one of the ([MAST-PUMP]) inlets were channeled through a conductive tubing of 1.9 cm inner diameter to four parallel 47mm filter holders installed in the rear hold using a vacuum pump (Diaphragm pumpME16 NT, VACUUBRAND BmbH & Co KG, Wertheim, Germany) at a minimum flow rate of 30 lpm (20lpm prior to may 2016). Air was conducted to an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) measuring and counting particles in the size range 0.25 - 32 µm every 60 seconds.

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the total dissolvable (i.e. acidified unfiltered whole seawater) Fe, Zn, Mn, Ni, Cd, Co, Cu, and Pb concentrations for 242 surface seawater samples. Trace metal analyses were performed with the goals of characterizing the surface seawater trace metal distribution across the open ocean and coastal regions in both the Atlantic and Pacific, and exploring metal-dependent ecosystem structure and metabolism. Some of the findings include high concentrations of iron (Fe) and manganese (Mn) in several regions, such as the North Atlantic Ocean and near the South Pacific islands, possibly due to Saharan dust and hydrothermal vent input, respectively. Elevated lead (Pb) was found in the North Pacific near southeast Asia, where anthropogenic sources may contribute. We also observe interbasin differences in concentrations for most of the metals, such as cobalt (Co), which is relatively high in the North Atlantic in comparison to the Pacific, perhaps due to dust deposition or continental weathering. There are also intrabasin differences in metal concentrations between oligotrophic and upwelling regions, exemplified by the higher cadmium (Cd) concentrations near the Peruvian coast, likely due to upwelling. Overall we captured high-resolution trace metal data that depicts the nuances in the metal distribution of the global ocean.

Understanding fish diversity patterns is critical for fisheries management amidst overfishing and climate change. Fish egg surveys have been used to characterize pelagic spawning fish communities, estimate biomass, and track population trends in response to perturbations. Environmental DNA (eDNA) metabarcoding has been implemented to rapidly and non-invasively survey marine ecosystems. To understand the efficacy of eDNA metabarcoding for assessing pelagic spawning fish community composition, concurrent eDNA metabarcoding and fish egg DNA barcoding off Scripps Institution of Oceanography’s Pier (La Jolla, CA) were conducted. Both methods revealed seasonal patterns in agreement with previous fish and fish egg surveys. Species richness was highest in late spring and summer. The presence and spawning of commercially important species and species of conservation concern were detected. Both methods showed overlap for pelagic spawning fishes for broadcast spawners, schooling fish, and locally abundant species. Some actively spawning species were not co-detected with eDNA, likely due to different sampling strategies, taxonomic biases, and abiotic/biotic factors influencing eDNA transport, shedding, and degradation. We identified key advantages and disadvantages of each method. Fish egg barcoding provided information on spawning trends but did not detect taxa with alternate reproduction strategies. Metabarcoding eDNA detected species not found in fish egg sampling, including demersal and viviparous bony fishes, non-spawning adults, Chondrichthyan, and Mammalian species, but missed abundant pelagic fish eggs. This study demonstrates that DNA barcoding of fish eggs and eDNA metabarcoding work best in tandem as each method identified unique fish taxa and provided complementary ecological and biological insight.

The western North Atlantic is a dynamic region characterized by the Gulf Stream western boundary current and inhabited by a diverse host of odontocete, or toothed whale, top predators. Their habitats are highly exploited by commercial fisheries, shipping, marine energy extraction, and naval exercises, subjecting them to a variety of potentially harmful interactions. Many of these species remain poorly understood due to the difficulties of observing them in the pelagic environment. Their habitat utilization and the impacts of anthropogenic activities are not well known. Over the past decade, passive acoustic data has become increasingly utilized for the study of a wide variety of marine animals, and offers several advantages over traditional line-transect visual survey methods. Passive acoustic devices can be deployed at offshore monitoring sites for long periods of time, enabling detection of even rare and cryptic species across seasons and sea states, and without altering animal behaviors. Here we utilized a large passive acoustic data set collected across a latitudinal habitat gradient in the western North Atlantic to address fundamental knowledge gaps in odontocete ecology. I approached the problem of discriminating between species based on spectral and temporal features of echolocation clicks by using machine learning to identify novel click types, and then matching these click types to species using spatiotemporal correlates. I was able to identify novel click types associated with short-beaked common dolphins, Risso’s dolphins, and short-finned pilot whales in this way. Next I characterized temporal patterns in presence and activity for ten different species across our monitoring sites at three different temporal scales: seasonal, lunar, and diel. I observed spatiotemporal separation of apparent competitors, and complex behavioral patterns modulated by interactions between the seasonal, lunar, and diel cycles. Finally I investigated the relationships between species presence and oceanographic covariates to predict habitat suitability across the region, and explored niche partitioning between potentially competitive species. The insights gained here significantly advance our understanding of toothed whale ecology in this region, and can be used for more effective population assessments and management in the face of anthropogenic threats and climate change.

