Description: Dataset: FHLOO

Description: To our knowledge, the FHL Ocean Observatory serves as the only multi-sensor array (~2 m from the surface) in the San Juan Islands archipelago that monitors for temperature, salinity, pH(total), carbon dioxide, dissolved oxygen, chlorophyll concentration, turbidity, and current velocity. In addition to the suite of ocean properties listed above, we also monitor the microplanktonic community using a camera system called the Imaging FlowCytoBot (IFCB). The IFCB is an automated imaging flow cytometer that is designed for the continuous monitoring of phytoplankton and microzooplankton. Using a laser-triggered, high-resolution camera, the IFCB generates images and optical data of individual plankton and other particles in the size range of 〉10-150 mm. Data produced by this project may be of interest to chemical and biological oceanographers, and climate scientists interested in the role of biogeochemistry in the global/regional climate system. This dataset includes pH, pCO2, temperature, salinity, and dissolved oxygen data recorded from 2018-2021. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/826798

Description: NSF Division of Biological Infrastructure (NSF DBI) FSML-1418875

Description: The stable isotope compositions of biogenic carbonates have been used for paleoceanographic and paleoclimatic reconstructions for decades, and produced some of the most iconic records in the field. However, we still lack a fully mechanistic understanding of the stable isotope proxies, especially the biological overprint on the environmental signals termed “vital effects”. A ubiquitous feature of stable isotope vital effects in marine calcifying organisms is a strong correlation between δ18O and δ13C in a range of values that are depleted from inorganic calcite/aragonite. Two mechanisms have been proposed to explain this correlation, one based on kinetic isotope effects during CO2(aq)-HCO3− inter-conversion, the other based on equilibrium isotope exchange during pH dependent speciation of the dissolved inorganic carbon (DIC) pool. Neither mechanism explains all the stable isotope features observed in biogenic carbonates. Here we present a fully kinetic model of biomineralization and its isotope effects using deep-sea corals as a test organism. A key component of our model is the consideration of the enzyme carbonic anhydrase in catalyzing the CO2(aq)-HCO3− inter-conversion reactions in the extracellular calcifying fluid (ECF). We find that the amount of carbonic anhydrase not only modulates the carbonate chemistry of the calcifying fluid, but also helps explain the slope of the δ18O-δ13C correlation. Differences in CA activity in the biomineralization process can possibly explain the observed range of δ18O-δ13C slopes in different calcifying organisms. A mechanistic understanding of stable isotope vital effects with numerical models can help us develop better paleoceanographic tracers.

Description: Accurate constraints on past ocean temperatures and compositions are critical for documenting climate change and resolving its causes. Most proxies for temperature are not thermodynamically based, appear to be subject to biological processes, require regional calibrations, and/or are influenced by fluid composition. As a result, their interpretation becomes uncertain when they are applied in settings not necessarily resembling those in which they were empirically calibrated. Independent proxies for past temperature could provide an important means of testing and/or expanding on existing reconstructions. Here we report measurements of abundances of stable isotopologues of calcitic and aragonitic benthic and planktic foraminifera and coccoliths, relate those abundances to independently estimated growth temperatures, and discuss the possible scope of equilibrium and kinetic isotope effects. The proportions of 13C–18O bonds in these samples exhibits a temperature dependence that is generally similar to that previously been reported for inorganic calcite and other biologically precipitated carbonatecontaining minerals (apatite from fish, reptile, and mammal teeth; calcitic brachiopods and molluscs; aragonitic coral and mollusks). Most species that exhibit non-equilibrium 18O/16O (d18O) and 13C/12C (δ13C) ratios are characterized by 13C–18O bond abundances that are similar to inorganic calcite and are generally indistinguishable from apparent equilibrium, with possible exceptions among benthic foraminiferal samples from the Arctic Ocean where temperatures are near-freezing. Observed isotope ratios in biogenic carbonates can be explained if carbonate minerals generally preserve a state of ordering that reflects the extent of isotopic equilibration of the dissolved inorganic carbon species.

Description: The calcite shells, or tests, of foraminifera provide a window into Earth history because they are archived in most marine sediments and contain useful geochemical proxies for paleoceanography. Previous observations of diurnal heterogeneity in proxies like Mg/Ca demonstrate a complex relationship between environmental conditions and test composition. The causes for this diurnal banding and the potential impact for proxy interpretation in systems other than Mg/Ca have yet to be determined. Recently, Mg and Na in shells of the planktic foraminifer species Orbulina universa have been observed to be high at the location of the primary organic sheet (POS), i.e. the organic template upon which the calcite test is formed. Here we use time-of-flight secondary ion mass spectrometry (ToF-SIMS), a chemical and isotope mapping technique with a spatial resolution of 300 nm, to show that Na banding is a consistent feature in the tests of 45 individual cultured O. universa. This banding occurs in two distinct forms: (1) sharp Na bands associated with organic sheets that are embedded in the calcite test after chamber formation; and (2) regular, thicker, but lower-amplitude Na bands that are found throughout the test. We use the pattern of the first type of banding to indicate the extent and sequence of calcite growth during chamber formation. Specifically, we show that new chamber formation involves growth over the previous chamber in Orbulina bilobata, a morphotype of O. universa that develops a second partial spherical chamber attached to the primary sphere. This is consistent with a bilamellar model of foraminiferal growth. However, a SIMS mapping survey of the morphologically more complex Globigerina bulloides and Neogloboquadrina dutertrei suggests that the pattern of growth during chamber formation and the prevalence of different types of Na bands may be species-specific. The wide, repeating Na bands that occur throughout the test of O. universa generally occur in an inverse pattern with respect to Mg banding for the first few days of the foraminifer's life, but this pattern changes as the organism ages. We use the magnitude, timing, and coherency between Na and Mg bands to put constraints on various proposed mechanisms for banding, including antiport Mg2+-2Na+ exchange and kinetic growth rate effects.

Description: Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain, Published online: 28 March 2018; doi:10.1038/nbt.4103 scGESTALT enables large-scale characterization of cell types and lineage relationships during vertebrate brain development.

Description: Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT, Published online: 23 October 2018; doi:10.1038/s41596-018-0058-x This protocol describes how to generate transgenic zebrafish expressing a barcode array that can be edited by CRISPR–Cas9 at multiple developmental stages. Single-cell RNA sequencing of edited barcodes and cellular transcriptomes allows reconstruction of lineage relationships.