Dataset Available Remotely Hosted

Sub-tropical coastal water Targeted Locus (Loci)

Authors: Ortmann, Alice
Published On: Dec 16 2015 20:44 UTC
DOI: https://doi.org/10.7266/N7VD6WF5
UDI: Y1.x133.006:0001
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Project Information

Funded By:
Gulf of Mexico Research Initiative

Funding Cycle:
The Alabama Marine Environmental Science Consortium (MESC)

Research Group:
Recovery: Plankton

Point of Contact

Robert Condon
Dauphin Island Sea Lab (DISL)
rcondon@disl.org

Data Collection Period
2009-07-01
to
2011-11-12
Theme keywords

growth, production, grazing, viral lysis, microbial loop, phytoplankton, chlorophyll a, prokaryote, microzooplankton, virus, protist, heterotrophic nano-flagellate, metagenome

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Abstract:

A two year study was undertaken to explore the factors driving seasonal patterns in bacterial abundance inshore (Mobile Bay, AL) and on the Alabama shelf in the northern Gulf of Mexico. Abiotic and biotic factors driving these patterns were identified, with temperature being an important factor in both locations, while salinity was important inshore.

Suggested Citation:

Ortmann, Alice. 2015. Sub-tropical coastal water Targeted Locus (Loci). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7VD6WF5

Purpose:

These experiments were designed to determine the relative roles of grazing and viral lysis on the microbial communities in Mobile Bay, AL.

Data Parameters and Units:

Run, BioSample, Sample Name, Library Name, MBases, MBytes, Experiment, SRA Sample, Sample Site (T35 29.79887 -88.20828 CP 30.0902 -88.2116 DI 30.25345 -88.04355 MB 30.4374 -88.0113), ammonium, bacterial abundance, chlorophyll, collection date (DD-MMM-YYYY), dissolved oxygen, nitrate, nitrite, phosphate, salinity, silicate, temperature

Methods:

Process_Description: Collection: Samples (26L) were collected from surface waters from four FOCAL stations (MB, DI, CP and T35), filtered through 150 um Nitex screen and kept in the dark until returned to the DISL. Physical parameters were obtained from CTD casts. Samples were processed in low light for nutrients, abundance of protists, prokaryotes and viruses and the concentration of chlorophyll a. Modified dilution experiments were carried out to determine the growth, grazing and viral lysis rates for phytoplankton and prokaryotes. Process_Description: Nutrients were measured using a Skalar + autoanalyzer. Samples were collected after filtration through a 0.7 um glass fiber filter. Samples were stored frozen prior to processing. Process_Description: Abundances: Phytoplankton was measured using chlorophyll a. Water was filtered through a 25 mm 0.7 um glass fiber filter and frozen immediately in liquid nitrogen, then stored at -86C until processing. Pigments were extracted in acetone/DMSO and determined using a Turner Fluorometer. Samples for protists, prokaryotes and viruses were fixed in 0.5% EM grade glutaraldehyde and flash frozen in liquid nitrogen. Samples were stored at -86C until processing. DAPI slides were prepared to determine protist numbers using epifluorescences microscopy while prokaryotes and viruses were counted using flow cytometry. Process_Description: Modified Dilution Experiments: To determine rates of growth, grazing and viral lysis, water was filtered through 0.7 um glass fiber filter and a 0.2 um Durapore filter. Virus free water was produced by passing the filtered water through a tangential flow filtration cartridge (30kDa). Two parallel dilution series were produced in triplicate. One with 0.2 um filtered water and one with virus free water. Samples were collected for chlorophyll a and prokaryote abundance at t=0 and t=24. Prokaryotes were also sampled at t=12. 1 L bottles were incubated in floating cages in the water to allow for ambient light and temperature conditions. Growth, grazing and viral lysis rates were determined from changes in the abundance of pigments or cells over time using linear regressions. Surface water was collected from 4 stations over 2 years and filtered through a 150 um Nitex screen followed by filtration through a 0.7 um glass fiber filter. Prokaryote cells were collected on a 142 mm 0.2 um Durapore filter that was stored at -20C until extraction. DNA was extracted from 1/16 of the filter. Triplicate PCR reactions amplified the V6 region of the bacterial 16S rRNA genes. Reactions were pooled and cleaned up with a Qiagen PCR clean up kit. The amplicons, which included barcodes and Ion Torrent adapters were pooled and sequenced using 100 bp kits on 316 chips. Ten different samples were pooled on each chip using 5 bp barcodes