Work Description

Date: 27 March, 2025

Dataset Title: Sediment Carbon and Nitrogen and Environmental Data, Middle Island Sinkhole, 2007–2021

Dataset Contact: Nathan Sheldon [email protected]

Dataset Creators:
Name: Cecilia M. Howard
Email: [email protected]
Institution: University of Michigan Department of Earth and Environmental Sciences
ORCID: https://orcid.org/0000-0001-7293-162X

Name: Diana Velazquez
Email: [email protected]
Institution: University of Michigan Department of Earth and Environmental Sciences
ORCID: https://orcid.org/0000-0001-8256-232X

Name: Kathryn I. Rico
Email: [email protected]
Institution: Arizona State University School of Earth and Space Exploration
ORCID: https://orcid.org/0000-0003-2761-8663

Name: Nathan D. Sheldon
Email: [email protected]
Institution: University of Michigan Department of Earth and Environmental Sciences
ORCID: https://orcid.org/0000-0003-3371-0036

Funding: University of Michigan (Department of Earth and Environmental Sciences Turner Award; Institute for Global Change Biology Graduate Fellowship); Geological Society of America (Graduate Research Grant)

Key Points:
- We compare year-to-year changes in the carbon and nitrogen chemistry of anoxic lake sediments to climate and environmental data to investigate links between the two.
- Deceases in ice cover and increases in lake temperature drive higher chlorophyll in the surface lake and increased organic carbon and nitrogen in the sediments.
- Despite low potential for physical mixing due to anoxic conditions, interannual variability in carbon and nitrogen occurs in sediments as deep as 12 cm.

Research Overview:
This study combines a field survey time series with analysis of remotely and locally sensed environmental and climate data. Field survey data consists of sediment chemistry from hand-push cores, and includes %Corg, %N, δ13Corg, Corg:N, collection month and year, and depth in sediment. Climate and environmental data for the region around Middle Island Sinkhole was pulled from publicly available NOAA databases (ERDDAP, National Data Buoy Center, NWS) for as much of the same time period as the sediment data as was available. These data included general weather information from the NDBC and NWS (air temperature, wind speed, wind direction, gust speed, monthly precipitation totals), as well as satellite-derived environmental data from a 0.25° area centered on MIS (ice cover, lake surface temperature, CDOM, DOC, Chlorophyll, suspended minerals). Data were processed to monthly and annual averages as described below in order to compare to sinkhole sediment chemistry.
Abstract: Records of recent past climate provide an essential window into understanding how changing climate influences environments and ecosystems such as lakes. Sediment carbon and nitrogen chemistry can offer insight into productivity and biochemistry, and anoxic sediments can often preserve short-term changes in these signals. We found that seasonal and annual changes in local ice season, chlorophyll, and precipitation influenced the amount and isotopic composition of carbon reaching the sediments of Middle Island Sinkhole, an anoxic sinkhole in Lake Huron. Carbon and nitrogen signals reflected the year or season of sample collection in sediments as deep as 12 cm. Our findings demonstrate that declining ice cover in this part of the Great Lakes is leading to increased export of organic carbon into sediments, but that in situ sediment processes may make teasing out short-term changes from sediment cores difficult even in an anoxic setting.

Geographic Location:
Geographic coverage is a 0.25° area centered on Middle Island Sinkhole (45.198722°, 83.3277040°):
NW corner: 45.327722°, -83.452704°
NE corner: 45.327722°, -83.202704°
SE corner: 45.073722°, -83.202704°
SW corner: 45.073722°, -83.452704°
A control site in Lake Huron with similar water depth and no anoxic groundwater influx was also sampled in 2013, 2015, and 2018 from near these coordinates: 45°12'16.02"N, 83°19'49.86"W

