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GCE-LTER Data Set Summary
Accession:
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MIC-GCED-1704
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Research Theme:
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Microbiology (Directed Study)
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Contributors:
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James T. Hollibaugh, Qian Liu, Bradley Tolar, Meredith Ross, Jelani Cheek, Corinne Sweeney, Natalie Wallsgrove, Brian Popp
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Title:
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Seasonal Distribution of Ammonia-Oxidizing Archaea and Ammonia-Oxidation Rates in the South Atlantic Bight from April to November 2014
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Abstract:
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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.
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DOI:
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10.6073/pasta/f7a582c38e6737c5843f6e8dd6da1899
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Key Words:
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ammonia, ammonia oxidizing archaea, amoA, Archaea, microbes, microbial, microbiology, nitrification, Nitrospina, South Atlantic Bight, Thaumarchaeota
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LTER Core Area:
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Inorganic Matter
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Research Themes:
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GCE3 Area2 - Patterns within the Domain, Microbiology, General Nutrient Chemistry |
Study Period:
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02-Apr-2014 to 07-Nov-2014
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Study Sites:
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GCE-OS -- Off-shore Transect, Georgia, USA
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Project References:
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Ammonia oxidation in the GCE domain |
Downloads:
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Data Table: MIC-GCED-1704 (Main data table for data set MIC-GCED-1704, 385 records)
Access: Public (released 07-Feb-2019)
Metadata: Text (ESA FLED),
XML (Ecological Metadata Language)
Data Formats: Spreadsheet (CSV) [65.61kb], Text File [64.02kb], MATLAB (GCE Toolbox) [449.99kb], MATLAB (Variables) [NaNkb], Text Report [98.39kb]
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") |
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Statistics:
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Generate script code to retrieve data tables for analysis in: MATLAB, R, SAS, SPSS |
Citation:
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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://dx.doi.org/10.6073/pasta/f7a582c38e6737c5843f6e8dd6da1899
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