Auxiliary material for
Relationship of Nitrogen Cycling Processes and Microbial Community Structure in Bed
Sediments to Seasonal Changes in the Yukon River at Pilot Station
Deborah A. Repert1, Jennifer C. Underwood1, Richard L. Smith1, Bongkeun Song2
1
United States Geological Survey, 3215 Marine St. E127, Boulder, Colorado 80303, USA
2
Department of Biology and Marine Biology, University of North Carolina Wilmington,
Wilmington, North Carolina 28403, USA
Journal of Geophysical Research – Biogeosciences, 2014
Introduction
Auxiliary material contains 5 tables and 3 figures. Table S1 shows river water field
measurements and nutrient concentrations corresponding to river water and sediment collection
time points used for laboratory incubations (TS01.pdf). Table S2 shows physical and nutrient
results from sediment and water incubations (FS02.pdf). Table S3 are correlation coefficients of
dominant genera and sediment characteristics and rates (TS03.pdf). Table S4 is discharge and
nutrient data from Pilot Station from 2008 to 2011 (TS04.pdf). Table S5 includes sediment
characteristics, biogeochemical rates and gene abundances from sediment and water incubations
(TS05.pdf). Figure S1 is a comparison of dissolved inorganic nitrogen and dissolved organic
nitrogen concentrations in river water collected from Pilot Station (FS01.pdf). Figure 2 is a heat
map showing abundance of phylum, dominant OTUs, and beta diversity between samples
(FS02.pdf). Figure 3 shows the linear relationship between denitrification and nitrate uptake
potential rates (FS03.pdf).
TS01.pdf: Field measurements of water temperature, pH, dissolved oxygen, specific
conductance, and alkalinity, and nutrient concentrations of ammonium, nitrate, total dissolved
nitrogen, dissolved organic carbon at time of sample collection.
1.1 Column “Date”, the date of river water and sediment sample collection
1.2 Column “WaterTemp”, the river water temperature in degrees Celcius
1.3 Column “field pH”, pH of the river water at the time of sampling
1.4 Column “DO”, dissolved oxygen concentration of the river water in µMolar
1.5 Column “SpCond”, specific conductance of the river water in µSiemens per cm
1.6 Column “Alk”, alkalinity of the river water in µequivalents calcium carbonate per Liter
1.7 Column “NH4+” ammonium concentration of the river water in µMolar
1.8 Column “NO3-” nitrate concentration of the river water in µMolar
1.9 Column “TDN” total dissolved nitrogen concentration of the river water in µMolar
1.10 Column “DOC” dissolved organic carbon concentration of the river water in µMolar
1.11 Column “DIC” dissolved inorganic carbon concentration of the river water in µMolar
TS02.pdf: Water samples collected from sediment plus river water incubations during the
CO2Prod incubation time period
2.1 Column “Amendment” details of incubation set-up and timepoint
2.2 Column “Rep” sample replicate
2.3 Column “Date Collected” date water sample collected from incubation bottles
2.4 Column “pH” pH of water sample
2.5 Column “Alk” alkalinity of the sample water in µequivalents calcium carbonate per Liter
2.6 Column “TDN” total dissolved nitrogen concentration of the sample water in µMolar
2.7 Column “DOC” dissolved organic carbon concentration of the sample water in µMolar
2.8 Column “DIC” dissolved inorganic carbon concentration of the sample water in µMolar
TS03.pdf: Correlation coefficients (r) of dominant genera level taxa compared to sediment
characteristics and biogeochemical processing rates.
3.1 Column “OTU Group” arbitrary group designation for the dominant operational taxonomic
units (OTUs)
3.2 Column “Number of OTUs” number of OTUs within each taxonomic group
3.3 Column “OTU Assignment” dominant taxa expressed as operational units
3.4 Column “Classification Level” taxonomic classification for the dominant OTUs
3.5 Column “Avg Abundance” average abundance in percent of the OTUs listed in column 3.1
3.6 Column “%C” r value for OTU vs. percent carbon of sediment used for microbial community
analysis
3.7 Column “%N” r value for OTU vs. percent nitrogen of sediment used for microbial
community analysis
3.8 Column “ExNH4” r value for OTU vs. KCl extractable sediment ammonium in µmol gDM-1
3.9 Column “ExTN” r value for OTU vs. KCl extractable sediment total nitrogen in µmol gDM-1
3.10 Column “DNF” r value for OTU vs. denitrification rate in µmol gDM-1 d-1
3.11 Column “NO3Up” r value for OTU vs. nitrate uptake rate in µmol gDM-1 d-1
3.12 Column “NNM” r value for OTU vs. net N mineralization rate in µmol gDM-1 d-1
3.13 Column “O2Con” r value for OTU vs. oxygen consumption rate in µmol gDM-1 d-1
3.14 Column “CO2Prod” r value for OTU vs. carbon dioxide production rate in µmol gDM-1 d-1
TS04.pdf: Dissolved organic carbon, total dissolved nitrogen and inorganic nitrogen species
collected from the Yukon River at Pilot Station from 2008 through 2011.
4.1 Column “Date” discharge measured and samples collected
4.2 Column “DOC” dissolved organic carbon concentration in µMolar
4.3 Column “TDN” total dissolved nitrogen concentration in µMolar
4.4 Column “NH4+” ammonium concentration in µMolar
4.5 Column “NO3-” nitrate concentration in µMolar
4.6 Column “DIN” dissolved inorganic nitrogen in µMolar, sum of inorganic nitrogen species
4.7 Column “DON” dissolved organic nitrogen concentration in µMolar, calculated by difference
of TDN and DIN
TS05.pdf: Measured sediment characteristics, including C and N content and gene abundance,
and biogeochemical potential rates of sediment and water incubations
5.1 Column “Parameter” measured sediment or rate parameter
5.2 Column “Units” unit of measure of each parameter
5.3 Column “4/8/2008” date of sediment and water incubation
5.4 Column “1/21/2009” date of sediment and water incubation
5.5 Column “5/18/2009” date of sediment and water incubation
5.6 Column “5/26/2010” date of sediment and water incubation
5.7 Column “3/14/2011” date of sediment and water incubation
5.8 Column “5/29/2011” date of sediment and water incubation
5.9 Column “9/14/2011” date of sediment and water incubation
FS01.pdf: Dissolved organic nitrogen (DON) relative to dissolved inorganic nitrogen (DIN)
concentrations during the 2010 and 2011 field seasons, including three time points (a, b and c;
blue circles and pie charts) comparing nitrate (NO3-), ammonium (NH4+) and organic nitrogen
(OrgN) concentration in river water samples collected during the 2011 field season. March, May
and Sept 2011 dates correspond to sediment collections for laboratory bioassays. Open triangles
are outliers and were not included in the Pearson r correlation.
FS02.pdf: Heat map illustrating average abundance of Phylum (a) and changes in abundance of
dominant operational taxonomic units (OTUs) between samples (b). Dominant OTUs are
classified at lowest depth available given 80% confidence. Minor Phylum, Bacteria and Archaea
level OTUs are, on average, less than 0.5% abundance and combined into one group. Letters in
parentheses next to duplicate taxa names indicate different OTU groups and correspond to OTU
Group designations in Table S3. Hierarchical clustering (c) illustrates beta differences between
samples.
FS03.pdf: Linear correlation of denitrification (DNF) potential rates relative to nitrate uptake
(NO3Up) potential rates in sediment and water incubations measured under ambient N conditions
in µmol N gDM-1 d-1.