Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Program Information
• Funding

Environmental and physical data associated with ocean acidification microbe adaptation.

For related research, go to: http://oceanography.ml.duke.edu/johnson/research/pico/

DIC: Water was sampled using a 5 L niskin bottle centered at 1 m with a bottle length of 0.7 m.  DIC was measured on mercuric chloride poisoned samples by acidification and subsequent quantification of released CO2 using a CO2 detector (Li-Cor 7000). DIC samples were collected following recommended procedures {Dickson et al., 2007} and measurements were calibrated against Certified Reference Materials provided by Dr. A. G. Dickson at Scripps Institution of Oceanography (SIO), University of California, San Diego (UCSD).   

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).

Bacteria: Bacterioplankton (i.e. ‘bacteria’) were enumerated using a FACSCalibur flow cytometer (Becton Dickinson) and populations characterized as previously described (Johnson et al., 2010).  Briefly, cells were excited with a 488 nm laser (15 mW Ar) and inelastic forward (<15°) scatter, inelastic side (90°) scatter (SSC), green (530 ± 30 nm) fluorescence, orange fluorescence (585 ± 42 nm), and red fluorescence (> 670 nm) emissions were measured.  Bacterioplankton were quantified by staining the samples with the nucleic acid stain SYBR Green –I (Molecular Probes Inc.) (Marie et al., 1997).

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.  

Certified reference materials were used to verify protocols (Inorganic Ventures: QCP-NT, QCP-NUT-1, CGSI1-1).  The detection limit was NO2 = 0.05 µM, NO3 = 0.1 µM, PO4 = 0.05 µM, SiOH4 = 0.2 µM).  Values measured below these limits are reported as zero.

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.  

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”

BCO-DMO Data Processing Notes:

- replaced NaN with nd
- added ISO DateTime column
- separated date and time into two columns

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.

Other PICO-related projects in BCO-DMO:
Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments

Collaborative Research: BoCP-Design: A multidomain microbial consortium to interrogate organic matter decomposition in a changing ocean

NSF2026: EAGER: Identifying microbes’ population-level environmental responses using Bayesian modeling

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.

NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).

In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.

Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.

PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)

NSF media releases for the Ocean Acidification Program:

Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification

Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?

Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)

Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)

Press Release 13-102 World Oceans Month Brings Mixed News for Oysters

Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)

Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants

Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)

Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)

Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)