Table of Contents

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

On September 23, 2017, on HRR cruise Leg 1 (R/V Point Sur PS18-09), samples were collected at 6 stations (S06, S11, S16, S21, SS, and GI) from the surface depth bottle in a CTD rosette. Triplicate 500-1000 milliliter (mL) samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer's instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5 nanograms per microliter (ng/µL) concentration for the amplicon library construction.

The full-length 18S rDNA region was amplified using 18S primers (Medlin et al. 1988; Edgar & Theriot 2004). Library construction and amplicon sequencing were performed at the Campbell Lab, Texas A&M University using Oxford Nanopore minION. The output sequencing results as fasta files were deposited in NCBI's GenBank under the project number PRJNA592369.

Fastq files for all six station samples were quality checked using FastQC. Resulting sequences were taxonomically annotated using BLAST search against PR2 database v5.0.0. The BLAST analysis used an assignment approach with similarity was ≥ 90% and query coverage was ≥ 1000 bp against the reference sequence. Any sequence that did not compile with this criterion was not used in this study. The following thresholds for identity with BLAST results were used for taxonomic assignment clustering: genus (95%), family (93%), class (92%), and order (90%). Archaeal and Bacterial sequences were removed from these results.

Additional tools used are:
Oxford Nanopore Technologies. Guppy protocol. Available at: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview [Accessed 21 Aug 2023].

- Saved the location table (station number, lat, lon, etc.) submitted as part of the dataset metadata in a separate spreadsheet.
- Imported the 6 original CSV files (provided in zip "HRR_18S_BLAST_results.zip") into the BCO-DMO system.
- Concatenated the 6 CSV files into a single data table.
- Joined the columns from the location table to the primary data table by matching on Station number.
- Saved final file as "922101_v1_hrr_18s_blast_results.csv".

NSF Award Abstract:
Hurricane Harvey is the strongest hurricane to hit the Texas coast in decades and the resulting tidal surges, flooding and terrestrial runoff have had a severe impact on the coastal ocean. The effects on the phytoplankton, the first link in the food chain, may be unprecedented. To determine how the phytoplankton community will respond to such drastic changes in salinity, nutrient inputs, and potential toxins, immediate and continuous sampling is the only way to fully capture the effects and to identify when conditions return to "normal". An automated, continuous phytoplankton imaging instrument that is deployed on the Texas coast records images of the phytoplankton and permits calculation of the abundance of different species. Together with molecular information on the genes that have been "turned on", or expressed, outcomes of this project will help determine the responses of individual types of phytoplankton. Extreme storms are expected to increase in frequency with future climate change, so the responses identified now will be valuable in predicting how such events will affect these primary producers, which in turn support most of the food webs in marine ecosystems, in the future.

High temporal resolution observations from the Imaging FlowCytobot (IFCB) have revealed that hurricanes in the Gulf of Mexico cause drastic changes in the phytoplankton community structure. The objectives of this RAPID project are: 1) to characterize the dynamics of the phytoplankton species in relation to the environmental variables along the Texas coast; 2) to assess the short and long-term changes in the phytoplankton community; and 3) to identify the strategies of the phytoplankton community for resource acquisition. To accomplish these objectives, this project will utilize IFCB time series to follow phytoplankton community structure during the recovery period from Hurricane Harvey. In addition, two RAPID response cruises (in late September and early October) to sample at 5 sites along a transect from Galveston to Port Aransas, TX. At each station, CTD profiles and water samples from surface and the chlorophyll maximum will be collected for nutrients, carbonate chemistry, and RNA sequencing for metatranscriptomic analysis. Metatranscriptomics can provide an indication of the metabolic strategies employed and functional relationships within the plankton community in response to changes in the environment. The advantage of a metatranscriptomic approach is that the entire molecular response to the environment is captured. So, while the response of phytoplankton to increased nutrient inputs from floodwater runoff is targeted, the responses to other environmental stresses (toxics, hypoxia, acidification) are also captured. Analyses of this time series using multivariate statistical techniques, such as principal component analysis (PCA), and network analysis, a powerful technique for identifying potential interactions among taxa, will provide insights on the environmental factors and metabolic responses structuring the community during the aftermath of the hurricane.

Related data from the The Texas Observatory for Algal Succession Time-Series (TOAST) can be found at the following: https://toast.tamu.edu/timeline?dataset=HRR_Cruise