Date Coverage:
MIS Carbon and Nitrogen Chemistry (%Corg, %N, Corg:N, δ13Corg): 2007-2021
Ice cover: 2006-12-01 to 2021-11-30
Lake Surface Temperature: 2006-12-01 to 2021-11-30
Colored Dissolved Organic Matter, Dissolved Organic Carbon, Chlorophyll, Suspended Minerals (MODIS): 2013-06-14 to 2017-10-20
Colored Dissolved Organic Matter, Dissolved Organic Carbon, Chlorophyll, Suspended Minerals (VIIRS): 2018-05-28 to 2021-11-30
Precipitation: 2007-2021
Air temperature, Wind Speed, Wind Direction, Gust Speed: 2012-2021

Methodology:
Field Methods: Sediment cores (15–30 cm) were collected by divers 1–3 times per year over the study period as manual push cores. Samples were collected in 2007 and in 2011–2021. Samples were not collected in 2020 due to the COVID-19 pandemic, and samples from 2007 and 2011 are excluded from some of the analysis due to lack of climate data. Cores were frozen within 1–2 days of collection and were stored in a -20°C freezer. Frozen cores were cut into segments using a tile saw (~1 cm for the top 3 cm of core, ~3 cm for the rest of the core) to allow for depth profiling. For most cores, the surface 1 cm includes microbial mat, while for some older cores, the bulk of the mat was removed. In 2013, 2015, and 2018, cores were also collected from a control site nearby in Lake Huron with a similar water depth and no anoxic groundwater input.
Sediment Chemistry: Sediments were freeze-dried, homogenized with a mortar and pestle, and then acidified using weak hydrochloric acid to remove inorganic carbon. 5–8 mg samples were loaded into tin capsules for analysis. Acidified samples were analyzed on a Costech ECS 4010 Elemental Analyzer for %Corg, %N, and Corg:N, and δ13Corg was measured on a Picarro G2201-i CM-CRDS. Weight percent carbon and nitrogen were calibrated to IAEA acetanilide and atropine standards, while δ13Corg was calibrated to IAEA caffeine and sucrose as well as lab-calibrated C3 and C4 sugar standards. Instrumental uncertainty for the EA was generally <1% for carbon and <0.3% for nitrogen. Instrumental uncertainty for the CM-CRDS was generally <0.3‰. For older cores (2007; 2011–2015), data was compiled from past analyses conducted using the same instruments.
Data Compilation: The NOAA ERDDAP database was used to compile lake data from a 0.25°x0.25° square centered on MIS (coordinates for each edge: N 45.327722°, E -83.202704°, S 45.073722°, W -83.452704°). Data products included colored dissolved organic matter (CDOM), dissolved organic carbon (DOC), chlorophyll, and suspended minerals acquired by the MODIS and VIIRS satellites (MODIS data from 2013–2017, VIIRS data from 2018–2021), and ice cover and lake (sea) surface temperature (LST) from the Great Lakes Surface Environmental Analysis. For documentation on these data products and the processing algorithms used to derive them: https://coastwatch.glerl.noaa.gov/satellite-data-products/ and https://coastwatch.glerl.noaa.gov/erddap/index.html. We compiled air temperature and wind data for 2012–2021 from several local NOAA weather stations and buoys (Thunder Bay Island (Station TBIM4), Thunder Bay Buoy (Station 45162), Alpena Harbor Light (Station APNM4), and Alpena (Station LPNM4)). For documentation on the weather station data products: https://www.ndbc.noaa.gov/faq/measdes.shtml. The measurements from TBIM4 were prioritized, as that station was closest to MIS and had the most continuous record of measurements; the other stations were used to fill in gaps in the dataset when TBIM4 was not recording data. Precipitation data (monthly summarized precipitation sum) was taken from the National Weather Service NOWData Database for the Alpena Area (https://www.weather.gov/wrh/Climate?wfo=apx).
Data Processing for Sediment Chemistry: Carbon and nitrogen data from sediment samples were compiled into a single dataset, with sample depth determined as the middle of the core slice. For the purposes of our analyses, “surface” samples were any with a depth less than or equal to 1.5 cm to include samples that still had microbial mat on the surface, while “sediment” samples were those deeper than 1.5 cm. “Deep” samples were those from greater than or equal to 6 cm depth. %Corg, %N, Corg:N, and δ13Corg were averaged by sampling year and depth range.
