Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
  • Problem Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

These data were published in the results publication Harcourt R, Garcia NS, Martiny AC (2024).  The data table for this dataset was derived from table S8 in Harcourt R, Garcia NS, Martiny AC (2024), with additional culture information (sample date, lat, lon, site location) from the Roscoff Culture Collection (RCC), Station Biologique de Roscoff.  See Harcourt R, Garcia NS, Martiny AC (2024) for additional related supplemental figures and tables.

We incubated serially transferred cultures of Synechococcus (CC9311, BL107, ROS8604, CC9902, representing two clades) in triplicate 1 L flasks at 16°C, 18°C, 20°C, 22°C, 25°C, and 27°C. We supplied ambient light (60 µmol quanta m^-2 s^-1) using white fluorescent lamps on a 12:12 light-dark cycle. We grew cultures in modified artificial seawater media. To ascertain that we did not impose growth rates upon cultures and the observed growth rates are a product of strain and environmental conditions, we used nutrient replete media and sampled prior to cultures encountering nutrient limitation; we supplied nitrate (NO₃^-) and phosphate (PO₄³⁻) in concentrations of 125 µM and 10 µM, respectively. Cells utilized a mean of 17% of the supplied nitrogen, and 22% of the supplied phosphorus, indicating cultures did not reach nutrient limitation. We transferred media and diluted cultures using an open flame in a hood in order to avoid contamination. We diluted weekly by approximately an order of magnitude to avoid nutrient limitation and maintain a stable growth rate.

We measured particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP), as well as cell enumeration by flow cytometry, following the methods outlined in Garcia et al. (2016). We sampled after seven doublings or one month to acclimate cells to the temperature conditions. We vacuum filtered POC, PON (150 mL), and POP (50 mL) samples onto pre-combusted GF/F Whatman glass filters (450°C) at 10 psi. We dried particulate organic carbon and particulate organic nitrogen samples at 50-80°C for a minimum of 48 hours and pelletized prior to analysis using a Flash EA 1112 NC Soil Analyzer (Thermo-Scientific, MA). We rinsed filtered particulate organic phosphorus samples with 0.17 M NaSO₄, immersed the filter in 2 mL of MgSO₄, dried at 80°C overnight, and combusted at 450°C for 2 hours. We then added 5 mL of 0.2 M HCl and baked the samples at 80-90°C. We measured particulate organic phosphorus samples via colorimetric assay following the Bermuda Atlantic Time-series methodology using a Genesys 10S UV-vis spectrophotometer (Thermo-Scientific) at 885 nm.

We measured culture cell density every two-three days and immediately prior to sampling using a NovoCyte 1000 flow cytometer (excitation laser 488 nm, emission peak 575 nm) and forward scatter. We assessed growth rate using flow cytometry based on increases in biomass measured across time points using the following equation: µ = ln(CD2)-ln(CD1))/(T2-T1), in which CD2 and CD1 are cell counts in cells/mL^-1 on the most recent count and the previous count, respectively, and T2 and T1 represent time points. We accounted for recent dilutions in accounting for growth rate; we counted cells prior to and after dilutions to ensure growth rate was accurately assessed. We counted the cells at a flow rate of 35 µL/min. To assess heterotrophic populations, we stained the cultures with SYBR Green (Thermo-Fisher) for 15 minutes at room temperature, vortexed them, and counted using the (excitation laser 488 nm, emission peak 520 nm) channel. We recorded duplicate cell counts at each sampling.

We measured cell diameter by microscopy under oil immersion at 1000x magnification using the Axioplan2 and AxioView 1.4.5 sizing software (Carl Zeiss, Goettingen, Germany) with reference to a staged micrometer (Ted Pella Inc., Redding, CA). To estimate cell diameter, we created a conversion factor determined by plotting the mean observed cell diameters and mean forward scatter values for several strains of Synechococcus.

Locations: Laboratory batch cultures in incubators from 16-25°C. The original isolation locations for the Synechococcus strains used were:
31.91, -124.17, Pacific Ocean, California Current
32.87, -117.26, Pacific Ocean, California Current
41.72, 3.55, Mediterranean Sea, Balearic Sea
48.72, -3.98, Atlantic Ocean, Britanny coast

Organism Identifier (LifeSciences Identifier, LSID):
Synechococcus, urn:lsid:marinespecies.org:taxname:160572

We used the software NovoExpress 1.5.6 to count cells. We used NovoExpress 1.5.6 and AxioView 1.4.5 to determine cell size.
 