Coccolithophorid algae are microscopic but prolific calcifiers in modern and ancient oceans. When the pH of seawater is modified, as may occur in the future due to ocean acidification, different species and strains of coccolithophorids have exhibited diverse calcification responses in laboratory culture. Since their biomineralization is a completely intracellular process, it is unclear why their response should be affected by extracellular seawater pH. Variations in the B/Cain coccoliths are potential indicators of pH shifts in the intracellular coccolith vesicle where calcification occurs, because B/Ca in abiogenic calcites increases at higher pH due to the greater abundance of borate ions, the only B species incorporated into calcite. We used a SIMS ion probe to measure B/Ca of coccoliths from three different strains of Emiliania huxleyi and one strain of Coccolithus braarudiibraarudiicultured under different seawater pH conditions to ascertain if the B/Ca can be used to elucidate how coccolithophorids respond to changing ocean pH.These data are interpreted with the aid of a conceptual model of cellular boron acquisition by coccolithophorids. Based on uptake in other plants, we infer that boron uptake by coccolithophorid cells is dominated by passive uptake of boric acid across the lipid bilayer. Subsequently, in the alkaline coccolith vesicle (C.V.), boron speciates according to the C.V. pH, and borate is incorporated into the coccolith. At increasing seawater pH, the relative abundance of the neutral boric acid in seawater decreases, lowering the potential B flux into the cell. Homeostasis or constant pH of the coccolith vesicle results in a decrease of the B/Cain the coccolith with increasing seawater pH. In contrast, if coccolith vesicle pH increases with increasing seawater pH, then the B/Ca will increase as the fraction of borate in the coccolith vesicle increases. The coccolith B/Ca is also expected to depend inversely on the dissolved inorganic carbon (DIC) concentration in the coccolith vesicle. The B/Ca in cultured coccoliths is much lower than that of foraminifera or corals and limits precision in the analysis. Modest variations in DIC or pH of the coccolith vesicle can account for the observed trends in B/Ca in cultured coccoliths. The model shows that paired measurements of B/Ca and B isotopic composition of the calcite could distinguish between regulation of pH or DIC in the coccolith vesicle. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-10-21.

Permafrost is warming globally which leads to widespread permafrost thaw. Particularly ice-rich permafrost is vulnerable to rapid thaw and erosion, impacting whole landscapes and ecosystems. Abrupt permafrost disturbances, such as retrogressive thaw slumps (RTS), expand by several meters each year and lead to an increased soil organic carbon release. We applied the disturbance detection algorithm LandTrendr for automated large-scale RTS mapping and high temporal thaw dynamic assessment to Northeast Siberia (8.1 × 10^6km^2). We adapted and parametrised the temporal segmentation algorithm for abrupt disturbance detection to incorporate Landsat+Sentinel-2 mosaics, conducted spectral filtering, spatial masking and filtering, and a binary machine-learning object classification of the disturbance output to separate between RTS and false positives (F1 score: 0.61). Ground truth data for calibration and validation of the workflow was collected from 9 known RTS cluster sites using very high-resolution RapidEye and PlanetScope imagery. The data set presents the results of the first automated detection and assessment of RTS and their temporal dynamics at large-scale for 2001–2019. We identified 50,895 RTS and a steady increase in RTS-affected area from 2001 to 2019 across Northeast Siberia, with a more abrupt increase from 2016 onward. Overall the RTS-affected area increased by 331% compared to 2000 (2000: 20,158 ha, 2001-2019: 66,699 ha). Contrary to this, focus sites show spatio-temporal variability in their annual RTS dynamics, with alternating periods of increased and decreased RTS development, indicating a close relationship to thaw drivers. The detected increase in RTS dynamics suggests advancing permafrost thaw and underlines the importance of assessing abrupt permafrost disturbances with high spatial and temporal resolution at large-scales. This consistenly obtained disturbance product will help to parametrise regional and global climate change models.