Data Processing for Weather Station Data: Data analysis was done using R version 4.3.2. Data from the four weather stations were combined by removing null data values and then filling the gaps according to a priority ranking based on proximity, where TBIM4 was the primary data source and missing data were filled in using data from station 45162, then APNM4, then LPNM4. We compared month-long blocks where all stations were recording data to confirm that the four stations were not notably different. Weather station data were then averaged by day.
Data Processing for Spatial Data: All data from MODIS and VIIRS were compiled into a single dataset for processing. We removed null data (land, cloud cover) and averaged the datasets by day to initially shrink the dataset into a more manageable size. The same processing was carried out for LST and ice cover. For all datasets we added the parameter “ice season,” which was determined as starting in November of the previous year and running until June (e.g., the 2018 ice season included data from November of 2017 through June of 2018). We calculated for each ice season the maximum ice and the duration of ice cover >0%, 50%, and 75%. For all climate parameters, we calculated the annual average and range across the region as well as the monthly averages and ranges. Only the annual averages are reported here, as they were determined to be more relevant.
Data Analysis: Data analysis was done in R version 4.3.2. Initial identification of sediment chemistry parameters with statistically significant interannual changes was done using Kruskal-Wallis rank sum tests on the different sediment depth groupings (full core, surface, sediments, intermediate sediments, and deep sediments) followed by a Wilcoxon test with a Bonferroni correction. We joined the annual average environmental data to the sediment chemistry data by year. We conducted principal components analyses using the prcomp function of the stats package with various subsets of data to identify relationships of interest for surface sediments (<1.5 cm depth; includes extensive microbial mat influence), deep sediments (>1.5 cm depth), and the full cores. PCA was limited to data from 2013–2021 due to the availability of some environmental data. For the sediment chemistry data, we calculated trimmed annual averages and standard errors of those trimmed averages, trimming 5% and 95% quantiles for each year to remove outliers. Means were then weighted by the number of data points for that year. This trimming and weighting was done separately for δ13Corg as there was a different number of samples analyzed than for Corg and N.
Using the cor_mat function in the rstatix package, we calculated a correlation matrix between sediment chemistry and environmental data. For the purposes of this manuscript, we included only the variables with the most significant correlations in the figure (δ13Corg, %Corg, %N, Corg:N, mean annual lake surface temperature, annual precipitation, days >75% ice cover, and average chlorophyll). We used the packages tidyverse and egg to visualize these relationships with cross plots of sediment chemistry against environmental parameters, plotting the trimmed mean, trimmed standard error, and the full data to show the range of values. Mean and standard error values for the control site in Lake Huron were also plotted for comparison.
Quality Control: Analytical standards (both IAEA and lab standards) were incorporated throughout analytical runs to ensure consistency and quality of sediment chemistry data. Random duplicate samples were also run spaced apart from each other within the same run or in separate runs to ensure sample consistency. For weather station data, measurements from multiple stations were combined to ensure thorough coverage. We compared month-long blocks where all stations were recording data to confirm that there were not statistically significant differences between the stations. We also compared the maximum annual ice cover for the study area to the maximum ice cover for the entirety of Lake Huron to confirm that the trends were consistent (p<0.05; the values for the study region were higher due to being coastal). For spatial data, we manually checked that there were no major data gaps, aside from winter-season gaps in lake data (chlorophyll, CDOM, DOC, SM) and used established available data products as our data source.