* File "S8_TableRevised.csv" was imported into the BCO-DMO data system for this dataset. Values "N/A" imported as missing data values. 
** Missing data values are displayed differently based on the file format you download.  They are blank in csv files, "NaN" in MatLab files, etc.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.  Can not start with a number]

* Links to strain information in the Roscoff Culture Collection (RCC) that were included in a "Reference" column in the data table were corrected by obtaining the correct links in the corresponding results journal publication Harcourt, R., Garcia, N. S., & Martiny, A. C. (2024).

* Additional isolation sample collection information was added to the data table from the RCC collection metadata (sample date, lat, lon, additional site location descriptions, and identifier for the strain in the RCC collection).

* Date converted to ISO 8601 format

* "m" removed from depth values and instead included in column description metadata, depth column was then typed as numeric type.

* LSID added for Synecococcus in metadata text (from World Register of Marine Species)

NSF abstract:
The elemental ratios of carbon, nitrogen, and phosphorus (C:N:P) have been considered fixed proportions in marine environments but recent work has demonstrated changes across latitudes. Such variation can have large implications for marine biogeochemistry and atmospheric CO_2 levels. As such, future variations in ocean community C:N:P could be a key feedback to global change. The elemental composition of particulate organic matter (POM) represents the aggregate value of diverse microorganisms as well as non-living particles. However, we currently do not understand how individual cells and particles contribute to observed variation in the C:N:P of POM. This project is determining the biomass C:N:P of individual microbial cells grown under a range of conditions and sampled from diverse ocean biomes. Because different individuals are likely to have different fates (e.g., loss to sinking, lysis, predation), understanding how the trait distribution of microbial biomass C:N:P relates to cell size and trophic mode and how environmental conditions affect each trait’s distribution offers new perspectives and insight into marine C, N, and P cycles. This project supports two PhD students and multiple undergraduate students. The PhD students are integrated into existing networks on microbiome science at each institution with opportunities to collaborate across diverse disciplines. Undergraduate students at both institutions are being recruited through existing training programs that target underrepresented groups. In addition, PI Hall is part of a collaborative of Ecologists and Poets at CSU, that look at ways to translate ecological relationships to non-traditional media to make it more accessible and impactful to the general public. This group is exploring the nature of individuality within the marine microbiome by creating trait distributions of written text and removing different modes of individuals (e.g., words) to better understand and communicate how individuals from the smallest organisms on the planet (marine microorganisms) can have large effects on the surrounding ecosystem (i.e., the planet). Results from this project are being incorporated into future projects of the working group at Colorado State University including public presentations, art installations, and published materials.

The aim of this project is to quantify the relationship between environmental conditions and marine microbial C:N:P by assessing the individuality in microbial elemental stoichiometry. To achieve this the project uses energy dispersive spectroscopy (EDS) to assess the stoichiometric trait distribution of populations and communities under different resource and temperature treatments and oceanographic field work across a broad latitudinal gradient. The researchers hypothesize that the relationship between the stoichiometry of particulate organic matter (POM) and environmental conditions are masked by distinct responses of individual constituents of the marine microbiome. They hypothesize that these distinct responses result in a multi-modal distribution of particulate carbon (C), nitrogen (N), and phosphorus (P) of the marine microbiome. The investigators are characterizing the distribution of three stoichiometric traits (biomass C:N, C:P, and N:P) for 50 marine isolates (both autotrophs and heterotrophs) under different resource and temperature environments. They are characterizing the same trait distribution for marine communities sampled from different regions of the ocean for the same resource and temperature environments as the population experiments. They are participating on an ocean going cruise to characterize stoichiometric trait distribution of the marine microbiome across natural gradients of resources and temperature. Understanding how constituent members of microbial communities alter their biomass in response to environmental change is providing a missing link between the variation in the ocean’s environment and particulate C:N:P ratios for diverse marine environments.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.