Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system

Diatoms serve as the major link between the marine carbon (C) and silicon (Si) biogeochemical cycles through their contributions to primary productivity and requirement for Si during cell wall formation. Although several culture-based studies have investigated the molecular response of diatoms to Si and nitrogen (N) starvation and replenishment, diatom silicon metabolism has been understudied in natural populations. A series of deckboard Si-amendment incubations were conducted using surface water collected in the California Upwelling Zone near Monterey Bay. Steep concentration gradients in macronutrients in the surface ocean coupled with substantial N and Si utilization led to communities with distinctly different macronutrient states: replete (‘healthy’), low N (‘N-stressed’), and low N and Si (‘N- and Si-stressed’). Biogeochemical measurements of Si uptake combined with metatranscriptomic analysis of communities incubated with and without added Si were used to explore the underlying m..., Metatranscriptome analysis
Seawater samples for metatranscriptome analysis were collected by filtration at <5 psi onto 47 mm, 1.2 µm pore-size polycarbonate membranes, flash frozen in liquid N2, and stored at -80°C. Total RNA was extracted from filters using the Trizol-RNeasy method with an additional bead beating step. In brief, filters were transferred to tubes containing RNase/DNase free 100 µm zirconia/silica beads with 1 mL of Trizol reagent, vortexed for 2 min, incubated at room temperature for 5 min, vortexed again for 2 min before following the standard Trizol RNA extraction protocol. The upper aqueous phase was transferred to a clean 1.5 mL tube with an equal volume of 70% alcohol, mixed, and added to QIAgen RNAeasy column. The standard RNeasy protocol with the optional on-column DNase treatment was followed.
RNA was quantified using a Qubit® RNA HS Assay, and RNA integrity was determined using the Agilent Bioanalyzer RNA 6000 Pico kit eukaryotic assay. Total RNA (500 ng) wa..., , # Assembly, annotation, and read counts from silicic acid and nitrogen stress experiments of marine microbial eukaryotes

More information about the collection, preparation, and analysis of samples can be found within the associated full length article.

### Associated article: Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system

Michael A. Maniscalco, Mark A. Brzezinski, Jeffrey W. Krause, Kimberlee Thamatrakoln
[doi: 10.3389/fmars.2023.1291294](https://doi.org/10.3389/fmars.2023.1291294)

File descriptions:

* \- DYEatom_Inc_counts.csv: Counts for all unique orfs within the metatranscriptomic assembly.

\- columns:

\- transcript- id of each transcript in metatrancriptome assembly

\- Si2control1_S94 - read counts mapped to each transcript from biological rep 1, control sample at Station 2

\- Si2control2_S95 - read counts mapped to each transcript from biologi...