Instrument and/or Software Specifications:
Carbon Isotope Measurements: Picarro G2201-i CM-CRDS calibrated to IAEA caffeine and sucrose standards as well as lab-calibrated C3 and C4 sugar standards.
Total Carbon and Nitrogen Measurements: Costech ECS 4010 Elemental Analyzer calibrated to IAEA acetanilide and atropine standards.

Files contained here:
Dataset filename: MIS_CarbonNitrogenChemistry.csv
Dataset description: This dataset includes sediment organic carbon and nitrogen chemistry along with sample collection information (collection location, depth in sediment, collection year and month) from Middle Island Sinkhole, MI and a nearby Lake Huron control site. Note that if this file is opened in Excel, some entries in the depth_range field may convert to dates (e.g., 9-12 converting to 12-Sept).
Column name: Units: Description/Code Explanation:
Year Year Sampling year
Location Sampling location. In combination with Site, Core, and Section, part of the full name for each sample; Code explanation: MIS = Middle Island Sinkhole, LH = Lake Huron
Month Month Sampling month; Code explanation: Numeric month codes (1 = January, etc.)
Site Specific sampling site where available; Code explanation: Arena = generally within MIS, P1,P4,P7,P10 = sampling post numbers, with increasing distance from the primary source of groundwater, A7,G7,M1,M2: Sampling locations away from the post line, LH = Lake Huron control site
Core Core sample number for the year the core was collected. In some cases, this is related to the post at which the sample was collected (see “Site”), in other cases it is numeric for the sampling year. Part of the full name for a sample; Code explanation: P1,P4,P7,P10 = sampling post numbers, with increasing distance from the primary source of groundwater. A7,G7,M1,M2 = Sampling locations away from the post line. Numeric = core number, related to order of sample collection that year.
Section The core segment, with increasing values indicating that the sample is deeper in the core. Part of the full name for a sample; Code explanation: 1A,1B,1C = the first three segments of the core; 2,3… = subsequent segments of the core
Depth cm Depth of the midpoint of the core section. Code explanation: increases down in core.
depth_range cm 3 cm ranges of depths for grouping samples; Code explanation: Mat = shallowest sample from a core. Some fields may convert to dates if opened in Excel (e.g., 9-12 to 12-Sept).
Molar_CN None Ratio of organic carbon to nitrogen
Corg % Percent organic carbon
N % Description: Percent nitrogen (acidified sample)
d13C ‰ Stable isotope composition of organic carbon

Dataset filename: MIS_CarbonNitrogenChemistry_TrimmedAnnualMeans_EnvironmentalAnnualAvg.csv
Dataset description: This dataset includes the trimmed annual mean values and standard errors of sediment organic carbon and nitrogen values for Middle Island Sinkhole, MI. The 5% and 95% quantiles were trimmed to remove outliers and calculate the trimmed mean and standard error. Separate calculations were done for δ13Corg due to differences in sample counts. The sample counts for both sets of data (Corg, N, Corg:N; δ13Corg) that were used to weight the means are included as well. The dataset also includes annual average values for various environmental parameters, derived from data products described in the Methods and Data Provenance sections. These environmental parameters are for the region around MIS, and include ice cover, lake surface temperature, chlorophyll, dissolved organic carbon, colored dissolved organic matter, suspended minerals, precipitation, and air temperature. These environmental parameters are associated with the sediment chemistry based on sampling year.
Column Name: Units: Description:
Year Year Sampling year
Corg % Trimmed mean of the percent organic carbon for a given sampling year
Corgse % Standard error of the trimmed mean percent organic carbon
Molar_CN None Trimmed mean of the ratio of organic carbon to nitrogen for a given sampling year
CNse None Standard error of the trimmed mean of the ratio of organic carbon to nitrogen
N % Trimmed mean of the percent nitrogen (acidified samples) for a given year
Nse % Standard error of the trimmed mean of the percent nitrogen
d13C ‰ Trimmed mean of the δ13Corg for a given year
d13Cse ‰ Standard error of the δ13Corg for a given year
Ccount Count Trimmed number of Corg, N, and Corg:N samples for a given year, used for weighting means and calculating standard error
d13Ccount Count Trimmed number of δ13Corg samples for a given year, used for weighting means and calculating standard error for δ13Corg.
days_50 Days Duration of >50% ice cover for the study region each year
days_75 Days Duration of >75% ice cover for the study region each year
maxice_avg % Average maximum ice cover for the study region each year.
CDOM_avg Absorp. Average colored dissolved organic matter for the study region each year.
chl_avg μg/L Average chlorophyll for the study region each year.
sm_avg mg/L Average suspended minerals for the study region each year.
DOC_avg mg/L Average dissolved organic carbon for the study region each year.
AirT_avg °C Average air temperature for the study region each year.
lst_avg °C Average lake surface temperature for the study region each year.
precip mm Sum of annual precipitation for the study region each year

