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GCE-LTER Data Set Summary

Accession: MIC-GCED-1704 Research Theme: Microbiology (Directed Study)
Contributors: James T. Hollibaugh, Qian Liu, Bradley Tolar, Meredith Ross, Jelani Cheek, Corinne Sweeney, Natalie Wallsgrove, Brian Popp
Title: Seasonal Distribution of Ammonia-Oxidizing Archaea and Ammonia-Oxidation Rates in the South Atlantic Bight from April to November 2014
Abstract: Previous work in nearshore waters of the Georgia USA coast has demonstrated mid-summer peaks in the abundance of Thaumarchaeota (blooms with 100 to 1,000-fold increases) accompanied by spikes in nitrite concentration. These studies were performed at one location, so the areal extent of the bloom is unknown, nor has it been demonstrated conclusively that it develops in inshore waters. We collected data on rates of ammonia oxidation and the distribution of Thaumarchaeota, ammonia-oxidizing Betaproteobacteria (AOB), nitrite-oxidizing Nitrospina and environmental variables during 6 cruises aboard the UNOLS vessel R/V Savannah from April to November 2014 on transects of the South Atlantic Bight to evaluate the areal extent and timing of the bloom. This data set includes measurements of Chlorophyll-a concentration, PAR attenuation coefficient, oxygen concenrations, temperature, salinity and nitogenous nutrient concentrations (nitrite, nitrite + nitrate, ammonium, urea), and estimates of Archaea, bacteria and diatom gene concentration based on quantitative PCR.
DOI: (not assigned)
Key Words: ammonia, ammonia oxidizing archaea, amoA, Archaea, microbes, microbial, microbiology, nitrification, Nitrospina, South Atlantic Bight, Thaumarchaeota
LTER Core Area: Other Site Research
Research Themes: GCE3 Area2 - Patterns within the Domain, Microbiology, General Nutrient Chemistry
Study Period: 02-Apr-2014 to 07-Nov-2014
Study Sites:
GCE-OS -- Off-shore Transect, Georgia, USA
» Download Geographic Coverage: Google Earth, ESRI Shapefile (polygons)
Project References: Ammonia oxidation in the GCE domain
Downloads: Information

Data Table: MIC-GCED-1704 (Main data table for data set MIC-GCED-1704, 385 records)

Access: GCE Members only (public release on 07-Feb-2019)

Metadata: Text (ESA FLED), XML (Ecological Metadata Language)

Data Formats: Spreadsheet (CSV) [65.61kb],  Text File [64.02kb],  Text Report [98.39kb],  MATLAB (GCE Toolbox) [449.99kb],  MATLAB (Variables) [NaNkb]

Column List:(hide)

Column Name Units Type Description
1 Cruise_Identifier none string R2R catalog identifier for this cruise
2 Date YYYY-MM-DD string Sampling date: MM/DD/YYYY
3 Time hh:mm string Time of day for CTD cast, sample collection, HH:MM, 24 hour clock, Eastern Standard Time
4 Station none string Station Identifier. ALTES, DOBES and SAPES are stations withing the estuary (HW and LW are high versus low tide), CRA is someone''s initials, SA is Saint Andrews Sound, SC is Saint Catherines Sound, SS is Saint Simon''s Sound, OS is Ossabaw Sound, WS is Wassaw Sound, MK### are channel markers in the Intracoastal Waterway, and letters followed by numbers are offshore transects with lowest number being closest to the shore.
5 CTD_Cast none string Sequential number of each CTD casts on each cruise
6 Depth (m) m floating-point Depth sampled in meters
7 Latitude degrees floating-point Latitude in decimal degrees
8 Longitude degrees floating-point Longitude in decimal degrees
9 Zone none string Arbitratry assignment of stations to zones in the study area identified by location and water properties: I = Inshore, N = Nearshore, M = midshelf, S = Shelf-break
10 Chlorophyll_a_Fluor mg/m^3 floating-point Relative Fluorescence measured by the fluometer on the Niskin roestte sampler converted to mg Chl a L-1 using a regression equation based on extracted chlorophyll data: Chl a = 1.7869RF - 2.2541, R² = 0.83
11 Chlorophyll_a_Conc ug/L floating-point Chlorophyll a concentration measured using a fluorometer
12 PAR_kz 1/m floating-point PAR attenuation coefficient kz in m-1 calculated as the slope of log(PAR) vs depth
13 Oxygen_Conc ml/L floating-point Dissolved oxygen concentration in mg L-1 from the oxygen sensor on the ship''s CTD
14 Temperature °C floating-point Water temperature from the CTD in Centigrade degrees
15 Salinity PSU floating-point Salinity calculated from water temperature and condictivity from the ship''s CTD, practical salinity units
16 Arch_amoA count/L exponential Concentration of genes for Archaeal ammonia monooxygenase subunit A determined by qPCR in units of copies L-1
17 Crenarchaeota_rrs count/L exponential Concentration of genes for Marine Group 1 Archaea (Thaumarchaeota) 16S rRNA determined by qPCR in units of copies L-1
18 Betaproteobacteria_amoA count/L exponential Concentration of genes for Betaproteobacteria ammonia monooxygenase subunit A determined by qPCR in units of copies L-1
19 Bacteria_rrs count/L exponential Concentration of genes for Bacteria 16S rRNA determined by qPCR in units of copies L-1
20 Nitrospina_rrs count/L exponential Concentration of genes for Nitrospina 16S rRNA determined by qPCR in units of copies L-1
21 Diatom_rrs count/L exponential Concentration of genes for diatom 18S rRNA determined by qPCR in units of copies L-1
22 Ammonia_Oxidation_Rate nanomoles/L/d floating-point Ammonia oxidation rate determined from conversion of 15N-labeled ammonium to 15N-labeled nitrite plus nitrate, in units of nmol L-1 d-1
23 Nitrite_Conc micromolar floating-point Nitrite concentration in 10-6 moles L-1
24 Flag_Nitrite_Conc none string QA/QC flags for Nitrite concentration in 10-6 moles L-1 (flagging criteria, where "x" is Nitrite_Conc: x<0="I")
25 NOx_Conc micromolar floating-point Nitrite plus nitrate concentration in 10-6 moles L-1
26 Flag_NOx_Conc none string QA/QC flags for Nitrite plus nitrate concentration in 10-6 moles L-1 (flagging criteria, where "x" is NOx_Conc: x<0="I")
27 Ammonium_Conc micromolar floating-point Ammonium concentration in 10-6 moles L-1
28 Urea_Conc micromolar floating-point Urea concentration in 10-6 moles L-1
29 Flag_Urea_Conc none string QA/QC flags for Urea concentration in 10-6 moles L-1 (flagging criteria, where "x" is Urea_Conc: x<0="I")
Citation: Hollibaugh, James T. 2017. Seasonal Distribution of Ammonia-Oxidizing Archaea and Ammonia-Oxidation Rates in the South Atlantic Bight from April to November 2014. Georgia Coastal Ecosystems LTER Project, University of Georgia, Long Term Ecological Research Network. http://gce-lter.marsci.uga.edu/data/MIC-GCED-1704

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This material is based upon work supported by the National Science Foundation under grants OCE-9982133, OCE-0620959 and OCE-1237140. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.