Georgia Coastal Ecosystems LTER Data Set Details

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GCE-LTER Data Set Summary

Accession:

MIC-GCED-1702

Research Theme:

Microbiology (Directed Study)

Contributors:

James T. Hollibaugh, Qian Liu, Meredith Ross, Jelani Cheek, Corinne Sweeney, Bradley Tolar, Patrick Hagan, Hannah Whitby, Annie Bratcher, Erica Malagon, Nicole Lynn-Bell, Jacob Shalack, Caroline Reddy, John Walker

Title:

Coupling between Sediment and Water Column Populations of Ammonia Oxidizing Thaumarchaeota in the Duplin River near Sapelo Island, Georgia

Abstract:

Populations of nitrifying organisms in the water column at Marsh Landing display a midsummer peak in the abundance of ammonia oxidizing Archaea (AOA) at the site, coinciding with a peak in nitrite concentration. Marsh Landing is at the mouth of the Duplin River, a dead-end tidal channel that drains an extensive area of salt marsh. While the lower Duplin River at Marsh Landing exchanges tidally with Doboy Sound and thus South Atlantic Bight (SAB) coastal waters, water in its upper reaches has a residence time of weeks. The work reported here had two goals: 1) test the hypothesis that the surrounding salt marsh is the source of nitrifiers seen in water samples taken at Marsh Landing; and 2) compare the seasonal dynamics of nitrifiers in surficial sediments with those in the water column. We sampled 6 stations along the ~20 km length of the Duplin River. We collected surface water samples (~0.20 m) at low- to mid-tide, monthly from April-December 2014. Sediment samples (top 1 cm) were collected at the same time from unvegetated creek bank at 2 locations on the Duplin River and from 4 locations spanning the creek bank-to-upland gradient of the saltmarsh accessible from the Teal Boardwalk. The abundance of ammonia oxidizing Archaea, Marine Group 1 Archaea (Thaumarchaeota), ammonia oxidizing Betaproteobacteria (AOB), Bacteria and Nitrospina, a nitrite oxidizing bacterium, were determined by quantitative PCR (qPCR) of DNA extracted from the samples. This data set contains the abundance estimates from April to December 2014 for sediment and water column samples, with corresponding water quality measurements (temperature, salinity and nitrogenous nutrient concentrations).

DOI:

10.6073/pasta/cc05fd510d50999d73d903cf10e308df

Key Words:

ammonia, ammonia oxidizing archaea, Archaea, estuaries, microbes, nitrate, nitrite, nitrogen compounds, salinity, salt marshes, sediments, temperature, Thaumarchaeota, urea, water

LTER Core Area:

Inorganic Matter

Research Themes:

GCE3 Area2 - Patterns within the Domain, Microbiology, General Nutrient Chemistry

Study Period:

09-Apr-2014 to 01-Dec-2014

Study Sites:

GCE10 -- Hunt Camp, Sapelo Island, Georgia, USA
ML -- Marsh Landing, Sapelo Island, Georgia, USA

» Download Geographic Coverage: Google Earth

Project References:

Ammonia oxidation in the GCE domain

Publications:

Hollibaugh, J.T., Liu, Q., Ross, M., Cheek, J., Sweeney, C., Tolar, B., Hagan, P., Whitby, H., Bratcher, A., Malagon, E., Lynn-Bell, N., Shalack, J., Reddy, C.M. and Walker, J.T. 2016. Poster: Coupling between Sediment and Water Column Populations of Ammonia Oxidizing Thaumarchaeota in a Salt Marsh Estuary.

Downloads:

Data Table: MIC-GCED-1702_Sediment (Sediment analyses for data set MIC-GCED-1702, 124 records)

Access: Public (released 10-Feb-2018)

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

Data Formats: Spreadsheet (CSV) [13.45kb], Text File [11.37kb], MATLAB (GCE Toolbox) [222.37kb], MATLAB (Variables) [132.80kb], Text Report [35.65kb]

Column List:(display)

Column	Name	Units	Type	Description
1	Date	YYYY-MM-DD hh:mm:ss	string	Date and time that the sample was taken
2	StationID	none	string	Station identifier and sample replicate identifier
3	Latitude	degrees	floating-point	Latitude of station sampled, decimal degree format
4	Longitude	degrees	floating-point	Longitude of station sampled, decimal degree format
5	Archaea_amoA	10^3 copies/g	floating-point	Abundance of Archaea ammonia monooxygenase genes, thousands of copies per gram wet sediment
6	Flag_Archaea_amoA	none	string	QA/QC flags for Abundance of Archaea ammonia monooxygenase genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Archaea_amoA: x<0="I", manual)
7	Crenarchaea_16S	10^3 copies/g	floating-point	Abundance of Crenarchaea 16S rRNA genes, thousands of copies per gram wet sediment
8	Flag_Crenarchaea_16S	none	string	QA/QC flags for Abundance of Crenarchaea 16S rRNA genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Crenarchaea_16S: x<0="I", manual)
9	Bacteria_amoA	10^3 copies/g	floating-point	Abundance of Betaproteobacteria ammonia monooxygenase genes, thousands of copies per gram wet sediment
10	Flag_Bacteria_amoA	none	string	QA/QC flags for Abundance of Betaproteobacteria ammonia monooxygenase genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Bacteria_amoA: x<0="I", manual)
11	Bacteria_16S	10^9 copies/g	floating-point	Abundance of Bacteria genes, billions of copies per gram wet sediment
12	Flag_Bacteria_16S	none	string	QA/QC flags for Abundance of Bacteria genes, billions of copies per gram wet sediment (flagging criteria, where "x" is Bacteria_16S: x<0="I", manual)
13	Nitrospina_16S	10^3 copies/g	floating-point	Abundance of Nitrospina 16S rRNA genes, thousands of copies per gram wet sediment
14	Flag_Nitrospina_16S	none	string	QA/QC flags for Abundance of Nitrospina 16S rRNA genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Nitrospina_16S: x<0="I", manual)

