Environmental and physical data associated with ocean acidification microbe adaptation from 2012-2014

Environmental and physical data associated with ocean acidification microbe adaptation from 2012-2014 Table of

pH: Water was sampled using a 5 L niskin bottle centered at 1 m with a bottle length of 0.7 m. pH was measured spectrophotometrically {Clayton and Byrne, 1993} in triplicate at standard temperature (25°C) immediately following collection.pH samples were collected following recommended procedures {Dickson et al., 2007}.
Secchi Depth: Secchi depth was measured in duplicate using a 20 cm disk with four alternating white and black quadrants (Cole Parmer #EW-05492-00) by lowering the disk until no longer visible and recording the depth.
Salinity: Water was sampled using a 5 L niskin bottle centered at 1 m with a bottle length of 0.7 m.Salinity was measured using a calibrated handheld digital refractometer (Atago PAL-06S), using a refractometer (Vista A366ATC), or using a Guideline Portasal 8410A all according to manufacturer's instructions and calibrated against known reference materials.
In situ salinity at the same depth was measured using a YSI Pro30.
Turbidity: Turbidity was measured in duplicate on discrete samples using a calibrated handheld turbidimeter (Orion AQ4500).
Dissolved Oxygen: Oxygen was measured optically in situ and atmospheric pressure measured near the sea surface using a calibrated probe (YSI ProODO) using manufactures recommendations.
Chlorophyll: Water was sampled using a 5 L niskin bottle centered at 1 m with a bottle length of 0.7 m.Methods described in Johnson et al. 2010: Chlorophyll concentrations were measured by filtering 25 mL of seawater sample onto a 0.22 µm pore size polycarbonate filter using gentle vacuum (<100 mm Hg) and extracting in 100% MeOH at -20°C in the dark for >24 h following (Holm-Hansen and Riemann, 1978).Fluorescence was measured using a Turner Designs 10-AU fluorometer following (Welschmeyer, 1994) that was calibrated against a standard chlorophyll solution (Ritchie, 2008).

Nutrients:
Water was filtered through a 0.22 µm Sterivex cartridge filter, Millipore #SVGPL10RC using a peristaltic pump input line at 1 m for later nutrient analysis (NO3, NO2, PO4, SiOH4) and water was placed into duplicate HCl-cleaned HDPE bottles (VWR#414004-110) and stored at -80°C until later analysis using an Astoria-Pacific A2 autoanalyzer following the manufacturer's recommended protocols running each replicate sample in duplicate.
Temperature: Water was sampled using a 5 L niskin bottle centered at 1 m with a bottle length of 0.7 m.Temperature was measured in duplicate using NIST traceable thermocouples (VWR#23609-232).In situ water temperature at the same depth was measured using a YSI Pro30.

Processing Description
Quality Scores (Q) as follows: 1=excellent (no known issues), 2=suspect, 3=poor (known reason to suspect data) Nutrients: Samples that had a mean concentration (mean of replicated samples) below the nominal detection limit are reported as zero.
Bacteria: Cells counts were normalized to volume sampled to determined cells per mL.Chlorophyll: >0.22 um referred to as "total" or simply "chlorophyll"

Dataset-specific Description
Used to measure temperature

Generic Instrument Description
An instrument that measures temperature digitally.
[ From the project website: Carbon dioxide is rising at ~3% per year in the atmosphere and oceans leading to increases in dissolved inorganic carbon and a reduction in pH.This trend is expected to continue for the foreseeable future and ocean pH is predicted to decrease substantially making the ocean more acidic, potentially affecting the marine ecosystem.
However, coastal estuaries are highly dynamic systems that often experience dramatic changes in environmental variables over short periods of times.In this study, the investigators are measuring key variables of the marine carbon system along with other potential forcing variables and characteristics of the ecosystem that may be affected by these pH changes.The goal of this project is to determine the time-scales and magnitude of natural variability that will be superimposed on any long term trends in ocean chemistry.This project is associated with Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments.[ table of contents | back to top ]

A
Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends.The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD.Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light.The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.a generic term used when specific type, make and model were not specified.In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.a laboratory or field device for the measurement of an index of refraction (refractometry).The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.that measures the proportion of oxygen (O2) in the gas or liquid being analyzed measures the clarity of a water sample.A beam of light is shown through a water sample.The turbidity, or its converse clarity, is read on a numerical scale.Turbidity determined by this technique is referred to as the nephelometric method from the root meaning "cloudiness".This word is used to form the name of the unit of turbidity, the NTU (Nephelometric Turbidity Unit).The meter reading cannot be used to compare the turbidity of different water samples unless the instrument is calibrated.Description from: http://www.gvsu.edu/wri/education/instructor-s-manual-turbidity-10.htm(One example is the Orion AQ4500 Turbidimeter) a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action.Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, typically made of glass or plastic and with a narrow neck, used for storing drinks or other liquids.
Research: Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments (OA microbe adaptation) Coverage: Neuse-Pamlico Sound to the Sargasso Sea Extracted from the NSF award abstract: This collaborative project by Duke University and Georgia Institute of Technology researchers will combine oceanographic and advanced molecular techniques to characterize the adaptive responses of microbial communities to multiple stressors associated with OA.In particular, microbial communities from estuarine and coastal ecosystems as well as open ocean waters will be incubated under conditions of increased acidity or temperature or both, and their activities will be measured and quantified.Preliminary data from time-series observations of a coastal temperate estuary shows that pH, temperature and other stressors vary over multiple space and time scales, and this variability is relatively higher than that observed in open ocean waters.Based on this evidence, the guiding hypothesis of this work is that microbes in coastal ecosystems are better adapted to ocean acidification as well as multiple stressors compared to similar microbes from the open ocean.To quantify the adaptive genetic, physiological and biogeochemical responses of microbes to OA, the team's specific goals are to: (1) characterize complex natural microbial community responses to multiple stressors using factorial mesocosm manipulations, (2) assemble a detailed view of genomic and physiological (including transcriptional) adaptations to OA at the single species level using cultured model marine microbes (e.g.Prochlorococcus, Synechococcus, Vibrio) identified as responsive to stressors in whole community mesocosm experiments, and (3) assess the power of model microbial strains and mesocosm experiments to predict microbial community responses to natural OA variability in a temporally dynamic, temperate estuary and along a trophic/pH gradient from the Neuse-Pamlico Sound to the Sargasso Sea.By comparing an estuarine ecosystem to its open ocean counterpart, this study will assess the sensitivity of microbial structure and function in response to ocean acidification.This project is associated with Pivers Island Coastal Observatory.

replaced NaN with nd -added ISO DateTime column -separated date and time into two columns [ table of contents | back to top ] Related Publications Parameters Parameter Description Units
table of contents | back to top ] Pivers Island Coastal Observatory (PICO) Website: http://oceanography.ml.duke.edu/johnson/research/pico/Coverage: 34.7181 deg N, 76.6707 deg W