Dataset: Transient exposure to novel high temperatures reshapes coastal phytoplankton communities

Name: Changes in seasonal phytoplankton community composition as a response to temperature at the San Pedro Ocean Time-series.
Published: 2021-06-01
Keywords: oceans

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Cite This Dataset

Project:

Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients (Phytoplankton Community Responses)

How does intensity and frequency of environmental variability affect phytoplankton growth? (Enviro variability and phytoplankton growth)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

David A. Hutchins (University of Southern California, USC)

Contact:

Joshua D. Kling (University of Southern California, USC)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-06-01

Restricted:

Validated:

Current State:

Preliminary and in progress

Changes in seasonal phytoplankton community composition as a response to temperature at the San Pedro Ocean Time-series.

Abstract:

Changes in seasonal phytoplankton community composition as a response to temperature at the San Pedro Ocean Time-series.

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Description

All scripts used to process elemental and sequencing data can be found on figshare at: https://doi.org/10.6084/m9.figshare.7603790.v2

Raw sequence data is available from NCBI under Bioproject PRJNA512541

Methods & Sampling

Sample Collection: Surface water for the experiment was collected from the Southern California Bight at the San Pedro Ocean Timeseries (SPOT) station (33˚33′ N, 118˚24′ W). Seasonal sampling in September 2016 (summer), November 2016 (fall), and May 2017 (spring) examined microbial communities collected at ambient surface water temperatures of 20.6°, 16.5° and 16.1°, respectively. Seawater was collected in carboys from 3 m depth, with 100 micron mesh prefiltration to remove zooplankton, and was then taken back to the University of Southern California, where it was stored overnight at collection temperature. Initial samples and the incubation-experiment setup used water combined from all the collection carboys. The remaining surface water was filtered through a 0.2 micron gravity filter and used for subsequent culture dilutions.

DNA collection and sequencing: Microbial diversity was sampled before nutrients were added, and at the end of the final temperature fluctuation cycle. Cells were filtered (1.2 micron polycarbonate) and stored in liquid nitrogen. Extractions used the DNeasy Power Soil kit (Qiagen, Hilden, Germany) modified to include a 10-min 65 degree celsius incubation before vortexing. Amplification and sequencing of the V4-V5 hypervariable region of the 16S rRNA gene was done using the primers 515F-Y (5′-GTGYCAGCMGCCGCGGTAA-3′) and 926R (5′-CCGYCAATTYMTTTRAGTTT-3′). These primers successfully amplify large proportions of known prokaryotes, and chloroplasts (via the 16S rRNA gene), as well as eukaryotes (via the 18S rRNA). Library prep and sequencing was done at Molecular Research DNA labs (MRDNA; Shallowater, TX, USA) on the Illumina Miseq plat-form producing 2 × 300 bp paired-end reads. DNA samples from the spring experiment were treated the same way as summer and fall DNA samples, but were sequenced on a different date. To avoid potential sequencing run-specific batch effects, each season was analyzed individually. The quality of DNA from one replicate in the spring future-constant treatment was low and consequently contained few reads. This replicate was excluded from sequence analysis.

Data Processing Description

Experimental setup: Because of the oligotrophic conditions and low biomass at SPOT, nutrients were added to stimulate photoautotrophic growth and so enable measurements of the effects of temperature on microbial communities. Each incubation experiment used triplicate one-liter flasks enriched with nitrate, silicate and phosphate added to final concentrations of 30, 30 and 2 micro molar, respectively. Iron, other trace metals, and vitamins were added at replete concentrations equivalent to Aquil medium to avoid micronutrient limitation. Enriched SPOT water was split into temperature treatments intended to simulate present and predicted-future surface-water temperatures at both constant and fluctuating temperatures. Present temperatures were set to match the temperature at SPOT at the time of collection. The present-constant treatments acted as our experimental control. Future temperatures were increased 4 °C (spring and fall) or 5 °C (summer) from the present temperature. The two fluctuating temperature treatments had the same means as the constant treatments, but they alternated between a warm phase above (+4 °C) and a cold phase below (−4 °C) the mean value sequentially every 24 h, yielding a 48 h complete thermal cycle.

Elemental analysis: To measure particulate organic carbon (POC) and nitrogen (PON),samples were filtered onto precombusted GF/F filters (2h at 450 °C) and analyzed using a Costech Elemental Combustion system (Valencia, CA, USA). POC was used to estimate bulk assemblage growth rates by recording the change in particulate organic carbon over 2 days, capturing growth during both cool and warm periods. To measure biogenic silica (BSi), samples were filtered onto 3 micron polycarbonate filters and measured to estimate diatom biomass. Similar to POC-derived growth rates, changes in BSi over two days were used to derive diatom-specific growth rates in our treatments. Cells were filtered onto precombusted GF/F filters for particulate organic phosphorus (POP) measurements. In addition to indirectly measuring Chlorophyll using in vivo fluorescence, we measured total chlorophyll by filtering onto GF/F filters and extracting in 90% acetone for 24h. Extracted Chlorophylla and in vivo fluorescence were measured on a Turner AU-10 (Turner Designs Inc., Sunnyvale, CA). During spring and fall experiments, carbon fixation rates were measured by spiking 30 ml of each enrichment with 50 microliter of 14C labeled sodium bicarbonate, then incubated for 3h, filtered onto GF/F filters, and placed in 4.5 ml of scintillation solution.Total radioactivity (TA) was measured using triplicate solutions of combined isotope and scintillation solution spiked with 100 μl of phenyethlamine. We accounted for filter absorption using 10ml from each replicate-enrichment spiked with identical amounts of isotopes and filtered immediately. Samples were incubated in the dark overnight and radioactivity was measured with a Tri-Carb 2500TR liquid scintillation counter after 24h (Beckman Coulter Inc., Brea, CA).