Data Provenance:
Dataset title: Dataset DOI or URL: Creator:
Ice Concentration from Great Lakes Surface Environmental Analysis (GLSEA) and NIC, Geodetic coordinate system (LAT, LON), 1995-present https://apps.glerl.noaa.gov/erddap/griddap/GL_Ice_Concentration_GCS.html CoastWatch Great Lakes Node
Sea Surface Temperature (SST) from Great Lakes Surface Environmental Analysis (GLSEA), Geodetic coordinate system (LAT, LON), 1995-present https://apps.glerl.noaa.gov/erddap/griddap/GLSEA_GCS.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Colored Dissolved Organic Matter, MODIS, Lake Huron (2013-2017) https://apps.glerl.noaa.gov/erddap/griddap/LH_CDOM_MODIS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Colored Dissolved Organic Matter, VIIRS, Lake Huron (2018-present) https://apps.glerl.noaa.gov/erddap/griddap/LH_CDOM_VIIRS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Dissolved Organic Carbon, MODIS, Lake Huron (2013-2017) https://apps.glerl.noaa.gov/erddap/griddap/LH_DOC_MODIS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Dissolved Organic Carbon, VIIRS, Lake Huron (2018-present) https://apps.glerl.noaa.gov/erddap/griddap/LH_DOC_VIIRS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Chlorophyll, MODIS, Lake Huron, (2013-2017) https://apps.glerl.noaa.gov/erddap/griddap/LH_CHL_MODIS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Chlorophyll, VIIRS, Lake Huron (2018-present) https://apps.glerl.noaa.gov/erddap/griddap/LH_CHL_VIIRS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Suspended Minerals, MODIS, Lake Huron (2013-2017) https://apps.glerl.noaa.gov/erddap/griddap/LH_SM_MODIS_SQ.html CoastWatch Great Lakes Node
Color Producing Agent (CPA) Suspended Minerals, VIIRS, Lake Huron (2018-present) https://apps.glerl.noaa.gov/erddap/griddap/LH_SM_VIIRS_SQ.html CoastWatch Great Lakes Node
NWS NOWData; Gaylord, MI; Precipitation; Alpena Area; Monthly Summarized Data; Precipitation Sum 2007–2024 https://www.weather.gov/wrh/Climate?wfo=apx NOAA Online Weather Data; Applied Climate Information System
Standard Meteorological Data; Station TBIM4 – Thunder Bay Island, MI https://www.ndbc.noaa.gov/station_history.php?station=tbim4 NOAA National Data Buoy Center
Standard Meteorological Data; Station 45162 – Thunder Bay Buoy, Alpena, MI https://www.ndbc.noaa.gov/station_page.php?station=45162 NOAA National Data Buoy Center
Standard Meteorological Data; Station APNM4 - Alpena Harbor Light, Alpena, MI https://www.ndbc.noaa.gov/station_history.php?station=apnm4 NOAA National Data Buoy Center
Standard Meteorological Data; Station LPNM4 - 9075065 - Alpena, MI https://www.ndbc.noaa.gov/station_history.php?station=lpnm4 NOAA National Data Buoy Center

Related publication(s):
Howard, C.M. (2025). Unraveling Records of Time and Environment in Microbial Ecosystems from the Archean to Today (Ph.D. Dissertation). University of Michigan. DOI: https://dx.doi.org/10.7302/25504
Howard, C.M., et al. (in prep). Climate-driven changes in sediment carbon and nitrogen of an anoxic Lake Huron sinkhole.

Use and Access:
This data set is made available under a Creative Commons Attribution 4.0 International license (CC BY 4.0).

To Cite Data:
Howard, C.M., Velazquez, D., Rico, K.I., and Sheldon, N.D. (2025). Sediment Carbon and Nitrogen and Environmental Data, Middle Island Sinkhole, 2007–2021 [Data set]. University of Michigan - Deep Blue Data.