Data Table: MIC-GCED-1702_Water (Water column analyses for data set MIC-GCED-1702, 150 records)

Access: Public (released 10-Feb-2018)

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

Data Formats: Spreadsheet (CSV) [33.01kb], Text File [28.80kb], MATLAB (GCE Toolbox) [274.23kb], MATLAB (Variables) [184.71kb], Text Report [57.30kb]

Column List:(display)

Column	Name	Units	Type	Description
1	Date	YYYY-MM-DD hh:mm:ss	string	Date and time that the sample was taken
2	StationID	none	string	Station identifier and sample replicate identifier
3	Latitude	degrees	floating-point	Latitude of station sampled, decimal degree format
4	Longitude	degrees	floating-point	Longitude of station sampled, decimal degree format
5	Depth	m	floating-point	Sample depth of collection
6	Flag_Depth	none	string	QA/QC flags for Sample depth of collection (flagging criteria, where "x" is Depth: x<0="I", x>4="Q")
7	Temperature	°C	floating-point	Water temperature at time of collection
8	Flag_Temperature	none	string	QA/QC flags for Water temperature at time of collection (flagging criteria, where "x" is Temperature: x<10="Q", x>35="Q")
9	Salinity	PSU	floating-point	Water salinity at time of collection
10	Flag_Salinity	none	string	QA/QC flags for Water salinity at time of collection (flagging criteria, where "x" is Salinity: x<0="I", x>35="Q")
11	Archaea_amoA	10^3 copies/g	floating-point	Abundance of Archaea ammonia monooxygenase genes, thousands of copies per gram wet sediment
12	Flag_Archaea_amoA	none	string	QA/QC flags for Abundance of Archaea ammonia monooxygenase genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Archaea_amoA: x<0="I", manual)
13	Crenarchaea_16S	10^3 copies/g	floating-point	Abundance of Crenarchaea 16S rRNA genes, thousands of copies per gram wet sediment
14	Flag_Crenarchaea_16S	none	string	QA/QC flags for Abundance of Crenarchaea 16S rRNA genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Crenarchaea_16S: x<0="I", manual)
15	Bacteria_amoA	10^3 copies/g	floating-point	Abundance of Betaproteobacteria ammonia monooxygenase genes, thousands of copies per gram wet sediment
16	Flag_Bacteria_amoA	none	string	QA/QC flags for Abundance of Betaproteobacteria ammonia monooxygenase genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Bacteria_amoA: x<0="I", manual)
17	Bacteria_16S	10^9 copies/g	floating-point	Abundance of Bacteria genes, billions of copies per gram wet sediment
18	Flag_Bacteria_16S	none	string	QA/QC flags for Abundance of Bacteria genes, billions of copies per gram wet sediment (flagging criteria, where "x" is Bacteria_16S: x<0="I", manual)
19	Nitrospina_16S	10^3 copies/g	floating-point	Abundance of Nitrospina 16S rRNA genes, thousands of copies per gram wet sediment
20	Flag_Nitrospina_16S	none	string	QA/QC flags for Abundance of Nitrospina 16S rRNA genes, thousands of copies per gram wet sediment (flagging criteria, where "x" is Nitrospina_16S: x<0="I", manual)
21	NO2_Conc	micromolar	floating-point	Concentration of nitrite
22	Flag_NO2_Conc	none	string	QA/QC flags for Concentration of nitrite (flagging criteria, where "x" is NO2_Conc: )
23	NOx_Conc	micromolar	floating-point	Concentration of undifferentiated nitrogen oxide compounds
24	Flag_NOx_Conc	none	string	QA/QC flags for Concentration of undifferentiated nitrogen oxide compounds (flagging criteria, where "x" is NOx_Conc: )
25	NH4_Conc	micromolar	floating-point	Concentration of ammonium
26	Flag_NH4_Conc	none	string	QA/QC flags for Concentration of ammonium (flagging criteria, where "x" is NH4_Conc: )
27	Urea_Conc	micromolar	floating-point	Concentration of urea
28	Flag_Urea_Conc	none	string	QA/QC flags for Concentration of urea (flagging criteria, where "x" is Urea_Conc: )
29	Field_Notes	none	string	Field notes recorded at the time of sample collection

Statistics:

Generate script code to retrieve data tables for analysis in: MATLAB, R, SAS, SPSS

Citation:

Hollibaugh, James T. 2017. Coupling between Sediment and Water Column Populations of Ammonia Oxidizing Thaumarchaeota in the Duplin River near Sapelo Island, Georgia. Georgia Coastal Ecosystems LTER Project, University of Georgia, Long Term Ecological Research Network. http://dx.doi.org/10.6073/pasta/cc05fd510d50999d73d903cf10e308df

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